PROJECT_NAME = @CMAKE_PROJECT_NAME@
@INCLUDE = Doxyfile-version
LAYOUT_FILE = @CMAKE_CURRENT_SOURCE_DIR@/DoxygenLayout.xml
INPUT = @CMAKE_CURRENT_SOURCE_DIR@ \
@CMAKE_SOURCE_DIR@/src \
@CMAKE_SOURCE_DIR@/api/legacy/include \
@CMAKE_SOURCE_DIR@/share/template
FILE_PATTERNS = *.c *.cpp *.h *.md
# CUDA files could be included like this, but currently produce a lot of
# warnings.
# FILE_PATTERNS += *.cu *.cuh
EXAMPLE_PATH = @CMAKE_SOURCE_DIR@
RECURSIVE = YES
EXCLUDE = @CMAKE_SOURCE_DIR@/src/external \
@CMAKE_SOURCE_DIR@/src/gromacs/linearalgebra/gmx_blas \
@CMAKE_SOURCE_DIR@/src/gromacs/linearalgebra/gmx_lapack \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.cpp \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.h \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/scanner.cpp \
@CMAKE_SOURCE_DIR@/src/api
EXCLUDE_PATTERNS = @CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_x86* \
@CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_intel* \
@CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_ibm* \
@CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_arm* \
@CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_sparc* \
@CMAKE_SOURCE_DIR@/src/gromacs/simd/impl_none
EXCLUDE_SYMBOLS = YY* yy* _gmx_sel_yy*
EXCLUDE_SYMBOLS += __STDC*
EXCLUDE_SYMBOLS += TEST TEST_F TEST_P TYPED_TEST_SUITE TYPED_TEST INSTANTIATE_TEST_SUITE_P
EXCLUDE_SYMBOLS += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES = YES
STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@
STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src \
@CMAKE_SOURCE_DIR@/src/include \
@CMAKE_SOURCE_DIR@/src/gromacs/*/include \
@CMAKE_SOURCE_DIR@/api/legacy/include
INCLUDE_PATH = @CMAKE_SOURCE_DIR@/src
HAVE_DOT = @DOXYGEN_DOT_FOUND@
DOT_PATH = @DOXYGEN_DOT_PATH@
MSCGEN_PATH = @DOXYGEN_MSCGEN_PATH@
DOTFILE_DIRS = @DEPGRAPH_DIR@
@DOXYGEN_EXTRA_SETTINGS@
ENABLED_SECTIONS = @DOXYGEN_SECTIONS@
MACRO_EXPANSION = YES
# Extract documentation also for code in headers within #ifdef __cplusplus
PREDEFINED = __cplusplus
# This is for cases where \cond does not work, so that #ifndef can also be used.
# thread_mpi also uses this, but it is now excluded from the documentation.
PREDEFINED += DOXYGEN
# This makes 'static gmx_inline' functions appear better in the documentation.
PREDEFINED += gmx_inline=inline
# This is for parser.cpp to make it produce code that Doxygen understands
# and that does not have unnecessary function declarations.
PREDEFINED += __STDC__ YYMALLOC=malloc YYFREE=free
EXTRA_PACKAGES += amssymb
JAVADOC_AUTOBRIEF = YES
BUILTIN_STL_SUPPORT = YES
INLINE_INHERITED_MEMB = YES
SORT_BY_SCOPE_NAME = YES
ALPHABETICAL_INDEX = YES
HTML_DYNAMIC_SECTIONS = YES
GENERATE_LATEX = NO
# Setting this to NO has a side effect to hide undocumented headers from the
# file list, which makes it generally look nicer.
VERBATIM_HEADERS = NO
STRIP_CODE_COMMENTS = NO
EXTRACT_LOCAL_CLASSES = NO
# This includes 'static inline' functions from headers in the documentation.
EXTRACT_STATIC = YES
ALIASES += Gromacs=GROMACS
ALIASES += linktodevmanual{2}="\2"
ALIASES += linktodevmanual{3}="\3"
DOT_IMAGE_FORMAT = svg
DOT_MULTI_TARGETS = YES
# According to Doxygen docs, this is required for svg support on IE
HTML_FILE_EXTENSION = .xhtml
OUTPUT_DIRECTORY = @HTML_OUTPUT_DIR@/doxygen