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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.621 by edhill, Fri Mar 3 18:36:53 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 remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
8  o moved ptracer ctrl index 17 -> 32    include it only where its needed
9    o move balancing of fluxes before the call of external_forcing_surf
10    o seaice:
11      - correct units of turning angles (now they are really in degrees)
12      - move computation of GWATX/Y out of main routine into dynsolver
13      - initialize GWATX/Y in seaice_init
14    o Apply mask on Fresh-Water flux (needed for SSH forcing).
15      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
16    o seaice: add runtime flags for turning angles (default to zero)
17    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
18      and trend from exf forcing and ctrl control adjustments
19    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
20      (since checkpoint57x_post)
21    o change the default rotation period to 86164.s = the Earth rotation
22    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
23      and based on a reference stratification. Tested within hs94.cs-32x32x5.
24    o seaice advection: add code for choosing between the default (2nd order
25      central differences) and multiDim advection schemes provided by
26      pkg/generic_advdiff
27    o seaice:
28      - removed all references to SEAICE_GRID.h fields from
29        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
30        (cubed-sphere configuration will change a little)
31      - grid computations in seaice_init are obsolete now.
32      - cleaned up code a little so that is easier to read (hopefully).
33      - added new (better?) discretizations of default advection and diffusion
34        (turn on with SEAICEuseFluxForm)
35      - replace 1 in 3d global fields by kSurface in growth.F
36      
37    checkpoint58a_post
38    o seaice:
39      - bug fix in advect.F
40    o shelfice:
41      - separate shelfice load anomaly from pload (breaks with time
42        dependent forcing), => introduce constant field shelficeLoadAnomaly.
43        Its default is 0., but it may be computed more cleverly from (unknown)
44        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
45        done offline. A good approximation of the pressure load anomaly is
46        necessary to avoid large initial adjustment processes underneath
47        deep-reaching shelfice.
48      - small fix in ISOMIP shelfice_thermodynamics
49      - add more sophisticated thermodynamics of Hellmer (1989), this is
50        now the default
51      - give a few constants more intuitive names
52    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
53      if bulk formulae are used in long integration (especially EmPmR). Turn
54      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
55      if balancePrintMean, the imbalance that is substracted is printed to
56      STDOUT.
57    o fix bug (typo) in obcs_apply_eta.F
58    o add a new package shelfice which enables us to model the circulation
59      underneath shelf-ice with draughts of hundreds of meters.
60     - works
61     - to do: + include improved thermodynamics
62              + check whether kSurfC (from model/inc/SURFACE.h) can be used
63                instead of new field kTopC
64              + can we use topoFile, Ro_surf and existing code in ini_depth.F
65                instead of new field R_shelfIce and new code in ini_depth.F
66                and ini_mask_etc.F?
67              + adjust vertical mixing schemes?
68    o seaice pkg:
69     - add a cpp-flag to include a simple formula for a salinity dependent
70       freezing point of sea water at the surface
71     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
72       meridional stresses are now different (and hopefully correct)
73    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
74       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
75       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
76    o pkg/diagnostics: add options and parameters for regional-statistics
77       diagnostics ; define regions by reading a region-mask from a file
78       (might add other options later)
79    o pkg/bulk_force:
80     - add option and parameters to use AIM surface-flux formulae.
81     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
82       others forcing fields (defined in PARM05, parameter file "data") are loaded
83       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
84     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
85     - use the right EXCH call for uwind,vwind (to work on CS-grid).
86     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
87       and parameters (note: calcWindStress replaces .NOT.readwindstress).
88     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
89    
90    checkpoint58
91    o add "--embed-source" option to genmake2 which, when the supporting
92      tools can be compiled (as determined by genmake2) will turn on the
93      embed_files package which then embeds the entire MITgcm source code
94      (*.[fFhc] + Makefile) used for the build within the executable
95      - requested by CNH but off by default
96      - adds a paltry <9MB to the mitgcmuv executable in most cases
97      - only writes the output when useEMBEDSRC in eedata is true
98    o clean up 3-dim. relaxation codes:
99      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
100      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
101      * Thanks to Tom Haine for testing!
102    
103    checkpoint57z_post
104    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
105      affects output (@ truncation level) of exp. plume_on_slope ; updated.
106    o fix the pickup behavior for obcs in combination with ptracers
107    o fix a bug in ptracers_external_fields_load
108    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
109      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
110    o transfered surface NH pressure to eta field (if exactConserv).
111    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
112         and update lab_sea output.txt file.
