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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.620 by mlosch, Fri Mar 3 10:21:29 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 move balancing of fluxes before the call of external_forcing_surf
8  o moved ptracer ctrl index 17 -> 32  o seaice:
9      - correct units of turning angles (now they are really in degrees)
10      - move computation of GWATX/Y out of main routine into dynsolver
11      - initialize GWATX/Y in seaice_init
12    o Apply mask on Fresh-Water flux (needed for SSH forcing).
13      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
14    o seaice: add runtime flags for turning angles (default to zero)
15    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
16      and trend from exf forcing and ctrl control adjustments
17    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
18      (since checkpoint57x_post)
19    o change the default rotation period to 86164.s = the Earth rotation
20    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
21      and based on a reference stratification. Tested within hs94.cs-32x32x5.
22    o seaice advection: add code for choosing between the default (2nd order
23      central differences) and multiDim advection schemes provided by
24      pkg/generic_advdiff
25    o seaice:
26      - removed all references to SEAICE_GRID.h fields from
27        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
28        (cubed-sphere configuration will change a little)
29      - grid computations in seaice_init are obsolete now.
30      - cleaned up code a little so that is easier to read (hopefully).
31      - added new (better?) discretizations of default advection and diffusion
32        (turn on with SEAICEuseFluxForm)
33      - replace 1 in 3d global fields by kSurface in growth.F
34      
35    checkpoint58a_post
36    o seaice:
37      - bug fix in advect.F
38    o shelfice:
39      - separate shelfice load anomaly from pload (breaks with time
40        dependent forcing), => introduce constant field shelficeLoadAnomaly.
41        Its default is 0., but it may be computed more cleverly from (unknown)
42        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
43        done offline. A good approximation of the pressure load anomaly is
44        necessary to avoid large initial adjustment processes underneath
45        deep-reaching shelfice.
46      - small fix in ISOMIP shelfice_thermodynamics
47      - add more sophisticated thermodynamics of Hellmer (1989), this is
48        now the default
49      - give a few constants more intuitive names
50    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
51      if bulk formulae are used in long integration (especially EmPmR). Turn
52      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
53      if balancePrintMean, the imbalance that is substracted is printed to
54      STDOUT.
55    o fix bug (typo) in obcs_apply_eta.F
56    o add a new package shelfice which enables us to model the circulation
57      underneath shelf-ice with draughts of hundreds of meters.
58     - works
59     - to do: + include improved thermodynamics
60              + check whether kSurfC (from model/inc/SURFACE.h) can be used
61                instead of new field kTopC
62              + can we use topoFile, Ro_surf and existing code in ini_depth.F
63                instead of new field R_shelfIce and new code in ini_depth.F
64                and ini_mask_etc.F?
65              + adjust vertical mixing schemes?
66    o seaice pkg:
67     - add a cpp-flag to include a simple formula for a salinity dependent
68       freezing point of sea water at the surface
69     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
70       meridional stresses are now different (and hopefully correct)
71    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
72       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
73       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
74    o pkg/diagnostics: add options and parameters for regional-statistics
75       diagnostics ; define regions by reading a region-mask from a file
76       (might add other options later)
77    o pkg/bulk_force:
78     - add option and parameters to use AIM surface-flux formulae.
79     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
80       others forcing fields (defined in PARM05, parameter file "data") are loaded
81       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
82     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
83     - use the right EXCH call for uwind,vwind (to work on CS-grid).
84     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
85       and parameters (note: calcWindStress replaces .NOT.readwindstress).
86     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
87    
88    checkpoint58
89    o add "--embed-source" option to genmake2 which, when the supporting
90      tools can be compiled (as determined by genmake2) will turn on the
91      embed_files package which then embeds the entire MITgcm source code
92      (*.[fFhc] + Makefile) used for the build within the executable
93      - requested by CNH but off by default
94      - adds a paltry <9MB to the mitgcmuv executable in most cases
95      - only writes the output when useEMBEDSRC in eedata is true
96    o clean up 3-dim. relaxation codes:
97      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
98      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
99      * Thanks to Tom Haine for testing!
100    
101    checkpoint57z_post
102    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
103      affects output (@ truncation level) of exp. plume_on_slope ; updated.
104    o fix the pickup behavior for obcs in combination with ptracers
105    o fix a bug in ptracers_external_fields_load
106    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
107      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
108    o transfered surface NH pressure to eta field (if exactConserv).
109    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
110         and update lab_sea output.txt file.
