From 4019ca8157136a68b6e43b31f166dc93acd81b4d Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 08 Feb 2019 08:14:57 +0000
Subject: [PATCH] Merge branch 'stretching-devel' into plane-new
---
src/io.c | 24 ++++
src/tape | 7 +
src/bondflip.c | 11 ++
config.guess | 137 +++++++++++---------------
src/energy.c | 4
src/initial_distribution.c | 2
src/general.h | 4
config.sub | 38 ++-----
src/restore.c | 10 +
src/energy.h | 2
src/vertexmove.c | 24 ++++
README.md | 5 +
12 files changed, 155 insertions(+), 113 deletions(-)
diff --git a/README.md b/README.md
index df6a955..4e76d54 100644
--- a/README.md
+++ b/README.md
@@ -63,3 +63,8 @@
THis line seemed to fixed everything:
libtoolize --force
+
+
+======= STATICALLY LINKING ==============
+./configure --enable-static LDFLAGS=-static
+
diff --git a/config.guess b/config.guess
index 2e9ad7f..1659250 100755
--- a/config.guess
+++ b/config.guess
@@ -1,8 +1,8 @@
#! /bin/sh
# Attempt to guess a canonical system name.
-# Copyright 1992-2016 Free Software Foundation, Inc.
+# Copyright 1992-2015 Free Software Foundation, Inc.
-timestamp='2016-10-02'
+timestamp='2015-08-20'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -27,7 +27,7 @@
# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
#
# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
#
# Please send patches to <config-patches@gnu.org>.
@@ -50,7 +50,7 @@
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright 1992-2016 Free Software Foundation, Inc.
+Copyright 1992-2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -186,12 +186,9 @@
*) machine=${UNAME_MACHINE_ARCH}-unknown ;;
esac
# The Operating System including object format, if it has switched
- # to ELF recently (or will in the future) and ABI.
+ # to ELF recently, or will in the future.
case "${UNAME_MACHINE_ARCH}" in
- earm*)
- os=netbsdelf
- ;;
- arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ arm*|earm*|i386|m68k|ns32k|sh3*|sparc|vax)
eval $set_cc_for_build
if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ELF__
@@ -240,10 +237,6 @@
UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
exit ;;
- *:LibertyBSD:*:*)
- UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'`
- echo ${UNAME_MACHINE_ARCH}-unknown-libertybsd${UNAME_RELEASE}
- exit ;;
*:ekkoBSD:*:*)
echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
exit ;;
@@ -275,42 +268,42 @@
ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
case "$ALPHA_CPU_TYPE" in
"EV4 (21064)")
- UNAME_MACHINE=alpha ;;
+ UNAME_MACHINE="alpha" ;;
"EV4.5 (21064)")
- UNAME_MACHINE=alpha ;;
+ UNAME_MACHINE="alpha" ;;
"LCA4 (21066/21068)")
- UNAME_MACHINE=alpha ;;
+ UNAME_MACHINE="alpha" ;;
"EV5 (21164)")
- UNAME_MACHINE=alphaev5 ;;
+ UNAME_MACHINE="alphaev5" ;;
"EV5.6 (21164A)")
- UNAME_MACHINE=alphaev56 ;;
+ UNAME_MACHINE="alphaev56" ;;
"EV5.6 (21164PC)")
- UNAME_MACHINE=alphapca56 ;;
+ UNAME_MACHINE="alphapca56" ;;
"EV5.7 (21164PC)")
- UNAME_MACHINE=alphapca57 ;;
+ UNAME_MACHINE="alphapca57" ;;
"EV6 (21264)")
- UNAME_MACHINE=alphaev6 ;;
+ UNAME_MACHINE="alphaev6" ;;
"EV6.7 (21264A)")
- UNAME_MACHINE=alphaev67 ;;
+ UNAME_MACHINE="alphaev67" ;;
"EV6.8CB (21264C)")
- UNAME_MACHINE=alphaev68 ;;
+ UNAME_MACHINE="alphaev68" ;;
"EV6.8AL (21264B)")
- UNAME_MACHINE=alphaev68 ;;
+ UNAME_MACHINE="alphaev68" ;;
"EV6.8CX (21264D)")
- UNAME_MACHINE=alphaev68 ;;
+ UNAME_MACHINE="alphaev68" ;;
"EV6.9A (21264/EV69A)")
- UNAME_MACHINE=alphaev69 ;;
+ UNAME_MACHINE="alphaev69" ;;
"EV7 (21364)")
- UNAME_MACHINE=alphaev7 ;;
+ UNAME_MACHINE="alphaev7" ;;
"EV7.9 (21364A)")
- UNAME_MACHINE=alphaev79 ;;
+ UNAME_MACHINE="alphaev79" ;;
