From c0d703a09da108f218b687beeec671f71b7a44c9 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Sat, 08 Mar 2014 18:25:50 +0000 Subject: [PATCH] Merge branch 'trisurf-polyel' --- src/bondflip.h | 2 src/main.c | 89 - src/io.c | 203 +++- src/tape | 18 src/bondflip.c | 311 +++--- src/initial_distribution.c | 67 + src/general.h | 4 src/general.c | 14 install-sh | 527 +++++++++++ src/vertexmove.c | 12 src/io.h | 50 + /dev/null | 1 src/timestep.c | 7 src/initial_distribution.h | 5 src/timestep.h | 2 missing | 510 +++++++++++ src/triangle.c | 2 depcomp | 791 +++++++++++++++++ 18 files changed, 2,286 insertions(+), 329 deletions(-) diff --git a/depcomp b/depcomp deleted file mode 120000 index 173ae3c..0000000 --- a/depcomp +++ /dev/null @@ -1 +0,0 @@ -/usr/share/automake-1.13/depcomp \ No newline at end of file diff --git a/depcomp b/depcomp new file mode 100755 index 0000000..4ebd5b3 --- /dev/null +++ b/depcomp @@ -0,0 +1,791 @@ +#! /bin/sh +# depcomp - compile a program generating dependencies as side-effects + +scriptversion=2013-05-30.07; # UTC + +# Copyright (C) 1999-2013 Free Software Foundation, Inc. + +# 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, 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, see <http://www.gnu.org/licenses/>. + +# 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. + +# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>. + +case $1 in + '') + echo "$0: No command. Try '$0 --help' for more information." 1>&2 + exit 1; + ;; + -h | --h*) + cat <<\EOF +Usage: depcomp [--help] [--version] PROGRAM [ARGS] + +Run PROGRAMS ARGS to compile a file, generating dependencies +as side-effects. + +Environment variables: + depmode Dependency tracking mode. + source Source file read by 'PROGRAMS ARGS'. + object Object file output by 'PROGRAMS ARGS'. + DEPDIR directory where to store dependencies. + depfile Dependency file to output. + tmpdepfile Temporary file to use when outputting dependencies. + libtool Whether libtool is used (yes/no). + +Report bugs to <bug-automake@gnu.org>. +EOF + exit $? + ;; + -v | --v*) + echo "depcomp $scriptversion" + exit $? + ;; +esac + +# Get the directory component of the given path, and save it in the +# global variables '$dir'. Note that this directory component will +# be either empty or ending with a '/' character. This is deliberate. +set_dir_from () +{ + case $1 in + */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;; + *) dir=;; + esac +} + +# Get the suffix-stripped basename of the given path, and save it the +# global variable '$base'. +set_base_from () +{ + base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'` +} + +# If no dependency file was actually created by the compiler invocation, +# we still have to create a dummy depfile, to avoid errors with the +# Makefile "include basename.Plo" scheme. +make_dummy_depfile () +{ + echo "#dummy" > "$depfile" +} + +# Factor out some common post-processing of the generated depfile. +# Requires the auxiliary global variable '$tmpdepfile' to be set. +aix_post_process_depfile () +{ + # If the compiler actually managed to produce a dependency file, + # post-process it. + if test -f "$tmpdepfile"; then + # Each line is of the form 'foo.o: dependency.h'. + # Do two passes, one to just change these to + # $object: dependency.h + # and one to simply output + # dependency.h: + # which is needed to avoid the deleted-header problem. + { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile" + sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile" + } > "$depfile" + rm -f "$tmpdepfile" + else + make_dummy_depfile + fi +} + +# A tabulation character. +tab=' ' +# A newline character. +nl=' +' +# Character ranges might be problematic outside the C locale. +# These definitions help. +upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ +lower=abcdefghijklmnopqrstuvwxyz +digits=0123456789 +alpha=${upper}${lower} + +if test -z "$depmode" || test -z "$source" || test -z "$object"; then + echo "depcomp: Variables source, object and depmode must be set" 1>&2 + exit 1 +fi + +# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. +depfile=${depfile-`echo "$object" | + sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} +tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} + +rm -f "$tmpdepfile" + +# Avoid interferences from the environment. +gccflag= dashmflag= + +# Some modes work just like other modes, but use different flags. We +# parameterize here, but still list the modes in the big case below, +# to make depend.m4 easier to write. Note that we *cannot* use a case +# here, because this file can only contain one case statement. +if test "$depmode" = hp; then + # HP compiler uses -M and no extra arg. + gccflag=-M + depmode=gcc +fi + +if test "$depmode" = dashXmstdout; then + # This is just like dashmstdout with a different argument. + dashmflag=-xM + depmode=dashmstdout +fi + +cygpath_u="cygpath -u -f -" +if test "$depmode" = msvcmsys; then + # This is just like msvisualcpp but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u='sed s,\\\\,/,g' + depmode=msvisualcpp +fi + +if test "$depmode" = msvc7msys; then + # This is just like msvc7 but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u='sed s,\\\\,/,g' + depmode=msvc7 +fi + +if test "$depmode" = xlc; then + # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information. + gccflag=-qmakedep=gcc,-MF + depmode=gcc +fi + +case "$depmode" in +gcc3) +## gcc 3 implements dependency tracking that does exactly what +## we want. Yay! Note: for some reason libtool 1.4 doesn't like +## it if -MD -MP comes after the -MF stuff. Hmm. +## Unfortunately, FreeBSD c89 acceptance of flags depends upon +## the command line argument order; so add the flags where they +## appear in depend2.am. Note that the slowdown incurred here +## affects only configure: in makefiles, %FASTDEP% shortcuts this. + for arg + do + case $arg in + -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; + *) set fnord "$@" "$arg" ;; + esac + shift # fnord + shift # $arg + done + "$@" + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + mv "$tmpdepfile" "$depfile" + ;; + +gcc) +## Note that this doesn't just cater to obsosete pre-3.x GCC compilers. +## but also to in-use compilers like IMB xlc/xlC and the HP C compiler. +## (see the conditional assignment to $gccflag above). +## There are various ways to get dependency output from gcc. Here's +## why we pick this rather obscure method: +## - Don't want to use -MD because we'd like the dependencies to end +## up in a subdir. Having to rename by hand is ugly. +## (We might end up doing this anyway to support other compilers.) +## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like +## -MM, not -M (despite what the docs say). Also, it might not be +## supported by the other compilers which use the 'gcc' depmode. +## - Using -M directly means running the compiler twice (even worse +## than renaming). + if test -z "$gccflag"; then + gccflag=-MD, + fi + "$@" -Wp,"$gccflag$tmpdepfile" + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + echo "$object : \\" > "$depfile" + # The second -e expression handles DOS-style file names with drive + # letters. + sed -e 's/^[^:]*: / /' \ + -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" +## This next piece of magic avoids the "deleted header file" problem. +## The problem is that when a header file which appears in a .P file +## is deleted, the dependency causes make to die (because there is +## typically no way to rebuild the header). We avoid this by adding +## dummy dependencies for each header file. Too bad gcc doesn't do +## this for us directly. +## Some versions of gcc put a space before the ':'. On the theory +## that the space means something, we add a space to the output as +## well. hp depmode also adds that space, but also prefixes the VPATH +## to the object. Take care to not repeat it in the output. +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + tr ' ' "$nl" < "$tmpdepfile" \ + | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \ + | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +sgi) + if test "$libtool" = yes; then + "$@" "-Wp,-MDupdate,$tmpdepfile" + else + "$@" -MDupdate "$tmpdepfile" + fi + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + + if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files + echo "$object : \\" > "$depfile" + # Clip off the initial element (the dependent). Don't try to be + # clever and replace this with sed code, as IRIX sed won't handle + # lines with