diff --git a/CMakeLists.txt b/CMakeLists.txt index c9b7e66a..17e127bc 100755 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -90,7 +90,7 @@ CHECK_ENABLE_FLAG( USE_DOXYGEN 1 ) CHECK_ENABLE_FLAG( USE_LATEX 1 ) FILE( MAKE_DIRECTORY "${${PROJ}_INSTALL_DIR}/doc" ) IF ( USE_DOXYGEN ) - SET( DOXYFILE_LATEX YES ) + SET( DOXYFILE_LATEX NO ) SET( DOXYFILE_IN "${${PROJ}_SOURCE_DIR}/doxygen/Doxyfile.in" ) SET( DOXY_HEADER_FILE "${${PROJ}_SOURCE_DIR}/doxygen/html/header.html" ) SET( DOXY_FOOTER_FILE "${${PROJ}_SOURCE_DIR}/doxygen/html/footer.html" ) diff --git a/IO/Reader.h b/IO/Reader.h index 6542a2ea..9dfc834b 100644 --- a/IO/Reader.h +++ b/IO/Reader.h @@ -87,7 +87,7 @@ std::shared_ptr getVariable( const std::string &path, const std::s * @brief Reformat the variable to match the mesh * @details This function modifies the dimensions of the array to match the mesh * @param[in] mesh The underlying mesh - * @param[in/out] variable The variable name to read + * @param[in,out] var The variable name to read */ void reformatVariable( const IO::Mesh &mesh, IO::Variable &var ); diff --git a/IO/Xdmf.h b/IO/Xdmf.h index c7d39801..ff9097bc 100644 --- a/IO/Xdmf.h +++ b/IO/Xdmf.h @@ -105,6 +105,7 @@ public: * @param[in] type The element type * @param[in] NumElements The number of elements * @param[in] dofMap The connectivity information (type x NumElements) + * @param[in] NumNodes The number of nodes * @param[in] x The x coordinates or the xy/xyz coordinates * @param[in] y The y coordinates (may be null) * @param[in] z The z coordinates (may be null) diff --git a/IO/netcdf.h b/IO/netcdf.h index 5fcc5d82..80c7d18a 100644 --- a/IO/netcdf.h +++ b/IO/netcdf.h @@ -123,6 +123,8 @@ Array getAtt( int fid, const std::string &att ); * @brief Write the dimensions * @details This function writes the grid dimensions to netcdf. * @param fid Handle to the open file + * @param names + * @param dims */ std::vector defDim( int fid, const std::vector &names, const std::vector &dims ); @@ -132,6 +134,10 @@ std::vector defDim( * @brief Write a variable * @details This function writes a variable to netcdf. * @param fid Handle to the open file + * @param var Variable to read + * @param dimids + * @param data + * @param rank_info */ template void write( int fid, const std::string &var, const std::vector &dimids, diff --git a/IO/silo.h b/IO/silo.h index a3edfeb7..aef994df 100644 --- a/IO/silo.h +++ b/IO/silo.h @@ -49,7 +49,7 @@ void close( DBfile *fid ); * @param[in] fid Handle to the open file * @param[in] name Name of variable */ -DataType varDataType( DBfile *dbfile, const std::string &name ); +DataType varDataType( DBfile *fid, const std::string &name ); /*! @@ -250,8 +250,6 @@ void writeMultiMesh( DBfile *fid, const std::string &meshname, * @param[in] varname Mesh name * @param[in] subVarNames Names of the sub meshes in the form "filename:meshname" * @param[in] subVarTypes Type of each submesh - * @param[in] ndim Dimension of variable (used to determine suffix) - * @param[in] nvar Number of subvariables (used to determine suffix) */ void writeMultiVar( DBfile *fid, const std::string &varname, const std::vector &subVarNames, const std::vector &subVarTypes ); diff --git a/analysis/analysis.h b/analysis/analysis.h index ec377995..1dc2a0c1 100644 --- a/analysis/analysis.h +++ b/analysis/analysis.h @@ -22,8 +22,8 @@ typedef Array BlobIDArray; * @param[in] SignDist SignDist * @param[in] vF vF * @param[in] vS vS - * @param[in] S S * @param[out] LocalBlobID The ids of the blobs + * @param[in] periodic Optional value * @return Returns the number of blobs */ int ComputeLocalBlobIDs( const DoubleArray& Phase, const DoubleArray& SignDist, @@ -48,12 +48,13 @@ int ComputeLocalPhaseComponent( const IntArray &PhaseID, int &VALUE, IntArray &C * @param[in] nx Number of elements in the x-direction * @param[in] ny Number of elements in the y-direction * @param[in] nz Number of elements in the z-direction + * @param[in] rank_info MPI communication info * @param[in] Phase Phase * @param[in] SignDist SignDist * @param[in] vF vF * @param[in] vS vS - * @param[in] S S - * @param[out] LocalBlobID The ids of the blobs + * @param[out] GlobalBlobID The ids of the blobs + * @param[in] comm MPI communicator * @return Returns the number of blobs */ int ComputeGlobalBlobIDs( int nx, int ny, int nz, const RankInfoStruct& rank_info, @@ -68,10 +69,11 @@ int ComputeGlobalBlobIDs( int nx, int ny, int nz, const RankInfoStruct& rank_inf * @param[in] nx Number of elements in the x-direction * @param[in] ny Number of elements in the y-direction * @param[in] nz