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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.613 by mlosch, Thu Feb 16 10:42:31 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 advection: add code for choosing between the default (2nd order
8  o moved ptracer ctrl index 17 -> 32    central differences) and multiDim advection schemes provided by
9      pkg/generic_advdiff
10    o seaice:
11      - removed all references to SEAICE_GRID.h fields from
12        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
13        (cubed-sphere configuration will change a little)
14      - grid computations in seaice_init are obsolete now.
15      - cleaned up code a little so that is easier to read (hopefully).
16      - added new (better?) discretizations of default advection and diffusion
17        (turn on with SEAICEuseFluxForm)
18      - replace 1 in 3d global fields by kSurface in growth.F
19      
20    checkpoint58a_post
21    o seaice:
22      - bug fix in advect.F
23    o shelfice:
24      - separate shelfice load anomaly from pload (breaks with time
25        dependent forcing), => introduce constant field shelficeLoadAnomaly.
26        Its default is 0., but it may be computed more cleverly from (unknown)
27        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
28        done offline. A good approximation of the pressure load anomaly is
29        necessary to avoid large initial adjustment processes underneath
30        deep-reaching shelfice.
31      - small fix in ISOMIP shelfice_thermodynamics
32      - add more sophisticated thermodynamics of Hellmer (1989), this is
33        now the default
34      - give a few constants more intuitive names
35    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
36      if bulk formulae are used in long integration (especially EmPmR). Turn
37      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
38      if balancePrintMean, the imbalance that is substracted is printed to
39      STDOUT.
40    o fix bug (typo) in obcs_apply_eta.F
41    o add a new package shelfice which enables us to model the circulation
42      underneath shelf-ice with draughts of hundreds of meters.
43     - works
44     - to do: + include improved thermodynamics
45              + check whether kSurfC (from model/inc/SURFACE.h) can be used
46                instead of new field kTopC
47              + can we use topoFile, Ro_surf and existing code in ini_depth.F
48                instead of new field R_shelfIce and new code in ini_depth.F
49                and ini_mask_etc.F?
50              + adjust vertical mixing schemes?
51    o seaice pkg:
52     - add a cpp-flag to include a simple formula for a salinity dependent
53       freezing point of sea water at the surface
54     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
55       meridional stresses are now different (and hopefully correct)
56    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
57       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
58       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
59    o pkg/diagnostics: add options and parameters for regional-statistics
60       diagnostics ; define regions by reading a region-mask from a file
61       (might add other options later)
62    o pkg/bulk_force:
63     - add option and parameters to use AIM surface-flux formulae.
64     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
65       others forcing fields (defined in PARM05, parameter file "data") are loaded
66       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
67     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
68     - use the right EXCH call for uwind,vwind (to work on CS-grid).
69     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
70       and parameters (note: calcWindStress replaces .NOT.readwindstress).
71     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
72    
73    checkpoint58
74    o add "--embed-source" option to genmake2 which, when the supporting
75      tools can be compiled (as determined by genmake2) will turn on the
76      embed_files package which then embeds the entire MITgcm source code
77      (*.[fFhc] + Makefile) used for the build within the executable
78      - requested by CNH but off by default
79      - adds a paltry <9MB to the mitgcmuv executable in most cases
80      - only writes the output when useEMBEDSRC in eedata is true
81    o clean up 3-dim. relaxation codes:
82      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
83      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
84      * Thanks to Tom Haine for testing!
85    
86    checkpoint57z_post
87    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
88      affects output (@ truncation level) of exp. plume_on_slope ; updated.
89    o fix the pickup behavior for obcs in combination with ptracers
90    o fix a bug in ptracers_external_fields_load
91    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
92      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
93    o transfered surface NH pressure to eta field (if exactConserv).
94    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
95         and update lab_sea output.txt file.
