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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.630 by mlosch, Wed Mar 15 13:06:14 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o seaice:
8  o moved ptracer ctrl index 17 -> 32    - modify advection so that it works also on the C-grid
9      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
10        problem in multi-tile runs with C-grid
11      - remove velocity clipping from seaice_dynsolver with C-grid
12    
13    checkpoint58b_post
14    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
15      update output.txt of exp. aim.5l_cs.thSI
16    o various mnc cleanups and improvements:
17      + shrink lookup tables by factor of ~4
18      + better error reporting when running out of lookup space
19      + able to handle longer path/file names (up to 500 chars)
20    o adjoint:
21      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
22      - TBD: "hidden" mom_vecinv recomp. in dynamics
23    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
24     (allow to differentiate between forcing components using new integer flags:
25      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
26     and add new flag to put Dissipation tendency out of Adams-Bashforth.
27    o ecco
28      - enable trend removal from SSH anomaly obs.
29    o adjoint
30      - a fix for PmEpR when #undef EXACT_CONSERV
31      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
32      - try to fix "hidden" recomp. in forward_step for NLFS
33        (NLFS seems broken sometimes after I checked it in)
34    o seaice:
35     - add c-grid version of the dynamic solver:
36       + three new routines that are the c-grid substitute lsr, dynsolver
37         and ostres
38       + put a few fields that were local to dynsolver into global common
39         blocks, so that I can move the computation of stresses etc into
40         seaice_lsr (saves coding but may break the adjoint).
41     - replace more hardwired parameters by runtime parameters
42     - add ice masks that mask the rhs of the implicit solvers where there
43       is no ice (commented out in seaice_dynsolver, because i am not sure
44       if this works properly), eventually this should replace the clipping
45       of ice velocities in seaice_dynsolver to +/-40cm/s.
46    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
47      include it only where its needed
48    o move balancing of fluxes before the call of external_forcing_surf
49    o seaice:
50      - correct units of turning angles (now they are really in degrees)
51      - move computation of GWATX/Y out of main routine into dynsolver
52      - initialize GWATX/Y in seaice_init
53    o Apply mask on Fresh-Water flux (needed for SSH forcing).
54      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
55    o seaice: add runtime flags for turning angles (default to zero)
56    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
57      and trend from exf forcing and ctrl control adjustments
58    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
59      (since checkpoint57x_post)
60    o change the default rotation period to 86164.s = the Earth rotation
61    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
62      and based on a reference stratification. Tested within hs94.cs-32x32x5.
63    o seaice advection: add code for choosing between the default (2nd order
64      central differences) and multiDim advection schemes provided by
65      pkg/generic_advdiff
66    o seaice:
67      - removed all references to SEAICE_GRID.h fields from
68        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
69        (cubed-sphere configuration will change a little)
70      - grid computations in seaice_init are obsolete now.
71      - cleaned up code a little so that is easier to read (hopefully).
72      - added new (better?) discretizations of default advection and diffusion
73        (turn on with SEAICEuseFluxForm)
74      - replace 1 in 3d global fields by kSurface in growth.F
75      
76    checkpoint58a_post
77    o seaice:
78      - bug fix in advect.F
79    o shelfice:
80      - separate shelfice load anomaly from pload (breaks with time
81        dependent forcing), => introduce constant field shelficeLoadAnomaly.
82        Its default is 0., but it may be computed more cleverly from (unknown)
83        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
84        done offline. A good approximation of the pressure load anomaly is
85        necessary to avoid large initial adjustment processes underneath
86        deep-reaching shelfice.
87      - small fix in ISOMIP shelfice_thermodynamics
88      - add more sophisticated thermodynamics of Hellmer (1989), this is
89        now the default
90      - give a few constants more intuitive names
91    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
92      if bulk formulae are used in long integration (especially EmPmR). Turn
93      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
94      if balancePrintMean, the imbalance that is substracted is printed to
95      STDOUT.
96    o fix bug (typo) in obcs_apply_eta.F
97    o add a new package shelfice which enables us to model the circulation
98      underneath shelf-ice with draughts of hundreds of meters.
99     - works
100     - to do: + include improved thermodynamics
101              + check whether kSurfC (from model/inc/SURFACE.h) can be used
102                instead of new field kTopC
103              + can we use topoFile, Ro_surf and existing code in ini_depth.F
104                instead of new field R_shelfIce and new code in ini_depth.F
105                and ini_mask_etc.F?
106              + adjust vertical mixing schemes?
107    o seaice pkg:
108     - add a cpp-flag to include a simple formula for a salinity dependent
109       freezing point of sea water at the surface
110     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
111       meridional stresses are now different (and hopefully correct)
112    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
113       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
114       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
115    o pkg/diagnostics: add options and parameters for regional-statistics
116       diagnostics ; define regions by reading a region-mask from a file
117       (might add other options later)
118    o pkg/bulk_force:
119     - add option and parameters to use AIM surface-flux formulae.
120     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
121       others forcing fields (defined in PARM05, parameter file "data") are loaded
122       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
123     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
124     - use the right EXCH call for uwind,vwind (to work on CS-grid).
