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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.622 by mlosch, Mon Mar 6 13:18:16 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   - add c-grid version of the dynamic solver:
9       + three new routines that are the c-grid substitute lsr, dynsolver
10         and ostres
11       + put a few fields that were local to dynsolver into global common
12         blocks, so that I can move the computation of stresses etc into
13         seaice_lsr (saves coding but may break the adjoint).
14     - replace more hardwired parameters by runtime parameters
15     - add ice masks that mask the rhs of the implicit solvers where there
16       is no ice (commented out in seaice_dynsolver, because i am not sure
17       if this works properly), eventually this should replace the clipping
18       of ice velocities in seaice_dynsolver to +/-40cm/s.
19    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
20      include it only where its needed
21    o move balancing of fluxes before the call of external_forcing_surf
22    o seaice:
23      - correct units of turning angles (now they are really in degrees)
24      - move computation of GWATX/Y out of main routine into dynsolver
25      - initialize GWATX/Y in seaice_init
26    o Apply mask on Fresh-Water flux (needed for SSH forcing).
27      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
28    o seaice: add runtime flags for turning angles (default to zero)
29    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
30      and trend from exf forcing and ctrl control adjustments
31    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
32      (since checkpoint57x_post)
33    o change the default rotation period to 86164.s = the Earth rotation
34    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
35      and based on a reference stratification. Tested within hs94.cs-32x32x5.
36    o seaice advection: add code for choosing between the default (2nd order
37      central differences) and multiDim advection schemes provided by
38      pkg/generic_advdiff
39    o seaice:
40      - removed all references to SEAICE_GRID.h fields from
41        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
42        (cubed-sphere configuration will change a little)
43      - grid computations in seaice_init are obsolete now.
44      - cleaned up code a little so that is easier to read (hopefully).
45      - added new (better?) discretizations of default advection and diffusion
46        (turn on with SEAICEuseFluxForm)
47      - replace 1 in 3d global fields by kSurface in growth.F
48      
49    checkpoint58a_post
50    o seaice:
51      - bug fix in advect.F
52    o shelfice:
53      - separate shelfice load anomaly from pload (breaks with time
54        dependent forcing), => introduce constant field shelficeLoadAnomaly.
55        Its default is 0., but it may be computed more cleverly from (unknown)
56        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
57        done offline. A good approximation of the pressure load anomaly is
58        necessary to avoid large initial adjustment processes underneath
59        deep-reaching shelfice.
60      - small fix in ISOMIP shelfice_thermodynamics
61      - add more sophisticated thermodynamics of Hellmer (1989), this is
62        now the default
63      - give a few constants more intuitive names
64    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
65      if bulk formulae are used in long integration (especially EmPmR). Turn
66      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
67      if balancePrintMean, the imbalance that is substracted is printed to
68      STDOUT.
69    o fix bug (typo) in obcs_apply_eta.F
70    o add a new package shelfice which enables us to model the circulation
71      underneath shelf-ice with draughts of hundreds of meters.
72     - works
73     - to do: + include improved thermodynamics
74              + check whether kSurfC (from model/inc/SURFACE.h) can be used
75                instead of new field kTopC
76              + can we use topoFile, Ro_surf and existing code in ini_depth.F
77                instead of new field R_shelfIce and new code in ini_depth.F
78                and ini_mask_etc.F?
79              + adjust vertical mixing schemes?
80    o seaice pkg:
81     - add a cpp-flag to include a simple formula for a salinity dependent
82       freezing point of sea water at the surface
83     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
84       meridional stresses are now different (and hopefully correct)
85    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
86       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
87       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
88    o pkg/diagnostics: add options and parameters for regional-statistics
89       diagnostics ; define regions by reading a region-mask from a file
90       (might add other options later)
91    o pkg/bulk_force:
92     - add option and parameters to use AIM surface-flux formulae.
93     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
94       others forcing fields (defined in PARM05, parameter file "data") are loaded
95       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
96     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
97     - use the right EXCH call for uwind,vwind (to work on CS-grid).
98     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
99       and parameters (note: calcWindStress replaces .NOT.readwindstress).
100     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
101    
102    checkpoint58
103    o add "--embed-source" option to genmake2 which, when the supporting
104      tools can be compiled (as determined by genmake2) will turn on the
105      embed_files package which then embeds the entire MITgcm source code
106      (*.[fFhc] + Makefile) used for the build within the executable
107      - requested by CNH but off by default
108      - adds a paltry <9MB to the mitgcmuv executable in most cases
109      - only writes the output when useEMBEDSRC in eedata is true
110    o clean up 3-dim. relaxation codes:
111      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
112      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
113      * Thanks to Tom Haine for testing!
