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TUV-x photolysis #1471

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0ec3468
TUV-x mods merged from tuvx_jun_cld branch
fvitt Jan 7, 2026
2511721
tuvx lib build/cmake updates
fvitt Jan 13, 2026
f193be9
changes for code review comments; remove unused modules
fvitt Jan 29, 2026
22003f5
scripts clean up as suggested by reviewer
fvitt Feb 3, 2026
9749a7d
minor code cleanup
fvitt Feb 3, 2026
e2ff919
futher changes per code review
fvitt Feb 4, 2026
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -2,6 +2,9 @@
buildnmlc
buildcppc

# Ignore ide configs
.vscode

# Ignore editor temporaries and backups
*~
.#*
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7 changes: 7 additions & 0 deletions .gitmodules
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Expand Up @@ -205,3 +205,10 @@ url = https://github.com/NCAR/CUPiD.git
fxtag = v0.4.0
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git

[submodule "tuv-x"]
path = libraries/tuv-x
url = https://github.com/NCAR/tuv-x.git
fxtag = ecf768a2b66
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@cacraigucar cacraigucar Feb 3, 2026

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We need a tag for this instance

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@fvitt fvitt Feb 3, 2026

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@K20shores, Can you make a new tag?

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@K20shores K20shores Feb 3, 2026

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Created: https://github.com/NCAR/tuv-x/tree/v0.14.1

tag: v0.14.1

fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/NCAR/tuv-x.git
11 changes: 11 additions & 0 deletions bld/namelist_files/namelist_definition.xml
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Expand Up @@ -7672,6 +7672,17 @@ Maximum zenith angle (degrees) used for photolysis.
Default: set by build-namelist.
</entry>

<entry id="tuvx_config_path" type="char*256" input_pathname="abs" category="chemistry"
group="tuvx_opts" valid_values="" >
Filepath of TUV-X configuration specification.
Default: NONE
</entry>

<entry id="tuvx_active" type="logical" category="chemistry"
group="tuvx_opts" valid_values="" >
Switch to turn on TUV-X photolysis.
Default: FALSE
</entry>

<!-- Namelist read by seq_drydep_mod and shared by CAM and CLM -->

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154 changes: 151 additions & 3 deletions cime_config/buildlib
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Expand Up @@ -7,7 +7,7 @@ create the cam library
# pylint: disable=unused-wildcard-import, bad-whitespace, too-many-locals
# pylint: disable=invalid-name
import sys, os, filecmp, shutil

from glob import glob

_CIMEROOT = os.environ.get("CIMEROOT")
if _CIMEROOT is None:
Expand All @@ -27,7 +27,7 @@ logger = logging.getLogger(__name__)

###############################################################################
def _build_fms(caseroot, libroot, bldroot):
###############################################################################
###############################################################################

with Case(caseroot) as case:

Expand Down Expand Up @@ -71,7 +71,7 @@ def _build_fms(caseroot, libroot, bldroot):

###############################################################################
def _build_cam(caseroot, libroot, bldroot):
###############################################################################
###############################################################################

with Case(caseroot, read_only=False) as case:

Expand Down Expand Up @@ -157,12 +157,160 @@ def _build_cam(caseroot, libroot, bldroot):
logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n", cmd, out, err)
expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc))

###############################################################################
def _run_cmd(command, working_dir):
###############################################################################

rc, out, err = run_cmd(command, from_dir=working_dir, verbose=True)
expect(rc == 0, f"Command {command} failed with rc={rc} out={out} err={err}")

###############################################################################
def _cmake_default_args(caseroot):
###############################################################################
# Returns a dictionary of CMake variables based on the Macros.cmake file for
# the build.

