Update teout standard name for check_energy; bring in check_energy di…

…agnostic output (#339)

Tag name (required for release branches): sima0_03_000
Originator(s): @jimmielin 

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

Closes ESCOMP/atmospheric_physics#161,
ESCOMP/atmospheric_physics#166,
ESCOMP/atmospheric_physics#176:
- Fixes Add check_energy related history output variables to
check_energy_diagnostics
ESCOMP/atmospheric_physics#161
- Fixes Need to remove old CAM suite definition files
[#166](ESCOMP/atmospheric_physics#166) as well
(but other PRs might get to it first) since I'm modifying the SDF files
in this PR anyway
- Fixes Update standard name for teout
[#176](ESCOMP/atmospheric_physics#176)
(updates teout standard name to
vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep)

Companion PRs:
- ESCOMP/atmospheric_physics#178
- ESCOMP/atmospheric_physics#169

Describe any changes made to build system: N/A

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary
datasets): N/A

List all files eliminated and why: N/A

List all files added and what they do: N/A

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)

```
Updates teout standard name to vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep
M       src/data/registry.xml
M       src/dynamics/mpas/dyn_comp.F90
M       src/dynamics/none/dyn_grid.F90
M       src/dynamics/se/dyn_comp.F90

Updates atmospheric_physics submodule.
M       .gitmodules
M       src/physics/ncar_ccpp

Notes that CAM7 test is preexisting failure.
M       test/existing-test-failures.txt
```

If there are new failures (compared to the
`test/existing-test-failures.txt` file),
have them OK'd by the gatekeeper, note them here, and add them to the
file.
If there are baseline differences, include the test and the reason for
the
diff. What is the nature of the change? Roundoff?

```
derecho/intel/aux_sima:
  SMS_Ln9.mpasa480_mpasa480.FKESSLER.derecho_intel.cam-outfrq_kessler_mpas_derecho (Overall: DIFF) details:
  SMS_Ln9.ne5pg3_ne5pg3_mg37.FKESSLER.derecho_intel.cam-outfrq_se_cslam (Overall: DIFF) details:
  SMS_Ln9.ne5pg3_ne5pg3_mg37.FTJ16.derecho_intel.cam-outfrq_se_cslam (Overall: DIFF) details:
    - baseline differences due to new thermo_water_update scheme in Kessler and TJ2016.

  
  SMS_Ln9.ne5pg3_ne5pg3_mg37.FCAM7.derecho_intel.cam-outfrq_se_cslam_analy_ic (Overall: FAIL) details:
    - pre-existing failure in CAM7 tests
```

```
derecho/gnu/aux_sima:
  SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_kessler_derecho (Overall: NLFAIL) details:
    FAIL SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_kessler_derecho NLCOMP
    - suite_kessler.xml changed to suite_kessler_test.xml, NLCOMP failure for physics_suite.
      the actual run passes BFB

  SMS_Ln9.mpasa480_mpasa480.FKESSLER.derecho_gnu.cam-outfrq_kessler_mpas_derecho (Overall: DIFF) details:
  SMS_Ln9.ne5pg3_ne5pg3_mg37.FKESSLER.derecho_gnu.cam-outfrq_se_cslam (Overall: DIFF) details:
  SMS_Ln9.ne5pg3_ne5pg3_mg37.FTJ16.derecho_gnu.cam-outfrq_se_cslam (Overall: DIFF) details:
    - baseline differences due to new thermo_water_update scheme in Kessler and TJ2016.

  SMS_Ln9.ne5pg3_ne5pg3_mg37.FCAM7.derecho_gnu.cam-outfrq_se_cslam_analy_ic (Overall: FAIL) details:
    - pre-existing failure in CAM7 tests
```

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:

CAM-SIMA date used for the baseline comparison tests if different than
latest:

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = atmos_phys0_08_000
+	fxtag         = 252b500a93c89f36ece7d8ba08fd8eb025279eaa
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_derecho/shell_commands

@@ -1 +1 @@
- ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler"
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler_test"

src/data/registry.xml

@@ -256,7 +256,7 @@
       <ic_file_input_names>tw_cur state_tw_cur</ic_file_input_names>
     </variable>
     <variable local_name="teout"
-              standard_name="vertically_integrated_total_energy_at_end_of_physics_timestep"
+              standard_name="vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep"
               units="J m-2" type="real" kind="kind_phys"
               allocatable="allocatable">
       <long_name>Total energy using dynamical core formula at the end of physics timestep</long_name>
@@ -343,7 +343,7 @@
       <data>vertically_integrated_total_energy_using_dycore_energy_formula</data>
       <data>vertically_integrated_total_water_at_start_of_physics_timestep</data>
       <data>vertically_integrated_total_water</data>
-      <data>vertically_integrated_total_energy_at_end_of_physics_timestep</data>
+      <data>vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep</data>
     </ddt>
     <ddt type="physics_tend">
       <data>tendency_of_air_temperature_due_to_model_physics</data>

src/dynamics/mpas/dyn_comp.F90

@@ -1072,8 +1072,8 @@ subroutine mark_variables_as_initialized()
         ! While we are not responsible for initializing or updating them, we still need to help mark them as initialized.
 
         ! These variables are to be set externally by the `check_energy_chng` CCPP physics scheme.
-        call mark_as_initialized('vertically_integrated_total_energy_at_end_of_physics_timestep')
         call mark_as_initialized('vertically_integrated_total_energy_using_dycore_energy_formula')
+        call mark_as_initialized('vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep')
         call mark_as_initialized('vertically_integrated_total_energy_using_dycore_energy_formula_at_start_of_physics_timestep')
         call mark_as_initialized('vertically_integrated_total_energy_using_physics_energy_formula')
         call mark_as_initialized('vertically_integrated_total_energy_using_physics_energy_formula_at_start_of_physics_timestep')

src/dynamics/none/dyn_grid.F90

@@ -703,7 +703,7 @@ subroutine find_energy_formula(file, grid_is_latlon)
       call mark_as_initialized("vertically_integrated_total_energy_using_dycore_energy_formula")
       call mark_as_initialized("vertically_integrated_total_water_at_start_of_physics_timestep")
       call mark_as_initialized("vertically_integrated_total_water")
-      call mark_as_initialized("vertically_integrated_total_energy_at_end_of_physics_timestep")
+      call mark_as_initialized("vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep")
 
    end subroutine find_energy_formula
 

src/dynamics/se/dyn_comp.F90

@@ -1873,7 +1873,7 @@ subroutine read_inidat(dyn_in)
    call mark_as_initialized("vertically_integrated_total_energy_using_dycore_energy_formula")
    call mark_as_initialized("vertically_integrated_total_water_at_start_of_physics_timestep")
    call mark_as_initialized("vertically_integrated_total_water")
-   call mark_as_initialized("vertically_integrated_total_energy_at_end_of_physics_timestep")
+   call mark_as_initialized("vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep")
 
 end subroutine read_inidat
 

test/existing-test-failures.txt

@@ -1 +1,4 @@
-All clear!
+SMS_Ln9.ne5pg3_ne5pg3_mg37.FCAM7.derecho_intel.cam-outfrq_se_cslam_analy_ic (Overall: FAIL) details:
+SMS_Ln9.ne5pg3_ne5pg3_mg37.FCAM7.derecho_gnu.cam-outfrq_se_cslam_analy_ic (Overall: FAIL) details:
+- CAM7 suite will not work without a PBL scheme
+- CAM7 suite will not work with snapshot fields in registry.xml even if initial_value is defined (CAM-SIMA#359)