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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1769 2012/11/15 15:37:25 mlosch Exp $ |
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$Name: $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
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o pkg/obcs: |
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- adding tidal velocity forcing capability to obcs |
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for usage example, see verification/seaice_obcs/input.tides |
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o pkg/seaice: |
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- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
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SEAICE_LSRrelaxU/V |
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- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
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o pkg/aim_v23: |
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- implement heating from friction (bottom friction and stratospheric drag). |
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o pkg/shap_filt: |
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- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
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dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
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o model/src: |
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- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
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time-constant addMass field from file (addMassFile); |
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- support for heating due to friction (and Kinetic Energy dissipation): |
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add option, run-time switch and 3-D field array + support code ; each pkg |
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or S/R can add heating contribution (if there is a sink of KE); the sum is |
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accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
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o pkg/seaice: |
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- complete merge of ITD code into seaice_growth.F |
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from MITgcm_contrib/torge/itd/code/ |
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no verification so far, but Torge Martin tested |
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"1-D test case and Beaufort set up; |
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deliver okay results after 1 model year." |
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- complete merge of SEAICE_SIZE.h into all relevant routines |
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- move computation of eta at Z-points into calc_viscosities |
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+ introduce global field etaZ |
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+ add different methods for computing etaZ, for now the old |
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method (simple averages of eta to Z-points) is hardwired |
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+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
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seaice_preconditioner |
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- simplify computations for SEAICE_ZETA_SMOOTHREG |
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- seaice_preconditioner: |
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+ replace one remaining press by pressLoc (mistake) |
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+ adjust printing of residuals |
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- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
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+ add (SEAICE.h) and rename some counters (initiliased in |
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seaice_init_fixed.F) |
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+ add _BEGIN/END_MASTER (myThid) around print statements |
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+ print total number of iterations and failures over SEAICE_monFreq |
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interval to STDOUT |
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- move control over output-messages by fgmres to seaice_jfnk to save |
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some operations |
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- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
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in order to make restarts with sol .ne. zero (fgmres with restarts) |
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(seaice_jfnk.F, seaice_fgmres.F) |
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- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
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a serious convergence problem when open boundaries are involved |
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o pkg/ggl90: fix computation of control volumes for the case of |
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ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
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up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
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o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
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o pkg/autodiff |
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- Add inAdMode switch for SEAICEuseDYNAMICS: |
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SEAICEuseDYNAMICSinAdMode |
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(extend logic in ADAUTODIFF_INADMODE_SET) |
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o pkg/seaice |
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- Step 1 of merging ice-thickness distribution (ITD) code from |
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MITgcm_contrib/torge/itd/ (author: Torge Martin) |
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The code implements concept laid out in Thorndike et al. (1975); |
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code is enabled via CPP flag SEAICE_ITD |
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nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
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code is not complete yet!! |
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- SEAICE_SIZE.h now included in almost all seaice routines |
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o verification (using seaice): |
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- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
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global_ocean.cs32x15.seaice ; update results. |
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- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
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- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
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offline_exf_seaice (previously compiling B-grid). |
78 |
o pkg/exf: |
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- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
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to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
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forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
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o pkg/layers (adjust changes from Sept 19): |
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- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
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this allows to remove "layers_maxNum" dimension from all layers arrays. |
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o pkg/layers (adjust changes from Sept 19): |
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- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
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- snap-shot extended to all type of layers (not just the 1rst type); |
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- remove layers variables when corresponding CPP option is undef. |
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o pkg/layers: |
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- rename pkg/layers variable and add new output (layer exist & un-weighted |
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velocity in layer) |
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o pkg/seaice: |
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- simplify (?) ocean-drag coefficent computations by using |
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the same routine in all three solvers (saves some code lines) |
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- remove global fields DRAGA and DRAGS from C-grid code and |
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declare them locally in lsr.F (the only place where they are |
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still used) |
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- update AD output of lab_sea.evp (very sensitive anyway). |
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o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
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(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
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and SEAICEuseJFNK=.true. A few things to note: |
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- involves a FGMRES, that is parallel but very inefficient, |
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because of many scalar products (global sums) in the Gram-Schmidt |
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orthogonalization method. Needs to be replaced. Original code |
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from J.-F. Lemieux |
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- preconditioner for FGMRES is a stripped down version of LSOR |
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- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
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preconditioner. For the preconditioner, the default is set to 10. |
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- Jacobian times vector is computed with finite differences |
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- marginally related to JFNK-solver: add a smooth regularization for |
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zeta with tanh that will improve convergence (Lemieux and Tremblay, |
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2009) for any implicit solver (not implemented for EVP because EVP |
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does not need this regularization in the first place). Define |
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SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
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o eesupp/src: |
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- check in genmake2 that intrinsic S/R flush is available. |
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- add S/R to flush IO unit (if intrinsic S/R flush is available) |
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- flush standard & error msg unit before MPI termination |
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- if debugMode, flush IO unit after printing msg |
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o pkg/ctrl: |
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- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
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to ctrl_set_unpack_xyz. |
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|
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checkpoint64 (2012/10/09) |
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o pkg/shelfice |
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- in mom_fluxform.F, mom_vecinv.F: |
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CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
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Bug fix KappaRU -> KappaRV |
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does not change verification/isomip but may change other setups |
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(presumably constant KappaRU=KappaRV) |
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- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
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o pkg/obcs: |
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- fixed some indexing bugs in obcs_seaice_sponge.F |
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- added obcs relaxation subroutines for HSALT and HSNOW |
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- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
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o pkg/seaice: |
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- add "multicategory" parameterization for snow in analogy to ice, |
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default is off for now. |
139 |
o pkg/obcs: |
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- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
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see verification/seaice_obcs/input.seaiceSponge for example application. |
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- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
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index setting by master-thread. This fix multi-threads Pb in previous modifs. |
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o pkg/layers : |
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- add diagnostics to pkg/layers |
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- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
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(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
148 |
o pkg/generic_advdiff/gad_implicit_r.F : |
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- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
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o pkg/seaice/seaice_growth.F: |
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- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
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o pkg/obcs: |
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- change default setting of OBCS_UVICE_OLD from defined to undef; |
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- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
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in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
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- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
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- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
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with Southern & Western OB at a tile edge (at least in a simple set-up). |
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o pkg/obcs: |
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- change settings of OB index in case OB coincides with tile edge (shared by |
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2 tiles), so that common OB location is registered by both tiles (instead of |
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only 1). However, for Southern and Western OB, index value = 0 is not |
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recognized as valid OB index (=default null value) and needs to be fixed. |
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- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
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- new parameter "OB_indexNone" for null index value (for now, still zero) |
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to replace hard-coded null index value of zero. |
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o pkg/exch2: |
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- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
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always check buffer-size (but outside the loop); move checking for valid |
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index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
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print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
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o pkg/ctrl (pack & unpack): |
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- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
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(locally defined) for different variables (+ remove the variable-specific |
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file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
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(to be extended to other local file names in ctrl.h). |
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o pkg/flt: |
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- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
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o pkg/mdsio: |
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- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
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o tools/genmake2: |
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- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
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(added by Alistair in version 1.51 for building without make depend); |
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- remove Header files list (H_SRC_FILES) from the dependence of targets |
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ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
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place in version 1.23): this save going through staf when unrelated header |
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file has been modified. |
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Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
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"make depend" step, still need to do "make links" before "make adtaf". |
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o eesupp/src (+ few pkg src files) & genmake2: |
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- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
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- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
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- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
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upper/lower case ; account for space between "#" and undef/define) |
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o pkg/flt (with exch2): |
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- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
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- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
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|
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checkpoint63s (2012/09/05) |
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o pkg/ecco: |
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- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
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- add more relevant #ifdef ALLOW_SMOOTH ones. |
203 |
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
204 |
o pkg/ctrl: |
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- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
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ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
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- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
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doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
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ctrlSmoothCorrel3D (new). |
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The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
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- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
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- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
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controls when useAtmWind, and vice versa. |
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- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
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- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
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#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
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- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
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#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
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- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
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replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
221 |
o pkg/smooth: |
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- remove un-necessary includes. |
223 |
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
224 |
Those CPP options were never defined, and not necessary. |
225 |
o model/src: |
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- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
227 |
- standard treatment of useSMOOTH. |
228 |
o pkg/autodiff: |
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- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
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useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
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o pkg/exch2: |
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- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
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+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
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- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
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and tiles to process mapping. |
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- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
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moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
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rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
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from w2_eeboot.F to w2_readparms.F. |
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o eesupp/src: |
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- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
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ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
243 |
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
244 |
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
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is defined (remove condition on usingMPI) to match cases where MPI_INIT |
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has been called. |
247 |
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
248 |
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
249 |
(so that on 1 proc, get same myPid independently of usingMPI) |
250 |
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
251 |
useCubedSphereExchange with EXCH-1 (safer). |
252 |
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
253 |
o pkg/ggl90: |
254 |
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
255 |
used in ALLOW_GGL90_SMOOTH code. |
256 |
o pkg/flt: |
257 |
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
258 |
floats at the Southern end of the domain). |
259 |
o eesupp/inc: |
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- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
261 |
but not used (and not to be used) anywhere, just for documentation. |
262 |
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
263 |
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
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a) can damage previously written records in any other multi-record files. |
265 |
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
266 |
o tools/genmake2: |
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- define variable MAKE within Makefile and use it in place of 'make'; |
268 |
- update AD_CONFIG.h (if needed) before building any of the executable |
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(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
270 |
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
271 |
- always print usual warning comment 'this file is automatically generated' |
272 |
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
273 |
o pkg/cheapaml: |
274 |
- updated to correspond to the code used in accepted paper (Nico Wienders). |
275 |
o pkg/exf: |
276 |
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
277 |
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
278 |
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
279 |
o pkg/exf, autodiff, ctrl, ecco and seaice: |
280 |
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
281 |
o pkg/ctrl, ecco: |
282 |
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
283 |
Depending on useAtmWind, one is inactive, and the other is active (see |
284 |
exf_getffields.F/exf_getsurfacefluxes.F). |
285 |
o tools/genmake2: |
286 |
- improve error msg when failing in 2nd test of check_for_broken_Ff |
287 |
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
288 |
- source local config file "genmake_local" just after processing the genmake2 |
289 |
command arguments (previously done before processing arg). |
290 |
o pkg/grdchk: |
291 |
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
292 |
to this routine from cost_final has been dropped in g_cost_final) |
293 |
- improve printed information (more explicit msg, no longer using "print *," |
294 |
fix fcpertminus printed value). |
295 |
o model/src: |
296 |
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
297 |
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
298 |
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
299 |
o pkg/dic: |
300 |
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
301 |
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
302 |
o pkg/grdchk: |
303 |
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
304 |
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
305 |
o pkg/autodiff/ctrl/grdchk : |
306 |
- attempt to sort out what works and what does not, |
307 |
with regard to I/O, and to warn/stop accordingly. |
308 |
o pkg/grdchk: |
309 |
- attempt to fix grdchk in the case of useSingleCpuIO. |
310 |
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
311 |
statements were moved from grdchk_main.F and into |
312 |
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
313 |
- a global sum is applied to record numbers icvrec/layer |
314 |
out of grdchk_loc so that they be passed to I/O routines. |
315 |
o pkg/smooth: |
316 |
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
317 |
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
318 |
o verification/testreport: |
319 |
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
320 |
- can also use compressed (gzip) reference output file; |
321 |
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
322 |
to be easier to collect by testreport. |
323 |
- update existing TLM output (half out-of-date by more than 3 yrs). |
324 |
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
325 |
- report run-time in each individual summary (previously only for AD test); |
326 |
for TLM test, add also TAF version. |
327 |
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
328 |
|
329 |
checkpoint63r (2012/08/15) |
330 |
o tools/genmake2: |
331 |
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
332 |
o pkg/ecco/ecco_cost_final.F : |
333 |
- fix fc print statements (to stdout and costfunction0000) so |
334 |
that the printed value is always after the global sum. |
335 |
o pkg/seaice/seaice_dynsolver.F : |
336 |
- fix ice strength assymptote at SEAICE_area_max<1 |
337 |
(no change for the standard case of SEAICE_area_max=1) |
338 |
o some cleaning: |
339 |
- pkg source files: ensure that all *.F files from each pkg included the |
340 |
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
341 |
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
342 |
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
343 |
includes; |
344 |
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
345 |
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
346 |
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
347 |
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
348 |
- update option-file CPP_OPTIONS.h of all AD experiments: |
349 |
* no longer include PACKAGES_CONFIG.h ; |
350 |
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
351 |
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
352 |
including ECCO_CPPOPTIONS.h). |
353 |
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
354 |
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
355 |
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
356 |
not necessary accurate). |
357 |
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
358 |
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
359 |
deliberately break compilation (a remainder that it needs to be customized) |
360 |
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
361 |
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
362 |
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
363 |
o tools/genamke2: |
364 |
- check for lapack. |
365 |
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
366 |
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
367 |
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
368 |
from both packages. |
369 |
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
370 |
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
371 |
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
372 |
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
373 |
o pkg/cost : add comments to explain special and/or untested setups. |
374 |
o pkg/exf: |
375 |
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
376 |
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
377 |
o verification/*/code_ad: |
378 |
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
379 |
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
380 |
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
381 |
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
382 |
o pkg/seaice : |
383 |
- added possibility to change ice strength/PRESS0 relationship to |
384 |
HEFF, according to the following run time parameters |
385 |
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
386 |
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
387 |
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
388 |
o pkg/ggl90 : |
389 |
- added run time flag mxlSurfFlag to include the code that ensure |
390 |
mixing between first and second level (previously included as a comment) |
391 |
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
392 |
- add test of newly added dumpAdByRec=T option where |
393 |
we write all records to one file per variable. |
394 |
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
395 |
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
396 |
to check that this code is ok with taf and compiles in adjoint. |
397 |
o pkg/autodiff : |
398 |
- added run time param dumpAdByRec : ad dump format switch. |
399 |
If true then write all records to one file per variable. |
400 |
Else write one file per record (remains the default). |
401 |
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
402 |
o pkg/seaice: |
403 |
- Added SEAICEuseTILT run time switch : if set to |
404 |
false then omit the tilt term in seaice dynamics. |
405 |
- Fix free drift calculation. |
406 |
o pkg/shelfice: |
407 |
When initializing SHELFICEDragQuadratic, set default to be |
408 |
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
409 |
but retain option to set it independently |
410 |
(inconsistenty spotted by Veronique Dansereau) |
411 |
o eesupp/inc: |
412 |
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
413 |
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
414 |
o model/src: |
415 |
- move balancing of relaxation terms to new S/R balance_relax.F. |
416 |
o pkg/autodiff: |
417 |
re-write active I/O high-level (control) S/R: |
418 |
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
419 |
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
420 |
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
421 |
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
422 |
- update and merge active_file_control_slice.flow into active_file_control.flow |
423 |
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
424 |
active_file_ad.F) keeping the argument list and function unchanged. |
425 |
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
426 |
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
427 |
- new low-level active I/O routines, one for each type (RL/RS), for active var |
428 |
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
429 |
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
430 |
right type. |
431 |
o autodiff and RS=real*4: |
432 |
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
433 |
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
434 |
- change argument type of 3-D mask argument to _RS to match type in the call |
435 |
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
436 |
o pkg/thsice: |
437 |
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
438 |
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
439 |
fresh-water flux: uniform correction or proportional to local precip. |
440 |
o pkg/ctrl: |
441 |
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
442 |
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
443 |
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
444 |
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
445 |
|
446 |
checkpoint63q (2012/07/30) |
447 |
o pkg/autodiff: |
448 |
note about monitor and snap-shot of ad-variables: |
449 |
a) need to apply ADEXCH before monitor or output of ad-vars to include |
450 |
overlap contributions (was done for adjDump but missing for monitor). |
451 |
b) since ADEXCH implies adding overlap values to interior array, machine |
452 |
truncation error is expected when adding an ADEXCH call in the middle of |
453 |
the time-stepping (although mathematically identical). |
454 |
modifs: |
455 |
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
456 |
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
457 |
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
458 |
apply ADEXCH before monitor or snap-shot of ad-variables: |
459 |
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
460 |
- implement new method (copy+adexch) for snap-shot and monitor of main model |
461 |
ad-vars (initially not used by default -> output unchanged). |
462 |
- change default (set to 2) to use new method and update few output_adm.txt |
463 |
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
464 |
and both tutorial_tracer_adjsens tests). |
465 |
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
466 |
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
467 |
o pkg/ctrl: |
468 |
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
469 |
generic control variables via |
470 |
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
471 |
Only required customization should be S/R ctrl_map_ini_genarr.F |
472 |
(routine in repository contains example) |
473 |
o pkg/exf: |
474 |
- fix and refine checking of surface-relaxation setting when using EXF |
475 |
o verification (adjoint exp): |
476 |
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
477 |
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
478 |
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
479 |
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
480 |
of KE that can occur with aggressive optimization |
481 |
+ put quadratic bottom drag calculation in separated loops (only done if |
482 |
using bottomDragQuadratic) |
483 |
o model/src: CG2D_NSA |
484 |
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
485 |
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
486 |
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
487 |
change cg2d residual target to be expressed in Wunits (=> do not normalise |
488 |
RHS ; this fix global_max Pb with TAF); update output. |
489 |
o verification/tutorial_tracer_adjsens: |
490 |
improve parameter consistency (and get rid of warnings): |
491 |
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
492 |
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
493 |
- use staggerTimeStep (for stability) in som81; use default rotation period. |
494 |
o pkg/exch2: |
495 |
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
496 |
reset to 0 = 1 long line in X) |
497 |
o pkg/mdsio: |
498 |
- fix reading of dimensions from meta file for large-size domain |
499 |
o model/src: |
500 |
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
501 |
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
502 |
Cubed-Sphere Exch with CS-corners inside the domain; |
503 |
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
504 |
globalArea and to set hasWetCSCorners. |
505 |
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
506 |
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
507 |
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
508 |
useCDscheme and useCubedSphereExchange). |
509 |
o pkg/seaice/seaice_growth.F : |
510 |
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
511 |
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
512 |
when the previous code was not correct. |
513 |
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
514 |
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
515 |
that term to QNET (essentially to set the melt/freeze water to 0degC). |
516 |
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
517 |
o verification/global_ocean.cs32x15/input.seaice : |
518 |
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
519 |
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
520 |
- update results (output.seaice.txt) accordingly. |
521 |
o verification/lab_sea/input/data.seaice : |
522 |
- remove SEAICEheatConsFix, which is now be tested |
523 |
in global_ocean.cs32x15. The presently coded fix |
524 |
is only consistent with real fresh water + nlfs. |
525 |
- update results (output.txt) accordingly. |
526 |
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
527 |
o AD_CONFIG.h file: |
528 |
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
529 |
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
530 |
add it explicitly in each fortran src file where it is needed. |
531 |
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
532 |
thus introducing potentially wrong dependency; therefore, better to include |
533 |
it only where it's really needed, and after any other included OPTIONS file |
534 |
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
535 |
or ALLOW_TANGENTLINEAR_RUN). |
536 |
|
537 |
checkpoint63p (2012/07/06) |
538 |
o pkg/autodiff: |
539 |
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
540 |
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
541 |
which are now read from new parameter file "data.autodiff" (inAdExact |
542 |
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
543 |
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
544 |
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
545 |
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
546 |
o verification/tutorial_tracer_adjsens/ |
547 |
- add extra sub-verification which uses "SOM" advection scheme |
548 |
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
549 |
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
550 |
and in data: |
551 |
multiDimAdvection=.TRUE., |
552 |
tempAdvScheme=81, |
553 |
saltAdvScheme=81, |
554 |
o model/src: |
555 |
- introduce ALLOW_BALANCE_RELAX which allow the removal |
556 |
of the global mean of relaxation terms by setting |
557 |
balanceThetaClimRelax and balanceSaltClimRelax |
558 |
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
559 |
This case is now treated appropriately in seaice_growth.F |
560 |
o pkg/seaice: |
561 |
- do balanceEmPmR and balanceQnet based on the net fluxes |
562 |
(SItflux) that enter the ocean+ice system rather than QNET |
563 |
and EMPMR. Works best in real fresh water. |
564 |
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
565 |
out of the diagnotics bloc, and stored in global arrays. |
566 |
|
567 |
checkpoint63o (2012/06/29) |
568 |
o vertical mixing schemes: |
569 |
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
570 |
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
571 |
to S/R FIND_RHO_SCALAR |
572 |
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
573 |
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
574 |
affects output (vermix.ggl90) at truncation level. |
575 |
o testreport: |
576 |
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
577 |
(nSx,nSy) for the number of threads (from eedata.mth) |
578 |
o model/src: |
579 |
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
580 |
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
581 |
o verification/tutorial_tracer_adjsens/ |
582 |
- compile with ALLOW_CG2D_NSA |
583 |
- run with nonlinFreeSurf=3 |
584 |
- update reference output_adm.txt |
585 |
o tools/genmake2: |
586 |
- add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ; |
587 |
refine usePROFILES switching off (only when NetCDF is not available). |
588 |
o verification (atmospheric set-up): |
589 |
- change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration |
590 |
o pkg/profiles : refine profiles and files handling. |
591 |
o model/src and pkg/ecco : introduce run-time switch usePROFILES. |
592 |
o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h : |
593 |
- changes to use model/src/the_main_loop.F rather than the ecco version |
594 |
in ecco type adjoint runs. |
595 |
o model/src: |
596 |
- move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID |
597 |
- move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC |
598 |
- update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL) |
599 |
o model/src: |
600 |
- fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before); |
601 |
update output of test experiment bottom_ctrl_5x5. |
602 |
o pkg/generic_advdiff: |
603 |
- implement vertical bi-harmonic diffusion (for now, only for T & S and |
604 |
only explicitly). |
605 |
o verification/bottom_ctrl_5x5/ |
606 |
update reference output (results changed quite some time ago, |
607 |
not sure when; but new reference results look ok in terms of grdchk) |
608 |
o verification/1D_ocean_ice_column/ |
609 |
For verification purposes, the exact adjoint rather than an approx. |
610 |
should be used (e.g., to comare against F.D. or TLM). |
611 |
removed autodiff_inadmode*_ad.F routines in code_ad/ |
612 |
Update results/ accordingly. |
613 |
o pkg/cal: |
614 |
- change cal_getdate.F so that output date is function of input time only |
615 |
(less ambiguous, not mixed up with input iteration number). |
616 |
- fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP). |
617 |
o pkg/diagnostics: |
618 |
- implement calendarDumps also for stats-diags |
619 |
- implement calendarDumps also for snap-shot output (negative freq) |
620 |
- for now, ignores calendarDumps if non-zero phase-lag. |
621 |
|
622 |
checkpoint63n (2012/06/04) |
623 |
o model/src: |
624 |
- recompute rSurfW & S to ensure consistent column thickness (needed for rStar) |
625 |
between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice; |
626 |
- use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more |
627 |
similar to calc_r_star.F); update results of experiment internal_wave and |
628 |
tutorial_global_oce_in_p (affected @ truncation level). |
629 |
o pkg/shelfice: |
630 |
- add parameterisation of advective-diffusive flux into the ice shelf |
631 |
according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd |
632 |
- simply eps3/3a computation |
633 |
o eesupp: |
634 |
- add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange |
635 |
between tiles, just fill-in edges assuming locally periodic subdomain) and |
636 |
add corresponding exchange subroutines (EXCH0); |
637 |
- new CG-solver version (_EX0) for disconnected-tiles special case. |
638 |
o model/src (CG-solvers): |
639 |
- modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached |
640 |
(similar final residual output and max-Iter number as with standard version); |
641 |
- allows to store and use lowest-residual solution (standard & _SR versions); |
642 |
- cleaning up (remove old, commented out code, LETS_MAKE_JAM ...). |
643 |
- by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h) |
644 |
o eesup/src: |
645 |
- global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef |
646 |
ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012) |
647 |
o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn |
648 |
|
649 |
checkpoint63m (2012/04/27) |
650 |
o pkg/shelfice: |
651 |
- account for partical cells in surface level below ice-shelf for hydrostatic |
652 |
pressure calculion (set uniformFreeSurfLev to F); update isomip experiments. |
653 |
o ad test experiments: |
654 |
- update and rename to "ad_optfile.local" local AD-optfile specific to a |
655 |
particular adjoint verification experiment (in verification/*/code_ad/) |
656 |
o pkg/seaice & pkg/exf: |
657 |
- Part two of ECCO-CLIVAR code merges. |
658 |
Completes merge of seaice area relax. code. |
659 |
Requires unified CPP option EXF_ALLOW_SEAICE_RELAX |
660 |
to be set in EXF_OPTIONS.h since this pkg controls its I/O |
661 |
(and avoids second CPP option in SEAICE_OPTIONS.h) |
662 |
- change default value of costIceStart & costIceEnd to a valid date. |
663 |
- add snowPrecip to HSNOW in seaice_growth |
664 |
o pkg/ptracers: |
665 |
- move ptracers summary and setup check into separated S/R ; add a check for |
666 |
valid PTRACERS_Iter0 value (error+stop or just warning). |
667 |
o pkg/cal (+ pkg/ecco): |
668 |
- avoid calling a S/R with 2 times the same arg (FWD: unless both are only used |
669 |
as input; and for AD, unless both are not differentiable (e.g., k index)). |
670 |
o model/src: |
671 |
- define internal flag "uniformFreeSurfLev" (=T when free-surface level-index |
672 |
is everywhere k=1) to speed-up some calculations (by pass kSurf reference); |
673 |
temporary set to usingZCoords value (to be changed to F when using shelfice). |
674 |
- hydrostatic pressure: implement partial cell near the surface also for |
675 |
Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on |
676 |
usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code). |
677 |
o pkg/ctrl/ctrl_init.F: |
678 |
- add a formal parameter to s/r ctrl_init_rec to print |
679 |
xx_$(ctrl_valiable)_file for easier debugging |
680 |
- move call of cal_* routines into the if-block where they are really |
681 |
needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having |
682 |
to specify a startdate |
683 |
o pkg/seaice: |
684 |
- update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and |
685 |
global_ocean.cs32x15/code versions). |
686 |
- turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for |
687 |
verification experiment global_ocean.cs32x15.seaice and update results. |
688 |
o pkg/exf: |
689 |
- new S/R EXF_GETFIELD_START to return starting-time of a forcing field |
690 |
(according to useExfYearlyFields). |
691 |
o pkg/cal: |
692 |
- move calendar setting & summary (previously in cal_readparams.F) into new |
693 |
S/R CAL_INIT_FIXED to be called later in the initialisation process, once |
694 |
length of the simulation is set (after SET_PARMS call); This is an attempt |
695 |
to fix Pb when, e.g.: pkg/longstep, modifies the length of the run. |
696 |
- For safety: keep a record of pkg/cal parameter settings status |
697 |
to allow to STOP if one pkg/cal S/R is called too early. |
698 |
- add a stop in all basic pkg/cal subroutines if called before setting is done. |
699 |
- modify cal_getdate.F: stop when nothing was returned; |
700 |
if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2); |
701 |
this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F. |
702 |
|
703 |
checkpoint63l (2012/04/04) |
704 |
o pkg/bbl: |
705 |
- fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc); |
706 |
update global_with_exf output.yearly.txt file. |
707 |
o pkg/cal: |
708 |
- start to clean-up cal_set.F ; fix for the case where baseTime is non-zero. |
709 |
- remove 2 unsused and very short (1 line only) functions ; |
710 |
- remove unsused subroutines from AD-Diff list. |
711 |
o model/src: |
712 |
- start to implement clean wait to stop in initialization S/R (config_check.F, |
713 |
packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage) |
714 |
o folowing PRINT_MESSAGE changes: |
715 |
- remove reminder multiple print to the same file (STDOUT) when multi-threads. |
716 |
o pkg/bbl: |
717 |
- modification so it can work with z* |
718 |
- replace deltaT with dTtracerLev(k) for asynchronous time stepping |
719 |
- global_with_exf/input.yearly verification; changes output.yearly.txt |
720 |
o eesupp/src: |
721 |
- PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR); |
722 |
writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1 |
723 |
- CHECK_THREADS: specific code if using OpenMP threading: improve checking of |
724 |
# of threads across processors (e.g., different env OMP_NUM_THREADS setting) |
725 |
- improve special preliminary call to EESET_PARMS (if eedata is read 2 times). |
726 |
- when using MPI, always set usingMPI=T ; set default accordingly and stop |
727 |
if not consistent. |
728 |
- ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread |
729 |
argument is zero (in case called within single-thread section). |
730 |
o pkg/fizhi: |
731 |
clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored |
732 |
in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO. |
733 |
o pkg/exch2: |
734 |
- add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to |
735 |
activate EXCH_IGNORE_CORNERS in vector EXCH S/R). |
736 |
- switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS) |
737 |
but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data |
738 |
with bad ones coming from a not-yet-updated halo. |
739 |
This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx. |
740 |
o pkg/frazil: |
741 |
move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F |
742 |
http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html |
743 |
o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy |
744 |
o verification/lab_sea |
745 |
* #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING |
746 |
* #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL |
747 |
* nTimeSteps 3 -> 4 |
748 |
* changed reference output accordingly |
749 |
o pkg/ctrl: |
750 |
* fix ctrl_get_gen for xx_sst, xx_sss |
751 |
o pkg/fizhi: |
752 |
- fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F |
753 |
update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d) |
754 |
- by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE); |
755 |
fix few out-of-bounds indices in referencing vars (initialise igrd to 1); |
756 |
clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array). |
757 |
o pkg/gmredi: |
758 |
- add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp |
759 |
o pkg/fizhi: |
760 |
- fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the |
761 |
(old)aces open64 tuv test. |
762 |
o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F |
763 |
o pkg/mom_vecinv: |
764 |
- fix 1 loop range in mom_vecinv.F to be like all the other loops which |
765 |
set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv |
766 |
with non-lin free-surf). |
767 |
o model/src: move k-loop outside of i/j-loops when (re-)computing R_low |
768 |
in ini/update_masks_etc.F in order to avoid -O3 optimization problems with |
769 |
some compilers (gfortran 4.6.0 on MacOS) |
770 |
o momentum: |
771 |
- separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM |
772 |
& MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised |
773 |
fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control. |
774 |
|
775 |
checkpoint63k (2012/03/17) |
776 |
o model/src: |
777 |
- selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum |
778 |
flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations. |
779 |
- SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version |
780 |
(#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp. |
781 |
o model/src: solve_*diagonal.F |
782 |
- replace division with multiplication by inverse (similar to original version) |
783 |
update output of AD exp. global_ocean.90x40x15. |
784 |
- fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F |
785 |
to enable the use of the vectorized & differentiable solve_tridiagonal.F |
786 |
- test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for |
787 |
vertical advection (to get solve_tridiagonal tested in AD mode). |
788 |
o pkg/seaice: ECCO-CLIVAR merge: |
789 |
1. seaice AREA relaxation |
790 |
* CPP option: SEAICE_ALLOW_AREA_RELAXATION |
791 |
* runtime flag: SEAICE_tauAreaObsRelax |
792 |
2. modified global mean cost imbalance code: CPP option |
793 |
ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION |
794 |
o another iteration on solve_*diagonal.F |
795 |
Make choices independent of AUTODIFF |
796 |
Default will be the adjoinable vectorized version. |
797 |
Alternative choices are: |
798 |
* non-adjoinable original version with low memory footprint: |
799 |
#define SOLVE_DIAGONAL_LOWMEMORY |
800 |
* still adjoinable but does not vectorize (k as inner-most loop): |
801 |
#define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef) |
802 |
o testreport |
803 |
- add option to use a home made wrapper around "make" |
804 |
- remove MITGCM_IEEE env. variable (no longer active) |
805 |
o pkg/shelfice |
806 |
- improve computation of friction velocity for velocity dependent |
807 |
exchange coefficients: include velocities into SHELFICEBoundaryLayer |
808 |
block to average velocities vertically |
809 |
- add TAF store directives for SHI_ALLOW_GAMMAFRICT |
810 |
o Modify diagonal solvers, now three versions (upon request): |
811 |
#ifndef SOLVE_DIAGONAL_AUTODIFF |
812 |
1. default version (dating back a while ago) |
813 |
#else /* def SOLVE_DIAGONAL_AUTODIFF */ |
814 |
# ifdef SOLVE_DIAGONAL_KINNER |
815 |
2. adjoinable version with k-innermost loop (G. Forget) |
816 |
# else |
817 |
3. adjoinable vectorized version of 2. |
818 |
# endif |
819 |
#endif /* SOLVE_DIAGONAL_AUTODIFF */ |
820 |
All flags are currently set within routines, but could/should be moved to CPP-options. |
821 |
Array bounds for 1. are as before, for 2.,3. cover the entire domain |
822 |
(could be changed for 1. too). |
823 |
o verification/lab_sea (fwd): |
824 |
- update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY, |
825 |
use 7 categories (except hb87), new solve4temp params (except salt_plume), |
826 |
constant salinity (=4) or variable salinity (salt_plume) done through |
827 |
SItracer. |
828 |
o pkg/seaice: |
829 |
- rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0; |
830 |
- remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t, |
831 |
SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz) |
832 |
from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when |
833 |
SEAICE_freeze got retired) but already better than previously with |
834 |
SEAICE_freeze=123456.7 deg.C; |
835 |
- move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS |
836 |
(safer multi-threaded setting); always set SEAICEuseEVP; |
837 |
- setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to |
838 |
SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report); |
839 |
stop if multiple specifications for the same coeff; make sure default |
840 |
SEAICE_mcPheePiston is compatible with drF(1) & deltaT. |
841 |
o pkg/obcs: |
842 |
- allow to switch to upwind 1rst order advection scheme for the advective |
843 |
flux computation at the open-boundary; disabled for adjoint built. |
844 |
o pkg/ptracers: |
845 |
- rename PTRACERS_RESTART.h -> PTRACERS_START.h |
846 |
- rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F |
847 |
- add parameter to decide when to start a tracer; use internal flag to |
848 |
know which tracer to step-forward; switch this internal flag at the top |
849 |
of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled |
850 |
for adjoint built. |
851 |
o pkg/seaice: |
852 |
- add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ; |
853 |
- move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ; |
854 |
- keep experiment offline_exf_seaice truly single category (set MULTDIM=1). |
855 |
o pkg/ecco: |
856 |
- fix writing of output file DiagnosCost_ClimSalt/Theta |
857 |
and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc). |
858 |
o pkg/seaice: |
859 |
- add missing initialisation of COR_ICE array in dynsolver.F |
860 |
- merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is |
861 |
compiled either way, and is tested in all exps (multidim was only tested |
862 |
in lab_sea ad before). |
863 |
- cosmetic change to prepare for future addition of ITD. no change to results. |
864 |
no defaults change. |
865 |
- added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise). |
866 |
- by lack of adequate verification experiments, I further used custom versions |
867 |
of global_ocean.cs32x15 to test multicat or not, with pickup or not. All |
868 |
should be correct. |
869 |
- avoid recomputations in ad. |
870 |
o array initialisation in adjoint mode: |
871 |
1) pkg/mom_common/mom_calc_ke.F: |
872 |
add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC): |
873 |
The S/R which calls MOM_CALC_KE initialises KE but in some recomputation |
874 |
part this initialisation is gone, resulting in Floating Point Exception |
875 |
(caught by open64 compiler with debug option). |
876 |
2) model/src/convective_weights.F |
877 |
set output convectCount over the full array range (instead of doing |
878 |
an update): this fix a similar issue when called within recomputation (adjoint) |
879 |
which could by-pass the initialisation (normally done in the caller S/R). |
880 |
o pkg/seaice: |
881 |
- final version of turbulent flux params, as agreed at MIT ice meet: |
882 |
SEAICE_mcPheePiston (default is ~ 0.000875) |
883 |
SEAICE_mcPheeTaper (default is 0.) |
884 |
SEAICE_frazilFrac (defualt is 1.) |
885 |
SEAICE_mcPheeStepFunc (default is false) |
886 |
- changes results at trunction error level |
887 |
- ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo |
888 |
o added pkg/frazil: |
889 |
- see frazil_description.tex for details |
890 |
- verification experiment is global_with_exf/input.yearly; changes output.yearly.txt |
891 |
o pkg/shelfice/shelfice_thermodynamics.F |
892 |
- fix exponents for velocity dependent exchange coefficients: change |
893 |
from 2/3(=0) to 0.66666666666666667 |
894 |
- move computation of velocity dependent exchange coefficients into |
895 |
separate loop, so that it applies to both thermodynamics |
896 |
- move some divisions by constants out of loops |
897 |
|
898 |
checkpoint63j (2012/02/16) |
899 |
o pkg/seaice: |
900 |
- overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc. |
901 |
- SItracer: added run time params, and allow coupling to ocn salinity. |
902 |
o pkg/seaice: remove (almost) all divisions by constants within loops |
903 |
in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d |
904 |
results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only |
905 |
those, caused by 1/QI -> recip_QI) -> update output.seaice.txt, |
906 |
output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt |
907 |
o pkg/seaice : |
908 |
- simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula |
909 |
= 1 or 2, using newly added run time parameter SEAICE_availHeatTaper. |
910 |
- fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148. |
911 |
- add permanent SItflux diag that corresponds to TFLUX but includes |
912 |
ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget. |
913 |
- allow activation/testing of a fix for suspected missing term in |
914 |
ocn-ice heat budget (to be confirmed). To test this, you want to |
915 |
undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param |
916 |
SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic. |
917 |
- no change in results, fwd or ad. |
918 |
o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below: |
919 |
- switch to variable freezing point. |
920 |
Results change : cg2d -> 1 digits; ad -> 3-6-6 digits. |
921 |
- bug fix : the sublimation term that was missing is now activated. |
922 |
Results change : cg2d -> 2 digits; ad -> 8-6-6 digits. |
923 |
- bug fix : flooding sign term for SIsal0.NE.0. |
924 |
Result change : cg2d -> 8 digits; ad -> 11-12-9 digits. |
925 |
o pkg/seaice: |
926 |
- unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT |
927 |
is now the default, and the old default constant freezing point is recovered |
928 |
with SEAICE_tempFrz0 = -1.96, |
929 |
SEAICE_dTempFrz_dS = 0., |
930 |
- retire SEAICE_freeze (= the old way of specifycing the constant freezing point) |
931 |
- remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there. |
932 |
- bug fix (thanks to M. Losch) : the sublimation term that was missing is now |
933 |
activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM. |
934 |
- bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) |
935 |
was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail). |
936 |
- bug fix (thanks to O. Jahn) : area loss for melting got messed up in |
937 |
seaice_growth r149 for legacy branch (no results change). |
938 |
- introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code |
939 |
from I. Fenty). |
940 |
- results did not change except for global_ocean.cs32x15, mostly due to the |
941 |
switch to variable freezing point (see above item for detail). |
942 |
o pkg/thsice: |
943 |
- fix and simplify interface to salt_plume pkg ; diagnose directly amount of |
944 |
seawater freezing in thsice_calc_thickn (not used). |
945 |
o pkg/seaice: turbulent flux term specification via run time params. |
946 |
- replace CPP switches with run time switches to facilitate testing |
947 |
- retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, |
948 |
GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR |
949 |
- added runtime parameter : SEAICEturbFluxFormula |
950 |
- move Mcphee constants to SEAICE_PARAMS.h |
951 |
- seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula; |
952 |
SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); |
953 |
remove seaice_summary call (moved to seaice_init_fixed) |
954 |
- seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on |
955 |
SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms) |
956 |
- seaice_summary.F : add missing report of read turbulent flux term set up |
957 |
and SITRACER. |
958 |
- seaice_check.F : check range; inform and stop if retired CPPs are used |
959 |
(incl. SEAICE_AGE). |
960 |
- seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without |
961 |
CPP switch, same computation as before for the different options. |
962 |
- change results at the truncation level. |
963 |
o pkg/seaice: |
964 |
- remove un-used parameters LAD & MAX_TICE ; add new run-time parameters: |
965 |
useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and |
966 |
SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY. |
967 |
- update verification/*/input*/data.seaice: |
968 |
to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY |
969 |
code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ; |
970 |
and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code, |
971 |
set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0. |
972 |
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY): |
973 |
- remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same |
974 |
algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0); |
975 |
difference in results only due to machine truncation. |
976 |
- remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using |
977 |
MaykutPolySatVap; keep MIN_LWDOWN. |
978 |
- adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation. |
979 |
- update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87, |
980 |
+ 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits). |
981 |
o pkg/salt_plume: |
982 |
- isolate saltPlumeFlux array exch into a specific S/R called from |
983 |
do_oceanic_phys.F |
984 |
- add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice. |
985 |
o verification: |
986 |
- move untested set-up to MITgcm_contrib/verification_other. |
987 |
o pkg/seaice: |
988 |
- retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER. |
989 |
o pkg/seaice: |
990 |
- seaice_solve4temp.F (keeping results unchanged): |
991 |
* add 2 future run-time params to select which saturation vapor pressure |
992 |
formula is used and how post-iteration fluxes are set. |
993 |
Temporary set these 2 params according to option SOLVE4TEMP_LEGACY; |
994 |
* New piece of code (not used) to update surf. atmos. heat flux F_ia using |
995 |
the linearized expression to stay consistent with tsurf finding. |
996 |
- seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x |
997 |
can be < 0. |
998 |
o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef): |
999 |
- remove from F_ia (and from it's derivative dFiDTs1) the contribution of |
1000 |
conductive heat flux F_c , and add it explicitly when updating tsurf as |
1001 |
solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf |
1002 |
so that now F_ia has a consistent meaning through the entire routine. |
1003 |
This causes differences at truncation level: update output of fwd exp. |
1004 |
global_ocean.cs32x15.seaice. |
1005 |
o pkg/seaice: |
1006 |
- lots of editing/cleaning in seaice_solve4temp.F + better documentation |
1007 |
of arrays, sign/direction of fluxes; no effect on results. |
1008 |
- replace hard coded 273.16 (=previous value of celsius2K) by celsius2K |
1009 |
in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part); |
1010 |
note: this should have been done before changing celsius2K default. |
1011 |
- to keep results unchanged, add back old value of celsius2K in verification |
1012 |
exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs |
1013 |
- replace hard coded seawater freezing temp in seaice_solve4temp.F (part |
1014 |
SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default |
1015 |
value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater |
1016 |
freezing temp is consistent with value in seaice_growth.F ; this causes |
1017 |
differences at machine truncation level: update lab_sea AD output (3/4). |
1018 |
o pkg/seaice: |
1019 |
- mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask |
1020 |
and climsst/sss even when using seaice (to prevent calculation that might |
1021 |
use SST on land); does not affect any verification exp. |
1022 |
- apply mask to taux,tauy (in seaice_get_dynforcing.F); update output |
1023 |
of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix. |
1024 |
o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness |
1025 |
over land (non-legacy code) |
1026 |
o vectorize salt_plume package: |
1027 |
- add extra code to salt_plume_frac and salt_plume_tendency_apply_s |
1028 |
- this code computes plumebk everywhere (also over land), thus requires |
1029 |
code to avoid divisions by zero and catch the case of kLev=Nr. |
1030 |
- efficiency of salt_plume_frac is still sub-optimal |
1031 |
o tools (genmake2): |
1032 |
- fix makefile NAME specification (option: -makefile NAME) by adding |
1033 |
"-f $MAKEFILE" in few places where it was missing including makedepend |
1034 |
command (contribution from Paul). |
1035 |
|
1036 |
checkpoint63i (2012/01/24) |
1037 |
o model/src: |
1038 |
- add factorized versions of some EOS code to find_rho.F, |
1039 |
define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX) |
1040 |
o model/src: |
1041 |
- add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h; |
1042 |
- change default celsius2K from 273.16 to 273.15 |
1043 |
- to keep results unchanged, add back old value of celsius2K in verification |
1044 |
exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd), |
1045 |
global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm). |
1046 |
o model/src: add a little initialisation trick to find_rho.F and find_alpha.F |
1047 |
to make TAF generate vectorizable code |
1048 |
o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows. |
1049 |
Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers |
1050 |
have flags that do this more efficiently. |
1051 |
o pkg/diagnostics/diagstats_calc.F |
1052 |
- for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact |
1053 |
o pkg/obcs (with exch2): |
1054 |
- derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F) |
1055 |
and remove code (in obcs_readparms.F) which was based on EXCH of indices |
1056 |
(through buffer) and did not account for exch2 (e.g., CS-grid) topology. |
1057 |
o pkg/exf and seaice exp: |
1058 |
- change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0) |
1059 |
so that switching off area & heff advection flags does not affect results. |
1060 |
- change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h |
1061 |
- keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef |
1062 |
EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update |
1063 |
results of verification experiments: 1D_ocean_ice_column(fwd), |
1064 |
global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8) |
1065 |
and offline_exf_seaice (all 4). |
1066 |
o pkg/seaice: |
1067 |
- remove array YNEG, RIVER, TMIX (replaced by local var) from common block; |
1068 |
remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef. |
1069 |
- fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY) |
1070 |
but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and |
1071 |
not multi-dim advection; |
1072 |
- fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and |
1073 |
SHORTWAVE_HEATING #undef. |
1074 |
o optim: make Makefile more robust (?) |
1075 |
o pkg/obcs: |
1076 |
* fix treatment of obcs_read_pickup for TAF |
1077 |
o pkg/shelfice: |
1078 |
* add missing initialisation of num_shifwflx |
1079 |
* new adjoint verification exp. for isomip |
1080 |
* change Prandtl and Schmidt numbers from generic formulations |
1081 |
(in terms of model diffus. and visc.) to separate runtime |
1082 |
parameters, with Holland and Jenkins (1999) default values. |
1083 |
o pkg/exf (interpolation): |
1084 |
- extended input field (2 rows) near the N & S poles: |
1085 |
* fill in with the symetric value (when even Nb of data in longitude) |
1086 |
* add average value at the poles only for scalar quantities ; for vector |
1087 |
component interpolation, skip the averaging and keep duplicated values, |
1088 |
unless the 2 components have same location (uvInterp=T) in which case |
1089 |
interpolate the 2 components together using S/R EXF_INTERP_UV. |
1090 |
- new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field |
1091 |
together: this allows to account properly for local orientation when |
1092 |
averaging at N & S pole. |
1093 |
- add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding |
1094 |
exf-interpolation near N & S poles. Undef by default. |
1095 |
- add debug check/print on 1rst iter if debugLevel >=2. |
1096 |
o pkg/exf: |
1097 |
- change masking flags definition (no longer "parameter"), put them in |
1098 |
common block and set them in S/R EXF_INIT_FIXED. |
1099 |
- change recognized masking flag from s,u,v to c,w,s since the mask |
1100 |
to use (maskC,W,S) depends on position on model grid and has little to |
1101 |
do with scalar/vector difference; fix masking if using P-coordinates. |
1102 |
- fix masking of wind-stress (was wrong if interpolated or read on A-grid) |
1103 |
and update results of exp. global_with_exf (x2). |
1104 |
- fix setting of zenith-angle table when SHORTWAVE_HEATING is undef. |
1105 |
o pkg/obcs |
1106 |
- S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate) |
1107 |
o pkg/exf (interpolation): |
1108 |
- assume periodicity in X only if input field cover full longitude range. |
1109 |
- improve search for lat. index (supposed to be faster, in ~log2(ny) steps, |
1110 |
and should vectorise). |
1111 |
- fix input lat of the 2 added row (in case we provide N.pole data). |
1112 |
|
1113 |
checkpoint63h (2011/12/30) |
1114 |
o pkg/seaice: |
1115 |
- change declaration of UVM from _RL to _RS in order to get B-grid |
1116 |
uIce,vIce monitor when _RS = real*4 |
1117 |
o pkg/offline: |
1118 |
- new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags); |
1119 |
- compute vertical velocity if not read from file (switch on exactConserv |
1120 |
& staggerTimeStep); |
1121 |
- fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq. |
1122 |
o verification: |
1123 |
- update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input) |
1124 |
with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m": |
1125 |
fix Pb in yG definition @ 2 missing corners (previously yG was averaged); |
1126 |
- update output of exp. global_ocean.cs32x15.viscA4 after changing |
1127 |
grid-file angles (used here for coriolis-3d); |
1128 |
- remove (or gzip) few files not needed to run fizhi-cs experiments. |
1129 |
o pkg/exf (vector interpolation): |
1130 |
- rotate vector component toward local grid-axis orientation using grid-angles |
1131 |
(stored in GRID.h) instead of locally computed rotation angle; keep old code |
1132 |
available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default). |
1133 |
o pkg/seaice: |
1134 |
- allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION |
1135 |
undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined. |
1136 |
o pkg/PKG_OPTIONS.h files: |
1137 |
- move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h", |
1138 |
outside of the #ifdef ALLOW_THISPKG / #endif block. |
1139 |
- update verification/*/code/PKG_OPTIONS.h files. |
1140 |
o add a verification experiment (offline_exf_seaice/input.seaice) that test |
1141 |
the B-grid LSOR solver |
1142 |
o pkg/seaice: sort out emissivity and long wave radiation step 2: |
1143 |
- add emissivity for snow and ice as new run-time parameters |
1144 |
(unfortunately) that default to the corresponding exf values; this |
1145 |
changes results in most verification experiments so that for backward |
1146 |
compatibility these parameter have to be set explicitly to inconsistent |
1147 |
values (ugly); |
1148 |
- the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired |
1149 |
emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp |
1150 |
until we agree how to handle this bug properly |
1151 |
o pkg/exf (interpolation): |
1152 |
- add a set of run-time param ({inputfield}_interpMethod), one for |
1153 |
each interpolated input field, to select the interpolation method |
1154 |
with a value of zero switching off the interpolation; |
1155 |
- print interpolation parameters to standard output; |
1156 |
- refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined |
1157 |
(to use instead runoff_interpMethod=0 in data.exf). |
1158 |
- simplify default setting of interpolation parameters (for all fields, |
1159 |
set position to match model grid cell-center position, leading to trivial |
1160 |
interpolation in case of regular Lat-Lon grid) and fix for the case of |
1161 |
non-uniform delY. |
1162 |
o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for |
1163 |
within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1. |
1164 |
this factor is absolutely required, because the lw exitance (= out-going |
1165 |
long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown, |
1166 |
where the reflectivity rho = 1-emissivity for conservation reasons. Once |
1167 |
this is established, we can remove the CPP-Flag (if we want to). |
1168 |
o pkg/seaice: |
1169 |
- qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and |
1170 |
ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined |
1171 |
- sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity |
1172 |
what the name implies (and not emissivity*BoltzmannConstant), this means |
1173 |
the old default value of 5.5e-8 now means |
1174 |
5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in |
1175 |
S/R exf_readparms |
1176 |
- FV-discretization of the B-grid LSOR solver, turn on with |
1177 |
SEAICE_LSRBNEW. This new solver also involves a slight re-organization |
1178 |
of the calling routine dynsolver, so that B and C-grid code look a |
1179 |
little more alike. |
1180 |
- fix index bugs in ostres.F (B-grid code) |
1181 |
o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better |
1182 |
o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the |
1183 |
default for SEAICE_emissivity, if useEXF; requires setting a wrong |
1184 |
parameter value in global_ocean.cs32x15/input.seaice/data.seaice for |
1185 |
backward compatiblity |
1186 |
o model/src: use sigmaR in calc_ivdc |
1187 |
|
1188 |
checkpoint63g (2011/12/16) |
1189 |
o pkg/seaice/seaice_growth.F: |
1190 |
fix heat conservation of the coupled ocean-seaice system. |
1191 |
when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of |
1192 |
solid vs liquid water treatment is resolved via QNET. |
1193 |
o pkg/seaice/seaice_growth.F: |
1194 |
add missing term for sublimation in saltFlux, which was breaking conservation. |
1195 |
o pkg/seaice/seaice_model.F: |
1196 |
Remove this patholigical case treatment in evolution branch, |
1197 |
where it is un-necessary and breaks conservation. |
1198 |
Update global_ocean.cs32x15/results accordingly for |
1199 |
output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt |
1200 |
o model/src: |
1201 |
useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in |
1202 |
external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE. |
1203 |
o pkg/obcs: |
1204 |
modify Stevens boundary conditions so that S/R obcs_calc_stevens computes |
1205 |
tendency for temperature and salinity that is then applied to update |
1206 |
theta and salt in S/R obcs_apply_ts; this requires proper masking of all |
1207 |
horizontal advection and diffusion contributions on the boundary (in |
1208 |
S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and |
1209 |
removing the mask in S/R timestep_tracer. The advantage of this approach is |
1210 |
that the updated tracer values include contributions from the surface |
1211 |
forcing and vertical diffusion. |
1212 |
This modification changes exp4.stevens because of vertical diffusion. |
1213 |
o model/src: |
1214 |
change non-curvilinear grid setting to also work with exch2 + blank tiles: |
1215 |
- move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst |
1216 |
face dimensions. |
1217 |
- new S/R INI_LOCAL_GRID to define model tile-local grid (using same units |
1218 |
as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID |
1219 |
and INI_SPHERICAL_POLAR_GRID. |
1220 |
change test-experiment global_ocean.90x40x15: |
1221 |
- split the domain in many more tiles (9x4 tiles of 10x10 each); |
1222 |
- switch to exch2 and remove 1 blank-tile (but only for MPI test). |
1223 |
- update results of both test (std & dwnslp). |
1224 |
o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in |
1225 |
tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation |
1226 |
o model/src: |
1227 |
- take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS |
1228 |
and fix initialisation when using sigma-coords. |
1229 |
o model/src: |
1230 |
- improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc. |
1231 |
to their current value at the beginning of forward_step.F": add a new run-time |
1232 |
switch "doResetHFactors" (default=false) and use it to do (or not) the resetting. |
1233 |
- set doResetHFactors=T in the following test exp: |
1234 |
global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS), |
1235 |
global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS) |
1236 |
and tutorial_global_oce_in_p (nonLinFS in p) |
1237 |
o pkg/ecco |
1238 |
- added IES cost term |
1239 |
o verification/advect_xz |
1240 |
- scale down the depth by 1/100 (from 200 km to just 2.km) |
1241 |
- add secondary test using divergent flow, r-star and implicit vertical advection. |
1242 |
- add note (check_conserve_TS.txt) and matlab script to check global |
1243 |
conservation of T & S with NonLin-FreeSurf and Adams-Bashforth. |
1244 |
o pkg/rbcs: |
1245 |
- add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F). |
1246 |
o pkg/obcs (Stevens BCs): |
1247 |
- fix various problems in the phase speed computations of the Stevens |
1248 |
boundary conditions: |
1249 |
- sign error for western and southern boundaries, |
1250 |
- time tendencies were underestimated by factor of dTracerLev and some just |
1251 |
zero (for multidim advection schemes) -> now estimate time tendencies |
1252 |
from difference between previous (n) time level and the one before (n-1); |
1253 |
this requires storing a field per tracer per boundary, also in the pickup |
1254 |
files. |
1255 |
- replace deltaTmom in cflMer/Zon computation with dTracerLev |
1256 |
- set default phase velocity to cflMer/Zon |
1257 |
- update verification experiment exp4.stevens |
1258 |
o pkg/generic_advdiff (implicit_r): |
1259 |
- fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf |
1260 |
(remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F); |
1261 |
- fix implicit vertical diffusion or advection with NonLin FreeSurf |
1262 |
(was using current recip_hFacC instead of future recip_hFacC): set future |
1263 |
recip_hFac in thermodynamics.F and pass & use it in all vertical implicit |
1264 |
solver S/R ; |
1265 |
- fill diagnostics of vertical advective fluxes (computed from tendency) |
1266 |
when using implicit vert. advection; |
1267 |
- update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion: |
1268 |
global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD), |
1269 |
tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD) |
1270 |
and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5. |
1271 |
o pkg/diagnostics: |
1272 |
- add diags for T & S tendency which goes through Adams-Bashforth. |
1273 |
|
1274 |
checkpoint63f (2011/11/30) |
1275 |
o pkg/obcs/obcs_calc_stevens.F: |
1276 |
- join some loops to reduce number of if-statements |
1277 |
- fix a bug in code for northern and southern boundaries. |
1278 |
o pkg/seaice/seaice_init_varia.F |
1279 |
- undo resetting UVM=0 that has slipped in unnoticed in r1.49 and |
1280 |
caused zero ice-velocities for the B-grid code |
1281 |
o pkg/seaice/seaice_init_fixed.F |
1282 |
- fix a bug in the initialisation of the second metric terms |
1283 |
k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0. |
1284 |
- this affects all seaice configurations with useCurviLinearGrid = .true. |
1285 |
and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms |
1286 |
= .true. (default) |
1287 |
- the only verification experiment affected is global_ocean.cs32x15: |
1288 |
icedyn, seaice, and seaice_dynmix (AD) |
1289 |
o pkg/thsice/thsice_diagnostics_state.F |
1290 |
- only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does |
1291 |
not contain garbage that can lead to surprises in diagstats_calc.F |
1292 |
o model/src: |
1293 |
- move bi,bj loops inside INTEGR_CONTINUITY ; |
1294 |
- call INTEGR_CONTINUITY directly from forward_step.F |
1295 |
(previously called from momentum_correction_step.F) |
1296 |
- call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F, |
1297 |
forward_step.F and pkg/ecco/the_main_loop.F |
1298 |
o model/src/do_oceanic_phys.F: |
1299 |
- reset addMass to zero only if useICEFRONT ; |
1300 |
- separated k-loop for rhoInSitu calculation ; |
1301 |
- add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P) |
1302 |
and at constant T,S (= WdRHOdP); |
1303 |
NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport |
1304 |
of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical |
1305 |
transport of locally-referenced potential density); |
1306 |
to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP) |
1307 |
o gluemnc: |
1308 |
- replace ncrcat with ncks when adding variables to *.glob.nc |
1309 |
- change the way variables without record dimensions are handled so that |
1310 |
files that have variables with and without record variables can be glued: |
1311 |
add a record dimension with a new unique name to be able to differentiate |
1312 |
between variable with and without a-prior record dimensions. Remove |
1313 |
this record dimension before adding the variable to the *.glob.nc file. |
1314 |
This procedure automatically works also for grid.*.nc files that do not |
1315 |
have any record dimension. |
1316 |
o verification/cpl_aim+ocn: |
1317 |
- generate new reference output on baudelaire (gfortran, mpich2) (previously |
1318 |
from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script. |
1319 |
o pkg/obcs/obcs_calc_stevens.F: |
1320 |
- add code for northern and southern boundaries. |
1321 |
- reorder some loops to save some operations and so that drFBar can be scalar |
1322 |
o model/src: |
1323 |
- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
1324 |
truncation) and add diagnostics for Adams-Bashforth tendency increment. |
1325 |
- update test-exp. AD output: |
1326 |
1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
1327 |
and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
1328 |
front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
1329 |
global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
1330 |
matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
1331 |
tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
1332 |
tutorial_plume_on_slope. |
1333 |
o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
1334 |
that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
1335 |
and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
1336 |
does not even come with an F77 compiler anymore, this should not be |
1337 |
a limitation |
1338 |
|
1339 |
checkpoint63e (2011/11/06) |
1340 |
o pkg/seaice adjoint of LSR: |
1341 |
- substantially rework STORE dirs. |
1342 |
- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
1343 |
this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
1344 |
and only perform SOLV_MAX_FIXED adjoint iters. |
1345 |
If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
1346 |
always goes to same record, meaning that the last forward field will be |
1347 |
the one used in the adjoint - an approximation. |
1348 |
- now produces non-zero LSR-related gradients, and acceptable gradients for |
1349 |
An's zonal (x-z) test case (to be checked in) |
1350 |
- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
1351 |
(but these are screwed up by the thermodynamics in the first place); |
1352 |
reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
1353 |
output_adm.txt also reflects changes to seaice_lsr |
1354 |
- global_ocean.cs32x15: |
1355 |
* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
1356 |
(output_adm.seaice.txt was updated) |
1357 |
* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
1358 |
(output_adm.seaice_dynmix.txt) |
1359 |
o test-exp. exp4+stevens: |
1360 |
- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
1361 |
o pkg/seaice (lsr solver): |
1362 |
- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
1363 |
update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
1364 |
- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
1365 |
- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
1366 |
into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
1367 |
- compute (with new S/R) and print initial (+ free-driff sol. if available) |
1368 |
and final residual of linearised system. |
1369 |
o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
1370 |
(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
1371 |
o pkg/obcs: Stevens BCs (still only for east and west) |
1372 |
- fix Stevens BCs by using intermediate velocities of previous |
1373 |
time step as "baroclinic" contribution rather velocity of one grid cell |
1374 |
inside the boundaries; more consistent but makes the entire treatment |
1375 |
more complicated, requires new pickup files and two new S/Rs: |
1376 |
obcs_copy_uv_n and obcs_save_uv_n |
1377 |
keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
1378 |
(undefined by default) |
1379 |
- silently move computation of some grid factors into separate loops to |
1380 |
save some recomputations |
1381 |
- add a hack for non-linear free surface |
1382 |
- add a verification experiment to exp4 that tests this code |
1383 |
o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
1384 |
|
1385 |
checkpoint63d (2011/10/25) |
1386 |
o pkg/obcs + seaice-dynamics: |
1387 |
- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
1388 |
solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
1389 |
values (consistent with an implicit method). |
1390 |
- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
1391 |
return to older implementation (same results as before); note that none of |
1392 |
the "experimental" OBCS_SEAICE options are implemented in the new version. |
1393 |
- switch test exp. seaice_obcs to use new version (update output). |
1394 |
o pkg/seaice: |
1395 |
- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
1396 |
- add parenthesis in Water-Ice drag calculations (evp & lsr); |
1397 |
- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
1398 |
and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
1399 |
- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
1400 |
and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
1401 |
o pkg/layers: |
1402 |
- Include potential density as new coordinate (Thanks to David Munday) |
1403 |
o pkg/dic: |
1404 |
- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
1405 |
carbonate computation/output to CALC_PCO2_APPROX |
1406 |
o pkg/generic_advdiff |
1407 |
- make TAF generate code that vectorizes: |
1408 |
gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
1409 |
o model/src: |
1410 |
- improve vectorization also for adjoint code of |
1411 |
solve_tridiagonal and solve_pentadiagonal. As this requires up to |
1412 |
5 new 3D-fields, this code is only turned on for the combination of |
1413 |
ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
1414 |
for singular matrix check (only for TARGET_NEC_SX). |
1415 |
- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
1416 |
ALLOW_AUTODIFF. This flag now needs to be set outside of |
1417 |
solve_tri/pentadiagonal.F |
1418 |
o pkg/exf: |
1419 |
- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
1420 |
optional namelist EXF_NML_OBCS). |
1421 |
- add many debug-print (to trace down where pkg/cal error msg comes from) |
1422 |
o pkg/mom_vecinv/mom_vi_hdissip.F |
1423 |
- rearrange loops so that vectorization is improved and in particular |
1424 |
the adjoint routine vectorizes. The code is a little longer now, but I |
1425 |
think easier to read. |
1426 |
Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
1427 |
o pkg/seaice: |
1428 |
- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
1429 |
o pkg/exch2: |
1430 |
- alternative code (without tile x tile matrix) for cumulated (global) sum; |
1431 |
used as default; keep using matrix version in adjustment.cs-32x32x1. |
1432 |
o tools/build_options: |
1433 |
- after merging some MPI and/or multi-threads specific optfiles so that |
1434 |
the modified default optfile support both built (using genmake2 -mpi |
1435 |
for the MPI built, using genmake2 -omp for OpenMP built), |
1436 |
move now obsolete optfiles to tools/build_options/unsupported/ |
1437 |
(add copy of email sent to support list in doc/optfiles_changes.txt) |
1438 |
|
1439 |
checkpoint63c (2011/09/28) |
1440 |
o pkg/ebm: |
1441 |
- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
1442 |
test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
1443 |
o pkg/seaice (SItracer pickup) |
1444 |
* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
1445 |
To be done: |
1446 |
- thorough testing of missing fields in S/R seaice_read_pickup |
1447 |
- thorough matching between generic tracers and specific fields used |
1448 |
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
1449 |
o pkg/grdchk: |
1450 |
- all procs calculate and print finite-difference gradient (for testreport) |
1451 |
- change description output used by testreport; |
1452 |
- AD testing: also compare and report Finite-difference gradient; |
1453 |
=> update all output_adm*.txt |
1454 |
o test exp. global_ocean_ebm: |
1455 |
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
1456 |
and turn on exactConserve; update (fwd) output. |
1457 |
o pkg/seaice (LSR): |
1458 |
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
1459 |
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
1460 |
* identical results with non-CS topology (but save up to half of EXCH calls) |
1461 |
* no much changes in cs-32 verification tests since no ice at face edges |
1462 |
(differences due to convergence criteria, since nb of iterations changed) |
1463 |
* expect some differences on lat-lon-cap grid. |
1464 |
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
1465 |
o pkg/exch2: |
1466 |
- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
1467 |
many tiles); until alternative coding is added, just add a stop. |
1468 |
o pkg/kpp: |
1469 |
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
1470 |
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
1471 |
o optfiles: |
1472 |
- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
1473 |
into corresponding standard one, which now support different build: |
1474 |
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
1475 |
- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
1476 |
o pkg/obcs (seaice): |
1477 |
- add missing EXCH for uIce,vIce after applying OBCS; |
1478 |
- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
1479 |
argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
1480 |
EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
1481 |
- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
1482 |
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
1483 |
and eedata.mth for MPI and mutlti-threaded testing. |
1484 |
o pkg/flt: |
1485 |
- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
1486 |
- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
1487 |
- fix pickup and trajectories + profiles output with multi-threads; |
1488 |
- add parameter to select group of fields to write along trajectory and |
1489 |
profile (default unchanged); |
1490 |
- only call PORT_RAND* function when flt_noise <> 0; |
1491 |
- add multi-threaded test for verification exp. flt_example. |
1492 |
o eesupp/src: |
1493 |
- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
1494 |
- USE_OMP_THREADING: check that number of threads (from eedata) matches |
1495 |
actual number (from env.var. setting). |
1496 |
o pkg/ebm: |
1497 |
- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
1498 |
- add multi-threaded test for verification exp. global_ocean_ebm |
1499 |
|
1500 |
checkpoint63b (2011/08/29) |
1501 |
o pkg/ebm: |
1502 |
- fix sign of runoff; |
1503 |
- update directly forcing fields (Qnet,EmPmR) to use standard |
1504 |
external_forcing_surf.F (remove ebm_forcing_surf.F); |
1505 |
- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
1506 |
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
1507 |
and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
1508 |
- update global_ocean_ebm parameters file data and update output (fwd+ad). |
1509 |
o verification/matrix_example: |
1510 |
- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
1511 |
MPI and mutlti-threaded testing. |
1512 |
o pkg/matrix: |
1513 |
- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
1514 |
- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
1515 |
- fix for multi-threaded (remove DATA statement); |
1516 |
- use standard DIFFERENT_MULTIPLE function; |
1517 |
- add MATRIX_OPTIONS.h |
1518 |
o verification/matrix_example: |
1519 |
To allow to split the domain in several tiles, change the domain size |
1520 |
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
1521 |
Western side) of land points. |
1522 |
o (*_)write_pickup: |
1523 |
- fix few bugs in mypackage_read/write_pickup.F |
1524 |
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
1525 |
array of length 1 (was caught by compiler syntax-check). |
1526 |
o pkg/diagnostics (velocity potential solver): |
1527 |
- fix initialisation of main diagonal matrix (for overlap values) |
1528 |
o tools/build_options: |
1529 |
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
1530 |
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
1531 |
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
1532 |
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
1533 |
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
1534 |
and use "-devel" testreport option for standard testing on baudelaire. |
1535 |
o pkg/grdchk: |
1536 |
- Assume that all gradient-check position are within the same tile |
1537 |
corresponding to global indices (iGloTile,jGloTile) and that |
1538 |
positions (i,j indices or nbeg) are local to this tile; |
1539 |
- set tile local-indices and proc. number according to tile global-indices; |
1540 |
- remove grdchkwhichproc from namelist (retired param); |
1541 |
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
1542 |
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
1543 |
o adding package bbl (Bottom Boundary Layer) |
1544 |
description in MITgcm/pkg/bbl/bbl_description.tex |
1545 |
example/test experiment in MITgcm_contrib/bbl |
1546 |
o adjoint verifications |
1547 |
- changed 5 experiments to multi-tiles |
1548 |
* global_ocean.90x40x15 |
1549 |
* obcs_ctrl |
1550 |
* offline_exf_seaice |
1551 |
* tutorial_dic_adjoffline |
1552 |
* tutorial_tracer_adjsens |
1553 |
changed reference output for those that crossed tile boundaries |
1554 |
(changed choices of gradient check positions) |
1555 |
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
1556 |
- temporary bug fix in grdchk_loc.F for obcs |
1557 |
o genmake2 & testreport |
1558 |
- add target "obj" (just for OBJFILES files) to Makefile; |
1559 |
- add option to specify FEXTRAFLAGS on command line. |
1560 |
o pkg/mypackage: |
1561 |
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
1562 |
|
1563 |
checkpoint63a (2011/08/02) |
1564 |
o pkg/diagnostics (velocity potential): |
1565 |
- fix velocity-potential calculation when using OBCS: balance net inflow |
1566 |
at each level (new S/R OBCS_DIAG_BALANCE). |
1567 |
- fix some of the problems with OBCS in stream-function calculation. |
1568 |
o pkg/exf/exf_readparms.F |
1569 |
- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
1570 |
EXF_NML_OBCS) more consistent, so that you need not have these lists |
1571 |
in data.exf when they are not used. |
1572 |
o optim/optim_readdata.F: |
1573 |
- add some output about obcs variables that might help debugging |
1574 |
- add a check about nvarlength |
1575 |
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
1576 |
o pkg/diagnostics (velocity potential): |
1577 |
- fix mask for OBCS (still problems in stream-function with OBCS); |
1578 |
- add specific parameter (default = main code CG2D params) for solver; |
1579 |
- in case of poor convergence, use solution corresponding to lowest residual. |
1580 |
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
1581 |
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
1582 |
and should be avoided where possible. |
1583 |
o model/src (rStar): |
1584 |
- include r* effect on reference-state (PhiRef) in totPhiHyd |
1585 |
(so that it's really the potential anomaly at the cell center); |
1586 |
affect solution only if z* with full pressure in EOS. |
1587 |
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
1588 |
update output (because of z* in totPhiHyd and viscA4 changes); |
1589 |
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
1590 |
@ constant r) until interpolation at constant r is implemented. |
1591 |
o pkg/diagnostics |
1592 |
- fix RCENTER diagnostics in case cell center is not at interface middle |
1593 |
o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
1594 |
this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
1595 |
that THETA and SALT are "conservative temperature" and "absolute |
1596 |
salinity" |
1597 |
o pkg/ctrl |
1598 |
- fix computation of endrec in s/r ctrl_init_rec |
1599 |
- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
1600 |
o pkg/seaice/seaice_growth.F |
1601 |
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
1602 |
remove then obsolete STORE directives |
1603 |
- fix STORE directives for tice and tices, so that only the |
1604 |
appropriate part of the fields are stored (and not the entire |
1605 |
field); update global_ocean.cs32x15.seaice AD output. |
1606 |
- cosmetic changes: adjust CPP flags and indentation for better |
1607 |
legibilty |
1608 |
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
1609 |
Chris Wilson) |
1610 |
o pkg/gmredi: |
1611 |
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
1612 |
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
1613 |
|
1614 |
checkpoint63 (2011/07/11) |
1615 |
o pkg/exch2: |
1616 |
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
1617 |
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
1618 |
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
1619 |
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
1620 |
o pkg/diagnostics: |
1621 |
- deal with pairs of post-processed diags which are computed together; in |
1622 |
particular, re-order list of diags within 1 file to save 2nd computation. |
1623 |
- add S/R to compute velocity stream-function (called after velocity-potential |
1624 |
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
1625 |
- add parameter to select grid-point location where PsiVEL == 0. |
1626 |
o eesupp/src: |
1627 |
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
1628 |
(specific S/R needed with exch2 topology - for now, just print an error msg) |
1629 |
o pkg/shelfice |
1630 |
- Implement friction velocity-dependent transfer coefficients following |
1631 |
Holland and Jenkins, JPO, 1999 |
1632 |
Original code by M. Losch with small modifs. |
1633 |
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
1634 |
and runtime flag SHELFICEuseGammaFrict |
1635 |
o verification lab_sea & global_ocean.cs32x15: |
1636 |
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
1637 |
does not miss some dependencies (but is slower) and also works with many files |
1638 |
(default makedepend limitation for AD built). |
1639 |
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
1640 |
o pkg/diagnostics: |
1641 |
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
1642 |
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
1643 |
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
1644 |
- Extend the use of "missing_value" setting from data.diagnostics for the case |
1645 |
of counter-diagnostics (where fraction-weight is zero). This applies both to |
1646 |
MNC and MDS output files. |
1647 |
o pkg/seaice/seaice_growth.F: |
1648 |
- add 'a priori' cap of latent heat flux based on actual mass considerations |
1649 |
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
1650 |
non-legacy seaice_solve4temp. |
1651 |
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
1652 |
flux taken from the ocean if the total actual latent heat fluxes exceed |
1653 |
the maximum) |
1654 |
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
1655 |
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
1656 |
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
1657 |
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
1658 |
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
1659 |
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
1660 |
o verification 1D_ocean_ice_column: |
1661 |
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
1662 |
update results |
1663 |
o pkg/diagnostics: |
1664 |
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
1665 |
which are not filled-up but computed from other diags ; In this case, the mate |
1666 |
diag points to the primary (filled-up) diag to used for post processing. |
1667 |
- Update Velocity-potential computation using post-processed diag framework. |
1668 |
==> Change the ordering of fields and time-periods in MDS output file |
1669 |
when using periodic averaging: now writes one time record with the full set |
1670 |
of fields for this time period, then the next time reccord (it used to be |
1671 |
one field with the full set of time records then the next field). |
1672 |
Note: this is now similar to NetCDF (MNC) output file. <== |
1673 |
|
1674 |
checkpoint62z (2011/06/21) |
1675 |
o adjoint monitor: |
1676 |
- Add adjoint monitor output for packages exf, seaice |
1677 |
and update relevant testreport output |
1678 |
o pkg/seaice: |
1679 |
- re-order diags inits so that they appear in order in available_diagnostics.log |
1680 |
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
1681 |
area/heff/hsnow preceeding thermodynamic growth/melt. |
1682 |
- modified diag: SIdA; output actual effect, as the description states. |
1683 |
