4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/seaice: |
8 |
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- remove code that resets useThSice in S/R seaice_readparms and |
9 |
|
replace by a warning in S/R seaice_check |
10 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
11 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
12 |
|
SEAICE_ITD is defined) |
13 |
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|
14 |
|
checkpoint64x (2014/05/24) |
15 |
|
o verification/lab_sea: |
16 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
17 |
|
- un-do the update after putting back local recip_Cp in few places. |
18 |
|
o pkg/salt_plume: modifications by An Nguyen: |
19 |
|
- add capability to do brine rejection (salt-plume) as function of |
20 |
|
volume+tracers (instead of only salinity tracer). |
21 |
|
- conserve volume by exchanging volume from each kLev to above to |
22 |
|
accommodate in-coming brine volume |
23 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
24 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
25 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
26 |
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- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
27 |
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- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
28 |
|
in East/West Arctic. |
29 |
|
o pkg/sbo: |
30 |
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- incorporate modifications from Katherine Quinn to enable the use of sbo |
31 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
32 |
|
output for future testreport verification (unfinished). |
33 |
|
o pkg/atm_phys: |
34 |
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- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
35 |
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skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
36 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
37 |
|
o pkg/seaice |
38 |
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seaice_calc_ice_strength.F: modify expression to avoid divisions |
39 |
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(affects truncation) |
40 |
|
seaice_do_ridging.F: clean up the insectarium |
41 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
42 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
43 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
44 |
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- add some debugging information and error messages (warnings) |
45 |
|
o model/src: modifications relatd to atmosphere p*: |
46 |
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- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
47 |
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- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
48 |
|
of vertical profile tRef in geopotential background and anomaly. |
49 |
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- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
50 |
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and pkg/atm_phys. |
51 |
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- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
52 |
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fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
53 |
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o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
54 |
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o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
55 |
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not used right now, but can be used in BGC packages to fix conservation. |
56 |
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o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
57 |
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other packages too. |
58 |
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o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
59 |
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SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
60 |
|
o model/src: |
61 |
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- since we have several heat capacity (even in model/src), define "recip_Cp" |
62 |
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as local variable (no longer in common block) to avoid any confusion. |
63 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
64 |
|
o pkg/exf: |
65 |
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- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
66 |
|
air density as function of air Temp, Humidity and atm pressure. |
67 |
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|
68 |
|
checkpoint64w (2014/05/02) |
69 |
|
o verification: |
70 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
71 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
72 |
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code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
73 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
74 |
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(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
75 |
|
o model/src: for atmosphere in p* coords: |
76 |
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- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
77 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
78 |
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but not yet activated. |
79 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
80 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
81 |
|
- this changes the results (but not for any verification experiment, because |
82 |
|
none tests this), but avoids having an extra field in the restart files |
83 |
|
o pkg/seaice: remove global variable TICE (not needed) |
84 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
85 |
|
seaice_diagnostics_state) |
86 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
87 |
|
- use specific read/write routines for reading and writing individual leves |
88 |
|
of a multilevel field |
89 |
|
o pkg/ctrl & model/inc: |
90 |
|
- move additional anomaly fields of control vars (related to options: |
91 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
92 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
93 |
|
o pkg/seaice: some small modifications to the ridging code |
94 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
95 |
|
seaice_growth |
96 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
97 |
|
computed only in one place and compute it in the same way as in |
98 |
|
seaice_growth |