125     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
126       and parameters (note: calcWindStress replaces .NOT.readwindstress).
127     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
128    
129    checkpoint58
130    o add "--embed-source" option to genmake2 which, when the supporting
131      tools can be compiled (as determined by genmake2) will turn on the
132      embed_files package which then embeds the entire MITgcm source code
133      (*.[fFhc] + Makefile) used for the build within the executable
134      - requested by CNH but off by default
135      - adds a paltry <9MB to the mitgcmuv executable in most cases
136      - only writes the output when useEMBEDSRC in eedata is true
137    o clean up 3-dim. relaxation codes:
138      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
139      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
140      * Thanks to Tom Haine for testing!
141    
142    checkpoint57z_post
143    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
144      affects output (@ truncation level) of exp. plume_on_slope ; updated.
145    o fix the pickup behavior for obcs in combination with ptracers
146    o fix a bug in ptracers_external_fields_load
147    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
148      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
149    o transfered surface NH pressure to eta field (if exactConserv).
150    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
151         and update lab_sea output.txt file.
152    o completing 3-dim. relaxation code: additional term
153         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
154      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
155      * At compile time, in "EXF_OPTIONS.h" set
156          #define  ALLOW_CLIMTEMP_RELAXATION
157          #define  ALLOW_CLIMSALT_RELAXATION
158      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
159          tauThetaClimRelax3Dim = 15552000.0,
160          tauSaltClimRelax3Dim  = 15552000.0,
161      * 3 cases:
162          1) Use a constant-in-time 3-dim. field
163          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
164          3) Real-time relax. to time-evolving prescribed field
165    o Adding Laplacian-type smoothness constraint on
166      initial and boundary (forcing) controls (ic, bc)
167      * enable at compile-time via
168        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
169      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
170      * Absolute scale somewhat unclear so far
171      * no area weighting was included since no other cost term does so far
172    
173    checkpoint57y_post
174    First step for a NLFS adjoint
175    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
176    o new init. routines for calc_r_star, calc_surf_dr
177    o still need to deal with ini_masks_etc
178    o testreport seemed happy
179    checkpoint57y_pre
180    
181    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
182    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
183    o add new offset feature to offline pkg (plus minor cleanup)
184    o cfc fixes for final year of integration
185    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
186      be in GCHEM_OPTIONS).
187    
188    checkpoint57x_post
189    o fix testreport Pb in multiple test experiment.
190    o cleanup our namelist syntax in verification:
191      - make it more F95 standards compliant (some work still needed)
192      - allows the vast majority of our tests to work with gfortran
193    o Non-Hydrostatic:
194     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
195     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
196    o Allow to apply AB on T,S rather than on AB(gT,gS):
197     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
198     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
199       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
200     - need a "clever" read_pickup to restart from the other AB formulation
201    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
202    o remove some unused variables (reduces number of compiler warnings)
203    o adjoint
204      * Disable useVariableViscosity for adjoint for time being
205        (there are a number of extensive recomputations)
206      * Initialize certain variables needed for adjoint
207    
208    checkpoint57w_post
209    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
210                 fix the singleCpuIO RS version of MDSWRITEFIELD
211       and add a WARNING if using globalFiles=T with multi-processors.
212    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
213      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
214    o tracer advection scheme:
215      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
216       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
217       was not very convenient).
218      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
219       (further tests needed for the implicit DST & Flux-Limiter schemes).
220    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
221      and sRef for convenience, handy, when you want to initialize
222      ptracers in a large domain with a constant non-zero value. Also,
223      untangle ptracers_init.F a little.
224    
225    checkpoint57v_post
226    o change dome exp. to use variable viscosity in side-drag terms.
227    o remove all the files from the cfc_offline test since they are now
228      incorporated into tutorial_cfc_offline which has been producing
229      identical results for a few days of testing
230    o add new parameter: sideDragFactor to enable half-slip-side BC
231      and change side-drag S/R to use viscosity from mom_calc_visc
232      (can switch back by setting sideDragFactor=0.); affects results at
233      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
234       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
235    o vorticity & strain are now computed without masking, to account for
236      no-slip-side BC in variable viscosity calculation ; mask is applied
237      anyway later on, before computing advection/coriolis terms.
238    o modify exp4 to test new obcs support for reading from external files
239      and for passive tracers
240    o fix behavior of ptracers_monitor when monitor output is written to a
241      netcdf-file; still not independent of monitor.F (writes in the same
242      file).
243    o change default value of tRef (put a uniform, meaningful value for ocean
244      & atmos) and initialize sRef (was missing, as Martin mentioned).
245    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
246      to be proportional to enstrophy dissipation length.  Thus,
247       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
248      This is now consistent with Smagorinsky and with the manual.
249    
250    checkpoint57u_post
251    o OBCS and PTRACERS: add open boundary support for passive tracers
252      - either use homogenous (pseudo) v.Neumann conditions or prescribe
253        OB-values from file; this is not different from the way theta and salinity
254        are treated
255      - however, Orlanski-radiation conditions are not supported, and the model
256        will stop if you use pTracers and Orlanski at the same time.
