From 0fb40c28545e8418469cf7d3600547dfe4083edb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 12:00:38 +0000
Subject: [PATCH] Merged with dump-state. Added some arg switches that need to be inished
---
src/main.c | 29 ++-
src/timestep.c | 1
src/io.c | 107 +++++++++++++
missing | 295 ++++++++++++++++++++++++++++++++++++
src/io.h | 12 +
5 files changed, 431 insertions(+), 13 deletions(-)
diff --git a/missing b/missing
index cdea514..f45d3d4 100755
--- a/missing
+++ b/missing
@@ -1,10 +1,20 @@
#! /bin/sh
+<<<<<<< HEAD
# Common wrapper for a few potentially missing GNU programs.
scriptversion=2012-06-26.16; # UTC
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+=======
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2012-01-06.13; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+>>>>>>> dump-state
# 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
@@ -25,6 +35,7 @@
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
+<<<<<<< HEAD
echo 1>&2 "Try '$0 --help' for more information"
exit 1
fi
@@ -41,17 +52,59 @@
# Back-compat with the calling convention used by older automake.
shift
;;
+=======
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+>>>>>>> dump-state
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
+<<<<<<< HEAD
Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
to PROGRAM being missing or too old.
+=======
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+>>>>>>> dump-state
Options:
-h, --help display this help and exit
-v, --version output version information and exit
+<<<<<<< HEAD
Supported PROGRAM values:
aclocal autoconf autoheader autom4te automake makeinfo
@@ -59,6 +112,25 @@
Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
'g' are ignored when checking the name.
+=======
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+>>>>>>> dump-state
Send bug reports to <bug-automake@gnu.org>."
exit $?
@@ -70,13 +142,19 @@
;;
-*)
+<<<<<<< HEAD
echo 1>&2 "$0: unknown '$1' option"
echo 1>&2 "Try '$0 --help' for more information"
+=======
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+>>>>>>> dump-state
exit 1
;;
esac
+<<<<<<< HEAD
# Run the given program, remember its exit status.
"$@"; st=$?
@@ -205,6 +283,223 @@
# Propagate the correct exit status (expected to be 127 for a program
# not found, 63 for a program that failed due to version mismatch).
exit $st
+=======
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG=\${$#}
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG=\${$#}
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+>>>>>>> dump-state
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
diff --git a/src/io.c b/src/io.c
index aab00bb..93fda4c 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,8 +11,11 @@
#include "initial_distribution.h"
#include "poly.h"
-
-
+#include <getopt.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <errno.h>
/** DUMP STATE TO DISK DRIVE **/
ts_bool dump_state(ts_vesicle *vesicle){
@@ -320,6 +323,106 @@
+ts_bool parse_args(int argc, char **argv){
+ int c, retval;
+ DIR *dir;
+ path[0]=0;
+while (1)
+ {
+ static struct option long_options[] =
+ {
+ {"force-from-tape", no_argument, &force_from_tape, 1},
+ {"tape", no_argument, 0, 't'},
+ {"output-file", required_argument, 0, 'o'},
+ {"directory", required_argument, 0, 'd'},
+ {"dump-file", required_argument,0, 'f'},
+ {0, 0, 0, 0}
+ };
+ /* getopt_long stores the option index here. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:fot",
+ long_options, &option_index);
+
+ /* Detect the end of the options. */
+ if (c == -1)
+ break;
+
+ switch (c)
+ {
+ case 0:
+ /* If this option set a flag, do nothing else now. */
+ if (long_options[option_index].flag != 0)
+ break;
+ printf ("option %s", long_options[option_index].name);
+ if (optarg)
+ printf (" with arg %s", optarg);
+ printf ("\n");
+ break;
+
+ case 't':
+ //check if tape exists. If not, fail immediately.
+ puts ("option -t\n");
+ break;
+
+ case 'o':
+ //set filename of master output file
+ printf ("option -o with value `%s'\n", optarg);
+ break;
+
+ case 'd':
+ //check if directory exists. If not create one. If creation is
+ //successful, set directory for output files.
