Merge pull request #31 from geoschem/release/8.0.2

Merge release 8.0.2 into main

Author: lizziel

.github/workflows/mac.yml

@@ -15,6 +15,7 @@ jobs:
   gnu:
     runs-on: macos-latest
     strategy:
+      fail-fast: false
       matrix:
         gcc_version: [12, 13, 14]
         build_type: [Debug, Release]
@@ -32,3 +33,7 @@ jobs:
 
       - name: Build
         run: cmake --build build  --verbose
+      
+      - name: Run tests
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build

.github/workflows/ubuntu.yml

@@ -1,19 +1,26 @@
 name: Ubuntu
 
-on: [pull_request, workflow_dispatch]
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
   cancel-in-progress: true
 
 jobs:
   gnu:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     strategy:
+      fail-fast: false
       matrix:
+        gcc_version: [12, 13, 14]
         build_type: [Debug, Release]
     env:
-      FC: gfortran
+      FC: gfortran-${{ matrix.gcc_version }}
 
     steps:
       - name: Checkout code
@@ -29,3 +36,7 @@ jobs:
 
       - name: Build
         run: cmake --build build  --verbose
+
+      - name: Run tests
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build

.github/workflows/windows.yml

@@ -0,0 +1,55 @@
+name: Windows
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gnu:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: [Debug, Release]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup MSYS2
+        uses: msys2/setup-msys2@v2
+        with:
+          update: true
+          install: >-
+            base-devel
+            mingw-w64-x86_64-toolchain
+            mingw-w64-x86_64-gcc
+            mingw-w64-x86_64-gcc-fortran
+            mingw-w64-x86_64-cmake
+            mingw-w64-x86_64-netcdf
+            mingw-w64-x86_64-netcdf-fortran
+          msystem: MINGW64
+
+      - name: Add MSYS2 mingw64 to PATH
+        shell: msys2 {0}
+        run: echo "C:/msys64/mingw64/bin" >> $GITHUB_PATH
+
+      - name: Configure with CMake
+        shell: msys2 {0}
+        run: cmake -G "MinGW Makefiles" -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build the project
+        shell: msys2 {0}
+        run: cmake --build build  --verbose
+
+      - name: Run tests
+        shell: msys2 {0}
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build

CHANGELOG.md

@@ -4,6 +4,13 @@ This file documents all notable changes to the Cloud-J repository since the init
 
 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).
 
+## [8.0.2] - 2015-03-25
+### Added
+- Added Github actions workflow to build on Windows
+- Added tests which compare the output of Cloud-J to some saved reference output
+- Added four optional output arguments to CLOUD_JX and made them required in PHOTO_JX to retrieve direct and diffuse fluxes
+- Added version and license badges to README
+
 ## [8.0.1] - 2024-09-30
 ### Added
 - Added error handling to exit the model if JVN_ is less than number of entries in FJX_j2j.dat

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Cloud-J/CMakeLists.txt
 
 cmake_minimum_required(VERSION 3.5)
-project(CLOUDJ VERSION 8.0.1 LANGUAGES Fortran)
+project(CLOUDJ VERSION 8.0.2 LANGUAGES Fortran)
 
 #-----------------------------------------------------------------------------
 # Add CMakeScripts/ to the module path
@@ -18,6 +18,11 @@ message("Cloud-J ${PROJECT_VERSION}")
 message("Current status: ${CLDJ_REPO_VERSION}")
 message("=================================================================")
 
+#-----------------------------------------------------------------------------
+# options
+#-----------------------------------------------------------------------------
+option(CLOUDJ_ENABLE_TESTS "Build the tests" ON)
+
 #-----------------------------------------------------------------------------
 # Set policies
 #-----------------------------------------------------------------------------
@@ -326,9 +331,9 @@ file(WRITE ${CMAKE_BINARY_DIR}/CloudJBuildProperties.txt
     "CloudJBuildProperties::INTERFACE_INCLUDE_DIRECTORIES:${BT_INCLUDES}\n"
 )
 
