From 42641cde38cfd1d27a2031604cc1397b5bd2849b Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 21 Mar 2014 20:57:24 +0000
Subject: [PATCH] Merge with trout-rnc.
---
src/main.c | 1
src/vertexmove.h | 2
src/io.c | 152 ++++++++
src/tape | 16
src/initial_distribution.c | 34 +
src/general.h | 15
src/vertexmove.c | 113 ++++++
src/io.h | 4
src/poly.h | 5
src/timestep.c | 22
src/poly.c | 96 +++-
src/bond.h | 1
src/bond.c | 11
aclocal.m4 | 570 +++++++++++++++++-------------
src/frame.c | 36 +
15 files changed, 764 insertions(+), 314 deletions(-)
diff --git a/aclocal.m4 b/aclocal.m4
index da06da5..72a1419 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,8 +1,7 @@
-# generated automatically by aclocal 1.11.3 -*- Autoconf -*-
+# generated automatically by aclocal 1.13.3 -*- Autoconf -*-
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -12,22 +11,20 @@
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.
+m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])])
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],,
-[m4_warning([this file was generated for autoconf 2.68.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
+[m4_warning([this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
-To do so, use the procedure documented by the package, typically `autoreconf'.])])
+To do so, use the procedure documented by the package, typically 'autoreconf'.])])
-# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 2002-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-
-# serial 1
# AM_AUTOMAKE_VERSION(VERSION)
# ----------------------------
@@ -35,10 +32,10 @@
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.11'
+[am__api_version='1.13'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.11.3], [],
+m4_if([$1], [1.13.3], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -54,24 +51,22 @@
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# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.11.3])dnl
+[AM_AUTOMAKE_VERSION([1.13.3])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
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_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
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# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
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+# '$srcdir', '$srcdir/..', or '$srcdir/../..'.
#
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@@ -90,7 +85,7 @@
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# start a VPATH build or use an absolute $srcdir.
#
# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
@@ -116,22 +111,19 @@
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
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-
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AC_DEFUN([AM_CONDITIONAL],
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- ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
- [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+[AC_PREREQ([2.52])dnl
+ m4_if([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
AC_SUBST([$1_TRUE])dnl
AC_SUBST([$1_FALSE])dnl
_AM_SUBST_NOTMAKE([$1_TRUE])dnl
@@ -150,16 +142,14 @@
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009,
-# 2010, 2011 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
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@@ -169,7 +159,7 @@
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#
# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
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- [depcc="$$1" am_compiler_list=])
+m4_if([$1], [CC], [depcc="$CC" am_compiler_list=],
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@@ -195,8 +186,8 @@
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- # in D'.
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+ # in D".
rm -rf conftest.dir
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
@@ -236,16 +227,16 @@
: > sub/conftest.c
for i in 1 2 3 4 5 6; do
echo '#include "conftst'$i'.h"' >> sub/conftest.c
- # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
- # Solaris 8's {/usr,}/bin/sh.
- touch sub/conftst$i.h
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > sub/conftst$i.h
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
- # We check with `-c' and `-o' for the sake of the "dashmstdout"
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# mode. It turns out that the SunPro C++ compiler does not properly
- # handle `-M -o', and we need to detect this. Also, some Intel
- # versions had trouble with output in subdirs
+ # handle '-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs.
am__obj=sub/conftest.${OBJEXT-o}
am__minus_obj="-o $am__obj"
case $depmode in
@@ -254,8 +245,8 @@
test "$am__universal" = false || continue
;;
nosideeffect)
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+ # After this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested.
