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Merge pull request #3013 from eagles-project/oscar-balwinder-mingxuan…
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…/mam-microphysics

Adds MAM4xx microphysics interface
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@bartgol
bartgol authored Nov 4, 2024
2 parents a6ea7a5 + b49cf67 commit 15602d7
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74 changes: 66 additions & 8 deletions components/eamxx/cime_config/namelist_defaults_scream.xml
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Expand Up @@ -268,6 +268,64 @@ be lost if SCREAM_HACK_XML is not enabled.
<cldFraction inherit="atm_proc_base"/>

<!-- MAM4xx namelist options -->

<!-- MAM4xx-Aerosol-Microphysics -->
<mam4_aero_microphys inherit="atm_proc_base">
<!--Aerosol Microphysics processes on/off switches -->
<mam4_do_cond type="logical" doc="Switch to enable aerosol microphysics condensation process">true</mam4_do_cond>
<mam4_do_newnuc type="logical" doc="Switch to enable aerosol microphysics nucleation process">true</mam4_do_newnuc>
<mam4_do_coag type="logical" doc="Switch to enable aerosol microphysics coagulation process">true</mam4_do_coag>
<mam4_do_rename type="logical" doc="Switch to enable aerosol microphysics rename process">true</mam4_do_rename>
<!-- LINOZ parameters -->
<mam4_o3_tau type="real" doc="Linoz tau parameter">172800.0</mam4_o3_tau>
<mam4_o3_sfc type="real" doc="Linoz surface parameter">3.0E-008</mam4_o3_sfc>
<mam4_o3_lbl type="integer" doc="Linoz lbl parameter">4</mam4_o3_lbl>
<mam4_psc_T type="real" doc="Linoz psc ozone loss temperature (K) threshold">193.0</mam4_psc_T>
<mam4_linoz_ymd type="integer" > 20100101</mam4_linoz_ymd>
<mam4_linoz_file_name type="file" doc="LINOZ chemistry file"> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/ne30pg2/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne30pg2_c20240724.nc</mam4_linoz_file_name>
<mam4_linoz_file_name hgrid="ne4np4.pg2" type="file" doc="LINOZ chemistry file"> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/ne4pg2/linoz1850-2015_2010JPL_CMIP6_10deg_58km_ne4pg2_c20240724.nc</mam4_linoz_file_name>
<!--Invariants-->
<mam4_oxid_ymd type="integer" > 20150101 </mam4_oxid_ymd>
<mam4_oxid_file_name type="file" doc="File containing oxidants data">${DIN_LOC_ROOT}/atm/scream/mam4xx/invariants/ne30pg2/oxid_1.9x2.5_L26_1850-2015_ne30pg2_c20241009.nc</mam4_oxid_file_name>
<mam4_oxid_file_name hgrid="ne4np4.pg2" type="file" doc="File containing oxidants data">${DIN_LOC_ROOT}/atm/scream/mam4xx/invariants/ne4pg2/oxid_1.9x2.5_L26_1850-2015_ne4pg2_c20241009.nc</mam4_oxid_file_name>
<mam4_chlorine_loading_ymd type="integer" doc="Cycle year for chlorine"> 20100101 </mam4_chlorine_loading_ymd>
<mam4_linoz_chlorine_file type="file" doc="File containing chlorine data"> ${DIN_LOC_ROOT}/atm/scream/mam4xx/linoz/Linoz_Chlorine_Loading_CMIP6_0003-2017_c20171114.nc</mam4_linoz_chlorine_file>
<!--Photolysis-->
<mam4_rsf_file type="file" doc="File containing photolysis data"> ${DIN_LOC_ROOT}/atm/scream/mam4xx/photolysis/RSF_GT200nm_v3.0_c080811.nc</mam4_rsf_file>
<mam4_xs_long_file type="file" doc="File containing photolysis data"> ${DIN_LOC_ROOT}/atm/scream/mam4xx/photolysis/temp_prs_GT200nm_JPL10_c130206.nc</mam4_xs_long_file>
<!--Vertical emissions-->
<verti_emiss_ymd type="integer"> 20100101 </verti_emiss_ymd>
<!-- For all other grids -->
<mam4_so2_verti_emiss_file_name type="file" doc="vertical emissions for so2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_so2_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_so2_verti_emiss_file_name>
<mam4_so4_a1_verti_emiss_file_name type="file" doc="vertical emissions for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_so4_a1_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_so4_a1_verti_emiss_file_name>
<mam4_so4_a2_verti_emiss_file_name type="file" doc="vertical emissions for ao4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_so4_a2_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_so4_a2_verti_emiss_file_name>
<mam4_pom_a4_verti_emiss_file_name type="file" doc="vertical emissions for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_pom_a4_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_pom_a4_verti_emiss_file_name>
<mam4_bc_a4_verti_emiss_file_name type="file" doc="vertical emissions for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_bc_a4_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_bc_a4_verti_emiss_file_name>
<mam4_num_a1_verti_emiss_file_name type="file" doc="vertical emissions for num_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_num_a1_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_num_a1_verti_emiss_file_name>
<mam4_num_a2_verti_emiss_file_name type="file" doc="vertical emissions for num_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_num_a2_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_num_a2_verti_emiss_file_name>
<mam4_num_a4_verti_emiss_file_name type="file" doc="vertical emissions for num_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_num_a4_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_num_a4_verti_emiss_file_name>
<mam4_soag_verti_emiss_file_name type="file" doc="vertical emissions for soag">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/elevated/cmip6_mam4_soag_elev_1x1_2010_clim_ne30pg2_c20241008.nc</mam4_soag_verti_emiss_file_name>

