From 37791bf67add4094040a9b8706450695805bf88f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 20 May 2016 18:35:21 +0000
Subject: [PATCH] Minimal changes to trisurf core to permit the trout rbc simulations with eliptical nucleus (optional parameters in tape R_nucleusX, R_nucleusY and R_nucleusZ) were added
---
python/tape | 2
src/io.c | 3
src/tape | 16 +-
src/neigh_test.c | 65 +++++++++
src/initial_distribution.c | 4
aclocal.m4 | 287 ++++++++++++-----------------------------
src/general.h | 6
src/vertexmove.c | 9 +
8 files changed, 180 insertions(+), 212 deletions(-)
diff --git a/aclocal.m4 b/aclocal.m4
index 9ecb44e..da47901 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.15 -*- Autoconf -*-
+# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
-# Copyright (C) 1996-2014 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,
@@ -20,63 +20,32 @@
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'.])])
-dnl pkg.m4 - Macros to locate and utilise pkg-config. -*- Autoconf -*-
-dnl serial 11 (pkg-config-0.29.1)
-dnl
-dnl Copyright © 2004 Scott James Remnant <scott@netsplit.com>.
-dnl Copyright © 2012-2015 Dan Nicholson <dbn.lists@gmail.com>
-dnl
-dnl This program is free software; you can redistribute it and/or modify
-dnl it under the terms of the GNU General Public License as published by
-dnl the Free Software Foundation; either version 2 of the License, or
-dnl (at your option) any later version.
-dnl
-dnl This program is distributed in the hope that it will be useful, but
-dnl WITHOUT ANY WARRANTY; without even the implied warranty of
-dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-dnl General Public License for more details.
-dnl
-dnl You should have received a copy of the GNU General Public License
-dnl along with this program; if not, write to the Free Software
-dnl Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-dnl 02111-1307, USA.
-dnl
-dnl As a special exception to the GNU General Public License, if you
-dnl distribute this file as part of a program that contains a
-dnl configuration script generated by Autoconf, you may include it under
-dnl the same distribution terms that you use for the rest of that
-dnl program.
+# pkg.m4 - Macros to locate and utilise pkg-config. -*- Autoconf -*-
+# serial 1 (pkg-config-0.24)
+#
+# Copyright © 2004 Scott James Remnant <scott@netsplit.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
-dnl PKG_PREREQ(MIN-VERSION)
-dnl -----------------------
-dnl Since: 0.29
-dnl
-dnl Verify that the version of the pkg-config macros are at least
-dnl MIN-VERSION. Unlike PKG_PROG_PKG_CONFIG, which checks the user's
-dnl installed version of pkg-config, this checks the developer's version
-dnl of pkg.m4 when generating configure.
-dnl
-dnl To ensure that this macro is defined, also add:
-dnl m4_ifndef([PKG_PREREQ],
-dnl [m4_fatal([must install pkg-config 0.29 or later before running autoconf/autogen])])
-dnl
-dnl See the "Since" comment for each macro you use to see what version
-dnl of the macros you require.
-m4_defun([PKG_PREREQ],
-[m4_define([PKG_MACROS_VERSION], [0.29.1])
-m4_if(m4_version_compare(PKG_MACROS_VERSION, [$1]), -1,
- [m4_fatal([pkg.m4 version $1 or higher is required but ]PKG_MACROS_VERSION[ found])])
-])dnl PKG_PREREQ
-
-dnl PKG_PROG_PKG_CONFIG([MIN-VERSION])
-dnl ----------------------------------
-dnl Since: 0.16
-dnl
-dnl Search for the pkg-config tool and set the PKG_CONFIG variable to
-dnl first found in the path. Checks that the version of pkg-config found
-dnl is at least MIN-VERSION. If MIN-VERSION is not specified, 0.9.0 is
-dnl used since that's the first version where most current features of
-dnl pkg-config existed.