more than a fixed number of characters (4096 in + # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; + # the IRIX cc adds comments like '#:fec' to the end of the + # dependency line. + tr ' ' "$nl" < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \ + | tr "$nl" ' ' >> "$depfile" + echo >> "$depfile" + # The second pass generates a dummy entry for each header file. + tr ' ' "$nl" < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ + >> "$depfile" + else + make_dummy_depfile + fi + rm -f "$tmpdepfile" + ;; + +xlc) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +aix) + # The C for AIX Compiler uses -M and outputs the dependencies + # in a .u file. In older versions, this file always lives in the + # current directory. Also, the AIX compiler puts '$object:' at the + # start of each line; $object doesn't have directory information. + # Version 6 uses the directory in both cases. + set_dir_from "$object" + set_base_from "$object" + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.u + tmpdepfile2=$base.u + tmpdepfile3=$dir.libs/$base.u + "$@" -Wc,-M + else + tmpdepfile1=$dir$base.u + tmpdepfile2=$dir$base.u + tmpdepfile3=$dir$base.u + "$@" -M + fi + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + do + test -f "$tmpdepfile" && break + done + aix_post_process_depfile + ;; + +tcc) + # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26 + # FIXME: That version still under development at the moment of writing. + # Make that this statement remains true also for stable, released + # versions. + # It will wrap lines (doesn't matter whether long or short) with a + # trailing '\', as in: + # + # foo.o : \ + # foo.c \ + # foo.h \ + # + # It will put a trailing '\' even on the last line, and will use leading + # spaces rather than leading tabs (at least since its commit 0394caf7 + # "Emit spaces for -MD"). + "$@" -MD -MF "$tmpdepfile" + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'. + # We have to change lines of the first kind to '$object: \'. + sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile" + # And for each line of the second kind, we have to emit a 'dep.h:' + # dummy dependency, to avoid the deleted-header problem. + sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile" + rm -f "$tmpdepfile" + ;; + +## The order of this option in the case statement is important, since the +## shell code in configure will try each of these formats in the order +## listed in this file. A plain '-MD' option would be understood by many +## compilers, so we must ensure this comes after the gcc and icc options. +pgcc) + # Portland's C compiler understands '-MD'. + # Will always output deps to 'file.d' where file is the root name of the + # source file under compilation, even if file resides in a subdirectory. + # The object file name does not affect the name of the '.d' file. + # pgcc 10.2 will output + # foo.o: sub/foo.c sub/foo.h + # and will wrap long lines using '\' : + # foo.o: sub/foo.c ... \ + # sub/foo.h ... \ + # ... + set_dir_from "$object" + # Use the source, not the object, to determine the base name, since + # that's sadly what pgcc will do too. + set_base_from "$source" + tmpdepfile=$base.d + + # For projects that build the same source file twice into different object + # files, the pgcc approach of using the *source* file root name can cause + # problems in parallel builds. Use a locking strategy to avoid stomping on + # the same $tmpdepfile. + lockdir=$base.d-lock + trap " + echo '$0: caught signal, cleaning up...' >&2 + rmdir '$lockdir' + exit 1 + " 1 2 13 15 + numtries=100 + i=$numtries + while test $i -gt 0; do + # mkdir is a portable test-and-set. + if mkdir "$lockdir" 2>/dev/null; then + # This process acquired the lock. + "$@" -MD + stat=$? + # Release the lock. + rmdir "$lockdir" + break + else + # If the lock is being held by a different process, wait + # until the winning process is done or we timeout. + while test -d "$lockdir" && test $i -gt 0; do + sleep 1 + i=`expr $i - 1` + done + fi + i=`expr $i - 1` + done + trap - 1 2 13 15 + if test $i -le 0; then + echo "$0: failed to acquire lock after $numtries attempts" >&2 + echo "$0: check lockdir '$lockdir'" >&2 + exit 1 + fi + + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + # Each line is of the form `foo.o: dependent.h', + # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" + # Some versions of the HPUX 10.20 sed can't process this invocation + # correctly. Breaking it into two sed invocations is a workaround. + sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \ + | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp2) + # The "hp" stanza above does not work with aCC (C++) and HP's ia64 + # compilers, which have integrated preprocessors. The correct option + # to use with these is +Maked; it writes dependencies to a file named + # 'foo.d', which lands next to the object file, wherever that + # happens to be. + # Much of this is similar to the tru64 case; see comments there. + set_dir_from "$object" + set_base_from "$object" + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir.libs/$base.d + "$@" -Wc,+Maked + else + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir$base.d + "$@" +Maked + fi + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile1" "$tmpdepfile2" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile" + # Add 'dependent.h:' lines. + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" + else + make_dummy_depfile + fi + rm -f "$tmpdepfile" "$tmpdepfile2" + ;; + +tru64) + # The Tru64 compiler uses -MD to generate dependencies as a side + # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'. + # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put + # dependencies in 'foo.d' instead, so we check for that too. + # Subdirectories are respected. + set_dir_from "$object" + set_base_from "$object" + + if test "$libtool" = yes; then + # Libtool generates 2 separate objects for the 2 libraries. These + # two compilations output dependencies in $dir.libs/$base.o.d and + # in $dir$base.o.d. We have to check for both files, because + # one of the two compilations can be disabled. We should prefer + # $dir$base.o.d over $dir.libs/$base.o.d because the latter is + # automatically cleaned when .libs/ is deleted, while ignoring + # the former would cause a distcleancheck panic. + tmpdepfile1=$dir$base.o.d # libtool 1.5 + tmpdepfile2=$dir.libs/$base.o.d # Likewise. + tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504 + "$@" -Wc,-MD + else + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir$base.d + tmpdepfile3=$dir$base.d + "$@" -MD + fi + + stat=$? + if test $stat -ne 0; then + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + do + test -f "$tmpdepfile" && break + done + # Same post-processing that is required for AIX mode. + aix_post_process_depfile + ;; + +msvc7) + if test "$libtool" = yes; then + showIncludes=-Wc,-showIncludes + else + showIncludes=-showIncludes + fi + "$@" $showIncludes > "$tmpdepfile" + stat=$? + grep -v '^Note: including file: ' "$tmpdepfile" + if test $stat -ne 0; then + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + echo "$object : \\" > "$depfile" + # The first sed program below extracts the file names and escapes + # backslashes for cygpath. The second sed program outputs the file + # name when reading, but also accumulates all include files in the + # hold buffer in order to output them again at the end. This only + # works with sed implementations that can handle large buffers. + sed < "$tmpdepfile" -n ' +/^Note: including file: *\(.*\)/ { + s//\1/ + s/\\/\\\\/g + p +}' | $cygpath_u | sort -u | sed -n ' +s/ /\\ /g +s/\(.*\)/'"$tab"'\1 \\/p +s/.\(.*\) \\/\1:/ +H +$ { + s/.*/'"$tab"'/ + G + p +}' >> "$depfile" + echo >> "$depfile" # make sure the fragment doesn't end with a backslash + rm -f "$tmpdepfile" + ;; + +msvc7msys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +#nosideeffect) + # This comment above is used by automake to tell side-effect + # dependency tracking mechanisms from slower ones. + +dashmstdout) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout, regardless of -o. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + # Remove '-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + test -z "$dashmflag" && dashmflag=-M + # Require at least two characters before searching for ':' + # in the target name. This is to cope with DOS-style filenames: + # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise. + "$@" $dashmflag | + sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + # Some versions of the HPUX 10.20 sed can't process this sed invocation + # correctly. Breaking it into two sed invocations is a workaround. + tr ' ' "$nl" < "$tmpdepfile" \ + | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \ + | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +dashXmstdout) + # This case only exists to satisfy depend.m4. It is never actually + # run, as this mode is specially recognized in the preamble. + exit 1 + ;; + +makedepend) + "$@" || exit $? + # Remove any Libtool call + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + # X makedepend + shift + cleared=no eat=no + for arg + do + case $cleared in + no) + set ""; shift + cleared=yes ;; + esac + if test $eat = yes; then + eat=no + continue + fi + case "$arg" in + -D*|-I*) + set fnord "$@" "$arg"; shift ;; + # Strip any option that makedepend may not understand. Remove + # the object too, otherwise makedepend will parse it as a source file. + -arch) + eat=yes ;; + -*|$object) + ;; + *) + set fnord "$@" "$arg"; shift ;; + esac + done + obj_suffix=`echo "$object" | sed 's/^.*\././'` + touch "$tmpdepfile" + ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" + rm -f "$depfile" + # makedepend may prepend the VPATH from the source file name to the object. + # No need to regex-escape $object, excess matching of '.' is harmless. + sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile" + # Some versions of the HPUX 10.20 sed can't process the last invocation + # correctly. Breaking it into two sed invocations is a workaround. + sed '1,2d' "$tmpdepfile" \ + | tr ' ' "$nl" \ + | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \ + | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" "$tmpdepfile".bak + ;; + +cpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + # Remove '-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + "$@" -E \ + | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ + -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ + | sed '$ s: \\$::' > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + cat < "$tmpdepfile" >> "$depfile" + sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvisualcpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + IFS=" " + for arg + do + case "$arg" in + -o) + shift + ;; + $object) + shift + ;; + "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") + set fnord "$@" + shift + shift + ;; + *) + set fnord "$@" "$arg" + shift + shift + ;; + esac + done + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile" + echo "$tab" >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +none) + exec "$@" + ;; + +*) + echo "Unknown depmode $depmode" 1>&2 + exit 1 + ;; +esac + +exit 0 + +# Local Variables: +# mode: shell-script +# sh-indentation: 2 +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/install-sh b/install-sh deleted file mode 120000 index 4fcda59..0000000 --- a/install-sh +++ /dev/null @@ -1 +0,0 @@ -/usr/share/automake-1.13/install-sh \ No newline at end of file diff --git a/install-sh b/install-sh new file mode 100755 index 0000000..377bb86 --- /dev/null +++ b/install-sh @@ -0,0 +1,527 @@ +#!/bin/sh +# install - install a program, script, or datafile + +scriptversion=2011-11-20.07; # UTC + +# This originates from X11R5 (mit/util/scripts/install.sh), which was +# later released in X11R6 (xc/config/util/install.sh) with the +# following copyright and license. +# +# Copyright (C) 1994 X Consortium +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to +# deal in the Software without restriction, including without limitation the +# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +# sell copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN +# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- +# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +# +# Except as contained in this notice, the name of the X Consortium shall not +# be used in advertising or otherwise to promote the sale, use or other deal- +# ings in this Software without prior written authorization from the X Consor- +# tium. +# +# +# FSF changes to this file are in the public domain. +# +# Calling this script install-sh is preferred over install.sh, to prevent +# 'make' implicit rules from creating a file called install from it +# when there is no Makefile. +# +# This script is compatible with the BSD install script, but was written +# from scratch. + +nl=' +' +IFS=" "" $nl" + +# set DOITPROG to echo to test this script + +# Don't use :- since 4.3BSD and earlier shells don't like it. +doit=${DOITPROG-} +if test -z "$doit"; then + doit_exec=exec +else + doit_exec=$doit +fi + +# Put in absolute file names if you don't have them in your path; +# or use environment vars. + +chgrpprog=${CHGRPPROG-chgrp} +chmodprog=${CHMODPROG-chmod} +chownprog=${CHOWNPROG-chown} +cmpprog=${CMPPROG-cmp} +cpprog=${CPPROG-cp} +mkdirprog=${MKDIRPROG-mkdir} +mvprog=${MVPROG-mv} +rmprog=${RMPROG-rm} +stripprog=${STRIPPROG-strip} + +posix_glob='?' +initialize_posix_glob=' + test "$posix_glob" != "?" || { + if (set -f) 2>/dev/null; then + posix_glob= + else + posix_glob=: + fi + } +' + +posix_mkdir= + +# Desired mode of installed file. +mode=0755 + +chgrpcmd= +chmodcmd=$chmodprog +chowncmd= +mvcmd=$mvprog +rmcmd="$rmprog -f" +stripcmd= + +src= +dst= +dir_arg= +dst_arg= + +copy_on_change=false +no_target_directory= + +usage="\ +Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE + or: $0 [OPTION]... SRCFILES... DIRECTORY + or: $0 [OPTION]... -t DIRECTORY SRCFILES... + or: $0 [OPTION]... -d DIRECTORIES... + +In the 1st form, copy SRCFILE to DSTFILE. +In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. +In the 4th, create DIRECTORIES. + +Options: + --help display this help and exit. + --version display version info and exit. + + -c (ignored) + -C install only if different (preserve the last data modification time) + -d create directories instead of installing files. + -g GROUP $chgrpprog installed files to GROUP. + -m MODE $chmodprog installed files to MODE. + -o USER $chownprog installed files to USER. + -s $stripprog installed files. + -t DIRECTORY install into DIRECTORY. + -T report an error if DSTFILE is a directory. + +Environment variables override the default commands: + CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG + RMPROG STRIPPROG +" + +while test $# -ne 0; do + case $1 in + -c) ;; + + -C) copy_on_change=true;; + + -d) dir_arg=true;; + + -g) chgrpcmd="$chgrpprog $2" + shift;; + + --help) echo "$usage"; exit $?;; + + -m) mode=$2 + case $mode in + *' '* | *' '* | *' +'* | *'*'* | *'?'* | *'['*) + echo "$0: invalid mode: $mode" >&2 + exit 1;; + esac + shift;; + + -o) chowncmd="$chownprog $2" + shift;; + + -s) stripcmd=$stripprog;; + + -t) dst_arg=$2 + # Protect names problematic for 'test' and other utilities. + case $dst_arg in + -* | [=\(\)!]) dst_arg=./$dst_arg;; + esac + shift;; + + -T) no_target_directory=true;; + + --version) echo "$0 $scriptversion"; exit $?;; + + --) shift + break;; + + -*) echo "$0: invalid option: $1" >&2 + exit 1;; + + *) break;; + esac + shift +done + +if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then + # When -d is used, all remaining arguments are directories to create. + # When -t is used, the destination is already specified. + # Otherwise, the last argument is the destination. Remove it from $@. + for arg + do + if test -n "$dst_arg"; then + # $@ is not empty: it contains at least $arg. + set fnord "$@" "$dst_arg" + shift # fnord + fi + shift # arg + dst_arg=$arg + # Protect names problematic for 'test' and other utilities. + case $dst_arg in + -* | [=\(\)!]) dst_arg=./$dst_arg;; + esac + done +fi + +if test $# -eq 0; then + if test -z "$dir_arg"; then + echo "$0: no input file specified." >&2 + exit 1 + fi + # It's OK to call 'install-sh -d' without argument. + # This can happen when creating conditional directories. + exit 0 +fi + +if test -z "$dir_arg"; then + do_exit='(exit $ret); exit $ret' + trap "ret=129; $do_exit" 1 + trap "ret=130; $do_exit" 2 + trap "ret=141; $do_exit" 13 + trap "ret=143; $do_exit" 15 + + # Set umask so as not to create temps with too-generous modes. + # However, 'strip' requires both read and write access to temps. + case $mode in + # Optimize common cases. + *644) cp_umask=133;; + *755) cp_umask=22;; + + *[0-7]) + if test -z "$stripcmd"; then + u_plus_rw= + else + u_plus_rw='% 200' + fi + cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;; + *) + if test -z "$stripcmd"; then + u_plus_rw= + else + u_plus_rw=,u+rw + fi + cp_umask=$mode$u_plus_rw;; + esac +fi + +for src +do + # Protect names problematic for 'test' and other utilities. + case $src in + -* | [=\(\)!]) src=./$src;; + esac + + if test -n "$dir_arg"; then + dst=$src + dstdir=$dst + test -d "$dstdir" + dstdir_status=$? + else + + # Waiting for this to be detected by the "$cpprog $src $dsttmp" command + # might cause directories to be created, which would be especially bad + # if $src (and thus $dsttmp) contains '*'. + if test ! -f "$src" && test ! -d "$src"; then + echo "$0: $src does not exist." >&2 + exit 1 + fi + + if test -z "$dst_arg"; then + echo "$0: no destination specified." >&2 + exit 1 + fi + dst=$dst_arg + + # If destination is a directory, append the input filename; won't work + # if double slashes aren't ignored. + if test -d "$dst"; then + if test -n "$no_target_directory"; then + echo "$0: $dst_arg: Is a directory" >&2 + exit 1 + fi + dstdir=$dst + dst=$dstdir/`basename "$src"` + dstdir_status=0 + else + # Prefer dirname, but fall back on a substitute if dirname fails. + dstdir=` + (dirname "$dst") 2>/dev/null || + expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$dst" : 'X\(//\)[^/]' \| \ + X"$dst" : 'X\(//\)$' \| \ + X"$dst" : 'X\(/\)' \| . 