114    
115    checkpoint57z_post
116    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
117      affects output (@ truncation level) of exp. plume_on_slope ; updated.
118    o fix the pickup behavior for obcs in combination with ptracers
119    o fix a bug in ptracers_external_fields_load
120    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
121      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
122    o transfered surface NH pressure to eta field (if exactConserv).
123    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
124         and update lab_sea output.txt file.
125    o completing 3-dim. relaxation code: additional term
126         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
127      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
128      * At compile time, in "EXF_OPTIONS.h" set
129          #define  ALLOW_CLIMTEMP_RELAXATION
130          #define  ALLOW_CLIMSALT_RELAXATION
131      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
132          tauThetaClimRelax3Dim = 15552000.0,
133          tauSaltClimRelax3Dim  = 15552000.0,
134      * 3 cases:
135          1) Use a constant-in-time 3-dim. field
136          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
137          3) Real-time relax. to time-evolving prescribed field
138    o Adding Laplacian-type smoothness constraint on
139      initial and boundary (forcing) controls (ic, bc)
140      * enable at compile-time via
141        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
142      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
143      * Absolute scale somewhat unclear so far
144      * no area weighting was included since no other cost term does so far
145    
146    checkpoint57y_post
147    First step for a NLFS adjoint
148    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
149    o new init. routines for calc_r_star, calc_surf_dr
150    o still need to deal with ini_masks_etc
151    o testreport seemed happy
152    checkpoint57y_pre
153    
154    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
155    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
156    o add new offset feature to offline pkg (plus minor cleanup)
157    o cfc fixes for final year of integration
158    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
159      be in GCHEM_OPTIONS).
160    
161    checkpoint57x_post
162    o fix testreport Pb in multiple test experiment.
163    o cleanup our namelist syntax in verification:
164      - make it more F95 standards compliant (some work still needed)
165      - allows the vast majority of our tests to work with gfortran
166    o Non-Hydrostatic:
167     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
168     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
169    o Allow to apply AB on T,S rather than on AB(gT,gS):
170     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
171     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
172       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
173     - need a "clever" read_pickup to restart from the other AB formulation
174    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
175    o remove some unused variables (reduces number of compiler warnings)
176    o adjoint
177      * Disable useVariableViscosity for adjoint for time being
178        (there are a number of extensive recomputations)
179      * Initialize certain variables needed for adjoint
180    
181    checkpoint57w_post
182    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
183                 fix the singleCpuIO RS version of MDSWRITEFIELD
184       and add a WARNING if using globalFiles=T with multi-processors.
185    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
186      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
187    o tracer advection scheme:
188      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
189       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
190       was not very convenient).
191      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
192       (further tests needed for the implicit DST & Flux-Limiter schemes).
193    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
194      and sRef for convenience, handy, when you want to initialize
195      ptracers in a large domain with a constant non-zero value. Also,
196      untangle ptracers_init.F a little.
197    
198    checkpoint57v_post
199    o change dome exp. to use variable viscosity in side-drag terms.
200    o remove all the files from the cfc_offline test since they are now
201      incorporated into tutorial_cfc_offline which has been producing
202      identical results for a few days of testing
203    o add new parameter: sideDragFactor to enable half-slip-side BC
204      and change side-drag S/R to use viscosity from mom_calc_visc
205      (can switch back by setting sideDragFactor=0.); affects results at
206      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
207       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
208    o vorticity & strain are now computed without masking, to account for
209      no-slip-side BC in variable viscosity calculation ; mask is applied
210      anyway later on, before computing advection/coriolis terms.
211    o modify exp4 to test new obcs support for reading from external files
212      and for passive tracers
213    o fix behavior of ptracers_monitor when monitor output is written to a
214      netcdf-file; still not independent of monitor.F (writes in the same
215      file).
216    o change default value of tRef (put a uniform, meaningful value for ocean
217      & atmos) and initialize sRef (was missing, as Martin mentioned).
218    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
219      to be proportional to enstrophy dissipation length.  Thus,
220       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
221      This is now consistent with Smagorinsky and with the manual.
222    
223    checkpoint57u_post
224    o OBCS and PTRACERS: add open boundary support for passive tracers
225      - either use homogenous (pseudo) v.Neumann conditions or prescribe
226        OB-values from file; this is not different from the way theta and salinity
227        are treated
228      - however, Orlanski-radiation conditions are not supported, and the model
229        will stop if you use pTracers and Orlanski at the same time.
230      - beefed up the rountine obcs_external_fields_load: now only those open
231        boundary values are overwritten with values from files for which there
232        are really files, otherwise the OB-fields remain untouched. This makes
233        it possible to use different OBs at different ends of the domain (as
234        with EXF)
235    o reduce number of exch calls in shap_filt (s2).