Number of elements in the z-direction - * @param[in] rank_in MPI communication info + * @param[in] rank_info MPI communication info * @param[in] PhaseID Array that identifies the phases * @param[in] VALUE Identifier for the phase to decompose * @param[out] GlobalBlobID The ids of the blobs for the phase + * @param[in] comm The communicator to use * @return Return the number of components in the specified phase */ int ComputeGlobalPhaseComponent( int nx, int ny, int nz, const RankInfoStruct& rank_info, @@ -82,10 +84,8 @@ int ComputeGlobalPhaseComponent( int nx, int ny, int nz, const RankInfoStruct& r * @brief Reorder the blobs * @details Reorder the blobs based on the number of cells they contain * largest first. - * @param[in] nx Number of elements in the x-direction - * @param[in] ny Number of elements in the y-direction - * @param[in] nz Number of elements in the z-direction - * @param[in/out] ID The ids of the blobs + * @param[in,out] ID The ids of the blobs + * @param[in] comm MPI communicator */ void ReorderBlobIDs( BlobIDArray& ID, const Utilities::MPI& comm ); @@ -117,8 +117,12 @@ struct ID_map_struct { * @details This functions computes the map of blob ids between iterations * @return Returns the map of the blob ids. Each final blob may have no source * ids, one parent, or multiple parents. Each src id may be a parent for multiple blobs. + * @param[in] nx Number of elements in the x-direction + * @param[in] ny Number of elements in the y-direction + * @param[in] nz Number of elements in the z-direction * @param[in] ID1 The blob ids at the first timestep * @param[in] ID2 The blob ids at the second timestep + * @param[in] comm The communicator to use */ ID_map_struct computeIDMap( int nx, int ny, int nz, const BlobIDArray& ID1, const BlobIDArray& ID2, const Utilities::MPI& comm ); @@ -127,7 +131,7 @@ ID_map_struct computeIDMap( int nx, int ny, int nz, const BlobIDArray& ID1, cons * @brief Compute the new global ids based on the map * @details This functions computes the time-consistent global ids for the * current global id index - * @param[in/out] map The timestep mapping for the ids + * @param[in,out] map The timestep mapping for the ids * @param[in] id_max The globally largest id used previously * @param[out] new_ids The newly renumbered blob ids (0:ids.max()) */ @@ -139,9 +143,9 @@ void getNewIDs( ID_map_struct& map, BlobIDType& id_max, std::vector& * @details This functions computes the map of blob ids between iterations. * Note: we also update the map to reflect the new ids * @param[out] new_ids The newly renumbered blob ids (0:ids.max()) - * @param[in/out] IDs The blob ids to renumber + * @param[in,out] IDs The blob ids to renumber */ -void renumberIDs( const std::vector& new_id_list, BlobIDArray& IDs ); +void renumberIDs( const std::vector& new_ids, BlobIDArray& IDs ); /*! diff --git a/analysis/distance.h b/analysis/distance.h index b3fc870e..99ac1cd4 100644 --- a/analysis/distance.h +++ b/analysis/distance.h @@ -24,6 +24,7 @@ inline bool operator<(const Vec& l, const Vec& r){ return l.x*l.x+l.y*l.y+l.z*l. * @param[in] ID Segmentation id * @param[in] Dm Domain information * @param[in] periodic Directions that are periodic + * @param[in] dx Cell size */ template void CalcDist( Array &Distance, const Array &ID, const Domain &Dm, @@ -36,6 +37,7 @@ void CalcDist( Array &Distance, const Array &ID, const Domain &Dm, * @param[in] ID Domain id * @param[in] Dm Domain information * @param[in] periodic Directions that are periodic + * @param[in] dx Cell size */ void CalcVecDist( Array &Distance, const Array &ID, const Domain &Dm, const std::array& periodic = {true,true,true}, const std::array& dx = {1,1,1} ); diff --git a/analysis/filters.h b/analysis/filters.h index 404fb265..65f52e32 100644 --- a/analysis/filters.h +++ b/analysis/filters.h @@ -25,7 +25,10 @@ void Med3D( const Array &Input, Array &Output ); * @details This routine performs a non-linear local means filter * @param[in] Input Input image * @param[in] Mean Mean value + * @param[in] Distance Distance * @param[out] Output Output image + * @param[in] d + * @param[in] h */ int NLM3D( const Array &Input, Array &Mean, const Array &Distance, Array &Output, const int d, const float h); diff --git a/analysis/imfilter.h b/analysis/imfilter.h index b1c4040a..1b998461 100644 --- a/analysis/imfilter.h +++ b/analysis/imfilter.h @@ -89,7 +89,7 @@ Array imfilter_separable( const Array& A, const std::vector imfilter_separable( const Array& A, const std::vector& Nh * This version works with separable filters and is more