diff --git a/physics/docs/ccpp_doxyfile b/physics/docs/ccpp_doxyfile new file mode 100644 index 000000000..91c80c221 --- /dev/null +++ b/physics/docs/ccpp_doxyfile @@ -0,0 +1,443 @@ +# Doxyfile 1.8.11 +DOXYFILE_ENCODING = UTF-8 +PROJECT_NAME = "Common Community Physics Package (CCPP) Scientific Documentation" +PROJECT_NUMBER = "" +PROJECT_BRIEF = " " +PROJECT_LOGO = img/dtc_logo.png +OUTPUT_DIRECTORY = doc +CREATE_SUBDIRS = NO +ALLOW_UNICODE_NAMES = NO +OUTPUT_LANGUAGE = English +BRIEF_MEMBER_DESC = YES +REPEAT_BRIEF = NO +ABBREVIATE_BRIEF = +ALWAYS_DETAILED_SEC = NO +INLINE_INHERITED_MEMB = NO +FULL_PATH_NAMES = NO +STRIP_FROM_PATH = +STRIP_FROM_INC_PATH = +SHORT_NAMES = NO +JAVADOC_AUTOBRIEF = NO +QT_AUTOBRIEF = NO +MULTILINE_CPP_IS_BRIEF = NO +INHERIT_DOCS = YES +SEPARATE_MEMBER_PAGES = YES +TAB_SIZE = 4 +ALIASES = +TCL_SUBST = +OPTIMIZE_OUTPUT_FOR_C = NO +OPTIMIZE_OUTPUT_JAVA = NO +OPTIMIZE_FOR_FORTRAN = YES +OPTIMIZE_OUTPUT_VHDL = NO +EXTENSION_MAPPING = .f=Fortranfixed \ + .F=Fortranfixed \ + .F90=FortranFree \ + .f90=FortranFree +MARKDOWN_SUPPORT = YES +AUTOLINK_SUPPORT = YES +BUILTIN_STL_SUPPORT = NO +CPP_CLI_SUPPORT = NO +SIP_SUPPORT = NO +IDL_PROPERTY_SUPPORT = YES +DISTRIBUTE_GROUP_DOC = YES +GROUP_NESTED_COMPOUNDS = NO +SUBGROUPING = YES +INLINE_GROUPED_CLASSES = NO +INLINE_SIMPLE_STRUCTS = NO +TYPEDEF_HIDES_STRUCT = YES +LOOKUP_CACHE_SIZE = 0 +EXTRACT_ALL = YES +EXTRACT_PRIVATE = YES +EXTRACT_PACKAGE = YES +EXTRACT_STATIC = YES +EXTRACT_LOCAL_CLASSES = YES +EXTRACT_LOCAL_METHODS = YES +EXTRACT_ANON_NSPACES = YES +HIDE_UNDOC_MEMBERS = NO +HIDE_UNDOC_CLASSES = NO +HIDE_FRIEND_COMPOUNDS = NO +HIDE_IN_BODY_DOCS = NO +INTERNAL_DOCS = YES + +CASE_SENSE_NAMES = NO + +HIDE_SCOPE_NAMES = NO + +HIDE_COMPOUND_REFERENCE= NO + +SHOW_INCLUDE_FILES = NO + +SHOW_GROUPED_MEMB_INC = NO + +FORCE_LOCAL_INCLUDES = NO + +INLINE_INFO = YES + +SORT_MEMBER_DOCS = NO + +SORT_BRIEF_DOCS = NO +SORT_MEMBERS_CTORS_1ST = NO +SORT_GROUP_NAMES = NO +SORT_BY_SCOPE_NAME = NO +STRICT_PROTO_MATCHING = NO +GENERATE_TODOLIST = YES +GENERATE_TESTLIST = YES +GENERATE_BUGLIST = YES +GENERATE_DEPRECATEDLIST= YES +ENABLED_SECTIONS = YES +MAX_INITIALIZER_LINES = 30 +SHOW_USED_FILES = YES +SHOW_FILES = YES +SHOW_NAMESPACES = YES +FILE_VERSION_FILTER = +LAYOUT_FILE = ccpp_dox_layout.xml +CITE_BIB_FILES = library.bib +QUIET = NO +WARNINGS = YES +WARN_IF_UNDOCUMENTED = NO +WARN_IF_DOC_ERROR = YES +WARN_NO_PARAMDOC = NO +WARN_AS_ERROR = NO +WARN_FORMAT = +WARN_LOGFILE = +INPUT = pdftxt/mainpage.txt \ + pdftxt/all_shemes_list.txt \ + pdftxt/GFSv15_suite.txt \ + pdftxt/GFSv15_suite_TKEEDMF.txt \ + pdftxt/CPT_adv_suite.txt \ + pdftxt/GSD_adv_suite.txt \ + pdftxt/GFS_RRTMG.txt \ + pdftxt/GFS_SFCLYR.txt \ + pdftxt/GFS_NSST.txt \ + pdftxt/GFS_NOAH.txt \ + pdftxt/GFS_SFCSICE.txt \ + pdftxt/GFS_HEDMF.txt \ + pdftxt/GFS_SATMEDMF.txt \ + pdftxt/GFS_GWDPS.txt \ + pdftxt/GFS_OZPHYS.txt \ + pdftxt/GFS_H2OPHYS.txt \ + pdftxt/GFS_RAYLEIGH.txt \ + pdftxt/GFS_SAMF.txt \ + pdftxt/GFS_SAMFdeep.txt \ + pdftxt/GFS_GWDC.txt \ + pdftxt/GFS_SAMFshal.txt \ + pdftxt/GFDL_cloud.txt \ +### pdftxt/GFS_SURFACE_PERT.txt \ + pdftxt/GFS_CALPRECIPTYPE.txt \ +### pdftxt/rad_cld.txt \ + pdftxt/CPT_CSAW.txt \ + pdftxt/CPT_MG3.txt \ + pdftxt/GSD_MYNN_EDMF.txt \ + pdftxt/GSD_CU_GF_deep.txt \ + pdftxt/GSD_RUCLSM.txt \ + pdftxt/GSD_THOMPSON.txt \ +### pdftxt/GFSphys_namelist.txt \ +### pdftxt/GFS_STOCHY_PHYS.txt \ + pdftxt/suite_input.nml.txt \ +### in-core MP + ../gfdl_fv_sat_adj.F90 \ +### time_vary + ../GFS_phys_time_vary.fv3.F90 \ + ../GFS_rad_time_vary.fv3.F90 \ + ../ozne_def.f \ + ../ozinterp.f90 \ + ../h2o_def.f \ + ../h2ointerp.f90 \ + ../aerclm_def.F \ + ../aerinterp.F90 \ + ../iccn_def.F \ + ../iccninterp.F90 \ + ../sfcsub.F \ + ../gcycle.F90 \ +### Radiation + ../radlw_main.f \ + ../radsw_main.f \ + ../radiation_aerosols.f \ + ../radiation_astronomy.f \ + ../radiation_clouds.f \ + ../radiation_gases.f \ + ../radiation_surface.f \ + ../radlw_param.f \ + ../radlw_datatb.f \ + ../radsw_param.f \ + ../radsw_datatb.f \ + ../dcyc2.f \ +### Land Surface + ../sfc_diff.f \ + ../sfc_nst.f \ + ../module_nst_model.f90 \ + ../module_nst_parameters.f90 \ + ../module_nst_water_prop.f90 \ + ../sfc_drv.f \ + ../sflx.f \ + ../namelist_soilveg.f \ + ../set_soilveg.f \ +### Sea Ice Surface + ../sfc_sice.f \ +### PBL + ../moninedmf.f \ + ../mfpbl.f \ + ../tridi.f \ +### satmedmf + ../satmedmfvdif.F \ + ../mfpblt.f \ + ../mfscu.f \ + ../tridi.f \ +### Orographic Gravity Wave + ../gwdps.f \ +### Rayleigh Dampling + ../rayleigh_damp.f \ +### Prognostic Ozone + ../ozphys_2015.f \ +### ../ozphys.f \ +### stratospheric h2o + ../h2ophys.f \ +### Deep Convection + ../samfdeepcnv.f \ +### Convective Gravity Wave + ../gwdc.f \ +### Shallow Convection + ../samfshalcnv.f \ + ../cnvc90.f \ +### Microphysics +### ../gscond.f \ +### ../precpd.f \ + ../module_bfmicrophysics.f \ +### GFDL cloud MP + ../gfdl_cloud_microphys.F90 \ + ../module_gfdl_cloud_microphys.F90 \ +### + ../GFS_MP_generic.F90 \ + ../calpreciptype.f90 \ +### stochy +### ../GFS_stochastics.F90 \ +### ../surface_perturbation.F90 \ +### ../../stochastic_physics/stochastic_physics.F90 \ +### CPT + ../m_micro.F90 \ +### ../micro_mg2_0.F90 \ + ../micro_mg3_0.F90 \ + ../micro_mg_utils.F90 \ + ../cldmacro.F \ + ../aer_cloud.F \ + ../cldwat2m_micro.F \ + ../wv_saturation.F \ + ../cs_conv_aw_adj.F90 \ + ../cs_conv.F90 \ +### GSD + ../cu_gf_driver.F90 \ + ../cu_gf_deep.F90 \ + ../cu_gf_sh.F90 \ + ../module_MYNNrad_pre.F90 \ + ../module_MYNNrad_post.F90 \ + ../module_MYNNPBL_wrapper.F90 \ + ../module_bl_mynn.F90 \ +### ../module_MYNNSFC_wrapper.F90 \ +### ../module_sf_mynn.F90 \ + ../sfc_drv_ruc.F90 \ + ../module_sf_ruclsm.F90 \ + ../namelist_soilveg_ruc.F90 \ + ../set_soilveg_ruc.F90 \ + ../module_soil_pre.F90 \ + ../mp_thompson_pre.F90 \ + ../module_mp_thompson_make_number_concentrations.F90 \ + ../mp_thompson.F90 \ + ../module_mp_thompson.F90 \ + ../module_mp_radar.F90 \ + ../mp_thompson_post.F90 \ +### utils + ../funcphys.f90 \ + ../physparam.f \ + ../physcons.F90 \ + ../radcons.f90 \ + ../mersenne_twister.f \ + compns_stochy.F90 + + +INPUT_ENCODING = UTF-8 +FILE_PATTERNS = *.f \ + *.F \ + *.F90 \ + *.f90 \ + *.nml \ + *.txt +RECURSIVE = YES +EXCLUDE = +EXCLUDE_SYMLINKS = NO +EXCLUDE_PATTERNS = +EXCLUDE_SYMBOLS = +EXAMPLE_PATH = ./ +EXAMPLE_PATTERNS = +EXAMPLE_RECURSIVE = NO +IMAGE_PATH = img +INPUT_FILTER = +FILTER_PATTERNS = +FILTER_SOURCE_FILES = NO +FILTER_SOURCE_PATTERNS = +USE_MDFILE_AS_MAINPAGE = +SOURCE_BROWSER = NO +INLINE_SOURCES = NO +STRIP_CODE_COMMENTS = YES +REFERENCED_BY_RELATION = YES +REFERENCES_RELATION = YES +REFERENCES_LINK_SOURCE = YES +SOURCE_TOOLTIPS = YES +USE_HTAGS = NO +VERBATIM_HEADERS = YES +#CLANG_ASSISTED_PARSING = NO +#CLANG_OPTIONS = +ALPHABETICAL_INDEX = NO +COLS_IN_ALPHA_INDEX = 5 +IGNORE_PREFIX = +GENERATE_HTML = YES +HTML_OUTPUT = html +HTML_FILE_EXTENSION = .html +HTML_HEADER = +HTML_FOOTER = +HTML_STYLESHEET = +HTML_EXTRA_STYLESHEET = ccpp_dox_extra_style.css +HTML_EXTRA_FILES = +HTML_COLORSTYLE_HUE = 220 +HTML_COLORSTYLE_SAT = 100 +HTML_COLORSTYLE_GAMMA = 80 +HTML_TIMESTAMP = NO +HTML_DYNAMIC_SECTIONS = NO +HTML_INDEX_NUM_ENTRIES = 100 +GENERATE_DOCSET = NO +DOCSET_FEEDNAME = "Doxygen generated docs" +DOCSET_BUNDLE_ID = org.doxygen.Project +DOCSET_PUBLISHER_ID = org.doxygen.Publisher +DOCSET_PUBLISHER_NAME = Publisher +GENERATE_HTMLHELP = NO +CHM_FILE = +HHC_LOCATION = +GENERATE_CHI = NO +CHM_INDEX_ENCODING = +BINARY_TOC = NO +TOC_EXPAND = NO +GENERATE_QHP = NO +QCH_FILE = +QHP_NAMESPACE = org.doxygen.Project +QHP_VIRTUAL_FOLDER = doc +QHP_CUST_FILTER_NAME = +QHP_CUST_FILTER_ATTRS = +QHP_SECT_FILTER_ATTRS = +QHG_LOCATION = +GENERATE_ECLIPSEHELP = NO +ECLIPSE_DOC_ID = org.doxygen.Project +DISABLE_INDEX = YES +GENERATE_TREEVIEW = YES +ENUM_VALUES_PER_LINE = 4 +TREEVIEW_WIDTH = 250 +EXT_LINKS_IN_WINDOW = NO +FORMULA_FONTSIZE = 10 +FORMULA_TRANSPARENT = YES +USE_MATHJAX = YES +MATHJAX_FORMAT = HTML-CSS +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2 +MATHJAX_EXTENSIONS = +MATHJAX_CODEFILE = +SEARCHENGINE = YES +SERVER_BASED_SEARCH = NO +EXTERNAL_SEARCH = NO +SEARCHENGINE_URL = +SEARCHDATA_FILE = searchdata.xml +EXTERNAL_SEARCH_ID = +EXTRA_SEARCH_MAPPINGS = +GENERATE_LATEX = YES +LATEX_OUTPUT = latex +LATEX_CMD_NAME = latex +MAKEINDEX_CMD_NAME = makeindex +COMPACT_LATEX = YES +PAPER_TYPE = a4 +EXTRA_PACKAGES = amsmath +LATEX_HEADER = +LATEX_FOOTER = +LATEX_EXTRA_STYLESHEET = +LATEX_EXTRA_FILES = +PDF_HYPERLINKS = YES +USE_PDFLATEX = YES +LATEX_BATCHMODE = NO +LATEX_HIDE_INDICES = YES +LATEX_SOURCE_CODE = NO + +LATEX_BIB_STYLE = plainnat + +LATEX_TIMESTAMP = NO + +GENERATE_RTF = NO + +RTF_OUTPUT = rtf +COMPACT_RTF = NO +RTF_HYPERLINKS = NO +RTF_STYLESHEET_FILE = +RTF_EXTENSIONS_FILE = +RTF_SOURCE_CODE = NO +GENERATE_MAN = NO +MAN_OUTPUT = man +MAN_EXTENSION = .3 +MAN_SUBDIR = +MAN_LINKS = NO +GENERATE_XML = NO +XML_OUTPUT = xml +XML_PROGRAMLISTING = YES +GENERATE_DOCBOOK = NO +DOCBOOK_OUTPUT = docbook +DOCBOOK_PROGRAMLISTING = NO +GENERATE_AUTOGEN_DEF = NO +GENERATE_PERLMOD = NO +PERLMOD_LATEX = NO +PERLMOD_PRETTY = YES +PERLMOD_MAKEVAR_PREFIX = +ENABLE_PREPROCESSING = NO +MACRO_EXPANSION = NO +EXPAND_ONLY_PREDEF = NO +SEARCH_INCLUDES = YES +INCLUDE_PATH = +INCLUDE_FILE_PATTERNS = +PREDEFINED = CCPP \ + MULTI_GASES \ + 0 +EXPAND_AS_DEFINED = +SKIP_FUNCTION_MACROS = YES +TAGFILES = +GENERATE_TAGFILE = +ALLEXTERNALS = NO +EXTERNAL_GROUPS = YES +EXTERNAL_PAGES = YES +PERL_PATH = /usr/bin/perl +CLASS_DIAGRAMS = YES +MSCGEN_PATH = +DIA_PATH = +HIDE_UNDOC_RELATIONS = NO +HAVE_DOT = YES +DOT_NUM_THREADS = 0 +DOT_FONTNAME = Helvetica +DOT_FONTSIZE = 10 +DOT_FONTPATH = +CLASS_GRAPH = NO +COLLABORATION_GRAPH = NO +GROUP_GRAPHS = YES +UML_LOOK = YES +UML_LIMIT_NUM_FIELDS = 10 +TEMPLATE_RELATIONS = NO +INCLUDE_GRAPH = YES +INCLUDED_BY_GRAPH = NO +CALL_GRAPH = YES +CALLER_GRAPH = NO +GRAPHICAL_HIERARCHY = YES +DIRECTORY_GRAPH = YES +DOT_IMAGE_FORMAT = svg +INTERACTIVE_SVG = NO +DOT_PATH = +DOTFILE_DIRS = +MSCFILE_DIRS = +DIAFILE_DIRS = +PLANTUML_JAR_PATH = +PLANTUML_INCLUDE_PATH = +DOT_GRAPH_MAX_NODES = 200 +MAX_DOT_GRAPH_DEPTH = 0 +DOT_TRANSPARENT = NO +DOT_MULTI_TARGETS = YES +GENERATE_LEGEND = YES +DOT_CLEANUP = YES