Merge branch 'release-clm5.0' of github.com:ESCOMP/ctsm into release-…

…clm5.0

.CLMTrunkChecklist → .CTSMTrunkChecklist

@@ -1,6 +1,6 @@
-Checklist of steps to do to make a CLM Trunk Tag        Mar/7th/2017
+Checklist of steps to do to make a CTSM Trunk Tag        Mar/7th/2017
 
-CLM Code Management team.
+CTSM Software Management team.
 
 See the wiki page for this on:
 

.github/ISSUE_TEMPLATE/01_bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a problem with the code
+
+---
+
+### Brief summary of bug
+
+[Give a one or two sentence summary. This could be the same as the issue title if you feel that is a sufficient summary.]
+
+### General bug information
+
+**CTSM version you are using:** [output of `git describe`]
+
+**Does this bug cause significantly incorrect results in the model's science?** [Yes / No]
+
+**Configurations affected:** [Fill this in if known.]
+
+### Details of bug
+
+[Fill in details here.]
+
+### Important details of your setup / configuration so we can reproduce the bug
+
+[Specify anything relevant: the compset, resolution, machine, compiler, any xml or namelist changes, etc. You don't have to repeat anything that you have already noted above.]
+
+### Important output or errors that show the problem
+
+[Fill this in with anything relevant that you haven't already noted; if there is nothing to add, delete this section.]

.github/ISSUE_TEMPLATE/02_support_needed.md

@@ -0,0 +1,36 @@
+---
+name: Support needed for model use
+about: Ask for help with using CTSM
+
+---
+
+### NOTE: Be sure to read the relevant documentation and user forums
+
+We have limited staff and ability to provide support. Here are some resources that might provide help:
+- User's Guide: https://escomp.github.io/ctsm-docs/doc/build/html/users_guide/index.html
+- CLM Forum: https://bb.cgd.ucar.edu/forums/land-modeling-clm
+- README files amongst the source code
+- GitHub CTSM issues: https://github.com/escomp/ctsm/issues/
+- Also make sure this issue is unique to CTSM and not really an issue with CESM or CIME
+
+### Details of support request
+
+[Fill in details here.]
+
+### Important details of your setup / configuration so we can better assist you
+
+**CTSM version you are using:** [output of `git describe`]
+
+**Have you made any modifications to code, xml files, etc.?** [Yes / No]
+
+[If Yes: Please point us to your modifications. However: In general we can NOT support problems with modified code. Try to show the problem without modifications.]
+
+**If you are having problems with a specific case: Is your case on a machine accessible to most CTSM developers (e.g., an NCAR machine)?** [Yes / No]
+
+If Yes:
+
+- Location of case directory: [Fill this in]
+
+- Location of run directory: [Fill this in]
+
+[If No: Please make sure you have included all important input and output needed to understand your issue, either by pasting it into the issue text, or by attaching relevant files. However: We are less likely to be able to reproduce your problem if the issue is NOT on an NCAR machine.]

.github/ISSUE_TEMPLATE/03_science_discussion.md

@@ -0,0 +1,7 @@
+---
+name: Science discussion
+about: We encourage the use of issues to discuss CTSM science developments
+
+---
+
+

.github/ISSUE_TEMPLATE/04_other.md

@@ -0,0 +1,7 @@
+---
+name: Other
+about: Other issues (enhancement, cleanup, documentation, etc.)
+
+---
+
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,15 +2,19 @@
 
 ### Specific notes
 
+Contributors other than yourself, if any:
+
 CTSM Issues Fixed (include github issue #):
 
 Are answers expected to change (and if so in what way)?
 
 Any User Interface Changes (namelist or namelist defaults changes)?
 
-Testing performed:
+Testing performed, if any:
 (List what testing you did to show your changes worked as expected)
 (This can be manual testing or running of the different test suites)
+(Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
+(aux_clm on cheyenne for gnu/pgi and hobart for gnu/pgi/nag is the standard for tags on master)
 
 **NOTE: Be sure to check your Coding style against the standard:**
 https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines

.gitignore

@@ -1,10 +1,10 @@
 # directories checked out by manage_externals, and other files created
 # by manage_externals
 manage_externals.log
-src/fates/
-tools/PTCLM/
-cime/
-components/
+/src/fates/
+/tools/PTCLM/
+/cime/
+/components/
 
 # ignore svn directories
 **/.svn/**
@@ -26,28 +26,35 @@ CMakeFiles/
 
 
 # unit testing directories
-src/unit_tests.*
+/src/unit_tests.*
+
+# files generated by the unit test build
+/src/dyn_subgrid/dynVarMod.F90
+/src/dyn_subgrid/dynVarTimeInterpMod.F90
+/src/dyn_subgrid/dynVarTimeUninterpMod.F90
+/src/utils/array_utils.F90
+/src/unit_test_stubs/utils/restUtilMod_stub.F90
+/src/unit_test_stubs/main/ncdio_pio_fake.F90
+/src/unit_test_stubs/main/ncdio_var.F90
+/src/unit_test_shr/unittestArrayMod.F90
 