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
1684 |
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
1685 |
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
1686 |
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
1687 |
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
1688 |
- added diagnostics for seaice generic tracers (SItr*). |
1689 |
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
1690 |
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
1691 |
I. Fenty: 18-Jun-2011: |
1692 |
Minor changes to seaice package: |
1693 |
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
1694 |
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
1695 |
- Differentiated "regularization variables" from "floor variables" |
1696 |
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
1697 |
* hiceMin became SEAICE_hice_reg (old hiceMin) |
1698 |
(with _reg meaning regularization variable) |
1699 |
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
1700 |
so as to ensure energy conservation when going between phases |
1701 |
- A22 was not used anywhere |
1702 |
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
1703 |
well-boundedness and smooth adjoint in seaice_growth.F |
1704 |
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
1705 |
because the old regularization always set heffActual >= 0.05 cm |
1706 |
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
1707 |
on AREA when HEFF > 0. |
1708 |
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
1709 |
requiring that DISABLE_AREA_FLOOR *not* be defined |
1710 |
Affected verifications: |
1711 |
- 1D_ocean_ice_column (output.txt output_adm.txt) |
1712 |
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
1713 |
o pkg/diagnostics: |
1714 |
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
1715 |
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
1716 |
(was _RL, now integer) with option = 0 to retrieve all levels. |
1717 |
- add pieces of code to compute velocity potential at each level (new diagnostics |
1718 |
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
1719 |
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
1720 |
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
1721 |
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
1722 |
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
1723 |
diagnostics counter-mate); check that definition of counter-diagnostic |
1724 |
includes a valid counter-mate (in diagnostics_set_levels.F). |
1725 |
o model/src (rStar): |
1726 |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
1727 |
affect solution only if z* with full pressure in EOS; |
1728 |
update output of test-exp global_ocean.90x40x15. |
1729 |
o pkg/seaice: |
1730 |
- introduce siEps=1e-5 parameter |
1731 |
- use areaMax in AREA update (part 4), consistent with ridging step (part 2.5). |
1732 |
- re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code. |
1733 |
- introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer. |
1734 |
For now it covers, and was tested for, ice salinity and age (attached to HEFF), |
1735 |
as well as ice cover age and ridging index (attached to AREA). |
1736 |
For now the run time parameters (in data.seaice/SEAICE_PARM03) are |
1737 |
SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA'). |
1738 |
Up to SItrMaxNum=3 tracers can be used simultaneously. |
1739 |
o pkg/salt_plume: |
1740 |
-introduce SPsalFRAC run time parameter that sets the fraction of the |
1741 |
salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically) |
1742 |
that gets vertically redistributed (fluxed down) by pkg/salt_plume. |
1743 |
o model debug options: |
1744 |
- Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored |
1745 |
in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h). |
1746 |
- Refine debug-msg printing selection (3 new levels): |
1747 |
debugMode : controls printing of debug messages (sequence of S/R calls). |
1748 |
debugLevel : controls printing of algorithm-relevant auxiliary/debug messages |
1749 |
debLevZero = 0 ; /* level of disabled aux. msg printing */ |
1750 |
debLevA = 1 ; /* level of minimum aux. msg printing */ |
1751 |
debLevB = 2 ; /* level of low aux. print (report read-file opening)*/ |
1752 |
debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */ |
1753 |
debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */ |
1754 |
debLevE = 5 ; /* level of extensive debug printing */ |
1755 |
New debugLevel default: with default debugMode value (=F), |
1756 |
= 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.; |
1757 |
and if debugMode=T, default debugLevel = 4 (debLevD). |
1758 |
Relation with previous settings: |
1759 |
debLevB (=2) corresponds to former debLevA (=1) |
1760 |
debLevD (=4) corresponds to former debLevB (=2) |
1761 |
Note: |
1762 |
a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before); |
1763 |
b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs); |
1764 |
to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5) |
1765 |
- Add new parameter (printResidualFreq, read from PARM02 namelist) to print |
1766 |
detailed CG solvers convergence; off (=0) by default, except if debugLevel=5. |
1767 |
o pkg/obcs: |
1768 |
- change OBCSfixTopo default from True to False (should not change the results); |
1769 |
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
1770 |
o pkg/thsice: |
1771 |
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
1772 |
2nd layer seaice sublimation (unlikely to happen) |
1773 |
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
1774 |
done in gad_advection & seaice_advection). |
1775 |
o adjoint: |
1776 |
bug fix spotted by Gael Forget: |
1777 |
seaice_advection and thsice_advection still had |
1778 |
legacy CPP options to avoid CS corner updates for adjoint |
1779 |
o pkg/seaice: |
1780 |
=> Change some of the defaults (2011/05/29): |
1781 |
- change SEAICEuseFluxForm default (from False to True) |
1782 |
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
1783 |
And print warnings if DIFF1 is not set in data.seaice and centered |
1784 |
avection scheme is used without any diffusion. |
1785 |
also: |
1786 |
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
1787 |
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
1788 |
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
1789 |
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
1790 |
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
1791 |
update results of test exp.: |
1792 |
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
1793 |
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
1794 |
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
1795 |
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
1796 |
seaice_obcs: output (SEAICEuseFluxForm=T) |
1797 |
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
1798 |
for standard fwd & AD lab_sea tests (to keep the same output). |
1799 |
o pkg/seaice/seaice_growth.F: |
1800 |
- use Ian Fenty's capping formulas for actual ice |
1801 |
thickness thoughout EVOLUTION branch. |
1802 |
- put treatment pathological case #2) in CPP brackets |
1803 |
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
1804 |
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
1805 |
o pkg/seaice: |
1806 |
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
1807 |
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
1808 |
also pass fac as a param, which can be 1. (to update the tendency |
1809 |
field) or the time step (to update the field itself). |
1810 |
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
1811 |
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
1812 |
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
1813 |
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
1814 |
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
1815 |
o pkg/seaice: |
1816 |
diffusion with centered advection scheme (diffus.F & advect.F): |
1817 |
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
1818 |
to just compute the laplacian of input-field. |
1819 |
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
1820 |
- fix flux-form version in diffus.F to conserve tracer. |
1821 |
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
1822 |
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
1823 |
|
1824 |
checkpoint62y (2011/05/26) |
1825 |
o pkg/seaice: |
1826 |
- seaice_growth.F : in EVOLUTION branch, always include |
1827 |
a_QSWbyATM_cover in qnet (as it should be). |
1828 |
- verification/global_ocean.cs32x15 : update results accordingly |
1829 |
(output.seaice.txt output_adm.seaice.txt). |
1830 |
o pkg/seaice + obcs: |
1831 |
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
1832 |
equivalent of assuming no tracer gradient outside the OB region. |
1833 |
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
1834 |
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
1835 |
after changes above); |
1836 |
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
1837 |
only at OB location (instead of over a band of OLx width). |
1838 |
o pkg/seaice: |
1839 |
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
1840 |
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
1841 |
o pkg/obcs: |
1842 |
- split header file "OBCS.h" into 4 separated files: |
1843 |
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
1844 |
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
1845 |
(contain no conditional statement which depends on OBCS options). |
1846 |
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
1847 |
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
1848 |
o ctrl, cost, grdchk & autodiff pkgs: |
1849 |
- make options file more standard (like other {PKG}_OPTIONS.h file but |
1850 |
with AD_CONFIG.h); clean-up some of the included header files. |
1851 |
o pkg/obcs: |
1852 |
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
1853 |
- apply tracer OB values to tracer field only at OB location (instead of |
1854 |
over a band of OLx width) |
1855 |
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
1856 |
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
1857 |
obcs_apply_tloc.F & obcs_apply_sloc.F |
1858 |
o obcs in model/src: |
1859 |
- call OBCS_APPLY_W only if NonHydrostatic. |
1860 |
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
1861 |
- reset dEtaHdt and wVel to zero outside OB interior region ; |
1862 |
- leave tracer unchanged outside OB interior region: This has no effect |
1863 |
on the solution but just to prevent unrealistic tracer value outside OB. |
1864 |
- zero out velocity outside OB interior region: This has no effect on |
1865 |
the solution but just to prevent unrealistic velocity outside OB. |
1866 |
o obcs and non-lin free-surf: |
1867 |
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
1868 |
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
1869 |
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
1870 |
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
1871 |
update results of test-exp. exp4(nlfs). |
1872 |
o exp4 (nlfs) test-exp: |
1873 |
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
1874 |
with NonLin-FreeSurf); update output.nlfs.txt |
1875 |
o obcs and 2d/3d solver norm: |
1876 |
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
1877 |
and outside OB interior region (will allow to place OB further inside the |
1878 |
domain). Depending on the domain, can affects cg2d-Norm (previous |
1879 |
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
1880 |
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
1881 |
e.g. in tutorial_plume_on_slope. |
1882 |
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
1883 |
o pkg rbcs: |
1884 |
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
1885 |
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
1886 |
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
1887 |
o pkg/shelfice/shelfice_init_fixed.F |
1888 |
fix CPP-flag combinations |
1889 |
o pkg/seaice: Merge iceage code of Pierre Rampal |
1890 |
* update/change/correct ice age calculations |
1891 |
* add age updates for pathological cases |
1892 |
Probably needs more testing... |
1893 |
|
1894 |
checkpoint62x (2011/05/13) |
1895 |
o pkg/mom_vecinv: |
1896 |
high-order vorticity scheme: use interior masks (maskInW & S) |
1897 |
to zero-out (outside OB) gradient of vorticity. |
1898 |
o verification exp.: |
1899 |
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
1900 |
hs94.128x64x5 and seaice_obcs ; update results. |
1901 |
o pkg/obcs: |
1902 |
fix bug in OBeta for YZ sections in obcs_exf_load.F |
1903 |
o pkg/ctrl, pkg/shelfice, and optim: |
1904 |
- add new control variable xx_shifwflx (fresh water flux underneath ice |
1905 |
shelves). This is almost as tedious as obcs-ctrl, because the |
1906 |
variables needs its own mask. |
1907 |
- add a cost function term that penalizes the deviation of xx_shifwflx |
1908 |
from the first guess (zero) in analogy to other control variables |
1909 |
o pkg/shelfice: |
1910 |
- start basic adjoint |
1911 |
o pkg/ctrl: |
1912 |
- remove extra 2D field "for good measure" when initializing in |
1913 |
ctrl_set_globfld_[xy/xz/yz].F |
1914 |
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
1915 |
- improve error messages in ctrl_set_unpack_* |
1916 |
o OBC implementation in momentum: |
1917 |
use interior masks (maskInC,W & S) in momentum S/R: |
1918 |
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
1919 |
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
1920 |
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
1921 |
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
1922 |
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
1923 |
(and also with Leith/Smagorinsky harmonic-viscosity). |
1924 |
Update output of experiment dome and exp4 (+nlfs). |
1925 |
o exp4 test-exp: |
1926 |
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
1927 |
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
1928 |
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
1929 |
time-varying OB at Western-side for wVel (NonHyd); update output. |
1930 |
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
1931 |
and biharmonic-viscosity ; also use prescribed time varying OB. |
1932 |
o pkg/obcs: |
1933 |
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
1934 |
o model/src: |
1935 |
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
1936 |
- initialise startTime & nIter0 with unlikely values: allows to set one |
1937 |
from the other without ambiguity. |
1938 |
o seaice_obcs test-exp.: |
1939 |
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
1940 |
o pkg/obcs: |
1941 |
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
1942 |
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
1943 |
o pkg/seaice: |
1944 |
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
1945 |
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
1946 |
- fixed bug in the initialization of sea ice salinity variable HSALT |
1947 |
in seaice_init_varia.F (removed dependence on ICE2WATR) |
1948 |
o fizhi-cs test exp.: |
1949 |
switch reference output convention for these 2 non-standard test-exp, |
1950 |
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
1951 |
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
1952 |
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
1953 |
o model/inc: |
1954 |
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
1955 |
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
1956 |
o pkg/seaice: |
1957 |
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
1958 |
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
1959 |
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
1960 |
and initial HSALT |
1961 |
|
1962 |
checkpoint62w (2011/04/26) |
1963 |
o pkg/mom_fluxform: |
1964 |
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
1965 |
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
1966 |
- update output of exp. global_ocean.90x40x15 |
1967 |
o pkg/mom_vecinv: |
1968 |
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
1969 |
o update seaice exp.: |
1970 |
use more consistent parameter values (remove "backward compatability only": |
1971 |
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
1972 |
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
1973 |
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
1974 |
o update test-exp global_ocean.90x40x15: |
1975 |
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
1976 |
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
1977 |
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
1978 |
o turn on zStar & viscA4 in standard set-up (dir input/) |
1979 |
and update output files: output.txt & output.dwnslp.txt |
1980 |
o new AD-test experiment: obcs_ctrl |
1981 |
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
1982 |
o pkg/dic: |
1983 |
fix two bugs in handling water vapour pressure in carbonate chemistry |
1984 |
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
1985 |
(add DIC Option = WATERVAP_BUG to recover old results) |
1986 |
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
1987 |
o adding allowInteriorFreezing option to check for water below freezing point |
1988 |
at depth and bring the negative heat anomaly to the surface level |
1989 |
o pkgs _fields_load: |
1990 |
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
1991 |
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
1992 |
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
1993 |
rbcs to get interpolation weights and time reccord number. |
1994 |
- fix multi-threading in aim_fields_load.F |
1995 |
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
1996 |
o external_fields_load: |
1997 |
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
1998 |
interpolation weights) to use in a periodic time-series ; do not divide by |
1999 |
time-step to convert to integer: |
2000 |
- this fixes case where externForcingPeriod is not multiple of time-step |
2001 |
(Thanks to Christopher L. Wolfe) |
2002 |
- this fixes case where externForcingPeriod is an odd multiple of time-step |
2003 |
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
2004 |
store index of time-record which is currently loaded: |
2005 |
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
2006 |
- needed for the adjoint but not yet used because of extensive recomputations; |
2007 |
(to be fixed soon) |
2008 |
|
2009 |
checkpoint62v (2011/04/02) |
2010 |
o verification/1D_ocean_ice_column added to test Ian Fenty's |
2011 |
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
2012 |
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
2013 |
(new velocity statistics after changing maskInW & maskInS definition) |
2014 |
o pkg/generic_advdiff with OBCS: |
2015 |
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
2016 |
equivalent to assumption of no tracer gradient outside the OB region. |
2017 |
This will affect the results if using obcs+biharmonic diffusion. |
2018 |
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
2019 |
o pkg/obcs: |
2020 |
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
2021 |
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
2022 |
in Interior region. No impact on solution but affects Velocity monitor stats. |
2023 |
o pkg/ptracers (adjoint) |
2024 |
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
2025 |
tape file for each tracer |
2026 |
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
2027 |
of parts of the adjoint code at run time. For now, there are only |
2028 |
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
2029 |
parameters are set in data.pkg. |
2030 |
This is the lazy coward's version of doing this, but still useful for |
2031 |
debugging. In order to do it right, everything needs to be moved to |
2032 |
pkg/autodiff. |
2033 |
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
2034 |
the end; this fixes the adjoint balancing code for open boundaries. |
2035 |
o pkg/ctrl: |
2036 |
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
2037 |
xx_${varname}period = 0., means time-independent control part |
2038 |
xx_${varname}period = -12., means one-year-periodic monthly control part |
2039 |
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
2040 |
clean up ctrl_init a little, remove unused variables |
2041 |
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
2042 |
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
2043 |
|
2044 |
checkpoint62u (2011/03/15) |
2045 |
o model/src: |
2046 |
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
2047 |
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
2048 |
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
2049 |
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
2050 |
o pkg/ctrl/obcs/ecco: |
2051 |
- remove obsolete, unused, and partially broken code: |
2052 |
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
2053 |
ALLOW_CTRL_OBCS_BALANCE |
2054 |
- put a stop statement into ecco/cost_obcsvol.F, but also add |
2055 |
cost_obcsvol to ecco_ad_diff.list |
2056 |
o pkg/ecco: fix counting cost function contributions for obcs (code |
2057 |
by Matt M.) and diffkr for diagnostics |
2058 |
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
2059 |
add cost penalty terms for initial uvel, vvel, eta controls |
2060 |
and I/O for prior error files |
2061 |
o pkg/mdsio: |
2062 |
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
2063 |
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
2064 |
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
2065 |
o pkg/ctrl: |
2066 |
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
2067 |
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
2068 |
unused and superfluous variables |
2069 |
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
2070 |
o pkg/ecco |
2071 |
- enable adjoint of Stevens OB |
2072 |
o pkg/ctrl/ecco/grdchk: |
2073 |
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
2074 |
Fortunately, we do not have any tests for the numerous cpp-flagged |
2075 |
option of "obcs as control parameters" so we will never know |
2076 |
if this is an improvement (but at least now things compile). |
2077 |
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
2078 |
- fix some problems within never used ifdefs to make the code compile |
2079 |
o pkg/obcs: |
2080 |
- Refine Interior mask definition to work with more complex OB (e.g. |
2081 |
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
2082 |
read in Interior mask from file. Check if Interior mask is consistent |
2083 |
with OB list of indices. |
2084 |
o pkg/seaice |
2085 |
- beginning code for a seaice tracer package, |
2086 |
but currently only used for seaice age: SEAICE_AGE |
2087 |
SEAICE_num = 4 |
2088 |
iTracer = 1: area-weighted ice age |
2089 |
= 2: volume-weighted ice age |
2090 |
= 3, 4: template for one-year vs. multi-year ice |
2091 |
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
2092 |
SEAICE_num |
2093 |
|
2094 |
checkpoint62t (2011/03/05) |
2095 |
o pkg/obcs: |
2096 |
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
2097 |
then normal component. This ensures that the normal component is set |
2098 |
correctly even when it conficts with tangential setting from an other OB. |
2099 |
Affects results of test-experiment seaice_obcs: update the output.txt |
2100 |
o pkg/obcs: |
2101 |
- add code to monitor statistics of dynamical fields at OB. |
2102 |
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
2103 |
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
2104 |
- change default: balance the Net inflow through all OB (instead of balancing |
2105 |
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
2106 |
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
2107 |
to match Nortern OB inflow (OBCS_balanceFacN=0). |
2108 |
o pkg/seaice: |
2109 |
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
2110 |
o pkg/seaice (seaice_growth v 1.113): |
2111 |
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
2112 |
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
2113 |
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
2114 |
runtime flag SEAICEareaFormula is kept but is inactive |
2115 |
o model/src: |
2116 |
- add new param to scale curvilinear grid distance and area when using |
2117 |
a different sphere radius from the grid-files. |
2118 |
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
2119 |
o adjoint: |
2120 |
- enable adjoint of Stevens OB |
2121 |
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
2122 |
(a bit delicate because of potentially modified adj. common block structure; |
2123 |
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
2124 |
|
2125 |
checkpoint62s (2011/02/15) |
2126 |
o pkg/seaice (seaice_growth v 1.112): |
2127 |
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
2128 |
computing the ice cover tendency from effective thickness tendencies. Include |
2129 |
Ian Fenty's formula. |
2130 |
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
2131 |
SEAICEareaFormula. |
2132 |
- simplify notations for the various d_HEFF/d_AREA terms. |
2133 |
o pkg/gmredi: |
2134 |
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
2135 |
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
2136 |
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
2137 |
o pkg/seaice (seaice_growth v 1.111): |
2138 |
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
2139 |
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
2140 |
also melt ice. |
2141 |
o pkg/seaice: |
2142 |
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
2143 |
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
2144 |
o pkg/cheapaml: |
2145 |
- from Nico Wienders: New version of this package. |
2146 |
o pkg/flt: |
2147 |
- add CPP options to prevent floats to re-enter the opposite side of |
2148 |
a periodic domain (default: keep periodicity) |
2149 |
o pkg/gmredi: |
2150 |
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
2151 |
(needed for multi-dim advection). |
2152 |
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
2153 |
o model/src: |
2154 |
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
2155 |
o tutorial_tracer_adjsens |
2156 |
- extend to NLFS and replace maskC by hFacC |
2157 |
(change reference output accordingly) |
2158 |
|
2159 |
checkpoint62r (2011/01/24) |
2160 |
o testreport: |
2161 |
- add option -deloutp (-do) to remove output file after successful run |
2162 |
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
2163 |
extract exact list of procs from this file ; adjust COMMAND by |
2164 |
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
2165 |
o pkg/ecco: replace old ineffective way of penalizing deviations from |
2166 |
first guess (of obcs) with code by Matt Mazloff |
2167 |
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
2168 |
exf/cal |
2169 |
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
2170 |
and handle case of obcs?period == 0 |
2171 |
Not affected by these changes: There is still an inconsistency in |
2172 |
the computation of start/endrec for the obcs variables for ALLOW_CAL |
2173 |
defined (see comment by Menemenlis, 7-Mar-2003) |
2174 |
- make S/R ctrl_get_gen_rec return something meaningful even if |
2175 |
ALLOW_CAL is not defined |
2176 |
- ctrl_getobcs?: simplify code so that it does not need to use |
2177 |
S/R exf_swapfields |
2178 |
o testreport: |
2179 |
allow to test MPI with different number of processors for each experiment: |
2180 |
create file "SIZE.h.mpi" in each build dir. |
2181 |
Note: update of "-command" argument not yet implemented. |
2182 |
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
2183 |
alleviate the need for additional 3D tapes when using |
2184 |
the non-inear free surface in the adjoint. This is done |
2185 |
by adding an 'update' of hfacc etc. to their current |
2186 |
value at the beginning of forward_step.F. |
2187 |
o pkg/seaice |
2188 |
seaice_lsr: move stress-divergence computations out of outer pseudo- |
2189 |
timestepping loop |
2190 |
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
2191 |
up, so that the calls of the ctrl_* subroutines are really at the end |
2192 |
of the routine. |
2193 |
o pkg/gmredi: |
2194 |
allow to specify a 2-D horizontal map and a 1-D vertical profil |
2195 |
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
2196 |
o pkg/seaice: |
2197 |
move lsr iterations from seaice_dynsolver to seaice_lsr. |
2198 |
o pkg/seaice: |
2199 |
reduce memory footprint of seaice mutldim advection tapes, |
2200 |
by using a 2D tape independent of the generic_advdiff ones, |
2201 |
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
2202 |
|
2203 |
checkpoint62q (2010/12/29) |
2204 |
o model/src: |
2205 |
- check horizontal grid-spacing for unset or zero/negative values. |
2206 |
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
2207 |
o pkg/flt: |
2208 |
- use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR |
2209 |
- precision of input and output files set according to readBinaryPrec |
2210 |
and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits. |
2211 |
- initial float position from tiled file was not converted to index space |
2212 |
(looks like a bug): fixed to make it similar to initial pos. global file. |
2213 |
o global_ocean.cs32x15: |
2214 |
change SIZE.h of AD set-up to get same tiling as with MPI. |
2215 |
Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11) |
2216 |
o model/src: |
2217 |
add flag to control printing of domain fields (bathymetry, hFac ...) in |
2218 |
ini_mask_etc (call to plot_fieds_xy*). |
2219 |
o pkg/thsice: |
2220 |
if useEXF, some forcing fields are not valid in overlap: fixed by computing |
2221 |
over the interior only + apply EXCH at the end (like with SEAICE advection). |
2222 |
o pkg/mdsio: |
2223 |
- add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer |
2224 |
to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS. |
2225 |
- change barrier call for safe multi-threads access to 3-D shared buffer. |
2226 |
- MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones) |
2227 |
- replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and |
2228 |
remove the 4 S/R MDS_PASS_WH_R4/8toRL/S. |
2229 |
o pkg/flt: |
2230 |
- add fourth-order Runge-Kutta integration |
2231 |
- add basic exch2 support (only 1 facet supported so far!) |
2232 |
o pkg/mdsio+rw: |
2233 |
new S/R to read local (or tile independent) vector (read counterpart of |
2234 |
mds_writevec_loc, and front-end write_glvec_rl/rs). |
2235 |
o global_ocean.cs32x15: additional input_ad.seaice experiment |
2236 |
that uses pkg/seaice rather than pkg/thsice. |
2237 |
(using multidim advection for seaice) |
2238 |
o towards more F95 syntax for array specification in namelist: |
2239 |
- change "data.diagnostics" (data.ptracers was changed before checkpoint62p) |
2240 |
of all verification experiments. |
2241 |
e.g.: line: fields(1,3)='ETAN ','ETANSQ ', |
2242 |
was changed to: fields(1:2,3)='ETAN ','ETANSQ ', |
2243 |
- finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles |
2244 |
o global_ocean.cs32x15: additional input.seaice experiment |
2245 |
that uses pkg/seaice rather than pkg/thsice. |
2246 |
|
2247 |
checkpoint62p (2010/12/17) |
2248 |
o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it |
2249 |
to THSICE_SIZE.h to avoid conflict with pkg/seaice. |
2250 |
o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint. |
2251 |
allow for use of multim. advection in seaice adjoint. |
2252 |
o pkg/seaice: add diagnostics for snow precipitation and sublimation flux |
2253 |
- first attempt to close budgets by taking into account the freshwater |
2254 |
flux implied by the sublimation of snow and ice. So far only the |
2255 |
volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag |
2256 |
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET |
2257 |
o eesupp/src: |
2258 |
new S/R with new option (NML_EXTENDED_F77) to change array specification |
2259 |
from F95 standard to commonly accepted extended F77 form. |
2260 |
This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5) |
2261 |
and to revert back to the original syntax (with -DNML_EXTENDED_F77) |
2262 |
for less tolerant f77 compiler (e.g., pgf77, g77). |
2263 |
o globalFiles: |
2264 |
commented out in parameter file "data" since it's not safe with MPI |
2265 |
(e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much |
2266 |
in this case); no longer commented out in restart test (tst_2+2). |
2267 |
o add adTapeDir to specify a special directory where adjoint tapes are |
2268 |
written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05 |
2269 |
and cannot be used together with mdsioLocalDir. |
2270 |
o nesting pkgs: |
2271 |
- packages_init_variables : put call to OBCS_INIT_VARIABLES in last position |
2272 |
- update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
2273 |
- add parameter files + utils dir + output from short run on beagle. |
2274 |
o pkg/seaice: |
2275 |
fix seaice_growth.F store directives; update results of exp. lab_sea.ad |
2276 |
o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid |
2277 |
unnecessary copying in adjoint code, requires new parameter NMAX_ITER |
2278 |
|
2279 |
checkpoint62o (2010/11/25) |
2280 |
o pkg/exf: |
2281 |
- change CPP option EXF_VERBOSE to run-time logical param exf_verbose. |
2282 |
o pkg/seaice: |
2283 |
- seaice_ocean_stress: split a loop for better vectorization of the |
2284 |
adjoint code |
2285 |
- seaice_growth.F: fix bug in conservation of freshwater connected to |
2286 |
capping of heff, put contribution into d_HEFFbyNEG |
2287 |
- replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat |
2288 |
by something more sensible (parameters that are what their name implies) |
2289 |
- change some defaults, so that by default exf-parameters are used for |
2290 |
things like rhoAir, cpAir,latent/sensible heat parameters, in order |
2291 |
to reproduce the old results, many data.seaice now contain funny values |
2292 |
for cpAir and latent heat of sublimation |
2293 |
o packages_readparms.F: move exf_readparms up in line so that |
2294 |
exf-parameters are visible for other packages (e.g. seaice) |
2295 |
o debugMode & debugLevel=2: |
2296 |
- differentiate between debugMode & debugLevel=2: |
2297 |
debugMode: controls printing of debug messages (sequence of S/R calls). |
2298 |
debugLevel: controls printing of algorithm intermediate results and stats. |
2299 |
- remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2"; |
2300 |
=> allows to print debug-stats without all sequence of call messages. |
2301 |
- switch control of debug print from debugLevel to debugMode in many S/R. |
2302 |
o pkg/obcs (obcs-sponge): |
2303 |
fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the |
2304 |
call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge) |
2305 |
o pkg/generic_advdiff: |
2306 |
- record overlap minimum size for each advection scheme; |
2307 |
- refine criteria on overlap minimum size; |
2308 |
- check and stop (in gad_check) if overlap size is too small. |
2309 |
o pkg/obcs: |
2310 |
- with ptracers: remove multiple calls to obcs_apply_ptracer (only done |
2311 |
once, in ptracers_implicit.F) |
2312 |
- with seaice: remove test on empty file name in obcs_apply_seaice (always |
2313 |
apply OB values when tile has OB) |
2314 |
o model/src, coriolis setting: |
2315 |
- integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical |
2316 |
useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from |
2317 |
files (selectCoriMap=3) with any grid. |
2318 |
- add parameter "fPrime" for constant second Coriolis coeff (default=0). |
2319 |
o pkg/seaice/seaice_growth.F: |
2320 |
a few cosmetic changes that reduce the number of lines of code |
2321 |
o pkg/obcs: add boundary conditions following Stevens (1990) |
2322 |
- the code follows old MOM/NAOSIM code |
2323 |
- so far it is only implemented for the eastern and western boundaries |
2324 |
and NOT for pTracers |
2325 |
o pkg/rbcs: |
2326 |
- replace rbcsInIter by rbcsForcingOffset, the time in seconds at the |
2327 |
beginning of the first rbcs forcing period. |
2328 |
- add option rbcsSingleTimeFiles that makes rbcs read forcing data like the |
2329 |
offline package, i.e., one file per time, labeled by iteration number; |
2330 |
deltaTrbcs sets the timestep with which the data was generated; |
2331 |
rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset. |
2332 |
- rbcsForcingCycle=0 makes forcing non-cyclic. |
2333 |
- make arithmetic safe for negative times and odd forcing periods. |
2334 |
|
2335 |
checkpoint62n (2010/11/09) |
2336 |
o pkg/seaice: |
2337 |
fix masking in free-drift S/R ; update results of exp. lab_sea.fd |
2338 |
o pkg/obcs: |
2339 |
New S/R to copy tracer value from the OB location to narrow band region |
2340 |
(width = same as overlap) beyond the OB: preserve OB value (needed for |
2341 |
high-order scheme) which were overwritten by EXCH call if in overlap |
2342 |
region. Applied to theta, salt, ptracer and advected seaice variables. |
2343 |
With seaice: use maskInC in similar way as in gad_advection.F, |
2344 |
in seaice_advection.F and advect.F. |
2345 |
Update output of experiment seaice_obcs and change exp4 to test OBCS with |
2346 |
4th order Adv.Scheme. for pasive salt and ptracer. |
2347 |
o tools/genmake2: |
2348 |
- when looking for an optfile (not specified), only search for Fortran compiler |
2349 |
(remove sym-link test + setting of CPP + makedepend check + C-compiler check) |
2350 |
- in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm |
2351 |
(instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong) |
2352 |
- set default for CPP to "cpp -traditional -P" (was the case without specifying |
2353 |
an optfile, but otherwise default was just "cpp". |
2354 |
- comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from) |
2355 |
- when "CC" is not set in the optfile, look for possible C compiler |
2356 |
(instead of just setting CC=cc) |
2357 |
- put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes: |
2358 |
=> add a ".F" to ".o" rule for source files with no "#include" (such as |
2359 |
port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS. |
2360 |
- move gfortran before g77 in list of possible Fortran compiler (consistent |
2361 |
with reference compiler switch from g77 to gfortran) |
2362 |
o pkg/seaice: |
2363 |
o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to |
2364 |
seaice_check that stops the model, when the CPP flag is used. |
2365 |
o seaice_growth.F: make capping of ice volume conserving by returning the |
2366 |
capped ice as freshwater to EmPmR. This does not change the verification |
2367 |
experiments but will change runs where the capping is acutally active |
2368 |
o change reference platform+compiler from faulks+g77 to baudelaire+gfortran |
2369 |
(except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5, |
2370 |
global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD), |
2371 |
lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd) |
2372 |
o tools/genmake2: |
2373 |
- merge genmake_warnings & genmake_errors into 1 log file: "genmake.log") |
2374 |
- change DUMPSTATE default to false (can use "-ds" option to switch it to T) |
2375 |
- clean previous genmake log files before anything else. |
2376 |
- change Makefile to remove testreport log files (*.tr_log) and genmake log |
2377 |
files only with "CLEAN" target (instead of "Clean"); |
2378 |
o pkg/generic_advdiff: |
2379 |
Change OBCS in multiDim advection (gad_advection.F): |
2380 |
Use maskInC to prevent intermediate update of tracer-field in OB regions, |
2381 |
thus keeping current-time-step OB values; and remove the call to OBCS_APPLY |
2382 |
which were applying future time-step OB values. |
2383 |
This way, all explicit calculations use current-time-step OB values |
2384 |
(simpler and more consistent). |
2385 |
Affects results when set-up uses time-varying OBC and multi-dim advection; |
2386 |
update output of experiment seaice_obcs. |
2387 |
o pkg/seaice: |
2388 |
move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h: |
2389 |
this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH & |
2390 |
SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY. |
2391 |
Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY |
2392 |
but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp |
2393 |
unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h) |
2394 |
o pkg aim (2010/10/26): |
2395 |
- Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation |
2396 |
formulation with obliquity, eccentricity, ... as run-time parameters, |
2397 |
- Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and |
2398 |
upward shortwave radition at the surface (all-sky and clear-sky). |
2399 |
o pkg/obcs: |
2400 |
- writing sections with globalFiles=T does not work: switch to tiled-files |
2401 |
when writing sections for OBCS (change pkg/rw/write_rec.F accordingly). |
2402 |
- fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F |
2403 |
- apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs |
2404 |
|
2405 |
checkpoint62m (2010/10/21) |
2406 |
o pkg/seaice: vectorize seaice_solve4temp.F |
2407 |
- move iterations loops outside of i/j-loops |
2408 |
- requires 2D arrays for TB and effConduct |
2409 |
- add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is |
2410 |
modified in this routine |
2411 |
- a little bit of clean up, adjusting indentation, etc. |
2412 |
- replaced a few TEN**a by exp(a*log(10.)) in new code for better |
2413 |
performance and '**TWO' by '**2' (because TWO is a float), |
2414 |
replaced ONE, ZERO |
2415 |
o eesupp/src: |
2416 |
fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube |
2417 |
o pkg/seaice/seaice_growth.F |
2418 |
Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and |
2419 |
merging process. The merged routine has two branches, and one activates the 'evolution' |
2420 |
branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now). |
2421 |
In summary, here is what the '10/10 revision' did consist of |
2422 |
part 1: seaice_growth.F revisions 1.71 to 1.75 |
2423 |
- Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged. |
2424 |
The emphasis here was on improving readability (e.g. by trying to use meaningful |
2425 |
variable names) and modularity (e.g. by adding arrays to store heff etc. updates). |
2426 |
part 1.5: |
2427 |
- revising the lab_sea experiment to make it a more useful (i.e. stable |
2428 |
and representative of an actual model run). This was done by generating a |
2429 |
(winter) pickup to start from, switching back the main experiment dynamic |
2430 |
solver from evp to lsr, having one of the experiments use the free drift solution. |
2431 |
part 2: seaice_growth.F revisions 1.76 to 1.85 |
2432 |
- Sorting out hard-coded constants that prevented heat and fresh water conservation. |
2433 |
- Sorting out the various fields units and sign (set early on and reset at the end) |
2434 |
to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and |
2435 |
fresh water stock is 'effective ice meters', and >0 implies more ice/snow. |
2436 |
- Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks, |
2437 |
and simplifying logical expressions to further improve readibility. |
2438 |
part 3: seaice_growth.F revisions 1.86 to 1.89 |
2439 |
- Re-organize the blocks of code more logically. |
2440 |
- Merging the '_if.F' pieces that add something new. |
2441 |
o pkg/thsice: |
2442 |
- vectorize thsice_solve4temp and thsice_get_exf. |
2443 |
Problem: thsice_solve4temp has an unvectorizable statement that |
2444 |
might also be problematic for TAF |
2445 |
- thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This |
2446 |
does not change the verifcation experiment, but will change all |
2447 |
experiments that have this flag undefined (not tested in verification); |
2448 |
a little reorganization to save a few 2D fields and recomputations |
2449 |
- 1st step of revisiting thsice adjoint (major recomp. sorted out) |
2450 |
- 2nd step: fix some store dirs |
2451 |
o seems to work somewhat, i.e. using ifort but not g77 |
2452 |
o likely cause are incomplete init. or recomputation |
2453 |
o start verification/global_ocean.cs32x15/input_ad.thsice |
2454 |
o pkg/obcs: add support for exch2 |
2455 |
- the position of the boundary and prescribed values are specified using |
2456 |
a global domain with exch2 facets stacked |
2457 |
- in x for N,S boundaries (like W2_mapIO=-1) |
2458 |
- in y for E,W boundaries (so E,W boundaries do not overlap) |
2459 |
o pkg/mdsio: add support for writing global sections with exch2 |
2460 |
file layout is as for obcs described above: |
2461 |
- for x-z sections, facets are stacked in x (like W2_mapIO=-1) |
2462 |
- for y-z sections, facets are stacked in y |
2463 |
o pkg/thsice: |
2464 |
- change a few routines for better vectorization: thsice_albedo.F, |
2465 |
thsice_step_temp.F, and in thsice_calc_thickn.F. Results are |
2466 |
not affected, but in particular the latter routine has changed |
2467 |
dramatically (not necessarily easier to read now). |
2468 |
- re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops |
2469 |
iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF. |
2470 |
o verification/lab_sea: |
2471 |
- overhaul of the forward model experiments. The main motivation |
2472 |
for this revision is that lab_sea has proven quite fragile (when |
2473 |
changing the sea-ice code, and switching platforms) to a point |
2474 |
when failures were very hard to attribute to specific code problems. |
2475 |
- the suspected reason for this fragility is noise amplification by evp so, |
2476 |
to start with, we decided to replace evp with lsr in the main experiment. |
2477 |
- the input.lsr experiment thus became obsolete and was removed. |
2478 |
- it was replaced with the input.fd experiment that uses an |
2479 |
analytical "free drift" solution as the ice velocity field. |
2480 |
- Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp) |
2481 |
will hopefully allow us to discriminate problems due to dynamic solvers |
2482 |
from problems due to the thermodynamic code. input.salt_plume (lsr) allows |
2483 |
us to test additional options, along with the salt plume package. |
2484 |
- Finally a pickup was generated (at the end of a one year run) to |
2485 |
make the tests more representative of an actual model run. Previously |
2486 |
the tests starting point was a 1m thickness of ice everywhere. |
2487 |
o pkg/seaice: |
2488 |
- introducing S\R seaice_freedrift.F that compute the |
2489 |
analytical solution to an approximate ice momentum |
2490 |
equation (i.e. the simple stress/coriolis balance). |
2491 |
- define SEAICE_ALLOW_FREEDRIFT to trigger the computation |
2492 |
of the free drift velocity field, and enable its use. |
2493 |
To actually use the free drift solution as the model ice |
2494 |
velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice. |
2495 |
o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata" |
2496 |
|
2497 |
checkpoint62l (2010/10/04) |
2498 |
o pkg/seaice: |
2499 |
-fix the USE_ORIGINAL_SBI version (for variable freezing point); |
2500 |
-use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new |
2501 |
version (with USE_ORIGINAL_SBI undef); |
2502 |
o add hooks for new packages OASIS, the package will follow |
2503 |
(hooks exclude the seaice pkg for now) |
2504 |
o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO |
2505 |
Option to use mdsio_read_whalos.F/mdsio_write_whalos.F, |
2506 |
rather than mdsio_readvector.F/mdsio_writevector.F, within |
2507 |
adread_adwrite.F to read/write adjoint-related tapes to disk. |
2508 |
o eesupp and pkg/mdsio: ALLOW_WHIO |
2509 |
Option to write/read 2D fields to files including tiles halos. |
2510 |
The main purpose is for adjoint related "tape I/O". |
2511 |
The secondary purpose is for debugging phases. |
2512 |
A word on those rather specifically intended purposes. |
2513 |
The code was meant to be stripped down to the bare minimum. |
2514 |
Typically, there is a unique and basic mapping to the global |
2515 |
buffer (tile by tile, then proc by proc, then level by level), and |
2516 |
byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not |
2517 |
meant to generate user friendly outputs of various shapes and forms. |
2518 |
Rather it is intended, for the knowledgeabale developers, |
2519 |
to be largely independent of the many mdsio options, to allow |
2520 |
outputs of tiles+halos in debugging phases and in adjoint runs, |
2521 |
and to allow some flexibility in tuning (adoint) I/O depending on each |
2522 |
file system behavior. With regard to tuning, most of the potential knobs |
2523 |
(to leave files open, to allocate the I/O indep. of usesinglecpuio, |
2524 |
to specify directories, to specify the typical size of I/O calls, etc.) |
2525 |
are not yet included, and will be added if they prove useful. |
2526 |
o pkg/seaice: |
2527 |
fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F |
2528 |
o pkg/seaice: |
2529 |
new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty |
2530 |
code (seaice_budget_ice_if.F) which enable to recover old standard |
2531 |
code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined. |
2532 |
temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F. |
2533 |
o model/src (rStar): |
2534 |
use simple average (not area weighted) of rStarFac at U,V point when using |
2535 |
vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection) |
2536 |
update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20. |
2537 |
|
2538 |
checkpoint62k (2010/09/17) |
2539 |
o adjoint |
2540 |
* changed verification/global_ocean.cs32x15 ; adjoint now tests |
2541 |
Adams-Bashforth 3 + NLFS + RSTAR |
2542 |
* some more modifs required for ECCO-GODAE v4 |
2543 |
o pkg/seaice |
2544 |
add SEAICE_AGE_VOL option to use volume instead of area for |
2545 |
integrating SEAICE_AGE |
2546 |
o model/src: |
2547 |
first check-in of sigma & hybrid-sigma coordinate code ; also includes |
2548 |
non-linear free-surface parts ; but pressure-gradient not yet coded. |
2549 |
o pkg/ptracers: |
2550 |
option for ptracer to convert Salt Relax into additional EmP. |
2551 |
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
2552 |
|
2553 |
checkpoint62j (2010/08/25) |
2554 |
o pkg/ggl90: |
2555 |
other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
2556 |
o pkg/dic: car_flux.F, phos_flux.F |
2557 |
- reduce number of exp-calls in order to improve performance |
2558 |
- clean up a little (replace fields by their macros, etc., fix |
2559 |
typo in CPP-flag) |
2560 |
o pkg/ggl90: minor changes |
2561 |
- GGL90diffKrS was removed --> always use GGL90diffKr |
2562 |
- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
2563 |
- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
2564 |
(commented out for now) |
2565 |
- change in max/min operations to ensure that smoothing is ok |
2566 |
- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
2567 |
- always use diffKrNrT as background profile (i.e. never use diffKr field) |
2568 |
o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
2569 |
o pkg/dic: |
2570 |
- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
2571 |
vectorization |
2572 |
- small bug fix in insol for the unlikely case of a cartesian grid |
2573 |
- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
2574 |
+ now vectorize, which also removes adjoint recomputations; |
2575 |
+ replace integer maksp1 by _RL maskp1 |
2576 |
+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
2577 |
|
2578 |
checkpoint62i (2010/07/21) |
2579 |
o pkg/flt: |
2580 |
- with OBCS: stop floats which enter the OB region |
2581 |
o model/src: |
2582 |
- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
2583 |
for implicit vertical advection. |
2584 |
o pkg/seaice: |
2585 |
- account for melting in seaice age evolution. |
2586 |
- remove double counting of seaice ridging effect on seaice age. |
2587 |
|
2588 |
checkpoint62h (2010/06/18) |
2589 |
o pkg/exch2: |
2590 |
- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
2591 |
o tools/genmake2 |
2592 |
- remove "-pdefault" option: redundant with the use of "packages.conf"; |
2593 |
- remove file pkg/pkg_default : set the default as a pkg group |
2594 |
("default_pkg_list") defined in pkg/pkg_groups; |
2595 |
- fix for case pkg/pkg_depend is missing (was hanging before); |
2596 |
- add option "-pgroups" to specify a different pkg_groups than the default. |
2597 |
o verification/adjustment.cs-32x32x1: |
2598 |
add a "minimal" set-up test (code_min & input_min) which only compiles |
2599 |
eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
2600 |
o tools/genmake2 |
2601 |
- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
2602 |
- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
2603 |
o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
2604 |
files are nearly the same anyway. |
2605 |
Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
2606 |
- redefinition of tau(i,i) (by a factor of ustar) |
2607 |
- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
2608 |
- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
2609 |
- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
2610 |
- replace |
2611 |
rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
2612 |
shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
2613 |
by |
