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Merge remote-tracking branch 'upstream/cam_development' into std_atm_fix_for_mpas
2 parents 8931195 + 54af3ee commit 2c9843f

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19 files changed

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-87
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19 files changed

+475
-87
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‎.gitmodules‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
[submodule "atmos_phys"]
3737
path = src/atmos_phys
3838
url = https://github.com/ESCOMP/atmospheric_physics
39-
fxtag = atmos_phys0_05_000
39+
fxtag = atmos_phys0_05_001
4040
fxrequired = AlwaysRequired
4141
fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
4242

@@ -144,28 +144,28 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
144144
[submodule "ccs_config"]
145145
path = ccs_config
146146
url = https://github.com/ESMCI/ccs_config_cesm.git
147-
fxtag = ccs_config_cesm1.0.0
147+
fxtag = ccs_config_cesm1.0.7
148148
fxrequired = ToplevelRequired
149149
fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
150150

151151
[submodule "cime"]
152152
path = cime
153153
url = https://github.com/ESMCI/cime
154-
fxtag = cime6.1.0
154+
fxtag = cime6.1.29
155155
fxrequired = ToplevelRequired
156156
fxDONOTUSEurl = https://github.com/ESMCI/cime
157157

158158
[submodule "cmeps"]
159159
path = components/cmeps
160160
url = https://github.com/ESCOMP/CMEPS.git
161-
fxtag = cmeps1.0.2
161+
fxtag = cmeps1.0.16
162162
fxrequired = ToplevelRequired
163163
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
164164

165165
[submodule "cdeps"]
166166
path = components/cdeps
167167
url = https://github.com/ESCOMP/CDEPS.git
168-
fxtag = cdeps1.0.48
168+
fxtag = cdeps1.0.53
169169
fxrequired = ToplevelRequired
170170
fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
171171

@@ -179,7 +179,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
179179
[submodule "parallelio"]
180180
path = libraries/parallelio
181181
url = https://github.com/NCAR/ParallelIO
182-
fxtag = pio2_6_2
182+
fxtag = pio2_6_3
183183
fxrequired = ToplevelRequired
184184
fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
185185

@@ -193,13 +193,13 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
193193
[submodule "clm"]
194194
path = components/clm
195195
url = https://github.com/ESCOMP/CTSM
196-
fxtag = ctsm5.2.027
196+
fxtag = ctsm5.3.002
197197
fxrequired = ToplevelRequired
198198
fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
199199

200200
[submodule "fms"]
201201
path = libraries/FMS
202202
url = https://github.com/ESCOMP/FMS_interface
203-
fxtag = fi_240516
203+
fxtag = fi_240828
204204
fxrequired = ToplevelRequired
205205
fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface

‎bld/configure‎

Lines changed: 7 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -2191,9 +2191,9 @@ sub write_filepath
21912191

21922192
if ($simple_phys) {
21932193
print $fh "$camsrcdir/src/physics/simple\n";
2194-
print $fh "$camsrcdir/src/atmos_phys/kessler\n";
2195-
print $fh "$camsrcdir/src/atmos_phys/held_suarez\n";
2196-
print $fh "$camsrcdir/src/atmos_phys/tj2016\n";
2194+
print $fh "$camsrcdir/src/atmos_phys/schemes/kessler\n";
2195+
print $fh "$camsrcdir/src/atmos_phys/schemes/held_suarez\n";
2196+
print $fh "$camsrcdir/src/atmos_phys/schemes/tj2016\n";
21972197
}
21982198

21992199
# Weak scaling fix. This has to come before physics/cam and before dycores
@@ -2334,9 +2334,10 @@ sub write_filepath
23342334
print $fh "$camsrcdir/src/physics/cam\n";
23352335

23362336
#Add the CCPP'ized subdirectories
2337-
print $fh "$camsrcdir/src/atmos_phys/tropopause_find\n";
2338-
print $fh "$camsrcdir/src/atmos_phys/zhang_mcfarlane\n";
2339-
print $fh "$camsrcdir/src/atmos_phys/dry_adiabatic_adjust\n";
2337+
print $fh "$camsrcdir/src/atmos_phys/schemes/tropopause_find\n";
2338+
print $fh "$camsrcdir/src/atmos_phys/schemes/zhang_mcfarlane\n";
2339+
print $fh "$camsrcdir/src/atmos_phys/schemes/dry_adiabatic_adjust\n";
2340+
print $fh "$camsrcdir/src/atmos_phys/schemes/utilities\n";
23402341