111    o completing 3-dim. relaxation code: additional term
112         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
113      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
114      * At compile time, in "EXF_OPTIONS.h" set
115          #define  ALLOW_CLIMTEMP_RELAXATION
116          #define  ALLOW_CLIMSALT_RELAXATION
117      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
118          tauThetaClimRelax3Dim = 15552000.0,
119          tauSaltClimRelax3Dim  = 15552000.0,
120      * 3 cases:
121          1) Use a constant-in-time 3-dim. field
122          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
123          3) Real-time relax. to time-evolving prescribed field
124    o Adding Laplacian-type smoothness constraint on
125      initial and boundary (forcing) controls (ic, bc)
126      * enable at compile-time via
127        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
128      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
129      * Absolute scale somewhat unclear so far
130      * no area weighting was included since no other cost term does so far
131    
132    checkpoint57y_post
133    First step for a NLFS adjoint
134    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
135    o new init. routines for calc_r_star, calc_surf_dr
136    o still need to deal with ini_masks_etc
137    o testreport seemed happy
138    checkpoint57y_pre
139    
140    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
141    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
142    o add new offset feature to offline pkg (plus minor cleanup)
143    o cfc fixes for final year of integration
144    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
145      be in GCHEM_OPTIONS).
146    
147    checkpoint57x_post
148    o fix testreport Pb in multiple test experiment.
149    o cleanup our namelist syntax in verification:
150      - make it more F95 standards compliant (some work still needed)
151      - allows the vast majority of our tests to work with gfortran
152    o Non-Hydrostatic:
153     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
154     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
155    o Allow to apply AB on T,S rather than on AB(gT,gS):
156     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
157     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
158       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
159     - need a "clever" read_pickup to restart from the other AB formulation
160    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
161    o remove some unused variables (reduces number of compiler warnings)
162    o adjoint
163      * Disable useVariableViscosity for adjoint for time being
164        (there are a number of extensive recomputations)
165      * Initialize certain variables needed for adjoint
166    
167    checkpoint57w_post
168    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
169                 fix the singleCpuIO RS version of MDSWRITEFIELD
170       and add a WARNING if using globalFiles=T with multi-processors.
171    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
172      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
173    o tracer advection scheme:
174      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
175       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
176       was not very convenient).
177      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
178       (further tests needed for the implicit DST & Flux-Limiter schemes).
179    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
180      and sRef for convenience, handy, when you want to initialize
181      ptracers in a large domain with a constant non-zero value. Also,
182      untangle ptracers_init.F a little.
183    
184    checkpoint57v_post
185    o change dome exp. to use variable viscosity in side-drag terms.
186    o remove all the files from the cfc_offline test since they are now
187      incorporated into tutorial_cfc_offline which has been producing
188      identical results for a few days of testing
189    o add new parameter: sideDragFactor to enable half-slip-side BC
190      and change side-drag S/R to use viscosity from mom_calc_visc
191      (can switch back by setting sideDragFactor=0.); affects results at
192      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
193       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
194    o vorticity & strain are now computed without masking, to account for
195      no-slip-side BC in variable viscosity calculation ; mask is applied
196      anyway later on, before computing advection/coriolis terms.
197    o modify exp4 to test new obcs support for reading from external files
198      and for passive tracers
199    o fix behavior of ptracers_monitor when monitor output is written to a
200      netcdf-file; still not independent of monitor.F (writes in the same
201      file).
202    o change default value of tRef (put a uniform, meaningful value for ocean
203      & atmos) and initialize sRef (was missing, as Martin mentioned).
204    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
205      to be proportional to enstrophy dissipation length.  Thus,
206       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
207      This is now consistent with Smagorinsky and with the manual.
208    
209    checkpoint57u_post
210    o OBCS and PTRACERS: add open boundary support for passive tracers
211      - either use homogenous (pseudo) v.Neumann conditions or prescribe
212        OB-values from file; this is not different from the way theta and salinity
213        are treated
214      - however, Orlanski-radiation conditions are not supported, and the model
215        will stop if you use pTracers and Orlanski at the same time.
216      - beefed up the rountine obcs_external_fields_load: now only those open
217        boundary values are overwritten with values from files for which there
218        are really files, otherwise the OB-fields remain untouched. This makes
219        it possible to use different OBs at different ends of the domain (as
220        with EXF)
221    o reduce number of exch calls in shap_filt (s2).
222    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
223      truncation level) 4/5 MLAdjust test results (11&12 digits match).
224    
225    checkpoint57t_post
226    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
227    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
228      same truncation, independent of the face number: affects affects several
229      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
230    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
231      note that biharmonic viscosity + no-slip was not tested in any experiment.