2>/dev/null || + echo X"$dst" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q' + ` + + test -d "$dstdir" + dstdir_status=$? + fi + fi + + obsolete_mkdir_used=false + + if test $dstdir_status != 0; then + case $posix_mkdir in + '') + # Create intermediate dirs using mode 755 as modified by the umask. + # This is like FreeBSD 'install' as of 1997-10-28. + umask=`umask` + case $stripcmd.$umask in + # Optimize common cases. + *[2367][2367]) mkdir_umask=$umask;; + .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;; + + *[0-7]) + mkdir_umask=`expr $umask + 22 \ + - $umask % 100 % 40 + $umask % 20 \ + - $umask % 10 % 4 + $umask % 2 + `;; + *) mkdir_umask=$umask,go-w;; + esac + + # With -d, create the new directory with the user-specified mode. + # Otherwise, rely on $mkdir_umask. + if test -n "$dir_arg"; then + mkdir_mode=-m$mode + else + mkdir_mode= + fi + + posix_mkdir=false + case $umask in + *[123567][0-7][0-7]) + # POSIX mkdir -p sets u+wx bits regardless of umask, which + # is incompatible with FreeBSD 'install' when (umask & 300) != 0. + ;; + *) + tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$ + trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0 + + if (umask $mkdir_umask && + exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1 + then + if test -z "$dir_arg" || { + # Check for POSIX incompatibilities with -m. + # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or + # other-writable bit of parent directory when it shouldn't. + # FreeBSD 6.1 mkdir -m -p sets mode of existing directory. + ls_ld_tmpdir=`ls -ld "$tmpdir"` + case $ls_ld_tmpdir in + d????-?r-*) different_mode=700;; + d????-?--*) different_mode=755;; + *) false;; + esac && + $mkdirprog -m$different_mode -p -- "$tmpdir" && { + ls_ld_tmpdir_1=`ls -ld "$tmpdir"` + test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1" + } + } + then posix_mkdir=: + fi + rmdir "$tmpdir/d" "$tmpdir" + else + # Remove any dirs left behind by ancient mkdir implementations. + rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null + fi + trap '' 0;; + esac;; + esac + + if + $posix_mkdir && ( + umask $mkdir_umask && + $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir" + ) + then : + else + + # The umask is ridiculous, or mkdir does not conform to POSIX, + # or it failed possibly due to a race condition. Create the + # directory the slow way, step by step, checking for races as we go. + + case $dstdir in + /*) prefix='/';; + [-=\(\)!]*) prefix='./';; + *) prefix='';; + esac + + eval "$initialize_posix_glob" + + oIFS=$IFS + IFS=/ + $posix_glob set -f + set fnord $dstdir + shift + $posix_glob set +f + IFS=$oIFS + + prefixes= + + for d + do + test X"$d" = X && continue + + prefix=$prefix$d + if test -d "$prefix"; then + prefixes= + else + if $posix_mkdir; then + (umask=$mkdir_umask && + $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break + # Don't fail if two instances are running concurrently. + test -d "$prefix" || exit 1 + else + case $prefix in + *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;; + *) qprefix=$prefix;; + esac + prefixes="$prefixes '$qprefix'" + fi + fi + prefix=$prefix/ + done + + if test -n "$prefixes"; then + # Don't fail if two instances are running concurrently. + (umask $mkdir_umask && + eval "\$doit_exec \$mkdirprog $prefixes") || + test -d "$dstdir" || exit 1 + obsolete_mkdir_used=true + fi + fi + fi + + if test -n "$dir_arg"; then + { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && + { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && + { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || + test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 + else + + # Make a couple of temp file names in the proper directory. + dsttmp=$dstdir/_inst.$$_ + rmtmp=$dstdir/_rm.$$_ + + # Trap to clean up those temp files at exit. + trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 + + # Copy the file name to the temp name. + (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && + + # and set any options; do chmod last to preserve setuid bits. + # + # If any of these fail, we abort the whole thing. If we want to + # ignore errors from any of these, just make sure not to ignore + # errors from the above "$doit $cpprog $src $dsttmp" command. + # + { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } && + { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } && + { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } && + { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } && + + # If -C, don't bother to copy if it wouldn't change the file. + if $copy_on_change && + old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` && + new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` && + + eval "$initialize_posix_glob" && + $posix_glob set -f && + set X $old && old=:$2:$4:$5:$6 && + set X $new && new=:$2:$4:$5:$6 && + $posix_glob set +f && + + test "$old" = "$new" && + $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1 + then + rm -f "$dsttmp" + else + # Rename the file to the real destination. + $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null || + + # The rename failed, perhaps because mv can't rename something else + # to itself, or perhaps because mv is so ancient that it does not + # support -f. + { + # Now remove or move aside any old file at destination location. + # We try this two ways since rm can't unlink itself on some + # systems and the destination file might be busy for other + # reasons. In this case, the final cleanup might fail but the new + # file should still install successfully. + { + test ! -f "$dst" || + $doit $rmcmd -f "$dst" 2>/dev/null || + { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null && + { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; } + } || + { echo "$0: cannot unlink or rename $dst" >&2 + (exit 1); exit 1 + } + } && + + # Now rename the file to the real destination. + $doit $mvcmd "$dsttmp" "$dst" + } + fi || exit 1 + + trap '' 0 + fi +done + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/missing b/missing deleted file mode 120000 index ba03d81..0000000 --- a/missing +++ /dev/null @@ -1 +0,0 @@ -/usr/share/automake-1.13/missing \ No newline at end of file diff --git a/missing b/missing new file mode 100755 index 0000000..f45d3d4 --- /dev/null +++ b/missing @@ -0,0 +1,510 @@ +#! /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 +# the Free Software Foundation; either version 2, 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, see <http://www.gnu.org/licenses/>. + +# 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. + +if test $# -eq 0; then +<<<<<<< HEAD + echo 1>&2 "Try '$0 --help' for more information" + exit 1 +fi + +case $1 in + + --is-lightweight) + # Used by our autoconf macros to check whether the available missing + # script is modern enough. + exit 0 + ;; + + --run) + # 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 + bison yacc flex lex help2man + +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 $? + ;; + + -v|--v|--ve|--ver|--vers|--versi|--versio|--version) + echo "missing $scriptversion (GNU Automake)" + exit $? + ;; + + -*) +<<<<<<< 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=$? + +# If it succeeded, we are done. +test $st -eq 0 && exit 0 + +# Also exit now if we it failed (or wasn't found), and '--version' was +# passed; such an option is passed most likely to detect whether the +# program is present and works. +case $2 in --version|--help) exit $st;; esac + +# Exit code 63 means version mismatch. This often happens when the user +# tries to use an ancient version of a tool on a file that requires a +# minimum version. +if test $st -eq 63; then + msg="probably too old" +elif test $st -eq 127; then + # Program was missing. + msg="missing on your system" +else + # Program was found and executed, but failed. Give up. + exit $st +fi + +perl_URL=http://www.perl.org/ +flex_URL=http://flex.sourceforge.net/ +gnu_software_URL=http://www.gnu.org/software + +program_details () +{ + case $1 in + aclocal|automake) + echo "The '$1' program is part of the GNU Automake package:" + echo "<$gnu_software_URL/automake>" + echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:" + echo "<$gnu_software_URL/autoconf>" + echo "<$gnu_software_URL/m4/>" + echo "<$perl_URL>" + ;; + autoconf|autom4te|autoheader) + echo "The '$1' program is part of the GNU Autoconf package:" + echo "<$gnu_software_URL/autoconf/>" + echo "It also requires GNU m4 and Perl in order to run:" + echo "<$gnu_software_URL/m4/>" + echo "<$perl_URL>" + ;; + esac +} + +give_advice () +{ + # Normalize program name to check for. + normalized_program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + + printf '%s\n' "'$1' is $msg." + + configure_deps="'configure.ac' or m4 files included by 'configure.ac'" + case $normalized_program in + autoconf*) + echo "You should only need it if you modified 'configure.ac'," + echo "or m4 files included by it." + program_details 'autoconf' + ;; + autoheader*) + echo "You should only need it if you modified 'acconfig.h' or" + echo "$configure_deps." + program_details 'autoheader' + ;; + automake*) + echo "You should only need it if you modified 'Makefile.am' or" + echo "$configure_deps." + program_details 'automake' + ;; + aclocal*) + echo "You should only need it if you modified 'acinclude.m4' or" + echo "$configure_deps." + program_details 'aclocal' + ;; + autom4te*) + echo "You might have modified some maintainer files that require" + echo "the 'automa4te' program to be rebuilt." + program_details 'autom4te' + ;; + bison*|yacc*) + echo "You should only need it if you modified a '.y' file." + echo "You may want to install the GNU Bison package:" + echo "<$gnu_software_URL/bison/>" + ;; + lex*|flex*) + echo "You should only need it if you modified a '.l' file." + echo "You may want to install the Fast Lexical Analyzer package:" + echo "<$flex_URL>" + ;; + help2man*) + echo "You should only need it if you modified a dependency" \ + "of a man page." + echo "You may want to install the GNU Help2man package:" + echo "<$gnu_software_URL/help2man/>" + ;; + makeinfo*) + echo "You should only need it if you modified a '.texi' file, or" + echo "any other file indirectly affecting the aspect of the manual." + echo "You might want to install the Texinfo package:" + echo "<$gnu_software_URL/texinfo/>" + echo "The spurious makeinfo call might also be the consequence of" + echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might" + echo "want to install GNU make:" + echo "<$gnu_software_URL/make/>" + ;; + *) + echo "You might have modified some files without having the proper" + echo "tools for further handling them. Check the 'README' file, it" + echo "often tells you about the needed prerequisites for installing" + echo "this package. You may also peek at any GNU archive site, in" + echo "case some other package contains this missing '$1' program." + ;; + esac +} + +give_advice "$1" | sed -e '1s/^/WARNING: /' \ + -e '2,$s/^/ /' >&2 + +# 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) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/src/bondflip.c b/src/bondflip.c index 478027d..23afbc9 100644 --- a/src/bondflip.c +++ b/src/bondflip.c @@ -11,6 +11,7 @@ #include "bondflip.h" //#include "io.h" #include<stdio.h> +#include<string.h> ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn){ /*c Vertex and triangle (lm and lp) indexing for bond flip: @@ -28,9 +29,9 @@ ts_vertex *it=bond->vtx1; ts_vertex *k=bond->vtx2; ts_uint nei,neip,neim; - ts_uint i; //j; - ts_double oldenergy, delta_energy; - // ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL; + ts_uint i,j; + ts_double oldenergy, delta_energy, dvol=0.0; + ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL; ts_vertex *kp,*km; @@ -73,112 +74,7 @@ // fprintf(stderr,"Bond will not be too long.. Continue.\n"); /* we make a bond flip. this is different than in original fortran */ -// 0. step. Get memory prior the flip - oldenergy=0; - oldenergy+=k->xk* k->energy; - oldenergy+=kp->xk* kp->energy; - oldenergy+=km->xk* km->energy; - oldenergy+=it->xk* it->energy; -// for(i=0;i<k->neigh_no;i++) oldenergy+=k->neigh[i]->xk*k->neigh[i]->energy; -// for(i=0;i<kp->neigh_no;i++) oldenergy+=kp->neigh[i]->xk*kp->neigh[i]->energy; -// for(i=0;i<km->neigh_no;i++) oldenergy+=km->neigh[i]->xk*km->neigh[i]->energy; -// for(i=0;i<it->neigh_no;i++) oldenergy+=it->neigh[i]->xk*it->neigh[i]->energy; -/* -fprintf(stderr,"*** Naslov k=%ld\n",(long)k); -fprintf(stderr,"*** Naslov it=%ld\n",(long)it); -fprintf(stderr,"*** Naslov km=%ld\n",(long)km); -fprintf(stderr,"*** Naslov kp=%ld\n",(long)kp); - -for(i=0;i<k->neigh_no;i++) - fprintf(stderr,"k sosed=%ld\n",(long)k->neigh[i]); -for(i=0;i<it->neigh_no;i++) - fprintf(stderr,"it sosed=%ld\n",(long)it->neigh[i]); - -for(i=0;i<km->neigh_no;i++) - fprintf(stderr,"km sosed=%ld\n",(long)km->neigh[i]); -for(i=0;i<kp->neigh_no;i++) - fprintf(stderr,"kp sosed=%ld\n",(long)kp->neigh[i]); - - -*/ -// fprintf(stderr,"I WAS HERE! Before bondflip!\n"); - ts_flip_bond(k,it,km,kp, bond); -// fprintf(stderr,"I WAS HERE! Bondflip successful!\n"); - -/* Calculating the new energy */ - delta_energy=0; - for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]); - for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]); - for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]); - for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]); - delta_energy+=k->xk* k->energy; - delta_energy+=kp->xk* kp->energy; - delta_energy+=km->xk* km->energy; - delta_energy+=it->xk* it->energy; -// for(i=0;i<k->neigh_no;i++) delta_energy+=k->neigh[i]->xk*k->neigh[i]->energy; -// for(i=0;i<kp->neigh_no;i++) delta_energy+=kp->neigh[i]->xk*kp->neigh[i]->energy; -// for(i=0;i<km->neigh_no;i++) delta_energy+=km->neigh[i]->xk*km->neigh[i]->energy; -// for(i=0;i<it->neigh_no;i++) delta_energy+=it->neigh[i]->xk*it->neigh[i]->energy; - delta_energy-=oldenergy; - // fprintf(stderr,"I WAS HERE! Got energy!\n"); -/* MONTE CARLO */ - if(delta_energy>=0){ -#ifdef TS_DOUBLE_DOUBLE - if(exp(-delta_energy)< drand48() ) -#endif -#ifdef TS_DOUBLE_FLOAT - if(expf(-delta_energy)< (ts_float)drand48()) -#endif -#ifdef TS_DOUBLE_LONGDOUBLE - if(expl(-delta_energy)< (ts_ldouble)drand48()) -#endif - { - //not accepted, reverting changes - // fprintf(stderr,"Failed to move, due to MC\n"); - -// ts_flip_bond(km,kp,it,k, bond); - ts_flip_bond(kp,km,k,it, bond); - - -/* -fprintf(stderr,"*** Naslov k=%d\n",k); -fprintf(stderr,"*** Naslov it=%d\n",it); -fprintf(stderr,"*** Naslov km=%d\n",km); -fprintf(stderr,"*** Naslov kp=%d\n",kp); -for(i=0;i<k->neigh_no;i++) - fprintf(stderr,"k sosed=%d\n",k->neigh[i]); -for(i=0;i<it->neigh_no;i++) - fprintf(stderr,"it sosed=%d\n",it->neigh[i]); - - -for(i=0;i<km->neigh_no;i++) - fprintf(stderr,"km sosed=%d\n",km->neigh[i]); -for(i=0;i<kp->neigh_no;i++) - fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]); -*/ - - - - // fprintf(stderr,"Reverted condition!\n"); - return TS_FAIL; - } - } - // fprintf(stderr,"Success\n"); - - -/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */ - return TS_SUCCESS; -} - - -ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp, -ts_bond *bond){ - - ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL; - ts_uint i,j; //lmidx, lpidx; -if(k==NULL || it==NULL || km==NULL || kp==NULL){ - fatal("ts_flip_bond: You called me with invalid pointers to vertices",999); -} +// find lm, lp // 1. step. We find lm and lp from k->tristar ! for(i=0;i<it->tristar_no;i++){ for(j=0;j<k->tristar_no;j++){ @@ -216,57 +112,150 @@ } } } -/* -// DEBUG TESTING! -fprintf(stderr,"*** Naslov k=%d\n",k); -fprintf(stderr,"*** Naslov it=%d\n",it); -fprintf(stderr,"*** Naslov km=%d\n",km); -fprintf(stderr,"*** Naslov kp=%d\n",kp); -for(i=0;i<k->neigh_no;i++) - fprintf(stderr,"k sosed=%d\n",k->neigh[i]); -for(i=0;i<it->neigh_no;i++) - fprintf(stderr,"it sosed=%d\n",it->neigh[i]); - - -// END DEBUG TESTING! -*/ if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999); -/* -//DEBUG TESTING -fprintf(stderr,"1. step: lm, lm2, lp1 and lp found!