Merge tag 'clm5.0.dev012' into release-clm5.0

Fixes for variable_year orbital mode Fixes for correctness and exact restartability with variable_year orbital mode: (1) Update max day length (max_dayl) each time step, rather than just updating it once in initialization (2) Update to a cime version that has a fix for datm, which updates the orbital parameters (used for solar zenith angle-based interpolation) each time step, rather than just once in initialization Fixes #379 Fixes #260
ESCOMP · May 18, 2018 · db586e2 · db586e2
2 parents edd59ca + e739c2c
commit db586e2
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diff --git a/.gitignore b/.gitignore
@@ -24,6 +24,10 @@ components/
 build/
 CMakeFiles/
 
+
+# unit testing directories
+src/unit_tests.*
+
 # cime_config
 buildnmlc
 buildcppc
@@ -57,6 +61,9 @@ surfdata_*.namelist
 clm.input_data_list
 clm.input_data_list.previous
 
+# Tools executables
+tools/mksurfdata_map/mksurfdata_map
+tools/mkprocdata_map/mkprocdata_map
 
 # build output
 *.o

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,49 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, politcal affiliation, veteran status, pregnancy, genetic information, personal appearance, choice of text editor or operating system, race, religion, or sexual identity and orientation, or any other characteristic protected under applicable US federal or state law. 
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+* Refusing to use the pronouns that someone requests
+* Intimidating, threatening, or hostile conduct; physical or verbal abuse; vandalism; arson; and sabotage
+* Alarming or threatening comments that might refer to, suggest, or promote a violent, intimidating, or threatening action
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. Alternatively, this behavior can be reported to individuals on the CTSM team, who will then have the responsibility to talk about the behavior to the core team. Another alternative for NCAR employees (when all individuals involved are NCAR employees) is to use the reporting methods of NCAR for this behavior (these options include anonymous reporting methods). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Retaliation against a person who initiates a complaint or an inquiry about such behaviors is equally prohibited.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/
diff --git a/Externals.cfg b/Externals.cfg
@@ -8,29 +8,29 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/cism-wrapper
-tag = cism2_1_46
+tag = release-v2.1.00
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/rtm
-tag = rtm1_0_65
+tag = rtm1_0_66
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/mosart
-tag = mosart1_0_30
+tag = mosart1_0_31
 required = True
 
 [cime]
 local_path = cime
 protocol = git
-repo_url = https://github.com/CESM-Development/cime
-tag = clm4518/n04/cime5.4.0-alpha.03
+repo_url = https://github.com/ESMCI/cime
+hash = a67dceae95567cc7529c4cfed153017f4b65b210
 required = True
 
 [externals_description]

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,14 +2,14 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NCAR/fates-release
-tag = fates_s1.4.1_a3.0.0_rev3
+tag = fates_s1.8.1_a3.0.0
 required = True
 
 [PTCLM]
 local_path = tools/PTCLM
 protocol = git
 repo_url = https://github.com/ESCOMP/ptclm
-tag = PTCLM2_171216c
+tag = PTCLM2_180214
 required = True
 
 [externals_description]

diff --git a/README b/README
@@ -5,6 +5,10 @@ offline-build and test scripts. This gives you everything you need
 to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in 
 place of a modeled atmosphere.
 
+For lists of current bugs (issues) and current development see the CTSM github page:
+
+https://github.com/ESCOMP/ctsm
+
 General directory structure:
 
 doc --------------- Documentation of CLM.
@@ -59,35 +63,39 @@ doc/Quickstart.userdatasets - Quick guide to using your own datasets.
 doc/IMPORTANT_NOTES --------- Some important notes about this version of 
                                                  clm, configuration modes and namelist items 
                                                  that are not validated or functional.
-doc/KnownBugs --------------- List of known bugs.
-doc/KnownLimitations -------- List of known limitations and workarounds.
 doc/ChangeLog --------------- Detailed list of changes for each model version.
 doc/ChangeSum --------------- Summary one-line list of changes for each 
-                                             model version.
+                              model version.
 doc/README ------------------ Documentation similar to this file
 doc/UsersGuide -------------- CLM Users Guide
 doc/CodeReference ----------- CLM Code Reference Guide
 