with Case(caseroot) as case:
macro_path = os.path.abspath(os.path.join(caseroot, "cmake_macros", ""))
args = "-DCONVERT_TO_MAKE=ON "
args += f"-DCASEROOT={caseroot} "
args += f"-DCOMPILER={case.get_value('COMPILER')} "
args += f"-DOS={case.get_value('OS')} "
args += f"-DMACH={case.get_value('MACH')} "
args += "-DCMAKE_C_COMPILER_WORKS=1 "
args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
args += f"-DDEBUG={case.get_value('DEBUG')} "
cmd = f"cmake {args} ."
rc, out, err = run_cmd(cmd, combine_output=True, from_dir=macro_path)
expect(rc == 0, f"Command {cmd} failed with rc={rc} out={out} err={err}")

arg_dict = {}
for line in out.splitlines():
if ":=" in line:
key, val = line.split(":=")
arg_dict[key.replace('CIME_SET_MAKEFILE_VAR','').strip()] = val.strip()

return arg_dict

###############################################################################
def _build_tuvx(caseroot, libroot, bldroot):
###############################################################################
# Builds the TUV-x library and updates the case variables used to set the
# include paths and linked libraries

with Case(caseroot) as case:
bldpath = os.path.join(bldroot, "tuv-x")
if not os.path.exists(bldpath):
os.makedirs(bldpath)
srcpath = os.path.abspath(os.path.join(case.get_value("COMP_ROOT_DIR_ATM"), \
"libraries", "tuv-x", ""))
logger.info("Building TUV-x in {} from source in {}\n".format(bldpath, srcpath))

arg_dict = _cmake_default_args(caseroot)
cmake_args = "-DCMAKE_VERBOSE_MAKEFILE=ON "
if case.get_value("MPILIB") != "mpi-serial":
cmake_args += "-DTUVX_ENABLE_MPI:BOOL=TRUE "
if case.get_value("DEBUG"):
cmake_args += "-DCMAKE_BUILD_TYPE=Debug "
else:
cmake_args += "-DCMAKE_BUILD_TYPE=Release "
cmake_args += "-DCMAKE_Fortran_COMPILER=mpif90 "
cmake_args += "-DCMAKE_C_COMPILER=mpicc "
cmake_args += "-DCMAKE_CXX_COMPILER=mpicxx "
cmake_args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
cmake_args += "-DCMAKE_C_COMPILER_WORKS=1 "
cmake_args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
if (case.get_value("MACH") == "izumi") :
cmake_args += f"-DCMAKE_PREFIX_PATH={arg_dict['NETCDF_PATH']} "
cmake_args += f"-DCMAKE_IGNORE_PATH={os.environ.get('PYTHONHOME')} "
if (case.get_value("MACH") == "izumi") and (case.get_value('COMPILER') == "nag") :
cmake_args += "-DCMAKE_Fortran_FLAGS='-C=all -g ' "
else :
cmake_args += f"-DCMAKE_Fortran_FLAGS='{arg_dict['FFLAGS']}' "
cmake_args += f"-DCMAKE_INSTALL_PREFIX='{libroot}' "
cmake_args += "-DTUVX_ENABLE_TESTS=OFF "
cmake_args += "-DTUVX_ENABLE_COVERAGE=OFF "
cmake_args += "-DTUVX_BUILD_CLI=OFF "
cmake_args += f"-DTUVX_INSTALL_INCLUDE_DIR='{_tuvx_include_dir(libroot)}' "
cmake_args += f"-DTUVX_INSTALL_MOD_DIR='{_tuvx_include_dir(libroot)}' "
cmake_args += srcpath

_run_cmd(f"cmake {cmake_args}", bldpath)
_run_cmd(case.get_value('GMAKE'), bldpath)
_run_cmd(f"{case.get_value('GMAKE')} install", bldpath)

# add TUV-x to include paths
incldir = os.environ.get('USER_INCLDIR')
if incldir is None:
incldir = ''
os.environ['USER_INCLDIR'] = incldir + \
f" -I{_tuvx_include_dir(libroot)} "

# create symlink to library in folder CIME expects libraries to be in
dst = os.path.join(libroot, "libtuvx.a")
if os.path.isfile(dst):
os.remove(dst)
os.symlink(_tuvx_lib_path(libroot), dst)
dst = os.path.join(libroot, "libyaml-cpp.a")
if os.path.isfile(dst):
os.remove(dst)
os.symlink(_yaml_cpp_lib_path(libroot), dst)