\n"); -fprintf(stderr,"--- Naslov lm=%ld",(long)lm); +/* backup old structure */ +/* need to backup: + * vertices k, kp, km, it + * triangles lm, lp, lm2, lp1 + * bond + */ +ts_vertex *bck_vtx[4]; +ts_triangle *bck_tria[4]; +ts_bond *bck_bond; +ts_vertex *orig_vtx[]={k,it,kp,km}; +ts_triangle *orig_tria[]={lm,lp,lm2,lp1}; -fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lm->vertex[0],(long)lm->vertex[1], (long)lm->vertex[2]); -fprintf(stderr,"--- Naslov lp=%ld",(long)lp); -fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lp->vertex[0],(long)lp->vertex[1], (long)lp->vertex[2]); -fprintf(stderr,"--- Naslov lm2=%ld",(long)lm2); -fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lm2->vertex[0],(long)lm2->vertex[1], (long)lm2->vertex[2]); -fprintf(stderr,"--- Naslov lp1=%ld",(long)lp1); -fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lp1->vertex[0],(long)lp1->vertex[1], (long)lp1->vertex[2]); - -for(i=0;i<lm->neigh_no;i++) - fprintf(stderr,"lm sosed=%ld\n",(long)lm->neigh[i]); -for(i=0;i<lp->neigh_no;i++) - fprintf(stderr,"lp sosed=%ld\n",(long)lp->neigh[i]); -// END DEBUG TESTING +//fprintf(stderr,"Backuping!!!\n"); + bck_bond=(ts_bond *)malloc(sizeof(ts_bond)); +for(i=0;i<4;i++){ +/* fprintf(stderr,"vtx neigh[%d]=",i); + for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx); + fprintf(stderr,"\n"); */ -/* -// DEBUG TESTING! + bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex)); + bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); + memcpy((void *)bck_vtx[i],(void *)orig_vtx[i],sizeof(ts_vertex)); + memcpy((void *)bck_tria[i],(void *)orig_tria[i],sizeof(ts_triangle)); + /* level 2 pointers */ -for(i=0;i<3;i++){ + bck_vtx[i]->neigh=(ts_vertex **)malloc(orig_vtx[i]->neigh_no*sizeof(ts_vertex *)); + bck_vtx[i]->tristar=(ts_triangle **)malloc(orig_vtx[i]->tristar_no*sizeof(ts_triangle *)); + bck_vtx[i]->bond=(ts_bond **)malloc(orig_vtx[i]->bond_no*sizeof(ts_bond *)); + bck_tria[i]->neigh=(ts_triangle **)malloc(orig_tria[i]->neigh_no*sizeof(ts_triangle *)); - if(lp1->neigh[i]==lp) fprintf(stderr,"Nasel sem par lp1->lp\n"); - if(lp->neigh[i]==lp1) fprintf(stderr,"Nasel sem par lp->lp1\n"); - if(lm2->neigh[i]==lm) fprintf(stderr,"Nasel sem par lm2->lm\n"); - if(lm->neigh[i]==lm2) fprintf(stderr,"Nasel sem par lm->lm2\n"); + memcpy((void *)bck_vtx[i]->neigh,(void *)orig_vtx[i]->neigh,orig_vtx[i]->neigh_no*sizeof(ts_vertex *)); + memcpy((void *)bck_vtx[i]->tristar,(void *)orig_vtx[i]->tristar,orig_vtx[i]->tristar_no*sizeof(ts_triangle *)); + memcpy((void *)bck_vtx[i]->bond,(void *)orig_vtx[i]->bond,orig_vtx[i]->bond_no*sizeof(ts_bond *)); + + memcpy((void *)bck_tria[i]->neigh,(void *)orig_tria[i]->neigh,orig_tria[i]->neigh_no*sizeof(ts_triangle *)); } -// END DEBUG TESTING! -*/ + memcpy(bck_bond,bond,sizeof(ts_bond)); +//fprintf(stderr,"Backup complete!!!\n"); +/* end backup vertex */ + +/* Save old energy */ + oldenergy=0; + oldenergy+=k->xk* k->energy; + oldenergy+=kp->xk* kp->energy; + oldenergy+=km->xk* km->energy; + oldenergy+=it->xk* it->energy; + //Neigbours of k, it, km, kp don't change its energy. + + if(vesicle->pswitch == 1){dvol = -lm->volume - lp->volume;} + +/* fix data structure for flipped bond */ + ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1); +/* Calculating the new energy */ + delta_energy=0; + delta_energy+=k->xk* k->energy; + delta_energy+=kp->xk* kp->energy; + delta_energy+=km->xk* km->energy; + delta_energy+=it->xk* it->energy; + //Neigbours of k, it, km, kp don't change its energy. + + delta_energy-=oldenergy; + if(vesicle->pswitch == 1){ + dvol = dvol + lm->volume + lp->volume; + delta_energy-= vesicle->pressure*dvol; + } + +/* MONTE CARLO */ + if(delta_energy>=0){ +#ifdef TS_DOUBLE_DOUBLE + if(exp(-delta_energy)< drand48() ) +#endif +#ifdef TS_DOUBLE_FLOAT + if(expf(-delta_energy)< (ts_float)drand48()) +#endif +#ifdef TS_DOUBLE_LONGDOUBLE + if(expl(-delta_energy)< (ts_ldouble)drand48()) +#endif + { + //not accepted, reverting changes + //restore all backups +// fprintf(stderr,"Restoring!!!\n"); + + for(i=0;i<4;i++){ +// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no ); + free(orig_vtx[i]->neigh); + free(orig_vtx[i]->tristar); + free(orig_vtx[i]->bond); + free(orig_tria[i]->neigh); + memcpy((void *)orig_vtx[i],(void *)bck_vtx[i],sizeof(ts_vertex)); + memcpy((void *)orig_tria[i],(void *)bck_tria[i],sizeof(ts_triangle)); +// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no ); + /* level 2 pointers are redirected*/ + } + memcpy(bond,bck_bond,sizeof(ts_bond)); + + for(i=0;i<4;i++){ + free(bck_vtx[i]); + free(bck_tria[i]); +/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no ); + for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx); + fprintf(stderr,"\n"); */ + } + + free(bck_bond); +// fprintf(stderr,"Restoration complete!!!\n"); + + return TS_FAIL; + } + } + /* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */ + // fprintf(stderr,"SUCCESS!!!\n"); + + // delete all backups + for(i=0;i<4;i++){ + free(bck_vtx[i]->neigh); + free(bck_vtx[i]->bond); + free(bck_vtx[i]->tristar); + free(bck_vtx[i]); + free(bck_tria[i]->neigh); + free(bck_tria[i]); +/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i); + for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx); + fprintf(stderr,"\n"); +*/ + } + free(bck_bond); + + return TS_SUCCESS; +} + + +ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp, +ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1){ + + ts_uint i; //lmidx, lpidx; +if(k==NULL || it==NULL || km==NULL || kp==NULL){ + fatal("ts_flip_bond: You called me with invalid pointers to vertices",999); +} // 2. step. We change the triangle vertices... (actual bond flip) for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp; for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km; @@ -323,34 +312,10 @@ vtx_remove_tristar(it,lm); vtx_remove_tristar(k,lp); //fprintf(stderr,"6. step: tristar corrected\n"); - -/* -//DEBUG TESTING -fprintf(stderr,"--- Naslov lm=%d",lm); - - -fprintf(stderr," vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]); -fprintf(stderr,"--- Naslov lp=%d",lp); -fprintf(stderr," vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]); -fprintf(stderr,"--- Naslov lm2=%d",lm2); -fprintf(stderr," vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]); -fprintf(stderr,"--- Naslov lp1=%d",lp1); -fprintf(stderr," vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]); - -for(i=0;i<lm->neigh_no;i++) - fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]); -for(i=0;i<lp->neigh_no;i++) - fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]); -// END DEBUG TESTING -*/ energy_vertex(k); energy_vertex(kp); energy_vertex(km); energy_vertex(it); - - // END modifications to data structure! - - return TS_SUCCESS; } diff --git a/src/bondflip.h b/src/bondflip.h index 8d7ee37..947555f 100644 --- a/src/bondflip.h +++ b/src/bondflip.h @@ -3,5 +3,5 @@ ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn); -ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp, ts_bond *bond); +ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp, ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1); #endif diff --git a/src/general.c b/src/general.c index ed06398..a600800 100644 --- a/src/general.c +++ b/src/general.c @@ -3,10 +3,20 @@ #include "general.h" #include<stdarg.h> +#include <sys/time.h> +#include <unistd.h> +#include <time.h> + + ts_uint ts_fprintf(FILE *fd, char *fmt, ...){ if(quiet) return TS_SUCCESS; - va_list ap; - va_start(ap,fmt); + va_list ap; + va_start(ap,fmt); + char tmbuf[255]; + struct timeval now; + gettimeofday(&now, 0); + strftime(tmbuf, sizeof tmbuf, "%Y-%m-%d %H:%M:%S", localtime(&now.tv_sec)); +fprintf(fd, "[%s] ",tmbuf); vfprintf(fd, fmt, ap); /* Call vfprintf */ va_end(ap); /* Cleanup the va_list */ return TS_SUCCESS; diff --git a/src/general.h b/src/general.h index e7e9545..3308faa 100644 --- a/src/general.h +++ b/src/general.h @@ -3,7 +3,6 @@ #include<stdarg.h> #include<stdio.h> - /* @brief This is a header file, defining general constants and structures. * @file header.h * @author Samo Penic @@ -260,8 +259,9 @@ ts_poly_list *poly_list; ts_double spring_constant; + ts_double pressure; + ts_int pswitch; } ts_vesicle; - diff --git a/src/initial_distribution.c b/src/initial_distribution.c index 382750b..7601f13 