2614 |
shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
2615 |
(changes results) |
2616 |
-> exf_bulkformulae v1.22, |
2617 |
update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
2618 |
(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
2619 |
output.txt 1.63 |
2620 |
offline_exf_seaice: output.seaicetd.txt 1.7 |
2621 |
seaice_obcs: output.txt 1.10) |
2622 |
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
2623 |
-> exf_bulkformulae v1.23, |
2624 |
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
2625 |
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
2626 |
Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
2627 |
o adjoint of exch-1: |
2628 |
- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
2629 |
(note: was already like this when using EXCH-2) and remove flow dir |
2630 |
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
2631 |
- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
2632 |
- update pkg/exch2 diff list. |
2633 |
|
2634 |
checkpoint62g (2010/05/19) |
2635 |
o eesupp/src (exch-1): |
2636 |
- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
2637 |
and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
2638 |
(renamed to exch1_*rx_cube.F). |
2639 |
- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
2640 |
to call new exch1 S/R ; update Makefile and .cvsignore. |
2641 |
- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
2642 |
exch2_xy_rx later) |
2643 |
Note: after updating your code, need to run "make clean" in eesupp/src |
2644 |
o test experiment bottom_ctrl_5x5: |
2645 |
new output_adm.txt with fewer grdchk & less monitor output. |
2646 |
o model/src: |
2647 |
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
2648 |
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
2649 |
beeing treated in the same way (ini_grid is not called a 2nd time). |
2650 |
o pkg/exf: |
2651 |
- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
2652 |
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
2653 |
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
2654 |
- cosmetic changes to exf_bulkformulae.F to make it look more like |
2655 |
exf_bulk_largeyeager04.F |
2656 |
o eesupp/src (exch-1): |
2657 |
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
2658 |
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
2659 |
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
2660 |
(even without using MPI). |
2661 |
- Message mode: move RecvAck setting (indicator of buffer being ready) |
2662 |
from send_put to recv_get S/R (was useless before, but not sure if |
2663 |
it's much more useful now); |
2664 |
- Switch the order of sync: MPI-proc 1rst and then threads; |
2665 |
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
2666 |
- fix AD code for communication mode ='get' (but not used). |
2667 |
o model/src: |
2668 |
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
2669 |
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
2670 |
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
2671 |
o pkg/ctrl: require a specific set of control variables and exf-flags for |
2672 |
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
2673 |
o model/src: |
2674 |
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
2675 |
1rst forward sweep, to avoid over-writing output files during recomputations |
2676 |
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
2677 |
b) 2nd version: |
2678 |
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
2679 |
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
2680 |
writePickupAtEnd) + seaice & ptracers output; |
2681 |
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
2682 |
o model/src: |
2683 |
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
2684 |
o pkg/exch2: |
2685 |
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
2686 |
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
2687 |
o pkg/autodiff & exch2: |
2688 |
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
2689 |
(for now, only if ALLOW_EXCH2 is defined). |
2690 |
o pkg/autodiff: |
2691 |
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
2692 |
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
2693 |
+ clean-up comments (_RS is not always real*4) |
2694 |
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
2695 |
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
2696 |
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
2697 |
o testreport (AD-tests): |
2698 |
no longer link files from dir "../input" (1rst link files from |
2699 |
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
2700 |
|
2701 |
checkpoint62f (2010/04/29) |
2702 |
o model/src/the_main_loop.F: |
2703 |
adjust store directives for seaice evp and multicategory according to |
2704 |
pkg/ecco/the_main_loop.F |
2705 |
o adjoint: |
2706 |
global_sum_ad was incomplete (noted many times by many people ;) |
2707 |
nice description by Jean U. as follows: |
2708 |
* allreduce(var) in global_sum.F can be interpreted as |
2709 |
reduce(sum) followed by broadcast of sum. |
2710 |
* The adjoint of that is |
2711 |
sum(adjoint) followed by broadcast(summed adjoint value) |
2712 |
or in other words, allreduce(sum, adjoint vars) |
2713 |
We were missing the sum(adjoint)! |
2714 |
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
2715 |
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
2716 |
The fix should produce 16-digit accuracy between |
2717 |
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
2718 |
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
2719 |
We'll probably change this yet again shortly |
2720 |
o eesupp/src: |
2721 |
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
2722 |
o pkg/icefront |
2723 |
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
2724 |
specification of addmass array based on a 2D field, which is added |
2725 |
at bottommost wet level at each horizontal location. |
2726 |
o model/src: |
2727 |
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
2728 |
layout; (not always compatible with delX,delY setting; commented out for now). |
2729 |
o pkg/exch2: |
2730 |
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
2731 |
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
2732 |
|
2733 |
checkpoint62e (2010/04/15) |
2734 |
o pkg/obcs: |
2735 |
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
2736 |
o pkg/dic: |
2737 |
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
2738 |
(note: not presently tested in any forward verification exp.) |
2739 |
update tutorial_global_oce_biogeo AD output file. |
2740 |
o pkg/exf: |
2741 |
- account for the variation of albedo as a function of zenith angle |
2742 |
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
2743 |
o build_options: |
2744 |
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
2745 |
o pkg/dic: |
2746 |
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
2747 |
- use binary pickup file for restart; |
2748 |
- initialise atmos-CO2 box from dic_pCO2 parameter; |
2749 |
- fix multi-threaded. |
2750 |
o pkg/rbcs: |
2751 |
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
2752 |
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
2753 |
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
2754 |
and update output.txt |
2755 |
o pkg/kpp: |
2756 |
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
2757 |
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
2758 |
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
2759 |
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
2760 |
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
2761 |
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
2762 |
o pkg/offline: |
2763 |
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
2764 |
(bug was added in version 1.10 on 2007-08-23). |
2765 |
o pkg/offline: |
2766 |
- no need to specify periodicExternalForcing, etc ... to use offline pack |
2767 |
- offline input files no longer just single prec --> parameter offlineLoadPrec |
2768 |
o verification/lab_sea: |
2769 |
change AD test to multi-tile setup and update all 4 AD output. |
2770 |
NOTE: while cost function values remain very similar, |
2771 |
gradients are very different, although gradient checks are self-consistent |
2772 |
Should try to get to the bottom of this (cost function summation order?) |
2773 |
o pkg/dic: |
2774 |
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
2775 |
a weakness of TAF that drops part of double precision in log10 derivative. |
2776 |
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
2777 |
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
2778 |
o pkg/ecco: |
2779 |
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
2780 |
update all 4 lab_sea AD output. |
2781 |
|
2782 |
checkpoint62d (2010/03/22) |
2783 |
o build_options: |
2784 |
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
2785 |
o remove unbalanced quote (single or double) in commented line of source code |
2786 |
(may cause some warning with some preprocessor/makedepend versions). |
2787 |
o pkg/seaice: |
2788 |
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
2789 |
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
2790 |
o testreport: |
2791 |
add option '-runonly' (short: '-ro') to just do the run part (without make). |
2792 |
o eesupp: remove JAM communication code (obsolete). |
2793 |
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
2794 |
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
2795 |
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
2796 |
(update also the output). |
2797 |
|
2798 |
checkpoint62c (2010/03/02) |
2799 |
o tools/build_options : |
2800 |
move (some) old optfiles from build_options/ to build_options/unsupported/ |
2801 |
o model/src and pkg/exf |
2802 |
surface relaxation -- separating data and data.exf options |
2803 |
The point is to ensure that we specify the surface relaxation |
2804 |
either in data or in data.exf (but not half and half) and to |
2805 |
avoid an accidental relaxation to 0 (which happened if a time |
2806 |
scale was specified but the file name was left empty) |
2807 |
o model/src model/inc and pkg/mom_common |
2808 |
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
2809 |
=> addition to the viscosity field as computed by others schemes |
2810 |
o tools/build_options: |
2811 |
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
2812 |
but keep the former optfile for few weeks for smooth transition |
2813 |
o pkg/ecco |
2814 |
- allow user defined cost function contributions |
2815 |
CPP: ALLOW_USERCOST_CONTRIBUTION |
2816 |
USAGE: compute contributions in cost_usercost_all.F |
2817 |
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
2818 |
the two options are complementary. |
2819 |
o pkg/smooth |
2820 |
- migration from contrib to the main repository |
2821 |
|
2822 |
checkpoint62b (2010/01/26) |
2823 |
o pkg/monitor: |
2824 |
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
2825 |
(in case someone forgot to update customized pieces of code) |
2826 |
o nonHydrostatic: |
2827 |
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
2828 |
- add a simple 2-D experiment (short_surf_wave) to test it. |
2829 |
o pkg/icefront: |
2830 |
adding the shell of, and the hooks to, a new package that |
2831 |
will model melting and freezing of vertical glacier ice fronts |
2832 |
o momentum: |
2833 |
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
2834 |
(without surf.pressure term: would need a 2nd filling since implicit term). |
2835 |
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
2836 |
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
2837 |
cannot deal with the former |
2838 |
o cleaning: |
2839 |
- remove all (except OpenAD) old TLM output from results_ad dirs. |
2840 |
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
2841 |
- comment out maskH definition (replaced by maskInC) |
2842 |
o pkg/monitor: |
2843 |
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
2844 |
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
2845 |
|
2846 |
checkpoint62a (2010/01/15) |
2847 |
o model/src: |
2848 |
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
2849 |
o pkg/diagnostics: |
2850 |
- add optional level number diagnostics (i.e., level number to be define |
2851 |
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
2852 |
- strictly check for valid parser-code(10) ; |
2853 |
- check if adding diag to the list from the right place. |
2854 |
o pkg/longstep: |
2855 |
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
2856 |
o diagnostics: |
2857 |
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
2858 |
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
2859 |
o pkg/diagnostics: |
2860 |
- Add option for writing vertical integral (sum of selected levels) of an output |
2861 |
field instead of writing output field levels. Activate this option on a per |
2862 |
output-file basis, by setting the 2nd character of fileflag to 'I'. |
2863 |
- Add field-specific information relative to level integral in 3rd postion |
2864 |
of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate |
2865 |
vertically (x level-thickness x hFac), "r"=same but without hFac. |
2866 |
o do_the_model_io: |
2867 |
- pass end-of-model-run flag as argument, from forward_step to diagnostics_write: |
2868 |
in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before |
2869 |
writing pickups and stopping. |
2870 |
o pkg/diagnostics (for now, only with mdsio): |
2871 |
- write time information to meta file (and modify accordingly rdmds.m) : |
2872 |
time-averaged diagnostics output: write starting and ending time of the |
2873 |
time-averaging interval ; snap-shot diagnostics output remains unchanged; |
2874 |
o pkg/timeave: |
2875 |
- S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously |
2876 |
always Nr), now assumed to be equal to number of levels of averaged field; |
2877 |
only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F |
2878 |
o pkg/sbo: |
2879 |
- fix ocean bottom pressure global-average & 2-D time-ave output (was |
2880 |
neither initialised nor filled). |
2881 |
- add starting iteration in suffix of global-average output file |
2882 |
(to avoid over-writing the file after a restart) |
2883 |
- use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb). |
2884 |
o time-average: |
2885 |
- use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj) |
2886 |
(pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf, |
2887 |
ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice) |
2888 |
this fix DIC_COST cumulative-time array (previously: bi,bj,k) |
2889 |
- fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice) |
2890 |
- fix missing accumulation for pkg/opps. |
2891 |
- cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0) |
2892 |
(pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81); |
2893 |
- fix initialisation of time-ave vars and do only full time-step increment |
2894 |
(i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81); |
2895 |
o pkg/layers: |
2896 |
- use standard RW pkg S/R to write the output |
2897 |
and remove local write_fld version (which had a problem). |
2898 |
- use simple cumulative-time array (no level index) to fix time-ave S/R calls. |
2899 |
- fix LAYERS_CALC argument list. |
2900 |
o pkg/timeave: |
2901 |
- store cumulative-time in a simple tiled array (drop the level index) |
2902 |
- add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array. |
2903 |
o pkg/ocn,aim_compon_interf |
2904 |
- changes for multi-threaded coupled run. (tested with ifort-11 on danton) |
2905 |
|
2906 |
checkpoint62 (2009/12/23) |
2907 |
o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output. |
2908 |
(was not previously tested in any other exp.) |
2909 |
o pkg/monitor: |
2910 |
- clean-up _RL/_RS version: add specific S/R for statistics with mask & volume: |
2911 |
mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one |
2912 |
(mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics. |
2913 |
- use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F). |
2914 |
- change del2 calculation. |
2915 |
- use interior masks (instead of maskH, <- to be remove). |
2916 |
- shorter monitor suffix for forcing stats ("forcing" instead of "extforcing"). |
2917 |
o mask & obcs: |
2918 |
- define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S). |
2919 |
- move global area computation from ini_masks_etc.F to ini_linear_phisurf.F |
2920 |
(called after packages_init_fixed) |
2921 |
o pkg/obcs: |
2922 |
- move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once. |
2923 |
Fixes bug in obcs+exf with nSx*nSy.GT.1 |
2924 |
- fix multi-tile handling in obcs balance code |
2925 |
o nonHydrostatic: |
2926 |
- Implement AB-3 for non-hydrostatic vertical momentum ; |
2927 |
(change ordering of var. stored in pickup file when using NH) |
2928 |
- move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D. |
2929 |
- add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x |
2930 |
(in prep. for new NH free surface form). |
2931 |
o pkg/obcs: |
2932 |
add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe |
2933 |
o model/src: |
2934 |
fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography |
2935 |
|
2936 |
checkpoint61z (2009/12/01) |
2937 |
o nonHydrostatic: |
2938 |
Fix missing vertical flux of vert. momentum near surface (k=1). This fixes |
2939 |
a spurious source of energy in simple baroclinic adjusment test case. |
2940 |
Update all non-hydrostatic exp output. |
2941 |
o model/src (3-d solver): |
2942 |
Change again 3-D solver free-surface RHS term when exactConserv=T: |
2943 |
simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1 |
2944 |
(which was not the case with previous formulation). |
2945 |
To recover previous version, just reset "oldFreeSurfTerm" to previous value. |
2946 |
Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW. |
2947 |
o nonHydrostatic: |
2948 |
- compatible with implicDiv2Dflow < 1 ; + implement implicit factor |
2949 |
for Non-Hydrostatic pressure gradient (similar to implicSurfPress). |
2950 |
- change 3-D solver to work with r* (for now, only with linear free-surf.) |
2951 |
- add few debug diagnostics (cg3d_x, residual) |
2952 |
o model/src: |
2953 |
fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b). |
2954 |
update output of exp. global_ocean.cs32x15.viscA4 |
2955 |
o update output of exp. global_ocean.cs32x15.icedyn after removing |
2956 |
#define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h |
2957 |
o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino) |
2958 |
o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output |
2959 |
for complex grids, for now only to "state", "adstate", "adexf", "adseaice" |
2960 |
o model: add Christopher Wolfe's implemetation of the single reduction cg2d |
2961 |
(d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and |
2962 |
runtime flag useSRCGSolver. Modify verification experiment global_with_exf |
2963 |
to test this code |
2964 |
o pkg/cd_code: |
2965 |
Change defaut D-grid time-stepping to get the same for D-grid momentum as for |
2966 |
C-grid momentum. D-grid velocity used to be stepped forward in time with |
2967 |
Adams-Bashforth only on surface pressure term. Tests show that using AB on |
2968 |
D-grid coriolis term improves stability (as expected from CD-scheme paper). |
2969 |
To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h). |
2970 |
Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2), |
2971 |
lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD), |
2972 |
tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens. |
2973 |
Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2, |
2974 |
global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD. |
2975 |
o pkg/obcs: |
2976 |
- fix bug in initialisation (broken since Oct 1rst modification) |
2977 |
for useOBCSprescribe without useEXF. |
2978 |
|
2979 |
checkpoint61y (2009/11/15) |
2980 |
o pkg/seaice |
2981 |
- change (once again) the discretization for the evp solver: rather than |
2982 |
squaring the averages of strain rates, average the squares to give |
2983 |
a better approximation to VP behavior (in simple test); this breaks |
2984 |
verification experiments that use EVP (lab_sea and lab_sea.hb87) |
2985 |
--> update outputs |
2986 |
o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit) |
2987 |
to improve vectorization of adjoint code on TARGET_NEC_SX |
2988 |
o verification/vermix: |
2989 |
- change vermix to a more "classical" 1d column with high vertical |
2990 |
resolution, seasonal heat flux forcing and constant wind forcing |
2991 |
--> update outputs |
2992 |
o pkg/seaice |
2993 |
- fix diagnostics of principal stress components for EVP |
2994 |
- add optional diagnostics of non-linear convergence for LSOR solver |
2995 |
- make maximum zeta a runtime parameter |
2996 |
o model/src (3-d solver): |
2997 |
Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49), |
2998 |
which consisted in removing the Surf. Non-Hydrostatic pressure from the |
2999 |
whole column and adding it to Eta (inspired from Casualli, 1999): |
3000 |
Only affects 3-D solver initial guess and only if using ExactConserv, |
3001 |
but tests did show a degradation of solver convergence. For this reason, |
3002 |
decide to disable this piece of code. |
3003 |
to recover previous version, just set zeroPsNH = exactConserv (line 78). |
3004 |
Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW |
3005 |
o pkg/ggl90: |
3006 |
- fix previous modif (unfortunatly has not been documented here). |
3007 |
o pkg/seaice/autodiff: |
3008 |
- add CPP flag to include clipping of zeta in EVP code; |
3009 |
although clipping of zeta is not necessary for EVP and not recommended |
3010 |
it was done by default, now clipping is disabled by default |
3011 |
- modify computation and store zetaC/Z in seaice_evp for TAF |
3012 |
- add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default) |
3013 |
- change seaice_calc_viscosities/strainrates for better |
3014 |
vectorization after AD by TAF |
3015 |
- rearrange common blocks in SEAICE.h once again for easier dumps of |
3016 |
adjoint output, adjust adcommon.h and g_common.h |
3017 |
- change flux form of default advection scheme for better vectorization |
3018 |
of adjoint code |
3019 |
- modify lab_sea/input.lsr to test the flux form of default advection |
3020 |
scheme |
3021 |
o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level |
3022 |
transition in checkpoint61r) |
3023 |
|
3024 |
checkpoint61x (2009/10/19) |
3025 |
o adjoint: adding two new verification experiments |
3026 |
* tutorial_global_biogeo: an online dic sensitivity experiment |
3027 |
(work with G. Forget) |
3028 |
* tutorial_dic_adjoffline: an offline dic sensitivity experiment |
3029 |
(an update of the Dutkiewicz et al., 2006 paper) |
3030 |
Both use the same CO2FLUX cost function, but different controls |
3031 |
Gradient checks look good, but some recomp. could still be traightened out |
3032 |
Should add xx_dic control variable to test at some point |
3033 |
o model/src: |
3034 |
add run-time parameters to check and/or mask initial Temp & Salt |
3035 |
o pkg/ptracers: |
3036 |
apply zonal filter (if used) to all passive tracers |
3037 |
|
3038 |
checkpoint61w (2009/10/12) |
3039 |
o adjoint: |
3040 |
* update and finish work on adjoint of dic package (G. Forget) |
3041 |
* start adjoint of offline package |
3042 |
* bug fix for cube-sphere TLM code (active_file_g.F) |
3043 |
o tutorial_global_oce_optim: |
3044 |
now tested with 4 tiles (change data.grdchk and update output_adm.txt) |
3045 |
and add SIZE.h_mpi for MPI testing |
3046 |
o pkg autodiff |
3047 |
- fix bug in autodiff_restore |
3048 |
- make genmake2 remove comments and empty lines from ad_input_code.f in |
3049 |
order to reduce file size (new script file remove_comments_sed) |
3050 |
o allows to specify vertical profile of vertical viscosity (viscArNr) |
3051 |
o pkg autodiff |
3052 |
autodiff_ini_model_io: comment out writing of grid information to netcdf |
3053 |
files, because at this time the grid fields are a bunch of zeros |
3054 |
(this is analogous to ini_mnc_vars.F) |
3055 |
o pkg seaice/autodiff: |
3056 |
left-over from removing the 3-time-level fields: |
3057 |
- small rearrangement of common blocks (SEAICE.h) |
3058 |
- fix field declaration in order to get meaningful output in |
3059 |
adseaice.*.nc (adcommon.h) |
3060 |
o pkg obcs: |
3061 |
- go through NH code only if nonHydrostatic=T |
3062 |
- fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart) |
3063 |
- move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields |
3064 |
=> Update output of experiment seaice_obcs |
3065 |
- useOBCSbalance: code is wrong with multi-tile / proc: add a stop. |
3066 |
- fix NH+Orlanski restart (add wvel OBC value in pickup file) |
3067 |
- fix restart for useOBCSprescribe + useEXF |
3068 |
o pkg ctrl |
3069 |
- make obcs as control parameter work also with useSingleCPUio |
3070 |
- replace a few sny and snx by Ny and Nx to be consistent with |
3071 |
ctrl_set_globfld_x/yz.F |
3072 |
o pkg seaice |
3073 |
- re-introduce global field frWtrAtm for the case of |
3074 |
ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
3075 |
- catch the case of an empty filename in seaice_cost_init_fixed.F |
3076 |
o pkg ecco: |
3077 |
- small bug fixes in the_main_loop |
3078 |
. fix order of monitor arguments |
3079 |
. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
3080 |
. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
3081 |
that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
3082 |
- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
3083 |
imbalance diagnostics for wmean_h/sflux = 0 |
3084 |
- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
3085 |
- catch the case of empty filenames in ecco_cost_init_fixed.F |
3086 |
and ecco_readparms.F |
3087 |
- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
3088 |
to make this statement meaningfull in ecco_cost_weights.F |
3089 |
o pkg zonal_filt: |
3090 |
- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
3091 |
- when using rStar, filter uVel*hFacW instead of uVel |
3092 |
(tested without topography: fix a Pb of growing instability with NLFS) |
3093 |
o pkg/aim/thsice: |
3094 |
-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
3095 |
(works as SST restoring) |
3096 |
o pkg/thsice: |
3097 |
-add specific parameter for salt restoring in slab mixed-layer |
3098 |
(by default equal to the temperature restoring) |
3099 |
|
3100 |
checkpoint61v (2009/09/21) |
3101 |
o pkg/kpp: |
3102 |
-add double diffusive contributions as a hack, turned off by default |
3103 |
for now, and the code can be excluded with a CPP-flag |
3104 |
EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
3105 |
-add a verification experiments to "vermix" to test this code |
3106 |
o pkg/mom_common: |
3107 |
Move computation of length scales to mom_init_fixed.F (avoid recomputation |
3108 |
at each time-steps*levels). |
3109 |
o pkg/layers: |
3110 |
Created a new package for computing volume fluxes in temperature or |
3111 |
[not yet implemented] density layers, e.g. for calculating residual |
3112 |
overturning circulations. |
3113 |
o pkg/diagnostics: |
3114 |
implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
3115 |
o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
3116 |
o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
3117 |
To avoid mixing type (RS/RL) of input/output array argument, |
3118 |
replace single mixed-type array with a pair from each type (RS/RL). |
3119 |
o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
3120 |
is now implemented for all pkgs (previously only done for the main pickup) |
3121 |
|
3122 |
checkpoint61u (2009/08/25) |
3123 |
o pkg/obcs: |
3124 |
- change OB?eta from _RS to _RL and put them into a separate commen block |
3125 |
- add code to read OB?eta from a file via obcs_prescribe_read: the code |
3126 |
compiles and does not destroy any other experiments, the data is read |
3127 |
properly, but the code is not tested in actual applications |
3128 |
o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
3129 |
create a meaningful unit attribute for the time coordinate variable |
3130 |
o pkg/ebm: add plenty of missing "_d 0" ; |
3131 |
update results of experiment global_ocean_ebm (fwd + adjoint tests) |
3132 |
Notes: several pieces of code only works for (very) specific set up |
3133 |
(domain size, lat range, etc ...); should be documented & stop if one |
3134 |
of those assumptions is not meet. |
3135 |
o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
3136 |
update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
3137 |
and offline_exf_seaice (seaicetd + adjoint). |
3138 |
o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
3139 |
update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
3140 |
seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
3141 |
o few changes to pass when compiling with strick checking of arguments |
3142 |
across S/R (allow to find few bugs in S/R calls). |
3143 |
o pkg/seaice: |
3144 |
- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
3145 |
2d-fields, for slightly better performance |
3146 |
|
3147 |
checkpoint61t (2009/07/22) |
3148 |
o pkg/seaice: |
3149 |
- remove unused variables in seaice_evp |
3150 |
- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
3151 |
o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
3152 |
named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
3153 |
each processor opens a different file (a fix from Matt). |
3154 |
o cg2d: |
3155 |
use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
3156 |
this reduces number of EXCH calls by 2 when using exch2. |
3157 |
For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
3158 |
directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
3159 |
o pkg/thsice: |
3160 |
add code for Near Infra-Red albedo (from Jeff) |
3161 |
(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
3162 |
o ini_model_io: |
3163 |
move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
3164 |
MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
3165 |
to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
3166 |
|
3167 |
checkpoint61s (2009/06/30) |
3168 |
o pkg/exch2 (exch2_rxN_cube*): |
3169 |
remove last BARRIER (no need to synchronise after getting data from shared |
3170 |
buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
3171 |
o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
3172 |
and generate new output (for the 2 tests) using default rotationPeriod. |
3173 |
o pkg/exch2: |
3174 |
- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
3175 |
(was already the case with AUTODIFF_EXCH2 defined) |
3176 |
- add bj in exch2 arrays and S/R. |
3177 |
- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
3178 |
MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
3179 |
o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
3180 |
- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
3181 |
GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
3182 |
- verification experiment natl_box.longstep |
3183 |
o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
3184 |
allow different versions of ifort (8 or 9) and different versions |
3185 |
of mpi (mpich or mpich2) to be used with the same optfile. |
3186 |
requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
3187 |
optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
3188 |
o pkg/seaice: |
3189 |
fix previous modif (3-level field removed) for old-pickup reading |
3190 |
|
3191 |
checkpoint61r (2009/06/25) |
3192 |
o pkg/seaice: |
3193 |
- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
3194 |
1. introduce fields for time step (N-1) |
3195 |
2. do not use levels 2 and 3 anymore (but keep them) |
3196 |
3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
3197 |
includes changes to pkg/thsice/thsice_get_velocity.F, |
3198 |
model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
3199 |
pkg/obcs/obcs_apply_uvice.F. |
3200 |
- completely remove code for leap-frog time stepping for second order |
3201 |
advection |
3202 |
- adjusted adjoint accordingly; |
3203 |
gradient checks have improved by an order of magnitude! |
3204 |
|
3205 |
checkpoint61q (2009/06/22) |
3206 |
o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
3207 |
- the boundary conditions along open boundaries are unclear, because the |
3208 |
associated masks are set to zero and are thus treated as closed when |
3209 |
applying the slip-boundary conditions. |
3210 |
- move initialisation of grid variables from seaice_init_varia to _fixed |
3211 |
o adding doc/diags_changes.txt |
3212 |
o model/src: |
3213 |
do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
3214 |
to avoid "_diags" naming if no relation to pkg/diagnostics. |
3215 |
ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
3216 |
file and only call PLOT_FIELD_XYZ if debugMode=T. |
3217 |
remove few PLOT_FIELD_XY calls outside initialisation. |
3218 |
remove few unnecessary BARRIER. |
3219 |
o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
3220 |
of salt_plume package in Southern Ocean |
3221 |
o pkg/thsice: |
3222 |
- fix hOceMxL in overlap (needed for sea-ice advection); |
3223 |
update output of experiment global_ocean.cs32x15.icedyn. |
3224 |
o pkg/seaice: |
3225 |
- make the (placeholder-)tracer IceAge a little more meaningful |
3226 |
by avoiding ridging of age due to convergent ice flow |
3227 |
- add diagnostics for surface temperature, atmospheric and oceanic |
3228 |
heat flux, and atmospheric and oceanic ice growth |
3229 |
|
3230 |
checkpoint61p (2009/06/10) |
3231 |
o eesupp (global_max & global_sum): |
3232 |
- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
3233 |
- remove starting & endding barrier (no longer needed) |
3234 |
o pkg/mdsio, writelocal: |
3235 |
works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
3236 |
(remove the STOP): uses shared buffer IO to store data from all threads |
3237 |
and then let master-thread write nThreads tiles. |
3238 |
o pkg/mdsio (read/write field): |
3239 |
- tiled IO done in 1 piece (all levels at a time); |
3240 |
- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
3241 |
- multi-threaded: allow to read/write local (non-shared) array |
3242 |
(was already working with singleCpuIO ; now works also without); |
3243 |
=> no longer needs barrier call after reading a file (added inside |
3244 |
mds_read/write field). |
3245 |
- move barrier calls outside gather/scatter_2d to mds_read/write_field |
3246 |
o pkg/obcs/exf |
3247 |
- exf_getffieldrec.F: add a few ". _d 0" and |
3248 |
add code to catch the case fldperiod = 0. |
3249 |
- obcs_precribe_read.F: change if statements so that they match |
3250 |
the variable type (_RL) |
3251 |
- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
3252 |
exf_iprec) as part of namelist EXF_NML_01 |
3253 |
o pkg/mdsio: |
3254 |
- read/write tiled (local) files: read/write 1-level tile chunk at a time |
3255 |
(instead of segment of length sNx); expected to speed up tiled IO. |
3256 |
o pkg/exch2: |
3257 |
- take buffer copy from/to array out of S/R exch2_send/recv into new |
3258 |
S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
3259 |
(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
3260 |
- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
3261 |
- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
3262 |
(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
3263 |
including Topology header file (and common blocks). |
3264 |
- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
3265 |
remove 2nd exch call in exch2_s3d_rx (no longer needed). |
3266 |
- document S/R arg. list (+ update some comments) |
3267 |
o pkg/seaice: |
3268 |
- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
3269 |
temperature and humidity over sea ice based on climatological values. |
3270 |
- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
3271 |
of LSR (this change is expected to change the results slightly because now |
3272 |
it uses slightly difference moduli from the second last LSR solution, but |
3273 |
that is more consistent with the stress computations; this part of the code |
3274 |
is not tested in the verification experiments) |
3275 |
- fix diagnostics for flux of ice in case of B-grid |
3276 |
- turn strain rates eij and press into global fields within global |
3277 |
common block in SEAICE.h for more straighforward diagnostics |
3278 |
- fix diagnostics for principal stress components, press, zeta, eta |
3279 |
to give something meaning full |
3280 |
o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
3281 |
new output (all 4 tests) using default rotationPeriod. |
3282 |
o pkg KPP: |
3283 |
- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
3284 |
- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
3285 |
and normal grid from 1 to Nr) |
3286 |
o Fix computations of L4rdt in mom_calc_visc.F |
3287 |
o eesupp: |
3288 |
new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
3289 |
should be called before a "stop" if we know that all process are going |
3290 |
to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
3291 |
|
3292 |
checkpoint61o (2009/05/26) |
3293 |
o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
3294 |
o model/src/ini_curvilinear_grid.F: |
3295 |
compute angleSin/CosC when they are not read from a file |
3296 |
o pkg/seaice: |
3297 |
add pseudo time stepping for LSOR |
3298 |
o pkg/exch2: |
3299 |
temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
3300 |
o pkg/seaice: |
3301 |
Adding separate sea ice albedo, drag coefficients, and HO in Southern |
3302 |
Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
3303 |
o SingleCpuIO: |
3304 |
fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
3305 |
o pkg/seaice: |
3306 |
put exchanged variable in (local) common block for MPI+Multi-Threads |
3307 |
to work (necessary with exch1, and for now with exch2 too). |
3308 |
o verification: to get more experiments tested with mpi, mth and mpi+mth, |
3309 |
change tiling of: |
3310 |
aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
3311 |
hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
3312 |
update output of exp: |
3313 |
exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
3314 |
tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
3315 |
+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
3316 |
(note: output.txt generated on faulks using only 1 tile) |
3317 |
o eesupp & mdsio (SingleCpuIO): |
3318 |
- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
3319 |
parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
3320 |
Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
3321 |
- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
3322 |
- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
3323 |
gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
3324 |
o pkg/exch2: |
3325 |
- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
3326 |
read parameter file "data.exch2" if it exists; otherwise try default regular |
3327 |
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
3328 |
- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
3329 |
with new code (not to be used, just as a backup solution). |
3330 |
- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
3331 |
in utils/exch2/input. |
3332 |
|
3333 |
checkpoint61n (2009/05/12) |
3334 |
o eesupp & mdsio (SingleCpuIO): |
3335 |
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
3336 |
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
3337 |
receive real*4 array (instead of real*8) to read/write 32.bit files. |
3338 |
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
3339 |
and remove new mapping S/R) |
3340 |
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
3341 |
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
3342 |
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
3343 |
when using exch2. Add S/R to map global io-buffer to global model array. |
3344 |
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
3345 |
|
3346 |
checkpoint61m (2009/04/29) |
3347 |
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
3348 |
and add 3 other S/R for other types (R4,R8,RS). |
3349 |
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
3350 |
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
3351 |
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
3352 |
- reduce number of macro definitions (keep only those which are used); |
3353 |
can always call directly the corrresponding S/R if needed. |
3354 |
- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
3355 |
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
3356 |
Fixed wrong type of arg in: |
3357 |
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
3358 |
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
3359 |
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
3360 |
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
3361 |
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
3362 |
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
3363 |
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
3364 |
o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
3365 |
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
3366 |
edges are closed (zero depth); might happen with "blank tiles"; |
3367 |
for now, disabled if using OBCS. |
3368 |
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
3369 |
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
3370 |
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
3371 |
to reduce length of 1.D array print in STDOUT. |
3372 |
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
3373 |
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
3374 |
o start to test MPI + multi-threaded (change testreport to skip tests |
3375 |
where number of tiles do not match). |
3376 |
o genmake2: add option "-omp" to turn on Open-MP ; |
3377 |
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
3378 |
o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
3379 |
and keep the original tile numbering. Note: compatible with old |
3380 |
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
3381 |
|
3382 |
checkpoint61l (2009/04/07) |
3383 |
o Overlaps had been forgotten in calculating ijk keys : fixed |
3384 |
o fix cyrus makedepend for gcc 4.4 |
3385 |
o experiment fizhi-cs-aqualev20: |
3386 |
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
3387 |
and generate new output. Note: new output is much closer to the old |
3388 |
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
3389 |
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
3390 |
o pkg/fizhi: |
3391 |
- change to avoid indices going deliberately over array-bounds |
3392 |
- remove unnecessary MPI stuff |
3393 |
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
3394 |
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
3395 |
does not go over array-bounds and therefore returns reliable output. |
3396 |
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
3397 |
this S/R has 4 output arguments, which are used inside "get_alarm"; |
3398 |
when it is called with the same variable "ndum" in place of several |
3399 |
output arguments, this produces weird side effect inside "get_alarm" |
3400 |
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
3401 |
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
3402 |
address) and produces error. |
3403 |
o tools/gemake2: (March 27-29 2009) |
3404 |
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
3405 |
testreport does). |
3406 |
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
3407 |
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
3408 |
update lab_sea.lsr & lab_sea.salt_plume results |
3409 |
o pkg/seaice: |
3410 |
Major overhaul of the LSOR solver: change discretization from original |
3411 |
finite differences to finite volume. The old routine is still in the |
3412 |
file seaice_lsr.F and can be turned on with the CPP-flag |
3413 |
SEAICE_OLD_AND_BAD_DISCRETIZATION |
3414 |
Along with this change, the discretization of the strain rates is changed. |
3415 |
The same flag turns on the old discretization in seaice_calc_strainrates.F |
3416 |
All verification experiments with seaice are affected (except for |
3417 |
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
3418 |
results by setting the above flag. |
3419 |
Further changes involve changes in defaults: |
3420 |
- ALLOW_FLOODING is defined and turned on by default |
3421 |
- SEAICEadvSnow = .true. is now the default |
3422 |
- SEAICEadvSalt = .true. is now the default |
3423 |
- SEAICEadvAge = .true. is now the default |
3424 |
- SEAICE_clipVelocities = .false. is now the default |
3425 |
(as per J. Zhang's recommendation) |
3426 |
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
3427 |
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
3428 |
- seaice_growth: replace computation of UG by a simple copy from wspeed |
3429 |
|
3430 |
checkpoint61k (2009/03/18) |
3431 |
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
3432 |
seaice_lsr: fixed a few metric terms, |
3433 |
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
3434 |
add more debugging diagnostics |
3435 |
seaice_evp: removed superfluous many metric terms of FV discretization |
3436 |
of stress divergence |
3437 |
affects lab_sea, lab_sea.hb87 |
3438 |
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
3439 |
of stress divergence for non-evp solver |
3440 |
(this part is not tested anywhere) |
3441 |
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
3442 |
they were effectively only half slip |
3443 |
affects lab_sea.hb87 |
3444 |
updated all relevant verification experiments (except lab_sea//output_adm.txt |
3445 |
which was left over, but fails at level 7 & 6) |
3446 |
|
3447 |
checkpoint61j (2009/03/17) |
3448 |
o pkg/seaice: turn a few hard wired parameters into run time parameters |
3449 |
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
3450 |
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
3451 |
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
3452 |
that are not cubed-sphere grids |
3453 |
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
3454 |
o pkg/ctrl: |
3455 |
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
3456 |
o non-hydrostatic (calc_gw.F): |
3457 |
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
3458 |
update output of exp. global_ocean.cs32x15.viscA4 |
3459 |
o remove backward compatibility for thetaMin,phiMin |
3460 |
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
3461 |
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
3462 |
interpolated wind field not only for curvilineargrid=.true., but also |
3463 |
for a rotated grid (rotateGrid=.true.) |
3464 |
o pkg/exf: add capability to bypass interpolation for runoff |
3465 |
by setting yet another CPP-flag |
3466 |
o eesupp/src, B-grid exchange: |
3467 |
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
3468 |
o autodiff |
3469 |
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
3470 |
allows to switch to single-prec common blocks; |
3471 |
corresponding switch occurs in tamc.h, integer isbyte |
3472 |
TAF store directivs "byte" and "kind" seem equivalent; |
3473 |
Most tamc.h have been updated correspondingly. |
3474 |
|
3475 |
checkpoint61i (2009/02/13) |
3476 |
o autodiff: |
3477 |
fix autodiff_sore/_restore indices for obcs |
3478 |
(spotted by I. Hoteit, M. Mazloff) |
3479 |
o pkg/autodiff, pkg/ctrl: |
3480 |
Add flag to reduce all tapelev I/O to single-prec. |
3481 |
In data.ctrl set |
3482 |
doSinglePrecTapelev = .TRUE. |
3483 |
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
3484 |
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
3485 |
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
3486 |
real fresh water flux (not yet) |
3487 |
o pkg/mdsio & rw: |
3488 |
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
3489 |
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
3490 |
o pkg/flt: |
3491 |
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
3492 |
init_fixed & ini_varia. |
3493 |
- clean-up & simplify linear interpolation S/R: |
3494 |
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
3495 |
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
3496 |
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
3497 |
- add vert. coordinate & horiz. indices to output files. |
3498 |
- change vertical position in initial condition, from index to depth [m]. |
3499 |
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
3500 |
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
3501 |
o pkg/ggl90: a few modifications: |
3502 |
- fix bottom boundary condition, and interpolation of KappaE |
3503 |
near top and bottom |
3504 |
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
3505 |
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
3506 |
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
3507 |
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
3508 |
(maintain temporary backward compatibility, until next checkpoint) |
3509 |
|
3510 |
checkpoint61h (2009/01/27) |
3511 |
o pkg/diagnostics with "periodic averaging diagnostics": |
3512 |
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
3513 |
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
3514 |
o pkg/obcs: fix loop ranges for balancing code |
3515 |
o pkg/flt: |
3516 |
- improve criteria for finding which tile owns a float. |
3517 |
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
3518 |
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
3519 |
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
3520 |
with ocean biogeo) |
3521 |
o pkg/flt: |
3522 |
- do some cleaning and fix the restart ; |
3523 |
- add output.txt in flt_example/results to get this pkg tested. |
3524 |
o genmake2: add an EXTENDED_SRC option and flag. |
3525 |
for now, cannot be turned on on command line (only through genmake_local) |
3526 |
o pkg/mdsio: read/write vector: |
3527 |
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
3528 |
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
3529 |
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
3530 |
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
3531 |
(drop to 4 digits matching for grad). But this test does not look very |
3532 |
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
3533 |
|
3534 |
checkpoint61g (2008/12/29) |
3535 |
o pkg/flt: |
3536 |
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
3537 |
+ make OPTIONS file more standard. |
3538 |
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
3539 |
- fix _BYTESWAPIO CPP-Flag |
3540 |
- standard reading of file-parameter "data.flt" |
3541 |
- fix argument list of S/R FLT_RESTART |
3542 |
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
3543 |
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
3544 |
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
3545 |
a still unfixed compiler/optimization bug |
3546 |
|
3547 |
checkpoint61f (2008/11/21) |
3548 |
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
3549 |
update results of global_ocean.cs32x15.icedyn test. |
3550 |
o move getcon.F from model/src to pkg/fizhi. |
3551 |
o pkg/exf: add parameter for extrapolation of temp up to the surface |
3552 |
and option to prevent negative evap (in bulk_largeyeager04 only). |
3553 |
o Prather Advection scheme: fix tracer conservation for divergent flow |
3554 |
(e.g., when using NonLin Free-Surface). |
3555 |
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
3556 |
o gmredi (Visbeck-variable-K): |
3557 |
- add more parameters to Visbeck-variable-K. |
3558 |
- use a 5 points average for dSigmaR in Visbeck-K calculation |
3559 |
(more "homogenous": same stencil and same weights as in dSigmaH) |
3560 |
- update output of ideal_2D_oce experiment. |
3561 |
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
3562 |
(#undef REAL4_IS_SLOW) |
3563 |
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
3564 |
coordinate variable |
3565 |
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
3566 |
(surface forcing fields), removes some of the functionality |
3567 |
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
3568 |
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
3569 |
probably not all: copy _RS surface flux fields to RL field before |
3570 |
calling DIAGNOSTICS_FILL |
3571 |
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
3572 |
real*4 (CALL EXCH_*_RS) versions. |
3573 |
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
3574 |
(generate new output). |
3575 |
|
3576 |
checkpoint61e (2008/10/23) |
3577 |
o gmredi (Visbeck-variable-K): |
3578 |
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
3579 |
- change computation of Visbeck-K where Slope > Smax : |
3580 |
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
3581 |
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
3582 |
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
3583 |
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
3584 |
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
3585 |
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
3586 |
does not become too large (to avoid precision problems in implicit-diffusion |
3587 |
solver); update ideal_2D_oce output. |
3588 |
o pkg ggl90: |
3589 |
- in ggl90_cal.F: compute only one set of visc/diff, used to |
