| aclocal.m4 | ●●●●● patch | view | raw | blame | history | |
| config.h | ●●●●● patch | view | raw | blame | history | |
| config.h.in | ●●●●● patch | view | raw | blame | history | |
| configure.ac | ●●●●● patch | view | raw | blame | history | |
| src/Makefile.am | ●●●●● patch | view | raw | blame | history | |
| src/dumpstate.c | ●●●●● patch | view | raw | blame | history | |
| src/dumpstate.h | ●●●●● patch | view | raw | blame | history | |
| src/io.c | ●●●●● patch | view | raw | blame | history | |
| src/io.h | ●●●●● patch | view | raw | blame | history | |
| src/main.c | ●●●●● patch | view | raw | blame | history |
aclocal.m4
@@ -20,6 +20,166 @@ If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'.])]) # pkg.m4 - Macros to locate and utilise pkg-config. -*- Autoconf -*- # serial 1 (pkg-config-0.24) # # Copyright © 2004 Scott James Remnant <scott@netsplit.com>. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # PKG_PROG_PKG_CONFIG([MIN-VERSION]) # ---------------------------------- AC_DEFUN([PKG_PROG_PKG_CONFIG], [m4_pattern_forbid([^_?PKG_[A-Z_]+$]) m4_pattern_allow([^PKG_CONFIG(_(PATH|LIBDIR|SYSROOT_DIR|ALLOW_SYSTEM_(CFLAGS|LIBS)))?$]) m4_pattern_allow([^PKG_CONFIG_(DISABLE_UNINSTALLED|TOP_BUILD_DIR|DEBUG_SPEW)$]) AC_ARG_VAR([PKG_CONFIG], [path to pkg-config utility]) AC_ARG_VAR([PKG_CONFIG_PATH], [directories to add to pkg-config's search path]) AC_ARG_VAR([PKG_CONFIG_LIBDIR], [path overriding pkg-config's built-in search path]) if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then AC_PATH_TOOL([PKG_CONFIG], [pkg-config]) fi if test -n "$PKG_CONFIG"; then _pkg_min_version=m4_default([$1], [0.9.0]) AC_MSG_CHECKING([pkg-config is at least version $_pkg_min_version]) if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) PKG_CONFIG="" fi fi[]dnl ])# PKG_PROG_PKG_CONFIG # PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND]) # # Check to see whether a particular set of modules exists. Similar # to PKG_CHECK_MODULES(), but does not set variables or print errors. # # Please remember that m4 expands AC_REQUIRE([PKG_PROG_PKG_CONFIG]) # only at the first occurence in configure.ac, so if the first place # it's called might be skipped (such as if it is within an "if", you # have to call PKG_CHECK_EXISTS manually # -------------------------------------------------------------- AC_DEFUN([PKG_CHECK_EXISTS], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl if test -n "$PKG_CONFIG" && \ AC_RUN_LOG([$PKG_CONFIG --exists --print-errors "$1"]); then m4_default([$2], [:]) m4_ifvaln([$3], [else $3])dnl fi]) # _PKG_CONFIG([VARIABLE], [COMMAND], [MODULES]) # --------------------------------------------- m4_define([_PKG_CONFIG], [if test -n "$$1"; then pkg_cv_[]$1="$$1" elif test -n "$PKG_CONFIG"; then PKG_CHECK_EXISTS([$3], [pkg_cv_[]$1=`$PKG_CONFIG --[]$2 "$3" 2>/dev/null` test "x$?" != "x0" && pkg_failed=yes ], [pkg_failed=yes]) else pkg_failed=untried fi[]dnl ])# _PKG_CONFIG # _PKG_SHORT_ERRORS_SUPPORTED # ----------------------------- AC_DEFUN([_PKG_SHORT_ERRORS_SUPPORTED], [AC_REQUIRE([PKG_PROG_PKG_CONFIG]) if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then _pkg_short_errors_supported=yes else _pkg_short_errors_supported=no fi[]dnl ])# _PKG_SHORT_ERRORS_SUPPORTED # PKG_CHECK_MODULES(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND], # [ACTION-IF-NOT-FOUND]) # # # Note that if there is a possibility the first call to # PKG_CHECK_MODULES might not happen, you should be sure to include an # explicit call to PKG_PROG_PKG_CONFIG in your configure.ac # # # -------------------------------------------------------------- AC_DEFUN([PKG_CHECK_MODULES], [AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl AC_ARG_VAR([$1][_CFLAGS], [C compiler flags for $1, overriding pkg-config])dnl AC_ARG_VAR([$1][_LIBS], [linker flags for $1, overriding pkg-config])dnl pkg_failed=no AC_MSG_CHECKING([for $1]) _PKG_CONFIG([$1][_CFLAGS], [cflags], [$2]) _PKG_CONFIG([$1][_LIBS], [libs], [$2]) m4_define([_PKG_TEXT], [Alternatively, you may set the environment variables $1[]_CFLAGS and $1[]_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details.]) if test $pkg_failed = yes; then AC_MSG_RESULT([no]) _PKG_SHORT_ERRORS_SUPPORTED if test $_pkg_short_errors_supported = yes; then $1[]_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "$2" 2>&1` else $1[]_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "$2" 2>&1` fi # Put the nasty error message in config.log where it belongs echo "$$1[]_PKG_ERRORS" >&AS_MESSAGE_LOG_FD m4_default([$4], [AC_MSG_ERROR( [Package requirements ($2) were not met: $$1_PKG_ERRORS Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. _PKG_TEXT])[]dnl ]) elif test $pkg_failed = untried; then AC_MSG_RESULT([no]) m4_default([$4], [AC_MSG_FAILURE( [The pkg-config script could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. _PKG_TEXT To get pkg-config, see <http://pkg-config.freedesktop.org/>.])[]dnl ]) else $1[]_CFLAGS=$pkg_cv_[]$1[]_CFLAGS $1[]_LIBS=$pkg_cv_[]$1[]_LIBS AC_MSG_RESULT([yes]) $3 fi[]dnl ])# PKG_CHECK_MODULES # Copyright (C) 2002-2013 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation config.h
@@ -16,6 +16,9 @@ /* Define to 1 if you have the `m' library (-lm). */ #define HAVE_LIBM 1 /* Define to 1 if you have the `xml2' library (-lxml2). */ /* #undef HAVE_LIBXML2 */ /* Define to 1 if your system has a GNU libc compatible `malloc' function, and to 0 otherwise. */ #define HAVE_MALLOC 1 config.h.in
@@ -15,6 +15,9 @@ /* Define to 1 if you have the `m' library (-lm). */ #undef HAVE_LIBM /* Define to 1 if you have the `xml2' library (-lxml2). */ #undef HAVE_LIBXML2 /* Define to 1 if your system has a GNU libc compatible `malloc' function, and to 0 otherwise. */ #undef HAVE_MALLOC configure.ac
@@ -17,6 +17,8 @@ AC_CHECK_LIB([gslcblas],[cblas_dgemm]) AC_CHECK_LIB([gsl],[gsl_blas_dgemm]) #AC_CHECK_LIB([xml2],[xmlNodeListGetString]) PKG_CHECK_MODULES([libxml2], [libxml-2.0]) # Checks for header files. AC_CHECK_HEADERS([stdlib.h string.h]) src/Makefile.am
@@ -1,6 +1,8 @@ bin_PROGRAMS = trisurf trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c shcomplex.c constvol.c trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c shcomplex.c constvol.c AM_CFLAGS = -Wall -Werror AM_CPPFLAGS = ${libxml2_CFLAGS} trisurf_LDADD = ${libcurl_LIBS} ${libxml2_LIBS} #shdiscoverdir=../ #shdiscover_PROGRAMS= shdiscover #shdiscover_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c energy.c sh.c shdiscover.c poly.c stats.c shcomplex.c src/dumpstate.c
New file @@ -0,0 +1,74 @@ #include <string.h> #include "general.h" #include <stdio.h> #include "initial_distribution.h" #include "vesicle.h" #include "dumpstate.h" #include <libxml/parser.h> #include <libxml/tree.h> ts_vesicle *vtk2vesicle(char *filename, ts_tape *tape){ ts_uint nshell=tape->nshell; ts_uint ncmax1=tape->ncxmax; ts_uint ncmax2=tape->ncymax; ts_uint ncmax3=tape->nczmax; ts_double stepsize=tape->stepsize; ts_uint no_vertices=5*nshell*nshell+2; ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize); vesicle->nshell=nshell; parse_vtk(filename, vesicle); exit(1); return vesicle; } ts_bool parse_vtk(char *filename, ts_vesicle *vesicle){ xmlDoc *doc; xmlNode *root_element=NULL; xmlNode *cur_node = NULL; doc = xmlReadFile(filename, NULL, 0); root_element=xmlDocGetRootElement(doc); cur_node=root_element->children; while(cur_node!