99 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
100 |
|
point exceptions over land |
101 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
102 |
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- move most of "PART 1" of S/R seaice_growth into a new and separate |
103 |
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S/R seaice_reg_ridge that will both regularize the state variable after |
104 |
|
advection call the actual ridging routine; |
105 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
106 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
107 |
|
- remove ridging code from seaice_advdiff |
108 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
109 |
|
more readable (this is probably subjective) |
110 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
111 |
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conditions in the correct category |
112 |
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- finally: add new ridging routine for ITD code |
113 |
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|
114 |
|
checkpoint64v (2014/04/11) |
115 |
|
o pkg/ecco: |
116 |
|
- add runtime parameters mdt[start,end]date[1,2] |
117 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
118 |
|
o pkg/seaice: |
119 |
|
- make deltaC a global variable, so that it can be used in ridging code |
120 |
|
- first step towards ridging: introduce new routines that compute |
121 |
|
ice strength based on ridging parameters |
122 |
|
- add diagnostic for HSNOWITD |
123 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
124 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
125 |
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- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
126 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
127 |
|
o verification/hs94.1x64x5: |
128 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
129 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
130 |
|
o autodiff: |
131 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
132 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
133 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
134 |
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- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
135 |
|
which are specific to TAF/TAMC). |
136 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
137 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
138 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
139 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
140 |
|
building mitgcmuv_ad (make adAll). |
141 |
|
o pkg/ecco: |
142 |
|
- cost_gencost_seaicev4.F: |
143 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
144 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
145 |
|
- add stop statement if old names siv4-[sst,vol] are used |
146 |
|
- add snapshots + cost reports for atmospheric longwave |
147 |
|
- remove factor 0.1 in front of wtau[u,v] |
148 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
149 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
150 |
|
o pkg/atm_phys: |
151 |
|
- add some diagnostics for Short-wave and for convection S/R. |
152 |
|
o pkg/seaice/seaice_growth: |
153 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
154 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
155 |
|
- rearrange loop order for better vector code in the same code block |
156 |
|
- rewrite the floeDiameter formula to have fewer divisions |
157 |
|
- (miraculously) none of this changes the results of seaice_itd |
158 |
|
o pkg/smooth: |
159 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
160 |
|
o pkg/salt_plume: |
161 |
|
- salt_plume_frac.F: |
162 |
|
clean up local param names |
163 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
164 |
|
o pkg/rw: |
165 |
|
- add RS version of S/R READ_MFLDS_LEV. |
166 |
|
o pkg/streamice: |
167 |
|
- fix the restart test by writing/reading pickup_streamice files. |
168 |
|
o pkg/seaice: |
169 |
|
- refine checks for jfnk-related parameters |
170 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
171 |
|
is no IMEX code to avoid confusion and surprises |
172 |
|
|
173 |
|
checkpoint64u (2014/03/07) |
174 |
|
o verification/MLAdjust: |
175 |
|
- rename secondary test suffix: |
176 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
177 |
|
0.leithD -> AhFlxF + switch to flux-form |
178 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
179 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
180 |
|
o pkg/mom_vecinv: |
181 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
182 |
|
to be before mom_calc_visc.F) |
183 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
184 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
185 |
|
this is simpler for the adjoint and for diagnostics. |
186 |
|
o model/src + pkg/momentum: |
187 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
188 |
|
(e.g., to add "thin-wall" where it is =1). |
189 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
190 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
191 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
192 |
|
coords; not working with CD-scheme neither. |
193 |
|
o pkg/seaice: |
194 |
|
- rename recently introduced parameters from (wrong name) AB to |
195 |
|
BDF (backward difference time discretisation) |
196 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
197 |
|
o tools/adjoint_options: |
198 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
199 |
|
|
200 |
|
checkpoint64t (2014/02/01) |
201 |
|
o pkg/ecco |
202 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
203 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
204 |
|
- replace hard-coded record number and period which only work for monthly |
205 |
|
with read-in runtime param that works for other periods (month,day,year) |
206 |
|
o pkg/thsice |
207 |
|
- corrected store directive fixes thsice adjoint gradient checks |
208 |
|
o genmake2 & testreport: |
209 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
210 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
211 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
212 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
213 |
|
o pkg/shelfice: |
214 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
215 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
216 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
217 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
218 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
219 |
|
o model/src/temp_integrate.F and salt_integrate.F |
220 |
|