if test "x$enable_dependency_tracking" = xyes; then
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else
@@ -263,7 +254,7 @@
fi
;;
msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok `-c -o', but also, the minuso test has
+ # This compiler won't grok '-c -o', but also, the minuso test has
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am__obj=conftest.${OBJEXT-o}
@@ -311,7 +302,7 @@
# AM_SET_DEPDIR
# -------------
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-# This macro is AC_REQUIREd in _AM_DEPENDENCIES
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AC_DEFUN([AM_SET_DEPDIR],
[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
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@@ -338,20 +333,18 @@
# Generate code to set up dependency tracking. -*- Autoconf -*-
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-# Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
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@@ -364,7 +357,7 @@
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mf=`echo "$mf" | sed -e 's/:.*$//'`
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@@ -376,21 +369,19 @@
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
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DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
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+ test -z "$am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
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# expansion.
for file in `sed -n "
s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`AS_DIRNAME(["$file"])`
@@ -408,7 +399,7 @@
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#
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# Do all the work for Automake. -*- Autoconf -*-
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-# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
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-AM_MISSING_PROG(MAKEINFO, makeinfo)
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AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
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AC_PROVIDE_IFELSE([AC_PROG_CXX],
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+AC_REQUIRE([AM_SILENT_RULES])dnl
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AC_CONFIG_COMMANDS_PRE(dnl
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[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
])
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@@ -555,14 +556,11 @@
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echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001, 2003, 2005, 2008, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-
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# AM_PROG_INSTALL_SH
# ------------------
@@ -577,15 +575,13 @@
install_sh="\${SHELL} $am_aux_dir/install-sh"
esac
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+AC_SUBST([install_sh])])
-# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+# Copyright (C) 2003-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
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@@ -602,13 +598,11 @@
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
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@@ -627,7 +621,7 @@
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
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case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
@@ -654,14 +648,11 @@
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
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-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
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@@ -670,11 +661,10 @@
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-
# AM_MISSING_HAS_RUN
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AC_DEFUN([AM_MISSING_HAS_RUN],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([missing])dnl
@@ -687,53 +677,21 @@
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
- am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
else
am_missing_run=
- AC_MSG_WARN([`missing' script is too old or missing])
+ AC_MSG_WARN(['missing' script is too old or missing])
fi
-])
-
-# Copyright (C) 2003, 2004, 2005, 2006, 2011 Free Software Foundation,
-# Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# serial 1
-
-# AM_PROG_MKDIR_P
-# ---------------
-# Check for `mkdir -p'.
-AC_DEFUN([AM_PROG_MKDIR_P],
-[AC_PREREQ([2.60])dnl
-AC_REQUIRE([AC_PROG_MKDIR_P])dnl
-dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
-dnl while keeping a definition of mkdir_p for backward compatibility.
-dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
-dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
-dnl Makefile.ins that do not define MKDIR_P, so we do our own
-dnl adjustment using top_builddir (which is defined more often than
-dnl MKDIR_P).
-AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
-case $mkdir_p in
- [[\\/$]]* | ?:[[\\/]]*) ;;
- */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-esac
])
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001, 2002, 2003, 2005, 2008, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-
-# serial 5
# _AM_MANGLE_OPTION(NAME)
# -----------------------
@@ -744,7 +702,7 @@
# --------------------
# Set option NAME. Presently that only means defining a flag for this option.
AC_DEFUN([_AM_SET_OPTION],
-[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+[m4_define(_AM_MANGLE_OPTION([$1]), [1])])
# _AM_SET_OPTIONS(OPTIONS)
# ------------------------
@@ -760,22 +718,16 @@
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 5
-
# AM_SANITY_CHECK
# ---------------
AC_DEFUN([AM_SANITY_CHECK],
[AC_MSG_CHECKING([whether build environment is sane])
-# Just in case
-sleep 1
-echo timestamp > conftest.file
# Reject unsafe characters in $srcdir or the absolute working directory
# name. Accept space and tab only in the latter.
am_lf='
@@ -786,32 +738,40 @@
esac
case $srcdir in
*[[\\\"\#\$\&\'\`$am_lf\ \ ]]*)
- AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
+ AC_MSG_ERROR([unsafe srcdir value: '$srcdir']);;
esac
-# Do `set' in a subshell so we don't clobber the current shell's
+# Do 'set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
- if test "$[*]" = "X"; then
- # -L didn't work.