+# PKG_PROG_PKG_CONFIG([MIN-VERSION])
+# ----------------------------------
AC_DEFUN([PKG_PROG_PKG_CONFIG],
[m4_pattern_forbid([^_?PKG_[A-Z_]+$])
m4_pattern_allow([^PKG_CONFIG(_(PATH|LIBDIR|SYSROOT_DIR|ALLOW_SYSTEM_(CFLAGS|LIBS)))?$])
@@ -98,19 +67,18 @@
PKG_CONFIG=""
fi
fi[]dnl
-])dnl PKG_PROG_PKG_CONFIG
+])# PKG_PROG_PKG_CONFIG
-dnl PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
-dnl -------------------------------------------------------------------
-dnl Since: 0.18
-dnl
-dnl Check to see whether a particular set of modules exists. Similar to
-dnl PKG_CHECK_MODULES(), but does not set variables or print errors.
-dnl
-dnl Please remember that m4 expands AC_REQUIRE([PKG_PROG_PKG_CONFIG])
-dnl only at the first occurence in configure.ac, so if the first place
-dnl it's called might be skipped (such as if it is within an "if", you
-dnl have to call PKG_CHECK_EXISTS manually
+# PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
+#
+# Check to see whether a particular set of modules exists. Similar
+# to PKG_CHECK_MODULES(), but does not set variables or print errors.
+#
+# Please remember that m4 expands AC_REQUIRE([PKG_PROG_PKG_CONFIG])
+# only at the first occurence in configure.ac, so if the first place
+# it's called might be skipped (such as if it is within an "if", you
+# have to call PKG_CHECK_EXISTS manually
+# --------------------------------------------------------------
AC_DEFUN([PKG_CHECK_EXISTS],
[AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl
if test -n "$PKG_CONFIG" && \
@@ -120,10 +88,8 @@
$3])dnl
fi])
-dnl _PKG_CONFIG([VARIABLE], [COMMAND], [MODULES])
-dnl ---------------------------------------------
-dnl Internal wrapper calling pkg-config via PKG_CONFIG and setting
-dnl pkg_failed based on the result.
+# _PKG_CONFIG([VARIABLE], [COMMAND], [MODULES])
+# ---------------------------------------------
m4_define([_PKG_CONFIG],
[if test -n "$$1"; then
pkg_cv_[]$1="$$1"
@@ -135,11 +101,10 @@
else
pkg_failed=untried
fi[]dnl
-])dnl _PKG_CONFIG
+])# _PKG_CONFIG
-dnl _PKG_SHORT_ERRORS_SUPPORTED
-dnl ---------------------------
-dnl Internal check to see if pkg-config supports short errors.
+# _PKG_SHORT_ERRORS_SUPPORTED
+# -----------------------------
AC_DEFUN([_PKG_SHORT_ERRORS_SUPPORTED],
[AC_REQUIRE([PKG_PROG_PKG_CONFIG])
if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then
@@ -147,17 +112,19 @@
else
_pkg_short_errors_supported=no
fi[]dnl
-])dnl _PKG_SHORT_ERRORS_SUPPORTED
+])# _PKG_SHORT_ERRORS_SUPPORTED
-dnl PKG_CHECK_MODULES(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND],
-dnl [ACTION-IF-NOT-FOUND])
-dnl --------------------------------------------------------------
-dnl Since: 0.4.0
-dnl
-dnl Note that if there is a possibility the first call to
-dnl PKG_CHECK_MODULES might not happen, you should be sure to include an
-dnl explicit call to PKG_PROG_PKG_CONFIG in your configure.ac
+# PKG_CHECK_MODULES(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND],
+# [ACTION-IF-NOT-FOUND])
+#
+#
+# Note that if there is a possibility the first call to
+# PKG_CHECK_MODULES might not happen, you should be sure to include an
+# explicit call to PKG_PROG_PKG_CONFIG in your configure.ac
+#
+#
+# --------------------------------------------------------------
AC_DEFUN([PKG_CHECK_MODULES],
[AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl
AC_ARG_VAR([$1][_CFLAGS], [C compiler flags for $1, overriding pkg-config])dnl
@@ -211,92 +178,9 @@
AC_MSG_RESULT([yes])
$3
fi[]dnl
-])dnl PKG_CHECK_MODULES
+])# PKG_CHECK_MODULES
-
-dnl PKG_CHECK_MODULES_STATIC(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND],
-dnl [ACTION-IF-NOT-FOUND])
-dnl ---------------------------------------------------------------------
-dnl Since: 0.29
-dnl
-dnl Checks for existence of MODULES and gathers its build flags with
-dnl static libraries enabled. Sets VARIABLE-PREFIX_CFLAGS from --cflags
-dnl and VARIABLE-PREFIX_LIBS from --libs.