esac
# A Pn.n version is a patched version.
# A Vn.n version is a released version.
# A Tn.n version is a released field test version.
# A Xn.n version is an unreleased experimental baselevel.
# 1.2 uses "1.2" for uname -r.
- echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
# Reset EXIT trap before exiting to avoid spurious non-zero exit code.
exitcode=$?
trap '' 0
@@ -383,16 +376,16 @@
exit ;;
i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
eval $set_cc_for_build
- SUN_ARCH=i386
+ SUN_ARCH="i386"
# If there is a compiler, see if it is configured for 64-bit objects.
# Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
# This test works for both compilers.
- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_64BIT_ARCH >/dev/null
then
- SUN_ARCH=x86_64
+ SUN_ARCH="x86_64"
fi
fi
echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
@@ -417,7 +410,7 @@
exit ;;
sun*:*:4.2BSD:*)
UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
- test "x${UNAME_RELEASE}" = x && UNAME_RELEASE=3
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
case "`/bin/arch`" in
sun3)
echo m68k-sun-sunos${UNAME_RELEASE}
@@ -642,13 +635,13 @@
sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
case "${sc_cpu_version}" in
- 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0
- 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
532) # CPU_PA_RISC2_0
case "${sc_kernel_bits}" in
- 32) HP_ARCH=hppa2.0n ;;
- 64) HP_ARCH=hppa2.0w ;;
- '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
esac ;;
esac
fi
@@ -687,11 +680,11 @@
exit (0);
}
EOF
- (CCOPTS="" $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
test -z "$HP_ARCH" && HP_ARCH=hppa
fi ;;
esac
- if [ ${HP_ARCH} = hppa2.0w ]
+ if [ ${HP_ARCH} = "hppa2.0w" ]
then
eval $set_cc_for_build
@@ -704,12 +697,12 @@
# $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
# => hppa64-hp-hpux11.23
- if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) |
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
grep -q __LP64__
then
- HP_ARCH=hppa2.0w
+ HP_ARCH="hppa2.0w"
else
- HP_ARCH=hppa64
+ HP_ARCH="hppa64"
fi
fi
echo ${HP_ARCH}-hp-hpux${HPUX_REV}
@@ -814,14 +807,14 @@
echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
exit ;;
F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
- FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
5000:UNIX_System_V:4.*:*)
- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
@@ -903,7 +896,7 @@
exit ;;
*:GNU/*:*:*)
# other systems with GNU libc and userland
- echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
exit ;;
i*86:Minix:*:*)
echo ${UNAME_MACHINE}-pc-minix
@@ -926,7 +919,7 @@
EV68*) UNAME_MACHINE=alphaev68 ;;
esac
objdump --private-headers /bin/sh | grep -q ld.so.1
- if test "$?" = 0 ; then LIBC=gnulibc1 ; fi
+ if test "$?" = 0 ; then LIBC="gnulibc1" ; fi
echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
arc:Linux:*:* | arceb:Linux:*:*)
@@ -972,9 +965,6 @@
ia64:Linux:*:*)
echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
- k1om:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
- exit ;;
m32r*:Linux:*:*)
echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
@@ -1000,9 +990,6 @@
eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
;;
- mips64el:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
- exit ;;
openrisc*:Linux:*:*)
echo or1k-unknown-linux-${LIBC}
exit ;;
@@ -1034,9 +1021,6 @@
exit ;;
ppcle:Linux:*:*)
echo powerpcle-unknown-linux-${LIBC}
- exit ;;
- riscv32:Linux:*:* | riscv64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
