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revision 1.1844 by heimbach, Fri Mar 29 23:21:39 2013 UTC revision 1.1907 by jmc, Mon Aug 5 17:41:43 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 verification/isomip, pkg/shelfic and OpenAD:  checkpoint64l (2013/08/05)
8    o model/src:
9      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
10      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
11        when using TAF but only if using OpenAD.
12    o pkg/mom_common+fluxform+vecinv:
13      - always set horiz. viscosity arrays to background value before calling
14        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
15        only when using variable horiz. viscosity (useVariableVisc=T);
16      - simplify mom_vecinv.F (only 1 block for momViscosity).
17    o pkg/mom_common: variable horiz. viscosity in NH code
18      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
19        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
20      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
21        useBiharmonicVisc & useVariableVisc.
22      - fix old bug (already in 1rst implementation of variable horizontal viscosity
23        in calc_gw.F, version 1.27, 2006/06/20):
24        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
25        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
26      - change background horiz viscosity in vertical momentum (gW) to always be
27        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
28        any type of variable viscosity, e.g., viscAh/4Grid)
29      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
30        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
31        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
32        default viscAh,viscA4 is zero).
33    o model/src:
34      - extend length of drC & recip_drC from Nr to Nr+1.
35    o Divided Adjoint (DIVA) with MPI:
36      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
37      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
38        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
39    
40    checkpoint64k (2013/07/23)
41    o tools/OAD_support:
42      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
43        and remove it from genmake2.
44    o tools/build_options:
45      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
46        MPI_HEADER_FILES list (let genmake2 find the missing headers)
47    o verification/halfpipe_streamice:
48      - change to driving stress formulation; update both Fwd & AD output.
49    o tools/genmake2 and Divided Adjoint with MPI:
50      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
51      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
52      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
53        Makefile, which is set by genmake2, and check which mpi-headers are needed.
54        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
55      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
56    o testreport:
57      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
58        perform additional runs (number of additional runs is "add_DIVA_runs" taken
59        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
60    o verification/lab_sea (AD test):
61      - change to test Divided Adjoint Run in this set-up (both standard AD test
62        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
63    o pkg atm_ & ocn_compon_interf:
64      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
65        staggerTimeStep implementation) and disable (retired) corresponding
66        parameter.
67    o pkg/offline:
68      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
69      - add S/R OFFLINE_CHECK to print offline parameter summary
70        and stop if loading a file that is not used;
71      - enable to calculate GMRedi tensor, KPP mixing and convective index
72        when the corresponding file(s) is/are not specified (but pkg is used).
73      - comment out resetting of monitorFreq (to endTime) since it still useful
74        for monitoring CFL numbers and checking offline fields.
75    o OpenAD:
76      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
77        smaller standard output) and generate new (smaller) output (on baudelaire
78        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
79    o model/src:
80      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
81        (where external_forcing_adjust was called) and change list of arguments;
82      - merge external_forcing_adjust.F into external_forcing_surf.F
83      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
84        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
85        previously in file "balance_relax.F", now removed); remove corresponding
86        arrays in FFIELDS.h.
87      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
88        a hack for getting back surfaceForcingS (loaded from file) when using
89        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
90      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
91        (was getting only 11 digits for AD-grad, due to different truncation
92         error in AD code).
93    
94    checkpoint64j (2013/07/04)
95    o pkg/offline:
96      - to enable the use of other features with pkg offline (e.g., obcs),
97        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
98      - comment out "allowFreezing" (now active) in 2 offline testing exp.
99    o pkg/exf ALLOW_RUNOFTEMP
100      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
101      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
102      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
103    o pkg/atm_phys:
104      - allows to add some damping on uVel,vVel (strength only function of k).
105    o verification, ad-tests:
106      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
107        global_ocean_ebm and offline_exf_seaice.thsice.
108    o verification/halfpipe_streamice:
109      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
110        flux input boundary conditions to be ignored; a fix for this bug changed
111        verification results for forward test.
112      - add adjoint test.
113    o pkg/ptracers:
114      - allow to restart without SOM pickup (resetting SOM to zero).
115    o pkg/gmredi:
116      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
117      - It uses mixing length theory and suppression by steering level effects to
118        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
119        to JPO, for more details).
120      - It also uses the diffusivity to calculate an eddy induced streamfunction
121        based on a PV closure (rather than a buoyancy closure as in GM).