236    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
237      truncation level) 4/5 MLAdjust test results (11&12 digits match).
238    
239    checkpoint57t_post
240    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
241    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
242      same truncation, independent of the face number: affects affects several
243      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
244    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
245      note that biharmonic viscosity + no-slip was not tested in any experiment.
246    o fix bug in non-linear free-surf side-drag ; generate new output for
247      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
248    o make mnc honor the writeBinaryPrec flag for most kinds of output
249    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
250    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
251      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
252    o add brackets in multi-terms sum to get same truncation, independent of
253      the face number (manage to get exactly same value of gU,gV at the cs-edge)
254      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
255    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
256      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
257      a maximum grid-scale Reynolds number.  Also, changes all length calculations
258      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
259      Suggested values of viscosity parameters found in mom_calc_visc.
260      Many new viscosity diagnostics available.
261    
262    checkpoint57s_post
263    o Add clearing-house for viscosity calculations, mom_calc_visc and
264      correct numerous bugs in LeithD and Smagorinsky discretizations.  
265      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
266      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
267      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
268      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
269      The Strain-Tension form is now called with useStrainTensonVisc=.true.
270      ViscAhStrain and viscAhTension are now retired.
271    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
272    o In response to JMC's bug report, genmake2 now ignores any soft-links
273      that it finds in the *current* directory when searching for files.
274      Soft-links found in any other source directories will still work as
275      they did before.
276    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
277      a C routine to unlimit the stack size
278    o mnc-ify pkg/aim snapshot vars
279    o mnc-ify pkg/land as requested by Daniel
280    o various changes to mnc including:
281      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
282      - output can now be grouped so that all files within a group
283          change the ITER portion of their names in lock-step together
284      - can now read ("global") PER-FACE (in addition to PER-TILE) files
285          and works with both EXCH1 and EXCH2 (but needs more testing)
286      - writing works for all verification test cases w/ g77 on Linux
287    
288    checkpoint57r_post
289    o make MNC variable initialization happen earlier
290    o add diagnostics for (almost) each term of the momentum Eq.
291    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
292    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
293    o remove MINIMAL_TAVE_OUTPUT option ;
294      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
295    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
296      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
297    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
298    o add time-dependent SST, SSS control
299    o cost terms in ecco/ modularized (new cost_generic.F)
300    o cost_averages routines are modularized (new cost_averagesgeneric.F)
301    o new infrastructure for seaice model vs. obs misfits in seaice/
302      * driver from the_main_loop.F is seaice_cost_driver.F
303      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
304      * gradient check in Exp. 6a of natl_box_adjoint/
305    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
306      (see README file)
307    
308    checkpoint57q_post
309    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
310    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
311      - bug was reported by Jean-Michel and Ian Fenty
312    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
313      update exp. cpl_aim+ocn output.
314    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
315      Needed for high-res. runs with large global files
316      to be able to limit tapelev size
317    o Changed some tests for adjoint:
318      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
319      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
320      * global_ocean.90x40x15/ back to default 3-level checkpointing
321    o Modifications to enable scripted COMMON to MODULE conversion
322      * verification/OpenAD/code/ has necessary scripts and description;
323      * converts, compiles and runs successfully;
324    
325    checkpoint57p_post
326    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
327    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
328      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
329    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
330    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
331      (was already the case for dissipation with mom_vecinv,
332       and also the case for grad.PhiHyd when staggered-timeStep)
333      This will allow to put dissipation out-off the AB time-stepping.
334     Unfortunately, affects truncation error. Update output of exp. that "fails"
335      (cg2d matching number) and leave the others for later: front_relax(10),
336      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
337      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
338    
339    checkpoint57o_post
340    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
341      (2) its ready to be documented during the 20050801 DocFest
342    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
343      for ideal_2D_oce and lab_sea on linux_ia32_g77
344    o set to #undef CTRL_SET_OLD_MAXCVARS_30
345      in global1x1_tot/code_seaice_adj to access indices 32, 33
346      (worth another tag)
347    
348    checkpoint57n_post
349    o adding precip control xx_precip 32
350    o adding swflux control xx_swflux 33
351    o Replacing 10 forcing penalty cost routines by 1 generic.
352    o Implementing partitioning in time-mean and variable adjustment
353      for atmos. state.
354    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
355  o in natl_box_adjoint:  o in natl_box_adjoint:
356    * updated: results_bulk/    * updated exp 1 to 10
357    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
358    o updated global1x1/*_seaice_adj/
359      to incorporate latest changes
360    o enable useSingleCpuIO for mdsio vector routines
361      (applies in particular to tapelev I/O)
362    o removed inefficient K-loop in all active_file*control*.F
363    
364  checkpoint57m_post  checkpoint57m_post
365  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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