+ //printf ("option -d with value `%s'\n", optarg);
+ dir = opendir(optarg);
+ if (dir)
+ {
+ /* Directory exists. */
+ closedir(dir);
+ }
+ else if (ENOENT == errno)
+ {
+ /* Directory does not exist. */
+ retval=mkdir(optarg, 0700);
+ if(retval){
+ fatal("Could not create requested directory. Check if you have permissions",1);
+ }
+ }
+ else
+ {
+ /* opendir() failed for some other reason. */
+ fatal("Could not check if directory exists. Reason unknown",1);
+ }
+ ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
+// sprintf(path,"%s", optarg);
+ strcpy(path, optarg);
+ // ts_fprintf(stdout,"ok!\n");
+
+ break;
+
+ case 'f':
+ //check if dump file specified exists. Defaults to dump.bin
+ break;
+
+ case '?':
+ /* getopt_long already printed an error message. */
+
+ ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
+ fatal("Ooops, read help first",1);
+ break;
+
+ default:
+ exit (1);
+ }
+ }
+
+ return TS_SUCCESS;
+
+}
+
+
+
+
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
printf("Number of vertices: %u\n",vlist->n);
diff --git a/src/io.h b/src/io.h
index 7ac2160..f76eb09 100644
--- a/src/io.h
+++ b/src/io.h
@@ -1,6 +1,18 @@
#ifndef _IO_H
#define _IO_H
+/** @ Global variables for I/O operations like filenames etc. */
+/*static char mastername[1024];
+static char prefixname[1024];
+static ts_bool restore=0;
+static char tape[1024]; */
+char path[1024];
+int force_from_tape;
+
+ts_bool parse_args(int argc, char **argv);
+
+
+
/** @brief Prints the position of vertices for the whole list
*
* The function is meant more or less as a debug tool, but can be used in production
diff --git a/src/main.c b/src/main.c
index 705d8de..0c955dc 100644
--- a/src/main.c
+++ b/src/main.c
@@ -21,6 +21,10 @@
int main(int argv, char *argc[]){
ts_uint inititer,mcsweeps, iterations;
ts_vesicle *vesicle, *vesicle1;
+
+
+parse_args(argv,argc);
+
/* THIS SHOULD GO INTO UNIT TEST
ts_bool retval;
ts_vertex_list *vlist=init_vertex_list(5);
@@ -64,19 +68,22 @@
vtx_list_free(vlist1);
printf("Tests complete.\n");
*/
+if(force_from_tape){
+ts_fprintf(stdout,"****************************************************\n");
+ts_fprintf(stdout,"**** Reinitializing initial geometry from tape *****\n");
+ts_fprintf(stdout,"****************************************************\n\n");
+vesicle=parsetape(&mcsweeps, &inititer, &iterations);
+} else {
+
+ts_fprintf(stdout,"**********************************************************************\n");
+ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
+ts_fprintf(stdout,"**********************************************************************\n\n");
vesicle1=parsetape(&mcsweeps, &inititer, &iterations);
-
-/*Testing */
-//vesicle->poly_list=init_poly_list(1400,20,vesicle->vlist);
-
-//poly_list_free(vesicle->poly_list);
-/*End testing*/
-
-dump_state(vesicle1);
-
vesicle=restore_state();
-//vesicle_free(vesicle1);
-run_simulation(vesicle1, mcsweeps, inititer, iterations);
+vesicle_free(vesicle1);
+}
+
+run_simulation(vesicle, mcsweeps, inititer, iterations);
write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);
diff --git a/src/timestep.c b/src/timestep.c
index d717abb..8ae5a30 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -22,6 +22,7 @@
centermass(vesicle);
cell_occupation(vesicle);
ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
+ dump_state(vesicle);
if(i>inititer){
write_vertex_xml_file(vesicle,i-inititer);
}
--
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