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Try to compile a simple program that uses NetCDF-Fortran and OpenMP
-#-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 if(NOT CLOUDJ_EXTERNAL_CONFIG AND NOT CLOUDJ_TRY_RUN_PASSED)
 
     # Format definitions with -D prefix
@@ -410,3 +415,19 @@ endif()
 # Add source code directory
 #-----------------------------------------------------------------------------
 add_subdirectory(src)
+
+#-----------------------------------------------------------------------------
+# Add test directory
+#-----------------------------------------------------------------------------
+if (CLOUDJ_ENABLE_TESTS)
+    enable_testing()
+
+    add_subdirectory(test)
+
+    #-----------------------------------------------------------------------------
+    # The executable needs the data tables, copy them into the bin directory if tests are enabled
+    #-----------------------------------------------------------------------------
+
+    add_custom_target(copy_table_data ALL ${CMAKE_COMMAND} -E copy_directory
+    ${PROJECT_SOURCE_DIR}/tables ${PROJECT_BINARY_DIR}/bin/tables)
+endif()

README.md

@@ -1,8 +1,18 @@
 # Cloud-J
 
-[![Ubuntu](https://github.com/geoschem/Cloud-J/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/geoschem/Cloud-J/actions/workflows/ubuntu.yml)
-[![Mac](https://github.com/geoschem/Cloud-J/actions/workflows/mac.yml/badge.svg)](https://github.com/geoschem/Cloud-J/actions/workflows/mac.yml)
-[![License](https://img.shields.io/badge/license-GPLv3-blue)](https://github.com/geoschem/Cloud-J/blob/main/LICENSE)
+<p>
+  <a href="https://github.com/geoschem/hemco/cloud-j"><img src="https://img.shields.io/github/v/release/geoschem/cloud-j?include_prereleases&label=Latest%20Pre-Release"></a>
+  <a href="https://github.com/geoschem/cloud-j/releases"><img src="https://img.shields.io/github/v/release/geoschem/cloud-j?label=Latest%20Stable%20Release"></a>
+  <a href="https://github.com/geoschem/cloud-j/releases/"><img src="https://img.shields.io/github/release-date/geoschem/cloud-j"></a>
+  <br />
+  <a href="https://doi.org/10.5281/zenodo.13862693"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13862693.svg" alt="DOI"></a>
+  <a href="https://github.com/geoschem/Cloud-J/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg"></a>
+  <a href="https://github.com/geoschem/Cloud-J/actions/workflows/ubuntu.yml"><img src="https://github.com/geoschem/Cloud-J/actions/workflows/ubuntu.yml/badge.svg" alt="Ubuntu"></a>
+  <a href="https://github.com/geoschem/Cloud-J/actions/workflows/mac.yml"><img src="https://github.com/geoschem/Cloud-J/actions/workflows/mac.yml/badge.svg" alt="Mac"></a>
+  <a href="https://github.com/geoschem/Cloud-J/actions/workflows/windows.yml"><img src="https://github.com/geoschem/Cloud-J/actions/workflows/windows.yml/badge.svg" alt="Windows"></a>
+</p>
+
+## Description
 
 Cloud-J is a multi-scattering eight-stream radiative transfer model for solar radiation based on Fast-J. It was originally developed by Michael J. Prather (UCI). For information about the origins and history of Cloud-J and its predecessor Fast-J please see the [history document](https://github.com/geoschem/cloud-j/blob/main/docs/History_of_Fast-J_photolysis_code.md) in the docs subdirectory of this repository.
 