+bld/README ------------------ Description of how to use the configure and
+                              build-namelist scripts.
 bld/configure --------------- Script to prepare CLM to be built.
+bld/build-namelist ---------- Script to build CLM namelists.
+
+cime_config/buildnml ------------- Build the CLM namelist for CIME
+cime_config/buildlib ------------- Build the CLM library
+cime_config/config_compsets.xml -- Define CLM compsets
+cime_config/config_component.xml - Define CLM XML settings
+cime_config/config_pes.xml ------- Define Processor layouts for various CLM grids and compsets
 
 test/tools/test_driver.sh -- Script for general software testing of 
                              CLM's offline tools.
 
-tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset 
+tools/mksurfdata_map ---------- Directory to build program to create surface dataset 
                                 at any resolution.
-tools/clm4_5/interpinic ------- Directory to build program to interpolate initial 
-                                conditions to any resolution.
-tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7 
+tools/mkdatadomain ------------ Directory to build program to create datm7 or docn7 
                                 domain files from clm files.
-tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded 
+tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded 
                                 format.
-tools/shared/ncl_scripts  ----- Directory of NCL and perl scripts to do various
+tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid
+tools/ncl_scripts  ------------ Directory of NCL and perl scripts to do various
                                 tasks. Most notably to plot perturbation error growth
                                 testing and to extract regional information from
                                 global datasets for single-point/regional simulations.
 
-bld/README ------------- Description of how to use the configure and
-                                        build-namelist scripts.
 
 =============================================================================================
 Source code directory structure:
@@ -112,7 +120,7 @@ scr_clm40 ------- CLM4.0 source code directory
 
          cd cime/scripts
          ./create_newcase            # get help on how to run create_newcase
-         ./create_newcase --case testI --res f19_g16 --compset I2000Clm50BgcCrop --mach cheyenne
+         ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm50BgcCrop --mach cheyenne
                                      # create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res
                                      # "I2000Clm50BgcCrop" case is clm5_0 active, datm8, and inactive ice/ocn
          cd testI

diff --git a/README.rst b/README.rst
@@ -17,8 +17,15 @@ https://escomp.github.io/ctsm-docs/
 
 For help with how to work with CTSM in git, see
 
-https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup
+https://github.com/ESCOMP/ctsm/wiki/Getting-started-with-CTSM-in-git
 
 and
 
-https://github.com/ESCOMP/ctsm/wiki/Getting-started-with-CTSM-in-git
+https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup
+
+To get updates on CTSM tags and important notes on CTSM developments
+join our low traffic email list:
+
+https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
+
+(Send email to [email protected] if you have problems with any of this)
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1569,12 +1569,15 @@ sub process_namelist_inline_logic {
   setup_logic_dynamic_roots($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_params_file($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_create_crop_landunit($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
+  setup_logic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_fertilizer($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_grainproduct($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_soilstate($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
-  setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
+    setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  }
   setup_logic_dynamic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_spinup($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl, $physv);
@@ -1742,6 +1745,10 @@ sub process_namelist_inline_logic {
   #######################################################################
   setup_logic_hydrology_switches($nl, $physv);
 
+  #########################################
+  # namelist group: clm_initinterp_inparm #
+  #########################################
+  setup_logic_initinterp($opts, $nl_flags, $definition, $defaults, $nl, $physv);
 }
 
 #-------------------------------------------------------------------------------
@@ -2069,6 +2076,18 @@ sub setup_logic_create_crop_landunit {
     }
   }
 }
+
+#-------------------------------------------------------------------------------
+
+sub setup_logic_subgrid {
+   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+   my $var = 'run_zero_weight_urban';
+   if ($physv->as_long() >= $physv->as_long("clm4_5")) {
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+   }
+}
+
 #-------------------------------------------------------------------------------
 