-dnl
-dnl Note that if there is a possibility the first call to
-dnl PKG_CHECK_MODULES_STATIC might not happen, you should be sure to
-dnl include an explicit call to PKG_PROG_PKG_CONFIG in your
-dnl configure.ac.
-AC_DEFUN([PKG_CHECK_MODULES_STATIC],
-[AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl
-_save_PKG_CONFIG=$PKG_CONFIG
-PKG_CONFIG="$PKG_CONFIG --static"
-PKG_CHECK_MODULES($@)
-PKG_CONFIG=$_save_PKG_CONFIG[]dnl
-])dnl PKG_CHECK_MODULES_STATIC
-
-
-dnl PKG_INSTALLDIR([DIRECTORY])
-dnl -------------------------
-dnl Since: 0.27
-dnl
-dnl Substitutes the variable pkgconfigdir as the location where a module
-dnl should install pkg-config .pc files. By default the directory is
-dnl $libdir/pkgconfig, but the default can be changed by passing
-dnl DIRECTORY. The user can override through the --with-pkgconfigdir
-dnl parameter.
-AC_DEFUN([PKG_INSTALLDIR],
-[m4_pushdef([pkg_default], [m4_default([$1], ['${libdir}/pkgconfig'])])
-m4_pushdef([pkg_description],
- [pkg-config installation directory @<:@]pkg_default[@:>@])
-AC_ARG_WITH([pkgconfigdir],
- [AS_HELP_STRING([--with-pkgconfigdir], pkg_description)],,
- [with_pkgconfigdir=]pkg_default)
-AC_SUBST([pkgconfigdir], [$with_pkgconfigdir])
-m4_popdef([pkg_default])
-m4_popdef([pkg_description])
-])dnl PKG_INSTALLDIR
-
-
-dnl PKG_NOARCH_INSTALLDIR([DIRECTORY])
-dnl --------------------------------
-dnl Since: 0.27
-dnl
-dnl Substitutes the variable noarch_pkgconfigdir as the location where a
-dnl module should install arch-independent pkg-config .pc files. By
-dnl default the directory is $datadir/pkgconfig, but the default can be
-dnl changed by passing DIRECTORY. The user can override through the
-dnl --with-noarch-pkgconfigdir parameter.
-AC_DEFUN([PKG_NOARCH_INSTALLDIR],
-[m4_pushdef([pkg_default], [m4_default([$1], ['${datadir}/pkgconfig'])])
-m4_pushdef([pkg_description],
- [pkg-config arch-independent installation directory @<:@]pkg_default[@:>@])
-AC_ARG_WITH([noarch-pkgconfigdir],
- [AS_HELP_STRING([--with-noarch-pkgconfigdir], pkg_description)],,
- [with_noarch_pkgconfigdir=]pkg_default)
-AC_SUBST([noarch_pkgconfigdir], [$with_noarch_pkgconfigdir])
-m4_popdef([pkg_default])
-m4_popdef([pkg_description])
-])dnl PKG_NOARCH_INSTALLDIR
-
-
-dnl PKG_CHECK_VAR(VARIABLE, MODULE, CONFIG-VARIABLE,
-dnl [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
-dnl -------------------------------------------
-dnl Since: 0.28
-dnl
-dnl Retrieves the value of the pkg-config variable for the given module.
-AC_DEFUN([PKG_CHECK_VAR],
-[AC_REQUIRE([PKG_PROG_PKG_CONFIG])dnl
-AC_ARG_VAR([$1], [value of $3 for $2, overriding pkg-config])dnl
-
-_PKG_CONFIG([$1], [variable="][$3]["], [$2])
-AS_VAR_COPY([$1], [pkg_cv_][$1])
-
-AS_VAR_IF([$1], [""], [$5], [$4])dnl
-])dnl PKG_CHECK_VAR
-
-# Copyright (C) 2002-2014 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,
@@ -308,10 +192,10 @@
# 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='1.15'
+[am__api_version='1.14'
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], [1.15], [],
+m4_if([$1], [1.14.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -327,14 +211,14 @@
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15])dnl
+[AM_AUTOMAKE_VERSION([1.14.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001-2014 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,
@@ -379,14 +263,15 @@
# configured tree to be moved without reconfiguration.
AC_DEFUN([AM_AUX_DIR_EXPAND],
-[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
-# Expand $ac_aux_dir to an absolute path.