@@ -1136,7 +1120,7 @@
# uname -m prints for DJGPP always 'pc', but it prints nothing about
# the processor, so we play safe by assuming i586.
# Note: whatever this is, it MUST be the same as what config.sub
- # prints for the "djgpp" host, or else GDB configure will decide that
+ # prints for the "djgpp" host, or else GDB configury will decide that
# this is a cross-build.
echo i586-pc-msdosdjgpp
exit ;;
@@ -1285,9 +1269,6 @@
SX-8R:SUPER-UX:*:*)
echo sx8r-nec-superux${UNAME_RELEASE}
exit ;;
- SX-ACE:SUPER-UX:*:*)
- echo sxace-nec-superux${UNAME_RELEASE}
- exit ;;
Power*:Rhapsody:*:*)
echo powerpc-apple-rhapsody${UNAME_RELEASE}
exit ;;
@@ -1301,9 +1282,9 @@
UNAME_PROCESSOR=powerpc
fi
if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then
- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_64BIT_ARCH >/dev/null
then
case $UNAME_PROCESSOR in
@@ -1325,7 +1306,7 @@
exit ;;
*:procnto*:*:* | *:QNX:[0123456789]*:*)
UNAME_PROCESSOR=`uname -p`
- if test "$UNAME_PROCESSOR" = x86; then
+ if test "$UNAME_PROCESSOR" = "x86"; then
UNAME_PROCESSOR=i386
UNAME_MACHINE=pc
fi
@@ -1356,7 +1337,7 @@
# "uname -m" is not consistent, so use $cputype instead. 386
# is converted to i386 for consistency with other x86
# operating systems.
- if test "$cputype" = 386; then
+ if test "$cputype" = "386"; then
UNAME_MACHINE=i386
else
UNAME_MACHINE="$cputype"
@@ -1398,7 +1379,7 @@
echo i386-pc-xenix
exit ;;
i*86:skyos:*:*)
- echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE} | sed -e 's/ .*$//'`
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
exit ;;
i*86:rdos:*:*)
echo ${UNAME_MACHINE}-pc-rdos
@@ -1409,25 +1390,23 @@
x86_64:VMkernel:*:*)
echo ${UNAME_MACHINE}-unknown-esx
exit ;;
- amd64:Isilon\ OneFS:*:*)
- echo x86_64-unknown-onefs
- exit ;;
esac
cat >&2 <<EOF
$0: unable to guess system type
-This script (version $timestamp), has failed to recognize the
-operating system you are using. If your script is old, overwrite
-config.guess and config.sub with the latest versions from:
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
-If $0 has already been updated, send the following data and any
-information you think might be pertinent to config-patches@gnu.org to
-provide the necessary information to handle your system.
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches@gnu.org> in order to provide the needed
+information to handle your system.
config.guess timestamp = $timestamp
diff --git a/config.sub b/config.sub
index dd2ca93..1acc966 100755
--- a/config.sub
+++ b/config.sub
@@ -1,8 +1,8 @@
#! /bin/sh
# Configuration validation subroutine script.
-# Copyright 1992-2016 Free Software Foundation, Inc.
+# Copyright 1992-2015 Free Software Foundation, Inc.
-timestamp='2016-11-04'
+timestamp='2015-08-20'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -33,7 +33,7 @@
# Otherwise, we print the canonical config type on stdout and succeed.
# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
# This file is supposed to be the same for all GNU packages
# and recognize all the CPU types, system types and aliases
@@ -53,7 +53,8 @@
me=`echo "$0" | sed -e 's,.*/,,'`
usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
Canonicalize a configuration name.
@@ -67,7 +68,7 @@
version="\
GNU config.sub ($timestamp)
-Copyright 1992-2016 Free Software Foundation, Inc.