=NULL){ // fprintf(stderr,"Node name is: %s\n",cur_node->name); if(strcmp((char *)cur_node->name,"UnstructuredGrid")==0) break; cur_node=cur_node->next; } cur_node=cur_node->children; while(cur_node!=NULL){ // fprintf(stderr,"Node name is: %s\n",cur_node->name); cur_node=cur_node->next; if(strcmp((char *)cur_node->name,"Piece")==0) break; } cur_node=cur_node->children; while(cur_node!=NULL){ fprintf(stderr,"Node name is: %s\n",cur_node->name); cur_node=cur_node->next; if(strcmp((char *)cur_node->name,"PointData")==0) vtk_index2vesicle(cur_node->children->next->children, vesicle); if(strcmp((char *)cur_node->name,"Points")==0) break; if(strcmp((char *)cur_node->name,"Cells")==0) break; } return TS_SUCCESS; } ts_bool vtk_index2vesicle(xmlNode *node, ts_vesicle *vesicle){ //fprintf(stderr, "vsebina: %s\n",node->content); ts_uint i; char *token; token = strtok((char *)node->content, " "); for(i=0;i<vesicle->vlist->n;i++){ vesicle->vlist->vtx[i]->idx=atoi(token); token=strtok(NULL," "); } //fprintf(stderr,"idx[11]=%d\n",vesicle->vlist->vtx[11]->idx); return TS_SUCCESS; } src/dumpstate.h
New file @@ -0,0 +1,31 @@ #ifndef _H_DUMPSTATE #define _H_DUMPSTATE #include <libxml/parser.h> #include <libxml/tree.h> typedef struct { long int npoints; long int ncells; long int idx; ts_double *x; ts_double *y; ts_double *z; long int neigh_idx1; long int neigh_idx2; } ts_vtk_data; ts_vesicle *vtk2vesicle(char *filename, ts_tape *tape); ts_bool parse_vtk(char *filename, ts_vesicle *vesicle); ts_bool vtk_index2vesicle(xmlNode *node, ts_vesicle *vesicle); #endif src/io.c
@@ -454,6 +454,7 @@ {"dump-filename", required_argument,0, 'f'}, {"tape-options",required_argument,0,'c'}, {"tape-template", required_argument,0,0}, {"dump-from-vtk",required_argument,0,0}, {0, 0, 0, 0} }; /* getopt_long stores the option index here. */ @@ -480,6 +481,9 @@ if(strcmp(long_options[option_index].name,"tape-template")==0){ strcpy(command_line_args.tape_templatefull,optarg); } if(strcmp(long_options[option_index].name,"dump-from-vtk")==0){ strcpy(command_line_args.dump_from_vtk,optarg); } break; case 'c': src/io.h
@@ -17,6 +17,7 @@ char tape_fullfilename[1024]; //name of the tape file char tape_templatefull[1024]; //name of the tape template file char tape_opts[1000]; //commandline tape options char dump_from_vtk[1024]; } ts_args; ts_args command_line_args; src/main.c
@@ -14,6 +14,7 @@ #include "poly.h" #include "sh.h" #include "shcomplex.h" #include "dumpstate.h" /** Entrance function to the program * @param argv is a number of parameters used in program call (including the program name @@ -28,7 +29,15 @@ force_from_tape=0; parse_args(argv,argc); // sets global variable command_line_args (defined in io.h) ts_fprintf(stdout,"Starting program...\n\n"); if(command_line_args.force_from_tape){ if(command_line_args.dump_from_vtk[0]!=0){ ts_fprintf(stdout,"************************************************\n"); ts_fprintf(stdout,"***** Dumping vesicle from VTK points list *****\n"); ts_fprintf(stdout,"************************************************\n\n"); tape=parsetape(command_line_args.tape_fullfilename); vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape); } else if(command_line_args.force_from_tape){ ts_fprintf(stdout,"************************************************\n"); ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n"); ts_fprintf(stdout,"************************************************\n\n");
