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revision 1.1807 by mlosch, Wed Jan 16 21:20:56 2013 UTC revision 1.1869 by jmc, Fri May 17 21:04:32 2013 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/seaice: add a line search option to the JFNK solver  o tools/OAD_support:
8      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
9        of array "ourStepOf" in function rvNextAction (revolve.F90).
10    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
11      - change pkg name (to be used with other atmospheric physics pkg)
12        but by-pass CVS when making the new pkg so that we keep the CVS history.
13    o pkg/offline:
14      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
15        (previously called from pkg/dic_surfforcing_init.F)
16    o model/src:
17      - re-order sequence of calls within packages_init_variables.F, using
18        standard order, except for:
19         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
20         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
21    o new pkg: atm_phys
22      - add entry point and source code (previously in contrib
23          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
24        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
25      - re-order sequence of calls within packages_readparms.F,
26         packages_init_fixed.F and packages_write_pickup.F
27        (but skip packages_init_variables.F because of TAF issues).
28      - update contrib/*/atm_gray/ experiment.
29    o pkg/seaice (ITD code):
30      - simplify and fix the writing of pickup-files for ITD case
31    o pkg/seaice (ITD code):
32      - introduce floe size dependent lateral melt for ITD case;
33      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
34      - update seaice_itd experiment main output.
35    o pkg/thsice:
36      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
37        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
38        changed accordingly pkg/atm2d.
39    
40    checkpoint64g (2013/05/01)
41    o pkg/exf ALLOW_RUNOFTEMP
42      - if defined,  river and glacier runoff temperature can be read-in from
43        runoftempfile; runoftempfile needs to have same format as runofffile
44    o pkg/thsice (& pkg/bulk_force):
45      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
46        for energy content of Precip + RunOff & Evap (like with pkg/exf).
47      - change computation domain to always be the interior (without overlap).
48      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
49    o verification/tutorial_global_oce_biogeo:
50      - add preliminary OpenAD setup (still has problems)
51    o pkg/seaice:
52      - turn some parameters for choosing the convergence criterion of
53        the inexact Newton method (JFNK) into runtime parameters for convenience
54      - clean up seaice_calc_viscosities.F: remove/retire two options for
55        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
56        the results of lab_sea/input because a division has been replaced by
57        a multiplication with the reciprocal (sumNorm)
58      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
59        convergence of solver (changes results, of course), and to test some
60        new features
61    o model/src:
62      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
63      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
64      - move forcing adjustment (balancing surface forcing) in specific S/R
65        where might also be applied exchanges (if needed) to forcing arrays.
66    o pkg/shelfice:
67      - allow to specify the Ice-Shelf mass per unit area (instead of
68        shelficeLoadAnomaly) and do the conversion from one to the other
69      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
70        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
71        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
72        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
73      - update isomip experiment forward output (get machine truncation error
74        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
75    o verification/offline_exf_seaice:
76      revise data.seaice in input.thermo and input_ad and update results accordingly
77        HO = 0.2, SEAICE_areaLossFormula = 2,
78        SEAICE_growMeltByConv = .TRUE.,
79        SEAICE_doOpenWaterMelt = .TRUE.,
80      Improve consistency with input.thsice and fix the spurious 500m ice corners
81    o verification/global_ocean.cs32x15:
82      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
83        in icedyn (thsice+seaice-dyn) test and update output.
84    o verification/offline_exf_seaice:
85      - adjust list of tested variables (with testreport) and update
86        standard test output with better slection of monitored fields.
87    o pkg/cd_code:
88      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
89        experiment lab_sea.hb87
90    o tools/genmake2:
91      - change default makedepend from the system default to tools/xmakedepend:
92        When no makedepend is specified, select tools/xmakedepend it the test pass,
93        otherwise select the system default (if exist and pass the test) or
94        try to build cyrus-makedepend ; stop if none of the 3 works.
95    o pkg/exf & pkg/thsice:
96      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
97        for energy content of Precip + RunOff & Evap. Assumes:
98       1) Rain has same temp as Air.
99       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
100       3) Run-Off comes at the temp of surface water (with same Cp)
101       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
102        put directly into Latent Heat flux & should use water-vapor heat capacity.
103       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
104        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
105    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
106        (compile when SEAICE_ALLOW_JFNK is defined)
107    o pkg/thsice:
108      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
109        implementation): move THSICE_AVE call after the advection (called directly
110        from thsice_do_advect.F).
111    o verification/global_ocean.90x40x15 and OpenAD:
112      New experiment for OpenAD is identical to the one in input_ad except that
113        multiDimAdvection=.FALSE.,
114      There is still an issue with this.
115    o pkg/thsice:
116      - account for ice velocity (ocean relative velocity) in turbulent heat flux
117        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
118        and offline_exf_seaice (main test).
