diff --git a/CHANGES b/CHANGES index 3ca5747c..b5b0cd17 100644 --- a/CHANGES +++ b/CHANGES @@ -1,4 +1,24 @@ Version 0.4.0 (currently in development) +* Antioch no longer header-only + - The parsing and a few "core" class implementations + have been move to .C files and their symbols are + in libantioch. Thus, users must now link against + libantioch in their applications. +* Added temperature exptrapolation capability to + KineticsTherory transport models +* Added API to allow resetting kinetics parameters +* Added capability to remove reaction from ReactionSet +* Added (optional) CppUnit-based unit testing + - Migration of the many existing unit tests to CppUnit + is still in progress. +* Added partial order support to kinetics + - Includes support for ChemKin-type specification + of forward and backward reaction orders +* Several enhancements and bugfixes to XML, ChemKin + parsing classes +* More testing of AD capabilities with (optional) + MetaPhsycL library +* Several other smaller bugfixes Version 0.3.1 * Critical Bugfix for NASA7 Thermo/ChemKin Parser diff --git a/Makefile.am b/Makefile.am index 4b1fce31..b64f9539 100644 --- a/Makefile.am +++ b/Makefile.am @@ -1,5 +1,3 @@ -BUILT_SOURCES = .license.stamp - # Doxygen support include $(top_srcdir)/doxygen/aminclude.am @@ -17,22 +15,9 @@ EXTRA_DIST = CHANGES LICENSE COPYING share # trying to remove stuff. dist-hook: chmod -R u+w $(distdir) - rm -rf `find $(distdir)/ -name .svn` rm -rf $(distdir)/share/aclocal/antioch.m4 cp -L $(top_srcdir)/share/aclocal/antioch.m4 $(distdir)/share/aclocal -#if SVN_CHECKOUT -# EXTRA_DIST += dist_version -# -#TODO: check if dist_version is needed in BUILT_SOURCES (in addition to EXTRA_DIST) -# BUILT_SOURCES = dist_version -# -#dist_version: FORCE -# @SVN_REVISION@ > $(top_srcdir)/dist_version -# -#FORCE: -#endif - # Tools in the auxiliary directory AUX_DIST = build-aux/install-sh AUX_DIST += build-aux/missing @@ -65,7 +50,7 @@ install-data-hook: cd $(DESTDIR)$(includedir) && mv config.replaced antioch_config.h ; # Install config file -BUILT_SOURCES += antioch_config.h +BUILT_SOURCES = antioch_config.h include_HEADERS = antioch_config.h # Additional files to be deleted by 'make distclean' @@ -107,11 +92,16 @@ MAINTAINERCLEANFILES += m4/lt~obsolete.m4 # works. #STAMPED_FILES = $(shell find $(top_srcdir)/src -name '*.h' -or -name '*.C') +# Since we don't distribute the lic_utils, check and make sure it's there. +# This way, we won't run this on distributed tarballs, only on the repos clones +if ANTIOCH_LICENSESTAMPEXISTS +BUILT_SOURCES += .license.stamp .license.stamp: $(top_srcdir)/LICENSE @$(top_srcdir)/src/common/lic_utils/update_license.pl $(top_srcdir)/LICENSE $(ANTIOCH_STAMPED_FILES) echo 'updated source license headers' >$@ CLEANFILES = .license.stamp +endif # ------------------------------------------- # Optional support for code coverage analysis diff --git a/configure.ac b/configure.ac index af73bd5e..5addcaf1 100644 --- a/configure.ac +++ b/configure.ac @@ -262,6 +262,11 @@ dnl----------------------------------------------- _AC_SRCDIRS(.) TOP_SEARCH_DIR=$ac_abs_top_srcdir +# Since we don't distribute the lic_utils, check and make sure it's there. +# This way, we won't run the license stamping perl script on distributed +# tarballs, only on the repository clones +AM_CONDITIONAL(ANTIOCH_LICENSESTAMPEXISTS, [test -f $TOP_SEARCH_DIR/src/common/lic_utils/update_license.pl]) + # We have to do this by subdirectory because otherwise distcheck # breaks as we start picking up files in the directories # that it uses. diff --git a/m4/common/gsl_new.m4 b/m4/common/gsl_new.m4 index cac1750e..33f0461a 100644 --- a/m4/common/gsl_new.m4 +++ b/m4/common/gsl_new.m4 @@ -52,7 +52,14 @@ fi # package requirement; if not specified, the default is to assume that # the package is optional -is_package_required=ifelse([$2], ,no, $2 ) +gsl_is_package_required=ifelse([$2], ,no, $2 ) + +if test "$gsl_is_package_required" != "yes"; then + if test "$gsl_is_package_required" != "no"; then + AC_MSG_ERROR([ Must specify "yes" or "no" for package requirement. + This is specified within the build system, not the command line.]) + fi +fi HAVE_GSL=0 @@ -82,14 +89,17 @@ HAVE_GSL=0 # Minimum version check #---------------------- - AC_PATH_PROG([GSL_CONFIG], - [gsl-config], + AC_PATH_PROG([GSL_CONFIG], + [gsl-config], []) - if test "x$GSL_CONFIG" = "x"; then - AC_MSG_ERROR([ Could not find gsl-config problem. - Please use --with-gsl to specify the location - of the GSL library. ]) + # Only error out if the user required GSL + if test "gsl_is_package_required" = "yes"; then + if test "x$GSL_CONFIG" = "x"; then + AC_MSG_ERROR([ Could not find gsl-config problem. + Please use --with-gsl to specify the location + of the GSL library. ]) + fi fi min_gsl_version=ifelse([$1], ,1.0, $1) @@ -130,7 +140,7 @@ HAVE_GSL=0 fi AC_MSG_CHECKING(for gsl - version >= $min_gsl_version) - version_succeeded=no + gsl_version_succeeded=no AC_LANG_PUSH([C++]) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[ @@ -145,14 +155,14 @@ HAVE_GSL=0 #endif ]])],[ AC_MSG_RESULT(yes) - version_succeeded=yes + gsl_version_succeeded=yes ],[ AC_MSG_RESULT(no) ]) AC_LANG_POP([C++]) - if test "$version_succeeded" != "yes";then - if test "$is_package_required" = yes; then + if test "$gsl_version_succeeded" != "yes";then + if test "$gsl_is_package_required" = yes; then AC_MSG_ERROR([ Your GSL version does not meet the minimum versioning @@ -168,42 +178,43 @@ HAVE_GSL=0 #------------------------- AC_LANG_PUSH([C]) - AC_CHECK_HEADER([gsl/gsl_math.h],[found_header=yes],[found_header=no]) + AC_CHECK_HEADER([gsl/gsl_math.h],[gsl_found_header=yes],[gsl_found_header=no]) AC_LANG_POP([C]) #------------------------------- # Check for a common function - # gamma function has been around + # gamma function has been around # since before v1.0 #------------------------------- + gsl_succeeded=no - AC_MSG_CHECKING([for -lgsl linkage]) + # Don't bother checking the lib unless we actually found the header + if test "$gsl_found_header" = "yes"; then + AC_MSG_CHECKING([for -lgsl linkage]) - AC_LANG_PUSH([C]) + AC_LANG_PUSH([C]) - AC_CHECK_LIB([gsl], - [gsl_sf_gamma], - [found_library=yes], - [found_library=no]) + AC_CHECK_LIB([gsl], + [gsl_sf_gamma], + [gsl_found_library=yes], + [gsl_found_library=no]) - AC_LANG_POP([C]) + AC_LANG_POP([C]) - CPPFLAGS="$ac_GSL_save_CPPFLAGS" - LDFLAGS="$ac_GSL_save_LDFLAGS" - LIBS="$ac_GSL_save_LIBS" - - succeeded=no - if test "$found_header" = yes; then - if test "$version_succeeded" = yes; then - if test "$found_library" = yes; then - succeeded=yes + if test "$gsl_version_succeeded" = yes; then + if test "$gsl_found_library" = yes; then + gsl_succeeded=yes fi