+Copyright 1992-2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -117,7 +118,7 @@
nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
knetbsd*-gnu* | netbsd*-gnu* | netbsd*-eabi* | \
- kopensolaris*-gnu* | cloudabi*-eabi* | \
+ kopensolaris*-gnu* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
@@ -301,7 +302,6 @@
| open8 | or1k | or1knd | or32 \
| pdp10 | pdp11 | pj | pjl \
| powerpc | powerpc64 | powerpc64le | powerpcle \
- | pru \
| pyramid \
| riscv32 | riscv64 \
| rl78 | rx \
@@ -429,7 +429,6 @@
| orion-* \
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
- | pru-* \
| pyramid-* \
| riscv32-* | riscv64-* \
| rl78-* | romp-* | rs6000-* | rx-* \
@@ -522,7 +521,7 @@
basic_machine=i386-pc
os=-aros
;;
- asmjs)
+ asmjs)
basic_machine=asmjs-unknown
;;
aux)
@@ -644,14 +643,6 @@
dpx2* | dpx2*-bull)
basic_machine=m68k-bull
os=-sysv3
- ;;
- e500v[12])
- basic_machine=powerpc-unknown
- os=$os"spe"
- ;;
- e500v[12]-*)
- basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
- os=$os"spe"
;;
ebmon29k)
basic_machine=a29k-amd
@@ -1032,7 +1023,7 @@
ppc-* | ppcbe-*)
basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
- ppcle | powerpclittle)
+ ppcle | powerpclittle | ppc-le | powerpc-little)
basic_machine=powerpcle-unknown
;;
ppcle-* | powerpclittle-*)
@@ -1042,7 +1033,7 @@
;;
ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
- ppc64le | powerpc64little)
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
basic_machine=powerpc64le-unknown
;;
ppc64le-* | powerpc64little-*)
@@ -1392,14 +1383,14 @@
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
| -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
- | -bitrig* | -openbsd* | -solidbsd* | -libertybsd* \
+ | -bitrig* | -openbsd* | -solidbsd* \
| -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
| -chorusos* | -chorusrdb* | -cegcc* \
| -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -midipix* | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
+ | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
| -linux-newlib* | -linux-musl* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* | -moxiebox* \
| -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
@@ -1408,8 +1399,7 @@
| -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
| -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
| -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* \
- | -onefs* | -tirtos* | -phoenix* | -fuchsia*)
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* | -tirtos*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-qnx*)
@@ -1540,8 +1530,6 @@
os=-dicos
;;
-nacl*)
- ;;
- -ios)
;;
-none)
;;
diff --git a/src/bondflip.c b/src/bondflip.c
index 66c40f7..13ec263 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -176,7 +176,6 @@
/* vesicle_volume(vesicle);
fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
*/
-
/* fix data structure for flipped bond */
ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1, vesicle->tape->w);
@@ -189,6 +188,12 @@
delta_energy+=it->xk* it->energy;
delta_energy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
//Neigbours of k, it, km, kp don't change its energy.
+ if(vesicle->tape->stretchswitch==1){
+ oldenergy+=lm->energy+lp->energy;
+ stretchenergy(vesicle,lm);
+ stretchenergy(vesicle,lp);
+ delta_energy+=lm->energy+lp->energy;
+ }
delta_energy-=oldenergy;
if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
@@ -334,6 +339,10 @@
// fprintf(stderr,"Restoration complete!!!\n");
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
+ if(vesicle->tape->stretchswitch==1){
+ stretchenergy(vesicle,lm);
+ stretchenergy(vesicle,lp);
+ }
return TS_FAIL;
}
diff --git a/src/energy.c b/src/energy.c
index 4d27995..1dae415 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -238,3 +238,7 @@
return vesicle->tape->F*ddp;
}
+
+void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle){
+ triangle->energy=vesicle->tape->xkA0/2.0*pow((triangle->area/vesicle->tlist->a0-1.0),2);
+}
diff --git a/src/energy.h b/src/energy.h
index 1b97fa9..9d1f47c 100644
--- a/src/energy.h
+++ b/src/energy.h
@@ -8,4 +8,6 @@
ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle);
inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w);
ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old);