- set X `ls -t "$srcdir/configure" conftest.file`
- fi
- rm -f conftest.file
- if test "$[*]" != "X $srcdir/configure conftest.file" \
- && test "$[*]" != "X conftest.file $srcdir/configure"; then
+ am_has_slept=no
+ for am_try in 1 2; do
+ echo "timestamp, slept: $am_has_slept" > conftest.file
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$[*]" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ if test "$[*]" != "X $srcdir/configure conftest.file" \
+ && test "$[*]" != "X conftest.file $srcdir/configure"; then
- # If neither matched, then we have a broken ls. This can happen
- # if, for instance, CONFIG_SHELL is bash and it inherits a
- # broken ls alias from the environment. This has actually
- # happened. Such a system could not be considered "sane".
- AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
-alias in your environment])
- fi
-
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
+ alias in your environment])
+ fi
+ if test "$[2]" = conftest.file || test $am_try -eq 2; then
+ break
+ fi
+ # Just in case.
+ sleep 1
+ am_has_slept=yes
+ done
test "$[2]" = conftest.file
)
then
@@ -821,45 +781,117 @@
AC_MSG_ERROR([newly created file is older than distributed files!
Check your system clock])
fi
-AC_MSG_RESULT(yes)])
+AC_MSG_RESULT([yes])
+# If we didn't sleep, we still need to ensure time stamps of config.status and
+# generated files are strictly newer.
+am_sleep_pid=
+if grep 'slept: no' conftest.file >/dev/null 2>&1; then
+ ( sleep 1 ) &
+ am_sleep_pid=$!
+fi
+AC_CONFIG_COMMANDS_PRE(
+ [AC_MSG_CHECKING([that generated files are newer than configure])
+ if test -n "$am_sleep_pid"; then
+ # Hide warnings about reused PIDs.
+ wait $am_sleep_pid 2>/dev/null
+ fi
+ AC_MSG_RESULT([done])])
+rm -f conftest.file
+])
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2009-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 1
+# AM_SILENT_RULES([DEFAULT])
+# --------------------------
+# Enable less verbose build rules; with the default set to DEFAULT
+# ("yes" being less verbose, "no" or empty being verbose).
+AC_DEFUN([AM_SILENT_RULES],
+[AC_ARG_ENABLE([silent-rules], [dnl
+AS_HELP_STRING(
+ [--enable-silent-rules],
+ [less verbose build output (undo: "make V=1")])
+AS_HELP_STRING(
+ [--disable-silent-rules],
+ [verbose build output (undo: "make V=0")])dnl
+])
+case $enable_silent_rules in @%:@ (((
+ yes) AM_DEFAULT_VERBOSITY=0;;
+ no) AM_DEFAULT_VERBOSITY=1;;
+ *) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
+esac
+dnl
+dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
+dnl do not support nested variable expansions.
+dnl See automake bug#9928 and bug#10237.
+am_make=${MAKE-make}
+AC_CACHE_CHECK([whether $am_make supports nested variables],
+ [am_cv_make_support_nested_variables],
+ [if AS_ECHO([['TRUE=$(BAR$(V))
+BAR0=false
+BAR1=true
+V=1
+am__doit:
+ @$(TRUE)
+.PHONY: am__doit']]) | $am_make -f - >/dev/null 2>&1; then
+ am_cv_make_support_nested_variables=yes
+else
+ am_cv_make_support_nested_variables=no
+fi])
+if test $am_cv_make_support_nested_variables = yes; then
+ dnl Using '$V' instead of '$(V)' breaks IRIX make.