3590 |
step forward TKE/T/S/momentum |
3591 |
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
3592 |
have Prandlt =1) |
3593 |
o gmredi (fm07): |
3594 |
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
3595 |
- allow to set few more params from data.gmredi |
3596 |
o pkg ggl90: |
3597 |
- add missing sqrt(2) factor in computation of mixing length |
3598 |
scale in ggl90_calc.F |
3599 |
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
3600 |
|
3601 |
checkpoint61d (2008/09/25) |
3602 |
o adjoint modifs |
3603 |
- adapt to new field rhoInSitu |
3604 |
- allow to revert from StoreDynVars2D, StoreDynVars3D |
3605 |
to individual fields |
3606 |
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
3607 |
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
3608 |
- save 1 rho computation. |
3609 |
- no longer modify T & S inland when using down_slope pkg. |
3610 |
o gad_som : allow to switch to SOM advection for T & S without corresponding |
3611 |
pickup files (using new S/R: MDS_CHECK4FILE). |
3612 |
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
3613 |
(for useSingleCpuIO to work in multi-threaded) |
3614 |
o pkg/shelfice: |
3615 |
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
3616 |
with SHELFICEtopoFile in data.shelfice |
3617 |
- move code for reading ice shelf topography and modifying hFacC into separate |
3618 |
subroutines of the shelfice package |
3619 |
- separate initialisation of "fixed" and "variable" variables |
3620 |
- kTopC is not (yet) replaced by kSurfC, although this is possible |
3621 |
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
3622 |
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
3623 |
and rename: |
3624 |
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
3625 |
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
3626 |
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
3627 |
|
3628 |
checkpoint61c (2008/08/30) |
3629 |
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
3630 |
to add mass source/sink of fluid in the interior (3-D generalisation |
3631 |
of oceanic real-fresh water flux). |
3632 |
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
3633 |
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
3634 |
o new pkg: down_slope |
3635 |
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
3636 |
- presently, modify T & S inland (dwnslp_calc_rho.F). |
3637 |
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
3638 |
- implementation for ocean in P-coords not tested. |
3639 |
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
3640 |
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
3641 |
(to facilitate conversion of oceanic pkg to p-coordinate). |
3642 |
o change FIND_RHO to FIND_RHO_2D : |
3643 |
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
3644 |
o new pkg: cheapaml |
3645 |
|
3646 |
checkpoint61b (2008/08/05) |
3647 |
o exch2: |
3648 |
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
3649 |
- no longer depend on the order sequence (N,S,E,W). |
3650 |
- 3rd exchange no longer needed (tested with 24 tiles). |
3651 |
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
3652 |
- exch_UV_A-grid readily available (but not yet tested). |
3653 |
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
3654 |
(both are no longer needed) in exch_uv: no effect in forward run; but |
3655 |
get truncation error differences with adjoint exch. |
3656 |
o exch2: |
3657 |
- change index-bounds storage (moved from target to local tile, |
3658 |
more intuitive this way) ; rename/remove some variables. |
3659 |
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
3660 |
|
3661 |
checkpoint61a (2008/07/29) |
3662 |
o exch2/matlab-topology-generator: |
3663 |
fix bug in index bounds for N-S internal exchange (hard to tell if this |
3664 |
had any effect on the solution). |
3665 |
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
3666 |
is exceeded |
3667 |
o testreport: modify syntax of awk, so that it works also with |
3668 |
awk, and not only with nawk and gawk |
3669 |
|
3670 |
checkpoint61 (2008/06/24) |
3671 |
o autodiff |
3672 |
Change default for TAF usage by removing argument '-nonew_arg' |
3673 |
This changes TAF subroutine argument list (ordering of active var.) |
3674 |
Omission of this flag leads to incompatibility w.r.t. TAMC |
3675 |
To restore TAMC-compatibility, need following modifs: |
3676 |
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
3677 |
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
3678 |
Tested TAF version is 1.9.22 |
3679 |
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
3680 |
|
3681 |
checkpoint60 (2008/06/19) |
3682 |
--->>> This is the last checkpoint for which generating the adjoint |
3683 |
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
3684 |
--->>> by default. |
3685 |
--->>> Future checkpoints will ommit this flag by default. |
3686 |
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
3687 |
o pkg/grdchk: Add gradient check to etan0 perturbations. |
3688 |
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
3689 |
o pkg/autodiff: more flexibility in zeroadj. |
3690 |
model/src: modifying do_oceanic_phys.F accordingly. |
3691 |
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
3692 |
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
3693 |
special setup of gmredi for which the adjoint is stable |
3694 |
enough for parameter optimization. |
3695 |
o bridging the gap between eddy stress and GM. |
3696 |
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
3697 |
along with a change in CPP option (now ALLOW_EDDYPSI). |
3698 |
-> when using GM w/ GM_AdvForm: |
3699 |
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
3700 |
is applied either in the tracer Eq. or in momentum Eq. |
3701 |
depending on data.gmredi (intro. GM_InMomAsStress). |
3702 |
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
3703 |
The key modifications are in model/src/taueddy_external_forcing.F |
3704 |
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
3705 |
|
3706 |
checkpoint59r (2008/05/29) |
3707 |
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
3708 |
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
3709 |
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
3710 |
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
3711 |
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
3712 |
mass points, when using mnc for output |
3713 |
- add runtime parameter (missing_value, missing_value_int) to override |
3714 |
default (which is the value of getcon('UNDEF')) |
3715 |
o pkg/mnc: prepare mnc for the actual use of missing values with the |
3716 |
diagnostics package: small fix in mnc_cw_readwrite.template and more |
3717 |
initialisation of never used fields |
3718 |
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
3719 |
versions |
3720 |
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
3721 |
thermodynamics sea ice solver does not blow up when some initial fields |
3722 |
are missing. |
3723 |
o move from external_forcing_surf.F to ini_forcing.F |
3724 |
the p-coord. hack consisting in using pLoad to set phi0surf ; |
3725 |
update output of tutorial_global_oce_in_p (affected @ truncation level). |
3726 |
o Freshen up a bit hs94.1x64x5, notably: |
3727 |
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
3728 |
exactConserv=.TRUE. |
3729 |
o pkg/generic_advdiff: |
3730 |
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
3731 |
applies to files where Temperature & Salinity 2nd Order moments are used. |
3732 |
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
3733 |
this uses a dynamically allocated internal state data structure |
3734 |
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
3735 |
and requires a fortran 90 compiler |
3736 |
|
3737 |
checkpoint59q (2008/05/06) |
3738 |
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
3739 |
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
3740 |
o Refresh tutorial_global_oce_biogeo, notably: |
3741 |
- change bathymetry (put back seamounts in ACC, use hFacs) |
3742 |
- change EOS (POLY3 --> JMD95Z) |
3743 |
- use Bryan-Lewis vertical diffusivity |
3744 |
- use multidimensional advection |
3745 |
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
3746 |
- change a couple of parameters in dic pkg |
3747 |
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
3748 |
o pkg/obcs: change default to OBCSfixTopo = .true., |
3749 |
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
3750 |
- replace "debugMode" with "debugLevel .GE. debLevB" |
3751 |
o implementation of TAF directives for gchem,cfc,dic |
3752 |
o remove "exp5" (replaced by tutorial_deep_convection). |
3753 |
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
3754 |
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
3755 |
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
3756 |
--> changes results in exp4, seaice_obcs |
3757 |
o tutorial_deep_convection : |
3758 |
update the set-up and increase resolution and domain size ; start |
3759 |
from pseudo initial conditions = output at t=120mn in order to see |
3760 |
something happening when running testreport. |
3761 |
o pkg/seaice: add os7mp as an advection scheme |
3762 |
add check for advection schemes |
3763 |
add a flag for restoring T and S underneath sea ice |
3764 |
o pkg/my82: add netcdf-support and diagnostics |
3765 |
o thsice pkg: |
3766 |
- Now hsMax limits snow height by turning it into ice following |
3767 |
flooding scheme (and now conserving energy) |
3768 |
- Slight rewriting of the formula in thsice_calc_thick.F |
3769 |
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
3770 |
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
3771 |
|
3772 |
checkpoint59p (2008/04/10) |
3773 |
o gchem / dic / cfc : |
3774 |
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
3775 |
- add new parameter files: "data.dic" & "data.cfc" ; |
3776 |
- various re-arrangement in initialisation & header file ; |
3777 |
- fix tutorial_global_oce_biogeo for multi-threaded test. |
3778 |
o pkg/dic: test for "pickup_dic" file when restarting ; |
3779 |
if no pickup-file, can restart with a re-initialised pH (same as it did |
3780 |
before) providing pickupStrictlyMatch is set to False. |
3781 |
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
3782 |
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
3783 |
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
3784 |
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
3785 |
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
3786 |
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
3787 |
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
3788 |
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
3789 |
scheme to use for vorticty-term ; |
3790 |
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
3791 |
(with default selectVortScheme, return to original discretisation) |
3792 |
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
3793 |
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
3794 |
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
3795 |
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
3796 |
also fix diagnostics VISCAHW & VISCA4W. |
3797 |
|
3798 |
checkpoint59o (2008/03/07) |
3799 |
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
3800 |
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
3801 |
move a few statemens out the main loop into separate loops |
3802 |
o pkg/shelfice: |
3803 |
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
3804 |
(kg/m^2/s), does not break tests, because in verification/isomip, |
3805 |
rhoConstFresh=rhoConst (by accident) |
3806 |
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
3807 |
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
3808 |
new file model/src/seawater.F, so that they are available for all pkgs. |
3809 |
- convert potential temperature into in-situ temperature. This changes the |
3810 |
isomip tests => update tests |
3811 |
o add a flag writePickupAtEnd (default=true) to be able to suppress |
3812 |
writing a pickup at the last timestep |
3813 |
o tools/mpack-1.6 : |
3814 |
- disable automake (not working) and autoconf (not needed). |
3815 |
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
3816 |
also cleaner with much less compilation warnings. |
3817 |
o pkg/profiles: |
3818 |
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
3819 |
(for "less than 32 characters name" compiler requirement) |
3820 |
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
3821 |
conditions that have a different sampling frequency than S/T/U/V obcs |
3822 |
o pkg/diagnostics (stats-diags): |
3823 |
- fix global Min/Max in case 1 processor get only empty tiles |
3824 |
o genmake2: replace (4 times) |
3825 |
make genmake_tc_1.o >> genmake_warnings 2>&1 |
3826 |
with |
3827 |
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
3828 |
echo $COMM >> genmake_warnings |
3829 |
$COMM >> genmake_warnings 2>&1 |
3830 |
to make genmake2 always see the value of CC as specified in the optfile. |
3831 |
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
3832 |
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
3833 |
- modify verification advect_cs test to test SOM-advection on CS-grid. |
3834 |
o pkg/ctrl: |
3835 |
- Rewrite of ctrl_map_ini_ecco.F, |
3836 |
introducing a generic routine (ctrl_map_ini_gen.F). |
3837 |
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
3838 |
|
3839 |
checkpoint59n (2008/02/09) |
3840 |
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
3841 |
number in dedicate array "hdiag": |
3842 |
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
3843 |
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
3844 |
- many small changes (integer format) for large number of diagnostics |
3845 |
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
3846 |
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
3847 |
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
3848 |
usingSphericalGrid, this allows to define the rotated grid coordinates |
3849 |
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
3850 |
geographical coordinates according to the inverse of the rotation defined |
3851 |
by the Euler angles, so that Coriolis parameter and online-interpolation by |
3852 |
exf works with the geographical coordinates on XC/YC/XG/YG. |
3853 |
Naturally, this feature does not work with all packages, so some |
3854 |
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
3855 |
profiles), because there the coordinates are assumed to be regular |
3856 |
spherical grid coordinates. |
3857 |
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
3858 |
- introduce isopycnal diffusion coefficient control. |
3859 |
o tools/adjoint_options: |
3860 |
- additional control vector components. |
3861 |
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
3862 |
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
3863 |
o pkg/mypackage: |
3864 |
- add example of read/write pickup for state-var ; |
3865 |
- add entry points to the main code for state-vars diags & write-pickup. |
3866 |
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
3867 |
transitions for useExfYearlyFields |
3868 |
- add new subroutine that determines the file to read from for |
3869 |
use*YearlyFields = .TRUE. and .FALSE. |
3870 |
- add a verification experiment to global_with_exf that tests |
3871 |
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
3872 |
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
3873 |
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
3874 |
subroutines (which could be generated from a template, because they are |
3875 |
almost identical), for now they are included in obcs_prescribe_read.F for |
3876 |
simplicity |
3877 |
o pkg/exf: |
3878 |
- add a little more diagnostic to exf_interp_read (in analogy to |
3879 |
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
3880 |
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
3881 |
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
3882 |
directive in routine lagran, and splitting a loop and making do while the |
3883 |
outermost loop (the latter requires the intoduction of index arrays) |
3884 |
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
3885 |
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
3886 |
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
3887 |
o verification/seaice_obcs: updated for restart test and latest options |
3888 |
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
3889 |
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
3890 |
for now this is only available for the C-grid code and also within |
3891 |
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
3892 |
|
3893 |
checkpoint59m (2008/01/14) |
3894 |
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
3895 |
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
3896 |
o gad_som : fix flux output (& diagnostics) to have same units as other |
3897 |
advection scheme fluxes (was previously multiplied by deltaT). |
3898 |
o added verification/seaice_obcs both to test seaice open boundaries |
3899 |
and to provide an example matlab scrpt for generating them |
3900 |
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
3901 |
o pkg/salt_plume: clean up salt_plume_frac.F to |
3902 |
remove redundancy in PlumeMethod 1 and 4 |
3903 |
o pkg/kpp: added saltplume diagnostics |
3904 |
o pkg/obcs and pkg/seaice: |
3905 |
- do not set uice and vice to zero when OB*icefile are unspecified |
3906 |
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
3907 |
- moved seaice tracer obcs after call to seaice_growth |
3908 |
o pkg/salt_plume: added various options for salt plume depth |
3909 |
criterion and for vertical distribution of the salt |
3910 |
|
3911 |
checkpoint59l (2007/12/18) |
3912 |
o pkg/ptracers: new version of ptracers pickup: |
3913 |
read meta file and write only fields which are needed to restart. |
3914 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
3915 |
o pkg/seaice: |
3916 |
- add timescale for melting due to warm mixed layer as a means of |
3917 |
setting SEAICE_availHeatFrac more conveniently |
3918 |
- add a CPP-flag/runtime parameter check for flooding algorithm |
3919 |
- reformulated availHeat in seaice_growth.F to be independent of AREA |
3920 |
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
3921 |
unit changes |
3922 |
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
3923 |
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
3924 |
SX vector computer. |
3925 |
o pkg/seaice: |
3926 |
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
3927 |
seaice forcing fields can now be read only through pkg/exf |
3928 |
- removed some unused halos |
3929 |
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
3930 |
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
3931 |
or U/VICE from U/VWIND before computing U/VSTRESS |
3932 |
|
3933 |
checkpoint59k (2007/11/30) |
3934 |
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
3935 |
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
3936 |
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
3937 |
all experiments pass when compile with un-initialised var. checking option. |
3938 |
o added pkg/salt_plume |
3939 |
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
3940 |
o pkg/seaice: new read/write pickup version. |
3941 |
read meta file and write only fields which are needed to restart. |
3942 |
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
3943 |
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
3944 |
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
3945 |
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
3946 |
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
3947 |
process. Fixed here by closing the domain at the Northern boundary. |
3948 |
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
3949 |
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
3950 |
a set of consecutive levels in/from a 3-D array. |
3951 |
o pkg/ptracers: |
3952 |
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
3953 |
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
3954 |
|
3955 |
checkpoint59j (2007/11/09) |
3956 |
o in pkgs: dic, obcs, offline, rbcs: |
3957 |
standard way to compute coeff. for time interpolation between 2 time reccords |
3958 |
which retains full precision (& make results less dependent on compiler). |
3959 |
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
3960 |
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
3961 |
packages instead of reading ice cover and wind speed separately |
3962 |
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
3963 |
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
3964 |
to allow to compile customized code before the update) |
3965 |
o cleaning-up: |
3966 |
- fix CPP instruction syntax in pkg/obcs |
3967 |
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
3968 |
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
3969 |
- fix some threads issue in IO parts. |
3970 |
o pkg/dic: |
3971 |
- add tons of "_d 0" (--> much better testreports !) |
3972 |
and then update outputs of tutorial_global_oce_biogeo |
3973 |
o pkg/mom_fluxform: |
3974 |
add a special version of momentum advection intended to conserve momentum |
3975 |
next to a bathymetry step or a coastline edge. (default = off = #undef) |
3976 |
o new read/write pickup version: |
3977 |
- for now, only implemented for main (mdsio) pickup file. |
3978 |
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
3979 |
and main pickup together. |
3980 |
- read meta file; read only what is needed to restart; stop if a field |
3981 |
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
3982 |
if it make sense (even if the restart is not perfect). |
3983 |
- if no meta file, assume that pickup to read corresponds exactly to |
3984 |
a pickup that would currently be written. |
3985 |
- read pickup written in the old format (until checkpoint59i) if it |
3986 |
recognizes an old meta file (no field-list). |
3987 |
- add a meta file in exp. which starts from a pickup: 2 cases: |
3988 |
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
3989 |
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
3990 |
b) a meta file describing the content of the associated pickup file |
3991 |
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
3992 |
o pkg/mdsio & pkg/rw: |
3993 |
- new routine to read a meta file ; new set of routine to read |
3994 |
Multiple-fields file (with meta file). |
3995 |
o added open boundary conditions capability for seaice |
3996 |
HSNOW, HSALT, UICE, and VICE |
3997 |
|
3998 |
checkpoint59i (2007/10/21) |
3999 |
o adjoint: |
4000 |
* fix multiDimAdvection adjoint |
4001 |
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
4002 |
and comlev1 size definition (maxpass vs. max. number of tracers) |
4003 |
* verification/global_ocean.90x45x15 adjoint now tests |
4004 |
NLFS and multiDimAdvection using DST3 (=30) |
4005 |
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
4006 |
o pkg/kpp: add "_d 0" to real constant (if missing); |
4007 |
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
4008 |
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
4009 |
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
4010 |
for internal parameters related to restart process (formerly from PARAMS.h) |
4011 |
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
4012 |
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
4013 |
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
4014 |
o pkg/monitor: |
4015 |
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
4016 |
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
4017 |
- account for deep Atmosphere factor and density factor (anelastic) |
4018 |
o added open boundary conditions capability for seaice HEFF and AREA |
4019 |
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
4020 |
thermodynamics |
4021 |
- requires a little reorganization, which affects the testreport results |
4022 |
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
4023 |
so that now the conservative form is tested |
4024 |
- add a few comments |
4025 |
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
4026 |
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
4027 |
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
4028 |
multidim-advection, for scheme 2 they are not filled) and transports, |
4029 |
thermodynamic growth rates |
4030 |
o change units of EmPmR (inside the code, + within coupling interface) |
4031 |
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
4032 |
Affects results @ truncation level (cg2d match) and update output of |
4033 |
experiments: lab_sea(6), global_ocean.90x40x15(10), |
4034 |
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
4035 |
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
4036 |
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
4037 |
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
4038 |
|
4039 |
checkpoint59h (2007/09/29) |
4040 |
o pkg/exf: |
4041 |
- improve vectorization by moving if-statement out of loops in |
4042 |
exf_mapfields, exf_radiation |
4043 |
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
4044 |
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
4045 |
o testreport: |
4046 |
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
4047 |
monitor & update offline_exf_seaice exp. output. |
4048 |
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
4049 |
o pkg/seaice: |
4050 |
- bug fix in the evp solver: boundary conditions were affected be |
4051 |
masking of zMax/zMin (changes results) |
4052 |
- minor bug fix in boundary conditions in seaice_calc_strainrates |
4053 |
(changes results for no_slip) |
4054 |
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
4055 |
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
4056 |
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
4057 |
stress formulation and no-slip boundary conditions |
4058 |
o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
4059 |
in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
4060 |
o pkg/seaice: a first HSALT time stepping equation has been checked in |
4061 |
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
4062 |
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
4063 |
without requiring DO-IF statements |
4064 |
o pkg/thsice: |
4065 |
use continuous power-law function for partition of energy between lateral |
4066 |
melting/freezing and thinning/thickening ; old code using step function |
4067 |
still available with #undef THSICE_FRACEN_POWERLAW |
4068 |
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
4069 |
o testreport: change AD testing : check against results/output_adm.txt |
4070 |
using same scripts as for forward test. |
4071 |
|
4072 |
checkpoint59g (2007/09/17) |
4073 |
o adjoint testing: in preparation for changing testreport: |
4074 |
- output format: cost and grad written on separated lines |
4075 |
- ad output results in directory "results" (instead of "results_ad") |
4076 |
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
4077 |
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
4078 |
o pkg/ecco: allow user defined cost function contributions |
4079 |
o testreport: |
4080 |
Allow to choose (per experiment) the list of tested output variables |
4081 |
and the main variable (used to issue a pass/FAIL ) ; |
4082 |
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
4083 |
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
4084 |
Also modify printing of summary: |
4085 |
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
4086 |
b) echo the list of tested variables in the individual summary.txt of |
4087 |
each experiment. |
4088 |
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
4089 |
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
4090 |
(but still depend on the tile decompostion of the domain). |
4091 |
o pkg/seaice: change a discretization detail to make the B-grid code |
4092 |
"more symmetric". This change is likely to remove all "ridges/leads" that |
4093 |
where quasi-aligned with the grid in B-grid solutions. It may also be |
4094 |
the solution to the stress coupling issues with the B-grid. |
4095 |
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
4096 |
remove .cvsignore from input dir. (since testreport no longer run here). |
4097 |
o pkg/thsice: |
4098 |
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
4099 |
- fix reshaping of sea-ice just after advection: |
4100 |
melt all the ice only if ice-volume is too small. |
4101 |
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
4102 |
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
4103 |
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
4104 |
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
4105 |
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
4106 |
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
4107 |
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
4108 |
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
4109 |
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
4110 |
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
4111 |
-> update output.txt |
4112 |
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
4113 |
this affects truncation error: -> update output.txt of exp: |
4114 |
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
4115 |
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
4116 |
|
4117 |
checkpoint59f (2007/08/21) |
4118 |
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
4119 |
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
4120 |
a bounded range (in forward mode) |
4121 |
o pkg/ecco, ctrl, autodiff and mom_common: |
4122 |
internal parameter controls, completements of implementations |
4123 |
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
4124 |
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
4125 |
(not seem any difference in testing results). |
4126 |
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
4127 |
at face corners. |
4128 |
o pkg/generic_advdiff: |
4129 |
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
4130 |
loop range indices for computing vertical advection tendency |
4131 |
and do the calculation in the interior only (no overlap) ; |
4132 |
for now, only implemented for SOM advection (to save CPU time). |
4133 |
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
4134 |
o exch2 adjoint |
4135 |
First set of changes: |
4136 |
- add exch2 hand-written adjoint templates |
4137 |
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
4138 |
This will require cleanup in pkg/autodiff/*.F |
4139 |
(changed routines currently kept separate in verif. code/) |
4140 |
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
4141 |
that used to hide exch2 or cubed-sphere specific code |
4142 |
(commented via 'cph-exch2') |
4143 |
o pkg/seaice |
4144 |
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
4145 |
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
4146 |
output of global_ocean.cs32x15.thsice . |
4147 |
|
4148 |
checkpoint59e (2007/07/26) |
4149 |
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
4150 |
for B-grid vector (not yet tested) and C-grid vector (<- only used |
4151 |
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
4152 |
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
4153 |
(#ifdef ALLOW_SALT_PLUME) |
4154 |
o gather_2d/scatter_2d: removed halo regions |
4155 |
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
4156 |
scheme and the corresponding test case (under front_relax dir). For now, |
4157 |
only available with Skew-flux form and not yet tested in realistic set-up. |
4158 |
adjoint: store directives updated, but gradient checks deteriorated, |
4159 |
so maybe GM/Redi adjoint is now broken. |
4160 |
o seaice adjoint |
4161 |
* add AREA, HEFF, HSNOW as control variable |
4162 |
(should not change lab_sea results) |
4163 |
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
4164 |
o pkg/seaice: |
4165 |
* added computation of saltFlux in seaice_growth; |
4166 |
For time being, sea ice salinity is assumed constant |
4167 |
contribution of snow flooding to freshening of sea ice is neglected. |
4168 |
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
4169 |
defaults to 0.0 in order to maintain backward compatibility. |
4170 |
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
4171 |
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
4172 |
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
4173 |
heat content used to melt or grow ice |
4174 |
* commented out cap of HICE: it helps keep ice thinner |
4175 |
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
4176 |
* applied OBCS T/S mask to HEFFM sea ice mask |
4177 |
|
4178 |
checkpoint59d (2007/06/21) |
4179 |
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
4180 |
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
4181 |
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
4182 |
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
4183 |
and change default value of parameter "GM_Small_Number"; |
4184 |
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
4185 |
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
4186 |
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
4187 |
o pkg/ecco: cost function when applying pkg/smooth to controls |
4188 |
o pkg/ctrl: add forcingPrecond run time parameter |
4189 |
o pkg/seaice: |
4190 |
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
4191 |
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
4192 |
changes verification/lab_sea |
4193 |
- rearrange implicit part of u-equation in LSR solver to make it easier to |
4194 |
read, understand, and debug. This causes changes at the truncation level. |
4195 |
- fix (serious) bug in the boundary conditions (sign error in the implicit |
4196 |
part) of the LSR solver. Changes all LSR results. |
4197 |
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
4198 |
is initilized with small values - does not change lab_sea results. |
4199 |
- added HsnowFile initialization capability |
4200 |
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
4201 |
initialization of pkg/smooth and application to control vector |
4202 |
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
4203 |
o dependencies: pkg/profiles requires pkg/cal |
4204 |
o pkg/profiles: |
4205 |
- added option ALLOW_PROFILES_GENERICGRID |
4206 |
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
4207 |
that interpolation information (grid points and coefficients) is provided |
4208 |
within the netcdf input files. |
4209 |
-> sample matlab scripts can be found in MITgcm_contrib/gael |
4210 |
that allow you to prepare netcdf input files. |
4211 |
- also modified: cleaner include statements, cleaner error print statements, |
4212 |
cleaner stops when error, and more tests of the netcdf input files consistency. |
4213 |
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
4214 |
o pkg/seaice: |
4215 |
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
4216 |
requires a new routine: seaice_diagnostics_fill.F |
4217 |
- make sure that seaice does not move if not forced (pressure replacement |
4218 |
method, Hibler and Ip, 1995), changes results |
4219 |
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
4220 |
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
4221 |
It is turned off by default (=-1.), because it changes the results. |
4222 |
- make it possible to read AREA from a file, too. |
4223 |
|
4224 |
checkpoint59c (2007/06/04) |
4225 |
o add S/R and diagnostics for oceanic mixed-layer depth |
4226 |
o move GMRedi call after all vertical mixing schemes (including KPP) |
4227 |
o pkg/thsice: |
4228 |
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
4229 |
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
4230 |
o pkg/obcs: |
4231 |
- bug fix for balance code |
4232 |
o pkg/seaice: |
4233 |
- allow values of SEAICE_elasticParm > 1 |
4234 |
- add new parameter SEAICE_evpTauRelax as an alternative |
4235 |
to SEAICE_elasticParm |
4236 |
- make lsr boundary conditions free slip (by default), changes result |
4237 |
- add code for no slip boundary conditions for lsr |
4238 |
- set minimum of zeta to zero (and not 4e8) (changes results) |
4239 |
- add a cap on AREA after advecting AREA if seaice_growth is not called |
4240 |
o change calculation of Visbeck K: |
4241 |
- no longer depend on tapering scheme; instead, compute slope (limited |
4242 |
by GM_maxSlope). this is equivalent to what was comuted before with |
4243 |
clipping or linear tappering. |
4244 |
- fix vertical averaging (wrong by 1/2 level) |
4245 |
- leave the old version (but will not be maintained) within |
4246 |
#ifdef OLD_VISBECK_CALC / #endif |
4247 |
- update output of exp. ideal_2D_oce |
4248 |
o change error catch in calc_r_star to improve vectorization |
4249 |
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
4250 |
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
4251 |
o adjoint: |
4252 |
Re-organized adjoint checkpointing according to Matt Mazloff |
4253 |
(but with modifs/completions/cleanups) |
4254 |
Storing is now bundled into large arrays to optimized I/O |
4255 |
(and second step in cleanup of the_main_loop) |
4256 |
|
4257 |
checkpoint59b (2007/05/16) |
4258 |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
4259 |
- export/import (between ocean & coupler) fields needed for ocean DIC. |
4260 |
o pkg/seaice: |
4261 |
- get rid of three more exchanges seaice_calc_viscosities (required |
4262 |
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
4263 |
- bug fix in seaice_ocean_stress (update of lab_sea required) |
4264 |
- reduce loop boundaries to necessary minimum also in seaice_evp |
4265 |
- go back to the old way of computing deltaC/Z as the adjoint likes that |
4266 |
better |
4267 |
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
4268 |
passive tracer to an Age Tracer) + update output.txt |
4269 |
o pkg/exf: |
4270 |
- implement A-grid / C-grid selection for wind-stress input files. |
4271 |
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
4272 |
for now, in exf_bulk_largeyeager04.F only : |
4273 |
- change implementation for case where windspeed + 2. components wind-stress |
4274 |
are read-in. AND use rhoConstFresh to convert evap. |
4275 |
o pkg/seaice: |
4276 |
- use correct EXCH_UV for wind-forcing (on A-grid). |
4277 |
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
4278 |
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
4279 |
o pkg/exf: |
4280 |
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
4281 |
EXF_INTERPOLATION: |
4282 |
- merge global_with_exf/code version of exf_interp_read.F |
4283 |
to the main code ; |
4284 |
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
4285 |
reading the file ; Important: This options needs to be defined to recover |
4286 |
previous code. |
4287 |
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
4288 |
- no longer loose real*8 precision along the way when using exf_iprec=64. |
4289 |
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
4290 |
- change discretisation of evp-solver in order to avoid another exchange |
4291 |
(changes lab_sea) and clean up a little |
4292 |
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
4293 |
help the adjoint (this also changes the results slightly) |
4294 |
- add a few "_d 0" where they had been missing in seaice_evp.F |
4295 |
- cleaning up: remove unused seaice_calc_rhs.F |
4296 |
o pkg/exf: some cleaning-up: |
4297 |
- change various "constants" into runtime parameters |
4298 |
- cleaned-up Large&Yeager04 routine which should eventually |
4299 |
replace exf_bulkformulae.F (changed names of S/R and CPP) |
4300 |
and merged various ALLOW_ATM_WIND options |
4301 |
only used with thsice pkg (in thsice_get_exf.F): |
4302 |
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
4303 |
which are used when useStabilityFct_overIce=TRUE (= the default) |
4304 |
- change default values of ice & snow emissivity and scale downward LW |
4305 |
by ice & snow emissivity. |
4306 |
o pkg/thsice: |
4307 |
fix few little problems, in thsice_calc_thickn.F: |
4308 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
4309 |
- melt only laterally if hIce < hThinIce (as the comments say) |
4310 |
and in thsice_extend.F: |
4311 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
4312 |
- start to form ice as soon as the minimum ice-volume is reachable. |
4313 |
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
4314 |
and cpl_aim+ocn |
4315 |
o pkg/kpp |
4316 |
- move computation of surface related input fields to KPP into a new |
4317 |
subroutine kpp_forcing_surf.F |
4318 |
- remove wrong (within bi,bj loops) EXCH calls. |
4319 |
- little cleaning (add argument myThid in last position, cvs header ...) |
4320 |
- for now, fix conservation problem by exchanging KPPviscAz (may not |
4321 |
be the best fix) |
4322 |
o pkg/seaice |
4323 |
- check for inconsistent evp parameter/cpp-flag combination |
4324 |
- remove leftover errIO flat for obsolete name list error handling |
4325 |
o OpenAD |
4326 |
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
4327 |
|
4328 |
checkpoint59a (2007/05/01) |
4329 |
o pkg/seaice: some parameter clarifications and a little bit of clean up |
4330 |
o pkg/thsice: rename run-time parameters: |
4331 |
himin -> hIceMin |
4332 |
himin0 -> hThinIce |
4333 |
hihig -> hThickIce |
4334 |
i0 -> i0swFrac |
4335 |
transCoef -> bMeltCoef |
4336 |
frac_energy -> fracMelting |
4337 |
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
4338 |
with default values (for now) that do not change the results. |
4339 |
remove old version of thsice vars advection in pkg/seaice. |
4340 |
o in FFIELDS.h: |
4341 |
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
4342 |
- make pLoad & sIceLoad always available (but still only used if |
4343 |
ATMOSPHERIC_LOADING is #define). |
4344 |
o pkg/kpp: replaced _KPP_RL with _RL |
4345 |
o bug fixes for vertical diffusivity computations when both KPP and |
4346 |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
4347 |
are no longer updating the vertical diffusivity array |
4348 |
(passed as argument) but are (re-) setting those arrays. |
4349 |
o pkg/seaice: fix bug in evp solver, while doing that |
4350 |
- change (improve?) discretization of stress computations for both |
4351 |
cgrid-lsr and evp solver |
4352 |
- add a new routine to compute strain rates |
4353 |
- the above changes lab_sea results |
4354 |
- add no slip conditions for evp solver (off by default), lsr-version |
4355 |
may follow |
4356 |
- fix exchange for shear at Z-points (does not change lab_sea) |
4357 |
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
4358 |
(to force the user to pick a time step since there is not "safe" way |
4359 |
of choosing it) |
4360 |
- add principal stress diagnostics |
4361 |
- rearrange fields for evp a little to avoid having to call a: too many |
4362 |
exchanges and b: exchanges for stress trensor components which we do |
4363 |
not have. |
4364 |
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
4365 |
of evp, complete rewrite for lsr case (latter is does not yet work |
4366 |
in all cases) |
4367 |
o pkg/kpp: add code to have mixing in shelf ice caverns |
4368 |
- add myThid to all kpp routines (long overdue) |
4369 |
|
4370 |
checkpoint59 (2007/04/19) |
4371 |
o pkg/exf: |
4372 |
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
4373 |
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
4374 |
- move exf header files from lower_case.h to UPPER_CASE.h ; |
4375 |
add missing cvs Header & Name |
4376 |
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
4377 |
- add namelist param. selectStressGridPosition, exf_monFreq |
4378 |
- retire many _CLIM routines, and remove data.exf_clim |
4379 |
+ params moved to data.exf |
4380 |
+ climsst, climsss now handled by exf_set_gen, i.e. |
4381 |
climss?period=0 refers to constant field, |
4382 |
climss?period=-12 to monthly forcing |
4383 |
- split up namelists in data.exf |
4384 |
o pkg/seaice: |
4385 |
- remove seaice_exch and seaice_exch_uv |
4386 |
- remove superfluous exchange of theta |
4387 |
- add myThid to seaice_budget_ocean/ice |
4388 |
- add new interface for atmospheric wind forcing (C-grid only) |
4389 |
+ new routine |
4390 |
+ two new field (taux, tauy for stress over ice) |
4391 |
+ removed one global field (DAIRN) for C-grid case only |
4392 |
o pkg/thsise |
4393 |
- 2nd set of modifs for thsice adjoint in conjunction with exf |
4394 |
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
4395 |
|
4396 |
checkpoint58y_post (2007/04/15) |
4397 |
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
4398 |
vertical diffusivity, similar to that in MOM4; turned on using |
4399 |
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
4400 |
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
4401 |
o Added capability for 3D specification of background vertical diffusion |
4402 |
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
4403 |
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
4404 |
"data" file that contains the 3D vertical diffusivity coefficients. |
4405 |
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
4406 |
- add code within pkg thsice to advect & diffuse sea-ice fields |
4407 |
similar to (and will replace) what has been added in seaice_advdiff.F, |
4408 |
but: - conserving Mass, Heat & Salt. |
4409 |
- better when using non-linear advection scheme (not yet fully tested) |
4410 |
- can also be used in atmospheric set-up (for now, only the diffusion). |
4411 |
|
4412 |
checkpoint58x_post (2007/04/04) |
4413 |
o IO option for global-file compact format: |
4414 |
- add options when generating topology (utils/exch2/matlab-topology-generator) |
4415 |
- add I/O capability (pkg/mdsio). |
4416 |
- adapt utils/matlab/rdmds.m to read this format. |
4417 |
for now long-line format not yet supported by pkg/mdsio (& exch2). |
4418 |
o shelfice: add a few diagnostics |
4419 |
|
4420 |
checkpoint58w_post (2007/03/13) |
4421 |
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
4422 |
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
4423 |
(and replace horiVertRatio in NH code). |
4424 |
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
4425 |
and tutorial_plume_on_slope (sensitive to truncation) |
4426 |
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
4427 |
directly to drive seaice model (C-grid only) |
4428 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
4429 |
- reintroduce computation of wind from stress, |
4430 |
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
4431 |
mass points to avoid tau = 0 |
4432 |
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
4433 |
o rdmnc.m: make it work with "global" files created with gluemnc |
4434 |
o rdmnc.m : some improvements in dealing with singleton dimension |
4435 |
(tested on all testreport mnc output files). |
4436 |
o genmake2: disable pkg/profiles if netcdf test fails. |
4437 |
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
4438 |
o move call to cal_readparms up to make calendar parameters/variable available |
4439 |
to all packages |
4440 |
|
4441 |
checkpoint58v_post (2007/02/08) |
4442 |
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
4443 |
useDynP_inEos_Zc tested. |
4444 |
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
4445 |
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
4446 |
and portions thereof. See read_cs.txt for description and examples. |
4447 |
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
4448 |
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
4449 |
following the great-circle arc between those 2 points. |
4450 |
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
4451 |
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
4452 |
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
4453 |
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
4454 |
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
4455 |
- still needs work (not working with some options ; efficiency to improve) |
4456 |
and serious testing. |
4457 |
- use this scheme for temperature & salinity in 2 advection test exp.: |
4458 |
advect_xy & advect_xz, respectively. |
4459 |
|
4460 |
checkpoint58u_post (2007/01/12) |
4461 |
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
4462 |
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
4463 |
o testreport: add option "-skipdir" to skip some test. |
4464 |
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
4465 |
momentum calculation. |
4466 |
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
4467 |
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
4468 |
remove checkpoint.F and the_correction_step.F (no longer used); |
4469 |
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
4470 |
o add option (linFSConserveTr) to correct for tracer source/sink due to |
4471 |
Linear Free surface |
4472 |
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
4473 |
o pkg/thsice: fix reading mnc-pickups |
4474 |
|
4475 |
checkpoint58t_post (2006/12/30) |
4476 |
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
4477 |
o pkg/mdsio: |
4478 |
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
4479 |
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
4480 |
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
4481 |
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
4482 |
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
4483 |
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
4484 |
- new S/R (to replace MDSWRITEMETA), which allows to write more |
4485 |
informations (variable names, time ...) to meta files. |
4486 |
- modify rdmds.m to give back the meta file content. |
4487 |
o pkg/diagnostics: change vertical interpolation to be safer, and more |
4488 |
flexible (define p-levels to interpolate to in data.diagnostics); |
4489 |
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
4490 |
diagnostic pointer. |
4491 |
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
4492 |
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
4493 |
o fix multi-category seaice: |
4494 |
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
4495 |
SEAICE_MULTICATEGORY |
4496 |
- fix short wave heat flux |
4497 |
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
4498 |
and allow to use EVP solver. Change forward lab_sea: test both EVP |
4499 |
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
4500 |
o Initial check-in of lab_sea adjoint |
4501 |
(very similar to natl_box_adjoint/code_seaice) |
4502 |
* used C-grid and EVP solver |
4503 |
* used KPP, GM/Redi |
4504 |
* uses inAdExact=.TRUE. |
4505 |
* gradient checks fail for both ADM and TLM |
4506 |
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
4507 |
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
4508 |
issue is related to forward mismatch between g77 an ifort |
4509 |
o pkg/seaice: overhaul of thermodynamics |
4510 |
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
4511 |
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
4512 |
- move a few global fields out of SEAICE.h into seaice_growth.F and |
4513 |
make them 2D (FICE/QNETO/ ...) |
4514 |
- remove FO (it is the same as QNETO) |
4515 |
- introduce a few local fields to avoid modifying external fields such |
4516 |
as atemp, etc. |
4517 |
|
4518 |
checkpoint58s_post (2006/12/11) |
4519 |
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
4520 |
changed exf_set_gen.F so that |
4521 |
genperiod=0 means input file is one time-constant field and |
4522 |
genperiod=-12 means input file contains 12 monthly means |
4523 |
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
4524 |
this affects truncation error ; generate new output file for exp. which |
4525 |
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
4526 |
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
4527 |
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
4528 |
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
4529 |
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
4530 |
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
4531 |
o start implementation of deep-atmosphere and anelastic formulation |
4532 |
o verification: remove 2nd copy of input files and use script "prepare_run" |
4533 |
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
4534 |
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
4535 |
o profiles: fix for multithreaded case |
4536 |
|
4537 |
o diagnostics: rename few diags: |
4538 |
s/'PRESSURE'/'RCENTER '/g |
4539 |
s/'TICE '/'oceFreez'/g |
4540 |
s/'TAUX '/'oceTAUX '/g |
4541 |
s/'TAUY '/'oceTAUY '/g |
4542 |
s/'SWFLUX '/'oceQsw '/g |
4543 |
s/DIFx/DFxE/g |
4544 |
s/DIFy/DFyE/g |
4545 |
and add few ocean-forcing diagnostics: |
4546 |
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
4547 |
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
4548 |
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
4549 |
as actual snow thickness. It now refers everywhere to effective snow |
4550 |
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
4551 |
|
4552 |
checkpoint58r_post (2006/11/17) |
4553 |
o modifications to pkg/seaice/growth.F, which change results of |
4554 |
lab_sea experiment: fixes pertain to melting snow over open water, to |
4555 |
