Merge pull request #1471 from fvitt/tuvx_photo

cam6_4_160: TUV-x photolysis

Author: fvitt

.gitignore

@@ -2,6 +2,9 @@
 buildnmlc
 buildcppc
 
+# Ignore ide configs
+.vscode
+
 # Ignore editor temporaries and backups
 *~
 .#*

.gitmodules

@@ -205,3 +205,10 @@ url = https://github.com/NCAR/CUPiD.git
 fxtag = v0.5.1
 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 = v0.14.3
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/tuv-x.git

bld/namelist_files/namelist_definition.xml

@@ -7750,6 +7750,17 @@ 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 -->
 

cime_config/buildlib

@@ -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:
@@ -27,7 +27,7 @@ logger = logging.getLogger(__name__)
 
 ###############################################################################
 def _build_fms(caseroot, libroot, bldroot):
-    ###############################################################################
+###############################################################################
 
     with Case(caseroot) as case:
 
@@ -71,7 +71,7 @@ def _build_fms(caseroot, libroot, bldroot):
 
 ###############################################################################
 def _build_cam(caseroot, libroot, bldroot):
-    ###############################################################################
+###############################################################################
 
     with Case(caseroot, read_only=False) as case:
 
@@ -157,12 +157,157 @@ 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 "
+        cmake_args += "-DCMAKE_BUILD_TYPE=Debug "
+        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)
 

cime_config/buildnml

@@ -231,6 +231,13 @@ 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():
 

cime_config/config_component.xml

@@ -227,6 +227,18 @@
     </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>

cime_config/testdefs/testmods_dirs/cam/carma_mixed_sulfate/user_nl_cam

@@ -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.
@@ -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'

cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/shell_commands

@@ -0,0 +1,2 @@
+./xmlchange ROF_NCPL=\$ATM_NCPL
+./xmlchange GLC_NCPL=\$ATM_NCPL

cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/user_nl_cam

@@ -0,0 +1,15 @@
+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'

cime_config/testdefs/testmods_dirs/cam/outfrq9s_tuvx_waccm_ma_mam5/user_nl_clm

@@ -0,0 +1,27 @@
+!----------------------------------------------------------------------------------
+! 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
+