efficient than a single filter. * @param[in] A The input array (Nx,Ny,Nz) * @param[in] H The filter [2*Nhx+1,2*Nhy+1,...] + * @param[in] Nh The filter size * @param[in] boundary The boundary conditions to apply (ndim): * fixed - Input array values outside the bounds of the array are * implicitly assumed to have the value X diff --git a/common/Communication.h b/common/Communication.h index 5baaa962..f14cc8a1 100644 --- a/common/Communication.h +++ b/common/Communication.h @@ -51,6 +51,7 @@ class fillHalo public: /*! * @brief Default constructor + * @param[in] comm Communicator to use * @param[in] info Rank and neighbor rank info * @param[in] n Number of local cells * @param[in] ng Number of ghost cells diff --git a/common/MPI.h b/common/MPI.h index ef2d9584..6e05135d 100644 --- a/common/MPI.h +++ b/common/MPI.h @@ -821,7 +821,7 @@ public: // Member functions * @return Output array for allGather */ template - std::vector allGather( const std::vector &x_in ) const; + std::vector allGather( const std::vector &x ) const; /*! diff --git a/common/Utilities.h b/common/Utilities.h index 8dcd8c8e..9389d538 100644 --- a/common/Utilities.h +++ b/common/Utilities.h @@ -30,6 +30,7 @@ using StackTrace::Utilities::sleep_s; * \details This routine will peform the default startup sequence * \param argc argc from main * \param argv argv from main + * \param multiple Intialize mpi with MPI_THREAD_MULTIPLE support? */ void startup( int argc, char **argv, bool multiple=true ); diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in index 8070b0e7..b654532f 100755 --- a/doxygen/Doxyfile.in +++ b/doxygen/Doxyfile.in @@ -379,12 +379,6 @@ MAX_INITIALIZER_LINES = 30 SHOW_USED_FILES = YES -# If the sources in your project are distributed over multiple directories -# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy -# in the documentation. The default is NO. - -SHOW_DIRECTORIES = YES - # Set the SHOW_FILES tag to NO to disable the generation of the Files page. # This will remove the Files entry from the Quick Index and from the # Folder Tree View (if specified). The default is YES. @@ -467,7 +461,7 @@ INPUT_ENCODING = UTF-8 # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py # *.f90 *.f *.for *.vhd *.vhdl -FILE_PATTERNS = *.h *.hh *.cu +FILE_PATTERNS = *.h *.hh # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. @@ -728,12 +722,6 @@ HTML_COLORSTYLE_GAMMA = 80 HTML_TIMESTAMP = YES -# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, -# files or namespaces will be aligned in HTML using tables. If set to -# NO a bullet list will be used. - -HTML_ALIGN_MEMBERS = YES - # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. For this to work a browser that supports @@ -850,7 +838,7 @@ TREEVIEW_WIDTH = 250 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. -GENERATE_LATEX = YES +GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be @@ -1005,18 +993,6 @@ GENERATE_XML = NO XML_OUTPUT = xml -# The XML_SCHEMA tag can be used to specify an XML schema, -# which can be used by a validating XML parser to check the -# syntax of the XML files. - -XML_SCHEMA = - -# The XML_DTD tag can be used to specify an XML DTD, -# which can be used by a validating XML parser to check the -# syntax of the XML files. - -XML_DTD = - # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that @@ -1174,11 +1150,6 @@ ALLEXTERNALS = NO EXTERNAL_GROUPS = YES -# The PERL_PATH should be the absolute path and name of the perl script -# interpreter (i.e. the result of `which perl'). - -PERL_PATH = /usr/bin/perl - #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- diff --git a/doxygen/DoxygenMainpage.h b/doxygen/DoxygenMainpage.h index d3dae521..0d42f215 100644 --- a/doxygen/DoxygenMainpage.h +++ b/doxygen/DoxygenMainpage.h @@ -4,8 +4,6 @@ * * - \ref IO "IO routines" * - \ref Utilities "Utility routines" - * - \ref silo "Access to silo routines" - * - \ref netcdf "Access to netcdf routines" * * \author James McClure */ diff --git a/threadpool/atomic_helpers.h b/threadpool/atomic_helpers.h index 32b67200..6d36312e 100644 --- a/threadpool/atomic_helpers.h +++ b/threadpool/atomic_helpers.h @@ -222,7 +222,6 @@ inline int32_atomic atomic_fetch_and_or( int32_atomic volatile *v, int32_atomic * \brief Fetch the current value and "ou" with given value * \details Perform *v = (*v) | x, returning the previous value * \return Returns the previous value before the "and" operation - * \param[in] v The pointer to the value to check and swap * \param[in] v The pointer to the value to check and or * \param[in] x The value to or */