122      - New files added to pkg/gmredi:
123        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
124          induced overturning streamfunction (called from gmredi_calc_tensor)
125        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
126          for use in gmredi_k3d
127        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
128          the eddy diffusivity
129    
130    checkpoint64i (2013/06/18)
131    o pkg/cheapaml:
132      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
133        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
134        with pkg/cheapaml.
135    o utils/python: add subpackage for cubed sphere function, first example is
136        simple cs.pcol to plot 2D fields on a map
137    o pkg/streamice:
138      - This is a new package in MITgcm, which solves dynamic equations for ice
139         sheets and ice streams
140      - At the moment it is independent of atmosphere/ocean dynamics, or any
141        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
142        ed that this will change)
143      - There is a new verification exercise that tests it, halfpipe_streamice,
144        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
145        rectangular embayment
146      - halfpipe_streamice is forward-only for now, will have TAF test soon
147      - for questions, email dgoldber@mit.edu
148    o pkg/thsice:
149      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
150        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
151      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
152         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
153      - allow precip from pkg/cheapaml to make snow over seaice.
154    o pkg/cfc:
155      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
156      - remove atmos CFC 2-D arrays from common bloc (now local variables)
157      - change some hard-coded constant to run time parameter for reading and
158        and interpolating atmospheric CFC ; keep same default as previously.
159      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
160      - put arguments in standard order: myTime, myIter, myThid
161      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
162        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
163      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
164      - new routine to print summary of CFC params and check for consistency.
165    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
166      similar to thsice_advdiff.
167      Note that for the B-grid case the routine parameters uc/vc are overwritten.
168    o pkg/cfc:
169      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
170        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
171      - fix interpolation of atmphspheric CFC between Sorthern and Northern
172        hemisphere value.
173    o pkg/seaice:
174      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
175    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
176                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
177      - requires an additional time level that is stored in the pickup
178      - you can start with AB2 from a pickup without this time level with
179        pickupStrictlyMatch = .false.
180    
181    checkpoint64h (2013/05/26)
182    o pkg/cheapaml:
183      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
184        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
185      - consistent treatment of uWind,vWind location: assume everywhere in
186        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
187        (Note: was already the case for Tair,Qair advection);
188        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
189      - compute diabatic forcing only in the interior (excluding overlap regions)
190      - fill in array "Qsw" (for short-wave heating);
191      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
192        before any update (consistent with MITgcm state var diagnostics);
193      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
194        non periodic ; + adjusted for uWind,vWind (C-grid).
195    o pkg/seaice:
196      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
197        add explicitly pkg/exf in experiments that currently use pkg/seaice.
198      - allows to compile pkg/seaice without pkg/exf.
199    o tools/OAD_support:
200      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
201        of array "ourStepOf" in function rvNextAction (revolve.F90).
202    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
203      - change pkg name (to be used with other atmospheric physics pkg)
204        but by-pass CVS when making the new pkg so that we keep the CVS history.
205    o pkg/offline:
206      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
207        (previously called from pkg/dic_surfforcing_init.F)
208    o model/src:
209      - re-order sequence of calls within packages_init_variables.F, using
210        standard order, except for:
211         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
212         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
213    o new pkg: atm_phys
214      - add entry point and source code (previously in contrib
215          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
216        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
217      - re-order sequence of calls within packages_readparms.F,
218         packages_init_fixed.F and packages_write_pickup.F
219        (but skip packages_init_variables.F because of TAF issues).
220      - update contrib/*/atm_gray/ experiment.
221    o pkg/seaice (ITD code):
222      - simplify and fix the writing of pickup-files for ITD case
223    o pkg/seaice (ITD code):
224      - introduce floe size dependent lateral melt for ITD case;
225      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
226      - update seaice_itd experiment main output.
227    o pkg/thsice:
228      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
229        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
230        changed accordingly pkg/atm2d.
231    
232    checkpoint64g (2013/05/01)
233    o pkg/exf ALLOW_RUNOFTEMP
234      - if defined,  river and glacier runoff temperature can be read-in from
235        runoftempfile; runoftempfile needs to have same format as runofffile
236    o pkg/thsice (& pkg/bulk_force):
237      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
238        for energy content of Precip + RunOff & Evap (like with pkg/exf).
239      - change computation domain to always be the interior (without overlap).
