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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.619 by mlosch, Fri Mar 3 07:52:57 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    - correct units of turning angles (now they are really in degrees)
9      - move computation of GWATX/Y out of main routine into dynsolver
10      - initialize GWATX/Y in seaice_init
11    o Apply mask on Fresh-Water flux (needed for SSH forcing).
12      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
13    o seaice: add runtime flags for turning angles (default to zero)
14    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
15      and trend from exf forcing and ctrl control adjustments
16    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
17      (since checkpoint57x_post)
18    o change the default rotation period to 86164.s = the Earth rotation
19    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
20      and based on a reference stratification. Tested within hs94.cs-32x32x5.
21    o seaice advection: add code for choosing between the default (2nd order
22      central differences) and multiDim advection schemes provided by
23      pkg/generic_advdiff
24    o seaice:
25      - removed all references to SEAICE_GRID.h fields from
26        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
27        (cubed-sphere configuration will change a little)
28      - grid computations in seaice_init are obsolete now.
29      - cleaned up code a little so that is easier to read (hopefully).
30      - added new (better?) discretizations of default advection and diffusion
31        (turn on with SEAICEuseFluxForm)
32      - replace 1 in 3d global fields by kSurface in growth.F
33      
34    checkpoint58a_post
35    o seaice:
36      - bug fix in advect.F
37    o shelfice:
38      - separate shelfice load anomaly from pload (breaks with time
39        dependent forcing), => introduce constant field shelficeLoadAnomaly.
40        Its default is 0., but it may be computed more cleverly from (unknown)
41        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
42        done offline. A good approximation of the pressure load anomaly is
43        necessary to avoid large initial adjustment processes underneath
44        deep-reaching shelfice.
45      - small fix in ISOMIP shelfice_thermodynamics
46      - add more sophisticated thermodynamics of Hellmer (1989), this is
47        now the default
48      - give a few constants more intuitive names
49    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
50      if bulk formulae are used in long integration (especially EmPmR). Turn
51      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
52      if balancePrintMean, the imbalance that is substracted is printed to
53      STDOUT.
54    o fix bug (typo) in obcs_apply_eta.F
55    o add a new package shelfice which enables us to model the circulation
56      underneath shelf-ice with draughts of hundreds of meters.
57     - works
58     - to do: + include improved thermodynamics
59              + check whether kSurfC (from model/inc/SURFACE.h) can be used
60                instead of new field kTopC
61              + can we use topoFile, Ro_surf and existing code in ini_depth.F
62                instead of new field R_shelfIce and new code in ini_depth.F
63                and ini_mask_etc.F?
64              + adjust vertical mixing schemes?
65    o seaice pkg:
66     - add a cpp-flag to include a simple formula for a salinity dependent
67       freezing point of sea water at the surface
68     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
69       meridional stresses are now different (and hopefully correct)
70    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
71       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
72       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
73    o pkg/diagnostics: add options and parameters for regional-statistics
74       diagnostics ; define regions by reading a region-mask from a file
75       (might add other options later)
76    o pkg/bulk_force:
77     - add option and parameters to use AIM surface-flux formulae.
78     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
79       others forcing fields (defined in PARM05, parameter file "data") are loaded
80       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
81     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
82     - use the right EXCH call for uwind,vwind (to work on CS-grid).
83     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
84       and parameters (note: calcWindStress replaces .NOT.readwindstress).
85     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
86    
87    checkpoint58
88    o add "--embed-source" option to genmake2 which, when the supporting
89      tools can be compiled (as determined by genmake2) will turn on the
90      embed_files package which then embeds the entire MITgcm source code
91      (*.[fFhc] + Makefile) used for the build within the executable
92      - requested by CNH but off by default
93      - adds a paltry <9MB to the mitgcmuv executable in most cases
94      - only writes the output when useEMBEDSRC in eedata is true
95    o clean up 3-dim. relaxation codes:
96      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
97      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
98      * Thanks to Tom Haine for testing!
99    
100    checkpoint57z_post
101    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
102      affects output (@ truncation level) of exp. plume_on_slope ; updated.
103    o fix the pickup behavior for obcs in combination with ptracers
104    o fix a bug in ptracers_external_fields_load
105    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
106      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
107    o transfered surface NH pressure to eta field (if exactConserv).
108    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
109         and update lab_sea output.txt file.