+ AM_V='$(V)'
+ AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
+else
+ AM_V=$AM_DEFAULT_VERBOSITY
+ AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
+fi
+AC_SUBST([AM_V])dnl
+AM_SUBST_NOTMAKE([AM_V])dnl
+AC_SUBST([AM_DEFAULT_V])dnl
+AM_SUBST_NOTMAKE([AM_DEFAULT_V])dnl
+AC_SUBST([AM_DEFAULT_VERBOSITY])dnl
+AM_BACKSLASH='\'
+AC_SUBST([AM_BACKSLASH])dnl
+_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
+])
+
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
# AM_PROG_INSTALL_STRIP
# ---------------------
-# One issue with vendor `install' (even GNU) is that you can't
+# One issue with vendor 'install' (even GNU) is that you can't
# specify the program used to strip binaries. This is especially
# annoying in cross-compiling environments, where the build's strip
# is unlikely to handle the host's binaries.
# Fortunately install-sh will honor a STRIPPROG variable, so we
-# always use install-sh in `make install-strip', and initialize
+# always use install-sh in "make install-strip", and initialize
# STRIPPROG with the value of the STRIP variable (set by the user).
AC_DEFUN([AM_PROG_INSTALL_STRIP],
[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-# Installed binaries are usually stripped using `strip' when the user
-# run `make install-strip'. However `strip' might not be the right
+# Installed binaries are usually stripped using 'strip' when the user
+# run "make install-strip". However 'strip' might not be the right
# tool to use in cross-compilation environments, therefore Automake
-# will honor the `STRIP' environment variable to overrule this program.
-dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+# will honor the 'STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be 'maybe'.
if test "$cross_compiling" != no; then
AC_CHECK_TOOL([STRIP], [strip], :)
fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006, 2008, 2010 Free Software Foundation, Inc.
+# Copyright (C) 2006-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-
-# serial 3
# _AM_SUBST_NOTMAKE(VARIABLE)
# ---------------------------
@@ -874,18 +906,16 @@
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
+# Copyright (C) 2004-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 2
-
# _AM_PROG_TAR(FORMAT)
# --------------------
# Check how to create a tarball in format FORMAT.
-# FORMAT should be one of `v7', `ustar', or `pax'.
+# FORMAT should be one of 'v7', 'ustar', or 'pax'.
#
# Substitute a variable $(am__tar) that is a command
# writing to stdout a FORMAT-tarball containing the directory
@@ -895,76 +925,114 @@
# Substitute a variable $(am__untar) that extract such
# a tarball read from stdin.
# $(am__untar) < result.tar
+#
AC_DEFUN([_AM_PROG_TAR],
[# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AC_SUBST([AMTAR], ['$${TAR-tar}'])
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
- [m4_case([$1], [ustar],, [pax],,
- [m4_fatal([Unknown tar format])])
-AC_MSG_CHECKING([how to create a $1 tar archive])
-# Loop over all known methods to create a tar archive until one works.
+
+# We'll loop over all known methods to create a tar archive until one works.
_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-_am_tools=${am_cv_prog_tar_$1-$_am_tools}
-# Do not fold the above two line into one, because Tru64 sh and
-# Solaris sh will not grok spaces in the rhs of `-'.
-for _am_tool in $_am_tools
-do
- case $_am_tool in
- gnutar)
- for _am_tar in tar gnutar gtar;
- do
- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
+m4_if([$1], [v7],
+ [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
- # tar/untar a dummy directory, and stop if the command works
+ [m4_case([$1],
+ [ustar],
+ [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
+ # There is notably a 21 bits limit for the UID and the GID. In fact,
+ # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
+ # and bug#13588).
+ am_max_uid=2097151 # 2^21 - 1
+ am_max_gid=$am_max_uid
+ # The $UID and $GID variables are not portable, so we need to resort
+ # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
+ # below are definitely unexpected, so allow the users to see them
+ # (that is, avoid stderr redirection).
+ am_uid=`id -u || echo unknown`
+ am_gid=`id -g || echo unknown`
+ AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
+ if test $am_uid -le $am_max_uid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi
+ AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
+ if test $am_gid -le $am_max_gid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi],
+
+ [pax],
+ [],
+
+ [m4_fatal([Unknown tar format])])
+
+ AC_MSG_CHECKING([how to create a $1 tar archive])
+
+ # Go ahead even if we have the value already cached. We do so because we
+ # need to set the values for the 'am__tar' and 'am__untar' variables.