119    
120    checkpoint64f (2013/03/31)
121    o verification/OpenAD:
122      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
123    o verification/isomip, pkg/shelfice and OpenAD:
124      - add OpenAD setup to this exp and make shelfice package work with OpenAD
125    o verification/tutorial_global_oce_biogeo:
126      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
127    o verification/offline_exf_seaice:
128      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
129    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
130      - add OpenAD setup to this exp and make ptracers package work with OpenAD
131    o pkg/seaice/seaice_evp.F:
132       mask the asymmetric contribution of the ice-ocean stress (when
133       the turningAngle is non-zero) over open water to avoid stripes
134       in the EVP-solutions after many EVP-substeps. This does not change
135       the verification experiment (because turningAngle=0 in that experiment),
136       but will affect other EVP solutions with turningAngle.ne.0
137    o verification, AD & TLM output:
138      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
139        additions and multiplications which affect results at machine truncation
140        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
141        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
142        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
143        digits of matching.
144    o pkg/seaice:
145       modify lsr-algorithm so that it vectorizes AND converges by using a
146       "zebra" method: split vector loop into two with step size 2; this
147       solves a general convergence problem for the JFNK solver on a vector
148       computer. It has the potential to even improve convergence for
149       non-vector machines, but it does change the results so it is turned
150       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
151       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
152    
153    checkpoint64e (2013/03/05)
154    o pkg/ecco and several verification experiments:
155       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
156       from ecco package, and revert to unified routine in model/src/
157       Adjust verification experiments accordingly, especially gloal_oce_llc90
158       Should conclude long-standing work by Gael to reconsile the_main_loop with
159       ECCO and will enable OpenAD's revolve loop in ECCO setup.
160    o pkg/generic_advdiff:
161      - implement compressible flow method for multi-dim advection (similar to
162        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
163        TAF generates many recomputations) to use it; no yet coded with implicit
164        vertical advection.
165      - change experiment advect_cs (new output) and advect_xy (same output)
166        to test compressible flow multi-dim advection.
167    o pkg/generic_advdiff:
168      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
169        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
170    o pkg/seaice:
171      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
172        bug affects two verification experiments (lab_sea and lab_sea.hb87),
173        recover old (wrong) results by setting noSlipFac = 2. in
174        seaice_calc_strainrates.F;
175      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
176      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
177        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
178      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
179    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
180      - new subroutines seaice_lsr_tridiagu/v
181      - introduce loop bounds i/jmin/max to be able to use a restricted
182        additive Schwarz method, but not used for now.
183      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
184      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
185    o OpenAD support
186       Reorganize S/R call for overall time-stepping loop to facilitate
187       OpenAD revolve loop replacement
188       (new S/R main_do_loop.F)
189    o model/src:
190      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
191      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
192        ADAMS_BASHFORTH2.
193    o pkg/cheapaml:
194      - add new parameter (default=F, same as before) to disable full domain
195        (including land) periodicity in X & Y dir.
196      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
197        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
198        into single S/R CHEAPAML_TIMESTEP.
199    
200    checkpoint64d (2013/02/17)
201    o pkg/monitor (angular momentum):
202      - do not add Eta contribution to the total AM if using rigid-lid;
203      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
204      - horizontal discretisation: compute Zonal wind contribution separately for
205        each component (instead of from cell centered averaged) and use the 4
206        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
207      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
208        FreeSurf) if using vectorInvariant momentum.
209    o model/src (horizontal grid):
210      - move initialisation of all horizontal grid arrays to null value
211        from specific horizontal grid S/R to main S/R INI_GRID;
212      - add 2 new arrays to project model C-grid velocity on to zonal direction
213        (similar to AngleCosC & -AngleSinC but at U and V point location) and
214        compute them in S/R CALC_GRID_ANGLES.
215    o pkg/seaice: replace a hard coded parameter by a runtime parameter
216        SEAICE_JFNK_tolIter
217    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
218        preconditioner for JFNK (run LSR into the overlaps as far as possible,
219        i.e OLx/y-2, but overwrite the solution in the overlaps)
220      - extend loop range in seaice_calc_viscosity
221      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
222      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
223      - slightly modify loops in tridiagonal solver lsr-preconditioner
224      - by default remove the extra exchange in seaice_preconditioner with a
225        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
226      - modify offline_exf_seaice so that old results without RAS are reproduced
227        for output.dyn_jfnk.txt
228      in seaice_fgmres.F (unrelated to RAS)
229      - add a cpp-flag option for a re-ordered mapping (potentially more
230        efficient), but because this changes the results, turn it off by
231        default
232      - replace the save statement by local common blocks
233    o utils/matlab:
234      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
235      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
236        instead of local script "load_cs.m".
237    o pkg/seaice:
238      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
239        to the scalarProductMetric and the unrolling. By chance this does not
240        change the verification experiment, because of the particular domain
241        decomposition
242    o pkg/diagnostics:
243      - change default missing_value from UNSET_RL to -999.
