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revision 1.1504 by heimbach, Mon Sep 26 18:24:26 2011 UTC revision 1.1538 by mlosch, Tue Nov 29 17:43:32 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/obcs/obcs_calc_stevens.F:
8      - join some loops to reduce number of if-statements
9      - fix a bug in code for northern and southern boundaries.
10    o pkg/seaice/seaice_init_varia.F
11      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
12        caused zero ice-velocities for the B-grid code
13    o pkg/seaice/seaice_init_fixed.F
14      - fix a bug in the initialisation of the second metric terms
15        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
16      - this affects all seaice configurations with useCurviLinearGrid = .true.
17        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
18        = .true. (default)
19      - the only verification experiment affected is global_ocean.cs32x15:
20        icedyn, seaice, and seaice_dynmix (AD)
21    o pkg/thsice/thsice_diagnostics_state.F
22      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
23        not contain garbage that can lead to surprises in diagstats_calc.F
24    o model/src:
25      - move bi,bj loops inside INTEGR_CONTINUITY ;
26      - call INTEGR_CONTINUITY directly from forward_step.F
27        (previously called from momentum_correction_step.F)
28      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
29        forward_step.F and pkg/ecco/the_main_loop.F
30    o model/src/do_oceanic_phys.F:
31      - reset addMass to zero only if useICEFRONT ;
32      - separated k-loop for rhoInSitu calculation ;
33      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
34        and at constant T,S (= WdRHOdP);
35      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
36        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
37        transport of locally-referenced potential density);
38        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
39    o gluemnc:
40      - replace ncrcat with ncks when adding variables to *.glob.nc
41      - change the way variables without record dimensions are handled so that
42        files that have variables with and without record variables can be glued:
43        add a record dimension with a new unique name to be able to differentiate
44        between variable with and without a-prior record dimensions. Remove
45        this record dimension before adding the variable to the *.glob.nc file.
46        This procedure automatically works also for grid.*.nc files that do not
47        have any record dimension.
48    o verification/cpl_aim+ocn:
49      - generate new reference output on baudelaire (gfortran, mpich2) (previously
50        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
51    o pkg/obcs/obcs_calc_stevens.F:
52      - add code for northern and southern boundaries.
53      - reorder some loops to save some operations and so that drFBar can be scalar
54    o model/src:
55      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
56        truncation) and add diagnostics for Adams-Bashforth tendency increment.
57      - update test-exp. AD output:
58        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
59      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
60        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
61        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
62        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
63        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
64        tutorial_plume_on_slope.
65    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
66      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
67      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
68      does not even come with an F77 compiler anymore, this should not be
69      a limitation
70    
71    checkpoint63e (2011/11/06)
72    o pkg/seaice adjoint of LSR:
73      - substantially rework STORE dirs.
74      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
75        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
76        and only perform SOLV_MAX_FIXED adjoint iters.
77        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
78        always goes to same record, meaning that the last forward field will be
79        the one used in the adjoint - an approximation.
80      - now produces non-zero LSR-related gradients, and acceptable gradients for
81        An's zonal (x-z) test case (to be checked in)
82      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
83        (but these are screwed up by the thermodynamics in the first place);
84        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
85        output_adm.txt also reflects changes to seaice_lsr
86      - global_ocean.cs32x15:
87        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
88          (output_adm.seaice.txt was updated)
89        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
90          (output_adm.seaice_dynmix.txt)
91    o test-exp. exp4+stevens:
92      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
93    o pkg/seaice (lsr solver):
94      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
95        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
96      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
97      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
98        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
99      - compute (with new S/R) and print initial (+ free-driff sol. if available)
100        and final residual of linearised system.
101    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
102      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
103    o pkg/obcs: Stevens BCs (still only for east and west)
104      - fix Stevens BCs by using intermediate velocities of previous
105        time step as "baroclinic" contribution rather velocity of one grid cell
106        inside the boundaries; more consistent but makes the entire treatment
107        more complicated, requires new pickup files and two new S/Rs:
108        obcs_copy_uv_n and obcs_save_uv_n
109        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
110        (undefined by default)
111      - silently move computation of some grid factors into separate loops to
112        save some recomputations
113      - add a hack for non-linear free surface
114      - add a verification experiment to exp4 that tests this code
115    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
116    
117    checkpoint63d (2011/10/25)
118    o pkg/obcs + seaice-dynamics:
119      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
120        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
121        values (consistent with an implicit method).
122      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
123        return to older implementation (same results as before); note that none of
124        the "experimental" OBCS_SEAICE options are implemented in the new version.
125      - switch test exp. seaice_obcs to use new version (update output).
126    o pkg/seaice:
127      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
128      - add parenthesis in Water-Ice drag calculations (evp & lsr);
129      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
130        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
131      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
132        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
133    o pkg/layers:
134      - Include potential density as new coordinate (Thanks to David Munday)
135    o pkg/dic:
136      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
137        carbonate computation/output to CALC_PCO2_APPROX
138    o pkg/generic_advdiff
139      - make TAF generate code that vectorizes:
140        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
141    o model/src:
142      - improve vectorization also for adjoint code of
143        solve_tridiagonal and solve_pentadiagonal. As this requires up to
144        5 new 3D-fields, this code is only turned on for the combination of
145        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
146        for singular matrix check (only for TARGET_NEC_SX).
147      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
148        ALLOW_AUTODIFF. This flag now needs to be set outside of
149        solve_tri/pentadiagonal.F
150    o pkg/exf:
151      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
152        optional namelist EXF_NML_OBCS).
153      - add many debug-print (to trace down where pkg/cal error msg comes from)
154    o pkg/mom_vecinv/mom_vi_hdissip.F
155      - rearrange loops so that vectorization is improved and in particular
156        the adjoint routine vectorizes. The code is a little longer now, but I
157        think easier to read.
158        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
159    o pkg/seaice:
160      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
161    o pkg/exch2:
162      - alternative code (without tile x tile matrix) for cumulated (global) sum;
163        used as default; keep using matrix version in adjustment.cs-32x32x1.
164    o tools/build_options:
165      - after merging some MPI and/or multi-threads specific optfiles so that
166        the modified default optfile support both built (using genmake2 -mpi
167        for the MPI built, using genmake2 -omp for OpenMP built),
168        move now obsolete optfiles to tools/build_options/unsupported/
169       (add copy of email sent to support list in doc/optfiles_changes.txt)
170    
171    checkpoint63c (2011/09/28)
172    o pkg/ebm:
173      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
174        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
175  o pkg/seaice (SItracer pickup)  o pkg/seaice (SItracer pickup)
176  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
177    To be done:    To be done:
178    - thorough testing of missing fields in S/R seaice_read_pickup    - thorough testing of missing fields in S/R seaice_read_pickup
179    - thorough matching between generic tracers and specific fields used    - thorough matching between generic tracers and specific fields used
180      (e.g. volume-weighted age, area-weighted age, salinity, ...)      (e.g. volume-weighted age, area-weighted age, salinity, ...)
181    o pkg/grdchk:
182      - all procs calculate and print finite-difference gradient (for testreport)
183      - change description output used by testreport;
184      - AD testing: also compare and report Finite-difference gradient;
185        => update all output_adm*.txt
186    o test exp. global_ocean_ebm:
187      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
188        and turn on exactConserve; update (fwd) output.
189  o pkg/seaice (LSR):  o pkg/seaice (LSR):
190    - print to STDOUT number of solver iterations at SEAICE_monFreq interval.    - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
191    - modify solver to deal cleanly with u/v switch at face edges (CS-grid):    - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
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