257      - beefed up the rountine obcs_external_fields_load: now only those open
258        boundary values are overwritten with values from files for which there
259        are really files, otherwise the OB-fields remain untouched. This makes
260        it possible to use different OBs at different ends of the domain (as
261        with EXF)
262    o reduce number of exch calls in shap_filt (s2).
263    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
264      truncation level) 4/5 MLAdjust test results (11&12 digits match).
265    
266    checkpoint57t_post
267    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
268    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
269      same truncation, independent of the face number: affects affects several
270      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
271    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
272      note that biharmonic viscosity + no-slip was not tested in any experiment.
273    o fix bug in non-linear free-surf side-drag ; generate new output for
274      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
275    o make mnc honor the writeBinaryPrec flag for most kinds of output
276    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
277    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
278      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
279    o add brackets in multi-terms sum to get same truncation, independent of
280      the face number (manage to get exactly same value of gU,gV at the cs-edge)
281      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
282    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
283      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
284      a maximum grid-scale Reynolds number.  Also, changes all length calculations
285      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
286      Suggested values of viscosity parameters found in mom_calc_visc.
287      Many new viscosity diagnostics available.
288    
289    checkpoint57s_post
290    o Add clearing-house for viscosity calculations, mom_calc_visc and
291      correct numerous bugs in LeithD and Smagorinsky discretizations.  
292      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
293      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
294      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
295      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
296      The Strain-Tension form is now called with useStrainTensonVisc=.true.
297      ViscAhStrain and viscAhTension are now retired.
298    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
299    o In response to JMC's bug report, genmake2 now ignores any soft-links
300      that it finds in the *current* directory when searching for files.
301      Soft-links found in any other source directories will still work as
302      they did before.
303    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
304      a C routine to unlimit the stack size
305    o mnc-ify pkg/aim snapshot vars
306    o mnc-ify pkg/land as requested by Daniel
307    o various changes to mnc including:
308      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
309      - output can now be grouped so that all files within a group
310          change the ITER portion of their names in lock-step together
311      - can now read ("global") PER-FACE (in addition to PER-TILE) files
312          and works with both EXCH1 and EXCH2 (but needs more testing)
313      - writing works for all verification test cases w/ g77 on Linux
314    
315    checkpoint57r_post
316    o make MNC variable initialization happen earlier
317    o add diagnostics for (almost) each term of the momentum Eq.
318    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
319    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
320    o remove MINIMAL_TAVE_OUTPUT option ;
321      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
322    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
323      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
324    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
325    o add time-dependent SST, SSS control
326    o cost terms in ecco/ modularized (new cost_generic.F)
327    o cost_averages routines are modularized (new cost_averagesgeneric.F)
328    o new infrastructure for seaice model vs. obs misfits in seaice/
329      * driver from the_main_loop.F is seaice_cost_driver.F
330      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
331      * gradient check in Exp. 6a of natl_box_adjoint/
332    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
333      (see README file)
334    
335    checkpoint57q_post
336    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
337    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
338      - bug was reported by Jean-Michel and Ian Fenty
339    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
340      update exp. cpl_aim+ocn output.
341    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
342      Needed for high-res. runs with large global files
343      to be able to limit tapelev size
344    o Changed some tests for adjoint:
345      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
346      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
347      * global_ocean.90x40x15/ back to default 3-level checkpointing
348    o Modifications to enable scripted COMMON to MODULE conversion
349      * verification/OpenAD/code/ has necessary scripts and description;
350      * converts, compiles and runs successfully;
351    
352    checkpoint57p_post
353    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
354    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
355      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
356    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
357    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
358      (was already the case for dissipation with mom_vecinv,
359       and also the case for grad.PhiHyd when staggered-timeStep)
360      This will allow to put dissipation out-off the AB time-stepping.
361     Unfortunately, affects truncation error. Update output of exp. that "fails"
362      (cg2d matching number) and leave the others for later: front_relax(10),
363      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
364      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
365    
366    checkpoint57o_post
367    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
368      (2) its ready to be documented during the 20050801 DocFest
369    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
370      for ideal_2D_oce and lab_sea on linux_ia32_g77
371    o set to #undef CTRL_SET_OLD_MAXCVARS_30
372      in global1x1_tot/code_seaice_adj to access indices 32, 33
373      (worth another tag)
374    
375    checkpoint57n_post
376    o adding precip control xx_precip 32
377    o adding swflux control xx_swflux 33
378    o Replacing 10 forcing penalty cost routines by 1 generic.
379    o Implementing partitioning in time-mean and variable adjustment
380      for atmos. state.
381    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
382  o in natl_box_adjoint:  o in natl_box_adjoint:
383    * updated: results_bulk/    * updated exp 1 to 10
384    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
385    o updated global1x1/*_seaice_adj/
386      to incorporate latest changes
387    o enable useSingleCpuIO for mdsio vector routines
388      (applies in particular to tapelev I/O)
389    o removed inefficient K-loop in all active_file*control*.F
390    
391  checkpoint57m_post  checkpoint57m_post
392  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)

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