Implements cam_thermo_water_update and CCPPized check_energy

.gitmodules

@@ -19,8 +19,8 @@
         fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
-	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = e95c172d7a5a0ebf054f420b08416228e211baa3
+	url           = https://github.com/jimmielin/atmospheric_physics
+	fxtag         = 7b188e35
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/config_component.xml

@@ -159,8 +159,8 @@
       <value compset="_CAM\d0%WX.*%SDYN">-nlev 145</value> -->
 
       <!-- Simple models -->
-<!--      <value compset="_CAM%ADIAB">-phys adiabatic</value>
-      <value compset="_CAM%DABIP04">-phys adiabatic</value> -->
+      <value compset="_CAM%ADIAB">--physics-suites adiabatic</value>
+<!--      <value compset="_CAM%DABIP04">-phys adiabatic</value> -->
       <value compset="_CAM%TJ16">--physics-suites tj2016 --analytic_ic</value>
 <!--      <value compset="_CAM%KESSLER">-phys kessler -chem terminator -analytic_ic</value> -->
       <value compset="_CAM%KESSLER">--physics-suites kessler --analytic_ic</value>

cime_config/namelist_definition_cam.xml

@@ -104,6 +104,10 @@
       <value hgrid="8x16" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-01-01_8x16_L26_c030228.nc</value>
       <value hgrid="8x16" ic_ymd="901" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-09-01_8x16_L26_c030918.nc</value>
       <value hgrid="8x16" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-01-01_8x16_L30_c090102.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="32">${DIN_LOC_ROOT}/atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L32_01-01-31_c221214.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="901" nlev="32">${DIN_LOC_ROOT}/atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-09-01-00000.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L30_c120315.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L26_c120525.nc</value>
       <value dyn="se" hgrid="ne5np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/homme/cami-mam3_0000-01_ne5np4_L30.140707.nc</value>
       <value dyn="se" hgrid="ne16np4" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/se/ape_topo_cam4_ne16np4_L26_c171020.nc</value>
       <value dyn="se" hgrid="ne16np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/se/ape_topo_cam4_ne16np4_L30_c171020.nc</value>

src/control/cam_comp.F90

@@ -29,6 +29,7 @@ module cam_comp
    use physics_types,             only: phys_state, phys_tend
    use physics_types,             only: dtime_phys
    use physics_types,             only: calday
+   use physics_types,             only: is_first_timestep, nstep
    use dyn_comp,                  only: dyn_import_t, dyn_export_t
 
    use perf_mod,                  only: t_barrierf, t_startf, t_stopf
@@ -148,9 +149,6 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       character(len=cx)        :: errmsg
       !-----------------------------------------------------------------------
 
-      dtime_phys = 0.0_r8
-      call mark_as_initialized('timestep_for_physics')
-
       call init_pio_subsystem()
 
       ! Initializations using data passed from coupler.
@@ -166,12 +164,20 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 
       call cam_ctrl_set_orbit(eccen, obliqr, lambm0, mvelpp)
 
-
       call timemgr_init(                                                      &
            dtime, calendar, start_ymd, start_tod, ref_ymd,                    &
            ref_tod, stop_ymd, stop_tod, curr_ymd, curr_tod,                   &
            perpetual_run, perpetual_ymd, initial_run_in)
 
+      dtime_phys = 0.0_r8
+      call mark_as_initialized('timestep_for_physics')
+
+      is_first_timestep = .true.
+      call mark_as_initialized('is_first_timestep')
+
+      nstep = get_nstep()
+      call mark_as_initialized('current_timestep_number')
+
       ! Get current fractional calendar day. Needs to be updated at every timestep.
       calday = get_curr_calday()
       call mark_as_initialized('fractional_calendar_days_on_end_of_current_timestep')
@@ -263,6 +269,10 @@ subroutine cam_timestep_init()
       use phys_comp, only: phys_timestep_init
       use stepon,    only: stepon_timestep_init
 
+      ! Update timestep flags in physics state
+      is_first_timestep = is_first_step()
+      nstep = get_nstep()
+
       !----------------------------------------------------------
       ! First phase of dynamics (at least couple from dynamics to physics)
       ! Return time-step for physics from dynamics.
@@ -509,10 +519,6 @@ subroutine cam_final(cam_out, cam_in)
       type(cam_out_t), pointer :: cam_out ! Output from CAM to surface
       type(cam_in_t),  pointer :: cam_in  ! Input from merged surface to CAM
 
-      !
-      ! Local variable
-      !
-      integer                  :: nstep   ! Current timestep number.
       !-----------------------------------------------------------------------
 
       call phys_final()
@@ -535,7 +541,6 @@ subroutine cam_final(cam_out, cam_in)
       call shr_sys_flush( iulog )   ! Flush all output to the CAM log file
 
       if (masterproc) then
-         nstep = get_nstep()
          write(iulog,9300) nstep-1,nstep
 9300     format (//'Number of completed timesteps:',i6,/,'Time step ',i6,     &
               ' partially done to provide convectively adjusted and ',        &