23412342
# Dynamics package and test utilities
23422343
print $fh "$camsrcdir/src/dynamics/$dyn\n";
@@ -2362,8 +2363,6 @@ sub write_filepath
23622363
print $fh "$camsrcdir/src/control\n";
23632364
print $fh "$camsrcdir/src/utils\n";
23642365
print $fh "$camsrcdir/src/utils/cam_ccpp\n";
2365-
print $fh "$camsrcdir/src/atmos_phys/utilities\n";
2366-
23672366

23682367
$fh->close;
23692368
}

‎ccs_config‎

Submodule ccs_config updated 116 files

‎cime_config/SystemTests/plb.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo
1212
from CIME.XML.standard_module_setup import *
1313
from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
14-
from CIME.utils import append_testlog
14+
from CIME.status import append_testlog
1515

1616
logger = logging.getLogger(__name__)
1717

‎cime_config/SystemTests/sct.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
from CIME.XML.standard_module_setup import *
1515
from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
1616
from CIME.test_status import *
17-
from CIME.utils import append_testlog
17+
from CIME.status import append_testlog
1818

1919

2020
logger = logging.getLogger(__name__)

‎cime_config/SystemTests/sub.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo
1212
from CIME.XML.standard_module_setup import *
1313
from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
14-
from CIME.utils import append_testlog
14+
from CIME.status import append_testlog
1515

1616

1717
logger = logging.getLogger(__name__)

‎cime_config/SystemTests/tmc.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
from CIME.XML.standard_module_setup import *
66
from CIME.SystemTests.system_tests_common import SystemTestsCommon
77
from CIME.test_status import *
8-
from CIME.utils import append_testlog
8+
from CIME.status import append_testlog
99
from CIME.baselines.performance import get_latest_cpl_logs
1010
import glob, gzip
1111

‎cime_config/config_component.xml‎

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -8,10 +8,10 @@
88
CAM
99
===============
1010
-->
11-
<desc atm="CAM70[%LT][%MT][%CCTS1][%CCTS4]" >CAM cam7 physics:</desc>
12-
<desc atm="CAM60[%1PCT][%4xCO2][%CCTS1][%CCTS2][%CFIRE][%CVBSX][%NUDG][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE][%WXIED][%HEMCO][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam6 physics:</desc>
13-
<desc atm="CAM50[%CCTS1][%CLB][%PORT][%RCO2][%MAM7][%SCAM][%SDYN][%WCSC][%WCTS][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam5 physics:</desc>
14-
<desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WX][%WXIE][%WXIED][%WCCM][%WCMD][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam4 physics:</desc>
11+
<desc atm="CAM70[%LT][%MT][%CT1S][%CT4S]" >CAM cam7 physics:</desc>
12+
<desc atm="CAM60[%1PCT][%4xCO2][%CT1S][%CT2S][%CFIRE][%CVBSX][%NUDG][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE][%WXIED][%HEMCO][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam6 physics:</desc>
13+
<desc atm="CAM50[%CT1S][%CLB][%PORT][%RCO2][%MAM7][%SCAM][%SDYN][%WCSC][%WCTS][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam5 physics:</desc>
14+
<desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WX][%WXIE][%WXIED][%WCCM][%WCMD][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam4 physics:</desc>
1515
<desc atm="CAM[%ADIAB][%DABIP04][%TJ16][%GRAYRAD][%HS94][%KESSLER][%RCO2][%SPCAMS][%SPCAMCLBS][%SPCAMM][%SPCAMCLBM]" >CAM simplified and non-versioned physics :</desc>
1616