fi fi - if test "$succeeded" = no; then - if test "$is_package_required" = yes; then + CPPFLAGS="$ac_GSL_save_CPPFLAGS" + LDFLAGS="$ac_GSL_save_LDFLAGS" + LIBS="$ac_GSL_save_LIBS" + + if test "$gsl_succeeded" = no; then + if test "$gsl_is_package_required" = yes; then AC_MSG_ERROR([GSL not found. Try either --with-gsl or setting GSL_DIR.]) else AC_MSG_NOTICE([optional GSL library not found]) diff --git a/src/Makefile.am b/src/Makefile.am index a6ee11a2..00203710 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -233,4 +233,4 @@ if CODE_COVERAGE_ENABLED CLEANFILES += *.gcda *.gcno endif -EXTRA_DIST = common +EXTRA_DIST = common/lcov diff --git a/src/thermo/include/antioch/stat_mech_thermo.h b/src/thermo/include/antioch/stat_mech_thermo.h index 59aea19e..1950ab16 100644 --- a/src/thermo/include/antioch/stat_mech_thermo.h +++ b/src/thermo/include/antioch/stat_mech_thermo.h @@ -516,9 +516,9 @@ namespace Antioch return CoeffType(1.5)*_chem_mixture.R(species); } - template - inline - CoeffType StatMechThermodynamics::cv_trans_over_R( const unsigned int species ) const + template + inline + CoeffType StatMechThermodynamics::cv_trans_over_R( const unsigned int /*species*/ ) const { return CoeffType(1.5); } diff --git a/src/transport/include/antioch/mixture_diffusion.h b/src/transport/include/antioch/mixture_diffusion.h index 74ace857..b5f9ebcd 100644 --- a/src/transport/include/antioch/mixture_diffusion.h +++ b/src/transport/include/antioch/mixture_diffusion.h @@ -192,11 +192,11 @@ namespace Antioch //! Invalid to call species diffusivity calculation with BinaryDiffusionBase model template - void private_species_diff_impl( unsigned int s, - const StateType& rho, - const StateType& cp, - const StateType& k, - StateType& D, + void private_species_diff_impl( unsigned int /*s*/, + const StateType& /*rho*/, + const StateType& /*cp*/, + const StateType& /*k*/, + StateType& /*D*/, AntiochPrivate::diffusion_tag >& /*tag*/ ) const { antioch_error(); diff --git a/test/gsl_unit/gsl_spliner_test.C b/test/gsl_unit/gsl_spliner_test.C index 138161da..63cdfac6 100644 --- a/test/gsl_unit/gsl_spliner_test.C +++ b/test/gsl_unit/gsl_spliner_test.C @@ -26,6 +26,7 @@ #include "antioch_config.h" +#ifdef ANTIOCH_HAVE_GSL #ifdef ANTIOCH_HAVE_CPPUNIT // C++ @@ -174,3 +175,4 @@ namespace AntiochTesting } // end namespace AntiochTesting #endif // ANTIOCH_HAVE_CPPUNIT +#endif // ANTIOCH_HAVE_GSL diff --git a/test/gsl_unit/gsl_spliner_test_base.h b/test/gsl_unit/gsl_spliner_test_base.h index e5209a52..485bf56c 100644 --- a/test/gsl_unit/gsl_spliner_test_base.h +++ b/test/gsl_unit/gsl_spliner_test_base.h @@ -29,6 +29,7 @@ #include "antioch_config.h" +#ifdef ANTIOCH_HAVE_GSL #ifdef ANTIOCH_HAVE_CPPUNIT #include @@ -143,5 +144,6 @@ namespace AntiochTesting } // end namespace AntiochTesting #endif // ANTIOCH_HAVE_CPPUNIT +#endif // ANTIOCH_HAVE_GSL #endif // ANTIOCH_GSL_SPLINER_TEST_BASE_H diff --git a/test/gsl_unit/gsl_spliner_vec_test.C b/test/gsl_unit/gsl_spliner_vec_test.C index e0112458..d7b09817 100644 --- a/test/gsl_unit/gsl_spliner_vec_test.C +++ b/test/gsl_unit/gsl_spliner_vec_test.C @@ -26,6 +26,7 @@ #include "antioch_config.h" +#ifdef ANTIOCH_HAVE_GSL #ifdef ANTIOCH_HAVE_CPPUNIT // C++ @@ -468,3 +469,4 @@ namespace AntiochTesting } // end namespace AntiochTesting #endif // ANTIOCH_HAVE_CPPUNIT +#endif // ANTIOCH_HAVE_GSL