113    o completing 3-dim. relaxation code: additional term
114         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
115      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
116      * At compile time, in "EXF_OPTIONS.h" set
117          #define  ALLOW_CLIMTEMP_RELAXATION
118          #define  ALLOW_CLIMSALT_RELAXATION
119      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
120          tauThetaClimRelax3Dim = 15552000.0,
121          tauSaltClimRelax3Dim  = 15552000.0,
122      * 3 cases:
123          1) Use a constant-in-time 3-dim. field
124          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
125          3) Real-time relax. to time-evolving prescribed field
126    o Adding Laplacian-type smoothness constraint on
127      initial and boundary (forcing) controls (ic, bc)
128      * enable at compile-time via
129        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
130      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
131      * Absolute scale somewhat unclear so far
132      * no area weighting was included since no other cost term does so far
133    
134    checkpoint57y_post
135    First step for a NLFS adjoint
136    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
137    o new init. routines for calc_r_star, calc_surf_dr
138    o still need to deal with ini_masks_etc
139    o testreport seemed happy
140    checkpoint57y_pre
141    
142    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
143    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
144    o add new offset feature to offline pkg (plus minor cleanup)
145    o cfc fixes for final year of integration
146    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
147      be in GCHEM_OPTIONS).
148    
149    checkpoint57x_post
150    o fix testreport Pb in multiple test experiment.
151    o cleanup our namelist syntax in verification:
152      - make it more F95 standards compliant (some work still needed)
153      - allows the vast majority of our tests to work with gfortran
154    o Non-Hydrostatic:
155     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
156     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
157    o Allow to apply AB on T,S rather than on AB(gT,gS):
158     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
159     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
160       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
161     - need a "clever" read_pickup to restart from the other AB formulation
162    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
163    o remove some unused variables (reduces number of compiler warnings)
164    o adjoint
165      * Disable useVariableViscosity for adjoint for time being
166        (there are a number of extensive recomputations)
167      * Initialize certain variables needed for adjoint
168    
169    checkpoint57w_post
170    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
171                 fix the singleCpuIO RS version of MDSWRITEFIELD
172       and add a WARNING if using globalFiles=T with multi-processors.
173    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
174      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
175    o tracer advection scheme:
176      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
177       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
178       was not very convenient).
179      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
180       (further tests needed for the implicit DST & Flux-Limiter schemes).
181    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
182      and sRef for convenience, handy, when you want to initialize
183      ptracers in a large domain with a constant non-zero value. Also,
184      untangle ptracers_init.F a little.
185    
186    checkpoint57v_post
187    o change dome exp. to use variable viscosity in side-drag terms.
188    o remove all the files from the cfc_offline test since they are now
189      incorporated into tutorial_cfc_offline which has been producing
190      identical results for a few days of testing
191    o add new parameter: sideDragFactor to enable half-slip-side BC
192      and change side-drag S/R to use viscosity from mom_calc_visc
193      (can switch back by setting sideDragFactor=0.); affects results at
194      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
195       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
196    o vorticity & strain are now computed without masking, to account for
197      no-slip-side BC in variable viscosity calculation ; mask is applied
198      anyway later on, before computing advection/coriolis terms.
199    o modify exp4 to test new obcs support for reading from external files
200      and for passive tracers
201    o fix behavior of ptracers_monitor when monitor output is written to a
202      netcdf-file; still not independent of monitor.F (writes in the same
203      file).
204    o change default value of tRef (put a uniform, meaningful value for ocean
205      & atmos) and initialize sRef (was missing, as Martin mentioned).
206    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
207      to be proportional to enstrophy dissipation length.  Thus,
208       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
209      This is now consistent with Smagorinsky and with the manual.
210    
211    checkpoint57u_post
212    o OBCS and PTRACERS: add open boundary support for passive tracers
213      - either use homogenous (pseudo) v.Neumann conditions or prescribe
214        OB-values from file; this is not different from the way theta and salinity
215        are treated
216      - however, Orlanski-radiation conditions are not supported, and the model
217        will stop if you use pTracers and Orlanski at the same time.
218      - beefed up the rountine obcs_external_fields_load: now only those open
219        boundary values are overwritten with values from files for which there
220        are really files, otherwise the OB-fields remain untouched. This makes
221        it possible to use different OBs at different ends of the domain (as
222        with EXF)
223    o reduce number of exch calls in shap_filt (s2).
224    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
225      truncation level) 4/5 MLAdjust test results (11&12 digits match).
226    
227    checkpoint57t_post
228    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
229    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
230      same truncation, independent of the face number: affects affects several
231      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
232    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
233      note that biharmonic viscosity + no-slip was not tested in any experiment.