- re-include store directives that were removed on Dec 27th. |
221 |
|
o model/src/external_forcing_surf.F |
222 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
223 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
224 |
|
turned off in the adjoint. The resolved issue dated back to July when |
225 |
|
EXTERNAL_FORCING_SURF call was moved. |
226 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
227 |
|
o pkg/exf/exf_check.F |
228 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
229 |
|
- streamline error output |
230 |
|
o pkg/streamice and aim_v23: |
231 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
232 |
|
Apple's /usr/bin/cpp knows what to do: |
233 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
234 |
|
Target: x86_64-apple-darwin13.0.0 |
235 |
|
|
236 |
|
checkpoint64s (2014/01/05) |
237 |
|
o tools/adjoint_options: |
238 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
239 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
240 |
|
o model/src: |
241 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
242 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
243 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
244 |
|
o model/src & pkg/ptracers: |
245 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
246 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
247 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
248 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
249 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
250 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
251 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
252 |
|
for now only implemented for in exf_interp_read.F |
253 |
|
o verification/advect_xy: |
254 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
255 |
|
o momentum diagnostics: |
256 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
257 |
|
- fix typo in diagnostics for momentum tendency from AB. |
258 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
259 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
260 |
|
|
261 |
|
checkpoint64r (2013/12/08) |
262 |
|
o verification/*/results: |
263 |
|
- Update reference output of experiments that were passing with just 13 digits |
264 |
|
(make it easier to detect future changes in results) |
265 |
|
o model/src & pkg/ptracers: |
266 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
267 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
268 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
269 |
|
o coupling interface pkgs: |
270 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
271 |
|
- change the config check to test the agreement of Ocean Depth |
272 |
|
with ATM land/sea mask (instead of ATM orography); |
273 |
|
- send to coupler the number of coupler time-steps to do for this run: |
274 |
|
this allows to check for consistency and don't need anymore to be |
275 |
|
specified in parameter file "data"; |
276 |
|
in coupler: |
277 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
278 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
279 |
|
o pkg/compon_communic: |
280 |
|
- add coupling send/receive for non-tiled integer vector; |
281 |
|
- add S/R to check and stop if any proc has an error (similar to |
282 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
283 |
|
o pkg/exch2: |
284 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
285 |
|
through list of all tiles my proc owns. |
286 |
|
o model/src: |
287 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
288 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
289 |
|
calling S/R); this affects AD results at machine truncation level: |
290 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
291 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
292 |
|
o tools/build_options: |
293 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
294 |
|
o coupling interface pkgs: |
295 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
296 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
297 |
|
to each S/R that needs it; remove un-used variables. |
298 |
|
- change component tile registration (cpl_register.F in both compon_interf |
299 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
300 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
301 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
302 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
303 |
|
a) can now use different tiling between atm & ocn comp. |
304 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
305 |
|
even if using the same tiling between atm & ocn). |
306 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
307 |
|
full land tiles); not yet tested. |
308 |
|
- check for valid mapping from comp. tile to coupler global array |
309 |
|
- improve report of tile registration results to log file. |
310 |
|
o pkg/exch2: |
311 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
312 |
|
tile-registration (CPL_REGISTER); |
313 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
314 |
|
store the local bi,bj indices of each tile; |
315 |
|
- also print bi,bj in local report to log file; |
316 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
317 |
|
Jun 2009 modif of pkg/exch2). |
318 |
|
o testing on baudelaire: |
319 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
320 |
|
get the full set of test done earlier |
321 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
322 |
|
o model/src/thermodynamics.F and routines called from it: |
323 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
324 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
325 |
|
velocity (outp) by adding bolus velocity. |
326 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
327 |
|
mass transport from velocity + lateral grid cell area |
328 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
329 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
330 |
|
in thermodynamics.F |
331 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
332 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
333 |
|
loop). |
334 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
335 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
336 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
337 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
338 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
339 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
340 |
|
tutorial_tracer_adjsens (+ TLM output). |
341 |
|
o tools/OAD_support and (verification/*/) code_oad: |
342 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
343 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