110    o completing 3-dim. relaxation code: additional term
111         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
112      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
113      * At compile time, in "EXF_OPTIONS.h" set
114          #define  ALLOW_CLIMTEMP_RELAXATION
115          #define  ALLOW_CLIMSALT_RELAXATION
116      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
117          tauThetaClimRelax3Dim = 15552000.0,
118          tauSaltClimRelax3Dim  = 15552000.0,
119      * 3 cases:
120          1) Use a constant-in-time 3-dim. field
121          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
122          3) Real-time relax. to time-evolving prescribed field
123    o Adding Laplacian-type smoothness constraint on
124      initial and boundary (forcing) controls (ic, bc)
125      * enable at compile-time via
126        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
127      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
128      * Absolute scale somewhat unclear so far
129      * no area weighting was included since no other cost term does so far
130    
131    checkpoint57y_post
132    First step for a NLFS adjoint
133    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
134    o new init. routines for calc_r_star, calc_surf_dr
135    o still need to deal with ini_masks_etc
136    o testreport seemed happy
137    checkpoint57y_pre
138    
139    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
140    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
141    o add new offset feature to offline pkg (plus minor cleanup)
142    o cfc fixes for final year of integration
143    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
144      be in GCHEM_OPTIONS).
145    
146    checkpoint57x_post
147    o fix testreport Pb in multiple test experiment.
148    o cleanup our namelist syntax in verification:
149      - make it more F95 standards compliant (some work still needed)
150      - allows the vast majority of our tests to work with gfortran
151    o Non-Hydrostatic:
152     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
153     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
154    o Allow to apply AB on T,S rather than on AB(gT,gS):
155     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
156     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
157       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
158     - need a "clever" read_pickup to restart from the other AB formulation
159    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
160    o remove some unused variables (reduces number of compiler warnings)
161    o adjoint
162      * Disable useVariableViscosity for adjoint for time being
163        (there are a number of extensive recomputations)
164      * Initialize certain variables needed for adjoint
165    
166    checkpoint57w_post
167    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
168                 fix the singleCpuIO RS version of MDSWRITEFIELD
169       and add a WARNING if using globalFiles=T with multi-processors.
170    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
171      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
172    o tracer advection scheme:
173      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
174       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
175       was not very convenient).
176      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
177       (further tests needed for the implicit DST & Flux-Limiter schemes).
178    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
179      and sRef for convenience, handy, when you want to initialize
180      ptracers in a large domain with a constant non-zero value. Also,
181      untangle ptracers_init.F a little.
182    
183    checkpoint57v_post
184    o change dome exp. to use variable viscosity in side-drag terms.
185    o remove all the files from the cfc_offline test since they are now
186      incorporated into tutorial_cfc_offline which has been producing
187      identical results for a few days of testing
188    o add new parameter: sideDragFactor to enable half-slip-side BC
189      and change side-drag S/R to use viscosity from mom_calc_visc
190      (can switch back by setting sideDragFactor=0.); affects results at
191      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
192       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
193    o vorticity & strain are now computed without masking, to account for
194      no-slip-side BC in variable viscosity calculation ; mask is applied
195      anyway later on, before computing advection/coriolis terms.
196    o modify exp4 to test new obcs support for reading from external files
197      and for passive tracers
198    o fix behavior of ptracers_monitor when monitor output is written to a
199      netcdf-file; still not independent of monitor.F (writes in the same
200      file).
201    o change default value of tRef (put a uniform, meaningful value for ocean
202      & atmos) and initialize sRef (was missing, as Martin mentioned).
203    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
204      to be proportional to enstrophy dissipation length.  Thus,
205       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
206      This is now consistent with Smagorinsky and with the manual.
207    
208    checkpoint57u_post
209    o OBCS and PTRACERS: add open boundary support for passive tracers
210      - either use homogenous (pseudo) v.Neumann conditions or prescribe
211        OB-values from file; this is not different from the way theta and salinity
212        are treated
213      - however, Orlanski-radiation conditions are not supported, and the model
214        will stop if you use pTracers and Orlanski at the same time.
215      - beefed up the rountine obcs_external_fields_load: now only those open
216        boundary values are overwritten with values from files for which there
217        are really files, otherwise the OB-fields remain untouched. This makes
218        it possible to use different OBs at different ends of the domain (as
219        with EXF)
220    o reduce number of exch calls in shap_filt (s2).
221    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
222      truncation level) 4/5 MLAdjust test results (11&12 digits match).
223    
224    checkpoint57t_post
225    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
226    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
227      same truncation, independent of the face number: affects affects several
228      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
229    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
230      note that biharmonic viscosity + no-slip was not tested in any experiment.