244    o pkg/layers: improve vectorization of layers_fluxcalc.F
245      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
246        time spent in this routine by more than a factor of 3 on an NEC-SX8
247      - step 2: replace search algorithm by a bisection algorithm found in
248        Press et al. Numerical Recipes in Fortran. This algorithm can be
249        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
250        For now, use this algorithm only for TARGET_NEC_SX defined.
251      - moved the search algorithm into a separate subroutine, that is kept
252        within the same file for automatic inlining.
253      - modified catching potential errors
254    o pkg/ecco:
255      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
256    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
257      - modifications for ALLOW_GENTIM2D_CONTROL
258      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
259      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
260      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
261      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
262    o model/src:
263      - account for moist thermodynamics in (dry) potential temperature equation;
264        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
265        and cpl_aim+ocn.
266      - also switch to standard compiler (gfortran, was using ifort previously)
267        for fizhi-cs experiments reference output.
268    o pkg/ctrl:
269      - 1st step toward generic time-varying control variable (2D) via CPP option
270        ALLOW_GENTIM2D_CONTROL
271      - note new namelist ctrl_nml_genarr in data.ctrl
272    o verification/global_ocean.cs32x15:
273      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
274        thsice calling sequence and update "output.icedyn.txt" output file.
275    o pkg/ptracers:
276      - from Ryan A.: code to allow to restart a tracer at regular time interval
277        specifying a reset frequency and a reset-phase (for each tracers).
278    o pkg/thsice:
279      - implement new sequence of calls for thsice+seaice:
280          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
281          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
282      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
283        in CPP_OPTIONS.h) to recover old sequence;
284      - update diagnostics for Intermediate State thsice diagnostics: now filled
285        just before advection (instead of just after advection in old sequence);
286      - update output of experiment offline_exf_seaice (standard test);
287      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
288        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
289    o pkg/aim_v23:
290      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
291      - use standard pkg/mdsio routines to read & write CO2 pickup file;
292      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
293      - Implement new sequence of calls for seaice advection (with thsice and
294        seaice diffusion): do ice advection after ice-Thermodynamic (previously
295        was done before); change aim_do_physics.F (split the bi,bj loops block);
296      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
297    o pkg/thsice:
298      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
299        where just seaice diffusion is used without seaice-dynamics.
300    
301    checkpoint64c (2013/01/18)
302    o pkg/seaice:
303      - add a parameter JFNKres_tFac that can replace JFNKres_t
304        (= JFNKres_tFac*JFNKresidual before JFNK solver)
305      - add a line search option to the JFNK solver
306      - move update of u/vIce and computation of initial residual into a separate
307        routine (same file); makes the code a little easier to read (?)
308      - the line search requires computation of the residual and for some reason
309        I cannot do the update of u/vIce at the beginning of the Newton loop
310        without changing the results, so we move computation of the new residual
311        also to the end of the Newton loop, even without the line search
312  o pkg/mdsio:  o pkg/mdsio:
313    - write missing value (corresponding to undefined array value) to meta files;    - write missing value (corresponding to undefined array value) to meta files;
314      skip this if missing value is one (UNSET_RL would be a better value for the      skip this if missing value is one (UNSET_RL would be a better value for the
315      case of undefined missing value but it's current the default missing-value);      case of undefined missing value but it's current the default missing-value);
316      Also update mdsio_read_meta.F (reading timeInterval & missing-value).      Also update mdsio_read_meta.F (reading timeInterval & missing-value).
317  o pkg/exf & thsice:  o pkg/exf & thsice:
318    - for diagnostics purpose, fill-up and update Qsw array (+ fill the diagnostics)    - for diagnostics purpose, fill-up and update Qsw array (+ fill the
319      even when SHORTWAVE_HEATING is #undef;      diagnostics) even when SHORTWAVE_HEATING is #undef;
320  o verification/cfc_example:  o verification/cfc_example:
321    - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to illustrate    - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
322      how to use it).      illustrate how to use it).
323  o verification/offline_exf_seaice:  o verification/offline_exf_seaice:
324    in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing    in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
325      files to only one time-record.      files to only one time-record.
326    in input.thermo: narrow the 2 bands of low initial ice-concentration near    in input.thermo: narrow the 2 bands of low initial ice-concentration near
327      N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for      N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
328      snapshot output; same mcPheePiston value as in thsice with surf-current=0.2m/s.      snapshot output; same mcPheePiston value as in thsice with
329        surf-current=0.2m/s.
330    in input.thsice: similar set-up as in input.thermo (channel with same seaice    in input.thsice: similar set-up as in input.thermo (channel with same seaice
331      initial conditions).      initial conditions).
332  o verification/cfc_example:  o verification/cfc_example:

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