Address review comments

src/data/air_composition.F90

@@ -559,13 +559,13 @@ subroutine water_composition_update(mmr, ncol, energy_formula, cp_or_cv_dycore,
          ! FV: moist pressure vertical coordinate does not need update.
       else if (energy_formula == ENERGY_FORMULA_DYCORE_SE) then
          ! SE
-         ! Note: species index subset to 1: because SIMA currently uses index 0. See #334.
+         ! Note: species index subset to 1: because SIMA currently uses index 0. See GitHub issue #334 in ESCOMP/CAM-SIMA.
          call get_cp(mmr(:ncol,:,:), .false., cp_or_cv_dycore(:ncol,:), &
                      factor=to_dry_factor, active_species_idx_dycore=thermodynamic_active_species_idx(1:), &
                      cpdry=cpairv(:ncol,:))
       else if (energy_formula == ENERGY_FORMULA_DYCORE_MPAS) then
          ! MPAS
-         ! Note: species index subset to 1: because SIMA currently uses index 0. See #334.
+         ! Note: species index subset to 1: because SIMA currently uses index 0. See GitHub issue #334 in ESCOMP/CAM-SIMA.
          call get_R(mmr(:ncol,:,:), thermodynamic_active_species_idx(1:), &
                     cp_or_cv_dycore(:ncol,:), fact=to_dry_factor, Rdry=rairv(:ncol,:))
 
@@ -699,7 +699,8 @@ subroutine get_cp_1hd(tracer, inv_cp, cp, factor, active_species_idx_dycore, cpd
       ! inv_cp: output inverse cp instead of cp
       logical,                   intent(in)  :: inv_cp
       real(kind_phys),           intent(out) :: cp(:,:)
-      ! if provided then tracer is not a mass mixing ratio
+      ! factor: to convert tracer to dry mixing ratio
+      ! if provided, then tracer is not a dry mass mixing ratio
       real(kind_phys), optional, intent(in)  :: factor(:,:)
       ! active_species_idx_dycore: array of indices for index of
       !    thermodynamic active species in dycore tracer array

src/data/cam_thermo.F90

@@ -241,10 +241,10 @@ subroutine cam_thermo_dry_air_update(mmr, T, ncol, pver, update_thermo_variables
 
       if (present(to_dry_factor)) then
         if (SIZE(to_dry_factor, 1) /= ncol) then
-          call endrun(subname//'DIM 1 of to_dry_factor is'//stringify((/SIZE(to_dry_factor,1)/))//'but should be'//stringify((/ncol/)))
+          call endrun(subname//'DIM 1 of to_dry_factor is '//stringify((/SIZE(to_dry_factor,1)/))//' but should be '//stringify((/ncol/)))
         end if
         if (SIZE(to_dry_factor, 2) /= pver) then
-          call endrun(subname//'DIM 2 of to_dry_factor is'//stringify((/SIZE(to_dry_factor,2)/))//'but should be'//stringify((/pver/)))
+          call endrun(subname//'DIM 2 of to_dry_factor is '//stringify((/SIZE(to_dry_factor,2)/))//' but should be '//stringify((/pver/)))
         end if
       end if
 
@@ -285,10 +285,10 @@ subroutine cam_thermo_water_update(mmr, ncol, pver, energy_formula, cp_or_cv_dyc
 
       if (present(to_dry_factor)) then
         if (SIZE(to_dry_factor, 1) /= ncol) then
-          call endrun(subname//'DIM 1 of to_dry_factor is'//stringify((/SIZE(to_dry_factor,1)/))//'but should be'//stringify((/ncol/)))
+          call endrun(subname//'DIM 1 of to_dry_factor is '//stringify((/SIZE(to_dry_factor,1)/))//' but should be '//stringify((/ncol/)))
         end if
         if (SIZE(to_dry_factor, 2) /= pver) then
-          call endrun(subname//'DIM 2 of to_dry_factor is'//stringify((/SIZE(to_dry_factor,2)/))//'but should be'//stringify((/pver/)))
+          call endrun(subname//'DIM 2 of to_dry_factor is '//stringify((/SIZE(to_dry_factor,2)/))//' but should be '//stringify((/pver/)))
         end if
       end if
 

src/dynamics/none/dyn_grid.F90

@@ -645,6 +645,11 @@ subroutine find_energy_formula(file, grid_is_latlon)
 
       ! Find which dynamical core is used in <file> and set the energy formulation
       ! (also called vc_dycore in CAM)
+      !
+      ! This functionality is only used to recognize the originating dynamical core
+      ! from the snapshot file in order to set the energy formulation when running
+      ! with the null dycore. Other dynamical cores set energy_formula_dycore at their
+      ! initialization.
 
       type(file_desc_t), intent(inout) :: file
       logical, intent(in)              :: grid_is_latlon

src/dynamics/se/dp_coupling.F90

@@ -784,10 +784,6 @@ subroutine derived_phys_dry(cam_runtime_opts, phys_state, phys_tend)
    ! Compute molecular viscosity(kmvis) and conductivity(kmcnd).
    ! Update zvirv registry variable; calculated for WACCM-X.
    !-----------------------------------------------------------------------------
-   ! **TEMP** TODO CHECK hplin: CAM has this if-clause for dry_air_species_num > 0
-   ! or otherwise uses zvirv = zvir. CAM-SIMA previously did not have this, and
-   ! instead has a switch for update_thermodynamic_variables. Check if we still want
-   ! this if-clause or change it to something else.
    if (dry_air_species_num > 0) then
       call cam_thermo_dry_air_update( &
            mmr                     = const_data_ptr, & ! dry MMR