<!-- For ne4 grids -->
<mam4_so2_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for so2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_so2_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_so2_verti_emiss_file_name>
<mam4_so4_a1_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_so4_a1_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_so4_a1_verti_emiss_file_name>
<mam4_so4_a2_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for so4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_so4_a2_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_so4_a2_verti_emiss_file_name>
<mam4_pom_a4_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_pom_a4_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_pom_a4_verti_emiss_file_name>
<mam4_bc_a4_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_bc_a4_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_bc_a4_verti_emiss_file_name>
<mam4_num_a1_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for num_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_num_a1_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_num_a1_verti_emiss_file_name>
<mam4_num_a2_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for num_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_num_a2_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_num_a2_verti_emiss_file_name>
<mam4_num_a4_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for num_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_num_a4_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_num_a4_verti_emiss_file_name>
<mam4_soag_verti_emiss_file_name hgrid="ne4np4.pg2" type="file" doc="vertical emissions for soag">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/elevated/cmip6_mam4_soag_elev_1x1_2010_clim_ne4pg2_c20241008.nc</mam4_soag_verti_emiss_file_name>

<!-- Mapping Files for finer resolutions -->
<aero_microphys_remap_file type="file" doc="File containing mapping data from the grid of frac land use files to the model grid. Unused if the grid is the same."/>
<aero_microphys_remap_file hgrid="ne120np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne120pg2_20231201.nc</aero_microphys_remap_file>
<aero_microphys_remap_file hgrid="ne256np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne256pg2_20231201.nc</aero_microphys_remap_file>
<aero_microphys_remap_file hgrid="ne512np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne512pg2_20231201.nc</aero_microphys_remap_file>
<aero_microphys_remap_file hgrid="ne1024np4.pg2">${DIN_LOC_ROOT}/atm/scream/maps/map_ne30pg2_to_ne1024pg2_20231201.nc</aero_microphys_remap_file>

</mam4_aero_microphys>

<!-- MAM4xx-Optics -->
<mam4_optics inherit="atm_proc_base">
<mam4_mode1_physical_properties_file type="file" doc="File containing optical properties for MAM4 mode 1, accumulation mode">${DIN_LOC_ROOT}/atm/scream/mam4xx/physprops/mam4_mode1_rrtmg_aeronetdust_c20240206.nc</mam4_mode1_physical_properties_file>
Expand All @@ -290,7 +348,7 @@ be lost if SCREAM_HACK_XML is not enabled.
<!-- MAM4xx-Surface-Emissions -->
<mam4_srf_online_emiss inherit="atm_proc_base">

<!-- For all other grids -->
<!-- For all other grids -->
<srf_emis_specifier_for_DMS type="file" doc="File containing surface emissions data for DMS">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/DMSflux.2010.ne30pg2_conserv.POPmonthlyClimFromACES4BGC_c20240816.nc</srf_emis_specifier_for_DMS>
<srf_emis_specifier_for_SO2 type="file" doc="File containing surface emissions data for SO2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so2_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_SO2>
<srf_emis_specifier_for_bc_a4 type="file" doc="File containing surface emissions data for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_bc_a4_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_bc_a4>
Expand All @@ -300,8 +358,8 @@ be lost if SCREAM_HACK_XML is not enabled.
<srf_emis_specifier_for_pom_a4 type="file" doc="File containing surface emissions data for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_pom_a4_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_pom_a4>
<srf_emis_specifier_for_so4_a1 type="file" doc="File containing surface emissions data for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so4_a1_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_so4_a1>
<srf_emis_specifier_for_so4_a2 type="file" doc="File containing surface emissions data for so4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne30pg2/surface/cmip6_mam4_so4_a2_surf_ne30pg2_2010_clim_c20240816.nc</srf_emis_specifier_for_so4_a2>
<!-- For ne4pg2 grid -->

<!-- For ne4pg2 grid -->
<srf_emis_specifier_for_DMS hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for DMS">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/DMSflux.2010.ne4pg2_conserv.POPmonthlyClimFromACES4BGC_c20240814.nc</srf_emis_specifier_for_DMS>
<srf_emis_specifier_for_SO2 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for SO2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so2_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_SO2>
<srf_emis_specifier_for_bc_a4 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for bc_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_bc_a4_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_bc_a4>
Expand All @@ -311,7 +369,7 @@ be lost if SCREAM_HACK_XML is not enabled.
<srf_emis_specifier_for_pom_a4 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for pom_a4">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_pom_a4_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_pom_a4>
<srf_emis_specifier_for_so4_a1 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for so4_a1">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so4_a1_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_so4_a1>
<srf_emis_specifier_for_so4_a2 hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for so4_a2">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/cmip6_mam4_so4_a2_surf_ne4pg2_2010_clim_c20240815.nc</srf_emis_specifier_for_so4_a2>


