BUILD_DEPENDS=	p5-XML-LibXML>0:textproc/p5-XML-LibXML	\

		libarchive>0:archivers/libarchive	\

		xcrysden:science/xcrysden	\

		bash:shells/bash

		libopenbabel.so:science/openbabel	\

.if defined(WITH_DEBUG)

CONFIGURE_ARGS+=--enable-debug-messages

.endif

.if ${ARCH:Mamd64*}

BUILD_DEPENDS+=	abinit:science/abinit

RUN_DEPENDS+=	abinit:science/abinit

CONFIGURE_ARGS+=--with-abinit

.endif

--- Documentation/reference/Makefile.am.orig	2020-07-07 14:26:13 UTC

+++ Documentation/reference/Makefile.am

@@ -81,11 +81,11 @@ GTKDOC_LIBS= \

 	@GTKS_LIBS@ @GLU_LIBS@ @EXTRA_LDFLAGS@ @EXTRA_LIBS@

 # This includes the standard gtk-doc make rules, copied by gtkdocize.

-include $(srcdir)/gtk-doc.make

+#include $(srcdir)/gtk-doc.make

 # Other files to distribute

 # e.g. EXTRA_DIST += version.xml.in

-EXTRA_DIST += version.in

+EXTRA_DIST = version.in

 # Files not to distribute

 # for --rebuild-types in $(SCAN_OPTIONS), e.g. $(DOC_MODULE).types

@@ -93,11 +93,11 @@ EXTRA_DIST += version.in

 DISTCLEANFILES = $(DOC_MODULE).types $(DOC_MODULE)-sections.txt

 # Comment this out if you want your docs-status tested during 'make check'

-if ENABLE_GTK_DOC

-TESTS_ENVIRONMENT = \

-  DOC_MODULE=$(DOC_MODULE) DOC_MAIN_SGML_FILE=$(DOC_MAIN_SGML_FILE) \

-  SRCDIR=$(abs_srcdir) BUILDDIR=$(abs_builddir)

-TESTS = $(GTKDOC_CHECK)

-endif

+#if ENABLE_GTK_DOC

+#TESTS_ENVIRONMENT = \

+#  DOC_MODULE=$(DOC_MODULE) DOC_MAIN_SGML_FILE=$(DOC_MAIN_SGML_FILE) \

+#  SRCDIR=$(abs_srcdir) BUILDDIR=$(abs_builddir)

+#TESTS = $(GTKDOC_CHECK)

+#endif

 #-include $(top_srcdir)/git.mk

--- configure.ac.orig	2020-07-07 14:26:13 UTC

+++ configure.ac

@@ -244,7 +244,7 @@ AC_ARG_ENABLE(python-module, AS_HELP_STRING([--enable-

 if test -n "$enable_python" -a "$enable_python" != "no" ; then

   AM_PATH_PYTHON(2.3.5)

   AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR(could not find Python headers)])

-  py_prefix=`$PYTHON -c "import sys; print sys.prefix"`

+  py_prefix=`$PYTHON -c "import sys; print (sys.prefix)"`

   PYTHON_INCLUDES="-I${py_prefix}/include/python${PYTHON_VERSION}"

   PKG_CHECK_MODULES(PYGTK, pygobject-2.0 pygtk-2.0, [have_pygtk=yes], [have_pygtk=no])

@@ -269,7 +269,6 @@ if test "$with_debug_messages" = "yes" ; then

 fi

 dnl Building the doc

-GTK_DOC_CHECK([1.3])

 dnl Test for plug-ins compilation

@@ -423,9 +422,9 @@ if test "x$enable_introspection" = "xyes" ; then

   dnl Add Python support for the PythonGI plug-in.

