Updates for GEOS-Chem

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Cloud-J README
+    url: https://github.com/geoschem/cloud-j
+    about: Please see the Cloud-J README and docs subdirectory on GitHub for more information

.github/ISSUE_TEMPLATE/new-feature-or-discussion.md

@@ -0,0 +1,13 @@
+---
+name: Request a new Cloud-J feature or start a discussion
+about: Use this form to request a new Cloud-J feature or start a discussion
+---
+
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### New Cloud-J feature or discussion
+
+Please provide a clear and concise overview of the discussion topic or new feature requested.

.github/ISSUE_TEMPLATE/question-issue.md

@@ -0,0 +1,14 @@
+---
+name: Ask a question about Cloud-J or report an issue with Cloud-J
+about: Use this form to ask a question about Cloud-J or to report an issue
+---
+
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### Description of your issue or question
+
+Please provide as much detail as possible. Always include the Cloud-J version number and any relevant configuration and log files.
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,20 @@
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### Describe the update
+
+Please provide a clear and concise overview of the update.
+
+### Expected changes
+
+Please provide details on how this update will impact model output and include plots or tables as needed.
+
+### Reference(s)
+
+If this is a science update, please provide a literature citation.
+
+### Related Github Issues and PRs
+
+Please link to the corresponding Github issue here. If fixing a bug, there should be an issue describing it with steps to reproduce.

.github/no-response.yml

@@ -0,0 +1,13 @@
+# Configuration for probot-no-response - https://github.com/probot/no-response
+
+# Number of days of inactivity before an Issue is closed for lack of response
+daysUntilClose: 60
+# Label requiring a response
+responseRequiredLabel: more information needed
+# Comment to post when closing an Issue for lack of response. Set to `false` to disable
+closeComment: >
+  This issue has been automatically closed because there has been no response
+  to our request for more information from the original author. With only the
+  information that is currently in the issue, we don't have enough information
+  to take action. Please reach out if you have or find the answers we need so
+  that we can investigate further.

.github/stale.yml

@@ -0,0 +1,20 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 30
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - never stale
+  - feature
+  - discussion
+  - future development
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. If there are no updates within 7 days it will be closed.
+  You can add the "never stale" tag to prevent the Stale bot from closing
+  this issue.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: Closing due to inactivity 

CHANGELOG.md

@@ -0,0 +1,48 @@
+# Changelog
+
+This file documents all notable changes to the Cloud-J repository since the initial commit under git version control.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [7.7.1] - TBD
+### Changed
+- Changed arguments of Init_Cldj to include root thread logical and LUT data directory
+- Renamed global variable FP to FPAR to avoid name conflict in other models
+- Changed FJX_scat-aer.dat format to expect 1 character greater width for R-eff and rho
+- Changed FJX_scat-aer.dat format to expect 2 characters greater width for QAA (data column 2)
+- Changed FJX_scat-aer.dat format to expect 1 character greater width for PAA (data columns 3-9)
+- Limit prints to single core
+- Renamed all modules to use .F90 suffix and cldj_ prefix
+
+## Added
+- Added CMake support
+- Added .gitignore, authors list, and contribution and support guidelines
+- Added module for error handling
+- Added C pre-processor blocks for compatibility with GEOS-Chem offline CTM, GCHP, GEOS, and CESM
+- Added new global variables RNAMES and BRANCH for species info
+- Added GitHub config and PR/issue templates
+- Added GitHub action for build tests
+
+### Fixed
+- Fixed bugs for compatibility with gfortran compilers
+- Fixed bugs for compatibility with intel compilers
+- Fixed bug in standalone model for computing ice water path input to Cloud_JX
+
+### Removed
+- Removed unnecessary whitespace printed to log
+- Removed CLDFLAG, LNRG, and NRANDO from CLOUD_JX argument list since they are global variables
+- Removed unused arguments in ICA_* subroutines
+- Removed unused common variables JXL_, JXL1_, and JXL2_
+- Removed redundant file close in initialization
+
+## [7.7]  - committed 2021-09-01
+### Changed
+- Replace files with version 7.7 from M. Prather's ftp site
+
+## [7.4d] - committed 2021-09-01
+### Changed
+- Replaced files with version 7.4d from M. Prather's ftp site
+
+## [7.3e] - committed 2021-09-01
+### Added
+- Added files for version 7.3e from M. Prather's ftp site

CMakeLists.txt

@@ -261,7 +261,16 @@ endif()
 #-----------------------------------------------------------------------------
 if(CLOUDJ_EXTERNAL_CONFIG AND GCCLASSIC_WRAPPER)
     target_compile_definitions(CloudJBuildProperties
-        INTERFACE MODEL_GCCLASSIC
+        INTERFACE MODEL_GEOSCHEM
+    )
+endif()
+
+#-----------------------------------------------------------------------------
+# For Cloud-J as submodule in GEOS-Chem "High Performance" (GCHP) superproject
+#-----------------------------------------------------------------------------
+if(CLOUDJ_EXTERNAL_CONFIG AND GCHP_WRAPPER)
+    target_compile_definitions(CloudJBuildProperties
+        INTERFACE MODEL_GEOSCHEM
     )
 endif()
 
@@ -271,12 +280,14 @@ endif()
 if(CLOUDJ_EXTERNAL_CONFIG AND MAPL_ESMF)
     target_link_libraries(CloudJBuildProperties
         INTERFACE $<LINK_ONLY:MAPL.base>
+	INTERFACE $<LINK_ONLY:MAPL.generic>
     )
     target_include_directories(CloudJBuildProperties 
         INTERFACE $<TARGET_PROPERTY:MAPL.base,INTERFACE_INCLUDE_DIRECTORIES>
+	INTERFACE $<TARGET_PROPERTY:MAPL.generic,INTERFACE_INCLUDE_DIRECTORIES>
     )
     target_compile_definitions(CloudJBuildProperties
-        INTERFACE ESMF_
+        INTERFACE MAPL_ESMF
     )
 endif()
 

src/Core/CMakeLists.txt

@@ -1,12 +1,12 @@
 # Cloud-J/src/Core/CMakeLists.txt
 
 add_library(CloudJ_Core STATIC EXCLUDE_FROM_ALL
-        cldj_cmn_mod.f90
-        cldj_error_mod.f90
-        cldj_init_mod.f90
-        cld_sub_mod.f90
-        fjx_sub_mod.f90
-        osa_sub_mod.f90
+        cldj_cmn_mod.F90
+        cldj_error_mod.F90
+        cldj_init_mod.F90
+        cldj_sub_mod.F90
+        cldj_fjx_sub_mod.F90
+        cldj_osa_sub_mod.F90
 )
 target_link_libraries(CloudJ_Core
 	PUBLIC CloudJBuildProperties