344 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
345 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
346 |
|
o model/src: |
347 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
348 |
|
retired list of parameters (routine FREEZE has been replace by surface |
349 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
350 |
|
o pkg/gmredi: |
351 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
352 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
353 |
|
- update output of FWD experiments: front_relax.bvp, |
354 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
355 |
|
|
356 |
|
checkpoint64q (2013/11/17) |
357 |
|
o verification: |
358 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
359 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
360 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
361 |
|
updating the input pickup_seaice files (previously wrong). |
362 |
|
o pkg/cost: |
363 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
364 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
365 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
366 |
|
cannot be applied to var in common block). |
367 |
|
o allows to get results independent of tile-per-proc setting (if using |
368 |
|
slower GLOBAL_SUM_SEND_RECV option). |
369 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
370 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
371 |
|
forward gradients: update output). |
372 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
373 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
374 |
|
o pkg/mom_common: |
375 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
376 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
377 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
378 |
|
ensure that all field value that are used are set. |
379 |
|
o tutorial_deep_convection (smag3d): |
380 |
|
- add missing scaling in mom_calc_smag_3d.F; |
381 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
382 |
|
o pkg/dic: |
383 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
384 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
385 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
386 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
387 |
|
o eesupp/src & pkg/mdsio: |
388 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
389 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
390 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
391 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
392 |
|
o verification/isomip: |
393 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
394 |
|
o tools/build_options: |
395 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
396 |
|
to get a working restart for all experiments, add "-fp-model source" |
397 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
398 |
|
|
399 |
|
checkpoint64p (2013/10/20) |
400 |
|
o pkg/autodiff: |
401 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
402 |
|
criteria, return to simple (default) tape IO format. |
403 |
|
o pkg/mdsio (+ eesupp/src): |
404 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
405 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
406 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
407 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
408 |
|
template) corresponding to simpler global mapping. |
409 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
410 |
|
to globalFile when parameter globalFiles is set to True. |
411 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
412 |
|
o pkg/autodiff: |
413 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
414 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
415 |
|
missing, just add a STOP if array type do not match. |
416 |
|
o pkg/exf: |
417 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
418 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
419 |
|
and rename array obsSIce to exf_iceFraction. |
420 |
|
o tutorial_deep_convection: |
421 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
422 |
|
for now all in this exp. code dir. |
423 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
424 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
425 |
|
o eesupp/src: |
426 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
427 |
|
very large number of processors did not work with existing set-up |
428 |
|
|
429 |
|
checkpoint64o (2013/09/25) |
430 |
|
o pkg/atm_phys & atm_compon_interf: |
431 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
432 |
|
o tools/build_options: |
433 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
434 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
435 |
|
remove CPP setting (was identical to genmake2 default). |
436 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
437 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
438 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
439 |
|
external forcing via taueddy_external_forcing.F |
440 |
|
- at the moment, it is very experimental and only works with the variable eddy |
441 |
|
diffusivity calculated in gmredi_k3d.F |
442 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
443 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
444 |
|
o testreport (& tools/do_tst_2+2): |
445 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
446 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
447 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
448 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
449 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
450 |
|
o pkg/atm_compon_interf: |
451 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
452 |
|
(which accumalate in time each coupling field) |
453 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
454 |
|
update accordingly + simplify aim_do_physics.F |
455 |
|
|
456 |
|
checkpoint64n (2013/08/26) |
457 |
|
o pkg/bbl: |
458 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
459 |
|
- replaced horizontal and vertical transport parameters with velocities |
460 |
|
- changes results for verification/global_with_exf.yearly |
461 |
|
o verification/halfpipe_streamice: |
462 |
|
- change to matrix construction; update both Fwd & AD output. |
463 |
|
o verification/tutorial_tracer_adjsens: |
464 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
465 |
|
rStar causes problems with OpenAD; update output. |
466 |
|
o tools: |
467 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
468 |
|
to local /tmp disk (but would be easy to move them back); |
469 |
|
- xmakedepend: apply the same switch for temp-files. |
470 |
|
o pkg/offline: |