1717
<!--
@@ -35,9 +35,9 @@
3535
CAM Options
3636
===============
3737
-->
38-
<desc option="CCTS1" >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA:</desc>
39-
<desc option="CCTS2" >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA and expanded isoprene and terpene oxidation:</desc>
40-
<desc option="CCTS4" >CAM-Chem troposphere/stratosphere simplified chemistry for climate simulations:</desc>
38+
<desc option="CT1S" >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA:</desc>
39+
<desc option="CT2S" >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA and expanded isoprene and terpene oxidation:</desc>
40+
<desc option="CT4S" >CAM-Chem troposphere/stratosphere simplified chemistry for climate simulations:</desc>
4141
<desc option="GEOSCHEM" >GEOS-Chem troposphere/stratosphere chemistry :</desc>
4242
<desc option="CFIRE" >CAM-Chem troposphere/stratosphere chem with simplified volatility basis set SOA scheme and fire emissons :</desc>
4343
<desc option="CLB" >CAM CLUBB - turned on by default in CAM60:</desc>
@@ -135,13 +135,13 @@
135135
<value compset="_CAM70">-phys cam7</value>
136136

137137
<!-- Modifiers for CAM runs (%.* includes SCAM runs) -->
138-
<value compset="_CAM.*(%CCTS1|%CFIRE)">-chem trop_strat_mam5_vbs</value>
138+
<value compset="_CAM.*(%CT1S|%CFIRE)">-chem trop_strat_mam5_vbs</value>
139139
<value compset="_CAM60.*%(GEOSCHEM)">-chem geoschem_mam4</value>
140140

141141
<value compset="%MAM7">-chem trop_mam7</value>
142142
<value compset="CAM60%CVBSX">-chem trop_strat_mam5_vbsext</value>
143-
<value compset="CAM60%CCTS2">-chem trop_strat_mam5_ts2</value>
144-
<value compset="CAM.*%CCTS4">-chem trop_strat_mam5_ts4</value>
143+
<value compset="CAM60%CT2S">-chem trop_strat_mam5_ts2</value>
144+
<value compset="CAM.*%CT4S">-chem trop_strat_mam5_ts4</value>
145145
<value compset="_CAM50%CLB">-clubb_sgs</value>
146146
<value compset="CAM%SPCAMS">-rad camrt -chem none -spcam_nx 32 -spcam_ny 1 -spcam_dx 4000 -spcam_dt 20 -phys spcam_sam1mom </value>
147147
<value compset="CAM%SPCAMCLBS">-rad camrt -chem none -spcam_nx 32 -spcam_ny 1 -spcam_dx 4000 -spcam_dt 20 -phys spcam_sam1mom -spcam_clubb_sgs </value>
@@ -153,7 +153,7 @@
153153

154154
<!-- Match against "%WC" to set defaults for all WACCM cases. -->
155155
<!-- Later settings of "-chem" take precedence over earlier ones. -->
156-
<value compset="_(CAM50|CAM60)%(WC|CC|CV|CF)">-age_of_air_trcs</value>
156+
<value compset="_(CAM50|CAM60)%(WC|CT|CV|CF)">-age_of_air_trcs</value>
157157
<value compset="_CAM40%WCCM">-chem waccm_ma</value>
158158
<value compset="_(CAM50|CAM60)%WCCM">-chem waccm_ma_mam5</value>
159159
<value compset="_(CAM50|CAM60)%WCMD">-chem waccm_mad_mam5</value>
@@ -169,7 +169,7 @@
169169

170170
<value compset="_CAM.*%SDYN">-offline_dyn</value>
171171
<value compset="_CAM\d0%SDYN_CLM">-nlev 56</value>
172-
<value compset="_CAM\d0%CC.*%SDYN">-nlev 56</value>
172+
<value compset="_CAM\d0%CT.*%SDYN">-nlev 56</value>
173173
<value compset="_CAM\d0%WC.*%SDYN">-nlev 88</value>
174174
<value compset="_CAM\d0%WX.*%SDYN">-nlev 145</value>
175175
<value compset="_CAM70%LT">-nlev 58 -model_top lt</value>
@@ -244,8 +244,8 @@
244244
<value compset="2000_CAM60%WCTS" >waccm_tsmlt_2000_cam6</value>
245245
<value compset="2000_CAM60%WCCM" >waccm_ma_2000_cam6</value>
246246
<value compset="2000_CAM60%WCSC" >waccm_sc_2000_cam6</value>
247-
<value compset="2000_CAM60%.*CCTS1" >2000_trop_strat_vbs_cam6</value>
248-
<value compset="2000_CAM60%GEOSCHEM" >2000_geoschem</value>
247+
<value compset="2000_CAM60%.*CT1S" >2000_trop_strat_vbs_cam6</value>
248+
<value compset="2000_CAM60%GEOSCHEM">2000_geoschem</value>
249249
<value compset="2000_CAM60%WXIE" >waccmx_ma_2000_cam6</value>
250250

