Upgrading to atmos_phys0_07_000 (#158)

Tag name (The PR title should also include the tag name):
`atmos_phys0_07_000`
Originator(s): @jimmielin

List all `development` PR URLs included in this PR and a short
description of each:
* #141 by @mattldawson @boulderdaze 
* #147 by @peverwhee 
* #144 by @mwaxmonsky 
* #151 by @mattldawson 
* #145 by @jimmielin 

List all test failures: N/A

.github/workflows/unit-tests.yaml

@@ -0,0 +1,72 @@
+name: unit-test-code-coverage
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  workflow_dispatch:
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gcc-toolchain:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout atmospheric_physics
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt update && sudo apt -y install libopenmpi-dev openmpi-bin
+
+      - name: Build pFUnit
+        run: |
+          git clone --depth 1 --branch v4.10.0 https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
+          cd pFUnit
+          pwd
+          cmake -B./build -S.
+          cd build
+          make install
+
+      - name: Build atmospheric_physics
+        run: |
+          cmake \
+            -DCMAKE_PREFIX_PATH=/home/runner/work/atmospheric_physics/atmospheric_physics/pFUnit/build/installed \
+            -DATMOSPHERIC_PHYSICS_ENABLE_CODE_COVERAGE=ON \
+            -B./build \
+            -S./test/unit-test
+          cd build
+          make
+
+      - name: Run tests
+        run: |
+          cd build && ctest -V --output-on-failure --output-junit test_results.xml
+
+      - name: Upload unit test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: unit-test-results
+          path: build/test_results.xml
+
+      - name: Setup GCov
+        run: |
+          python3 -m venv venv
+          source venv/bin/activate
+          pip3 install gcovr
+
+      - name: Run Gcov
+        run: |
+          source venv/bin/activate
+          cd build
+          gcovr -r .. --filter '\.\./schemes' --html atmospheric_physics_code_coverage.html --txt
+
+      - name: Upload code coverage results
+        uses: actions/upload-artifact@v4
+        with:
+          name: code-coverage-results
+          path: build/atmospheric_physics_code_coverage.html
+

.gitignore

@@ -0,0 +1,7 @@
+**/*.DS_Store
+**/*.pyc
+**/build/
+**/CMakeCache.txt
+**/CMakeFiles/
+.vscode
+xcode/

doc/ChangeLog

@@ -1,5 +1,77 @@
 ===============================================================
 
+Tag name: atmos_phys0_07_000
+Originator(s): jimmielin
+Date: November 18, 2024
+One-line Summary: Implement CCPPized check_energy_chng and check_energy_fix
+Github PR URL:
+
+This PR fixes the following NCAR/atmospheric_physics Github issues: #114
+
+- Implements check_energy_chng. The routine computes total energies using physics and dycore formula and takes in boundary fluxes of vapor, liquid+ice, ice, sensible heat, and writes to log significant energy conservation errors.
+In order to take in the scheme name and fluxes from the last calling physics scheme (usually zero) a check_energy_zero_fluxes has to be ran before the scheme, then the physics scheme to be checked, then check_energy_chng.
+
+- Implements check_energy_fix. The routine computes the heating rate required for global mean total energy conservation which is later applied by apply_heating_rate.
+Supporting routines include the global mean calculator for total energy (check_energy_gmean) - stored in separate folder to prevent CAM from building it.
+The global means are very useful for diagnosing model state (as the computed energy numbers include all model state incl. constituents) through a simple one-line printout. check_energy_gmean_diagnostics implements this.
+At the end of the timestep check_energy_save_teout has to be ran in order to save total energies at the end of the timestep for use in the next timestep.
+
+- Diagnostics of intermediate quantities used in check_energy_diagnostics.
+
+- Implements dycore_energy_consistency_adjust which adjusts temperature and temperature tendencies for the MPAS and SE dynamical cores.
+
+Code reviewed by:
+
+List all existing files that have been added (A), modified (M), or deleted (D),
+and describe the changes:
+
+- Docs:
+M       doc/ChangeLog
+
+- check_energy_chng and supporting routines:
+A       schemes/check_energy/check_energy_chng.F90
+A       schemes/check_energy/check_energy_chng.meta
+A       schemes/check_energy/check_energy_chng_namelist.xml
+A       schemes/check_energy/check_energy_scaling.F90
+A       schemes/check_energy/check_energy_scaling.meta
+A       schemes/check_energy/check_energy_zero_fluxes.F90
+A       schemes/check_energy/check_energy_zero_fluxes.meta
+
+- check_energy_fix and supporting routines:
+A       schemes/check_energy/check_energy_fix.F90
+A       schemes/check_energy/check_energy_fix.meta
+A       schemes/check_energy/check_energy_gmean/check_energy_gmean.F90
+A       schemes/check_energy/check_energy_gmean/check_energy_gmean.meta
+A       schemes/check_energy/check_energy_save_teout.F90
+A       schemes/check_energy/check_energy_save_teout.meta
+
+- check_energy related diagnostics:
+A       schemes/sima_diagnostics/check_energy_diagnostics.F90
+A       schemes/sima_diagnostics/check_energy_diagnostics.meta
+
+- check_energy_gmean "nstep, te" atm.log output:
+A       schemes/sima_diagnostics/check_energy_gmean_diagnostics.F90
+A       schemes/sima_diagnostics/check_energy_gmean_diagnostics.meta
+
+- dycore_energy_consistency_adjust and applications in simple physics:
+A       schemes/check_energy/dycore_energy_consistency_adjust.F90
+A       schemes/check_energy/dycore_energy_consistency_adjust.meta
+M       suites/suite_held_suarez_1994.xml
+M       suites/suite_kessler.xml
+
+- add check_energy to SDFs:
+M       suites/suite_cam7.xml
+
+- adiabatic SDF:
+A       suites/suite_adiabatic.xml
+
+
+List and Describe any test failures: N/A
+
+Summarize any changes to answers: none
+
+===============================================================
+
 Tag name:
 Originator(s): jimmielin
 Date: October 17, 2024