<!-- For ne4pg2 grid -->
<srf_emis_specifier_for_DMS hgrid="ne4np4.pg2" type="file" doc="File containing surface emissions data for DMS">${DIN_LOC_ROOT}/atm/scream/mam4xx/emissions/ne4pg2/surface/DMSflux.2010.ne4pg2_conserv.POPmonthlyClimFromACES4BGC_c20240814.nc</srf_emis_specifier_for_DMS>
Expand Down Expand Up @@ -576,9 +634,9 @@ be lost if SCREAM_HACK_XML is not enabled.
<surf_lw_flux_up >0.0</surf_lw_flux_up>
<surf_mom_flux type="array(real)">0.0,0.0</surf_mom_flux>
<!-- Note: MAM4xx-ACI needs dry aerosol diameter (dgnum), currently set to aitken model nominal diameter, remove it once all of MAM4xx is integrated -->
<dgnum type="real" doc="Dry aerosol particles diameter [m]">2.6e-08</dgnum>
<dgnumwet type="real" doc="Wet aerosol particles diameter [m]">0.41417721820867320E-007</dgnumwet>
<wetdens type="real" doc="Wet density of interstitial aerosol [kg/m3]">0.15100083211582764E+004</wetdens>
<dgnum type="array(real)" doc="Dry aerosol particles diameters (one per mode) [m]">1.37146e-07 ,3.45899e-08 ,1.00000e-06 ,9.99601e-08</dgnum>
<dgnumwet type="array(real)" doc="Wet aerosol particles diameter [m]">1.37452e-07 ,3.46684e-08 ,1.00900e-06 ,9.99601e-08</dgnumwet>
<wetdens type="array(real)" doc="Wet density of interstitial aerosol [kg/m3]">5.08262e-12 ,1.54035e-13 ,3.09018e-13 ,9.14710e-22</wetdens>
<bc_c1 type="real">0.0</bc_c1>
<bc_c3 type="real">0.0</bc_c3>
<bc_c4 type="real">0.0</bc_c4>
Expand Down Expand Up @@ -646,7 +704,7 @@ be lost if SCREAM_HACK_XML is not enabled.
<!--
These options are meant for power users to debug the code.
They are not meant to be used for typical eamxx simulations.
-->
-->
<driver_debug_options>
<force_crash_nsteps type="integer"
doc="Force simulation to fail at a specific atmosphere timestep">
Expand Down
17 changes: 17 additions & 0 deletions ...s/eamxx/cime_config/testdefs/testmods_dirs/scream/mam4xx/aero_microphysics/shell_commands
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@@ -0,0 +1,17 @@

#!/bin/sh
#------------------------------------------------------
# MAM4xx adds additionaltracers to the simulation
# Increase number of tracers for MAM4xx simulations
#------------------------------------------------------

$CIMEROOT/../components/eamxx/cime_config/testdefs/testmods_dirs/scream/mam4xx/update_eamxx_num_tracers.sh -b

#------------------------------------------------------
#Update IC file and add drydep process
#------------------------------------------------------
$CIMEROOT/../components/eamxx/scripts/atmchange initial_conditions::Filename='$DIN_LOC_ROOT/atm/scream/init/screami_mam4xx_ne4np4L72_c20240208.nc' -b
$CIMEROOT/../components/eamxx/scripts/atmchange physics::atm_procs_list="mac_aero_mic,rrtmgp,mam4_aero_microphys" -b



3 changes: 2 additions & 1 deletion components/eamxx/src/physics/mam/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ add_subdirectory(${EXTERNALS_SOURCE_DIR}/mam4xx ${CMAKE_BINARY_DIR}/externals/ma
# EAMxx mam4xx-based atmospheric processes
add_library(mam
eamxx_mam_microphysics_process_interface.cpp
${SCREAM_BASE_DIR}/src/physics/rrtmgp/shr_orb_mod_c2f.F90
eamxx_mam_optics_process_interface.cpp
eamxx_mam_dry_deposition_process_interface.cpp
eamxx_mam_aci_process_interface.cpp
Expand All @@ -54,7 +55,7 @@ target_include_directories(mam PUBLIC
${EXTERNALS_SOURCE_DIR}/haero
${EXTERNALS_SOURCE_DIR}/mam4xx/src
)
target_link_libraries(mam PUBLIC physics_share scream_share mam4xx haero)
target_link_libraries(mam PUBLIC physics_share csm_share scream_share mam4xx haero)

#if (NOT SCREAM_LIB_ONLY)
# add_subdirectory(tests)
Expand Down
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