Add regression test against original cloud chemistry module

src/chemistry/aerosol/cloud_aqueous_chemistry.F90

@@ -3,6 +3,9 @@
 !----------------------------------------------------------------------------------
 module cloud_aqueous_chemistry
 
+#define USE_MAM
+#undef USE_CARMA
+
   use shr_kind_mod, only : r8 => shr_kind_r8
   use cam_logfile,  only : iulog
   use physics_buffer,only: physics_buffer_desc, pbuf_get_index, pbuf_add_field, dtype_r8
@@ -38,7 +41,12 @@ subroutine sox_inti
     use spmd_utils,   only : masterproc
     use phys_control, only : phys_getopts
     use carma_flags_mod, only : carma_do_cloudborne
-    use clouds, only : sox_cldaero_init
+#ifdef USE_MAM
+    use mam_clouds, only : sox_cldaero_init
+#endif
+#ifdef USE_CARMA
+    use carma_clouds, only : sox_cldaero_init
+#endif
 
     logical :: modal_aerosols
 
@@ -129,7 +137,7 @@ subroutine sox_inti
        endif
        return
     end if
-
+    
     call sox_cldaero_init()
 
   end subroutine sox_inti
@@ -186,7 +194,7 @@ subroutine setsox( state, &
 #ifdef USE_MAM
     use mam_clouds,      only : sox_cldaero_update, sox_cldaero_create_obj, sox_cldaero_destroy_obj
 #endif
-#ifdef USE_CLOUDS
+#ifdef USE_CARMA
     use carma_clouds,    only : sox_cldaero_update, sox_cldaero_create_obj, sox_cldaero_destroy_obj
 #endif
     use cloud_utilities, only : cldaero_conc_t

