Add TUV-x to CAM

.gitignore

@@ -15,6 +15,7 @@ src/dynamics/fv3/atmos_cubed_sphere
 libraries/FMS
 libraries/mct
 libraries/parallelio
+libraries/tuv-x
 src/atmos_phys
 src/dynamics/mpas/dycore
 share
@@ -23,6 +24,9 @@ src/hemco
 buildnmlc
 buildcppc
 
+# ignore ide configs
+.vscode
+
 # Ignore editor temporaries and backups
 *~
 .#*

Externals_CAM.cfg

@@ -71,6 +71,13 @@ sparse = ../.mpas_sparse_checkout
 hash = b8c33daa
 required = True
 
+[TUV-x]
+local_path = libraries/tuv-x
+protocol = git
+repo_url = https://github.com/NCAR/tuv-x.git
+hash = ccda76c0553064a9b7b0eba73162ddeee6d8eaff
+required = True
+
 [hemco]
 local_path = src/hemco
 tag = hemco-cesm1_2_1_hemco3_6_3_cesm

bld/namelist_files/namelist_definition.xml

@@ -7352,6 +7352,17 @@ 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, imp
-
+from glob import glob
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
@@ -21,6 +21,7 @@ from CIME.case import Case
 from CIME.utils import run_sub_or_cmd, expect, run_cmd
 from CIME.buildlib import parse_input
 from CIME.build import get_standard_makefile_args
+from CIME.XML.env_build import EnvBuild
 
 logger = logging.getLogger(__name__)
 
@@ -113,12 +114,150 @@ 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, "Command {} failed with rc={}".format(command, rc))
+
+###############################################################################
+def _cmake_default_args(caseroot):
+###############################################################################
+# Returns a dictionary of CMake variables based on the Macros.cmake file for
+# the build.
+
+    build = EnvBuild(case_root=caseroot)
+    with Case(caseroot) as case:
+        macro_path = os.path.abspath(os.path.join(caseroot, "cmake_macros", ""))
+        args = "-DCONVERT_TO_MAKE=ON "
+        args += "-DCASEROOT={} ".format(caseroot)
+        args += "-DCOMPILER={} ".format(build.get_value("COMPILER"))
+        args += "-DOS={} ".format(build.get_value("OS"))
+        args += "-DMACH={} ".format(case.get_value("MACH"))
+        args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
+        args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        cmd = "cmake {} .".format(args)
+        rc, out, err = run_cmd(cmd, combine_output=True, from_dir=macro_path)
+        expect(rc == 0, "Command {} failed with rc={} out={} err={}".format(cmd, rc, out, 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
+
+    build = EnvBuild(case_root=caseroot)
+    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)
+        if build.get_value("MPILIB") == "mpi-serial":
+            cmake_args = "-DCMAKE_Fortran_COMPILER={} ".format(arg_dict["SFC"])
+        else:
+            cmake_args = "-DCMAKE_Fortran_COMPILER={} ".format(arg_dict["MPIFC"])
+            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_C_COMPILER_WORKS=1 "
+        cmake_args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        cmake_args += "-DTUVX_ENABLE_TESTS=OFF "
+        cmake_args += "-DTUVX_ENABLE_COVERAGE=OFF "
+        cmake_args += "-DCMAKE_Fortran_FLAGS='{}' ".format(arg_dict["FFLAGS"])
+        cmake_args += "-DCMAKE_INSTALL_PREFIX='{}' ".format(libroot)
+        cmake_args += "-DTUVX_INSTALL_INCLUDE_DIR='{}' ".format(_tuvx_include_dir(libroot))
+        cmake_args += "-DTUVX_INSTALL_MOD_DIR='{}' ".format(_tuvx_include_dir(libroot))
+        cmake_args += srcpath
+
+        _run_cmd("cmake {}".format(cmake_args), bldpath)
+        _run_cmd(case.get_value("GMAKE"), bldpath)
+        _run_cmd("{} install".format(case.get_value("GMAKE")), bldpath)
+
+        # add TUV-x to include paths
+        incldir = os.environ.get('USER_INCLDIR')
+        if incldir is None:
+            incldir = ''
+        os.environ['USER_INCLDIR'] = incldir + \
+            " -I{} ".format(_tuvx_include_dir(libroot))
+
+        # create simlink 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)
+
+###############################################################################
+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), \
+           "TUV-x include directory not found at {}".format(coreinc))
+    return coreinc
+
+###############################################################################
+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), \
+           "TUV-x library not found at {}".format(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, \
+           "TUV-x not found at {}".format(libroot))
+    expect(len(corepaths)<2, \
+           "Multiple TUV-x versions found at {}".format(libroot))
+    expect(os.path.exists(corepaths[0]), \
+           "TUV-x install directory not found at {}".format(corepaths[0]))
+    return corepaths[0]
+
+###############################################################################
+def _tuvx_package_dir(libroot):
+###############################################################################
+# Returns the path to the TUV-x CMake package
+
+    paths = glob(os.path.join(libroot, "tuvx*", "cmake", "tuvx*" ))
+    expect(len(paths)>0, \
+           "TUV-x package not found at {}".format(libroot))
+    expect(len(paths)<2, \
+           "Multiple TUV-x versions found at {}".format(libroot))
+    expect(os.path.exists(paths[0]), \
+           "TUV-x package directory not found at {}".format(paths[0]))
+    return paths[0]
 
 ###############################################################################
 
 
 def _main_func():
     caseroot, libroot, bldroot = parse_input(sys.argv)
+    _build_tuvx(caseroot, libroot, bldroot)
     _build_cam(caseroot, libroot, bldroot)
 
 

cime_config/buildnml

@@ -211,6 +211,17 @@ def buildnml(case, caseroot, compname):
         if (os.path.isfile(file1)) and (not os.path.isfile(file2)):
             shutil.copy(file1,file2)
 
+        # Temporary copy of TUV-x data for development
+        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)
+        shutil.copy2(os.path.join(srcroot, "cime_config", "tuvx_MOZART.json"), \
+                     os.path.join(rundir, "tuvx_MOZART.json"))
+        shutil.copy2(os.path.join(srcroot, "cime_config", "tuvx_MOZART_TS1.json"), \
+                     os.path.join(rundir, "tuvx_MOZART_TS1.json"))
+
 ###############################################################################
 def _main_func():
 

cime_config/config_component.xml

@@ -203,6 +203,18 @@
     </desc>
   </entry>
 
+  <entry id="CAM_LINKED_LIBS">
+    <type>char</type>
+    <valid_values></valid_values>
+    <default_value>-ltuvx -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>