+
+void stretchenergy(ts_vesicle *vesicle, ts_triangle *triangle);
#endif
diff --git a/src/general.h b/src/general.h
index c530a68..c9cc537 100644
--- a/src/general.h
+++ b/src/general.h
@@ -195,11 +195,13 @@
ts_double znorm;
ts_double area; // firstly needed for sh.c
ts_double volume; // firstly needed for sh.c
+ ts_double energy;
};
typedef struct ts_triangle ts_triangle;
struct ts_triangle_list{
ts_uint n;
+ ts_double a0;
ts_triangle **tria;
};
typedef struct ts_triangle_list ts_triangle_list;
@@ -273,6 +275,8 @@
long int pswitch;
long int constvolswitch;
long int constareaswitch;
+ long int stretchswitch;
+ ts_double xkA0;
ts_double constvolprecision;
char *multiprocessing;
long int brezveze0;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 0274038..4956900 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -112,7 +112,7 @@
vesicle->sphHarmonics=NULL;
}
-
+ vesicle->tlist->a0=sqrt(3)/4*pow((vesicle->tape->dmax+1.0)/2.0,2);
return TS_SUCCESS;
}
diff --git a/src/io.c b/src/io.c
index c6a35cb..943d96b 100644
--- a/src/io.c
+++ b/src/io.c
@@ -826,6 +826,7 @@
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
+ //ts_double senergy=0.0;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -974,9 +975,26 @@
}
fprintf(fh,"</DataArray>\n");
-
- fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
+ fprintf(fh,"</PointData>\n<CellData>\n");
+
+ if(vesicle->tape->stretchswitch==1){
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
+ for(i=0;i<blist->n;i++){
+ fprintf(fh, "0.0 ");
+ }
+ for(i=0;i<monono*polyno+filno*(fonono-1);i++){
+ fprintf(fh,"0.0 ");
+ }
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
+ }
+ fprintf(fh,"</DataArray>\n");
+ }
+
+
+
+ fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
@@ -1165,6 +1183,8 @@
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
+ CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
+ CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
diff --git a/src/restore.c b/src/restore.c
index c89ff6d..989a87b 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -16,13 +16,14 @@
#include "poly.h"
#include "initial_distribution.h"
#include "io.h"
+#include <math.h>
ts_vesicle *parseDump(char *dumpfname) {
xmlDocPtr doc;
xmlNodePtr cur, cur1,cur2;
ts_vesicle *vesicle=NULL;
doc = xmlParseFile(dumpfname);
-
+ int i;
if (doc == NULL ) {
fatal("Dump file could not be found or parsed. It is correct file?",1);
}
@@ -86,7 +87,12 @@
init_normal_vectors(vesicle->tlist);
mean_curvature_and_energy(vesicle);
sweep_attraction_bond_energy(vesicle);
-
+ if(vesicle->tape->stretchswitch==1){
+ vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2);
+ for(i=0;i<vesicle->tlist->n;i++){
+ stretchenergy(vesicle, vesicle->tlist->tria[i]);
+ }
+ }
/* TODO: filaments */
// ts_fprintf(stdout,"Restoration completed\n");
diff --git a/src/tape b/src/tape
index 9d7363b..5e1be37 100644
--- a/src/tape
+++ b/src/tape
@@ -23,6 +23,11 @@
#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
constareaswitch=0
+
+#Stretching
+stretchswitch=1
+xkA0=1.0
+
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=0
@@ -56,7 +61,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=2000
+mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=0
diff --git a/src/vertexmove.c b/src/vertexmove.c
index eec552e..e74fa74 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -21,7 +21,7 @@
ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
@@ -121,7 +121,10 @@
for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
}
-
+ //stretching energy 1 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
+ }
delta_energy=0;
@@ -200,6 +203,17 @@
}
/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
+
+ //stretching energy 2 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle, vtx->tristar[i]);
+ dstretchenergy+=vtx->tristar[i]->energy;
+ }
+ }
+
+ delta_energy+=dstretchenergy;
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -246,6 +260,12 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //stretching energy 3 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle,vtx->tristar[i]);
+ }
+ }
// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
if(vesicle->tape->constvolswitch == 1){
--
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