96    o completing 3-dim. relaxation code: additional term
97         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
98      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
99      * At compile time, in "EXF_OPTIONS.h" set
100          #define  ALLOW_CLIMTEMP_RELAXATION
101          #define  ALLOW_CLIMSALT_RELAXATION
102      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
103          tauThetaClimRelax3Dim = 15552000.0,
104          tauSaltClimRelax3Dim  = 15552000.0,
105      * 3 cases:
106          1) Use a constant-in-time 3-dim. field
107          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
108          3) Real-time relax. to time-evolving prescribed field
109    o Adding Laplacian-type smoothness constraint on
110      initial and boundary (forcing) controls (ic, bc)
111      * enable at compile-time via
112        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
113      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
114      * Absolute scale somewhat unclear so far
115      * no area weighting was included since no other cost term does so far
116    
117    checkpoint57y_post
118    First step for a NLFS adjoint
119    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
120    o new init. routines for calc_r_star, calc_surf_dr
121    o still need to deal with ini_masks_etc
122    o testreport seemed happy
123    checkpoint57y_pre
124    
125    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
126    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
127    o add new offset feature to offline pkg (plus minor cleanup)
128    o cfc fixes for final year of integration
129    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
130      be in GCHEM_OPTIONS).
131    
132    checkpoint57x_post
133    o fix testreport Pb in multiple test experiment.
134    o cleanup our namelist syntax in verification:
135      - make it more F95 standards compliant (some work still needed)
136      - allows the vast majority of our tests to work with gfortran
137    o Non-Hydrostatic:
138     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
139     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
140    o Allow to apply AB on T,S rather than on AB(gT,gS):
141     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
142     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
143       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
144     - need a "clever" read_pickup to restart from the other AB formulation
145    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
146    o remove some unused variables (reduces number of compiler warnings)
147    o adjoint
148      * Disable useVariableViscosity for adjoint for time being
149        (there are a number of extensive recomputations)
150      * Initialize certain variables needed for adjoint
151    
152    checkpoint57w_post
153    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
154                 fix the singleCpuIO RS version of MDSWRITEFIELD
155       and add a WARNING if using globalFiles=T with multi-processors.
156    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
157      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
158    o tracer advection scheme:
159      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
160       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
161       was not very convenient).
162      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
163       (further tests needed for the implicit DST & Flux-Limiter schemes).
164    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
165      and sRef for convenience, handy, when you want to initialize
166      ptracers in a large domain with a constant non-zero value. Also,
167      untangle ptracers_init.F a little.
168    
169    checkpoint57v_post
170    o change dome exp. to use variable viscosity in side-drag terms.
171    o remove all the files from the cfc_offline test since they are now
172      incorporated into tutorial_cfc_offline which has been producing
173      identical results for a few days of testing
174    o add new parameter: sideDragFactor to enable half-slip-side BC
175      and change side-drag S/R to use viscosity from mom_calc_visc
176      (can switch back by setting sideDragFactor=0.); affects results at
177      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
178       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
179    o vorticity & strain are now computed without masking, to account for
180      no-slip-side BC in variable viscosity calculation ; mask is applied
181      anyway later on, before computing advection/coriolis terms.
182    o modify exp4 to test new obcs support for reading from external files
183      and for passive tracers
184    o fix behavior of ptracers_monitor when monitor output is written to a
185      netcdf-file; still not independent of monitor.F (writes in the same
186      file).
187    o change default value of tRef (put a uniform, meaningful value for ocean
188      & atmos) and initialize sRef (was missing, as Martin mentioned).
189    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
190      to be proportional to enstrophy dissipation length.  Thus,
191       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
192      This is now consistent with Smagorinsky and with the manual.
193    
194    checkpoint57u_post
195    o OBCS and PTRACERS: add open boundary support for passive tracers
196      - either use homogenous (pseudo) v.Neumann conditions or prescribe
197        OB-values from file; this is not different from the way theta and salinity
198        are treated
199      - however, Orlanski-radiation conditions are not supported, and the model
200        will stop if you use pTracers and Orlanski at the same time.
201      - beefed up the rountine obcs_external_fields_load: now only those open
202        boundary values are overwritten with values from files for which there
203        are really files, otherwise the OB-fields remain untouched. This makes
204        it possible to use different OBs at different ends of the domain (as
205        with EXF)
206    o reduce number of exch calls in shap_filt (s2).
207    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
208      truncation level) 4/5 MLAdjust test results (11&12 digits match).
209    
210    checkpoint57t_post
211    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
212    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
213      same truncation, independent of the face number: affects affects several
214      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
215    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
216      note that biharmonic viscosity + no-slip was not tested in any experiment.
