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Bring hotfixes for ccpp-framework and ccpp-physics from release/public-v4 back to master #113

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merged 6 commits into from
May 11, 2020
Merged

Bring hotfixes for ccpp-framework and ccpp-physics from release/public-v4 back to master #113

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7b748e1
Update CCPP version number from 3 to 4
climbfuji May 6, 2020
7f09418
gfsphysics/GFS_layer/GFS_physics_driver.F90: update comment on locati…
climbfuji May 6, 2020
a63d75f
Add no_nsst CCPP suites from public release
climbfuji May 6, 2020
e8f00d1
Update .gitmodules and submodule pointers for ccpp-framework and ccpp…
climbfuji May 6, 2020
0847728
Bugfixes for CCPP: check for and correct syntax of \htmlinclude lines
climbfuji May 11, 2020
8b67de4
Revert change to .gitmodules and update submodule pointers for ccpp-f…
climbfuji May 11, 2020
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12 changes: 8 additions & 4 deletions .gitmodules
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Expand Up @@ -4,9 +4,13 @@
branch = dev/emc
[submodule "ccpp/framework"]
path = ccpp/framework
url = https://github.com/NCAR/ccpp-framework
branch = master
#url = https://github.com/NCAR/ccpp-framework
#branch = master
url = https://github.com/climbfuji/ccpp-framework
branch = bugfixes_from_public_release
[submodule "ccpp/physics"]
path = ccpp/physics
url = https://github.com/NCAR/ccpp-physics
branch = master
#url = https://github.com/NCAR/ccpp-physics
#branch = master
url = https://github.com/climbfuji/ccpp-physics
branch = bugfixes_from_public_release
2 changes: 1 addition & 1 deletion ccpp/framework
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Submodule framework updated 19 files
+1 −1 CMakeLists.txt
+ − doc/DevelopersGuide/CCPP_VARIABLES_FV3.pdf
+ − doc/DevelopersGuide/CCPP_VARIABLES_SCM.pdf
+0 −15 doc/DevelopersGuide/Makefile
+12 −0 doc/DevelopersGuide/README.md
+0 −23 doc/DevelopersGuide/acknow.tex
+0 −2 doc/DevelopersGuide/chap_appendix.tex
+0 −328 doc/DevelopersGuide/chap_hostmodel.tex
+0 −12 doc/DevelopersGuide/chap_intro.tex
+0 −158 doc/DevelopersGuide/chap_schemes.tex
+0 −69 doc/DevelopersGuide/host_cap_template.F90
+ − doc/DevelopersGuide/images/ccpp_design_with_ccpp_prebuild.pdf
+ − doc/DevelopersGuide/images/dtc_logo.png
+0 −39 doc/DevelopersGuide/main.tex
+0 −28 doc/DevelopersGuide/preface.tex
+0 −129 doc/DevelopersGuide/scheme_template.F90
+0 −81 doc/DevelopersGuide/scheme_template.meta
+0 −28 doc/DevelopersGuide/title.tex
+3 −1 scripts/metadata_parser.py
2 changes: 1 addition & 1 deletion ccpp/physics
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Submodule physics updated 30 files
+1 −1 CMakeLists.txt
+4 −3 physics/cires_ugwp.F90
+0 −67 physics/dcyc2.meta
+467 −0 physics/docs/ccppv4_doxyfile
+292 −257 physics/docs/library.bib
+46 −23 physics/docs/pdftxt/CPT_adv_suite.txt
+17 −0 physics/docs/pdftxt/GFS_OCEAN.txt
+1 −1 physics/docs/pdftxt/GFS_OZPHYS.txt
+117 −0 physics/docs/pdftxt/GFS_UGWPv0.txt
+0 −1 physics/docs/pdftxt/GFSv14_suite.txt
+0 −1 physics/docs/pdftxt/GFSv15_suite.txt
+0 −1 physics/docs/pdftxt/GFSv15_suite_TKEEDMF.txt
+127 −0 physics/docs/pdftxt/GFSv15p2_no_nsst_suite.txt
+133 −0 physics/docs/pdftxt/GFSv15p2_suite.txt
+167 −0 physics/docs/pdftxt/GFSv16beta_no_nsst_suite.txt
+176 −0 physics/docs/pdftxt/GFSv16beta_suite.txt
+150 −82 physics/docs/pdftxt/GSD_adv_suite.txt
+0 −21 physics/docs/pdftxt/UGWPv0.txt
+27 −20 physics/docs/pdftxt/all_shemes_list.txt
+15 −11 physics/docs/pdftxt/mainpage.txt
+100 −0 physics/docs/pdftxt/suite_FV3_GFS_v15p2.xml.txt
+99 −0 physics/docs/pdftxt/suite_FV3_GFS_v15p2_no_nsst.xml.txt
+100 −0 physics/docs/pdftxt/suite_FV3_GFS_v16beta.xml.txt
+97 −0 physics/docs/pdftxt/suite_FV3_GFS_v16beta_no_nsst.xml.txt
+143 −32 physics/docs/pdftxt/suite_input.nml.txt
+5 −14 physics/m_micro.F90
+0 −4 physics/mp_thompson.F90
+0 −2 physics/sfc_drv_ruc.F90
+3 −6 physics/sfc_nst.f
+11 −7 physics/sfc_ocean.F
2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_CPT_v0.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_CPT_v0" lib="ccppphys" ver="3">
