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revision 1.525 by edhill, Sat Jul 30 00:58:40 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 move balancing of fluxes before the call of external_forcing_surf
8    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  o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
327    (2) its ready to be documented during the 20050801 DocFest    (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  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    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  checkpoint57n_post
335  o adding precip control xx_precip 32  o adding precip control xx_precip 32

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