+ _am_tools=${am_cv_prog_tar_$1-$_am_tools}
+
+ for _am_tool in $_am_tools; do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar; do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ AM_RUN_LOG([cat conftest.dir/file])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+ done
rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
- rm -rf conftest.dir
- if test -s conftest.tar; then
- AM_RUN_LOG([$am__untar <conftest.tar])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
-done
-rm -rf conftest.dir
-AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
-AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+ AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+ AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+
AC_SUBST([am__tar])
AC_SUBST([am__untar])
]) # _AM_PROG_TAR
diff --git a/src/bond.c b/src/bond.c
index a348d61..ce255ca 100644
--- a/src/bond.c
+++ b/src/bond.c
@@ -35,6 +35,17 @@
return blist->bond[blist->n-1];
}
+
+ts_bool bond_vector(ts_bond *bond){
+
+ bond->x = bond->vtx1->x - bond->vtx2->x;
+ bond->y = bond->vtx1->y - bond->vtx2->y;
+ bond->z = bond->vtx1->z - bond->vtx2->z;
+
+ return TS_SUCCESS;
+}
+
+
ts_bool bond_list_free(ts_bond_list *blist){
ts_uint i;
for(i=0;i<blist->n;i++){
diff --git a/src/bond.h b/src/bond.h
index e2be586..34cdba5 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -20,6 +20,7 @@
*/
ts_bond *bond_add(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2);
+ts_bool bond_vector(ts_bond *bond);
ts_bool bond_list_free(ts_bond_list *blist);
diff --git a/src/frame.c b/src/frame.c
index d2d7e10..aeaef21 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -22,7 +22,7 @@
vtx[i]->y-=vesicle->cm[1];
vtx[i]->z-=vesicle->cm[2];
}
-
+//move polymers for the same vector as we moved vesicle
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
vesicle->poly_list->poly[i]->vlist->vtx[j]->x-=vesicle->cm[0];
@@ -30,22 +30,24 @@
vesicle->poly_list->poly[i]->vlist->vtx[j]->z-=vesicle->cm[2];
}
}
+//move filaments for the same vector as we moved vesicle
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->x-=vesicle->cm[0];
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->y-=vesicle->cm[1];
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->z-=vesicle->cm[2];
+ }
+ }
-
- vesicle->cm[0]=0;
- vesicle->cm[1]=0;
- vesicle->cm[2]=0;
+ vesicle->cm[0]=0.0;
+ vesicle->cm[1]=0.0;
+ vesicle->cm[2]=0.0;
return TS_SUCCESS;
}
ts_bool cell_occupation(ts_vesicle *vesicle){
ts_uint i,j,cellidx, n=vesicle->vlist->n;
- //ts_double shift;
- //ts_double dcell;
- //shift=(ts_double) vesicle->clist->ncmax[0]/2;
- //dcell=1.0/(1.0 + vesicle->stepsize);
- //`fprintf(stderr, "Bil sem tu\n");
cell_list_cell_occupation_clear(vesicle->clist);
for(i=0;i<n;i++){
@@ -56,17 +58,21 @@
cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->vlist->vtx[i]);
}
+//Add all polymers to cells
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
cellidx=vertex_self_avoidance(vesicle, vesicle->poly_list->poly[i]->vlist->vtx[j]);
cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->poly_list->poly[i]->vlist->vtx[j]);
}
}
+//Add all filaments to cells
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ cellidx=vertex_self_avoidance(vesicle, vesicle->filament_list->poly[i]->vlist->vtx[j]);
+ cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->filament_list->poly[i]->vlist->vtx[j]);
+ }
+ }
+
-
-
- //fprintf(stderr, "Bil sem tu\n");
- //if(dcell);
- //if(shift);
return TS_SUCCESS;
}
diff --git a/src/general.h b/src/general.h
index 3308faa..79da2ba 100644
--- a/src/general.h
+++ b/src/general.h
@@ -166,10 +166,11 @@
ts_uint idx;
ts_vertex *vtx1;
ts_vertex *vtx2;
- ts_double bond_length;
- ts_double bond_length_dual;
- ts_bool tainted;
+ ts_double bond_length;
+ ts_double bond_length_dual;
+ ts_bool tainted; //TODO: remove
ts_double energy;
+ ts_double x,y,z;
};
typedef struct ts_bond ts_bond;
@@ -256,11 +257,17 @@
ts_double cm[3];
ts_double volume;
ts_spharm *sphHarmonics;
-
+// Polymers outside the vesicle and attached to the vesicle membrane (polymer brush):
ts_poly_list *poly_list;
+// Filaments inside the vesicle (not attached to the vesicel membrane:
+ ts_poly_list *filament_list;
+
ts_double spring_constant;
ts_double pressure;
ts_int pswitch;
+
+ ts_double R_nucleus;