src/chemistry/aerosol/cloud_aqueous_chemistry_snapshot.F90

@@ -0,0 +1,152 @@
+! Captures inputs and output to cloud aqueous chemistry routines
+module cloud_aqueous_chemistry_snapshot
+
+  use shr_kind_mod, only : r8 => shr_kind_r8
+
+  implicit none
+  private
+
+  public :: cloud_snapshot_init, cloud_snapshot_capture_input, cloud_snapshot_capture_output
+
+contains
+
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+  subroutine cloud_snapshot_init()
+
+    use cam_history, only : addfld, horiz_only
+
+    integer :: i_elem
+    character(len=10) :: index_string
+
+    call addfld( 'cloud_press_in',       (/ 'lev' /), 'I', 'Pa',       'mid-point pressure' )
+    call addfld( 'cloud_pdel_in',        (/ 'lev' /), 'I', 'Pa',       'pressure thickness of levels' )
+    call addfld( 'cloud_tfld_in',        (/ 'lev' /), 'I', 'K',        'temperature' )
+    call addfld( 'cloud_mbar_in',        (/ 'lev' /), 'I', 'AMU',      'mean wet atmopheric mass' )
+    call addfld( 'cloud_lwc_in',         (/ 'lev' /), 'I', 'kg kg-1',  'cloud liquid water content' )
+    call addfld( 'cloud_cldfrc_in',      (/ 'lev' /), 'I', 'unitless', 'cloud fraction' )
+    call addfld( 'cloud_cldnum_in',      (/ 'lev' /), 'I', 'kg-1',     'droplet number concentration' )
+    call addfld( 'cloud_xhnm_in',        (/ 'lev' /), 'I', 'cm-3',     'total atmospheric density' )
+    do i_elem = 1, 7
+      write(index_string, '(I10)') i_elem
+      call addfld( 'cloud_invariants_'//trim(adjustl(index_string))//'_in', (/ 'lev' /), 'I', 'unknown', 'invariant' )
+    end do
+    do i_elem = 1, 26
+      write(index_string, '(I10)') i_elem
+      call addfld( 'cloud_qcw_'//trim(adjustl(index_string))//'_in', (/ 'lev' /), 'I', 'vmr', 'cloud-borne aerosol' )
+      call addfld( 'cloud_qcw_'//trim(adjustl(index_string))//'_out', (/ 'lev' /), 'I', 'vmr', 'transported species' )
+      call addfld( 'cloud_qin_'//trim(adjustl(index_string))//'_in', (/ 'lev' /), 'I', 'vmr', 'transported species' )
+      call addfld( 'cloud_qin_'//trim(adjustl(index_string))//'_out', (/ 'lev' /), 'I', 'vmr', 'transported species' )
+    end do
+    call addfld( 'cloud_xphlwc_out',     (/ 'lev' /), 'I', 'unitless', 'ph value multiplied by cloud liquid water content' )
+    do i_elem = 1, 4
+      write(index_string, '(I10)') i_elem
+      call addfld( 'cloud_aqso4_'//trim(adjustl(index_string))//'_out',   horiz_only, 'I', 'unknown', 'aqueous phase chemistry' )
+      call addfld( 'cloud_aqh2so4_'//trim(adjustl(index_string))//'_out', horiz_only, 'I', 'unknown', 'aqueous phase chemistry' )
+    end do
+    call addfld( 'cloud_aqso4_h2o2_out', horiz_only,  'I', 'kg m-2',   'SO4 aqueous phase chemistry due to H2O2?' )
+    call addfld( 'cloud_aqso4_o3_out',   horiz_only,  'I', 'kg m-2',   'SO4 aqueous phase chemistry due to O3?' )
+
+  end subroutine cloud_snapshot_init
+
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+  subroutine cloud_snapshot_capture_input(ncol, lchnk, loffset, dtime, press, &
+    pdel, tfld, mbar, lwc, cldfrc, cldnum, xhnm, invariants, qcw, qin)
+
+    use cam_history, only : outfld
+    use cam_logfile, only : iulog
+    use spmd_utils,  only : is_main_process => masterproc
+
+    integer,          intent(in)    :: ncol              ! num of columns in chunk
+    integer,          intent(in)    :: lchnk             ! chunk id
+    integer,          intent(in)    :: loffset           ! offset of chem tracers in the advected tracers array
+    real(r8),         intent(in)    :: dtime             ! time step (sec)
+    real(r8),         intent(in)    :: press(:,:)        ! midpoint pressure ( Pa )
+    real(r8),         intent(in)    :: pdel(:,:)         ! pressure thickness of levels (Pa)
+    real(r8),         intent(in)    :: tfld(:,:)         ! temperature
+    real(r8),         intent(in)    :: mbar(:,:)         ! mean wet atmospheric mass ( amu )
+    real(r8), target, intent(in)    :: lwc(:,:)          ! cloud liquid water content (kg/kg)
+    real(r8), target, intent(in)    :: cldfrc(:,:)       ! cloud fraction
+    real(r8),         intent(in)    :: cldnum(:,:)       ! droplet number concentration (#/kg)
+    real(r8),         intent(in)    :: xhnm(:,:)         ! total atms density ( /cm**3)
+    real(r8),         intent(in)    :: invariants(:,:,:)
+    real(r8), target, intent(in)    :: qcw(:,:,:)        ! cloud-borne aerosol (vmr)
+    real(r8),         intent(in)    :: qin(:,:,:)        ! transported species ( vmr )
+
+    integer :: i_elem
+    character(len=10) :: index_string
+
+#if 0
+    if (is_main_process) then
+      write(iulog,*) "*****************************"
+      write(iulog,*) "Cloud Chemistry scalar inputs"
+      write(iulog,*) "*****************************"
+      write(iulog,*) "ncol: ", ncol
+      write(iulog,*) "lchnk: ", lchnk
+      write(iulog,*) "loffset: ", loffset
+      write(iulog,*) "dtime: ", dtime
+      write(iulog,*) "press dims: ", size(press, dim=1), size(press, dim=2)
+      write(iulog,*) "invariants dims: ", size(invariants, dim=1), size(invariants, dim=2), size(invariants, dim=3)
+      write(iulog,*) "qcw dims: ", size(qcw, dim=1), size(qcw, dim=2), size(qcw, dim=3)
+      write(iulog,*) "qin dims: ", size(qin, dim=1), size(qin, dim=2), size(qin, dim=3)
+    end if
+#endif
+    call outfld( 'cloud_press_in',  press(:ncol,:),  ncol, lchnk )
+    call outfld( 'cloud_pdel_in',   pdel(:ncol,:),   ncol, lchnk )
+    call outfld( 'cloud_tfld_in',   tfld(:ncol,:),   ncol, lchnk )
+    call outfld( 'cloud_mbar_in',   mbar(:ncol,:),   ncol, lchnk )
+    call outfld( 'cloud_lwc_in',    lwc(:ncol,:),    ncol, lchnk )
+    call outfld( 'cloud_cldfrc_in', cldfrc(:ncol,:), ncol, lchnk )
+    call outfld( 'cloud_cldnum_in', cldnum(:ncol,:), ncol, lchnk )
+    call outfld( 'cloud_xhnm_in',   xhnm(:ncol,:),   ncol, lchnk )
+    do i_elem = 1, 7
+      write(index_string, '(I10)') i_elem
+      call outfld( 'cloud_invariants_'//trim(adjustl(index_string))//'_in', invariants(:ncol,:,i_elem), ncol, lchnk )
+    end do
+    do i_elem = 1, 26
+      write(index_string, '(I10)') i_elem
+      call outfld( 'cloud_qcw_'//trim(adjustl(index_string))//'_in', qcw(:ncol,:,i_elem), ncol, lchnk )
+      call outfld( 'cloud_qin_'//trim(adjustl(index_string))//'_in', qin(:ncol,:,i_elem), ncol, lchnk )
+    end do
+
+  end subroutine cloud_snapshot_capture_input
+
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+  subroutine cloud_snapshot_capture_output(ncol, lchnk, qcw, qin, xphlwc, &
+    aqso4, aqh2so4, aqso4_h2o2, aqso4_o3)
+
+    use cam_history, only : outfld
+
+    integer,          intent(in)   :: ncol              ! num of columns in chunk
+    integer,          intent(in)   :: lchnk             ! chunk id
+    real(r8), target, intent(in)   :: qcw(:,:,:)        ! cloud-borne aerosol (vmr)
+    real(r8),         intent(in)   :: qin(:,:,:)        ! transported species ( vmr )
+    real(r8),         intent(in)   :: xphlwc(:,:)       ! pH value multiplied by lwc
+
+    real(r8),         intent(in)   :: aqso4(:,:)        ! aqueous phase chemistry
+    real(r8),         intent(in)   :: aqh2so4(:,:)      ! aqueous phase chemistry
+    real(r8),         intent(in)   :: aqso4_h2o2(:)     ! SO4 aqueous phase chemistry due to H2O2 (kg/m2)
+    real(r8),         intent(in)   :: aqso4_o3(:)       ! SO4 aqueous phase chemistry due to O3 (kg/m2)
+
+    integer :: i_elem
+    character(len=10) :: index_string
+
+    call outfld( 'cloud_xphlwc_out',     xphlwc(:ncol,:),     ncol, lchnk )
+    call outfld( 'cloud_aqso4_h2o2_out', aqso4_h2o2(:ncol),   ncol, lchnk )
+    call outfld( 'cloud_aqso4_o3_out',   aqso4_o3(:ncol),     ncol, lchnk )
+    do i_elem = 1, 4
+      write(index_string, '(I10)') i_elem
+      call outfld( 'cloud_aqso4_'//trim(adjustl(index_string))//'_out',   aqso4(:ncol,i_elem),   ncol, lchnk )
+      call outfld( 'cloud_aqh2so4_'//trim(adjustl(index_string))//'_out', aqh2so4(:ncol,i_elem), ncol, lchnk )
+    end do
+    do i_elem = 1, 26
+      write(index_string, '(I10)') i_elem
+      call outfld( 'cloud_qcw_'//trim(adjustl(index_string))//'_out', qcw(:ncol,:,i_elem), ncol, lchnk )
+      call outfld( 'cloud_qin_'//trim(adjustl(index_string))//'_out', qin(:ncol,:,i_elem), ncol, lchnk )
+    end do
+
+  end subroutine cloud_snapshot_capture_output
+
+end module cloud_aqueous_chemistry_snapshot