471 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
472 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
473 |
|
output files) and apply r* scaling at each time-step (function of the time |
474 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
475 |
|
o adjoint with OpenAD: |
476 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
477 |
|
package openad. This package has to be compiled for all runs with OpenAD |
478 |
|
instead of specifying code_oad_all as a modification directory. |
479 |
|
- link the fortran templates from tools/OAD_support to the build directory |
480 |
|
for preprocessing to avoid conflicts between different setups compiled |
481 |
|
simultaneously and simplify cleanup. |
482 |
|
o pkg/exf: |
483 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
484 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
485 |
|
o model/src: |
486 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
487 |
|
(similar to do_fields_blocking_exchanges.F). |
488 |
|
o tools/genmake2: |
489 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
490 |
|
built, will stop if things go wrong with staf). |
491 |
|
- fix target "adobj" (left from TAF version-2 transition) |
492 |
|
o pkg/diagnostics: |
493 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
494 |
|
this replace/extend the use of logical param "settingDiags" (to check |
495 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
496 |
|
New S/R to print error message and stop when pkgStatus is not right. |
497 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
498 |
|
|
499 |
|
checkpoint64m (2013/08/13) |
500 |
|
o model/inc: |
501 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
502 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
503 |
|
o pkg/kpp & aim_v23: |
504 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
505 |
|
o pkg/seaice: |
506 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
507 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
508 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
509 |
|
o eesupp/src: |
510 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
511 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
512 |
|
o switch to TAF version-2: |
513 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
514 |
|
are used in I/O routines of adjoint state and associated common blocks |
515 |
|
that are used in adcommon.h (backward compatible with version-1) |
516 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
517 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
518 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
519 |
|
out except for diva). |
520 |
|
- the major change with TAF version-2 is that both the differentiated |
521 |
|
routines and the forward routines (new) are returned as part of the TAF |
522 |
|
output source code. Update genmake2 accordingly. |
523 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
524 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
525 |
|
output show minor changes (machine truncation level); update the few AD & |
526 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
527 |
|
|
528 |
|
checkpoint64l (2013/08/05) |
529 |
|
o model/src: |
530 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
531 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
532 |
|
when using TAF but only if using OpenAD. |
533 |
|
o pkg/mom_common+fluxform+vecinv: |
534 |
|
- always set horiz. viscosity arrays to background value before calling |
535 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
536 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
537 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
538 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
539 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
540 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
541 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
542 |
|
useBiharmonicVisc & useVariableVisc. |
543 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
544 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
545 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
546 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
547 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
548 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
549 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
550 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
551 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
552 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
553 |
|
default viscAh,viscA4 is zero). |
554 |
|
o model/src: |
555 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
556 |
|
o Divided Adjoint (DIVA) with MPI: |
557 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
558 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
559 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
560 |
|
|
561 |
|
checkpoint64k (2013/07/23) |
562 |
|
o tools/OAD_support: |
563 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
564 |
|
and remove it from genmake2. |
565 |
|
o tools/build_options: |
566 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
567 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
568 |
|
o verification/halfpipe_streamice: |
569 |
|
- change to driving stress formulation; update both Fwd & AD output. |
570 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
571 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
572 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
573 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
574 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
575 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
576 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
577 |
|
o testreport: |
578 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
579 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
580 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
581 |
|
o verification/lab_sea (AD test): |
582 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
583 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
584 |
|
o pkg atm_ & ocn_compon_interf: |
585 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
586 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
587 |
|
parameter. |
588 |
|
o pkg/offline: |
589 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
590 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
591 |
|
and stop if loading a file that is not used; |
592 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
593 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
594 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
595 |
|