251251
<value compset="2000_CAM40_SLND_SICE_DOCN%SOMAQP">aquaplanet_cam4</value>
@@ -258,7 +258,7 @@
258258
<value compset="2000_CAM\d0%WC.*_SLND_SICE_DOCN%AQP">aquaplanet_waccm_2000</value>
259259

260260
<value compset="2010_CAM60" >2010_cam6</value>
261-
<value compset="2010_CAM60%.*CCTS1" >2010_trop_strat_vbs_cam6</value>
261+
<value compset="2010_CAM60%.*CT1S" >2010_trop_strat_vbs_cam6</value>
262262
<value compset="2010_CAM60%WCTS" >waccm_tsmlt_2010_cam6</value>
263263
<value compset="2010_CAM60%WCSC" >waccm_sc_2010_cam6</value>
264264
<value compset="2010_CAM60%GEOSCHEM">2010_geoschem</value>
@@ -278,9 +278,9 @@
278278
<value compset="HIST_CAM60%WCCM" >waccm_ma_hist_cam6</value>
279279
<value compset="HIST_CAM60%WCMD" >waccm_ma_hist_cam6</value>
280280
<value compset="HIST_CAM40%WCMD" >waccm_ma_hist_cam4</value>
281-
<value compset="HIST_CAM.*CCTS1" >hist_trop_strat_vbs_cam6</value>
282-
<value compset="HIST_CAM.*CCTS4" >hist_trop_strat_ts4_cam7</value>
283-
<value compset="HIST_CAM60%.*CCTS[12]%NUDG">hist_trop_strat_nudged_cam6</value>
281+
<value compset="HIST(C_|E_|_)CAM.*CT1S">hist_trop_strat_vbs_cam6</value>
282+
<value compset="HISTC_CAM7.*CT4S" >hist_trop_strat_ts4_cam7</value>
283+
<value compset="HIST_CAM60%.*CT[12]S%NUDG">hist_trop_strat_nudged_cam6</value>
284284
<value compset="HIST_CAM60%CVBSX" >hist_trop_strat_vbsext_cam6</value>
285285
<value compset="HIST_CAM60%CFIRE" >hist_trop_strat_vbsfire_cam6</value>
286286
<value compset="HIST_CAM60%GEOSCHEM">hist_geoschem</value>
@@ -309,8 +309,8 @@
309309
<value compset="_CAM60%WCCM%SDYN" >sd_waccm_ma_cam6</value>
310310
<value compset="_CAM60%WCMD%SDYN" >sd_waccm_ma_cam6</value>
311311
<value compset="_CAM40%WCMD%SDYN" >sd_waccm_ma_cam4</value>
312-
<value compset="_CAM60%.*CCTS1%SDYN" >sd_trop_strat_vbs_cam6</value>
313-
<value compset="_CAM60%.*CCTS2%SDYN" >sd_trop_strat2_cam6</value>
312+
<value compset="_CAM60%.*CT1S%SDYN" >sd_trop_strat_vbs_cam6</value>
313+
<value compset="_CAM60%.*CT2S%SDYN" >sd_trop_strat2_cam6</value>
314314
<value compset="_CAM60%SDYN_CLM50" >sd_cam6</value>
315315

316316
<value compset="2000_CAM%DABIP04" >dabi_p2004</value>
@@ -437,7 +437,7 @@
437437
<value compset="^SSP126_">$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc</value>
438438
<value compset="^SSP245_">$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc</value>
439439
<value compset="^SSP370_">$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc</value>
440-
<value compset="^HIST_" >$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</value>
440+
<value compset="^HIST" >$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</value>
441441
<value compset="^2000_" >$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</value>
442442
<value compset="^2010_" >$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</value>
443443
<value compset="^1850_" >$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</value>

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