240      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
241    o verification/tutorial_global_oce_biogeo:
242      - add preliminary OpenAD setup (still has problems)
243    o pkg/seaice:
244      - turn some parameters for choosing the convergence criterion of
245        the inexact Newton method (JFNK) into runtime parameters for convenience
246      - clean up seaice_calc_viscosities.F: remove/retire two options for
247        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
248        the results of lab_sea/input because a division has been replaced by
249        a multiplication with the reciprocal (sumNorm)
250      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
251        convergence of solver (changes results, of course), and to test some
252        new features
253    o model/src:
254      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
255      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
256      - move forcing adjustment (balancing surface forcing) in specific S/R
257        where might also be applied exchanges (if needed) to forcing arrays.
258    o pkg/shelfice:
259      - allow to specify the Ice-Shelf mass per unit area (instead of
260        shelficeLoadAnomaly) and do the conversion from one to the other
261      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
262        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
263        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
264        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
265      - update isomip experiment forward output (get machine truncation error
266        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
267    o verification/offline_exf_seaice:
268      revise data.seaice in input.thermo and input_ad and update results accordingly
269        HO = 0.2, SEAICE_areaLossFormula = 2,
270        SEAICE_growMeltByConv = .TRUE.,
271        SEAICE_doOpenWaterMelt = .TRUE.,
272      Improve consistency with input.thsice and fix the spurious 500m ice corners
273    o verification/global_ocean.cs32x15:
274      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
275        in icedyn (thsice+seaice-dyn) test and update output.
276    o verification/offline_exf_seaice:
277      - adjust list of tested variables (with testreport) and update
278        standard test output with better slection of monitored fields.
279    o pkg/cd_code:
280      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
281        experiment lab_sea.hb87
282    o tools/genmake2:
283      - change default makedepend from the system default to tools/xmakedepend:
284        When no makedepend is specified, select tools/xmakedepend it the test pass,
285        otherwise select the system default (if exist and pass the test) or
286        try to build cyrus-makedepend ; stop if none of the 3 works.
287    o pkg/exf & pkg/thsice:
288      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
289        for energy content of Precip + RunOff & Evap. Assumes:
290       1) Rain has same temp as Air.
291       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
292       3) Run-Off comes at the temp of surface water (with same Cp)
293       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
294        put directly into Latent Heat flux & should use water-vapor heat capacity.
295       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
296        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
297    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
298        (compile when SEAICE_ALLOW_JFNK is defined)
299    o pkg/thsice:
300      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
301        implementation): move THSICE_AVE call after the advection (called directly
302        from thsice_do_advect.F).
303    o verification/global_ocean.90x40x15 and OpenAD:
304      New experiment for OpenAD is identical to the one in input_ad except that
305        multiDimAdvection=.FALSE.,
306      There is still an issue with this.
307    o pkg/thsice:
308      - account for ice velocity (ocean relative velocity) in turbulent heat flux
309        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
310        and offline_exf_seaice (main test).
311    
312    checkpoint64f (2013/03/31)
313    o verification/OpenAD:
314      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
315    o verification/isomip, pkg/shelfice and OpenAD:
316    - add OpenAD setup to this exp and make shelfice package work with OpenAD    - add OpenAD setup to this exp and make shelfice package work with OpenAD
317  o verification/offline_exf_seaice: replace adjoint experiment.  o verification/tutorial_global_oce_biogeo:
318      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
319    o verification/offline_exf_seaice:
320      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
321  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
322    - add OpenAD setup to this exp and make ptracers package work with OpenAD    - add OpenAD setup to this exp and make ptracers package work with OpenAD
323  o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean  o pkg/seaice/seaice_evp.F:
324    stress (when the turningAngle is non-zero) over open water to avoid     mask the asymmetric contribution of the ice-ocean stress (when
325    stripes in the EVP-solutions after many EVP-substeps. This does not change     the turningAngle is non-zero) over open water to avoid stripes
326    the verification experiment (because turningAngle=0 in that experiment), but     in the EVP-solutions after many EVP-substeps. This does not change
327    will affect other EVP solutions with turningAngle.ne.0     the verification experiment (because turningAngle=0 in that experiment),
328       but will affect other EVP solutions with turningAngle.ne.0
329  o verification, AD & TLM output:  o verification, AD & TLM output:
330    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
331      additions and multiplications which affect results at machine truncation      additions and multiplications which affect results at machine truncation

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