<suite name="FV3_CPT_v0" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_RRTMGP.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_RRTMGP" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_RRTMGP" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_coupled.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_coupled" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_coupled" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_csawmg.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_csawmg" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_csawmg" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_csawmgshoc.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_csawmgshoc" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_csawmgshoc" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_gfdlmp.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_gfdlmp" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_gfdlmp" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_gfdlmp_noahmp.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_gfdlmp_noahmp" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_gfdlmp_noahmp" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_gfdlmp_regional.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_gfdlmp_regional" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_gfdlmp_regional" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_gfdlmp_regional_c768.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_gfdlmp_regional_c768" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_gfdlmp_regional_c768" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_h2ophys.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_h2ophys" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_h2ophys" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_myj.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_myj" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_myj" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_ntiedtke.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_ntiedtke" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_ntiedtke" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_ozphys_2015.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_ozphys_2015" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_ozphys_2015" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_sas.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_sas" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_sas" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_satmedmf.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_satmedmf" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_satmedmf" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_satmedmf_coupled.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_satmedmf_coupled" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_satmedmf_coupled" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_satmedmfq.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_satmedmfq" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_satmedmfq" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_shinhong.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_shinhong" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_shinhong" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_stretched.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_stretched" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_stretched" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_2017_ysu.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_2017_ysu" lib="ccppphys" ver="3">
<suite name="FV3_GFS_2017_ysu" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_cpld_rasmgshoc.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_cpld_rasmgshoc" lib="ccppphys" ver="3">
<suite name="FV3_GFS_cpld_rasmgshoc" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_cpldnst_rasmgshoc.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_cpldnst_rasmgshoc" lib="ccppphys" ver="3">
<suite name="FV3_GFS_cpldnst_rasmgshoc" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_rasmgshoc.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_rasmgshoc" lib="ccppphys" ver="3">