for monitoring CFL numbers and checking offline fields. |
596 |
|
o OpenAD: |
597 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
598 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
599 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
600 |
|
o model/src: |
601 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
602 |
|
(where external_forcing_adjust was called) and change list of arguments; |
603 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
604 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
605 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
606 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
607 |
|
arrays in FFIELDS.h. |
608 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
609 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
610 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
611 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
612 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
613 |
|
error in AD code). |
614 |
|
|
615 |
|
checkpoint64j (2013/07/04) |
616 |
|
o pkg/offline: |
617 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
618 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
619 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
620 |
|
o pkg/exf ALLOW_RUNOFTEMP |
621 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
622 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
623 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
624 |
|
o pkg/atm_phys: |
625 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
626 |
|
o verification, ad-tests: |
627 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
628 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
629 |
|
o verification/halfpipe_streamice: |
630 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
631 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
632 |
|
verification results for forward test. |
633 |
|
- add adjoint test. |
634 |
|
o pkg/ptracers: |
635 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
636 |
|
o pkg/gmredi: |
637 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
638 |
|
- It uses mixing length theory and suppression by steering level effects to |
639 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
640 |
|
to JPO, for more details). |
641 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
642 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
643 |
|
- New files added to pkg/gmredi: |
644 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
645 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
646 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
647 |
|
for use in gmredi_k3d |
648 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
649 |
|
the eddy diffusivity |
650 |
|
|
651 |
|
checkpoint64i (2013/06/18) |
652 |
|
o pkg/cheapaml: |
653 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
654 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
655 |
|
with pkg/cheapaml. |
656 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
657 |
|
simple cs.pcol to plot 2D fields on a map |
658 |
|
o pkg/streamice: |
659 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
660 |
|
sheets and ice streams |
661 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
662 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
663 |
|
ed that this will change) |
664 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
665 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
666 |
|
rectangular embayment |
667 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
668 |
|
- for questions, email dgoldber@mit.edu |
669 |
|
o pkg/thsice: |
670 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
671 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
672 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
673 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
674 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
675 |
|
o pkg/cfc: |
676 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
677 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
678 |
|
- change some hard-coded constant to run time parameter for reading and |
679 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
680 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
681 |
|
- put arguments in standard order: myTime, myIter, myThid |
682 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
683 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
684 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
685 |
|
- new routine to print summary of CFC params and check for consistency. |
686 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
687 |
|
similar to thsice_advdiff. |
688 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
689 |
|
o pkg/cfc: |
690 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
691 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
692 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
693 |
|
hemisphere value. |
694 |
|
o pkg/seaice: |
695 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
696 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
697 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
698 |
|
- requires an additional time level that is stored in the pickup |
699 |
|
- you can start with AB2 from a pickup without this time level with |
700 |
|
pickupStrictlyMatch = .false. |
701 |
|
|
702 |
|
checkpoint64h (2013/05/26) |
703 |
|
o pkg/cheapaml: |
704 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
705 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
706 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
707 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
708 |
|
(Note: was already the case for Tair,Qair advection); |
709 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
710 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
711 |
|
- fill in array "Qsw" (for short-wave heating); |
712 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
713 |
|
before any update (consistent with MITgcm state var diagnostics); |
714 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
715 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
716 |
|
o pkg/seaice: |
717 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
718 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
719 |
|
- allows to compile pkg/seaice without pkg/exf. |
720 |
|
o tools/OAD_support: |
721 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
722 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
723 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
724 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
725 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