217    o fix bug in non-linear free-surf side-drag ; generate new output for
218      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
219    o make mnc honor the writeBinaryPrec flag for most kinds of output
220    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
221    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
222      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
223    o add brackets in multi-terms sum to get same truncation, independent of
224      the face number (manage to get exactly same value of gU,gV at the cs-edge)
225      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
226    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
227      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
228      a maximum grid-scale Reynolds number.  Also, changes all length calculations
229      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
230      Suggested values of viscosity parameters found in mom_calc_visc.
231      Many new viscosity diagnostics available.
232    
233    checkpoint57s_post
234    o Add clearing-house for viscosity calculations, mom_calc_visc and
235      correct numerous bugs in LeithD and Smagorinsky discretizations.  
236      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
237      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
238      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
239      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
240      The Strain-Tension form is now called with useStrainTensonVisc=.true.
241      ViscAhStrain and viscAhTension are now retired.
242    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
243    o In response to JMC's bug report, genmake2 now ignores any soft-links
244      that it finds in the *current* directory when searching for files.
245      Soft-links found in any other source directories will still work as
246      they did before.
247    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
248      a C routine to unlimit the stack size
249    o mnc-ify pkg/aim snapshot vars
250    o mnc-ify pkg/land as requested by Daniel
251    o various changes to mnc including:
252      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
253      - output can now be grouped so that all files within a group
254          change the ITER portion of their names in lock-step together
255      - can now read ("global") PER-FACE (in addition to PER-TILE) files
256          and works with both EXCH1 and EXCH2 (but needs more testing)
257      - writing works for all verification test cases w/ g77 on Linux
258    
259    checkpoint57r_post
260    o make MNC variable initialization happen earlier
261    o add diagnostics for (almost) each term of the momentum Eq.
262    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
263    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
264    o remove MINIMAL_TAVE_OUTPUT option ;
265      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
266    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
267      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
268    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
269    o add time-dependent SST, SSS control
270    o cost terms in ecco/ modularized (new cost_generic.F)
271    o cost_averages routines are modularized (new cost_averagesgeneric.F)
272    o new infrastructure for seaice model vs. obs misfits in seaice/
273      * driver from the_main_loop.F is seaice_cost_driver.F
274      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
275      * gradient check in Exp. 6a of natl_box_adjoint/
276    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
277      (see README file)
278    
279    checkpoint57q_post
280    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
281    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
282      - bug was reported by Jean-Michel and Ian Fenty
283    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
284      update exp. cpl_aim+ocn output.
285    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
286      Needed for high-res. runs with large global files
287      to be able to limit tapelev size
288    o Changed some tests for adjoint:
289      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
290      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
291      * global_ocean.90x40x15/ back to default 3-level checkpointing
292    o Modifications to enable scripted COMMON to MODULE conversion
293      * verification/OpenAD/code/ has necessary scripts and description;
294      * converts, compiles and runs successfully;
295    
296    checkpoint57p_post
297    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
298    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
299      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
300    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
301    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
302      (was already the case for dissipation with mom_vecinv,
303       and also the case for grad.PhiHyd when staggered-timeStep)
304      This will allow to put dissipation out-off the AB time-stepping.
305     Unfortunately, affects truncation error. Update output of exp. that "fails"
306      (cg2d matching number) and leave the others for later: front_relax(10),
307      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
308      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
309    
310    checkpoint57o_post
311    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
312      (2) its ready to be documented during the 20050801 DocFest
313    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
314      for ideal_2D_oce and lab_sea on linux_ia32_g77
315    o set to #undef CTRL_SET_OLD_MAXCVARS_30
316      in global1x1_tot/code_seaice_adj to access indices 32, 33
317      (worth another tag)
318    
319    checkpoint57n_post
320    o adding precip control xx_precip 32
321    o adding swflux control xx_swflux 33
322    o Replacing 10 forcing penalty cost routines by 1 generic.
323    o Implementing partitioning in time-mean and variable adjustment
324      for atmos. state.
325    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
326  o in natl_box_adjoint:  o in natl_box_adjoint:
327    * updated: results_bulk/    * updated exp 1 to 10
328    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
329    o updated global1x1/*_seaice_adj/
330      to incorporate latest changes
331    o enable useSingleCpuIO for mdsio vector routines
332      (applies in particular to tapelev I/O)
333    o removed inefficient K-loop in all active_file*control*.F
334    
335  checkpoint57m_post  checkpoint57m_post
336  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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