<suite name="FV3_GFS_rasmgshoc" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_gf.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_gf" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_gf" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_gf_thompson.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_gf_thompson" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_gf_thompson" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_mynn.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_mynn" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_mynn" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_ras.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_ras" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_ras" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_rasmgshoc.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_rasmgshoc" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_rasmgshoc" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_thompson.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_thompson" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_thompson" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15_thompson_mynn.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15_thompson_mynn" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15_thompson_mynn" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="time_vary">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15p2.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15p2" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15p2" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15p2_coupled.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15p2_coupled" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15p2_coupled" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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91 changes: 91 additions & 0 deletions ccpp/suites/suite_FV3_GFS_v15p2_no_nsst.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15p2_no_nsst" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
<scheme>fv_sat_adj</scheme>
</subcycle>
</group>
<group name="time_vary">
<subcycle loop="1">
<scheme>GFS_time_vary_pre</scheme>
<scheme>GFS_rrtmg_setup</scheme>
<scheme>GFS_rad_time_vary</scheme>
<scheme>GFS_phys_time_vary</scheme>
</subcycle>
</group>
<group name="radiation">
<subcycle loop="1">
<scheme>GFS_suite_interstitial_rad_reset</scheme>
<scheme>GFS_rrtmg_pre</scheme>
<scheme>rrtmg_sw_pre</scheme>
<scheme>rrtmg_sw</scheme>
<scheme>rrtmg_sw_post</scheme>
<scheme>rrtmg_lw_pre</scheme>
<scheme>rrtmg_lw</scheme>
<scheme>rrtmg_lw_post</scheme>
<scheme>GFS_rrtmg_post</scheme>
</subcycle>
</group>
<group name="physics">
<subcycle loop="1">
<scheme>GFS_suite_interstitial_phys_reset</scheme>
<scheme>GFS_suite_stateout_reset</scheme>
<scheme>get_prs_fv3</scheme>
<scheme>GFS_suite_interstitial_1</scheme>
<scheme>GFS_surface_generic_pre</scheme>
<scheme>GFS_surface_composites_pre</scheme>
<scheme>dcyc2t3</scheme>
<scheme>GFS_surface_composites_inter</scheme>
<scheme>GFS_suite_interstitial_2</scheme>
</subcycle>
<!-- Surface iteration loop -->
<subcycle loop="2">
<scheme>sfc_diff</scheme>
<scheme>GFS_surface_loop_control_part1</scheme>
<scheme>sfc_ocean</scheme>
<scheme>lsm_noah</scheme>
<scheme>sfc_sice</scheme>
<scheme>GFS_surface_loop_control_part2</scheme>
</subcycle>
<!-- End of surface iteration loop -->
<subcycle loop="1">
<scheme>GFS_surface_composites_post</scheme>
<scheme>sfc_diag</scheme>
<scheme>sfc_diag_post</scheme>
<scheme>GFS_surface_generic_post</scheme>
<scheme>GFS_PBL_generic_pre</scheme>
<scheme>hedmf</scheme>
<scheme>GFS_PBL_generic_post</scheme>
<scheme>GFS_GWD_generic_pre</scheme>
<scheme>cires_ugwp</scheme>
<scheme>cires_ugwp_post</scheme>
<scheme>GFS_GWD_generic_post</scheme>
<scheme>rayleigh_damp</scheme>
<scheme>GFS_suite_stateout_update</scheme>
<scheme>ozphys_2015</scheme>
<scheme>h2ophys</scheme>
<scheme>GFS_DCNV_generic_pre</scheme>
<scheme>get_phi_fv3</scheme>
<scheme>GFS_suite_interstitial_3</scheme>
<scheme>samfdeepcnv</scheme>
<scheme>GFS_DCNV_generic_post</scheme>
<scheme>GFS_SCNV_generic_pre</scheme>
<scheme>samfshalcnv</scheme>
<scheme>GFS_SCNV_generic_post</scheme>
<scheme>GFS_suite_interstitial_4</scheme>
<scheme>cnvc90</scheme>
<scheme>GFS_MP_generic_pre</scheme>
<scheme>gfdl_cloud_microphys</scheme>
<scheme>GFS_MP_generic_post</scheme>
<scheme>maximum_hourly_diagnostics</scheme>
</subcycle>
</group>
<group name="stochastics">
<subcycle loop="1">
<scheme>GFS_stochastics</scheme>
</subcycle>
</group>
<!-- <finalize></finalize> -->
</suite>
2 changes: 1 addition & 1 deletion ccpp/suites/suite_FV3_GFS_v15plus.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>

<suite name="FV3_GFS_v15plus" lib="ccppphys" ver="3">
<suite name="FV3_GFS_v15plus" lib="ccppphys" ver="4">
<!-- <init></init> -->
<group name="fast_physics">
<subcycle loop="1">
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