+
} ts_vesicle;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 7601f13..3c27e55 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -37,10 +37,42 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
ts_vesicle *vesicle;
+ ts_vertex *vtx;
+
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);
+ // Nucleus:
+ vesicle->R_nucleus=tape->R_nucleus;
+
+ //Initialize grafted polymers (brush):
+ vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
vesicle->spring_constant=tape->kspring;
poly_assign_spring_const(vesicle);
+
+ //Initialize filaments (polymers inside the vesicle):
+ vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
+ poly_assign_filament_xi(vesicle,tape);
+
+ ts_uint i,j;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
+ vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
+ }
+ }
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ }
+ }
+ }
+
+
+// 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 */
diff --git a/src/io.c b/src/io.c
index db4e64f..b222081 100644
--- a/src/io.c
+++ b/src/io.c
@@ -36,6 +36,8 @@
fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
/* dump poly list */
fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* dump filament list */
+ fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/*dump vertices*/
@@ -118,6 +120,43 @@
}
}
+
+ /*dump filamentes grandes svinjas */
+ for(i=0;i<vesicle->filament_list->n;i++){
+ fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ }
+
+ /* dump filamentes vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
+ fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* dump vtx1 and vtx2 offsets */
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
+// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+
+
/* pointer offsets for fixing the restored pointers */
/* need pointers for
vlist->vtx
@@ -180,6 +219,9 @@
/* restore poly list */
vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* restore filament list */
+ vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/* prerequisity. Bonds must be malloced before vertexes are recreated */
@@ -319,6 +361,61 @@
vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
retval=fread(&idx,sizeof(ts_uint),1,fh);
vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
+ }
+ }
+
+ /*restore filaments */
+ vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+
+ }
+
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
+ }
+
+ }
+ }
+
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
}
}
@@ -664,8 +761,8 @@
/* Here comes header of the file */
//find number of extra vtxs and bonds of polymeres
- ts_uint monono=0, polyno=0, poly_idx=0;
- ts_bool poly=0;
+ ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
+ ts_bool poly=0, fil=0;
if(vesicle->poly_list!=NULL){
if(vesicle->poly_list->poly[0]!=NULL){
polyno=vesicle->poly_list->n;
@@ -673,8 +770,17 @@
poly=1;
}
}
+
+ if(vesicle->filament_list!=NULL){
+ if(vesicle->filament_list->poly[0]!=NULL){
+ filno=vesicle->filament_list->n;
+ fonono=vesicle->filament_list->poly[0]->vlist->n;
+ fil=1;
+ }
+ }
+
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
@@ -684,6 +790,16 @@
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%u ", poly_idx);
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
fprintf(fh,"%u ", poly_idx);
}
}
@@ -698,6 +814,14 @@
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
}
}
}
@@ -720,14 +844,26 @@
}
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
+// fprintf(stderr,"was here\n");
+
+ }
+ }
+
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno;i++){
+ for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
fprintf(fh,"3 ");
}
@@ -797,11 +933,15 @@
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_INT("nfil",&tape->nfil),
+ CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ 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("xi",&tape->xi),
CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
CFG_SIMPLE_INT("nymax", &tape->ncymax),
diff --git a/src/io.h b/src/io.h
index eb0b737..bfc6173 100644
--- a/src/io.h
+++ b/src/io.h
@@ -16,6 +16,9 @@
long int nczmax;
long int npoly;
long int nmono;
+ long int nfil;
+ long int nfono;
+ long int R_nucleus;
long int pswitch;
char *multiprocessing;
long int brezveze0;
@@ -25,6 +28,7 @@
ts_double dmax;
