Feature/cp mconv

[ywkawai]

close #551
close #553

[Copilot]

Pull request overview

This PR adds a moist convective adjustment (MCONV) cumulus parameterization pathway and extends the PBL/turbulence plumbing to handle tracer (QV) vertical diffusion, alongside a refactor that splits physics variable initialization into Init vs Setup phases and wires physics history output accordingly.

Changes:

• Add a new DG moist convective adjustment cumulus scheme and integrate it into the atmospheric CP component.
• Extend BL/PBL turbulence tendency computation to include tracer tendencies and update the boundary-layer test case outputs/config accordingly.
• Refactor multiple physics “vars” modules to introduce a Setup method and call these from AtmosComponent_setup_vars; adjust RK time integration initialization logic.

Reviewed changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
model/atm_nonhydro3d/test/case/boundary_layer/visualize/visualize.sh	Adds QV/BL_QV_t plots and reorders plotted fields.
model/atm_nonhydro3d/test/case/boundary_layer/run.conf	Enables QV history output and adds BL_QV_t history item.
model/atm_nonhydro3d/test/case/boundary_layer/mod_user.F90	Updates boundary-layer initial conditions (surface potential temperature + RH-based QV init logic).
model/atm_nonhydro3d/test/case/boundary_layer/init.conf	Renames TEMP0→SFC_POTT and changes ENV_RH default.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_tb_vars.F90	Introduces Setup method; shifts variable-object setup responsibilities.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_sfc.F90	Passes default surface temp into vars initialization; removes separate default-value call.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_sfc_vars.F90	Splits vars init vs setup; moves allocation/registration into Setup.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_rd_vars.F90	Splits vars init vs setup for radiation variables.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_mp_vars.F90	Splits vars init vs setup for microphysics variables.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_cp.F90	Adds CP type for moist convective adjustment; integrates tendency calculation/finalize hooks.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_cp_vars.F90	Adds Setup, tendency-field getter helper, and expands history writing for CP vars.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_bl.F90	Extends BL tendency computation to include tracer tendencies and apply them to forcing terms.
model/atm_nonhydro3d/src/atmos/mod_atmos_phy_bl_vars.F90	Adds Setup and registers BL tracer tendency variables (but currently with range/count issues).
model/atm_nonhydro3d/src/atmos/mod_atmos_component.F90	Calls physics vars Setup for activated components during Atmos vars setup.
model/atm_nonhydro3d/src/admin/mod_dg_driver.F90	Adds CP vars history output in normal and restart-read output paths.
FElib/src/Makefile	Adds cumulus directory and CP object(s) to the build.
FElib/src/fluid_dyn_solver/scale_atm_dyn_dgm_driver_trcadv3d.F90	Fixes/ensures local mesh pointer is set before per-cell update.
FElib/src/depend	Adds dependency line for the new cumulus adjustment object.
FElib/src/cumulus/scale_atm_phy_cp_dgm_mconv_adjustment.F90	New moist convective adjustment DG implementation producing density/rhot/rhoqv tendencies and rain flux.
FElib/src/common/scale_timeint_rk.F90.erb	Updates RK init logic for stage 1 and adds var0 initialization (OpenACC present-list needs update).
FElib/src/common/scale_timeint_rk.F90	Same RK change as template; currently missing var0 mapping in OpenACC present(...).
FElib/src/bl_turbulence/scale_atm_phy_bl_dgm_mynn_lv2.F90	Extends MYNN lv2 visc/diff coef calc to include Rtot gradient term in stability metrics.
FElib/src/bl_turbulence/scale_atm_phy_bl_dgm_common.F90	Extends BL common vertical diffusion solver to handle QA tracer components in the block system.

Comments suppressed due to low confidence (3)

FElib/src/common/scale_timeint_rk.F90:2227

• The OpenACC region writes to var0_2d(i,j,varID), but var0_2d is not included in the present(...) clause. With OpenACC enabled this can fail at runtime due to missing device data mapping.

    if ( nowstage == 1 .and. (.not. this%imex_flag) ) then
      !$omp parallel do
      !$acc parallel loop collapse(2) present( q, varTmp_2d )
      do j=js, je
      do i=is, ie
        var0_2d(i,j,varID) = q(i,j)

FElib/src/common/scale_timeint_rk.F90:2593

• The OpenACC region writes to var0_3d(i,j,k,varID), but var0_3d is not listed in the present(...) clause. This is likely to cause an OpenACC runtime error (data not present on device).

    if ( nowstage == 1 .and. (.not. this%imex_flag) ) then
      !$omp parallel do collapse(2)
      !$acc parallel loop collapse(3) present( q, varTmp_3d )
      do k=ks, ke
      do j=js, je
      do i=is, ie
        var0_3d(i,j,k,varID) = q(i,j,k)
        varTmp_3d(i,j,k,varID) = q(i,j,k)

model/atm_nonhydro3d/src/atmos/mod_atmos_phy_bl_vars.F90:193

• This loop iterates iq=1,QA (global tracer count) but indexes tracer metadata as TRACER_NAME(this%QS+iq-1). With the current BL setup (QS_BL=QA, QA_BL=0) this will immediately reference tracers outside the BL range and can go out of bounds when QA>1.

    do iq = 1, QA
      iv = ATMOS_PHY_BL_TENDS_NUM1 + iq 
      qtrc_tp_vinfo_tmp%keyID = iv
      qtrc_tp_vinfo_tmp%NAME  = 'BL_'//trim(TRACER_NAME(this%QS+iq-1))//'_t'
      qtrc_tp_vinfo_tmp%DESC  = 'tendency of rho*'//trim(TRACER_NAME(this%QS+iq-1))//' in BL process'
      qtrc_tp_vinfo_tmp%UNIT  = 'kg/m3/s'

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