232    o fix bug in non-linear free-surf side-drag ; generate new output for
233      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
234    o make mnc honor the writeBinaryPrec flag for most kinds of output
235    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
236    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
237      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
238    o add brackets in multi-terms sum to get same truncation, independent of
239      the face number (manage to get exactly same value of gU,gV at the cs-edge)
240      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
241    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
242      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
243      a maximum grid-scale Reynolds number.  Also, changes all length calculations
244      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
245      Suggested values of viscosity parameters found in mom_calc_visc.
246      Many new viscosity diagnostics available.
247    
248    checkpoint57s_post
249    o Add clearing-house for viscosity calculations, mom_calc_visc and
250      correct numerous bugs in LeithD and Smagorinsky discretizations.  
251      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
252      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
253      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
254      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
255      The Strain-Tension form is now called with useStrainTensonVisc=.true.
256      ViscAhStrain and viscAhTension are now retired.
257    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
258    o In response to JMC's bug report, genmake2 now ignores any soft-links
259      that it finds in the *current* directory when searching for files.
260      Soft-links found in any other source directories will still work as
261      they did before.
262    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
263      a C routine to unlimit the stack size
264    o mnc-ify pkg/aim snapshot vars
265    o mnc-ify pkg/land as requested by Daniel
266    o various changes to mnc including:
267      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
268      - output can now be grouped so that all files within a group
269          change the ITER portion of their names in lock-step together
270      - can now read ("global") PER-FACE (in addition to PER-TILE) files
271          and works with both EXCH1 and EXCH2 (but needs more testing)
272      - writing works for all verification test cases w/ g77 on Linux
273    
274    checkpoint57r_post
275    o make MNC variable initialization happen earlier
276    o add diagnostics for (almost) each term of the momentum Eq.
277    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
278    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
279    o remove MINIMAL_TAVE_OUTPUT option ;
280      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
281    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
282      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
283    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
284    o add time-dependent SST, SSS control
285    o cost terms in ecco/ modularized (new cost_generic.F)
286    o cost_averages routines are modularized (new cost_averagesgeneric.F)
287    o new infrastructure for seaice model vs. obs misfits in seaice/
288      * driver from the_main_loop.F is seaice_cost_driver.F
289      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
290      * gradient check in Exp. 6a of natl_box_adjoint/
291    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
292      (see README file)
293    
294    checkpoint57q_post
295    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
296    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
297      - bug was reported by Jean-Michel and Ian Fenty
298    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
299      update exp. cpl_aim+ocn output.
300    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
301      Needed for high-res. runs with large global files
302      to be able to limit tapelev size
303    o Changed some tests for adjoint:
304      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
305      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
306      * global_ocean.90x40x15/ back to default 3-level checkpointing
307    o Modifications to enable scripted COMMON to MODULE conversion
308      * verification/OpenAD/code/ has necessary scripts and description;
309      * converts, compiles and runs successfully;
310    
311    checkpoint57p_post
312    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
313    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
314      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
315    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
316    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
317      (was already the case for dissipation with mom_vecinv,
318       and also the case for grad.PhiHyd when staggered-timeStep)
319      This will allow to put dissipation out-off the AB time-stepping.
320     Unfortunately, affects truncation error. Update output of exp. that "fails"
321      (cg2d matching number) and leave the others for later: front_relax(10),
322      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
323      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
324    
325    checkpoint57o_post
326    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
327      (2) its ready to be documented during the 20050801 DocFest
328    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
329      for ideal_2D_oce and lab_sea on linux_ia32_g77
330    o set to #undef CTRL_SET_OLD_MAXCVARS_30
331      in global1x1_tot/code_seaice_adj to access indices 32, 33
332      (worth another tag)
333    
334    checkpoint57n_post
335    o adding precip control xx_precip 32
336    o adding swflux control xx_swflux 33
337    o Replacing 10 forcing penalty cost routines by 1 generic.
338    o Implementing partitioning in time-mean and variable adjustment
339      for atmos. state.
340    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
341  o in natl_box_adjoint:  o in natl_box_adjoint:
342    * updated: results_bulk/    * updated exp 1 to 10
343    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
344    o updated global1x1/*_seaice_adj/
345      to incorporate latest changes
346    o enable useSingleCpuIO for mdsio vector routines
347      (applies in particular to tapelev I/O)
348    o removed inefficient K-loop in all active_file*control*.F
349    
350  checkpoint57m_post  checkpoint57m_post
351  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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