100644 --- a/src/initial_distribution.c +++ b/src/initial_distribution.c @@ -9,36 +9,61 @@ #include "triangle.h" #include "initial_distribution.h" #include "energy.h" +#include "poly.h" +#include "io.h" ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){ - ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell); + ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell); ts_bool retval; - ts_uint no_vertices=5*nshell*nshell+2; - - - - ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize); - -//TODO: debugging only. Please remove ASAP! - vesicle->bending_rigidity=25.0; - - vesicle->nshell=nshell; - retval = vtx_set_global_values(vesicle); - retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist); - retval = init_vertex_neighbours(vesicle->vlist); - vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist); + ts_uint no_vertices=5*nshell*nshell+2; + ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize); + vesicle->nshell=nshell; + //retval = vtx_set_global_values(vesicle); + retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist); + retval = init_vertex_neighbours(vesicle->vlist); + vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist); // retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh - retval = init_triangles(vesicle); - retval = init_triangle_neighbours(vesicle); - retval = init_common_vertex_triangle_neighbours(vesicle); - retval = init_normal_vectors(vesicle->tlist); - retval = mean_curvature_and_energy(vesicle); - ts_fprintf(stderr,"initial_distribution finished!\n"); + retval = init_triangles(vesicle); + retval = init_triangle_neighbours(vesicle); + retval = init_common_vertex_triangle_neighbours(vesicle); + retval = init_normal_vectors(vesicle->tlist); + retval = mean_curvature_and_energy(vesicle); + ts_fprintf(stdout,"initial_distribution finished!\n"); if(retval); return vesicle; } + +ts_vesicle *create_vesicle_from_tape(ts_tape *tape){ + ts_vesicle *vesicle; + vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize); + vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist); + vesicle->spring_constant=tape->kspring; + poly_assign_spring_const(vesicle); + + vesicle->nshell=tape->nshell; + vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */ + vesicle->bending_rigidity=tape->xk0; + vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */ + ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0); + vesicle->stepsize=tape->stepsize; + vesicle->clist->ncmax[0]=tape->ncxmax; + vesicle->clist->ncmax[1]=tape->ncymax; + vesicle->clist->ncmax[2]=tape->nczmax; + vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */ + + vesicle->pressure= tape->pressure; + vesicle->pswitch=tape->pswitch; + + return vesicle; + +} + + + + + ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){ /* Some often used relations */ const ts_double s1= sin(2.0*M_PI/5.0); diff --git a/src/initial_distribution.h b/src/initial_distribution.h index 7b3e2ba..20bbf18 100644 --- a/src/initial_distribution.h +++ b/src/initial_distribution.h @@ -1,6 +1,8 @@ +#include "io.h" + + /** @brief initial bond length */ #define A0 1.2 - /** @brief Creates initial distribution of vertices * @@ -10,6 +12,7 @@ */ ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize); +ts_vesicle *create_vesicle_from_tape(ts_tape *tape); /** Sets the initial position of the vertexes to dipyramid * diff --git a/src/io.c b/src/io.c index 547c51c..d4a9cc4 100644 --- a/src/io.c +++ b/src/io.c @@ -11,11 +11,14 @@ #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){ +ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){ /* save current state with wrong pointers. Will fix that later */ ts_uint i,j,k; @@ -128,14 +131,15 @@ */ fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh); - + + fwrite(&iteration, sizeof(ts_uint),1,fh); fclose(fh); return TS_SUCCESS; } /** RESTORE DUMP FROM DISK **/ -ts_vesicle *restore_state(){ +ts_vesicle *restore_state(ts_uint *iteration){ ts_uint i,j,k; FILE *fh=fopen("dump.bin","rb"); ts_uint retval; @@ -313,10 +317,112 @@ vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required! } + retval=fread(iteration,sizeof(ts_uint),1,fh); if(retval); fclose(fh); return vesicle; } + + + +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, &(command_line_args.force_from_tape), 1}, + {"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 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; + +} + @@ -417,11 +523,11 @@ fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n", vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy, vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0); - for(j=0;j<vlist->vtx[i]->neigh_no;j++){ + for(j=0;j<vlist->vtx[i]->bond_no;j++){ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual); } fprintf(fh,"\n"); - for(j=0;j<vlist->vtx[i]->neigh_no;j++){ + for(j=0;j<vlist->vtx[i]->bond_no;j++){ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length); } fprintf(fh,"\n"); @@ -647,74 +753,63 @@ -ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){ - long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // THIS IS DUE TO CONFUSE BUG! - char *buf=malloc(255*sizeof(char)); - long int brezveze0=1; +ts_tape *parsetape(char *filename){ + // long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG! + ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape)); + tape->multiprocessing=calloc(255,sizeof(char)); + /* long int brezveze0=1; long int brezveze1=1; long int brezveze2=1; - ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0; + ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0; long int iter=1000, init=1000, mcsw=1000; - +*/ cfg_opt_t opts[] = { - CFG_SIMPLE_INT("nshell", &nshell), - CFG_SIMPLE_INT("npoly", &npoly), - CFG_SIMPLE_INT("nmono", &nmono), - CFG_SIMPLE_FLOAT("dmax", &dmax), - CFG_SIMPLE_FLOAT("xk0",&xk0), - CFG_SIMPLE_FLOAT("k_spring",&kspring), - CFG_SIMPLE_FLOAT("stepsize",&stepsize), - CFG_SIMPLE_INT("nxmax", &ncxmax), - CFG_SIMPLE_INT("nymax", &ncymax), - CFG_SIMPLE_INT("nzmax", &nczmax), - CFG_SIMPLE_INT("iterations",&iter), - CFG_SIMPLE_INT("mcsweeps",&mcsw), - CFG_SIMPLE_INT("inititer", &init), - CFG_SIMPLE_BOOL("quiet",&quiet), - CFG_SIMPLE_STR("multiprocessing",buf), - CFG_SIMPLE_INT("smp_cores",&brezveze0), - CFG_SIMPLE_INT("cluster_nodes",&brezveze1), - CFG_SIMPLE_INT("distributed_processes",&brezveze2), + CFG_SIMPLE_INT("nshell", &tape->nshell), + CFG_SIMPLE_INT("npoly", &tape->npoly), + CFG_SIMPLE_INT("nmono", &tape->nmono), + CFG_SIMPLE_FLOAT("dmax", &tape->dmax), + CFG_SIMPLE_FLOAT("xk0",&tape->xk0), + CFG_SIMPLE_INT("pswitch",&tape->pswitch), + CFG_SIMPLE_FLOAT("pressure",&tape->pressure), + CFG_SIMPLE_FLOAT("k_spring",&tape->kspring), + CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize), + CFG_SIMPLE_INT("nxmax", &tape->ncxmax), + CFG_SIMPLE_INT("nymax", &tape->ncymax), + CFG_SIMPLE_INT("nzmax", &tape->nczmax), + CFG_SIMPLE_INT("iterations",&tape->iterations), + CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps), + CFG_SIMPLE_INT("inititer", &tape->inititer), + CFG_SIMPLE_BOOL("quiet",&tape->quiet), + CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing), + CFG_SIMPLE_INT("smp_cores",&tape->brezveze0), + CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1), + CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2), CFG_END() }; cfg_t *cfg; ts_uint retval; cfg = cfg_init(opts, 0); - retval=cfg_parse(cfg, "tape"); + retval=cfg_parse(cfg, filename); if(retval==CFG_FILE_ERROR){ fatal("No tape file.",100); } else if(retval==CFG_PARSE_ERROR){ fatal("Invalid tape!",100); } - ts_vesicle *vesicle; - *iterations=iter; - *inititer=init; - *mcsweeps=mcsw; - vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize); - vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist); - vesicle->spring_constant=kspring; - poly_assign_spring_const(vesicle); - - - vesicle->nshell=nshell; - vesicle->dmax=dmax*dmax; - vesicle->bending_rigidity=xk0; - vesicle->stepsize=stepsize; - vesicle->clist->ncmax[0]=ncxmax; - vesicle->clist->ncmax[1]=ncymax; - vesicle->clist->ncmax[2]=nczmax; - vesicle->clist->max_occupancy=8; cfg_free(cfg); - free(buf); - // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell); - - return vesicle; + /* global variables are set automatically */ + quiet=tape->quiet; + return tape; +} +ts_bool tape_free(ts_tape *tape){ + free(tape->multiprocessing); + free(tape); + return TS_SUCCESS; } diff --git a/src/io.h b/src/io.h index 7ac2160..c8dfd17 100644 --- a/src/io.h +++ b/src/io.h @@ -1,6 +1,49 @@ #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; + + +typedef