src/chemistry/modal_aero/aero_model.F90

@@ -187,6 +187,7 @@ subroutine aero_model_init( pbuf2d )
     use modal_aero_gasaerexch, only: modal_aero_gasaerexch_init
     use modal_aero_newnuc,     only: modal_aero_newnuc_init
     use modal_aero_rename,     only: modal_aero_rename_init
+    use cloud_aqueous_chemistry_snapshot, only : cloud_snapshot_init
 
     ! args
     type(physics_buffer_desc), pointer :: pbuf2d(:,:)
@@ -544,6 +545,8 @@ subroutine aero_model_init( pbuf2d )
 
     call aero_wetdep_init()
 
+    call cloud_snapshot_init()
+
   end subroutine aero_model_init
 
   !=============================================================================
@@ -960,7 +963,8 @@ subroutine aero_model_gasaerexch( state, loffset, ncol, lchnk, troplev, delt, re
     use modal_aero_gasaerexch, only : modal_aero_gasaerexch_sub
     use modal_aero_newnuc,     only : modal_aero_newnuc_sub
     use modal_aero_data,       only : cnst_name_cw, qqcw_get_field
-
+    use cloud_aqueous_chemistry_snapshot, only : cloud_snapshot_capture_input, &
+                                                 cloud_snapshot_capture_output
     !-----------------------------------------------------------------------
     !      ... dummy arguments
     !-----------------------------------------------------------------------
@@ -1060,7 +1064,29 @@ subroutine aero_model_gasaerexch( state, loffset, ncol, lchnk, troplev, delt, re
       dvmrcwdt(:ncol,:,:) = vmrcw(:ncol,:,:)
 