masking EVAP under sea ice, and to using the correct AREA variable for |
4556 |
computations of EVAP, PRECIP, HSNOW, and GHEFF |
4557 |
o add ability to read bathy, salt, and theta using MNC (off by def) |
4558 |
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
4559 |
both are turned off by default and do no change any results |
4560 |
o seaice advection with pkg/thsice: a step toward the use of non-linear |
4561 |
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
4562 |
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
4563 |
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
4564 |
in natl_box (affects results @ truncation level: update output.txt) |
4565 |
o multi-threading and IO: |
4566 |
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
4567 |
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
4568 |
(needed to work with SingleCpuIO): tested in all verif. exp. |
4569 |
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
4570 |
affects the results (but none of the verification test uses this scheme). |
4571 |
o Adding some pkg/diagnostics capability to pkg/seaice |
4572 |
(will certainly be subject to changes) |
4573 |
o ctrl: adding new control variables: |
4574 |
lwflux, lwdown, evap, snowprecip, apressure, runoff |
4575 |
|
4576 |
checkpoint58q_post (2006/10/20) |
4577 |
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
4578 |
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
4579 |
high_res_cube configuration by 4% on Columbia. |
4580 |
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
4581 |
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
4582 |
dynamical allocation (seems to work in multi-threaded). |
4583 |
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
4584 |
single CPU io) so that TAF does not have to see EESUPPORT.h |
4585 |
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
4586 |
|
4587 |
checkpoint58p_post (2006/09/08) |
4588 |
o obcs: stop if obcs is used with useCDscheme = .true. |
4589 |
o shelfice: |
4590 |
- fix a sign error so that no slip at shelfice interface works |
4591 |
- remove stop for combination non-hydrostatic code and shelfice. That does |
4592 |
not mean, that the results are correct, but at least they are numerically |
4593 |
stable |
4594 |
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
4595 |
o added adjoint exch routined for all exch*3d* routines |
4596 |
and updated flow directives |
4597 |
|
4598 |
checkpoint58o_post (2006/08/28) |
4599 |
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
4600 |
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
4601 |
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
4602 |
and clean-up reading/writing of pickup files. |
4603 |
o fix local version of read/write pickup (NH part) in rotating_tank/code |
4604 |
o simplify EXCH interface: |
4605 |
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
4606 |
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
4607 |
o added the regrid package |
4608 |
o shelfice: |
4609 |
- add a simple boundary layer scheme to reduce noise |
4610 |
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
4611 |
|
4612 |
checkpoint58n_post (2006/08/14) |
4613 |
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
4614 |
local variable (not in common block). |
4615 |
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
4616 |
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
4617 |
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
4618 |
to work with SingleCpuIO. |
4619 |
o add "_d 0" to real constant of pkg/cfc subroutines ; |
4620 |
update exp. cfc_exemple & tutorial_cfc_offline output files. |
4621 |
o multi-threading and IO: |
4622 |
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
4623 |
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
4624 |
- barrier before and after reading. |
4625 |
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
4626 |
- avoid using MDS_WRITELOCAL for LAND pkg output. |
4627 |
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
4628 |
common-block variables ; Allows multi-threading with master-thread IO. |
4629 |
o change default MAX_NO_THREADS from 32 to 4 ; |
4630 |
and stop cleanly when MAX_NO_THREADS is too small. |
4631 |
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
4632 |
|
4633 |
checkpoint58m_post (2006/07/17) |
4634 |
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
4635 |
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
4636 |
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
4637 |
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
4638 |
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
4639 |
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
4640 |
add MITgcm_tutorials (= code + all the tutorials) |
4641 |
o ecco, option to compute cost for total ssh (mean+anom) |
4642 |
o consistent with addition of ptracer and ssh in pkg/profiles |
4643 |
o profiles: adding ptracer and ssh |
4644 |
o testreport: change multi-test output-file name |
4645 |
(from output.txt.{name} to output.{name}.txt) |
4646 |
o profiles: now ok for mutli-tiles case |
4647 |
o seaice: add 4 parameters for different advection schemes for area, |
4648 |
(effective) seaice thickness, enthalphy, and snow height. Their default |
4649 |
is the standard parameter SEAICEadvScheme |
4650 |
o calc_gw: |
4651 |
- add cosFacU in zonal viscous flux (harmonic.visc.). |
4652 |
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
4653 |
of tutorial_plume_on_slope. |
4654 |
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
4655 |
o calc_gw: true flux-form, account for horizontal grid spacing. |
4656 |
update rotating_tank results, but not plume_on_slope (affected at |
4657 |
truncation level, 11 digits). |
4658 |
|
4659 |
checkpoint58l_post (2006/07/12) |
4660 |
o calc_gw: |
4661 |
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
4662 |
- remove side-drag for now (need to fix it); update plume_on_slope results. |
4663 |
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
4664 |
o commit code to make SST/SSS weights spatially variable |
4665 |
(based on either variable in-situ or variable initial T/S weights) |
4666 |
o pkg/ecco: |
4667 |
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
4668 |
now based on horizontally varying weights wthetaLev, wsaltLev |
4669 |
* cost_averagesflags now returns year indices in addition to day, month |
4670 |
* sflux balance is performed on annual basis |
4671 |
(sflxumm, sfluxmm2, bal_sfluxmm) |
4672 |
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
4673 |
including separate counting and multipliers |
4674 |
o pkg/rbcs |
4675 |
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
4676 |
|
4677 |
checkpoint58k_post (2006/07/06) |
4678 |
o testreport: |
4679 |
- always build in dir. "build" (if not there, mkdir build instead of building |
4680 |
& running in input) |
4681 |
- run in dir run (if it exists), in build otherwise. |
4682 |
- call prepare_run (if input/prepare_run exists) |
4683 |
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
4684 |
o pkg/exf modifications to interpolation and rotation routines for more |
4685 |
reasonable treatment of North Pole singularity: for tracers North Pole |
4686 |
value is set to northernmost zonal-mean value, for zonal velocity it is |
4687 |
set to zero, and for meridional velocity it is set to northernmost value. |
4688 |
o pkg/exf/exf_check_range.F |
4689 |
- add tile index to diagnostics and move stop statement to the very |
4690 |
end of the routine. |
4691 |
o pkg/diagnostics: (diagnostics_main_init.F) |
4692 |
define title of isomorphic variables according to the current config. |
4693 |
o pkg/thsice with pkg/seaice dynamics: |
4694 |
- fix domain of computation (interior only, required for exf) and do exchanges |
4695 |
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
4696 |
o towards a standard way of dealing with multi-threading in MONITOR |
4697 |
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
4698 |
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
4699 |
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
4700 |
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
4701 |
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
4702 |
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
4703 |
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
4704 |
o tracer advection: |
4705 |
- clean-up and simplify calc_common_factors.F |
4706 |
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
4707 |
advection subroutine (but still not used within DST advection S/R) |
4708 |
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
4709 |
|
4710 |
checkpoint58j_post (2006/06/15) |
4711 |
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
4712 |
from file (collects calls previously in FORWARD_STEP) |
4713 |
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
4714 |
o adjoint store dir. adjusted accordingly |
4715 |
o genmake2 |
4716 |
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
4717 |
|
4718 |
checkpoint58i_post (2006/06/14) |
4719 |
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
4720 |
on wind stress (SEAICEstressFactor defaults to 1.) |
4721 |
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
4722 |
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
4723 |
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
4724 |
on CS-grid: no longer loosing mass. |
4725 |
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
4726 |
o pkg/ggl90: fix sloppy output and fix a bug |
4727 |
o pkg/seaice: added SEAICEuseEVPpickup parameter |
4728 |
- Set to false in order to start EVP solver with |
4729 |
non-EVP pickup files when using SEAICEuseEVP |
4730 |
- fix sign error in diffusion in seaice_calc_rhs |
4731 |
|
4732 |
checkpoint58h_post (2006/06/07) |
4733 |
* Modifications for bottom topography control |
4734 |
o replace hFacC by _hFacC at various places |
4735 |
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
4736 |
o add non-self-adjoint cg2d_nsa |
4737 |
o update autodiff support routines |
4738 |
o re-initialise hfac after ctrl_depth_ini |
4739 |
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
4740 |
* Adding verification for 5x5 box (4-layer) bottom topography control |
4741 |
|
4742 |
checkpoint58g_post (2006/06/07) |
4743 |
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
4744 |
used for mean seasonal cycle, mean diurnal cycle); add an example |
4745 |
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
4746 |
o pkg/ggl90: |
4747 |
- add parameter (minimum surface kinetic energy) |
4748 |
- fix bug (avoiding division by zero) |
4749 |
o couple pkg/thsice to pkg/seaice: |
4750 |
- modify advection in seaice to accomodate new scalar fields to be advected |
4751 |
- only muliDimAdection scheme work with seaice/thsice |
4752 |
- mapping of thsice-variables to seaice-variables, back and forth |
4753 |
- does not break the verification experiments, but does not give the |
4754 |
desired results either |
4755 |
o pkg/seaice |
4756 |
- make (default) second order advection a bit less confusing? |
4757 |
|
4758 |
checkpoint58f_post (2006/06/05) |
4759 |
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
4760 |
to pkg/seaice): |
4761 |
- new routines thsice_map_exf and thsice_get_exf provide the interface |
4762 |
- add an additional formal parameter to thsice_solve4temp |
4763 |
o pkg/exf: |
4764 |
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
4765 |
- correct Stefan-Boltzmann constant |
4766 |
- new parameter for longwave surface emittance |
4767 |
- separate some stuff from exf_bulkformulae into new routines |
4768 |
exf_radiation, exf_wind |
4769 |
- add new parameters and constants: longwave emissivity for ocean, ice |
4770 |
and snow, evaporation parameters over ice |
4771 |
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
4772 |
either wind from stress or stress from wind |
4773 |
o pkg/thSIce: |
4774 |
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
4775 |
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
4776 |
and THSICE_CALC_THICKN |
4777 |
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
4778 |
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
4779 |
to make debugging easier. |
4780 |
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
4781 |
o pkg/bulk_force: |
4782 |
- clean-up comments and parameters ; |
4783 |
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
4784 |
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
4785 |
generate new output for test-experiment: aim.5l_cs.thSI |
4786 |
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
4787 |
testreport accordingly |
4788 |
|
4789 |
checkpoint58e_post (2006/05/17) |
4790 |
o SEAICE_CGRID adjoint done |
4791 |
o R_STAR adjoint implemented. |
4792 |
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
4793 |
* need to sort out init. of h0facc, etc. |
4794 |
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
4795 |
to be able to use it in pure forward. |
4796 |
|
4797 |
checkpoint58d_post (2006/04/21) |
4798 |
o upgrade simple test-experiment to tutorial example: |
4799 |
step.1: duplicate the experiment and (step.2) will remove the old copy. |
4800 |
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
4801 |
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
4802 |
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
4803 |
tutorial_global_oce_biogeo <- copy of dic_example |
4804 |
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
4805 |
tutorial_plume_on_slope <- copy of plume_on_slope |
4806 |
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
4807 |
tutorial_global_oce_optim <- empty for now (David ?) |
4808 |
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
4809 |
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
4810 |
o correct a sign problem in cost_scat.F |
4811 |
o obcs and ptracers: fix boundary conditions for advections schemes |
4812 |
with larger stencil |
4813 |
o thsice adjoint: start |
4814 |
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
4815 |
completeness |
4816 |
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
4817 |
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
4818 |
o ptracers adjoint: |
4819 |
* avoid extensive recomputatations |
4820 |
* fix missing re-init. of gptr (missed by TAF) |
4821 |
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
4822 |
me to turn off the excessive output to STDOUT that this package produces |
4823 |
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
4824 |
and add those terms in Vector-Invariant formulation. |
4825 |
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
4826 |
if the control period (xx_hfluxperiod etc) is 0 |
4827 |
o in profiles pkg, clean routines and fix details |
4828 |
o in ecco pkg, reading ssh data: |
4829 |
fix problem in case the model does not start at iter0=0 |
4830 |
o fix mnc-pickup/restart for ptracers |
4831 |
o new package prifiles: |
4832 |
code to compute profile-based cost by Gael Forget |
4833 |
(modifs in ecco, ctrl, autodiff) |
4834 |
o Benign bug fix in initialization (spotted by M. Mazloff) of |
4835 |
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
4836 |
|
4837 |
checkpoint58c_post (2006/03/23) |
4838 |
o adjoint: finish NLFS adjoint and provide reference output in |
4839 |
verification/global_ocean.90x40x15/results_ad_nlfs |
4840 |
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
4841 |
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
4842 |
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
4843 |
with SEAICE_CGRID defined. |
4844 |
o move calendarDumps from "data" to "data.cal" and clean-up the code |
4845 |
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
4846 |
o add useEXF & useCAL flags (for now, set in hard-coded way) |
4847 |
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
4848 |
(were missing in NH mode, and wrong in quasihydrostatic mode). |
4849 |
waiting for Chris updated version of calc_gw to add those CALLs. |
4850 |
o fix bug in quasihydrostatic S/R ; |
4851 |
add a test for this option: global_ocean.90x40x15.qshyd |
4852 |
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
4853 |
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
4854 |
o add on/off flag useOffLine for package OFFLINE |
4855 |
o seaice: |
4856 |
- modify advection so that it works also on the C-grid |
4857 |
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
4858 |
problem in multi-tile runs with C-grid |
4859 |
- add flags for clipping ice velocities and/or masking solver forcing |
4860 |
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
4861 |
C-grid solver |
4862 |
- added a few comments to seaice_diffusion.F |
4863 |
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
4864 |
are now exclusive) |
4865 |
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
4866 |
required re-ordering the code a little: |
4867 |
+ make DAIRN global variable (defined in SEAICE) |
4868 |
+ move computation of the viscosities eta and zeta into a new separate |
4869 |
routine (because I need to recompute them in seaice_ocean_stress.F) |
4870 |
|
4871 |
checkpoint58b_post (2006/03/13) |
4872 |
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
4873 |
update output.txt of exp. aim.5l_cs.thSI |
4874 |
o various mnc cleanups and improvements: |
4875 |
+ shrink lookup tables by factor of ~4 |
4876 |
+ better error reporting when running out of lookup space |
4877 |
+ able to handle longer path/file names (up to 500 chars) |
4878 |
o adjoint: |
4879 |
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
4880 |
- TBD: "hidden" mom_vecinv recomp. in dynamics |
4881 |
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
4882 |
(allow to differentiate between forcing components using new integer flags: |
4883 |
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
4884 |
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
4885 |
o ecco |
4886 |
- enable trend removal from SSH anomaly obs. |
4887 |
o adjoint |
4888 |
- a fix for PmEpR when #undef EXACT_CONSERV |
4889 |
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
4890 |
- try to fix "hidden" recomp. in forward_step for NLFS |
4891 |
(NLFS seems broken sometimes after I checked it in) |
4892 |
o seaice: |
4893 |
- add c-grid version of the dynamic solver: |
4894 |
+ three new routines that are the c-grid substitute lsr, dynsolver |
4895 |
and ostres |
4896 |
+ put a few fields that were local to dynsolver into global common |
4897 |
blocks, so that I can move the computation of stresses etc into |
4898 |
seaice_lsr (saves coding but may break the adjoint). |
4899 |
- replace more hardwired parameters by runtime parameters |
4900 |
- add ice masks that mask the rhs of the implicit solvers where there |
4901 |
is no ice (commented out in seaice_dynsolver, because i am not sure |
4902 |
if this works properly), eventually this should replace the clipping |
4903 |
of ice velocities in seaice_dynsolver to +/-40cm/s. |
4904 |
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
4905 |
include it only where its needed |
4906 |
o move balancing of fluxes before the call of external_forcing_surf |
4907 |
o seaice: |
4908 |
- correct units of turning angles (now they are really in degrees) |
4909 |
- move computation of GWATX/Y out of main routine into dynsolver |
4910 |
- initialize GWATX/Y in seaice_init |
4911 |
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
4912 |
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
4913 |
o seaice: add runtime flags for turning angles (default to zero) |
4914 |
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
4915 |
and trend from exf forcing and ctrl control adjustments |
4916 |
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
4917 |
(since checkpoint57x_post) |
4918 |
o change the default rotation period to 86164.s = the Earth rotation |
4919 |
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
4920 |
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
4921 |
o seaice advection: add code for choosing between the default (2nd order |
4922 |
central differences) and multiDim advection schemes provided by |
4923 |
pkg/generic_advdiff |
4924 |
o seaice: |
4925 |
- removed all references to SEAICE_GRID.h fields from |
4926 |
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
4927 |
(cubed-sphere configuration will change a little) |
4928 |
- grid computations in seaice_init are obsolete now. |
4929 |
- cleaned up code a little so that is easier to read (hopefully). |
4930 |
- added new (better?) discretizations of default advection and diffusion |
4931 |
(turn on with SEAICEuseFluxForm) |
4932 |
- replace 1 in 3d global fields by kSurface in growth.F |
4933 |
|
4934 |
checkpoint58a_post (2006/02/13) |
4935 |
o seaice: |
4936 |
- bug fix in advect.F |
4937 |
o shelfice: |
4938 |
- separate shelfice load anomaly from pload (breaks with time |
4939 |
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
4940 |
Its default is 0., but it may be computed more cleverly from (unknown) |
4941 |
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
4942 |
done offline. A good approximation of the pressure load anomaly is |
4943 |
necessary to avoid large initial adjustment processes underneath |
4944 |
deep-reaching shelfice. |
4945 |
- small fix in ISOMIP shelfice_thermodynamics |
4946 |
- add more sophisticated thermodynamics of Hellmer (1989), this is |
4947 |
now the default |
4948 |
- give a few constants more intuitive names |
4949 |
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
4950 |
if bulk formulae are used in long integration (especially EmPmR). Turn |
4951 |
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
4952 |
if balancePrintMean, the imbalance that is substracted is printed to |
4953 |
STDOUT. |
4954 |
o fix bug (typo) in obcs_apply_eta.F |
4955 |
o add a new package shelfice which enables us to model the circulation |
4956 |
underneath shelf-ice with draughts of hundreds of meters. |
4957 |
- works |
4958 |
- to do: + include improved thermodynamics |
4959 |
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
4960 |
instead of new field kTopC |
4961 |
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
4962 |
instead of new field R_shelfIce and new code in ini_depth.F |
4963 |
and ini_mask_etc.F? |
4964 |
+ adjust vertical mixing schemes? |
4965 |
o seaice pkg: |
4966 |
- add a cpp-flag to include a simple formula for a salinity dependent |
4967 |
freezing point of sea water at the surface |
4968 |
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
4969 |
meridional stresses are now different (and hopefully correct) |
4970 |
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
4971 |
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
4972 |
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
4973 |
o pkg/diagnostics: add options and parameters for regional-statistics |
4974 |
diagnostics ; define regions by reading a region-mask from a file |
4975 |
(might add other options later) |
4976 |
o pkg/bulk_force: |
4977 |
- add option and parameters to use AIM surface-flux formulae. |
4978 |
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
4979 |
others forcing fields (defined in PARM05, parameter file "data") are loaded |
4980 |
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
4981 |
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
4982 |
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
4983 |
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
4984 |
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
4985 |
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
4986 |
|
4987 |
checkpoint58 (2006/01/12) |
4988 |
o add "--embed-source" option to genmake2 which, when the supporting |
4989 |
tools can be compiled (as determined by genmake2) will turn on the |
4990 |
embed_files package which then embeds the entire MITgcm source code |
4991 |
(*.[fFhc] + Makefile) used for the build within the executable |
4992 |
- requested by CNH but off by default |
4993 |
- adds a paltry <9MB to the mitgcmuv executable in most cases |
4994 |
- only writes the output when useEMBEDSRC in eedata is true |
4995 |
o clean up 3-dim. relaxation codes: |
4996 |
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
4997 |
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
4998 |
* Thanks to Tom Haine for testing! |
4999 |
|
5000 |
checkpoint57z_post (2005/12/31) |
5001 |
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
5002 |
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
5003 |
o fix the pickup behavior for obcs in combination with ptracers |
5004 |
o fix a bug in ptracers_external_fields_load |
5005 |
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
5006 |
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
5007 |
o transfered surface NH pressure to eta field (if exactConserv). |
5008 |
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
5009 |
and update lab_sea output.txt file. |
5010 |
o completing 3-dim. relaxation code: additional term |
5011 |
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
5012 |
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
5013 |
* At compile time, in "EXF_OPTIONS.h" set |
5014 |
#define ALLOW_CLIMTEMP_RELAXATION |
5015 |
#define ALLOW_CLIMSALT_RELAXATION |
5016 |
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
5017 |
tauThetaClimRelax3Dim = 15552000.0, |
5018 |
tauSaltClimRelax3Dim = 15552000.0, |
5019 |
* 3 cases: |
5020 |
1) Use a constant-in-time 3-dim. field |
5021 |
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
5022 |
3) Real-time relax. to time-evolving prescribed field |
5023 |
o Adding Laplacian-type smoothness constraint on |
5024 |
initial and boundary (forcing) controls (ic, bc) |
5025 |
* enable at compile-time via |
5026 |
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
5027 |
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
5028 |
* Absolute scale somewhat unclear so far |
5029 |
* no area weighting was included since no other cost term does so far |
5030 |
|
5031 |
checkpoint57y_post (2005/12/08) |
5032 |
First step for a NLFS adjoint |
5033 |
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
5034 |
o new init. routines for calc_r_star, calc_surf_dr |
5035 |
o still need to deal with ini_masks_etc |
5036 |
o testreport seemed happy |
5037 |
checkpoint57y_pre (2005/12/08) |
5038 |
|
5039 |
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
5040 |
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
5041 |
o add new offset feature to offline pkg (plus minor cleanup) |
5042 |
o cfc fixes for final year of integration |
5043 |
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
5044 |
be in GCHEM_OPTIONS). |
5045 |
|
5046 |
checkpoint57x_post (2005/12/04) |
5047 |
o fix testreport Pb in multiple test experiment. |
5048 |
o cleanup our namelist syntax in verification: |
5049 |
- make it more F95 standards compliant (some work still needed) |
5050 |
- allows the vast majority of our tests to work with gfortran |
5051 |
o Non-Hydrostatic: |
5052 |
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
5053 |
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
5054 |
o Allow to apply AB on T,S rather than on AB(gT,gS): |
5055 |
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
5056 |
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
5057 |
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
5058 |
- need a "clever" read_pickup to restart from the other AB formulation |
5059 |
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
5060 |
o remove some unused variables (reduces number of compiler warnings) |
5061 |
o adjoint |
5062 |
* Disable useVariableViscosity for adjoint for time being |
5063 |
(there are a number of extensive recomputations) |
5064 |
* Initialize certain variables needed for adjoint |
5065 |
|
5066 |
checkpoint57w_post (2005/11/03) |
5067 |
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
5068 |
fix the singleCpuIO RS version of MDSWRITEFIELD |
5069 |
and add a WARNING if using globalFiles=T with multi-processors. |
5070 |
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
5071 |
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
5072 |
o tracer advection scheme: |
5073 |
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
5074 |
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
5075 |
was not very convenient). |
5076 |
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
5077 |
(further tests needed for the implicit DST & Flux-Limiter schemes). |
5078 |
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
5079 |
and sRef for convenience, handy, when you want to initialize |
5080 |
ptracers in a large domain with a constant non-zero value. Also, |
5081 |
untangle ptracers_init.F a little. |
5082 |
|
5083 |
checkpoint57v_post (2005/10/13) |
5084 |
o change dome exp. to use variable viscosity in side-drag terms. |
5085 |
o remove all the files from the cfc_offline test since they are now |
5086 |
incorporated into tutorial_cfc_offline which has been producing |
5087 |
identical results for a few days of testing |
5088 |
o add new parameter: sideDragFactor to enable half-slip-side BC |
5089 |
and change side-drag S/R to use viscosity from mom_calc_visc |
5090 |
(can switch back by setting sideDragFactor=0.); affects results at |
5091 |
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
5092 |
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
5093 |
o vorticity & strain are now computed without masking, to account for |
5094 |
no-slip-side BC in variable viscosity calculation ; mask is applied |
5095 |
anyway later on, before computing advection/coriolis terms. |
5096 |
o modify exp4 to test new obcs support for reading from external files |
5097 |
and for passive tracers |
5098 |
o fix behavior of ptracers_monitor when monitor output is written to a |
5099 |
netcdf-file; still not independent of monitor.F (writes in the same |
5100 |
file). |
5101 |
o change default value of tRef (put a uniform, meaningful value for ocean |
5102 |
& atmos) and initialize sRef (was missing, as Martin mentioned). |
5103 |
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
5104 |
to be proportional to enstrophy dissipation length. Thus, |
5105 |
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
5106 |
This is now consistent with Smagorinsky and with the manual. |
5107 |
|
5108 |
checkpoint57u_post |
5109 |
o OBCS and PTRACERS: add open boundary support for passive tracers |
5110 |
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
5111 |
OB-values from file; this is not different from the way theta and salinity |
5112 |
are treated |
5113 |
- however, Orlanski-radiation conditions are not supported, and the model |
5114 |
will stop if you use pTracers and Orlanski at the same time. |
5115 |
- beefed up the rountine obcs_external_fields_load: now only those open |
5116 |
boundary values are overwritten with values from files for which there |
5117 |
are really files, otherwise the OB-fields remain untouched. This makes |
5118 |
it possible to use different OBs at different ends of the domain (as |
5119 |
with EXF) |
5120 |
o reduce number of exch calls in shap_filt (s2). |
5121 |
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
5122 |
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
5123 |
|
5124 |
checkpoint57t_post (2005/10/03) |
5125 |
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
5126 |
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
5127 |
same truncation, independent of the face number: affects affects several |
5128 |
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
5129 |
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
5130 |
note that biharmonic viscosity + no-slip was not tested in any experiment. |
5131 |
o fix bug in non-linear free-surf side-drag ; generate new output for |
5132 |
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
5133 |
o make mnc honor the writeBinaryPrec flag for most kinds of output |
5134 |
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
5135 |
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
5136 |
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
5137 |
o add brackets in multi-terms sum to get same truncation, independent of |
5138 |
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
5139 |
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
5140 |
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
5141 |
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
5142 |
a maximum grid-scale Reynolds number. Also, changes all length calculations |
5143 |
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
5144 |
Suggested values of viscosity parameters found in mom_calc_visc. |
5145 |
Many new viscosity diagnostics available. |
5146 |
|
5147 |
checkpoint57s_post (2005/09/20) |
5148 |
o Add clearing-house for viscosity calculations, mom_calc_visc and |
5149 |
correct numerous bugs in LeithD and Smagorinsky discretizations. |
5150 |
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
5151 |
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
5152 |
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
5153 |
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
5154 |
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
5155 |
ViscAhStrain and viscAhTension are now retired. |
5156 |
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
5157 |
o In response to JMC's bug report, genmake2 now ignores any soft-links |
5158 |
that it finds in the *current* directory when searching for files. |
5159 |
Soft-links found in any other source directories will still work as |
5160 |
they did before. |
5161 |
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
5162 |
a C routine to unlimit the stack size |
5163 |
o mnc-ify pkg/aim snapshot vars |
5164 |
o mnc-ify pkg/land as requested by Daniel |
5165 |
o various changes to mnc including: |
5166 |
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
5167 |
- output can now be grouped so that all files within a group |
5168 |
change the ITER portion of their names in lock-step together |
5169 |
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
5170 |
and works with both EXCH1 and EXCH2 (but needs more testing) |
5171 |
- writing works for all verification test cases w/ g77 on Linux |
5172 |
|
5173 |
checkpoint57r_post (2005/09/07) |
5174 |
o make MNC variable initialization happen earlier |
5175 |
o add diagnostics for (almost) each term of the momentum Eq. |
5176 |
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
5177 |
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
5178 |
o remove MINIMAL_TAVE_OUTPUT option ; |
5179 |
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
5180 |
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
5181 |
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
5182 |
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
5183 |
o add time-dependent SST, SSS control |
5184 |
o cost terms in ecco/ modularized (new cost_generic.F) |
5185 |
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
5186 |
o new infrastructure for seaice model vs. obs misfits in seaice/ |
5187 |
* driver from the_main_loop.F is seaice_cost_driver.F |
5188 |
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
5189 |
* gradient check in Exp. 6a of natl_box_adjoint/ |
5190 |
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
5191 |
(see README file) |
5192 |
|
5193 |
checkpoint57q_post (2005/08/19) |
5194 |
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
5195 |
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
5196 |
- bug was reported by Jean-Michel and Ian Fenty |
5197 |
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
5198 |
update exp. cpl_aim+ocn output. |
5199 |
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
5200 |
Needed for high-res. runs with large global files |
5201 |
to be able to limit tapelev size |
5202 |
o Changed some tests for adjoint: |
5203 |
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
5204 |
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
5205 |
* global_ocean.90x40x15/ back to default 3-level checkpointing |
5206 |
o Modifications to enable scripted COMMON to MODULE conversion |
5207 |
* verification/OpenAD/code/ has necessary scripts and description; |
5208 |
* converts, compiles and runs successfully; |
5209 |
|
5210 |
checkpoint57p_post (2005/08/01) |
5211 |
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
5212 |
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
5213 |
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
5214 |
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
5215 |
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
5216 |
(was already the case for dissipation with mom_vecinv, |
5217 |
and also the case for grad.PhiHyd when staggered-timeStep) |
5218 |
This will allow to put dissipation out-off the AB time-stepping. |
5219 |
Unfortunately, affects truncation error. Update output of exp. that "fails" |
5220 |
(cg2d matching number) and leave the others for later: front_relax(10), |
5221 |
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
5222 |
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
5223 |
|
5224 |
checkpoint57o_post (2005/07/30) |
5225 |
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
5226 |
(2) its ready to be documented during the 20050801 DocFest |
5227 |
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
5228 |
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
5229 |
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
5230 |
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
5231 |
(worth another tag) |
5232 |
|
5233 |
checkpoint57n_post (2005/07/29) |
5234 |
o adding precip control xx_precip 32 |
5235 |
o adding swflux control xx_swflux 33 |
5236 |
o Replacing 10 forcing penalty cost routines by 1 generic. |
5237 |
o Implementing partitioning in time-mean and variable adjustment |
5238 |
for atmos. state. |
5239 |
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
5240 |
o in natl_box_adjoint: |
5241 |
* updated exp 1 to 10 |
5242 |
(but does not have time-mean vs. variable split results yet) |
5243 |
o updated global1x1/*_seaice_adj/ |
5244 |
to incorporate latest changes |
5245 |
o enable useSingleCpuIO for mdsio vector routines |
5246 |
(applies in particular to tapelev I/O) |
5247 |
o removed inefficient K-loop in all active_file*control*.F |
5248 |
|
5249 |
checkpoint57m_post (2005/07/28) |
5250 |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
5251 |
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
5252 |
o pkg/exch2: filling of face-corner halo regions is optional |
5253 |
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
5254 |
|
5255 |
checkpoint57l_post (2005/07/14) |
5256 |
tag before updating tutorials (pre-release-2) |
5257 |
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
5258 |
for output and interpolation of input fields onto model grid) |
5259 |
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
5260 |
Affects results of exp. rotating_tank ; update output.txt. |
5261 |
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
5262 |
and taking the square quantity and/or using a fraction-weight field. |
5263 |
o fix aim_diagnostics_init.F mate numbers. |
5264 |
o add mnc output capability to diagnostics/diagstat and update |
5265 |
our cvsignore files for the ACSII output generated |
5266 |
|
5267 |
checkpoint57k_post (2005/07/02) |
5268 |
o lab_sea now uses diagnostics package and provides a suite of |
5269 |
new EXF diagnostics output. |
5270 |
|
5271 |
checkpoint57j_post (2005/06/30) |
5272 |
o exf |
5273 |
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
5274 |
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
5275 |
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
5276 |
* extended diagnostics output |
5277 |
- now includes all EXF variables |
5278 |
- hs, hl moved to common block |
5279 |
- separate S/R for diagnostics, called after ctrl vector is added |
5280 |
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
5281 |
- EXFqnet contains true Qnet (i.e. includes qsw) |
5282 |
* updated verif. lab_sea, global_with_exf |
5283 |
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
5284 |
to ensure that diagnostics sees a true EXFqnet |
5285 |
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
5286 |
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
5287 |
several times with different frequencies. |
5288 |
o mnc-ify the thsice package as requested by Daniel Enderton |
5289 |
- the monitor--MNC output needs work |
5290 |
- many attributes need to be added (most are currently blank) |
5291 |
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
5292 |
- many attributes need to be added (most are currently blank) |
5293 |
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
5294 |
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
5295 |
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
5296 |
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
5297 |
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
5298 |
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
5299 |
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
5300 |
|
5301 |
checkpoint57i_post (2005/06/19) |
5302 |
o Diagnostics package was changed: diagnostic allocation is now deactivated |
5303 |
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
5304 |
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
5305 |
add 1rst Order upwind vertical Shear. |
5306 |
o add a quick fix for A/B checkpointing in OFFLINE mode |
5307 |
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
5308 |
end-run around the C/Fortran linking horror in eesup/src/timers.F |
5309 |
o added pkg/runclock: allows user to terminate run based on wall clock |
5310 |
o added non-hydrostatic scaling parameter: nh_am2 |
5311 |
o pkg/my82: futile attempt to make results compiler-independent by adding |
5312 |
some "_d 0", etc. no effect. |
5313 |
o for mnc output, fill the 'T' coordinate var with myTime and create a |
5314 |
separate 'iter' variable for iteration count |
5315 |
o pkg/diagnostics: |
5316 |
add new capability: output of Global/Regional & per-level statistics ; |
5317 |
tested against monitor output (including land & thSIce) on various exp. |
5318 |
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
5319 |
|
5320 |
checkpoint57h_done (2005/05/19) |
5321 |
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
5322 |
data.diagnostics, data.gchem, data.ptracers) is done. |
5323 |
|
5324 |
o pkg/diagnostics: prepare for Global/Regional statistics. |
5325 |
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
5326 |
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
5327 |
and rename it: DIFFERENT_MULTIPLE |
5328 |
|
5329 |
checkpoint57h_post (2005/05/14) |
5330 |
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
5331 |
o pkg/diagnostics: change output frequency, now in seconds (instead |
5332 |
of Nb of iterations). This requires to change data.diagnostics. |
5333 |
checkpoint57h_pre (2005/05/12) |
5334 |
|
5335 |
o in mnc, let the user create the output dir if both mnc_outdir_date |
5336 |
and mnc_outdir_num are false |
5337 |
o add fflags() to pkg/diagnostics which allows one to specify, on a |
5338 |
per-file basis, the file precision [default behavior is unchanged] |
5339 |
o added diagnostics to pkg/kpp, including computation of mixed layer |
5340 |
depth based on a temperature/density criterion |
5341 |
o updated verification/natl_box to test the new pkg/kpp diagnostics |
5342 |
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
5343 |
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
5344 |
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
5345 |
not mnc -- this mistake was found by JMC and is now corrected |
5346 |
|
5347 |
checkpoint57g_post (2005/04/15) |
5348 |
o add Adams-Bashforth 3rd Order time stepping: |
5349 |
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
5350 |
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
5351 |
checkpoint57g_pre (2005/04/15) |
5352 |
|
5353 |
o make lambda[Theta,Salt]ClimRelax spatially varying |
5354 |
(default remains spatially uniform constant based on tau) |
5355 |
o added new control variables |
5356 |
* init. uVel, vVel, etanN |
5357 |
* lambda[Theta,Salt]ClimRelax |
5358 |
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
5359 |
(suggested by G. Forget) |
5360 |
|
5361 |
checkpoint57f_post (2005/04/06) |
5362 |
o add parameter "baseTime" = model base time = time at iteration zero |
5363 |
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
5364 |
account for baseTime shift |
5365 |
o move Coriolis arrays from PARAMS.h to GRID.h |
5366 |
checkpoint57f_pre (2005/04/06) |
5367 |
|
5368 |
o mnc-ifying the seaice package |
5369 |
o introduced an alternative length scale calculation for use in the limiting |
5370 |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
5371 |
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
5372 |
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
5373 |
as well as grad(vort3). Made it compatible with both approximate form |
5374 |
for the cubed sphere and full form of these gradients. Added flag |
5375 |
useFullLeith to select between approximate and full form. |
5376 |
o add "d0" in getcon.F to reduce differences between compilers/platforms |
5377 |
update output.txt of exp. fizhi-gridalt-hs |
5378 |
o change port_rand funtion to allow to set the seed. |
5379 |
o fix obscure MNC bug involving conversion between reals and integers |
5380 |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
5381 |
new version is now more standards-compliant |
5382 |
o adjoint-related modifications |
5383 |
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
5384 |
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
5385 |
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
5386 |
|
5387 |
checkpoint57e_post (2005/02/28) |
5388 |
o Adding eddy stress controls a la Ferreira et al. |
5389 |
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
5390 |
|
5391 |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
5392 |
update output.txt of exp. fizhi-gridalt-hs |
5393 |
o add more "Z" dimensions and associated coordinate vars to MNC |
5394 |
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
5395 |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
5396 |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
5397 |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
5398 |
months and years. Requires pkg/cal. |
5399 |
o diagnostics: add pickup functionality |
5400 |
- off by default for backwards compatibility |
5401 |
- current version only uses MDSIO -- MNC will be added |
5402 |
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
5403 |
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
5404 |
|
5405 |
checkpoint57d_post (2005/02/11) |
5406 |
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
5407 |
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
5408 |
output from the diagnostics package |
5409 |
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
5410 |
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
5411 |
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
5412 |
o add coordinate variables to the MNC output from the diagnostics package |
5413 |
o change MNC-flags default value: true when useMNC=TRUE |
5414 |
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
5415 |
the ability (off by default) to read the grid information using MNC |
5416 |
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
5417 |
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
5418 |
o do snap-shot diagnostics at the middle of the time-interval (instead of |
5419 |
at the end). |
5420 |
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
5421 |
new test for AIM with thSIce + slab-ocean |
5422 |
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
5423 |
o move state variable diagnostics to the beginning of the time step ; |
5424 |
(note: still needs some work specially for snap-shot diagnostics) |
5425 |
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
5426 |
|
5427 |
checkpoint57c_post (2005/01/27) |
5428 |
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
5429 |
o generate new output.txt files on faulks with g77 & the new -ieee option |
5430 |
checkpoint57c_pre (2005/01/27) |
5431 |
|
5432 |
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
5433 |
update output.txt of exp. global_ocean.90x40x15 |
5434 |
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
5435 |
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
5436 |
o add saltFlux(+File) forcing capability with periodicExternalForcing |
5437 |
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
5438 |
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
5439 |
o improvements for the MNC output from DIAGNOSTICS: |
5440 |
- correct handling of the unlimitied dimension |
5441 |
- all dims now have associated coordinate variables |
5442 |
- variables located at U, V, and Corner ("Z") points are now written |
5443 |
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
5444 |
*all* data points are output |
5445 |
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
5446 |
o added pkg/seaice/seaice_monitor.F |
5447 |
o mdsio_readfield.F can now read files visible only to master MPI process. |
5448 |
o pkg/seaice: some test code for ice-modified ocean stress |
5449 |
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
5450 |
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
5451 |
spurious negative numbers for precipitation and humidity. Will cause |
5452 |
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
5453 |
o pkg/ctrl/ |
5454 |
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
5455 |
May be enabled via doPackDiag |
5456 |
* introduce z-scaling of |
5457 |
+ gradient (doZscalePack) and |
5458 |
+ control (doZscaleUnpack) |
5459 |
o pkg/mdsio/ |
5460 |
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
5461 |
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
5462 |
|
5463 |
checkpoint57b_post (2004/12/20) |
5464 |
o simplify options in diagnostics_fill arguments (remove weird combinations) |
5465 |
o fix MNC coordinate variables so that they now contain per-face index |
5466 |
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
5467 |
general, EXCH2 grids are only aligned to a "local" coordinate system |
5468 |
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
5469 |
o Implement instantaneous output within pkg diagnostics: |
5470 |
setting a negative frequency in data.diagnostics produces |
5471 |
"snap-shot" output (as opposed to time-average if freq > 0) |
5472 |
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
5473 |
NOTE: change ptracer diagnostics name: use 2 characters to work with |
5474 |
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
5475 |
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
5476 |
becomes the coordinate variable for the 'T' dimension |
5477 |
o add CF-style coordinate variables to MNC |
5478 |
- just a first cut: numbers are meaningless on the cubesphere and |
5479 |
missing along the T axis but otherwise it works! |
5480 |
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
5481 |
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
5482 |
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
5483 |
this is based directly on what the model compute, so that the content of |
5484 |
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
5485 |
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
5486 |
o clean up build options files for SunOS, in particular |
5487 |
- remove -traditional from xmakedepend |
5488 |
- change -xarch=v9 to -xarch=native for f77 |
5489 |
- restore use of make (not gmake) |
5490 |
- add CC=gcc if using g77 |
5491 |
o changes per discussion of AM, JMC, & EH3 today: |
5492 |
- move redundant "grid" variables out of "state" -- in preparation of |
5493 |
creating proper CF-style coordinate variables and in recognition |
5494 |
that any/all grid variables can be easily copied (eg. w/NCO) from |
5495 |
the grid files into any of the other NetCDF files |
5496 |
- *always* output grid variables with MDSIO (this will eventually be |
5497 |
changed) |
5498 |
- output MNC grid file if useMNC is true |
5499 |
o every instance of _END_MASTER() has been found and replaced with |
5500 |
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
5501 |
preprocessors |
5502 |
o re-arrange diagnostics pkg initialisation: |
5503 |
- allow each package to extend the available diagnostics list |
5504 |
- add some checking and fix small problems (multi-threaded, ...) |
5505 |
- new S/R diagnostics_fill (replace fill_diagnostics): |
5506 |
look through the short list of active diag. (instead of the long list) |
5507 |
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
5508 |
|
5509 |
checkpoint57a_post (2004/12/10) |
5510 |
o this set of changes restores TAMC compatibility |
5511 |
tested for global_ocean.90x40x15 adjoint on trough |
5512 |
(what a pain) |
5513 |
|
5514 |
checkpoint57a_pre (2004/12/10) |
5515 |
o some modifs in tools/build_options for sunos |
5516 |
o call ctrl_pack for ctrl at end for optimcycle=0 |
5517 |
|
5518 |
checkpoint57 (2004/12/09) |
5519 |
o add horizontal bi-harmonic viscosity for vertical velocity |
5520 |
- new parameter viscA4W (defaults to viscA4) |
5521 |