ts_double stepsize;
ts_double kspring;
+ ts_double xi;
ts_double pressure;
long int iterations;
long int inititer;
diff --git a/src/main.c b/src/main.c
index e9685fc..588e277 100644
--- a/src/main.c
+++ b/src/main.c
@@ -47,6 +47,7 @@
vtx_set_global_values(vesicle);
vesicle->pressure=tape->pressure;
vesicle->dmax=tape->dmax*tape->dmax;
+ poly_assign_filament_xi(vesicle,tape);
if(command_line_args.reset_iteration_count) start_iteration=tape->inititer-1;
else start_iteration++;
diff --git a/src/poly.c b/src/poly.c
index 2057db1..5cfc6e0 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -6,6 +6,17 @@
#include<math.h>
#include"energy.h"
+ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
+ ts_uint i;
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]->k = tape->xi;
+ }
+
+ return TS_SUCCESS;
+}
+
+
ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
ts_uint i;
@@ -20,8 +31,10 @@
ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly));
poly->vlist = init_vertex_list(n);
poly->blist = init_bond_list();
- poly->grafted_vtx = grafted_vtx;
- grafted_vtx->grafted_poly = poly;
+ if (grafted_vtx!=NULL){
+ poly->grafted_vtx = grafted_vtx;
+ grafted_vtx->grafted_poly = poly;
+ }
ts_uint i;
for(i=0;i<n-1;i++){
@@ -38,45 +51,72 @@
}
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
ts_uint i=0,j=0; //idx;
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
+ ts_double dphi,dh;
+ ts_uint ji;
- if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
+ // Grafting polymers:
+ if (vlist!=NULL){
+ if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
- while(i<n_poly){
- gvtxi = rand() % vlist->n;
- if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
- i++;
+ while(i<n_poly){
+ gvtxi = rand() % vlist->n;
+ if (vlist->vtx[gvtxi]->grafted_poly == NULL){
+ poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
+ i++;
+ }
}
}
-
+ else
+ {
+ for(i=0;i<n_poly;i++){
+ poly_list->poly[i] = init_poly(n_mono, NULL);
+ }
+ }
+
poly_list->n = n_poly;
-/* Make straight poylmers normal to membrane. Dist. between poly vertices put to 1*/
- for (i=0;i<poly_list->n;i++){
+ if (vlist!=NULL){
+ /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ for (i=0;i<poly_list->n;i++){
+
+ xnorm=0.0;
+ ynorm=0.0;
+ znorm=0.0;
+ for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
+ xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
+ ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
+ znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ }
+ normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ xnorm=xnorm/normlength;
+ ynorm=ynorm/normlength;
+ znorm=znorm/normlength;
- xnorm=0.0;
- ynorm=0.0;
- znorm=0.0;
- for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
- xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
- ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
- znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
+ poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
+ poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ }
}
- normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
- xnorm=xnorm/normlength;
- ynorm=ynorm/normlength;
- znorm=znorm/normlength;
-
- for (j=0;j<poly_list->poly[i]->vlist->n;j++){
- poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ }
+ else
+ {
+ /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
+ dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ for(i=0;i<poly_list->n;i++){
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ ji = j + i*poly_list->poly[i]->vlist->n;
+ poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->z = ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
+ }
}
}
diff --git a/src/poly.h b/src/poly.h
index 9bdec52..26dd444 100644
--- a/src/poly.h
+++ b/src/poly.h
@@ -1,11 +1,12 @@
#ifndef _POLY_H
#define _POLY_H
+#include"io.h"
#include"general.h"
ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx);
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist);
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle);
ts_bool poly_free(ts_poly *poly);
@@ -13,4 +14,6 @@
ts_bool poly_assign_spring_const(ts_vesicle *vesicle);
+ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape);
+
#endif
diff --git a/src/tape b/src/tape
index 4254270..bd62b6c 100644
--- a/src/tape
+++ b/src/tape
@@ -14,13 +14,25 @@