726 |
|
o pkg/offline: |
727 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
728 |
|
(previously called from pkg/dic_surfforcing_init.F) |
729 |
|
o model/src: |
730 |
|
- re-order sequence of calls within packages_init_variables.F, using |
731 |
|
standard order, except for: |
732 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
733 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
734 |
|
o new pkg: atm_phys |
735 |
|
- add entry point and source code (previously in contrib |
736 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
737 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
738 |
|
- re-order sequence of calls within packages_readparms.F, |
739 |
|
packages_init_fixed.F and packages_write_pickup.F |
740 |
|
(but skip packages_init_variables.F because of TAF issues). |
741 |
|
- update contrib/*/atm_gray/ experiment. |
742 |
|
o pkg/seaice (ITD code): |
743 |
|
- simplify and fix the writing of pickup-files for ITD case |
744 |
|
o pkg/seaice (ITD code): |
745 |
|
- introduce floe size dependent lateral melt for ITD case; |
746 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
747 |
|
- update seaice_itd experiment main output. |
748 |
|
o pkg/thsice: |
749 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
750 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
751 |
|
changed accordingly pkg/atm2d. |
752 |
|
|
753 |
|
checkpoint64g (2013/05/01) |
754 |
|
o pkg/exf ALLOW_RUNOFTEMP |
755 |
|
- if defined, river and glacier runoff temperature can be read-in from |
756 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
757 |
|
o pkg/thsice (& pkg/bulk_force): |
758 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
759 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
760 |
|
- change computation domain to always be the interior (without overlap). |
761 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
762 |
|
o verification/tutorial_global_oce_biogeo: |
763 |
|
- add preliminary OpenAD setup (still has problems) |
764 |
|
o pkg/seaice: |
765 |
|
- turn some parameters for choosing the convergence criterion of |
766 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
767 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
768 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
769 |
|
the results of lab_sea/input because a division has been replaced by |
770 |
|
a multiplication with the reciprocal (sumNorm) |
771 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
772 |
|
convergence of solver (changes results, of course), and to test some |
773 |
|
new features |
774 |
|
o model/src: |
775 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
776 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
777 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
778 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
779 |
|
o pkg/shelfice: |
780 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
781 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
782 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
783 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
784 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
785 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
786 |
|
- update isomip experiment forward output (get machine truncation error |
787 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
788 |
|
o verification/offline_exf_seaice: |
789 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
790 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
791 |
|
SEAICE_growMeltByConv = .TRUE., |
792 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
793 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
794 |
|
o verification/global_ocean.cs32x15: |
795 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
796 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
797 |
|
o verification/offline_exf_seaice: |
798 |
|
- adjust list of tested variables (with testreport) and update |
799 |
|
standard test output with better slection of monitored fields. |
800 |
|
o pkg/cd_code: |
801 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
802 |
|
experiment lab_sea.hb87 |
803 |
|
o tools/genmake2: |
804 |
|
- change default makedepend from the system default to tools/xmakedepend: |
805 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
806 |
|
otherwise select the system default (if exist and pass the test) or |
807 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
808 |
|
o pkg/exf & pkg/thsice: |
809 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
810 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
811 |
|
1) Rain has same temp as Air. |
812 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
813 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
814 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
815 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
816 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
817 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
818 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
819 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
820 |
|
o pkg/thsice: |
821 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
822 |
|
implementation): move THSICE_AVE call after the advection (called directly |
823 |
|
from thsice_do_advect.F). |
824 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
825 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
826 |
|
multiDimAdvection=.FALSE., |
827 |
|
There is still an issue with this. |
828 |
|
o pkg/thsice: |
829 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
830 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
831 |
|
and offline_exf_seaice (main test). |
832 |
|
|
833 |
|
checkpoint64f (2013/03/31) |
834 |
|
o verification/OpenAD: |
835 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
836 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
837 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
838 |
|
o verification/tutorial_global_oce_biogeo: |
839 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
840 |
|
o verification/offline_exf_seaice: |
841 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
842 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
843 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
844 |
|
o pkg/seaice/seaice_evp.F: |
845 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
846 |
|
the turningAngle is non-zero) over open water to avoid stripes |
847 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
848 |
|
the verification experiment (because turningAngle=0 in that experiment), |