234    o fix bug in non-linear free-surf side-drag ; generate new output for
235      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
236    o make mnc honor the writeBinaryPrec flag for most kinds of output
237    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
238    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
239      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
240    o add brackets in multi-terms sum to get same truncation, independent of
241      the face number (manage to get exactly same value of gU,gV at the cs-edge)
242      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
243    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
244      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
245      a maximum grid-scale Reynolds number.  Also, changes all length calculations
246      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
247      Suggested values of viscosity parameters found in mom_calc_visc.
248      Many new viscosity diagnostics available.
249    
250    checkpoint57s_post
251    o Add clearing-house for viscosity calculations, mom_calc_visc and
252      correct numerous bugs in LeithD and Smagorinsky discretizations.  
253      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
254      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
255      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
256      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
257      The Strain-Tension form is now called with useStrainTensonVisc=.true.
258      ViscAhStrain and viscAhTension are now retired.
259    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
260    o In response to JMC's bug report, genmake2 now ignores any soft-links
261      that it finds in the *current* directory when searching for files.
262      Soft-links found in any other source directories will still work as
263      they did before.
264    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
265      a C routine to unlimit the stack size
266    o mnc-ify pkg/aim snapshot vars
267    o mnc-ify pkg/land as requested by Daniel
268    o various changes to mnc including:
269      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
270      - output can now be grouped so that all files within a group
271          change the ITER portion of their names in lock-step together
272      - can now read ("global") PER-FACE (in addition to PER-TILE) files
273          and works with both EXCH1 and EXCH2 (but needs more testing)
274      - writing works for all verification test cases w/ g77 on Linux
275    
276    checkpoint57r_post
277    o make MNC variable initialization happen earlier
278    o add diagnostics for (almost) each term of the momentum Eq.
279    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
280    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
281    o remove MINIMAL_TAVE_OUTPUT option ;
282      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
283    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
284      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
285    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
286    o add time-dependent SST, SSS control
287    o cost terms in ecco/ modularized (new cost_generic.F)
288    o cost_averages routines are modularized (new cost_averagesgeneric.F)
289    o new infrastructure for seaice model vs. obs misfits in seaice/
290      * driver from the_main_loop.F is seaice_cost_driver.F
291      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
292      * gradient check in Exp. 6a of natl_box_adjoint/
293    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
294      (see README file)
295    
296    checkpoint57q_post
297    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
298    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
299      - bug was reported by Jean-Michel and Ian Fenty
300    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
301      update exp. cpl_aim+ocn output.
302    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
303      Needed for high-res. runs with large global files
304      to be able to limit tapelev size
305    o Changed some tests for adjoint:
306      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
307      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
308      * global_ocean.90x40x15/ back to default 3-level checkpointing
309    o Modifications to enable scripted COMMON to MODULE conversion
310      * verification/OpenAD/code/ has necessary scripts and description;
311      * converts, compiles and runs successfully;
312    
313    checkpoint57p_post
314    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
315    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
316      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
317    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
318    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
319      (was already the case for dissipation with mom_vecinv,
320       and also the case for grad.PhiHyd when staggered-timeStep)
321      This will allow to put dissipation out-off the AB time-stepping.
322     Unfortunately, affects truncation error. Update output of exp. that "fails"
323      (cg2d matching number) and leave the others for later: front_relax(10),
324      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
325      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
326    
327    checkpoint57o_post
328    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
329      (2) its ready to be documented during the 20050801 DocFest
330    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
331      for ideal_2D_oce and lab_sea on linux_ia32_g77
332    o set to #undef CTRL_SET_OLD_MAXCVARS_30
333      in global1x1_tot/code_seaice_adj to access indices 32, 33
334      (worth another tag)
335    
336    checkpoint57n_post
337    o adding precip control xx_precip 32
338    o adding swflux control xx_swflux 33
339    o Replacing 10 forcing penalty cost routines by 1 generic.
340    o Implementing partitioning in time-mean and variable adjustment
341      for atmos. state.
342    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
343  o in natl_box_adjoint:  o in natl_box_adjoint:
344    * updated: results_bulk/    * updated exp 1 to 10
345    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
346    o updated global1x1/*_seaice_adj/
347      to incorporate latest changes
348    o enable useSingleCpuIO for mdsio vector routines
349      (applies in particular to tapelev I/O)
350    o removed inefficient K-loop in all active_file*control*.F
351    
352  checkpoint57m_post  checkpoint57m_post
353  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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