   AM_PATH_PYTHON(2.3)

   AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR(could not find Python headers)])

-  PYTHON_INCLUDES="`python-config --cflags`"

+  PYTHON_INCLUDES="`${PYTHON}-config --cflags`"

   AC_SUBST(PYTHON_INCLUDES)

-  PYTHON_LIBS="`python-config --libs`"

+  PYTHON_LIBS="`${PYTHON}-config --libs`"

   AC_SUBST(PYTHON_LIBS)

   AC_MSG_CHECKING(for pygobject overrides directory)

@@ -434,9 +433,10 @@ if test "x$enable_introspection" = "xyes" ; then

   if test "x$overrides_dir" = "x" ; then

     overrides_dir="${pyexecdir}/gi/overrides"

   fi

-  if ! test -w $overrides_dir ; then

-    overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides

-  fi

+  # Do not test -w $overrides_dir to allow build as non-root

+  #if ! test -w $overrides_dir ; then

+  #  overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides

+  #fi

   AC_MSG_RESULT($overrides_dir)

 else

   overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides

@@ -446,12 +446,12 @@ AM_CONDITIONAL([WITH_GOBJECT_INTROSPECTION], [test "x$

 dnl AC_PROG_CC set the CC variable and detect if we use the GNU compiler

 dnl We now append some various CFLAGS depending on platform and choice

 dnl of the user.

-AC_ARG_WITH(strict-cflags, AS_HELP_STRING([--with-strict-cflags], [if set or absent some correctness cflags are appended to the CFLAGS variable. Appended values dependent on the platform and code branch (default on Unix for development is Wall Wno-unused W Werror ansi pedantic-errors).]), [STRICT_CFLAGS=$withval], [STRICT_CFLAGS="no"])

+AC_ARG_WITH(strict-cflags, AS_HELP_STRING([--with-strict-cflags], [if set or absent some correctness cflags are appended to the CFLAGS variable. Appended values dependent on the platform and code branch (default on Unix for development is Wall Wno-unused W ansi ).]), [STRICT_CFLAGS=$withval], [STRICT_CFLAGS="no"])

 flags='Wall W ansi'

 flags_cpp='Wall W ansi'

 if test "$GCC" = "yes" -a "$STRICT_CFLAGS" = "yes"; then

-  flags=$flags' Werror Wpedantic std=c99'

-  flags_cpp=$flags_cpp' Werror Wpedantic'

+  flags=$flags' std=c99'

+  flags_cpp=$flags_cpp' '

 fi

 for fl in $flags ; do

   case " $CFLAGS " in

--- lib/plug-ins/abinit/ab_symmetry.c.orig	2020-07-07 14:26:13 UTC

+++ lib/plug-ins/abinit/ab_symmetry.c

@@ -458,7 +458,7 @@ gpointer startThreadSymmetry(gpointer data _U_)

   char *spGrp;

   double box[3][3], genAfm[3], *xred;

   int i, *typat, grpId, grpMagnId;

-  AbError errno;

+  AbError error;

   VisuNodeArrayIter iter;

   AbinitData *dt;

@@ -492,13 +492,13 @@ gpointer startThreadSymmetry(gpointer data _U_)

   /* Ask for the calculation of the symmetries. */

   DBG_fprintf(stderr, "AB symmetry(%p): Ready to get symmetries from ABINIT.\n",

               (gpointer)g_thread_self());

-  errno = ab_symmetry_get_group(dt->sym, &spGrp, &grpId,

+  error = ab_symmetry_get_group(dt->sym, &spGrp, &grpId,

 				 &grpMagnId, genAfm);

   DBG_fprintf(stderr, "AB symmetry(%p): return from ABINIT (%d).\n",

-              (gpointer)g_thread_self(), errno);

-  if (errno == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED)

+              (gpointer)g_thread_self(), error);

+  if (error == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED)

     g_free(spGrp);

-  else if (errno != AB_ERROR_SYM_NOT_PRIMITIVE)

+  else if (error != AB_ERROR_SYM_NOT_PRIMITIVE)

     dt->error = g_error_new(TOOL_FILE_FORMAT_ERROR, TOOL_FILE_FORMAT_ERROR_METHOD,

                             "An error occured in ABINIT plug-in.");

   abinit_mutexUnlock();

@@ -517,7 +517,7 @@ static void updateSymmetries(VisuData *dataObj, gdoubl

   gchar *bravais[7] = {"triclinic", "monoclinic", "orthorhombic",

 		       "tetragonal", "trigonal", "hexagonal", "cubic"};

   gchar *center[7] = {"F", "F", "I", "P", "A", "B", "C"};

-  AbError errno;

+  AbError error;

 #ifdef G_THREADS_ENABLED

   GThread *ld_thread;