     ! aqueous chemistry ...
-
+      call cloud_snapshot_capture_input( &
+              ! pbuf,     &
+              ncol,     &
+              lchnk,    &
+              loffset,  &
+              delt,     &
+              pmid,     &
+              pdel,     &
+              tfld,     &
+              mbar,     &
+              cwat,     &
+              cldfr,    &
+              cldnum,   &
+              airdens,  &
+              invariants, &
+              vmrcw,    &
+              vmr      &
+              ! xphlwc,   &
+              ! aqso4,    &
+              ! aqh2so4,  &
+              ! aqso4_h2o2, &
+              ! aqso4_o3  &
+              )
       if( has_sox ) then
          call setsox( state, &
               pbuf,     &
@@ -1099,6 +1125,29 @@ subroutine aero_model_gasaerexch( state, loffset, ncol, lchnk, troplev, delt, re
          call outfld( 'XPH_LWC',    xphlwc(:ncol,:),   ncol, lchnk )
 
       endif
+      call cloud_snapshot_capture_output( &
+              ! pbuf,     &
+              ncol,     &
+              lchnk,    &
+              ! loffset,  &
+              ! delt,     &
+              ! pmid,     &
+              ! pdel,     &
+              ! tfld,     &
+              ! mbar,     &
+              ! cwat,     &
+              ! cldfr,    &
+              ! cldnum,   &
+              ! airdens,  &
+              ! invariants, &
+              vmrcw,    &
+              vmr,      &
+              xphlwc,   &
+              aqso4,    &
+              aqh2so4,  &
+              aqso4_h2o2, &
+              aqso4_o3  &
+              )
 
 !   Tendency due to aqueous chemistry
     dvmrdt = (vmr - dvmrdt) / delt

src/chemistry/modal_aero/mam_clouds.F90

@@ -461,16 +461,16 @@ subroutine sox_cldaero_update( state, &
     do n = 1, ntot_amode
        m = lptr_so4_cw_amode(n)
        l = m - loffset
+       aqso4(:,n)=0._r8
+       aqh2so4(:,n)=0._r8
        if (l > 0) then
-          aqso4(:,n)=0._r8
           do k=1,pver
              do i=1,ncol
                 aqso4(i,n)=aqso4(i,n)+dqdt_aqso4(i,k,l)*adv_mass(l)/mbar(i,k) &
                      *pdel(i,k)/gravit ! kg/m2/s
              enddo
           enddo
 
-          aqh2so4(:,n)=0._r8
           do k=1,pver
              do i=1,ncol
                 aqh2so4(i,n)=aqh2so4(i,n)+dqdt_aqh2so4(i,k,l)*adv_mass(l)/mbar(i,k) &

test/chemistry/CMakeLists.txt

@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 3.6)
+
+project(
+  cam_chemistry_tests
+  VERSION 0.1.0
+  LANGUAGES Fortran
+)
+
+option(CAMCHEM_ENABLE_MEMCHECK "Enable memory checking with valgrind" ON)
+option(CAMCHEM_ENABLE_MPI "Build with MPI support" OFF)
+option(CAMCHEM_ENABLE_OPENMP "Build with OpenMP support" OFF)
+
+include(cmake/dependencies.cmake)
+
+# Copy test data
+add_custom_target(copy_test_data ALL ${CMAKE_COMMAND} -E copy_directory
+  ${CMAKE_CURRENT_SOURCE_DIR}/data ${CMAKE_BINARY_DIR}/test/chemistry/data)
+
+enable_testing()
+
+add_subdirectory(cloud_aqueous_chemistry)

test/chemistry/Dockerfile

@@ -0,0 +1,31 @@
+FROM fedora:41
+
+RUN dnf -y update \
+    && dnf -y install \
+        cmake \
+        gcc \
+        gcc-c++ \
+        gcc-fortran \
+        gdb \
+        git \
+        lapack-devel \
+        lcov \
+        m4 \
+        make \
+        netcdf-fortran-devel \
+        python3 \
+        python3-pip \
+        valgrind \
+    && dnf clean all
+
+COPY . /cam
+
+RUN cd /cam/test/chemistry \
+    && mkdir build \
+    && cd build \
+    && cmake \
+         -D CMAKE_BUILD_TYPE=DEBUG \
+         .. \
+    && make
+
+WORKDIR /cam/test/chemistry/build

test/chemistry/README.md

@@ -0,0 +1,22 @@
+Chemistry Tests
+===============
+
+Tests in this folder are used to support the porting of CAM-Chem functionality to CAM-SIMA.
+
+To build and run the test suite, from this folder run:
+
+```
+mkdir build
+cd build
+cmake ..
+make
+make test
+```
+
+To run the tests in a Docker container, from the `CAM/test/chemistry` folder run:
+
+```
+docker build -t cam-test ../../ -f Dockerfile
+docker run -it cam-test bash
+make test
+```