849 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
850 |
|
o verification, AD & TLM output: |
851 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
852 |
|
additions and multiplications which affect results at machine truncation |
853 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
854 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
855 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
856 |
|
digits of matching. |
857 |
|
o pkg/seaice: |
858 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
859 |
|
"zebra" method: split vector loop into two with step size 2; this |
860 |
|
solves a general convergence problem for the JFNK solver on a vector |
861 |
|
computer. It has the potential to even improve convergence for |
862 |
|
non-vector machines, but it does change the results so it is turned |
863 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
864 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
865 |
|
|
866 |
|
checkpoint64e (2013/03/05) |
867 |
|
o pkg/ecco and several verification experiments: |
868 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
869 |
|
from ecco package, and revert to unified routine in model/src/ |
870 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
871 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
872 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
873 |
|
o pkg/generic_advdiff: |
874 |
|
- implement compressible flow method for multi-dim advection (similar to |
875 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
876 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
877 |
|
vertical advection. |
878 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
879 |
|
to test compressible flow multi-dim advection. |
880 |
|
o pkg/generic_advdiff: |
881 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
882 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
883 |
|
o pkg/seaice: |
884 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
885 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
886 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
887 |
|
seaice_calc_strainrates.F; |
888 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
889 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
890 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
891 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
892 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
893 |
|
- new subroutines seaice_lsr_tridiagu/v |
894 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
895 |
|
additive Schwarz method, but not used for now. |
896 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
897 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
898 |
|
o OpenAD support |
899 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
900 |
|
OpenAD revolve loop replacement |
901 |
|
(new S/R main_do_loop.F) |
902 |
|
o model/src: |
903 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
904 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
905 |
|
ADAMS_BASHFORTH2. |
906 |
|
o pkg/cheapaml: |
907 |
|
- add new parameter (default=F, same as before) to disable full domain |
908 |
|
(including land) periodicity in X & Y dir. |
909 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
910 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
911 |
|
into single S/R CHEAPAML_TIMESTEP. |
912 |
|
|
913 |
|
checkpoint64d (2013/02/17) |
914 |
|
o pkg/monitor (angular momentum): |
915 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
916 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
917 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
918 |
|
each component (instead of from cell centered averaged) and use the 4 |
919 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
920 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
921 |
|
FreeSurf) if using vectorInvariant momentum. |
922 |
|
o model/src (horizontal grid): |
923 |
|
- move initialisation of all horizontal grid arrays to null value |
924 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
925 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
926 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
927 |
|
compute them in S/R CALC_GRID_ANGLES. |
928 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
929 |
|
SEAICE_JFNK_tolIter |
930 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
931 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
932 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
933 |
|
- extend loop range in seaice_calc_viscosity |
934 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
935 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
936 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
937 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
938 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
939 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
940 |
|
for output.dyn_jfnk.txt |
941 |
|
in seaice_fgmres.F (unrelated to RAS) |
942 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
943 |
|
efficient), but because this changes the results, turn it off by |
944 |
|
default |
945 |
|
- replace the save statement by local common blocks |
946 |
|
o utils/matlab: |
947 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
948 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
949 |
|
instead of local script "load_cs.m". |
950 |
|
o pkg/seaice: |
951 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
952 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
953 |
|
change the verification experiment, because of the particular domain |
954 |
|
decomposition |
955 |
o pkg/diagnostics: |
o pkg/diagnostics: |
956 |
- change default missing_value from UNSET_RL to -999. |
- change default missing_value from UNSET_RL to -999. |
957 |
o pkg/layers: improve vectorization of layers_fluxcalc.F |
o pkg/layers: improve vectorization of layers_fluxcalc.F |
958 |
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
959 |
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
960 |
- step 2: replace search algorithm by a bisection algorithm found in |
- step 2: replace search algorithm by a bisection algorithm found in |
961 |
Press et al. Numerical Recipes in Fortran. This algorithm can be |
Press et al. Numerical Recipes in Fortran. This algorithm can be |
962 |
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
963 |
For now, use this algorithm only for TARGET_NEC_SX defined. |
For now, use this algorithm only for TARGET_NEC_SX defined. |
964 |
- moved the search algorithm into a separate subroutine, that is kept |
- moved the search algorithm into a separate subroutine, that is kept |