From ee84bde159fa91d6f1907cf3d8c39cfe50638444 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Wed, 12 Nov 2014 18:51:28 +0000
Subject: [PATCH] Started writting vtk dump file restoration
---
src/Makefile.am | 4
src/dumpstate.c | 74 ++++++++++++++
src/main.c | 11 ++
configure.ac | 2
src/io.c | 4
config.h.in | 3
config.h | 3
aclocal.m4 | 160 ++++++++++++++++++++++++++++++++
src/dumpstate.h | 31 ++++++
src/io.h | 1
10 files changed, 291 insertions(+), 2 deletions(-)
diff --git a/aclocal.m4 b/aclocal.m4
index 3a9a040..da47901 100644
--- a/aclocal.m4
+++ b/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
diff --git a/config.h b/config.h
index ac9c24a..b730cc2 100644
--- a/config.h
+++ b/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
diff --git a/config.h.in b/config.h.in
index f865b7a..d480e81 100644
--- a/config.h.in
+++ b/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
diff --git a/configure.ac b/configure.ac
index 2ebed26..3d3e095 100644
--- a/configure.ac
+++ b/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])
diff --git a/src/Makefile.am b/src/Makefile.am
index b81035d..5091e90 100644
--- a/src/Makefile.am
+++ b/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
diff --git a/src/dumpstate.c b/src/dumpstate.c
new file mode 100644
index 0000000..4d7dde2
--- /dev/null
+++ b/src/dumpstate.c
@@ -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;
+}
diff --git a/src/dumpstate.h b/src/dumpstate.h
new file mode 100644
index 0000000..fdf54f6
--- /dev/null
+++ b/src/dumpstate.h
@@ -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
diff --git a/src/io.c b/src/io.c
index ead2de3..f913762 100644
--- a/src/io.c
+++ b/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':
diff --git a/src/io.h b/src/io.h
index ec04fb1..69de4e9 100644
--- a/src/io.h
+++ b/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;
diff --git a/src/main.c b/src/main.c
index 7d3726a..c55d30a 100644
--- a/src/main.c
+++ b/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");
--
Gitblit v1.9.3