 sub setup_logic_cnfire {
@@ -2103,7 +2122,7 @@ sub setup_logic_cnfire {
 sub setup_logic_cnprec {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
-  if ( $physv->as_long() >= $physv->as_long("clm5_0") && &value_is_true($nl->get_value('use_cn')) ) {
+  if ( $physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true($nl_flags->{'use_cn'}) ) {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults,
                  $nl, 'ncrit', 'use_cn'=>$nl_flags->{'use_cn'});
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults,
@@ -2363,7 +2382,10 @@ sub setup_logic_initial_conditions {
     }
     if ($opts->{'ignore_ic_date'}) {
       if ( &value_is_true($nl_flags->{'use_crop'}) ) {
-        $log->fatal_error("using ignore_ic_date is incompatable with crop!");
+        $log->warning("using ignore_ic_date is incompatable with crop! If you choose to ignore this error, " . 
+                      "the counters since planting for crops will be messed up. \nSo you should ignore at " . 
+                      "least the first season for crops. And since it will impact the 20 year means, ideally the " .
+                      "first 20 years should be ignored.");
       }
     } elsif ($opts->{'ignore_ic_year'}) {
        $settings{'ic_md'} = $ic_date;
@@ -2386,9 +2408,9 @@ sub setup_logic_initial_conditions {
           # Delete any date settings, except for crop
           delete( $settings{'ic_ymd'} );
           delete( $settings{'ic_md'}  );
-          if ( &value_is_true($nl_flags->{'use_crop'}) ) {
-             $settings{'ic_md'} = $ic_date;
-          }
+          #if ( &value_is_true($nl_flags->{'use_crop'}) ) {
+             #$settings{'ic_md'} = $ic_date;
+          #}
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_sim_years" );
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_how_close" );
           foreach my $sim_yr ( split( /,/, $nl->get_value("init_interp_sim_years") )) {
@@ -3705,6 +3727,26 @@ sub setup_logic_lnd2atm {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_initinterp {
+   #
+   # Options related to init_interp
+   #
+   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+   if ($physv->as_long() >= $physv->as_long("clm4_5")) {
+      my $var = 'init_interp_method';
+      if ( &value_is_true($nl->get_value("use_init_interp"))) {
+         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var);
+      } else {
+         if (defined($nl->get_value($var))) {
+            $log->fatal_error("$var can only be set if use_init_interp is true");
+         }
+      }
+   }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_fates {
     #
     # Set some default options related to Ecosystem Demography

diff --git a/bld/namelist_files/namelist_defaults_clm4_0.xml b/bld/namelist_files/namelist_defaults_clm4_0.xml
@@ -105,14 +105,14 @@ irrig=".false." crop="off" lnd_tuning_mode="clm4_0_GSWP3v1"
 >lnd/clm2/initdata_map/clmi.I1850Clm40CnGswGs.1441-01-01.0.9x1.25_gx1v6_simyr1850_c170823.nc
 </finidat>
 
-<finidat hgrid="0.9x1.25" maxpft="17" mask="gx1v6" bgc="none" ic_ymd="06010101" ic_tod="0" sim_year="1850" glc_nec="0"
+<finidat hgrid="0.9x1.25" maxpft="17" mask="gx1v6" bgc="none" ic_ymd="33620101" ic_tod="0" sim_year="1850" glc_nec="0"
 irrig=".false." crop="off" lnd_tuning_mode="clm4_0_CRUv7"
->lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.0601-01-01.0.9x1.25_gx1v6_simyr1850_c171224.nc
+>lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.3362-01-01.0.9x1.25_gx1v6_simyr1850_c171222.nc
 </finidat>
 
-<finidat hgrid="0.9x1.25" maxpft="17" mask="gx1v6" bgc="cn"   ic_ymd="06010101" ic_tod="0" sim_year="1850" glc_nec="0"
+<finidat hgrid="0.9x1.25" maxpft="17" mask="gx1v6" bgc="cn"   ic_ymd="33620101" ic_tod="0" sim_year="1850" glc_nec="0"
 irrig=".false." crop="off" lnd_tuning_mode="clm4_0_CRUv7"
->lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.0601-01-01.0.9x1.25_gx1v6_simyr1850_c171224.nc
+>lnd/clm2/initdata_map/clmi.I1850Clm40CnCruGs.3362-01-01.0.9x1.25_gx1v6_simyr1850_c171222.nc
 </finidat>
 
 <!-- Initial files at 0.9x1.25 or 1.9x2.5 native resolution -->