- affects only non-hydrostatic code |
5522 |
- to be done: no-slip lateral boundary conditions |
5523 |
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
5524 |
o implement Implicit Vertical advection for pTracers |
5525 |
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
5526 |
(implemented also for implicit vertical diffusion & advection) |
5527 |
o OBCS: extend application of tracer open boundary conditions |
5528 |
to a strip beyond the boundary of width Olx/Oly |
5529 |
o add call monitor to TAF set of required calls (flow directives) |
5530 |
and include in natl_box_adjoint |
5531 |
o untangle a few ifdefs related to cost, ctrl, autodiff |
5532 |
untangel a few ALLOW_ECCO_OPTIMIZATION |
5533 |
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
5534 |
(theta2, salt2 in ecco_cost_weights) |
5535 |
|
5536 |
checkpoint56c_post (2004/12/03) |
5537 |
o OBCS as control variables |
5538 |
- update ctrl_ad_diff.list, obcs_ad_diff.list |
5539 |
- remove balance of obcs controls from default |
5540 |
- fix index bug nobcs in ctrl_init |
5541 |
- fix dummy fields filen in ctrl_pack |
5542 |
- add dummy weights for obcs |
5543 |
o lsopt: comment out fort.94 output |
5544 |
o optim: |
5545 |
- remove unnecessary header files |
5546 |
- adjusted namelists |
5547 |
- add xerbla.F to Makefile |
5548 |
o exf: |
5549 |
- multiple modifications of exf_check_range |
5550 |
- unit change in exf_init_runoff from [m/year] to [m/s] |
5551 |
o mdsio: |
5552 |
- i/o-vector change debugLevel from debLevA to debLevB |
5553 |
|
5554 |
checkpoint56b_post (2004/12/01) |
5555 |
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
5556 |
is called from DO_THE_MODEL_IO |
5557 |
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
5558 |
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
5559 |
- clean up PTRACERS_WRITE_TIMEAVE a little |
5560 |
o add another verification experiment that tests both the cfc-pkg and |
5561 |
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
5562 |
reactive tendencies treated inline with regular timestepping |
5563 |
o testreport previously did a lousy job of comparing small numbers, so |
5564 |
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
5565 |
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
5566 |
testreport. |
5567 |
o ptracers_monitor: bug fix for MPI |
5568 |
|
5569 |
checkpoint56a_post (2004/11/28) |
5570 |
o GCHEM: finish reorganizating the package |
5571 |
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
5572 |
(introduces another 3D-array for each passive tracer, but only if |
5573 |
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
5574 |
gchemTendency is not needed because the timestep is done separately) |
5575 |
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
5576 |
- GCHEM is now---more or less cleanly---separate from PTRACERS |
5577 |
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
5578 |
so clear to me how that should be done in a general way. |
5579 |
o CFC: improve formatting of output in CFC_ATMOS |
5580 |
o PTRACERS: |
5581 |
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
5582 |
that ALL experiments with ptracers enable can be checked. This makes |
5583 |
GCHEM_MONITOR obsolete. |
5584 |
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
5585 |
monitorFreq |
5586 |
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
5587 |
o add PTRACERS (PTR0[1-5]) to testreport output |
5588 |
o exf_check_range: |
5589 |
* default changed to .TRUE. |
5590 |
* will check values for niter0 if debLevA, every timestep if debLevB |
5591 |
* STOP in exf_check_range if 'out of range' |
5592 |
* range chosen generous to allow for potential extema |
5593 |
TBD: a version with stricter range |
5594 |
permitted range would be runtime parameters |
5595 |
o GMredi: |
5596 |
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
5597 |
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
5598 |
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
5599 |
o GCHEM: |
5600 |
- move call to GCHEM_FORCING_SEP, so that it is now called before |
5601 |
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
5602 |
- introduced a useGCHEM runtime flag and applied it everywhere. |
5603 |
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
5604 |
this flag is now only visible within GCHEM-pkg routines. |
5605 |
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
5606 |
be replaced by a 3D array that is computed before thermodynamics; for |
5607 |
this, the tracer ID iTracer had to be included into the parameter list |
5608 |
of ptracers_forcing |
5609 |
- set up forward_step to call gchem_forcing, that will replace |
5610 |
gchem_forcing_int in ptracers_forcing |
5611 |
- cleaning up |
5612 |
o small cleaning of exch2: remove files that are also in eesupp/src |
5613 |
|
5614 |
checkpoint56 (2004/11/17) |
5615 |
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
5616 |
o mnc: cleanup "full" files--fixes out-of-memory problem |
5617 |
o ECCO-GODAE |
5618 |
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
5619 |
* fully merged and updated from SIO code |
5620 |
windstress sign change affects |
5621 |
- exf_inscal_[u/v]stress |
5622 |
- sign of xx_tau[u/v] adjustments |
5623 |
- signs in cost_scat |
5624 |
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
5625 |
* natl_box_adjoint updated and compressed |
5626 |
* 2-level checkpoint switch added |
5627 |
(tested in EXP. 1 of natl_box_adjoint) |
5628 |
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
5629 |
o SVD |
5630 |
* first complete, non-hacked version for SVD calculations |
5631 |
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
5632 |
performed via direct access files admtlm_vector.it???? |
5633 |
(via ctrl_[un]pack) |
5634 |
* optimcycle is used for ARPACK iteration counter |
5635 |
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
5636 |
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
5637 |
and add linear transforms where necessary |
5638 |
* controls are initial/final SST, SSS (can be extended; need to check |
5639 |
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
5640 |
o mdsio: filename info to both stderr, stdout |
5641 |
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
5642 |
from sign change |
5643 |
|
5644 |
checkpoint55j_post (2004/11/10) |
5645 |
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
5646 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
5647 |
o add consistent build directories and .cvsignore files to verification |
5648 |
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
5649 |
o make all subroutines 30 or less characters in length for certain older |
5650 |
compilers to work (a thorough search only turns up two routines in |
5651 |
pkg/ptracers) |
5652 |
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
5653 |
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
5654 |
|
5655 |
checkpoint55i_post (2004/10/28) |
5656 |
o change arrays for total vertical diffusivity (2.D if explicit, |
5657 |
3.D if implicit) ; each ptracer uses its own background value. |
5658 |
o added mnc/NetCDF output capability to ocn_compon_interf |
5659 |
- added bits to verification/cpl_aim+ocn so that it can run on |
5660 |
ITRDA and other clusters without the mpirun "-wd" option |
5661 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
5662 |
configuration |
5663 |
o give MNC the ability to create additional files rather than |
5664 |
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
5665 |
- the default is just less than 2GB which is a practical limit |
5666 |
on many systems |
5667 |
o Compute the non-local term using either KPP vertical diffusivity (=default) |
5668 |
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
5669 |
|
5670 |
checkpoint55h_post (2004/10/20) |
5671 |
o add verification test "vermix" |
5672 |
o remove all the *_ioinc flags and replace with the single global |
5673 |
outputTypesInclusive flag |
5674 |
o allow to set a vertical profile of vertical diffusivity for T & S |
5675 |
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
5676 |
o useMNC moved from data.mnc to data.pkg |
5677 |
|
5678 |
checkpoint55g_post (2004/10/14) |
5679 |
o Renaming carbon AD experiments to comply with testreport conventions |
5680 |
o Updating adjoint of Held-Suarez hs94.1x64x5 |
5681 |
o Fixing directives for non-ECCO forward_step, after ECCO directives |
5682 |
have been fixed to avoid recomp. of do_oceanic_phys |
5683 |
Works well for global_ocean.90x40x15, |
5684 |
but recomp. issue remains for carbon |
5685 |
o Updating adjoint output for natl_box_adjoint after |
5686 |
pkg/ecco has been modified (see taga c55d_post) |
5687 |
|
5688 |
checkpoint55f_post (2004/10/13) |
5689 |
o rename to timeave_init_fixed |
5690 |
|
5691 |
checkpoint55e_post (2004/10/13) |
5692 |
o some delicate re-shuffle of store directives to avoid one |
5693 |
extra call of do_oceanic_physics |
5694 |
affects ecco_the_main_loop.F, do_oceanic_physics.F |
5695 |
checkpoint_lev1_directives.h |
5696 |
o NB: this may break global_ocean adjoint temporarily, |
5697 |
but it is clear how to fix it. Will do later, need this now. |
5698 |
|
5699 |
checkpoint55d_post (2004/10/11) |
5700 |
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
5701 |
o ecco_cost_weights is modified to 1x1 runs |
5702 |
o modifs to allow observations to be read in as |
5703 |
single file or yearly files |
5704 |
o enable to read exf forcing fields as either |
5705 |
single file or yearly files (flag useExfYearlyFields) |
5706 |
checkpoint55d_pre (2004/10/08) |
5707 |
|
5708 |
o switch between 2-level and 3-level checkpointing |
5709 |
o add ability of MNC to write local and "partial" (eg. 2D slices where |
5710 |
the full 3D field is never actually stored) arrays to NetCDF files |
5711 |
with the correct (that is, the complete multi-dimensional) set of |
5712 |
array indicies |
5713 |
- used in mom_vecinv() to write the diagFreq output |
5714 |
- tested (demonstrated) in verification/aim.5l_cs |
5715 |
o further mnc-ification |
5716 |
- add verification/lab_sea to the list with mnc setups |
5717 |
- fix undefined mnc v-names in cd_code |
5718 |
- add kpp to mnc output (both snapshot and timeave) |
5719 |
o non-hydrostatic code |
5720 |
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
5721 |
in calc_gw.F |
5722 |
- defaults to viscAh |
5723 |
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
5724 |
friction or Leith) in non-hydrostatic mode, as long as there is |
5725 |
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
5726 |
o pkg/cost |
5727 |
extend simple cost functions to treat time mean quantities |
5728 |
(T,U,V) via cost_accumulate_state from cost_tile |
5729 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
5730 |
be 2 times larger than the minimum size the advection scheme requires. |
5731 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
5732 |
o GGL90 (Gaspar's TKE mixed layer) |
5733 |
- add horizontal diffusion of TKE, requires exchanges in |
5734 |
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
5735 |
default. In OPA there is no horizontal diffusion of TKE but the |
5736 |
mixing coefficients are computed from a horizontal average of TKE of |
5737 |
6 points or so. I think that diffusion has a little more physical |
5738 |
justification. |
5739 |
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
5740 |
was in vain) |
5741 |
- mask tke-variable in ggl90_init |
5742 |
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
5743 |
o fix biharmonic diffusion on CS-grid. |
5744 |
o more obcs stuff |
5745 |
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
5746 |
for reading boundary values. This routine is called from |
5747 |
obcs_prescribe_read |
5748 |
- updated obcs_check |
5749 |
- changed sponge layer relaxation parameter units for days to seconds |
5750 |
- turned off sponge layer by default |
5751 |
- changed argument list of OBCS_CALC to myTime+deltaTclock |
5752 |
- fixed about 35 bugs in obcs_external_fields_load |
5753 |
|
5754 |
checkpoint55c_post (2004/09/23) |
5755 |
o obcs stuff |
5756 |
- new runtime flags useOBCSprescribe, useOBCSbalance |
5757 |
- re-arranged obcs_calc |
5758 |
- moved exf_getobcs to obcs_prescibe_read |
5759 |
obcs_prescibe_read is called after ORLANSKI stuff |
5760 |
and independent of it (executable can contain all). |
5761 |
- updated obcs_check |
5762 |
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
5763 |
These may be necessary only if tangential velocities are |
5764 |
prescribed at OB, not sure, needs testing. |
5765 |
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
5766 |
which simplifies the calls and passes the ifc check-bounds test |
5767 |
|
5768 |
checkpoint55b_post (2004/09/22) |
5769 |
o add a 2D scalar, Z location, exchange_2 routine. |
5770 |
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
5771 |
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
5772 |
affects advect_cs results (for the wrong reason): update output.txt |
5773 |
o use a more standard discretization for biharmonic viscosity ; |
5774 |
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
5775 |
affects results of dome set-up: update output.txt |
5776 |
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
5777 |
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
5778 |
|
5779 |
checkpoint55a_post (2004/09/20) |
5780 |
o merged code to |
5781 |
* prescribe/read time-dependent open boundaries |
5782 |
(works in conjunction with exf, cal) |
5783 |
* sponge layer code for open boundaries |
5784 |
* each boundary N/S/E/W now has its own CPP option |
5785 |
(healthy for the adjoint) |
5786 |
|
5787 |
checkpoint55 (2004/09/17) |
5788 |
o up-to-date adjoint of previous breaks |
5789 |
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
5790 |
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
5791 |
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
5792 |
- carbon: * remove tr1-related adjoint verification |
5793 |
* add ptracer as control variable |
5794 |
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
5795 |
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
5796 |
|
5797 |
checkpoint54f_post (2004/09/16) |
5798 |
o in verification/carbin/ remove experiment related to |
5799 |
ALLOW_PASSIVE_TRACER (array tr1 etc) |
5800 |
code_ad/ input_ad/ results_ad |
5801 |
|
5802 |
o add two new packages |
5803 |
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
5804 |
+ subject to optimization (memory) |
5805 |
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
5806 |
+ subject to reordering (many GOTOs in the original code) |
5807 |
+ so far opps is called for every (i,j) point, and then operates in |
5808 |
the vertical; one may want to reorder the scheme in order operate in |
5809 |
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
5810 |
fields) |
5811 |
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
5812 |
- all verification tests compile and run with linux_ia32_g77 |
5813 |
- defaults are compatible with current input files--nothing |
5814 |
should change if you were not previously using MNC |
5815 |
- MNC output has been added in numerous places (eg. timeave) |
5816 |
but there are still a few writes not yet do-able with MNC |
5817 |
(this is in progress) |
5818 |
- flags now allow for either/or/both use of MDSIO and MNC and |
5819 |
documentation will soon follow |
5820 |
- numerous small formatting cleanups for ProTeX |
5821 |
o add version info (via BUILD_INFO.h) to MNC and stdout |
5822 |
|
5823 |
checkpoint54e_post (2004/09/02) |
5824 |
o add two new packages |
5825 |
- pp81 (Packanowski and Philander, 1981), Richardson number and |
5826 |
stratification dependent mixing |
5827 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
5828 |
- these scheme operate in a similar manner as KPP (without ghat, of |
5829 |
course), however there is only one diffusivity that is used for both |
5830 |
temperature and salinity (and passive tracers) |
5831 |
o add offline package |
5832 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
5833 |
provided by Stephanie Dutkiewicz |
5834 |
o genmake2: add ability to search for C compilers and cleanup test output |
5835 |
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
5836 |
|
5837 |
checkpoint54d_post (2004/07/27) |
5838 |
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
5839 |
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
5840 |
leading to additional shift by 5 days each year of integration |
5841 |
(i.e. leading to considerable offset over the years) |
5842 |
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
5843 |
o start with no AB and no initial filtering (staggerTimeStep): |
5844 |
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
5845 |
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
5846 |
(external loading & cpl import/export stay in forward_step.F) |
5847 |
o update coupling interface to work with new staggerTimeStep |
5848 |
o change MDSIO ptracers_pickup. |
5849 |
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
5850 |
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
5851 |
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
5852 |
|
5853 |
checkpoint54c_post (2004/07/18) |
5854 |
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
5855 |
this affects (truncation error) output.txt of test-exp: |
5856 |
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
5857 |
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
5858 |
o change Qnet to always be the net heat flux, (+upward). |
5859 |
affects (truncation error) output of natl_box exp.: updated |
5860 |
o define the max number of passive tracers in PTRACERS_SIZE.h |
5861 |
o start to test mnc routinely in exp0 |
5862 |
o add sea-ice loading (sIceLoad) as a new forcing field. |
5863 |
|
5864 |
checkpoint54b_post (2004/07/08) |
5865 |
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
5866 |
impressive on Altix and Opteron systems) |
5867 |
o diagnostics can now write NetCDF files through the mnc package |
5868 |
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
5869 |
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
5870 |
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
5871 |
affects (truncation error) output of lab_sea & natl_box exp.: updated |
5872 |
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
5873 |
|
5874 |
checkpoint54a_post (2004/07/06) |
5875 |
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
5876 |
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
5877 |
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
5878 |
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
5879 |
+ internal_wave (shift in writing cg2d_ini_res) |
5880 |
checkpoint54a_pre (2004/07/05) |
5881 |
|
5882 |
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
5883 |
- modified verification/lab_sea and natl_box_adjoint accordingly |
5884 |
|
5885 |
checkpoint54 (2004/07/02) |
5886 |
checkpoint53g_post (2004/07/02) |
5887 |
o prepare splitting of thermodynamics: store convect.counter in common block |
5888 |
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
5889 |
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
5890 |
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
5891 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
5892 |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
5893 |
o restore adjointability |
5894 |
|
5895 |
checkpoint53f_post (2004/06/25) |
5896 |
o modifications that affect AIM experiment results (update output.txt): |
5897 |
- no advection of S at top interface Nr (pkg/generic_advdiff) |
5898 |
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
5899 |
o AIM pkg: |
5900 |
- include stability function into surf.Flux derivative relative to Tsurf |
5901 |
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
5902 |
|
5903 |
checkpoint53e_post |
5904 |
o merged cylindrical coord configuration |
5905 |
o added rotating_tank experiment |
5906 |
checkpoint53e_pre |
5907 |
|
5908 |
checkpoint53d_post (2004/06/14) |
5909 |
o faulks upgraded: re-generate output.txt that have changed: |
5910 |
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
5911 |
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
5912 |
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
5913 |
o added Sadourny discretization of Coriolis |
5914 |
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
5915 |
- re-enabled use of omega3 (useAbsVorticity) |
5916 |
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
5917 |
vector-invariant equations |
5918 |
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
5919 |
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
5920 |
hopefully without new bugs |
5921 |
- still to do: biharmonic friction for non-hydrostatic w |
5922 |
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
5923 |
o regenerated output for global_ocean_ebm (using -ieee) |
5924 |
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
5925 |
of mom_common/ |
5926 |
- simple re-arrangement of instructions within computing loop |
5927 |
checkpoint53d_pre (2004/05/21) |
5928 |
|
5929 |
checkpoint53c_post (2004/05/21) |
5930 |
o new version of coupler for AIM+thSIce and Ocean models |
5931 |
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
5932 |
- land: change Evaporation of snow |
5933 |
- aim with thSIce: fix bug in snow-precip. |
5934 |
o changes to calc_gw.F |
5935 |
- bug fix for w^2 term near the bottom boundary |
5936 |
- (hopefully) improve the lateral slip boundary condtions for use with |
5937 |
partial/looped cells |
5938 |
- because the bug fix changes two verification experiments anyway (exp5 |
5939 |
and plume on slope), change the lateral boundary condition from half slip |
5940 |
to the value of no_slip_sides |
5941 |
o ebm package wasnt quite up to the parallel task. Fixed that. |
5942 |
o Adjoint of EBM package + verification |
5943 |
* TLM OK |
5944 |
* ADM not sufficient accuracy yet (needs further testing) |
5945 |
|
5946 |
checkpoint53b_post (2004/05/14) |
5947 |
o Commiting new energy balance model to repository |
5948 |
* package is pkg/ebm |
5949 |
* verif. is verification/global_ocean_ebm |
5950 |
* references are in ebm_driver.F |
5951 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
5952 |
C Global thermohaline circulation. Part I: |
5953 |
C Sensitivity to atmospheric moisture transport. |
5954 |
C J. Climate 12(1), 71-82 |
5955 |
C * X. Wang, P. Stone and J. Marotzke, 1999: |
5956 |
C Global thermohaline circulation. Part II: |
5957 |
C Sensitivity with interactive transport. |
5958 |
C J. Climate 12(1), 83-91 |
5959 |
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
5960 |
C Destabilization of the thermohaline circulation |
5961 |
C by atmospheric eddy transports. |
5962 |
C J. Climate 7(12), 1870-1882 |
5963 |
o Will need long integration testing. |
5964 |
checkpoint53b_pre (2004/05/14) |
5965 |
|
5966 |
o created pkg/mom_common in preparation for variable viscosity code |
5967 |
o renamed and split ini_mnc_io |
5968 |
o pkg/land: only liquid water can diffuse or run-off |
5969 |
o AIM using land: soil wetness availability account for snow |
5970 |
o added printMapIncludesZeros to EEPARMS namelist |
5971 |
|
5972 |
checkpoint53a_post (2004/05/11) |
5973 |
o restore TAMC compatiility for exf_constants.h |
5974 |
(no usage of _d in .h) |
5975 |
o Additional storing in KPP in an attempt to fix |
5976 |
TAMC problem with adjoint of KPP code. |
5977 |
(no success...) |
5978 |
Identical code works fine with TAF. |
5979 |
o Fixed verification/natl_box_adjoint experiments. |
5980 |
Initial conditions for Experiments 4 and 5 are now |
5981 |
set to "SEAICE_initialHEFF=0", which is more reasonable, |
5982 |
and hence gives results closer to that of Experiment 2. |
5983 |
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
5984 |
|
5985 |
checkpoint53 (2004/05/06) |
5986 |
o stable checkpoint with up to date adjoint |
5987 |
TLM tests only run for 1st grdchk at the moment. Its unclear if |
5988 |
this is a code problem or a problem with resetting code for g_ |
5989 |
variables that is being autogenerated wrong. |
5990 |
Otherwise: |
5991 |
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
5992 |
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
5993 |
are both still in chaos following their security messes. |
5994 |
|
5995 |
checkpoint52n_post (2004/05/06) |
5996 |
o various build (mostly genmake2) changes including: |
5997 |
- ability to build/run more easily within Cygwin and MacOS X |
5998 |
- more complicated Makefiles with a stronger dependence on Gnu Make |
5999 |
o pkg/seaice modifications |
6000 |
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
6001 |
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
6002 |
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
6003 |
- changed proxy for geostrophic velocity and updated |
6004 |
verification/lab_sea/results/* accordingly |
6005 |
- removed ADI dynamic solver from pkg/seaice |
6006 |
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
6007 |
they caused a segmentation fault under certain circumstances |
6008 |
- removed unused field WATR |
6009 |
o bug fix in exf-package: |
6010 |
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
6011 |
now reflect that. |
6012 |
o small fixes in the cal-package: |
6013 |
- set reference date to first of January for the 'model'-calendar |
6014 |
- failing of cal_CheckDate in cal_FullDate now actually results in a |
6015 |
warning |
6016 |
o small modifications in exf-package to increase flexibility: |
6017 |
- change climtempfreeze from a constant to a runtime parameter that |
6018 |
is specified in data.exf_clim (default = -1.9) |
6019 |
- introduce runtime parameter windstressmax (default = 2.0) that is |
6020 |
specified in data.exf |
6021 |
o fix in pkg/thsice: |
6022 |
- update Evap (Tsf changes) to be consistent with Latent heat flux |
6023 |
- maintain snow precipitation unchanged (even if Tsf >=0). |
6024 |
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
6025 |
|
6026 |
checkpoint52m_post (2004/04/18) |
6027 |
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
6028 |
this does not change any of the results, because myIter=0 in swfrac always |
6029 |
lead to jwtype=2 (the default anyway), but the call makes little sense |
6030 |
as a default |
6031 |
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
6032 |
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
6033 |
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
6034 |
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
6035 |
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
6036 |
o extending useSingleCpuIO option to work with new exch2 I/O format |
6037 |
- old-style, missing-tile I/O is still accessible by defining CPP |
6038 |
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
6039 |
o monitor package can write to NetCDF files and/or STDOUT |
6040 |
o fix re-definition bug in MNC_GRID_INIT_ALL() |
6041 |
o doc/api_reference added |
6042 |
- a framework for building an API Reference Manual using all |
6043 |
the "protex" comments embedded in the code |
6044 |
- see pkg/generic_advdiff, pkg/mnc for examples |
6045 |
o MNC: |
6046 |
- make myThid the last argument for all subroutines |
6047 |
- new default for the grid files: NO halos |
6048 |
- add useMNC and other run-time flags |
6049 |
- separate per-file-group handling of the unlimited dimension |
6050 |
- early initialization of MNC w/ flags read at the eeboot stage |
6051 |
and lookup tables set in initialize_fixed |
6052 |
- write all MNC output to a freshly-created directory |
6053 |
o thermodynamics sea-ice (thsice) is now tested with testreport. |
6054 |
o test exp. advect_cs: use the standard cs32 grid ; update output. |
6055 |
o Added functionality to grdchk: |
6056 |
pick global i,j,k position (or nearest wet) where to perform check. |
6057 |
|
6058 |
checkpoint52l_post (2004/03/11) |
6059 |
o new land formulation: |
6060 |
a) use ground enthalpy as prognostic variable to ensure exact |
6061 |
energy conservation. |
6062 |
b) account for water temperature and for latent heat of freezing |
6063 |
in all processes (rain, run-off, ground storage) |
6064 |
c) compute surface and ground temperature implicitly. |
6065 |
o aim_v23 modification for new land model: |
6066 |
a) Treat separately land / ocean / sea-ice surface fluxes |
6067 |
to allow implicit computation of land & sea-ice surface temp. |
6068 |
b) add snow precipitation. |
6069 |
checkpoint52l_pre (2004/03/11) |
6070 |
|
6071 |
o fix problem (when 1 tile is empty) in min/max monitor. |
6072 |
o fix bug in timeAve (u,vZetatave in common block) |
6073 |
o no restoring terms under ice for pkg/seaice |
6074 |
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
6075 |
o bug fix for pkg/seaice pickups |
6076 |
o change MNC call locations and add coordinate attributes |
6077 |
o mask vorticity at the corner ; affects global_ocean.cs output |
6078 |
o fix ini_curvilinear_grid ; test CS experiments with mpi |
6079 |
o aim.5l_cs: modify sea-ice fraction input file ; update output |
6080 |
o exf: Adding simple range check routine for exf fields after read |
6081 |
|
6082 |
checkpoint52k_post (2004/02/23) |
6083 |
o removed top-level directory "diags" |
6084 |
- we migrated these functions to pkg/timeave a long time ago |
6085 |
o fixed bug introduced in pkg/monitor |
6086 |
o accuracy ctrlprec = 32 insuffient for gradient checks using |
6087 |
averaged fields (I/O via cost_averages) |
6088 |
-> use ctrl.h in active_file*.F to control I/O precision. |
6089 |
o paramter list of CALL ADTHE_MAIN_LOOP |
6090 |
o added initial do_the_model_io to ecco |
6091 |
o set all ...Freq to zero after cost_final |
6092 |
taveFreq, dumpFreq, pChkptFreq |
6093 |
o MAIN and ECCO differentiability restored |
6094 |
|
6095 |
checkpoint52j_post (2004/02/18) |
6096 |
o fix nchklev in tamc.h for global_ocean... |
6097 |
o Bringing flow and store directives up-to-date |
6098 |
o Really weird thing! |
6099 |
call do_the_model_io from the_main_loop with parameters |
6100 |
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
6101 |
TAF places a faulty re-call of initialise_varia |
6102 |
after cost_final call which should not be there! |
6103 |
checkpoint52j_pre (2004/02/03) |
6104 |
|
6105 |
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
6106 |
error messages |
6107 |
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
6108 |
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
6109 |
debug output |
6110 |
o modfied mdsio_writefield.F to handle non-global files under exch2 |
6111 |
o update AIM Cubed-Sphere exp (aim.5l_cs): |
6112 |
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
6113 |
o update AIM Equatorial Channel exp: |
6114 |
use standard aim_v23 pkg and change the SST fields to be more realistic. |
6115 |
o globalFile now works with exch2 |
6116 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
6117 |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
6118 |
o limit timeave output for hi-res integrations |
6119 |
|
6120 |
checkpoint52i_post (2004/01/21) |
6121 |
o removed CPP_EEOPTIONS.h from verification/*/code |
6122 |
o updated the tiling for global_ocean_pressure |
6123 |
checkpoint52i_pre (2004/01/20) |
6124 |
|
6125 |
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
6126 |
the old pkg/aim). |
6127 |
|
6128 |
checkpoint52h_pre (2004/01/20) |
6129 |
o shortened offending lines in exch2_send_rx?.template |
6130 |
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
6131 |
o genmake2: add build & execute test for NetCDF code |
6132 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
6133 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
6134 |
o added useSingleCPUIO flag to monitor.F and mon_out.F |
6135 |
o added temporary hack for sea-ice dynamics on the cube: |
6136 |
metric terms are ignored and it is assumed that |
6137 |
there is no sea-ice on cube faces 1, 2, 4, and 5. |
6138 |
|
6139 |
checkpoint52f_post (2004/01/09) |
6140 |
o added exch2 cube routines to pkg/exch2 |
6141 |
o modified hs94.cs-32x32x5 to use it |
6142 |
o added new grid files to hs94.cs-32x32x5 |
6143 |
checkpoint52f_pre (2004/01/07) |
6144 |
|
6145 |
checkpoint52e_post (2004/01/07) |
6146 |
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
6147 |
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
6148 |
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
6149 |
to work with implicit vertical advection and AB ; |
6150 |
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
6151 |
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
6152 |
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
6153 |
checkpoint52e_pre (2004/01/02) |
6154 |
|
6155 |
o fix bug in impldiff when Nr=1 or Nr=2. |
6156 |
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
6157 |
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
6158 |
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
6159 |
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
6160 |
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
6161 |
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
6162 |
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
6163 |
|
6164 |
checkpoint52d_post (2003/12/16) |
6165 |
o re-tiled many expts to allow comparison in multi-processor mode |
6166 |
- updated output accordingly |
6167 |
- changed hs94.128x64x5 to use intial T from file rather than use the |
6168 |
random number generator |
6169 |
o add infrastructure in model routines for fizhi and gridalt packages |
6170 |
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
6171 |
o changes to permit hi-res, cubed-sphere, configuration |
6172 |
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
6173 |
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
6174 |
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
6175 |
of surface winds for the cube |
6176 |
(A verification experiment, based on global_ocean.cs32x15, but with |
6177 |
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
6178 |
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
6179 |
complete with example surface forcing files and matlab scripts to look |
6180 |
at the output and compare it with that of global_ocean.cs32x15.) |
6181 |
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
6182 |
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
6183 |
to conform to the common rule. |
6184 |
o check-in the first version of the coupler + interfaces for multi-components |
6185 |
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
6186 |
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
6187 |
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
6188 |
- ocean and atmos. share the same horizontal grid (no interpolation). |
6189 |
- exchanges between component and coupler is done in forward_step |
6190 |
o new verification experiment, cpl_aim+ocn: |
6191 |
coupled ocean - AIM atmosphere on cs32 grid. |
6192 |
|
6193 |
checkpoint52d_pre (2003/12/06) |
6194 |
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
6195 |
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
6196 |
|
6197 |
checkpoint52c_post (2003/11/25) |
6198 |
o Fixing OPTIONS files for use of exf: |
6199 |
- ALLOW_ECCO not needed |
6200 |
- ECCO_CPPOPTIONS.h should not be included from |
6201 |
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
6202 |
as has been the case in the past |
6203 |
- All cal/exf related options are currently set in |
6204 |
single header file. Should remain so until we |
6205 |
agree on a consistent new policy. |
6206 |
o Removed all CPP options for cal package. |
6207 |
cal has no more CPP options. |
6208 |
o modified STOREs in GAD_ADVECTION |
6209 |
o corrected key comp. for passkey |
6210 |
|
6211 |
checkpoint52b_post (2003/11/23) |
6212 |
o new version: "thsice" of thermodynamic sea-ice pkg: |
6213 |
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
6214 |
- modify fluxes but do not change theta directly; |
6215 |
- light cleaning of bulk_force pkg (still needed with thsice). |
6216 |
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
6217 |
+ output_thsice.txt to test thsice & bulk_force pkgs. |
6218 |
o put back grid & coriolis monitor output. |
6219 |
checkpoint52b_pre (2003/11/23) |
6220 |
|
6221 |
o call "do_the_model_io" at the beginning (=> dump initial state) |
6222 |
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
6223 |
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
6224 |
(need info on NUMBER_OF_PTRACERS) |
6225 |
o missing PTRACERS headers in some routines |
6226 |
o default tamc.h in pkg/autodiff supposed to crash |
6227 |
to ensure proper customization |
6228 |
|
6229 |
checkpoint52a_post (2003/11/17) |
6230 |
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
6231 |
- moved surfaceTendencyTice from pkg/seaice to main code |
6232 |
- subroutine FREEZE_SURFACE now limits only surface temperature |
6233 |
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
6234 |
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
6235 |
- keep the old version of FREEZE for backward compatibility; |
6236 |
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
6237 |
- corresponding modifs for TAF directives |
6238 |
o added surface flux output variables to TIMEAVE_STATVARS |
6239 |
o time-averaged output for pkg/ptracers |
6240 |
o fix problem with ECCO-related divided adjoint |
6241 |
snapshot file was missing some ad-variables, |
6242 |
but no warning issued by TAF |
6243 |
|
6244 |
checkpoint52a_pre (2003/11/12) |
6245 |
o some bug fixes for #undef REAL4_IS_SLOW |
6246 |
|
6247 |
checkpoint52 = ecco_c52_e35 |
6248 |
o after testing adjoints of checkpoint51u_post |
6249 |
|
6250 |
checkpoint51u_post (2003/11/06) |
6251 |
o this is the post-merge tag of the ecco-branch |
6252 |
(needs another clean checkout and re-testing) |
6253 |
o various natl_box_adjoint configs and results |
6254 |
but no input fields |
6255 |
o obcs adjoint not yet merged! |
6256 |
o adding ECCO global 1x1 and 2x2 degree configs |
6257 |
o updated/extended some store directives for seaice |
6258 |
o pkg/ecco now containes ecco-specific part of cost function |
6259 |
o top level routines the_main_loop, forward_step |
6260 |
supersede those in model/src/ |
6261 |
previous input data.cost now in data.ecco |
6262 |
(new namelist ecco_cost_nml) |
6263 |
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
6264 |
|
6265 |
checkpoint51t_post (2003/11/04) |
6266 |
o this is the pre-merge tag of the ecco-branch |
6267 |
|
6268 |
checkpoint51s_post (2003/11/04) |
6269 |
o cleanup: removed various obsolete #define-s |
6270 |
o pkg/grdchk |
6271 |
- renamed 'ph-grd 3' to 'grad-res' |
6272 |
- merged from ecco-branch |
6273 |
(remaining bug fixes for obcs gradient checks) |
6274 |
- additional high-precision output for testreport |
6275 |
(grep for 'precision_grdchk_result') |
6276 |
|
6277 |
checkpoint51r_post (2003/11/03) |
6278 |
o cleaned up or removed CPP_OPTIONS.h files |
6279 |
o updated results for some of the tests to reflect the new |
6280 |
optfiles (-ieee: -O0 instead of -O3) |
6281 |
|
6282 |
checkpoint51q_post (2003/10/30) |
6283 |
o cd_code: |
6284 |
- moved cd_scheme.F -> cd_code_scheme.F |
6285 |
- separate read_checkpoint from cd_code_ini_vars.F |
6286 |
- separated cd_code part from write_checkpoint |
6287 |
- updated AD_SOURCE, generated .flow |
6288 |
- added CD_CODE_VARS.h to the_main_loop |
6289 |
- Moving cd_code specific store dir.s to pkg/cd_code |
6290 |
o ctrl package totally restructured |
6291 |
- pack/unpack now optional and decoupled from |
6292 |
xx_/adxx_ I/O |
6293 |
- ctrl_pack/unpack cleaned |
6294 |
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
6295 |
- confined inclusion of AD_CONFIG.h to where necessary. |
6296 |
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
6297 |
|
6298 |
checkpoint51p_post (2003/10/30) |
6299 |
o create initial cd_code package |
6300 |
- WARNING: the initialization of fields within packages |
6301 |
is broken because INI_FIELDS (where READ_CHECKPOINT is |
6302 |
called) is called *before* PACKAGES_INIT_VARIABLES. |
6303 |
This seems to be backwards since |
6304 |
1) its important to initially zero the entire field including |
6305 |
the "halo" region |
6306 |
2) zeroing needs to be done *before* reading pickup info |
6307 |
and the pickup call might or might not happen in any |
6308 |
particular run |
6309 |
- this needs an overhaul for R2 |
6310 |
o cleanup verification/*/code/GMREDI_OPTIONS.h |
6311 |
o cleanup testreport |
6312 |
|
6313 |
checkpoint51o_post (2003/10/27) |
6314 |
o bringing AD-related verif's up to date with genmake2 |
6315 |
- carbon/ |
6316 |
- global_ocean.90x40x15/ |
6317 |
- hs.94.1x64x5/ |
6318 |
- (front_relax/ ) |
6319 |
o (more) consistent directory structure for AD-related verif.'s |
6320 |
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
6321 |
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
6322 |
o bug fix in find_alpha.F for MDJWF: |
6323 |
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
6324 |
change rho -> rho-rhoConst |
6325 |
- replace call find_rho to find_rhonum |
6326 |
o initialisation of rFlx extended to full array (required by TAF) |
6327 |
and shifted to thermodynamics |
6328 |
o removed PTRACERS.h in ptracers routine |
6329 |
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
6330 |
o Correcting initialisations for fVerU, fVerV. |
6331 |
o helping TAF to recognize dependency on kUp for |
6332 |
fVerU, fVerV |
6333 |
o Replacing delZ by delR in pkg/ctrl/ |
6334 |
checkpoint51o_pre (2003/10/24) |
6335 |
|
6336 |
o undid all of cp51 pending some cleanups and discussion |
6337 |
o added the [#include "AD_CONFIG.h"] statement to all files that need |
6338 |
it for adjoint/tl #defines |
6339 |
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
6340 |
o removed tools/genmake since it no longer works |
6341 |
|
6342 |
checkpoint51n_post (2003/10/23) |
6343 |
o modifications to make FREEZE flux visible to pkg/kpp |
6344 |
- moved surfaceTendencyTice from pkg/seaice to main code |
6345 |
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
6346 |
- subroutine FREEZE now limits only surface temperature |
6347 |
(this means new output.txt for global_ocean.90x40x15, |
6348 |
global_ocean.cs32x15, and global_with_exf) |
6349 |
o added surface flux output variables to TIMEAVE_STATVARS |
6350 |
|
6351 |
checkpoint51n_pre (2003/10/23) |
6352 |
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
6353 |
o added [#include "AD_CONFIG.h"] to all files that use the following |
6354 |
defines: |
6355 |
- ALLOW_ADJOINT_RUN |
6356 |
- ALLOW_TANGENTLINEAR_RUN |
6357 |
- ALLOW_ECCO_OPTIMIZATION |
6358 |
|
6359 |
checkpoint51m_post (2003/10/21) |
6360 |
o incorporating changes to get TAMC/TAF working in genmake2 |
6361 |
- added new TAMC/TAF targets to the Makefile |
6362 |
- various cleanups related to package handling |
6363 |
- these changes should have no impact on the forward model |
6364 |
|
6365 |
checkpoint51l_post (2003/10/20) |
6366 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
6367 |
- faster algorithm for cal_addtime.F |
6368 |
- higher precision arithmetic, where needed |
6369 |
- pkg/exf *startdate variables changed from calendar date to |
6370 |
model integration time |
6371 |
|
6372 |
checkpoint51l_pre (2003/10/17) |
6373 |
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
6374 |
o enable to apply restoring on S & T only in a latitude band. |
6375 |
o update output (external_forcing_surf modif. change truncation errors) |
6376 |
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
6377 |
|
6378 |
checkpoint51k_post (2003/10/16) |
6379 |
o change default to: useNHMTerms=.FALSE. |
6380 |
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
6381 |
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
6382 |
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
6383 |
exp1, ideal_2D_oce |
6384 |
- change data file of oceanic exp (leave the results unchanged for now) |
6385 |
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
6386 |
o set gravitySign automatically according to the vertical coordinate used |
6387 |
(and change sign: back to "logical" value: +1 when R increases downward) |
6388 |
o added an include barrier to the default CPP_OPTIONS.h and |
6389 |
removed the #include "PACKAGES_CONFIG.h" from it |
6390 |
o fix a bug in mom_fluxform (from chk51j_post) |
6391 |
|
6392 |
checkpoint51j_post (2003/10/10) |
6393 |
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
6394 |
o adjusted some flow directives (dynamics, thermodynamics) |
6395 |
o added cubed-sphere case to test cost function |
6396 |
o heckpoint_lev?_directives.h now include |
6397 |
pkg-specific directives, whenever those are enabled. |
6398 |
o Moving pkg-specific flow directives to corresponding pkg |
6399 |
Moving pkg-specific differentiation list to corresponding pkg |
6400 |
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
6401 |
---> conventions are |
6402 |
- pkg_ad.flow |
6403 |
- pkg_ad_diff.list |
6404 |
- pkg_ad_check_lev?_dir.h |
6405 |
|
6406 |
checkpoint51i_post (2003/10/09) |
6407 |
o merge of the branch-genmake2 |
6408 |
- knowingly breaks the older genmake |
6409 |
- automatic generation of all ALLOW_${PKG_NAME} defines |
6410 |
- new testreport supersedes older testscript |
6411 |
o large number of package inclusion and header cleanups |
6412 |
checkpoint51i_pre (2003/10/08) |
6413 |
|
6414 |
o new output for adjoin of global ocean vector invariant |
6415 |
o fix for checkpoint of thermodynamic seaice and bulk_force |
6416 |
o Steph gchem various cleanups |
6417 |
|
6418 |
checkpoint 51h_pre |
6419 |
o fixed some single quotes |
6420 |
o modify gchem pkg to be more versatile |
6421 |
o modifications to clean up dic pkg |
6422 |
o add pkg/cfc |
6423 |
|
6424 |
checkpoint51g_post (2003/10/02) |
6425 |
o provide links for ARPACK and ADM*TLM |
6426 |
o start removing verification/vero/ |
6427 |
o update AD-related stuff |
6428 |
(in particular some IF-statements in model/src/ routines) |
6429 |
o adding to verification/global_ocean.90x40x15/ adjoint of |
6430 |
vector invariant setup |
6431 |
|
6432 |
checkpoint51f_post (2003/10/02) |
6433 |
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
6434 |
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
6435 |
of tracer Green's fucntions for ocean inversion project. |
6436 |
|
6437 |
checkpoint51f_pre (2003/08/07) |
6438 |
o Added on-the-fly spatial interpolation capability |
6439 |
"USE_EXF_INTERPOLATION" to pkg/exf. |
6440 |
- This is a temporary Cartesian-grid hack until |
6441 |
the super-duper ESMF coupler becomes available. |
6442 |
- See verification/global_with_exf/README for usage example. |
6443 |
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
6444 |
flags and modified pkg/seaice accordingly. |
6445 |
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
6446 |
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
6447 |
non-local transport term. |
6448 |
|
6449 |
checkpoint51e_post (2003/08/03) |
6450 |
o pkg/mom_vecinv: |
6451 |
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
6452 |
- add time-ave diagnostic of vorticity advection. |
6453 |
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
6454 |
o atmospheric geopotential: - include water vapor effect; |
6455 |
- use p^kappa in p* scaling. |
6456 |
o land pkg: read initial state from files. |
6457 |
o AIM : add stratospheric drag in the upper level |
6458 |
|
6459 |
checkpoint51d_post (2003/07/18) |
6460 |
o change function ILNBLNK (=> last non-blank char.) to return zero |
6461 |
(instead of the string length) when the string. char is empty |
6462 |
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
6463 |
o modif's to restore TAMC compatibility |
6464 |
- avoid "_d" constructs in PARAMETER declarations |
6465 |
- avoid interrupting lines by comment lines |
6466 |
o Use cluster local disks for purely local I/O |
6467 |
vs. globally visible disks needed for ctrl stuff |
6468 |
(merged from ecco-branch) |
6469 |
- new active_file_loc... and mdsio_..._loc routines |
6470 |
- affected packages: autodiff, ctrl, grdchk, mdsio |
6471 |
|
6472 |
checkpoint51c_post (2003/07/08) |
6473 |
o introducing integer flag debugLevel |
6474 |
- debLevZero: suppress all output |
6475 |
- debLevA: standard |
6476 |
- debLevB: equivalent to current debugMode=.TRUE. |
6477 |
o introducing pathname variable mdsioLocalDir for mdsio |
6478 |
that can be specified at runtime |
6479 |
(relevant for cluster I/O to local disk) |
6480 |
` |
6481 |
>>>checkpoint51b_post |
6482 |
adjoint of ptracers |
6483 |
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
6484 |
o extended state in checkpoint_lev?, etc. |
6485 |
o alternative ctrl/cost with tr1 or ptracer |
6486 |
o new comlev1_bibj_ptracers |
6487 |
o new ptracers.flow |
6488 |
o made ptracers_forcing same as external_forcing_s |
6489 |
o added verification for adjoint with ptracers |
6490 |
- adm. grdchk fail so far |
6491 |
- tlm. grdchk OK |
6492 |
- checked tapelev/comlev recomputations: OK |
6493 |
<<<checkpoint51b_pre |
6494 |
|
6495 |
checkpoint51a_post (2003/06/25) |
6496 |
o added code for biogeochemistry package |
6497 |
- new pkgs: dic, gchem |
6498 |
- new subroutine in ptracers |
6499 |
o modify code for biogeo packages |
6500 |
- in model/src and pkg/ptracers |
6501 |
|
6502 |
checkpoint51 (2003/06/24) |
6503 |
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
6504 |
- autodiff, ctrl, exf, grdchk, seaice |
6505 |
kept separate packages |
6506 |
- cost, ecco, obcs |
6507 |
o updating verification/internal_wave, verification/lab_sea |
6508 |
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
6509 |
|
6510 |
checkpoint50i_post (2003/06/23) |
6511 |
o Preparing next differentiable checkpoint and sync |
6512 |
of MAIN vs. ecco-branch |
6513 |
- 1st step: this one is differentiable |
6514 |
- 2nd step: next(! not this) checkpoint will have updated packages |
6515 |
from ecco-branch) |
6516 |
|
6517 |
checkpoint50h_post (2003/06/20) |
6518 |
o new package "land": provide surface BC for AIM. |
6519 |
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
6520 |
o AIM: use true log-P extrapolation for near surface temp (= as in |
6521 |
F.Molteni paper) ; update aim.5l_cs output. |
6522 |
o New variable in PARM03 for more flexible pickups |
6523 |
o somewhat cleaned package initialisation sequence for |
6524 |
ctrl/ cost/ ecco/ in packages_... routines |
6525 |
|
6526 |
checkpoint50g_post (2003/05/23) |
6527 |
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
6528 |
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
6529 |
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
6530 |
made the default because of faster convergence than ADI |
6531 |
|
6532 |
checkpoint50f_post (2003/05/23) |
6533 |
o exf totally restructured |
6534 |
- replaced all exf_set_ routines by one generic exf_set_gen.F |
6535 |
and made sure it's still differentiable |
6536 |
- split exf_getffields.F into new exf_bulkformulae.F |
6537 |
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
6538 |
- updated adjoint/makefile and relevant verif. accordingly |
6539 |
|
6540 |
checkpoint50f_pre (2003/05/23) |
6541 |
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
6542 |
+ change Evap over land. (update aim.5l_cs output) |
6543 |
o added missing .cvsignores and made uniform across expts |
6544 |
o changed configuration of tidal_basin_2d expt |
6545 |
o added pkg/debug functions for tracing code in fatal crashes |
6546 |
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
6547 |
o new fn in pkg/monitor to stop model if solution grows too big |
6548 |
o removed lots of single quotes from comments |
6549 |
|
6550 |
checkpoint50e_post (2003/05/14) |
6551 |
o make KPP work with PTRACERS |
6552 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
6553 |
nearly a copy of kpp_transport_s |
6554 |
- there is no analogue to SurfaceTendencyS, so I have to use |
6555 |
gPtr(of the surface layer) instead |
6556 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
6557 |
checkpoint50e_pre (2003/05/13) |
6558 |
|
6559 |
checkpoint50d_post (2003/05/13) |
6560 |
o change kpp output from multiple-record state files to single-record state |
6561 |
files analogous to write_state.F |
6562 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
6563 |
analogous to the cg2d-related output. |
6564 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
6565 |
so that writing to internal file fn (with length 512) fails. |
6566 |
checkpoint50d_pre (2003/05/12) |
6567 |
|
6568 |
checkpoint50c_post (2003/05/12) |
6569 |
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
6570 |
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
6571 |
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
6572 |
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
6573 |
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
6574 |
|
6575 |
checkpoint50c_pre (2003/04/30) |
6576 |
Merging from release1_p13: |
6577 |
o bug fix for pkg/seaice dynamic solver |
6578 |
o Added SEAICE_initialHEFF to pkg/seaice |
6579 |
|
6580 |
checkpoint50b_post (2003/04/17) |
6581 |
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
6582 |
o in order to put the momForcing out of the Adams-Bashforth: |
6583 |
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
6584 |
to timestep.F |
6585 |