@@ -82,6 +92,21 @@ cd cloudj_rundir
 ./cloudj_standalone | tee cloudj.log 2>&1
 ```
 
+
+## How to run the tests
+Cloud-J ensures correctness by testing all changes against known output. This means that anytime that input data
+or an algorithm changes the [reference output](test/expected_output/reference_output.txt) will need to be updated.
+
+To run the tests, compile Cloud-J and then run `make test` or `ctest` from within the build directory.
+
+```
+make test
+```
+
+```
+ctest
+```
+
 ## Debugging
 
 If you wish to build Cloud-J with compiler debug flags on simply run the following command in your build folder prior to the <tt>make</tt> command.

src/Core/cldj_fjx_sub_mod.F90

@@ -119,7 +119,8 @@ MODULE CLDJ_FJX_SUB_MOD
 !-----------------------------------------------------------------------
       subroutine PHOTO_JX (U0,SZA,RFL,SOLF, LPRTJ, PPP,ZZZ,TTT,HHH,    &
                        DDD,RRR,OOO, CCC, LWP,IWP,REFFL,REFFI,AERSP,    &
-                       NDXAER, L1U,ANU,NJXU, VALJXX,SKPERD,SWMSQ,OD18, LDARK,RC)
+                       NDXAER, L1U,ANU,NJXU, VALJXX,SKPERD,SWMSQ,OD18, &
+                       LDARK,FSBOT,FJBOT,FLXD,FJFLX,RC)
 !  PHOTO_JX is the gateway to single column fast-JX calculations:
 !    calc J's for a single column atmosphere (aka Indep Colm Atmos or ICA)
 !    needs P, T, O3, clds, aersls, SZA (not lat or long), albedos, ...
@@ -149,12 +150,16 @@ subroutine PHOTO_JX (U0,SZA,RFL,SOLF, LPRTJ, PPP,ZZZ,TTT,HHH,    &
       integer, intent(in)                    :: L1U   ! cloud-j input
       integer, intent(in)                    :: NJXU  ! cloud-j input
 ! reports out the JX J-values, upper level program converts to CTM chemistry J's
-      real*8,intent(out), dimension(L1U-1,NJXU):: VALJXX ! cloud-j output
-      real*8,intent(out), dimension(S_+2,L1U)  :: SKPERD ! cloud-j output
-      real*8,  intent(out), dimension(6)       :: SWMSQ  ! cloud-j output
-      real*8,  intent(out), dimension(L1U)     :: OD18   ! cloud-j output
-      logical, intent(out)                     :: LDARK  ! cloud-j output
-      integer, intent(inout)                   :: RC     ! cloud-j output
+      real*8,  intent(out), dimension(L1U-1,NJXU) :: VALJXX
+      real*8,  intent(out), dimension(S_+2,L1U)   :: SKPERD
+      real*8,  intent(out), dimension(6)          :: SWMSQ
+      real*8,  intent(out), dimension(L1U)        :: OD18
+      logical, intent(out)                        :: LDARK
+      real*8,  intent(out), dimension(W_+W_r)     :: FSBOT
+      real*8,  intent(out), dimension(W_+W_r)     :: FJBOT
+      real*8,  intent(out), dimension(L1U,W_+W_r) :: FLXD
+      real*8,  intent(out), dimension(L1U,W_+W_r) :: FJFLX
+      integer, intent(inout)                      :: RC
 
 !-----------------------------------------------------------------------
       character(len=255)  ::  thisloc, errmsg
@@ -164,10 +169,10 @@ subroutine PHOTO_JX (U0,SZA,RFL,SOLF, LPRTJ, PPP,ZZZ,TTT,HHH,    &
       real*8, dimension(L1_)   :: TTJ,HHJ,DDJ,RRJ,OOJ,CCJ
       integer,dimension(L1_)   :: JXTRA
 !
-      real*8, dimension(W_+W_r)       :: FJTOP,FJBOT,FSBOT,FLXD0
+      real*8, dimension(W_+W_r)       :: FJTOP, FLXD0
       real*8, dimension(5,W_+W_r)     :: FIBOT
-      real*8, dimension(L1_,W_+W_r)   :: AVGF, FJFLX
-      real*8, dimension(L1_,W_+W_r)   :: DTAUX, FLXD
+      real*8, dimension(L1_,W_+W_r)   :: AVGF
+      real*8, dimension(L1_,W_+W_r)   :: DTAUX
       real*8, dimension(8,L1_,W_+W_r) :: POMEGAX
 !
       real*8, dimension(L1_)        ::  DTAU600