 #endif

@@ -571,9 +571,9 @@ static void updateSymmetries(VisuData *dataObj, gdoubl

 	  /* We get then the space group. */

           DBG_fprintf(stderr, "AB symmetry: get group.\n");

-	  errno = ab_symmetry_get_group(sym, &spGrp, &grpId,

+	  error = ab_symmetry_get_group(sym, &spGrp, &grpId,

 					 &grpMagnId, genAfm);

-	  if (errno == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED)

+	  if (error == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED)

 	    {

 	      str = g_strdup_printf("%s (#%d)", spGrp, grpId);

 	      gtk_label_set_text(GTK_LABEL(lblSymId), str);

@@ -629,7 +629,7 @@ static void updateSymmetries(VisuData *dataObj, gdoubl

 	  /* If the bravais lattice doesn't match with the xred bravais

 	     lattice, we print a message. */

-	  if (errno == AB_ERROR_SYM_BRAVAIS_XRED)

+	  if (error == AB_ERROR_SYM_BRAVAIS_XRED)

 	    gtk_widget_show(lblSymWarning);

 	  else

 	    gtk_widget_hide(lblSymWarning);

--- m4/libxc.m4.orig	2020-07-07 14:26:13 UTC

+++ m4/libxc.m4

@@ -57,17 +57,13 @@ AC_DEFUN([AC_CHECK_LIBXC],

   LIBS="$LIBS -lxc"

    AC_MSG_CHECKING([for LIBXC library])

-   AC_LINK_IFELSE([[

-program main

-

-  call xc_f90_family_from_id()

-end]], ac_libxc_ok=yes, ac_libxc_ok=no)

+   ac_libxc_ok=yes

    AC_MSG_RESULT([$ac_libxc_ok])

    LIBS="$LIBS_SVG"

    LDFLAGS="$LDFLAGS_SVG"

    FCFLAGS="$FCFLAGS_SVG"

    if test "$ac_libxc_ok" = "yes"; then

-      LIBXC_LIBS="-lxc"

+      LIBXC_LIBS="-lxc -lxcf90"

       AS_IF([test -n "$LIBXC_PATH_LIBDIR"], [LIBXC_LIBS="-L$LIBXC_PATH_LIBDIR $LIBXC_LIBS"])

       AC_SUBST([LIBXC_LIBS])

    fi

--- src/coreTools/atoms_yaml.c.orig	2020-07-07 14:26:13 UTC

+++ src/coreTools/atoms_yaml.c

@@ -1270,19 +1270,7 @@ static int posinp_yaml_forces(yaml_parser_t *parser, P

   return done;

 }

-#if SYSTEM_X11 == 1

-static char* strdup(const char *src)

-{

-  char *dest;

-  size_t ln;

-  ln = strlen(src);

-  dest = malloc(sizeof(char) * (ln + 1));

-  memcpy(dest, src, sizeof(char) * ln);

-  dest[ln] = '\0';

-  return dest;

-}

-#endif

 static int posinp_yaml_external_potential(const PosinpDict *dict, PosinpAtoms *atoms, char **message)

 {

   int done;

lib/girepository-1.0/v_sim-3.8.typelib

lib/libv_sim-3.la

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cinchonidine.xsf.bz2

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cnt.Benzen_on_Ag111

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/collisions.ascii

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h2o-dens.cube.bz2

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nq-netcdf.cdl

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nq-netcdf.nc

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_collisions.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_isolate.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_load.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_plot.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_rightMenu.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pygi_rotate.v_sim.py

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/si1002x1-o_DS1_DEN-etsf.nc

%%PORTEXAMPLES%%%%EXAMPLESDIR%%/silane.nc

share/gir-1.0/v_sim-3.8.gir

%%DATADIR%%/pixmaps/abinit.png

%%DATADIR%%/pixmaps/archives.png

%%DATADIR%%/pixmaps/cube.png

%%DATADIR%%/pixmaps/msym.png

%%DATADIR%%/pixmaps/nanoquanta.png

%%DATADIR%%/pixmaps/pythongi.png

%%DATADIR%%/pixmaps/stock-pythongi_20.png

%%DATADIR%%/pixmaps/xsf.png