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
6586 |
o re-generate output for highly sensitive test-exp: |
6587 |
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
6588 |
|
6589 |
checkpoint50b_pre (2003/04/17) |
6590 |
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
6591 |
o corrected CPP option mismatch in exf_Bulk... functions for case |
6592 |
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
6593 |
|
6594 |
checkpoint50a_post (2003/03/21) |
6595 |
o Bug fix for merging between c50 and KPP. |
6596 |
ikey was passed from thermodynamics to kpp_calc via |
6597 |
common block rather than being recomputed in kpp_calc, |
6598 |
in contradiction with new key itdkey. |
6599 |
New key ikppkey created, and tamc.h headers updated. |
6600 |
|
6601 |
checkpoint50 (2003/03/08) |
6602 |
- 2nd step of merge with ecco-branch: |
6603 |
merge changes in ecco-branch back into main trunk |
6604 |
- bug fix in find_alpha |
6605 |
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
6606 |
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
6607 |
- merged some sliced AD support routines |
6608 |
|
6609 |
checkpoint49 (2003/03/06) |
6610 |
merged from ecco-branch: |
6611 |
o exf: |
6612 |
- Enable initialisation of forcing fields to constant |
6613 |
(runtime) values. |
6614 |
- in exf_getffields.F |
6615 |
Reduce i-/j-loop to interior domain, discarding overlaps. |
6616 |
That also fixes wrong TAF-key computations for key_1, key_2 |
6617 |
with bulf formulae. |
6618 |
- exf_init.F modify #ifdef for exf_init_evap |
6619 |
- exf_getffieldrec.F, ctrl_getrec.F |
6620 |
The following INT-usages are not safe: |
6621 |
fldsecs = int(fldsecs/fldperiod)*fldperiod |
6622 |
fldcount = int(fldsecs/fldperiod) + 1 |
6623 |
and were modified. |
6624 |
o autodiff: checkpoint_lev... |
6625 |
- updated storing for bulk formulae (some arrays were missing) |
6626 |
- added state for seaice package |
6627 |
- synchronized with main branch |
6628 |
o DIVA: |
6629 |
Modif.s in |
6630 |
- the_main_loop.F |
6631 |
- the_model_main.F |
6632 |
and added cost_final_restore.F cost_final_store.F |
6633 |
o With these changes, it is possible to fully separate |
6634 |
the first forward run to compute the cost function (mdthe_main_loop) |
6635 |
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
6636 |
into separate model executions. |
6637 |
This enables better tuning of DIVA to given queue sizes. |
6638 |
o Loss of cost function value in consecutive DIVA runs is |
6639 |
fixed by storing to 'costfinal' file. |
6640 |
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
6641 |
beginning/end of adjoint integration is accounted for. |
6642 |
The current changes apply to TAF-1.4.26. |
6643 |
TAF has one remaining bug, requiring one manual change |
6644 |
(see MITgcm manual). |
6645 |
o cal: synchronized between MAIN and ecco-branch |
6646 |
|
6647 |
checkpoint48i_post (2003/03/05) |
6648 |
o Changes to restore differentiability of code w.r.t. previous tag |
6649 |
(mostly adding new routines to make list and replacing |
6650 |
pressure by totPhiHyd). |
6651 |
o Updated and merged grdchk package |
6652 |
- has both ADM and TLM checks |
6653 |
- works for single- and multi-proc. |
6654 |
- output cleaned |
6655 |
- worked successfully for parallel DIVA |
6656 |
o genmake: |
6657 |
- Adding -platform=SP4 |
6658 |
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
6659 |
o Modif. for DIVA: |
6660 |
ctrl_unpack should not be called in intermediate DIVA interval. |
6661 |
(similar thing would apply for active files such as |
6662 |
tbar, sbar, psbar, which should not be reinitialised; |
6663 |
only relevant for ecco-branch) |
6664 |
|
6665 |
checkpoint48h_post (2003/02/28) |
6666 |
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
6667 |
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
6668 |
o Added SEAICE_initialHEFF to pkg/seaice |
6669 |
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
6670 |
|
6671 |
checkpoint48g_post (2003/02/18) |
6672 |
--- EOS: |
6673 |
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
6674 |
store total Potential in totPhyHyd for diagnostics & EOS. |
6675 |
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
6676 |
--- Pressure/geopotential gradient: |
6677 |
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
6678 |
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
6679 |
( changes results of global_ocean_pressure ) |
6680 |
o NLFS + z-coord.: add eta*Rho' contribution. |
6681 |
o accurate phiHyd when using interface-W at the middle between 2 centers |
6682 |
( changes results of ideal_2D_oce ) |
6683 |
o includes r* 2nd term in potential gradient. |
6684 |
|
6685 |
checkpoint48f_post (2003/02/18) |
6686 |
Merging from release1_p12: |
6687 |
o Modifications for using pkg/exf with pkg/seaice |
6688 |
- improved description of the various forcing configurations |
6689 |
- added basic radiation bulk formulae to pkg/exf |
6690 |
- units/sign fix for evap computation in exf_getffields.F |
6691 |
- updated verification/global_with_exf/results/output.txt |
6692 |
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
6693 |
(SBO) core products, including oceanic mass, center-of-mass, |
6694 |
angular, and bottom pressure (see pkg/sbo/README.sbo). |
6695 |
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
6696 |
to avoid negative values in shallow regions. |
6697 |
- updated verification/natl_box/results/output.txt |
6698 |
- updated verification/lab_sea/results/output.txt |
6699 |
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
6700 |
o Added useSingleCpuIO option (see PARAMS.h). |
6701 |
o Updated useSingleCpuIO option in mdsio_writefield.F to |
6702 |
work with multi-field files, e.g., for single-file pickup. |
6703 |
o pkg/seaice: |
6704 |
- bug fix in growth.F: QNET for no shortwave case |
6705 |
- added HeffFile for specifying initial sea-ice thickness |
6706 |
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
6707 |
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
6708 |
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
6709 |
o pkg/seaice: |
6710 |
- adjoint-friendly modifications |
6711 |
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
6712 |
|
6713 |
checkpoint48e_post (2003/02/12) |
6714 |
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
6715 |
o dynamics: change definition of computational domain & adapt mom_fluxform |
6716 |
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
6717 |
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
6718 |
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
6719 |
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
6720 |
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
6721 |
inverted_barometer solid-body.cs-32x32x1 |
6722 |
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
6723 |
|
6724 |
checkpoint48d_post (2003/02/09) |
6725 |
o in preparation for r*: |
6726 |
a) use pre-computed gradient of hydrostatic potential: |
6727 |
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
6728 |
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
6729 |
=> affects results of glob_oce_pressure (different truncation error) |
6730 |
update output.txt of ideal_2D_oce & global_ocean_pressure |
6731 |
|
6732 |
checkpoint48d_pre (2003/02/08) |
6733 |
o in preparation for r*: |
6734 |
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
6735 |
pass the 2 comp. of the grad. as arguments to momentum S/R. |
6736 |
but for the moment, only used if it does not change the results. |
6737 |
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
6738 |
|
6739 |
checkpoint48c_post (2003/02/06) |
6740 |
Modifications in treatment of initial flux forcing controls |
6741 |
to avoid extra storing of flux fields. |
6742 |
|
6743 |
checkpoint48c_pre (2003/01/21) |
6744 |
o Added tidal_basin_2d experiment (currently 1D!) |
6745 |
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
6746 |
|
6747 |
checkpoint48b_post (2003/01/27) |
6748 |
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
6749 |
(modification to pressure gradient not yet implemented) |
6750 |
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
6751 |
(for U & V) that are used for vertical advection of momentum. |
6752 |
|
6753 |
checkpoint48a_post (2003/01/24) |
6754 |
o In preparation for r*, use temp. array to compute vertical transport |
6755 |
in flux-form momentum pkg. => change results of few test-exp. |
6756 |
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
6757 |
lab_sea, natl_box & plume_on_slope |
6758 |
|
6759 |
checkpoint48 (2003/01/23) |
6760 |
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
6761 |
|
6762 |
checkpoint47j_post (2003/01/21) |
6763 |
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
6764 |
o moved adexch from forward_step to addummy_in_stepping |
6765 |
o added exch in ctrl_map_... |
6766 |
o aveFreq.=0. at end of cost_final to avoid overwrite in |
6767 |
reverse checkpointing loop |
6768 |
o Yet more changes in gmredi: |
6769 |
* adgmredi_calc_tensor |
6770 |
avoiding all recomputation of gmredi_slope_limit |
6771 |
* adgmredi_x/y/rtransport |
6772 |
added flag for excessive storing to avoid recomp. of |
6773 |
u/v/rtans, dTdx/y/z |
6774 |
-> this is not really necessary and very memory-consuming |
6775 |
* adgmredi_slope_psi: |
6776 |
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
6777 |
* gmredi_slope_limit |
6778 |
re-activated full calculation of taperfct for case 'ac02' |
6779 |
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
6780 |
|
6781 |
checkpoint47i_post (2003/01/13) |
6782 |
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
6783 |
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
6784 |
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
6785 |
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
6786 |
o gmredi: fix few bugs. |
6787 |
|
6788 |
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
6789 |
This will be a good checkpoint to plug into the ecco-branch. |
6790 |
o few modif.'s to get latest version adjointed |
6791 |
(mainly kick out code in ini_linear_phisurf) |
6792 |
o modif's to run adjoint with exactConserv |
6793 |
o case GM_BOLUS_ADVEC should be cleaned |
6794 |
S/R gmredi_slope_psi should be cleaned |
6795 |
o verification/carbon now has exactConserv=.TRUE. |
6796 |
|
6797 |
checkpoint47g_post (2003/01/10) |
6798 |
o time-average AIM output: becomes independent from statvars time-average |
6799 |
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
6800 |
o After TAF bug fix: |
6801 |
Tested adjoint of gmredi package. |
6802 |
Tests were done with checkpoint47 rather than with latest |
6803 |
checkpoint47f_post since the latter is broken for the adjoint |
6804 |
verification/carbon/ contains both ADM and TLM gradient checks. |
6805 |
Here they are, before they get changed/lost/stolen. |
6806 |
Mostly modif.'s to fix numerical sensitivities. |
6807 |
Gradient checks OK for |
6808 |
- GM_taper_scheme: |
6809 |
* clipping |
6810 |
* ac02 |
6811 |
* linear |
6812 |
* glw91 |
6813 |
* dm95 |
6814 |
* ldd97 |
6815 |
- GMREDI_OPTIONS: |
6816 |
* GM_VISBECK_VARIABLE_K |
6817 |
* GM_NON_UNITY_DIAGONAL |
6818 |
* GM_EXTRA_DIAGONAL |
6819 |
* GM_BOLUS_ADVEC |
6820 |
in conjunction with data.gmredi parameters to be checked in |
6821 |
in a few minutes under verification/carbon/code/ |
6822 |
|
6823 |
checkpoint47f_post (2002/12/28) |
6824 |
Merging from release1_p10: |
6825 |
o modifications for using pkg/exf with pkg/seaice |
6826 |
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
6827 |
and SEAICE_EXTERNAL_FLUXES |
6828 |
- pkg/exf CPP options EXF_READ_EVAP and |
6829 |
EXF_NO_BULK_COMPUTATIONS |
6830 |
- usage examples are Experiments 8 and 9 in |
6831 |
verification/lab_sea/README |
6832 |
- verification/lab_sea default experiment now uses |
6833 |
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
6834 |
|
6835 |
checkpoint47e_post (2002/12/27) |
6836 |
o created a tag prior to creating a branch |
6837 |
|
6838 |
checkpoint47d_post (2002/12/16) |
6839 |
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
6840 |
at the bottom boundary had an erroneous half slip boundary condition |
6841 |
o added bottom drag and no slip boundary condition capabilities to |
6842 |
oceanic pressure coordinates code |
6843 |
o added new verification experiment global_ocean_pressure, this experiment is |
6844 |
also described in the tutorial section of the manual |
6845 |
checkpoint47d_pre (2002/12/16) |
6846 |
|
6847 |
checkpoint47c_post (2002/12/16) |
6848 |
o Added a verification experiment for a global cubed-sphere ocean run |
6849 |
- verification/global_ocean.cubed32x32x30 |
6850 |
- uses pkg/therm_seaice and pkg/bulk_forcing |
6851 |
|
6852 |
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
6853 |
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
6854 |
when using P-coordinate; only implemented for atmospheric config. |
6855 |
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
6856 |
NOTES: requires option NONLIN_FRSURF to be "#define". |
6857 |
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
6858 |
|
6859 |
checkpoint47b_post (2002/12/05) |
6860 |
Merging from release1_p9: |
6861 |
o pkg/seaice |
6862 |
- removed GOTO's and added taf directives |
6863 |
- double precision constants to reduce the g77 (Linux) |
6864 |
to F77 (SGI) differences reported in release1_p8 |
6865 |
o tools/genmake |
6866 |
- added SGI options |
6867 |
o verification/testscript |
6868 |
- updated to that of checkpoint47a_post |
6869 |
o verification/global_ocean.90x40x15/input/eedata |
6870 |
- modified for SGI f77 compatibility |
6871 |
o verification/lab_sea |
6872 |
- added description of sea-ice model |
6873 |
- added missing matlab routines |
6874 |
- added test of thermodynamics parallelization |
6875 |
|
6876 |
checkpoint47a_post (2002/11/23) |
6877 |
o new pkg: aim_v23 |
6878 |
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
6879 |
for now, keep the same surface forcing as before. |
6880 |
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
6881 |
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
6882 |
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
6883 |
o add diagnostic of surface correction term in monitor output |
6884 |
|
6885 |
o bulk_force and therm_seaice |
6886 |
- Two packages: bulk_force (Bulk forcing) |
6887 |
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
6888 |
- Earlier integration from Stephaine Dutkiewicz |
6889 |
and Patrick Heimbach. |
6890 |
- Two ifdef statements for compile time, |
6891 |
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
6892 |
|
6893 |
checkpoint47 (2002/11/15) |
6894 |
differentiable version of checkpoint46n_post |
6895 |
o bug fix in quasihydrostaticterms |
6896 |
o * "clean" adjoint code (in terms of extensive recomputations) |
6897 |
can now be obtained for all GMREDI options (i.e. for |
6898 |
- GM_VISBECK_VARIABLE_K |
6899 |
- GM_NON_UNITY_DIAGONAL |
6900 |
- GM_EXTRA_DIAGONAL |
6901 |
- GM_BOLUS_ADVEC ) |
6902 |
* However, wrong gradient check problem remains unsolved. |
6903 |
* New CPP options have been introduced for different |
6904 |
tapering schemes |
6905 |
o external_fields_load now part of differentiation list |
6906 |
o pressure needs multiple storing; |
6907 |
would be nice to have store_pressure at beginning or |
6908 |
end of forward_step, e.g. by having phiHyd global (5-dim.) |
6909 |
(NB: pressure is needed for certain cases in find_rho, |
6910 |
which is also invoked through convective_adjustment). |
6911 |
o recomputations in find_rho for cases |
6912 |
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
6913 |
o #define ATMOSPHERIC_LOADING should be differentiable |
6914 |
o ini_forcing shifted to begining of initialise_varia |
6915 |
o Incorporating QNVS line search routines into MITgcm |
6916 |
(this is separate code, and therefore not under pkg) |
6917 |
lsopt/, optim/ |
6918 |
o Updated verification/carbon/ |
6919 |
- #define GM_VISBECK_VARIABLE_K |
6920 |
- GM_taper_scheme = 'ldd97' |
6921 |
|
6922 |
checkpoint46n_post (2002/11/12) |
6923 |
Merging from release1_p8: |
6924 |
o verification/natl_box: |
6925 |
updating new external_fields_load routine |
6926 |
o New package: pkg/seaice |
6927 |
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
6928 |
The sea-ice code is based on Hibler (1979-1980). |
6929 |
Two sea-ice dynamic solvers, ADI and LSR, are included. |
6930 |
In addition to computing prognostic sea-ice variables and diagnosing |
6931 |
the forcing/external data fields that drive the ocean model, |
6932 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
6933 |
The implied surface heat flux is then stored in variable |
6934 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
6935 |
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
6936 |
non-local transport term. Because this call precedes model |
6937 |
thermodynamics, temperature under sea-ice may not be "exactly" at |
6938 |
the freezing point by the time theta is dumped or time-averaged. |
6939 |
N.B.: fairly large differences in accuracy occur across |
6940 |
different platforms/compilers; comparison between |
6941 |
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
6942 |
generated output gives: |
6943 |
T S U V |
6944 |
C D M c m s m s m s m s |
6945 |
n p a R g m m e . m m e . m m e . m m e . |
6946 |
f n k u 2 i a a d i a a d i a a d i a a d |
6947 |
g d e n d n x n . n x n . n x n . n x n . |
6948 |
|
6949 |
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
6950 |
o GAD: |
6951 |
- generated new common blocks to account for call of |
6952 |
same gad routines with differing traceridentities |
6953 |
(needed to modify tracerIdentity indices in GAD.h) |
6954 |
- generated separate common blocks for case useCubedSphereExchange |
6955 |
(Department of Futurology) |
6956 |
- parameter lists to gmredi_?transport: added tracerIdentity |
6957 |
- added new key indices to tamc.h |
6958 |
o external_fields_load: |
6959 |
- added this routine to TAF list |
6960 |
- needed to make some common blocks global and additional storing |
6961 |
along the same lines as exf package (checkpoint_lev?_directives.h) |
6962 |
o exf: |
6963 |
updated external forcing package |
6964 |
- bug fixes carried over from ecco-branch |
6965 |
(missing OBCS_OPTIONS.h in two routines) |
6966 |
- enable easy to use "no forcing". |
6967 |
- added exf I/O for atmospheric loading |
6968 |
- added exf I/O for runoff data |
6969 |
- transfered scaling between exf <-> MITgcm to exf namelist |
6970 |
o Adding new verification experiment global_with_exf. |
6971 |
This verification experiment is almost identical to the |
6972 |
global_ocean.90x40x15 experiment, except that it uses |
6973 |
the exf (and cal) package instead of the |
6974 |
external_fields_load routine (cf README file). |
6975 |
|
6976 |
checkpoint46m_post (2002/11/07) |
6977 |
o modified testscript to return -- when there are no lines of "%MON" output |
6978 |
o added new flag "quasiHydrostatic" for QH mode |
6979 |
and new routine quasihydrostaticterms() |
6980 |
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
6981 |
New routine: mom_u_coriolis_nh() |
6982 |
o fixed sign of non-hydrostatic metric terms in u and v equations. |
6983 |
Depend on correct sign of gravitySign. |
6984 |
o added work.pc* to .cvsignore in aim directories using ifc |
6985 |
o introduced flag for controllin non-hydrostatic metric terms |
6986 |
o removed gravitySign from PARM04 |
6987 |
o switched to g77/ifc from pgf77 in aim experiments |
6988 |
|
6989 |
checkpoint46l_post (2002/11/01) |
6990 |
o made convective adjustment work with pressure coordinates: |
6991 |
- changed the direction of k-loop in convective_adjustment.F for the |
6992 |
case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
6993 |
- adjusted the reference pressure k-index in convective_adjustment.F |
6994 |
- adjusted the convection condition in convect.F (in analogy to |
6995 |
calc_ivdc.F) |
6996 |
- convective_adjustment no longer computes anything on the halos |
6997 |
- removed the warnings about negative salinity from find_rho.F and |
6998 |
find_alpha.F; instead the new routine look_for_neg_salinity, called |
6999 |
at the beginning of find_rho, find_alpha, and find_beta, does a |
7000 |
check of the entire slice, if CPP-option |
7001 |
CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
7002 |
checkpoint46l_pre (2002/10/23) |
7003 |
|
7004 |
checkpoint46k_post (2002/10/23) |
7005 |
o fixed the verification/global_ocean.90x40x15 experiment: |
7006 |
- new bathymetry (the world according to A., JMC, and M.) |
7007 |
- new initial fields and forcing fields (*.bin files) |
7008 |
- new POLY3.COEFFS (for the next release one should switch to a full |
7009 |
equation of state: JMD95P or MDJWF) |
7010 |
- fixed several errors and redundancies in the data file |
7011 |
- experiment uses looped cells |
7012 |
- added matlab directory with diagnostic scripts for plotting of output |
7013 |
|
7014 |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
7015 |
- read AIM physics parameters from a file (data.aimphys) |
7016 |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
7017 |
|
7018 |
checkpoint46j_post (2002/10/07) |
7019 |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
7020 |
o move wVel computation at the end of the time step, in S/R integr_continuity |
7021 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
7022 |
o update timeave pkg for wVel diagnostic. |
7023 |
checkpoint46j_pre (2002/09/27) |
7024 |
|
7025 |
checkpoint46i_post (2002/09/25) |
7026 |
o Clean up AIM package (and keep the results unchanged): |
7027 |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
7028 |
declare all the variables _RL ; use _d 0 for all numerical constants. |
7029 |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
7030 |
|
7031 |
checkpoint46h_post (2002/09/25) |
7032 |
o cleaned up the use of rhoNil and rhoConst. |
7033 |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
7034 |
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
7035 |
and the dynamical equations are all divided by rhoConst |
7036 |
o introduced new parameter rhoConstFresh, a reference density of fresh |
7037 |
water, to remove the fresh water flux's dependence on rhoNil. The default |
7038 |
value is 999.8 kg/m^3 |
7039 |
o cleanup up external_forcing.F and external_forcing_surf.F |
7040 |
- can now be used by both OCEANIC and OCEANICP |
7041 |
checkpoint46h_pre (2002/09/18) |
7042 |
|
7043 |
Added code to convert surface volume flux (fresh water) into |
7044 |
a mass flux when using P coordinates in the ocean (OCEANICP). |
7045 |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
7046 |
|
7047 |
checkpoint46g_post (2002/09/18) |
7048 |
o Include a new diagnostic variable phiHydLow for the ocean model |
7049 |
- in z-coordinates, it is the bottom pressure anomaly |
7050 |
- in p-coordinates, it is the sea surface elevation |
7051 |
- in both cases, these variable have global drift, reflecting the mass |
7052 |
drift in z-coordinates and the volume drift in p-coordinates |
7053 |
- included time averaging for phiHydLow, be aware of the drift! |
7054 |
o depth-dependent computation of Bo_surf for pressure coordinates |
7055 |
in the ocean (buoyancyRelation='OCEANICP') |
7056 |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
7057 |
Theta, Salinity, and Pressure in the parameter list. This routine is |
7058 |
presently contained in find_rho.F. This routine does not give the |
7059 |
correct density for 'POLY3', which would be a z-dependent reference |
7060 |
density. |
7061 |
o cleaned up find_rho |
7062 |
- removed obsolete 'eqn' from the parameter list. |
7063 |
o added two new verification experiments: gop and goz |
7064 |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
7065 |
checkpoint46g_pre (2002/09/16) |
7066 |
|
7067 |
checkpoint46f_post (2002/09/16) |
7068 |
o Enable tangent linear (forward mode) gradient checks: |
7069 |
- extended active file handling to g_... files |
7070 |
- added TANGENT_SIMULATION to theSimulationMode |
7071 |
- extended grdchk package accordingly |
7072 |
o added tangent linear setup in verification/carbon/code_ftl |
7073 |
o added adjoint setup in verification/front_relax/code_ad |
7074 |
|
7075 |
checkpoint46e_post (2002/09/05) |
7076 |
o Added new equation of state -> MDJWF |
7077 |
- EOS of McDougall et al., 2002, JAOT, submitted |
7078 |
- caveat: the equation of state is only valid for a smaller (more |
7079 |
realistic?) range of values than JMD95P/Z and UNESCO |
7080 |
- added masks to the calculation of pressure in store_pressure |
7081 |
- added more check values for density in check_eos (ini_eos.F), some of |
7082 |
the old check values are out of the range of the MDJWF-eos, so don't |
7083 |
expect perfect matches for those |
7084 |
checkpoint46e_pre (2002/08/19) |
7085 |
|
7086 |
checkpoint46d_post (2002/08/19) |
7087 |
o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
7088 |
'OCEANICP', also initialised field pressure correctly in ini_eos in the |
7089 |
case of pressure coordinates. eosType='JMD95Z' in |
7090 |
combination with buoyancyRelation='OCEANICP' now causes an error. |
7091 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
7092 |
in find_alpha/beta. |
7093 |
checkpoint46d_pre (2002/08/15) |
7094 |
|
7095 |
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
7096 |
so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
7097 |
|
7098 |
checkpoint46c_post (2002/08/15) |
7099 |
o Changes necessary for ocean in p-coordinates |
7100 |
- Added new buoyancy relation = 'OCEANICP' |
7101 |
- Added new parameters = gravitySign (this used to be contained inside |
7102 |
the factor dRdZ which I added when we first switched to R coordinates). |
7103 |
X GM/Redi is not compatible (yet) |
7104 |
X bottom drag and no-slip need to be debugged. |
7105 |
checkpoint46c_pre (2002/08/07) |
7106 |
|
7107 |
checkpoint46b_post (2002/08/07) |
7108 |
o Added new equation of state -> JMD95Z and JMD95P |
7109 |
- EOS of Jackett and McDougall, 1995, JAOT |
7110 |
- moved all EOS parameters into EOS.h |
7111 |
- new routines ini_eos.F, store_pressure.F |
7112 |
o Added UNESCO EOS, but not recommended because it requires |
7113 |
in-situ temperature (see JMD95) |
7114 |
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
7115 |
unesco.f to be used with POLY3 |
7116 |
checkpoint46b_pre (2002/07/31) |
7117 |
|
7118 |
checkpoint46a_post (2002/07/31) |
7119 |
o Added (atmospheric) pressure loading |
7120 |
- new field in FFIELDS.h, etc... |
7121 |
- new cpp flag ATMOSPHERIC_LOADING |
7122 |
o Changed hFacC to _hFacC in calc_phi_hyd.F |
7123 |
o Added SHORTWAVE_HEATING to some files for consistency |
7124 |
checkpoint46a_pre (2002/07/13) |
7125 |
|
7126 |
checkpoint46 (2002/07/13) |
7127 |
further merges from release1_p5 |
7128 |
o new ctrl package |
7129 |
- adopted from ECCO environment to enable optimization |
7130 |
- added Eliassen Palm fluxes to controls |
7131 |
o added Eliassen Palm flux controls to gradient check package |
7132 |
o cost package |
7133 |
- Compatible with new ctrl package |
7134 |
- added Eliassen Palm cost hooks |
7135 |
- modif's of existing cost functions |
7136 |
o Adjoint-related bug fixes in kpp: |
7137 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
7138 |
- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
7139 |
o autodiff package |
7140 |
- flow directives: |
7141 |
+ new for S/R do_the_model_io |
7142 |
+ enhanced for S/R checkpoint |
7143 |
+ new gmredi.flow |
7144 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
7145 |
disable adcommon.h/g_common.h by default. |
7146 |
- fixed problem for adjoint of global_max |
7147 |
o modified verification/carbon/ |
7148 |
o New setup for adjoint of global_ocean |
7149 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
7150 |
o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
7151 |
o incorporated hooks for sponge layer code (external_forcing.F) |
7152 |
|
7153 |
checkpoint45d_post (2002/07/12) |
7154 |
o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
7155 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
7156 |
(affects plume_on_slope "cg2d" output) |
7157 |
o add new parameter deltaTfreesurf for free-surface time stepping |
7158 |
o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
7159 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
7160 |
o change phiMin in exp1 (to agree with documentation) |
7161 |
o add new flags: |
7162 |
- T,S forcing inside/outside Adams-Bashforth |
7163 |
- turn off temp,salt advection and/or forcing |
7164 |
- for each tracer, define internal flag for multiDimAdvection & A-B |
7165 |
o monitor: change definition of KE to check conservation of Energy |
7166 |
|
7167 |
checkpoint45c_post (2002/05/30) |
7168 |
o Removed f90 comments ("!") |
7169 |
o Modified initialisations to enable exf package for MITgcm |
7170 |
(without invoking ECCO_PACKAGE). |
7171 |
o modifications to gradient check package (Martin Losch) |
7172 |
- enable centered differences |
7173 |
- modified format of standard output |
7174 |
|
7175 |
checkpoint45b_post (2002/05/30) |
7176 |
o cleaned exchange calls in cg2d |
7177 |
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
7178 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
7179 |
to configure barotropic setup (Martin Losch) |
7180 |
o moved some initialisations within bi,bj loop in dynamics |
7181 |
(TAF flow dependency) |
7182 |
o in initialise_varia, moved call packages_init_variables |
7183 |
before convective_adjustment_init |
7184 |
(corresponding adjustment of TAF tape initialisation). |
7185 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
7186 |
|
7187 |
checkpoint45a_post (2002/05/01) |
7188 |
o compute Rho over the whole domain (extend iMin,jMin indices) |
7189 |
o specific exchange for X-slice domain (case Ny=1) |
7190 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
7191 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
7192 |
|
7193 |
checkpoint44h_post = checkpoint45 |
7194 |
o Fix to restore differentiability: |
7195 |
place at which packages_init_variables is called in |
7196 |
initialise_varia is crucial for reverse control flow. |
7197 |
o modifications in GMRedi to enable stable adjoint |
7198 |
(corresponding modif's in thermodynamics, dynamics) |
7199 |
o added missing hook for sponge layer code in external_forcing |
7200 |
o modified test cost functions |
7201 |
o storing in gad_advection (plus removal of write(0,*)! |
7202 |
o missing headers TR1.h added in convective_adjustment routines |
7203 |
o errorMessageUnit set non-equal zero in eeboot |
7204 |
(conflict on some platforms, e.g. IBM SP3) |
7205 |
o modified carbon verif. |
7206 |
|
7207 |
checkpoint44h_pre (2002/03/14) |
7208 |
o vertical grid option: allow to put the Interface at the middle between |
7209 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
7210 |
o GM Advective form: Tracers are advected using the residual transport (= |
7211 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
7212 |
|
7213 |
checkpoint44g_post (2002/03/05) |
7214 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
7215 |
results) ; ifdef missing in thermodynamics.F |
7216 |
|
7217 |
checkpoint44f_pre,checkpoint44f_post |
7218 |
o added PTRACERS package |
7219 |
This allows an arbitrary number of passive tracers to be integrated |
7220 |
forward simultaneously with the dynamicaly model. |
7221 |
+ Implemented so far: |
7222 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
7223 |
- I/O and checkpointing |
7224 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
7225 |
+ Not implemented so far: |
7226 |
- KPP |
7227 |
- OBCS |
7228 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
7229 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
7230 |
line in data.pkg. |
7231 |
+ This package is disabled by default since it increases storage. |
7232 |
|
7233 |
|
7234 |
o testscript: added -cleanup option |
7235 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
7236 |
b) enable to filter 2D fields. |
7237 |
|
7238 |
checkpoint44e_pre,post |
7239 |
o re-wrote convective adjustment to use pre-calculated weights |
7240 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
7241 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
7242 |
Original calls to convect() still in place. |
7243 |
|
7244 |
chkpt44d_pre,post |
7245 |
o added missing EXCLUDE_MONITOR flags |
7246 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
7247 |
(incompatible typ in MIN/MAX expressions caused problems |
7248 |
on IBM SP3) |
7249 |
o in genmake added variable MAKEDEPEND |
7250 |
plus resetting for case SunOS |
7251 |
o added timer_stats.c routine for IBM SP3 |
7252 |
o removed variables in dynamics |
7253 |
!!! I forgot to create tag chkpt44d_pre !!! |
7254 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
7255 |
|
7256 |
o real fresh water flux implemented with non-linear free-surface. |
7257 |
|
7258 |
chkpt44c_pre,post |
7259 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
7260 |
USE_NATURAL_BCS in solve_for_P); |
7261 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
7262 |
|
7263 |
checkpoint44b_pre/_post |
7264 |
o merge of relevant stuff from the ecco-branch: |
7265 |
- genmake: removed $S64 overwrite for case SunOS |
7266 |
- pkg/exf: update and corrections for field swapping and obcs |
7267 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
7268 |
harmonized between ECCO and MITgcm |
7269 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
7270 |
updated checkpointing_lev... lists for obcs |
7271 |
- model/src: minor changes in forward_step, plot_field |
7272 |
added directive for divided adjoint in the_main_loop |
7273 |
- pkg/mdsio: added mdsio_gl_slice |
7274 |
|
7275 |
o check parameters & config (chkpt44a_pre,post) |
7276 |
o OBC and NonLin_FrSurf. |
7277 |
|
7278 |
checkpoint44 (2002/01/18) |
7279 |
o fix bug in mom_vi_del2uv |
7280 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
7281 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
7282 |
o update AIM experiments (NCEP input files) |
7283 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
7284 |
o added some stuff for AD |
7285 |
|
7286 |
checkpoint43 (2001/09/28) |
7287 |
o added two new advection tests |
7288 |
o added global 4x4 degree ocean test |
7289 |
o added test of H&S94 with free surface on cube |
7290 |
o some final mods for gradient check, adjoint,... |
7291 |
|
7292 |
checkpoint42 (2001/09/27) |
7293 |
Fixed AD-related problems: |
7294 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
7295 |
(mainly thermodynamics.F) |
7296 |
o New store directives for multi-dim. advection schemes |
7297 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
7298 |
* new common block and key passkey |
7299 |
(mainly gad_advection.F) |
7300 |
o Modified store directives for split of dynamics/thermodynamics |
7301 |
for the case ALLOW_KPP |
7302 |
o Cleaned argument list for timestep_tracer.F |
7303 |
|
7304 |
checkpoint41 (2001/09/27) |
7305 |
o re-formatted/added comments in prologues of key subroutines |
7306 |
to work with protex |
7307 |
|
7308 |
checkpoint40 (2001/09/27) |
7309 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
7310 |
o added FLT (floats) package from Arne along with demo. experiment |
7311 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
7312 |
implementation of forward-in-time forcing terms |
7313 |
o more mods for non-linear free-surface including new variable |
7314 |
o modified multi-dim method to work on cube |
7315 |
o bug fix in KPP (from DM) |
7316 |
|
7317 |
checkpoint40pre9 (2001/09/27) |
7318 |
o added DST advection schemes |
7319 |
o fix MPI bug on SGI's |
7320 |
o modifications for non-linear free-surface |
7321 |
o fixed conditionals for fixed flow/passive tracer only mode |
7322 |
o added tension/strain form of stress tensor |
7323 |
o changes to commenting of arguments for TAF/TAMC |
7324 |
o added/updated many matlab scripts |
7325 |
o added multi-dimensional advection method for tracers |
7326 |
|
7327 |
checkpoint40pre8 (2001/09/05) |
7328 |
o new package rw/ |
7329 |
Added method for dumping intermediate local arrays: |
7330 |
mdsio_writetile - same as mdsio_writefield except works from inside |
7331 |
bi,bj loop |
7332 |
mdsio_writelocal - same as mdsio_writetile except works for local |
7333 |
arrays |
7334 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
7335 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
7336 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
7337 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
7338 |
control flux-form versus vector invariant code. |
7339 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
7340 |
or genmake -DISABLE ... |
7341 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
7342 |
(additional storing is now needed for case vecinv; |
7343 |
currently nothing implemented to switch this storing off |
7344 |
in case fluxform is used since no CPP flag available). |
7345 |
|
7346 |
checkpoint40pre7 (2001/08/14) |
7347 |
o bug fix in dynamics.F |
7348 |
calc_viscosity called before k=1,Nr loop. |
7349 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
7350 |
o cleaned initialisations in ctrl_map_ini |
7351 |
related to TAF |
7352 |
|
7353 |
checkpoint40pre6 (2001/08/13) |
7354 |
o split dynamics into thermodynamics & dynamics |
7355 |
o corresponding split of calc_diffusivity into |
7356 |
calc_diffusivity, calc_viscosity |
7357 |
(kpp_calc_diff, kpp_calc_visc). |
7358 |
o Added diffkr, kapgm to control variables |
7359 |
o bug fix in gmredi_slope_limit for ldd97 |
7360 |
|
7361 |
checkpoint40pre5 (2001/07/31) |
7362 |
o proper initialization of Adams-Bashforth time stepping |
7363 |
+ uses forward step for very first step of model (iter=0) |
7364 |
o re-generated *all* output since almost all output is modified by this |
7365 |
change (sorry but we've been putting this one off for about 2 years) |
7366 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
7367 |
*not* regenerated since they are already out of date and I don't |
7368 |
want to create the impression that they are suddenly working. |
7369 |
o removed KAP stuff for DEC's |
7370 |
o modified/added many .cvsignore files in */code and */input |
7371 |
o added new expt "solid-body.cs-32x32x1" |
7372 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
7373 |
is not necessarily any better than the current one... |
7374 |
|
7375 |
checkpoint40pre4 (2001/07/30) |
7376 |
o added re-initialisations of utrans,vtrans,rtrans in |
7377 |
calc_common_factors which are crucial for TAF. |
7378 |
o extended iMin,jMin range for calc_common_factors, |
7379 |
calc_diffusivity |
7380 |
o added option ALLOW_PASSIVE_TRACER |
7381 |
o a few minor updates and fixes |
7382 |
|
7383 |
checkpoint40pre3 (2001/07/13) |
7384 |
o created calc_gtr1.F for gad package |
7385 |
o split the_main_loop and re-introduced forward_step |
7386 |
o some recomputations of nIter0 for TAMC |
7387 |
|
7388 |
checkpoint40pre2 (2001/07/13) |
7389 |
o Updated to latest branch of AJA, JMC |
7390 |
o Added gradient check package |
7391 |
o Added routines for passive tracer handling |
7392 |
o Added carbon sequestration sensitivity experiment |
7393 |
|
7394 |
checkpoint39 (2001/05/14) |
7395 |
o Modifications and fixes to support TAMC |
7396 |
(mainly missing or wrong directives) |
7397 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
7398 |
in addummy_in_stepping |
7399 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
7400 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
7401 |
o Included following packages: |
7402 |
cal: calendar |
7403 |
exf: external forcing |
7404 |
ecco: essential routines to control use of cal, exf |
7405 |
(NB: this is not the full ECCO environment) |
7406 |
o disabled some packages by default in genmake |
7407 |
|
7408 |
checkpoint38 (2001/04/10) |
7409 |
o see notes_c37_adj.txt |
7410 |
o corrected wrong layer index in external_forcing_t |
7411 |
o replaced the_main_loop/forward_step by the_main_loop |
7412 |
o removed forceoutput from write_state |
7413 |
(replaced criteria for initial/final state) |
7414 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
7415 |
|
7416 |
checkpoint37 (2001/03/13) |
7417 |
o mdsio.F routine split and packaged in pkg/mdsio |
7418 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
7419 |
used unless genmake -disable=mdsio) |
7420 |
o allow a more precise surface-geopotential gradient for the atmosphere |
7421 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
7422 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
7423 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
7424 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
7425 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
7426 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
7427 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
7428 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
7429 |
and after) unless activating 2 commented lines in initialise-varia. |
7430 |
o Non-Hydrostatic pickup file Pb fixed. |
7431 |
o bug with Rigid-lid version (since c35) fixed. |
7432 |
|
7433 |
checkpoint36 (2001/02/20) |
7434 |
o implement Crank-Nickelson barotropic time-stepping |
7435 |
o recover Time-Average diagnostics |
7436 |
o fix Pb in checkpoint (PR#19) |
7437 |
o AIM become a standard package ; clean unused CPP_kees |
7438 |
|
7439 |
checkpoint35 (2001/02/08) |
7440 |
o subtantial rewrite of dynamics.f |
7441 |
o allows staggered time-stepping |
7442 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
7443 |
o added bottom drag (linear + quadratic) |
7444 |
|
7445 |
checkpoint34 (2001/01/30) |
7446 |
o Modified exchange routines for correct reverse simulation. |
7447 |
o Added verification output to comply with bug fix in impldiff.F |
7448 |
as of c33 (exp2, natl_box). |
7449 |
o Corrected store directives in dynamics.F |
7450 |
o Corrected array boundaries in impldiff.F |
7451 |
o Corrected array dimensions in gmredi. |
7452 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
7453 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
7454 |
o Added mdsio_gl.F for ECCO purposes. |
7455 |
|
7456 |
checkpoint33 (2000/11/30) |
7457 |
o Fixed bug in lower BC in impldiff.F |
7458 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
7459 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
7460 |
- Removed verification/natl_box/code/external_fields_scale.F |
7461 |
(did not differ from that in model/src) |
7462 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
7463 |
(see FFIELDS.h for description) |
7464 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
7465 |
kpp_calc.F and kpp_transport_t.F |
7466 |
- Removed model/src/external_fields_scale.F and calls to it |
7467 |
- verification/natl_box uses flux data with "atmospheric" sign so |
7468 |
a special version of external_fields_load.F is used to |
7469 |
change the data as it's read in. This way, the arrays |
7470 |
have the right units and signs at all times tha a user could |
7471 |
possibly use them. |
7472 |
o Corrected genmake to delete a temporary file during configuration |
7473 |
|
7474 |
checkpoint32 (2000/11/13) |
7475 |
o Scaling of forcing fields moved from external_forcing.F to |
7476 |
external_fields_scale.F, called directly after loading fields. |
7477 |
o Surface relaxation terms added to surface tendency fields in |
7478 |
extra subroutine. |
7479 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
7480 |
fields. |
7481 |
o Changes in GMRedi to comply with packaging structure. |
7482 |
o Modifications and bug fixes in KPP package. |
7483 |
o Verification experiment for KPP added (verification/nat_box/) |
7484 |
|
7485 |
checkpoint31 (2000/09/11) |
7486 |
o Packages interface brought in line with defined standard |
7487 |
-> new routines packages_...F |
7488 |
-> changes in initialise_fixed.F, initialise_varia.F |
7489 |
-> enables initialisation interface for ECCO package |
7490 |
o Rescaling of external forcing fields immediately after read |
7491 |
(removed from external_forcing.F) |
7492 |
-> new: surface_fields_scale.F |
7493 |
-> affects ini_foorcing.F, external_fields_load.F |
7494 |
o Computation of surface tendencies before tendency updates. |
7495 |
-> new: external_forcing_surf.F |
7496 |
o Change of variable names useGMRedi, useKPP, useECCO |
7497 |
o Further changes in dynamics.F, impldiff.F for TAMC |
7498 |
o Tested for experiments 0, 2, 4. |
7499 |
- not yet tested for GMRedi. |
7500 |
- not yet tested for KPP. |
7501 |
|
7502 |
checkpoint30 (2000/07/13) |
7503 |
o Updates for OBCs |
7504 |
o New experiment for test OBCs (internal_wave) |
7505 |
o New output.txt in verification/exp4/results/ |
7506 |
o Updates for KPP: calculation of viscosity corrected, new variables |
7507 |
kpp_dumpFreq and kpp_taveFreq |
7508 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
7509 |
and entry for T90 in genmake |
7510 |
|
7511 |
checkpoint29 (2000/06/21) |
7512 |
o packaged KPP and GM/Redi |
7513 |
|
7514 |
checkpoint28 (2000/06/09) |
7515 |
o Corrected initialization of hFacMin for difference vertical coordinates |
7516 |
o Modified calculation of partial cell thickness to more robust algorithm |
7517 |
o config_summary.F: replaced write_1D_... by write_0D_... |
7518 |
read_write.F: added subroutines write_0D_... |
7519 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
7520 |
included some initialisations required for TAMC. |
7521 |
o routine calc_isoslopes: modified sqrt computation to make it |
7522 |
differentiable for zero argument. |
7523 |
o routines dynamics, impldiff: |
7524 |
included store directives and tape key computations required for TAMC. |
7525 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
7526 |
|
7527 |
checkpoint27 (2000/04/10) |
7528 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
7529 |
formulation works properly with variable resolution. |
7530 |
o restructured the calling tree between the_model_main() and dynamics() |
7531 |
o split initialise() into initialise_fixed() and initialise_varia() |
7532 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
7533 |
in new routine ini_psurf() |
7534 |
|
7535 |
checkpoint26 (2000/04/05) |
7536 |
o moved some #ifdef in optional routines to encompass everything |
7537 |
except the argument declarations. This was using up some memory. |
7538 |
o fixed macros like _ADT to work with both versions of Linux cpp |
7539 |
o cleaned up some unused and uninitialized variables |
7540 |
(helps when debugging with strict compile options) |
7541 |
o split up CPP_EEOPTIONS.h into options and macros |
7542 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
7543 |
o patch for 2 processor JAM mode |
7544 |
|
7545 |
checkpoint25 (2000/03/15) |
7546 |
o updates for OBCs and NH |
7547 |
o dramatically reduced memory usage |
7548 |
o added "JAM" routines for use on Artic network |
7549 |
o parameterization of convection by implicit vertical diffusion |
7550 |
o added a diagnostic of convective index |
7551 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
7552 |
(this is was partly for OBCs and NH but also in anticipation of |
7553 |
an explicit free-surface option) |
7554 |
o initial state input files for U and V |
7555 |
|
7556 |
checkpoint24 (1999/08/02) |
7557 |
o Removed some spurious "REAL"s |
7558 |
o Updated KPP to latest version from JPL |
7559 |
o Added a COS(latitude) in horizontal viscosity |
7560 |
|
7561 |
checkpoint23 (1999/05/26) |
7562 |
o Added del^4 diffusion for salt and temperature |
7563 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
7564 |
|
7565 |
checkpoint22 (1999/05/18) |
7566 |
o Made many small changes: implicit none, format(i5), etc... |
7567 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
7568 |
|
7569 |
checkpoint21 (1999/05/18) |
7570 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
7571 |
o Split-up mid-level I/O routines |
7572 |
o Updated input data for experiments 0,1,2,4 and 5 |
7573 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
7574 |
|
7575 |
checkpoint20 (1999/03/22) |
7576 |
o Tidied up open-boundaries some more |
7577 |
o Added non-hydrostatic code |
7578 |
o Fixed some input data |
7579 |
o Modified MPI start-up to work in "coupled" context. |
7580 |
|
7581 |
checkpoint19 (1998/12/15) |
7582 |
o Tidied up directory structure for verification experiments. |
7583 |
o Added new code for open boundaries. |
7584 |
o Corrected advective terms near boundaries. |
7585 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
7586 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
7587 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
7588 |
|
7589 |
checkpoint18 (1998/11/30) |
7590 |
o Further changes for optional code generation with |
7591 |
CPP - ugh! |
7592 |
|
7593 |
checkpoint17 (1998/11/03) |
7594 |
o Beginning to incorporating modularity |
7595 |
for supporting atmos. and ocean configs. |
7596 |
o Small changes for TAMC complinace |
7597 |
o New ultra simple test case. Barotropic box |
7598 |
configuration "exp0". |
7599 |
|
7600 |
checkpoint16 (1998/10/28) |
7601 |
o Minor changes to exchange routines to support |
7602 |
accumulation in reverse mode. Adjoint of an |
7603 |
assignment is an addition. |
7604 |
o Changes to support compilation by TAMC (LR(1) |
7605 |
syntax) and by g77 under Linux ( 72 character |
7606 |
limit ). |
7607 |
|
7608 |
checkpoint15 (1998/09/29) |
7609 |
Rewrote exchange routines to allow |
7610 |
o General tile <-> tile connectivity. |
7611 |
o TAMC reverse mode flag ( is this really needed? ) |
7612 |
o Variable width overlap and exchange region widths. |
7613 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
7614 |
shmput/shmget, VIA, SYSV shmem and every other cool |
7615 |
communication method. |
7616 |
|
7617 |
checkpoint14 (1998/09/09) |
7618 |
Consistent isomorphism chages made. These allow dynamical core |
7619 |
to support both pressure and meters as a vertical coordinate. |
7620 |
|
7621 |
checkpoint13 (1998/07/17) |
7622 |
Release which corrects global_max problem and a couple |
7623 |
of KGM time-averaging diagnostic errors. Also contains |
7624 |
a double-gyre experiment setup as well as the baseline |
7625 |
4 degree global template. The double gyre template is |
7626 |
organised to allow it to be applied automatically to |
7627 |
the baseline configuration. |
7628 |
|
7629 |
branch-point-rdot |
7630 |
A few tidy-ups have been made bt the real point of this |
7631 |
check-point (excuse the pun) is to allow a branch to be |
7632 |
made for the purposes of adding the rDot alterations. |
7633 |
I don't want to commit the rDot to the main-trunk until |
7634 |
we've actually tested it... |
7635 |
|
7636 |
checkpoint12 (1998/07/08) |
7637 |
Tidy up and added generic genmake script (formerly |
7638 |
configure script). |
7639 |
Released to testers. |
7640 |
|
7641 |
checkpoint11 (1998/07/02) |
7642 |
Re-arranged initialise() and introduced ini_vertical_grid() |
7643 |
and ini_masks_etc(). |
7644 |
|
7645 |
checkpoint10 (1998/07/01) |
7646 |
Introduced the configure script. |
7647 |
Separated out the diags package. |
7648 |
Added template for writing time-averages of tile/intermediate quantities. |
7649 |
Updated SIZE.h in exp2 and made the data big-endian. |
7650 |
|
7651 |
checkpoint9 (1998/06/22) |
7652 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
7653 |
General tidy-up. |
7654 |
SST.bin SSS.bin added to verification/exp2 |
7655 |
|
7656 |
checkpoint8 (1998/06/22) |
7657 |
Inludes time-dependant forcing and time-averaging. |
7658 |
Works at 4x4 and 2.8125x2.8125 global |
7659 |
|
7660 |
checkpoint7-4degree-ref |
7661 |
Branch from checkpoint7. Released for application to |
7662 |
global modeling and general modeling - process studies, regional |
7663 |
model etc.. |
7664 |
Configured for verification/exp2 - 4 degree global, two process. |
7665 |
|
7666 |
checkpoint7 (1998/06/15) |
7667 |
Created by cnh |
7668 |
Simple 4 degree global simulation |
7669 |
configuration. |
7670 |
Includes climatological wind, |
7671 |
hydrography, bathymetry etc |
7672 |
Does not include Heat Flux and E-P |
7673 |
|
7674 |
checkpoint6 (1998/06/08) |
7675 |
Created by cnh |
7676 |
merged checkpoint5 with CD and |
7677 |
spherical polar code. |
7678 |
Still some problems with GM Redi |
7679 |
abd full topography. |
7680 |
|
7681 |
checkpoint5 (1998/06/08) |
7682 |
Created by AJA |
7683 |
contains updates to GM Redi |
7684 |
and reordered timestepping loop |
7685 |
for Implicit Diffusion. |
7686 |
|
7687 |
checkpoint4 (1998/05/30) |
7688 |
Created by cnh |
7689 |
Contains memory saving macros ( _rdxc etc..) for when |
7690 |
grid variations are limited. |
7691 |
Contains polynomial coeffs for EOS and knudsen program |
7692 |
for generation. |
7693 |
|
7694 |
checkpoint3 (1998/05/26) |
7695 |
Created by cnh |
7696 |
Added extra flags for runtime options |
7697 |
Added this file |
7698 |
Added implicit free-surface |
7699 |
Added pre-conditioner |
7700 |
Put compare01 into repository ( compare01/... ) |
7701 |
Put data and eedata into repository ( verification/exp1 ) |
7702 |
|
7703 |
checkpoint2 |
7704 |
Created by AJA |
7705 |
Added GM/Redi |
7706 |
|
7707 |
checkpoint1 |
7708 |
Created by AJA |
7709 |
Restructured kloop in dynamics.F |
7710 |
Added non-linear EOS |
7711 |
|
7712 |
baseline |
7713 |
Original checked in code |