###############################################################################
def _tuvx_include_dir(libroot):
###############################################################################
# Returns the path to the TUV-x include directory

coreinc = os.path.join(libroot, "include")
expect(os.path.exists(coreinc), f"TUV-x include directory not found at {coreinc}")

return coreinc

###############################################################################
def _yaml_cpp_lib_path(libroot):
###############################################################################
# Returns the path to the yaml-cpp library

corelib = os.path.join(libroot, "lib64", "libyaml-cpp.a")
if not os.path.exists(corelib):
corelib = os.path.join(libroot, "lib64", "libyaml-cppd.a")
if not os.path.exists(corelib):
corelib = os.path.join(libroot, "lib", "libyaml-cpp.a")
expect(os.path.exists(corelib), f"yaml-cpp library not found at {corelib}")

return corelib

###############################################################################
def _tuvx_lib_path(libroot):
###############################################################################
# Returns the path to the TUV-x library

corelib = os.path.join(_tuvx_install_dir(libroot), "lib64", "libtuvx.a")
if not os.path.exists(corelib):
corelib = os.path.join(_tuvx_install_dir(libroot), "lib", "libtuvx.a")
expect(os.path.exists(corelib), f"TUV-x library not found at {corelib}")

return corelib

###############################################################################
def _tuvx_install_dir(libroot):
###############################################################################
# Returns the path to the TUV-x install directory

corepaths = glob(os.path.join(libroot, "tuvx*"))
expect(len(corepaths)>0, f"TUV-x not found at {libroot}")
expect(len(corepaths)<2, f"Multiple TUV-x versions found at {libroot}")
expect(os.path.exists(corepaths[0]), f"TUV-x install directory not found at {corepaths[0]}")

return corepaths[0]

###############################################################################


def _main_func():
caseroot, libroot, bldroot = parse_input(sys.argv)
_build_tuvx(caseroot, libroot, bldroot)
_build_fms(caseroot, libroot, bldroot)
_build_cam(caseroot, libroot, bldroot)

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7 changes: 7 additions & 0 deletions cime_config/buildnml
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Expand Up @@ -214,6 +214,13 @@ def buildnml(case, caseroot, compname):
logger.info("GEOS-Chem config file copy: file1 %s file2 %s ", file1, file2)
shutil.copy(file1,file2)

# Copy TUV-x data to rundir
dest_data = os.path.join(rundir, "data")
if os.path.exists(dest_data):
shutil.rmtree(dest_data)
shutil.copytree(os.path.join(srcroot, "libraries", "tuv-x", "data"), \
dest_data)

###############################################################################
def _main_func():

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12 changes: 12 additions & 0 deletions cime_config/config_component.xml
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Expand Up @@ -221,6 +221,18 @@
</desc>
</entry>

<entry id="CAM_LINKED_LIBS">
<type>char</type>
<valid_values></valid_values>
<default_value>-ltuvx -lyaml-cpp -lstdc++</default_value>
<group>build_component_cam</group>
<file>env_build.xml</file>
<desc>
CAM linked libraries. The libraries are built by CAM's buildlib script and should be included
during linking of the model executable.
</desc>
</entry>