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
pressure=0.1
-####### Polymer definitions ###########
+####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=300
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
k_spring=800
+
+####### Filament (inside the vesicle) definitions ###########
+# nfil is a number of filaments inside the vesicle
+nfil=1
+# nfono is a number of monomers in each filament
+nfono=300
+# Persistence lenght of the filaments (in units l_min)
+xi=100
+
+####### Nucleus (inside the vesicle) ###########
+# Radius of an impenetrable hard sphere inside the vesicle
+R_nucleus=5
####### Cell definitions ############
nxmax=60
@@ -32,7 +44,7 @@
#how many MC sweeps between subsequent records of states to disk
mcsweeps=500
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
-inititer=1
+inititer=0
#how many records do you want on the disk iteration are there in a run?
iterations=20
diff --git a/src/timestep.c b/src/timestep.c
index 92a4a25..d631d42 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -23,7 +23,7 @@
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){
+ if(i>=inititer){
write_vertex_xml_file(vesicle,i-inititer);
}
}
@@ -56,15 +56,25 @@
}
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- rnvec[0]=drand48();
- rnvec[1]=drand48();
- rnvec[2]=drand48();
- retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ rnvec[0]=drand48();
+ rnvec[1]=drand48();
+ rnvec[2]=drand48();
+ retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
+ }
}
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ rnvec[0]=drand48();
+ rnvec[1]=drand48();
+ rnvec[2]=drand48();
+ retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
+ }
}
+
// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
if(retval);
return TS_SUCCESS;
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 7f6391f..da8e70f 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -254,3 +254,116 @@
//END MONTE CARLOOOOOOO
return TS_SUCCESS;
}
+
+
+
+
+ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+ ts_uint i;
+ ts_bool retval;
+ ts_uint cellidx;
+ ts_double delta_energy;
+ ts_double costheta,sintheta,phi,r;
+ ts_double dist[2];
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx,backupneigh[2];
+ ts_bond backupbond[2];
+
+ //backup vertex:
+ memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->bond_no;i++){
+ dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
+ if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+
+ //self avoidance check with distant vertices
+ cellidx=vertex_self_avoidance(vesicle, vtx);
+ //check occupation number
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
+ if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+ //backup bonds
+ for(i=0;i<vtx->bond_no;i++){
+ memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
+ vtx->bond[i]->bond_length=sqrt(dist[i]);
+ bond_vector(vtx->bond[i]);
+ }
+
+ //backup neighboring vertices:
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
+ }
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ delta_energy=0;
+
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ delta_energy += vtx->energy - backupvtx.energy;
+ }
+
+ for(i=0;i<vtx->neigh_no;i++){
+ if(vtx->neigh[i]->bond_no == 2){
+ vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
+ delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
+ }
+ }
+
+ // poly->k is filament persistence length (in units l_min)
+ delta_energy *= poly->k;
+
+ 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
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->bond_no;i++){
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ }
+
+ return TS_FAIL;
+ }
+ }
+
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ if(vtx->cell!=vesicle->clist->cell[cellidx]){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
+ }
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
+ return TS_SUCCESS;
+}
diff --git a/src/vertexmove.h b/src/vertexmove.h
index 6387ab8..c58ee64 100644
--- a/src/vertexmove.h
+++ b/src/vertexmove.h
@@ -2,3 +2,5 @@
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn);
ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn);
+
+ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn);
--
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