231    o fix bug in non-linear free-surf side-drag ; generate new output for
232      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
233    o make mnc honor the writeBinaryPrec flag for most kinds of output
234    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
235    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
236      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
237    o add brackets in multi-terms sum to get same truncation, independent of
238      the face number (manage to get exactly same value of gU,gV at the cs-edge)
239      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
240    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
241      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
242      a maximum grid-scale Reynolds number.  Also, changes all length calculations
243      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
244      Suggested values of viscosity parameters found in mom_calc_visc.
245      Many new viscosity diagnostics available.
246    
247    checkpoint57s_post
248    o Add clearing-house for viscosity calculations, mom_calc_visc and
249      correct numerous bugs in LeithD and Smagorinsky discretizations.  
250      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
251      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
252      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
253      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
254      The Strain-Tension form is now called with useStrainTensonVisc=.true.
255      ViscAhStrain and viscAhTension are now retired.
256    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
257    o In response to JMC's bug report, genmake2 now ignores any soft-links
258      that it finds in the *current* directory when searching for files.
259      Soft-links found in any other source directories will still work as
260      they did before.
261    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
262      a C routine to unlimit the stack size
263    o mnc-ify pkg/aim snapshot vars
264    o mnc-ify pkg/land as requested by Daniel
265    o various changes to mnc including:
266      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
267      - output can now be grouped so that all files within a group
268          change the ITER portion of their names in lock-step together
269      - can now read ("global") PER-FACE (in addition to PER-TILE) files
270          and works with both EXCH1 and EXCH2 (but needs more testing)
271      - writing works for all verification test cases w/ g77 on Linux
272    
273    checkpoint57r_post
274    o make MNC variable initialization happen earlier
275    o add diagnostics for (almost) each term of the momentum Eq.
276    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
277    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
278    o remove MINIMAL_TAVE_OUTPUT option ;
279      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
280    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
281      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
282    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
283    o add time-dependent SST, SSS control
284    o cost terms in ecco/ modularized (new cost_generic.F)
285    o cost_averages routines are modularized (new cost_averagesgeneric.F)
286    o new infrastructure for seaice model vs. obs misfits in seaice/
287      * driver from the_main_loop.F is seaice_cost_driver.F
288      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
289      * gradient check in Exp. 6a of natl_box_adjoint/
290    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
291      (see README file)
292    
293    checkpoint57q_post
294    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
295    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
296      - bug was reported by Jean-Michel and Ian Fenty
297    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
298      update exp. cpl_aim+ocn output.
299    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
300      Needed for high-res. runs with large global files
301      to be able to limit tapelev size
302    o Changed some tests for adjoint:
303      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
304      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
305      * global_ocean.90x40x15/ back to default 3-level checkpointing
306    o Modifications to enable scripted COMMON to MODULE conversion
307      * verification/OpenAD/code/ has necessary scripts and description;
308      * converts, compiles and runs successfully;
309    
310    checkpoint57p_post
311    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
312    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
313      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
314    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
315    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
316      (was already the case for dissipation with mom_vecinv,
317       and also the case for grad.PhiHyd when staggered-timeStep)
318      This will allow to put dissipation out-off the AB time-stepping.
319     Unfortunately, affects truncation error. Update output of exp. that "fails"
320      (cg2d matching number) and leave the others for later: front_relax(10),
321      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
322      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
323    
324    checkpoint57o_post
325    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
326      (2) its ready to be documented during the 20050801 DocFest
327    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
328      for ideal_2D_oce and lab_sea on linux_ia32_g77
329    o set to #undef CTRL_SET_OLD_MAXCVARS_30
330      in global1x1_tot/code_seaice_adj to access indices 32, 33
331      (worth another tag)
332    
333    checkpoint57n_post
334    o adding precip control xx_precip 32
335    o adding swflux control xx_swflux 33
336    o Replacing 10 forcing penalty cost routines by 1 generic.
337    o Implementing partitioning in time-mean and variable adjustment
338      for atmos. state.
339    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
340  o in natl_box_adjoint:  o in natl_box_adjoint:
341    * updated: results_bulk/    * updated exp 1 to 10
342    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
343    o updated global1x1/*_seaice_adj/
344      to incorporate latest changes
345    o enable useSingleCpuIO for mdsio vector routines
346      (applies in particular to tapelev I/O)
347    o removed inefficient K-loop in all active_file*control*.F
348    
349  checkpoint57m_post  checkpoint57m_post
350  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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