<entry id="CAM_NML_USE_CASE">
<type>char</type>
<valid_values></valid_values>
Expand Down
8 changes: 5 additions & 3 deletions cime_config/testdefs/testmods_dirs/cam/carma_mixed_sulfate/user_nl_cam
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@@ -1,6 +1,6 @@
mfilt=1,1,1,1,1,1
ndens=1,1,1,1,1,1
nhtfrq=3,3,3,3,3,3
mfilt=1,1,1,1,1,1,1,1,1,1
ndens=1,1,1,1,1,1,1,1,1,1
nhtfrq=3,3,3,3,3,3,3,3,3,3
inithist='ENDOFRUN'
pbuf_global_allocate=.false.
history_carma=.true.
Expand All @@ -11,3 +11,5 @@ solar_data_type='FIXED'
solar_data_ymd=20000101
carma_maxretries = 40
ubc_specifier = 'T->MSIS', 'Q->2.d-8vmr', 'CH4->2.d-10vmr', 'H->MSIS', 'N->MSIS', 'O->MSIS', 'O2->MSIS', 'H2->TGCM', 'NO->SNOE'
tuvx_active = .true.
tuvx_config_path = '$COMP_ROOT_DIR_ATM/src/chemistry/pp_waccm_ma_sulfur/tuvx_config.json'
2 changes: 2 additions & 0 deletions cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/shell_commands
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@@ -0,0 +1,2 @@
./xmlchange ROF_NCPL=\$ATM_NCPL
./xmlchange GLC_NCPL=\$ATM_NCPL
15 changes: 15 additions & 0 deletions cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/user_nl_cam
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mfilt=1,1,1,1,1,1,1,1,1
ndens=1,1,1,1,1,1,1,1,1
nhtfrq=9,9,9,9,9,9,9,9,9
write_nstep0=.true.
inithist='ENDOFRUN'

tuvx_active = .true.
tuvx_config_path = '$COMP_ROOT_DIR_ATM/src/chemistry/pp_waccm_ma_mam5/tuvx_config.json'

fincl2 = 'TUVX_DOSE_RATE_01','TUVX_DOSE_RATE_02','TUVX_DOSE_RATE_03','TUVX_DOSE_RATE_04','TUVX_DOSE_RATE_05',
'TUVX_DOSE_RATE_06','TUVX_DOSE_RATE_07','TUVX_DOSE_RATE_08','TUVX_DOSE_RATE_09','TUVX_DOSE_RATE_10',
'TUVX_DOSE_RATE_11','TUVX_DOSE_RATE_12','TUVX_DOSE_RATE_13','TUVX_DOSE_RATE_14','TUVX_DOSE_RATE_15',
'TUVX_DOSE_RATE_16','TUVX_DOSE_RATE_17','TUVX_DOSE_RATE_18','TUVX_DOSE_RATE_19','TUVX_DOSE_RATE_20',
'TUVX_DOSE_RATE_21','TUVX_DOSE_RATE_22','TUVX_DOSE_RATE_23','TUVX_DOSE_RATE_24',
'TUVX_DOSE_RATE_25','TUVX_DOSE_RATE_26','TUVX_DOSE_RATE_27','TUVX_DOSE_RATE_28'
27 changes: 27 additions & 0 deletions cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/user_nl_clm
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!----------------------------------------------------------------------------------
! Users should add all user specific namelist changes below in the form of
! namelist_var = new_namelist_value
!
! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
! are set in the CLM_NAMELIST_OPTS env variable.
!
! EXCEPTIONS:
! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting
! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting
! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting
! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting
! Set irrigate by the CLM_BLDNML_OPTS -irrig setting
! Set dtime with L_NCPL option
! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options
! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
! (includes $inst_string for multi-ensemble cases)
! Set glc_grid with CISM_GRID option
! Set glc_smb with GLC_SMB option
! Set maxpatch_glcmec with GLC_NEC option
! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable
!----------------------------------------------------------------------------------
hist_nhtfrq = 9
hist_mfilt = 1
hist_ndens = 1

3 changes: 3 additions & 0 deletions cime_config/testdefs/testmods_dirs/cam/outfrq9s_waccm_ma_mam4/user_nl_cam
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Expand Up @@ -5,3 +5,6 @@ inithist='ENDOFRUN'
nlte_use_extco2 = .true.
fincl2 = 'QRL_TOT','QRLNLTE','QCO2','QO3','QHC2S','QNO','QO3P',
'QCO2ext','TCO2ext','PCO2ext','CO2_ext','N2_ext','O_ext','O2_ext'

tuvx_active = .true.
tuvx_config_path = '$COMP_ROOT_DIR_ATM/src/chemistry/pp_waccm_ma_mam5/tuvx_config.json'
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