 # cime_config
 buildnmlc
 buildcppc
 
-# don't ignore cism build utilities directory
-!components/cism/**/build
-
 # configure / build files
-bld/**/CESM_cppdefs
-bld/**/Filepath
-bld/**/config_cache.xml
-bld/**/lnd_in
-bld/**/drv_flds_in
+/bld/**/CESM_cppdefs
+/bld/**/Filepath
+/bld/**/config_cache.xml
+/bld/**/lnd_in
+/bld/**/drv_flds_in
 
 # build-naemlist testing
-bld/unit_testers/lnd_in*
-bld/unit_testers/drv_flds_in*
-bld/unit_testers/temp_file.txt*
-bld/unit_testers/user_nl_clm_real_parameters*
-bld/unit_testers/env_run.xml
+/bld/unit_testers/lnd_in*
+/bld/unit_testers/drv_flds_in*
+/bld/unit_testers/temp_file.txt*
+/bld/unit_testers/user_nl_clm_real_parameters*
+/bld/unit_testers/env_run.xml
 
 # tools testing output
 td.*.status
@@ -58,18 +65,27 @@ test_driver_*.sh
 # mksurfdata output
 surfdata_*.log
 surfdata_*.namelist
+landuse.timeseries_*.namelist
+landuse.timeseries_*.log
+landuse_timeseries_*.txt
 clm.input_data_list
 clm.input_data_list.previous
+*.stdout.txt.o*
 
 # Tools executables
-tools/mksurfdata_map/mksurfdata_map
-tools/mkprocdata_map/mkprocdata_map
+/tools/mksurfdata_map/mksurfdata_map
+/tools/mkprocdata_map/mkprocdata_map
+
+# mksurfdata output files
+/tools/mksurfdata_map/surfdata_*.nc
+/tools/mksurfdata_map/landuse.timeseries_*.nc
 
 # mkmapdata output files
-tools/mkmapdata/PET*.RegridWeightGen.Log
-tools/mkmapdata/regrid.*.out
-tools/mkmapdata/regrid.*.err
-tools/mkmapdata/regrid.o*
+/tools/mkmapdata/PET*.RegridWeightGen.Log
+/tools/mkmapdata/regrid.*.out
+/tools/mkmapdata/regrid.*.err
+/tools/mkmapdata/regrid.o*
+/tools/mkmapdata/map*.nc
 
 # build output
 *.o

CONTRIBUTING.md

@@ -1,11 +1,15 @@
 ## How to contribute:
 
-It's recommended that you first contact [email protected] to discuss the changes or additions that you propose.
-Work with them to think about the design and implemention of the changes as well as the planning
-and scheduling for the change to come into CTSM.
-
-It's also recommened that you join the [email protected] google groups in order 
-to be informed about the science that is happening in CTSM as well as the latest develepments and tags.
+We recommend that you first open an issue (https://github.com/escomp/ctsm/issues/) to
+discuss the changes or additions that you propose. Through the issue discussion, you can
+work with other CTSM developers to think about the design and implementation of the changes
+as well as the planning and scheduling for the change to come into CTSM. An alternative is
+to contact the key software and science developers via [email protected]. Making
+contact early in your project will increase the likelihood that your developments can come
+into CTSM.
+
+We also recommend that you join the [email protected] google groups in order 
+to be informed about the science that is happening in CTSM as well as the latest developments and tags.
 The ctsm-dev group is here:
 
 https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
@@ -41,4 +45,4 @@ Code conventions: https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines
 
 #### Code of Conduct:
 
-See the "CODE_OF_CONDUCT.md" file for expectations of how to work in the community.
+See the `CODE_OF_CONDUCT.md` file for expectations of how to work in the community.

Externals.cfg

@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/cism-wrapper
-tag = release-v2.1.01
+tag = release-cesm2.0.04
 externals = Externals_CISM.cfg
 required = True
 
@@ -30,7 +30,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime_cesm2_0_rel_03
+tag = cime5.6.10
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_clm4_5.xml

@@ -502,7 +502,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 </init_interp_attributes>
 
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false."
->hgrid=1.9x2.5 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
+>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
 </init_interp_attributes>
 
 <!--
@@ -577,10 +577,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Present day crop spinup at 2-degree with irrigation on -->
-<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
+<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="2000"
-         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."  use_init_interp=".true."
->lnd/clm2/initdata_map/clmi.IGM2000GSWP3CLM50BGCCROPIRR.2011-01-01.1.9x2.5_gx1v6_gl5_simyr2000_c170419.nc
+         ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
+>lnd/clm2/initdata_map/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c180715.nc
 </finidat>
 