struct { + long int nshell; + long int ncxmax; + long int ncymax; + long int nczmax; + long int npoly; + long int nmono; + long int pswitch; + char *multiprocessing; + long int brezveze0; + long int brezveze1; + long int brezveze2; + ts_double xk0; + ts_double dmax; + ts_double stepsize; + ts_double kspring; + ts_double pressure; + long int iterations; + long int inititer; + long int mcsweeps; + long int quiet; +} ts_tape; + +typedef struct{ + ts_int force_from_tape; + ts_int reset_iteration_count; +} ts_args; + +ts_args command_line_args; + +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 @@ -48,8 +91,9 @@ ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text); ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno); ts_bool write_master_xml_file(ts_char *filename); -ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations); +ts_tape *parsetape(char *filename); +ts_bool tape_free(ts_tape *tape); -ts_bool dump_state(ts_vesicle *vesicle); -ts_vesicle *restore_state(); +ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration); +ts_vesicle *restore_state(ts_uint *iteration); #endif diff --git a/src/main.c b/src/main.c index 705d8de..a89cecf 100644 --- a/src/main.c +++ b/src/main.c @@ -19,67 +19,38 @@ */ int main(int argv, char *argc[]){ -ts_uint inititer,mcsweeps, iterations; -ts_vesicle *vesicle, *vesicle1; -/* THIS SHOULD GO INTO UNIT TEST -ts_bool retval; - ts_vertex_list *vlist=init_vertex_list(5); -ts_vertex_list *vlist1; -ts_bond_list *blist=init_bond_list(); -ts_triangle_list *tlist=init_triangle_list(); -ts_cell_list *clist=init_cell_list(3,3,3,0.3); + ts_vesicle *vesicle; + ts_tape *tape; + ts_uint start_iteration=0; + parse_args(argv,argc); // sets global variable command_line_args (defined in io.h) + ts_fprintf(stdout,"Starting program...\n\n"); + if(force_from_tape){ + ts_fprintf(stdout,"************************************************\n"); + ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n"); + ts_fprintf(stdout,"************************************************\n\n"); + tape=parsetape("tape"); + vesicle=create_vesicle_from_tape(tape); + } else { -retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]); -if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n"); + ts_fprintf(stdout,"**********************************************************************\n"); + ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n"); + ts_fprintf(stdout,"**********************************************************************\n\n"); + tape=parsetape("tape"); + vesicle=restore_state(&start_iteration); -retval=vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]); -if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n"); -fprintf(stderr,"Was here"); -retval=vtx_remove_neighbour(vlist->vtx[1],vlist->vtx[0]); -vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]); -fprintf(stderr,"Was here too!\n"); + if(command_line_args.reset_iteration_count) start_iteration=0; + else start_iteration++; -vlist->vtx[0]->x=1.0; -vlist->vtx[0]->x=1.1; -vlist1=vertex_list_copy(vlist); -bond_add(blist, vlist->vtx[1],vlist->vtx[0]); -triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]); + if(start_iteration>=tape->iterations){ + ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n"); + return 0; + } + } -triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]); - -printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex); -cell_add_vertex(clist->cell[0], vlist->vtx[0]); -printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex); -printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->vertex[0]->x); -cell_list_cell_occupation_clear(clist); -printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex); -cell_add_vertex(clist->cell[0], vlist->vtx[0]); - - -triangle_list_free(tlist); -bond_list_free(blist); -vtx_list_free(vlist); -cell_list_free(clist); - -vtx_list_free(vlist1); -printf("Tests complete.\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); -write_master_xml_file("test.pvd"); -write_dout_fcompat_file(vesicle,"dout"); -vesicle_free(vesicle); - -return 0; //program finished perfectly ok. We return 0. + run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration); + write_master_xml_file("test.pvd"); + write_dout_fcompat_file(vesicle,"dout"); + vesicle_free(vesicle); + tape_free(tape); + return 0; //program finished perfectly ok. We return 0. } diff --git a/src/tape b/src/tape index f3c8bad..59b417a 100644 --- a/src/tape +++ b/src/tape @@ -1,16 +1,22 @@ ####### Vesicle definitions ########### # nshell is a number of divisions of dipyramid nshell=17 -# dmax is the max. bond length +# dmax is the max. bond length (in units l_min) dmax=1.7 -# bending rigidity of the membrane +# bending rigidity of the membrane (in units kT) xk0=25.0 -# max step size +# max step size (in units l_min) stepsize=0.15 + +# Pressure calculations +# (pswitch=1: calc. p*dV energy contribution) +pswitch = 0 +# pressure difference: p_inside - p_outside (in units l_min^3/kT): +pressure=0.0 ####### Polymer definitions ########### # npoly is a number of polymers attached to npoly distinct vertices on vesicle -npoly=2 +npoly=20 # nmono is a number of monomers in each polymer nmono=10 # Spring constant between monomers of the polymer @@ -24,11 +30,11 @@ ####### Program Control ############ #how many MC sweeps between subsequent records of states to disk -mcsweeps=5000 +mcsweeps=500 #how many initial mcsweeps*inititer MC sweeps before recording to disk? inititer=1 #how many records do you want on the disk iteration are there in a run? -iterations=10000 +iterations=10 #shut up if we are using cluster!!! diff --git a/src/timestep.c b/src/timestep.c index d717abb..92a4a25 100644 --- a/src/timestep.c +++ b/src/timestep.c @@ -9,19 +9,20 @@ #include "frame.h" #include "io.h" -ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){ +ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){ ts_uint i, j; centermass(vesicle); cell_occupation(vesicle); - ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps); - for(i=0;i<inititer+iterations;i++){ + if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps); + for(i=start_iteration;i<inititer+iterations;i++){ for(j=0;j<mcsweeps;j++){ single_timestep(vesicle); } 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,i); if(i>inititer){ write_vertex_xml_file(vesicle,i-inititer); } diff --git a/src/timestep.h b/src/timestep.h index e25234d..dd18481 100644 --- a/src/timestep.h +++ b/src/timestep.h @@ -1,5 +1,5 @@ #ifndef _TIMESTEP_H #define _TIMESTEP_H ts_bool single_timestep(ts_vesicle *vesicle); -ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations); +ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_simulation); #endif diff --git a/src/triangle.c b/src/triangle.c index dc53487..311e138 100644 --- a/src/triangle.c +++ b/src/triangle.c @@ -150,6 +150,7 @@ // fprintf(stderr,"*** tria_number=%d\n",tria->neigh_no); tria->neigh=(ts_triangle **)realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *)); if(tria->neigh == NULL){ + fprintf(stderr,"Ooops: tria->neigh_no=%d\n",tria->neigh_no); fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100); } /* we repeat the procedure for neighbour */ @@ -168,6 +169,7 @@ // fprintf(stderr,"*** ntria_number=%d\n",ntria->neigh_no); ntria->neigh=(ts_triangle **)realloc(ntria->neigh,ntria->neigh_no*sizeof(ts_triangle *)); if(ntria->neigh == NULL){ + fprintf(stderr,"Ooops: ntria->neigh_no=%d\n",ntria->neigh_no); fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100); } return TS_SUCCESS; diff --git a/src/vertexmove.c b/src/vertexmove.c index 86b8533..7f6391f 100644 --- a/src/vertexmove.c +++ b/src/vertexmove.c @@ -18,7 +18,7 @@ ts_double dist; ts_bool retval; ts_uint cellidx; - ts_double delta_energy,oenergy; + ts_double delta_energy,oenergy,dvol=0.0; ts_double costheta,sintheta,phi,r; //This will hold all the information of vtx and its neighbours ts_vertex backupvtx[20]; @@ -83,7 +83,9 @@ memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex)); } - + if(vesicle->pswitch == 1){ + for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume; + }; delta_energy=0; //update the normals of triangles that share bead i. @@ -97,6 +99,12 @@ energy_vertex(vtx->neigh[i]); delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy); } + + if(vesicle->pswitch == 1){ + for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume; + delta_energy-=vesicle->pressure*dvol; + }; + /* No poly-bond energy for now! if(vtx->grafted_poly!=NULL){ delta_energy+= -- Gitblit v1.9.3