 <!-- FATES on for 2000 (MUST be an exact match - can't interpolate files for FATES -->
@@ -971,7 +971,7 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <stream_year_last_ndep  use_cn=".true."   sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_last_ndep>
 
 <stream_year_first_ndep use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >1850</stream_year_first_ndep>
-<stream_year_last_ndep  use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >2000</stream_year_last_ndep>
+<stream_year_last_ndep  use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >2015</stream_year_last_ndep>
 
 <stream_year_first_ndep use_cn=".true."   sim_year="constant" sim_year_range="1850-2100" >1850</stream_year_first_ndep>
 <stream_year_last_ndep  use_cn=".true."   sim_year="constant" sim_year_range="1850-2100" >2100</stream_year_last_ndep>
@@ -1064,13 +1064,13 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_last_popdens>
 
 <stream_year_first_popdens use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >1850</stream_year_first_popdens>
-<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >2010</stream_year_last_popdens>
+<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1850-2000" >2016</stream_year_last_popdens>
 
 <stream_year_first_popdens use_cn=".true."   sim_year="constant" sim_year_range="1850-2100" >1850</stream_year_first_popdens>
-<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1850-2100" >2010</stream_year_last_popdens>
+<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1850-2100" >2016</stream_year_last_popdens>
 
 <stream_year_first_popdens use_cn=".true."   sim_year="constant" sim_year_range="2000-2100" >1850</stream_year_first_popdens>
-<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="2000-2100" >2010</stream_year_last_popdens>
+<stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="2000-2100" >2016</stream_year_last_popdens>
 
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." >lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc</stream_fldfilename_popdens>
 
@@ -1104,13 +1104,13 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_last_urbantv>
 
 <stream_year_first_urbantv phys="clm5_0" sim_year="constant" sim_year_range="1850-2000" >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="1850-2000" >2010</stream_year_last_urbantv>
+<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="1850-2000" >2106</stream_year_last_urbantv>
 
 <stream_year_first_urbantv phys="clm5_0" sim_year="constant" sim_year_range="1850-2100" >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="1850-2100" >2010</stream_year_last_urbantv>
+<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="1850-2100" >2106</stream_year_last_urbantv>
 
 <stream_year_first_urbantv phys="clm5_0" sim_year="constant" sim_year_range="2000-2100" >1850</stream_year_first_urbantv>
-<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="2000-2100" >2010</stream_year_last_urbantv>
+<stream_year_last_urbantv  phys="clm5_0" sim_year="constant" sim_year_range="2000-2100" >2106</stream_year_last_urbantv>
 
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 

bld/namelist_files/namelist_definition_clm4_5.xml

@@ -2432,20 +2432,24 @@ to the atmosphere) (but using the 'general' method will typically have
 only a very minor impact on results in this case). For this method to
 work, the input finidat file needs to be at the same resolution as the
 current configuration. So this is a less general form of
-init_interp. However, it can be used when transitioning from a spinup
-run to a transient run, or in other cases where the only difference is
-in internal memory allocation. In order to catch possible problems, this
-uses a different algorithm for finding the input point for each output
-point, which ensures that each active output point is associated with
-exactly one input point with the same latitude, longitude and type. This
-method requires (a) the same grid for input and output, within roundoff;
-(b) any non-zero-weight point in the input must have memory allocated
-for it in this grid cell in the output (this will be satisfied if the
-point is non-zero-weight on the surface dataset or if it's a point for
-which we allocate memory even for zero-weight points); (c) any active
-point in the output (based on the surface dataset and rules for
-determining active points) must have a matching point in this grid cell
-in the input.
+init_interp. However, it can be used in cases where the only difference
+is in internal memory allocation. In order to catch possible problems,
+this uses a different algorithm for finding the input point for each
+output point, which ensures that each active output point is associated
+with exactly one input point with the same latitude, longitude and
+type. This method requires (a) the same grid for input and output,
+within roundoff; (b) any non-zero-weight point in the input must have
+memory allocated for it in this grid cell in the output (this will be
+satisfied if the point is non-zero-weight on the surface dataset or if
+it's a point for which we allocate memory even for zero-weight points);
+(c) any active point in the output (based on the surface dataset and
+rules for determining active points) must have a matching point in this
+grid cell in the input. (Note that this generally can NOT be used when
+transitioning from a spinup run to a transient run, because spinup runs
+typically have irrigation off and transient runs have irrigation on, and
+the presence/absence of irrigation affects the subgrid structure; if it
+weren't for that difference, then this option would be useful for this
+use case.)
 
 </entry>