-am_aux_dir=`cd "$ac_aux_dir" && pwd`
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
])
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -417,7 +302,7 @@
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -608,7 +493,7 @@
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -684,7 +569,7 @@
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -774,8 +659,8 @@
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target (and possibly the TAP driver). The
-# system "awk" is bad on some platforms.
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -848,11 +733,7 @@
END
AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
fi
-fi
-dnl The trailing newline in this macro's definition is deliberate, for
-dnl backward compatibility and to allow trailing 'dnl'-style comments
-dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
-])
+fi])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
@@ -881,7 +762,7 @@
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001-2014 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,
@@ -892,7 +773,7 @@
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh+set}" != xset; then
+if test x"${install_sh}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -902,7 +783,7 @@
fi
AC_SUBST([install_sh])])
-# Copyright (C) 2003-2014 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,
@@ -923,7 +804,7 @@
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001-2014 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,
@@ -973,7 +854,7 @@
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997-2014 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,
@@ -1012,7 +893,7 @@
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001-2014 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,
@@ -1041,7 +922,7 @@
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -1088,7 +969,7 @@
# For backward compatibility.
AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
-# Copyright (C) 2001-2014 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,
@@ -1107,7 +988,7 @@
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996-2014 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,
@@ -1188,7 +1069,7 @@
rm -f conftest.file
])
-# Copyright (C) 2009-2014 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,
@@ -1248,7 +1129,7 @@
_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
])
-# Copyright (C) 2001-2014 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,
@@ -1276,7 +1157,7 @@
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006-2014 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,
@@ -1295,7 +1176,7 @@
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004-2014 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,
diff --git a/python/tape b/python/tape
index baaac60..74ebbf0 100644
--- a/python/tape
+++ b/python/tape
@@ -52,7 +52,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=20
+mcsweeps=200000
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=0
diff --git a/src/general.h b/src/general.h
index 547680e..dccee34 100644
--- a/src/general.h
+++ b/src/general.h
@@ -260,6 +260,9 @@
long int nfil;
long int nfono;
long int R_nucleus;
+ ts_double R_nucleusX;
+ ts_double R_nucleusY;
+ ts_double R_nucleusZ;
long int pswitch;
long int constvolswitch;
long int constareaswitch;
@@ -307,6 +310,9 @@
ts_int pswitch;
ts_tape *tape;
ts_double R_nucleus;
+ ts_double R_nucleusX;
+ ts_double R_nucleusY;
+ ts_double R_nucleusZ;
ts_double area;
} ts_vesicle;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 4c82b35..ae7de0b 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -52,7 +52,9 @@
ts_vertex *vtx;
ts_tape *tape=vesicle->tape;
vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
-
+ vesicle->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
+ vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
+ vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
//Initialize grafted polymers (brush):
diff --git a/src/io.c b/src/io.c
index c35d42b..2461de5 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1031,6 +1031,9 @@
CFG_SIMPLE_INT("nfil",&tape->nfil),
CFG_SIMPLE_INT("nfono",&tape->nfono),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
+ CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
+ CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
diff --git a/src/neigh_test.c b/src/neigh_test.c
new file mode 100644
index 0000000..49ea775
--- /dev/null
+++ b/src/neigh_test.c
@@ -0,0 +1,65 @@
+#include<stdio.h>
+#include<math.h>
+#include "general.h"
+#include "vertex.h"
+#include "bond.h"
+#include "triangle.h"
+#include "cell.h"
+#include "vesicle.h"
+#include "io.h"
+#include "initial_distribution.h"
+#include "frame.h"
+#include "timestep.h"
+
+/** Entrance function to the program
+ * @param argv is a number of parameters used in program call (including the program name
+ * @param argc is a pointer to strings (character arrays) which holds the arguments
+ * @returns returns 0 on success, any other number on fail.
+*/
+
+int main(int argv, char *argc[]){
+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);
+
+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");
+
+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=vertex_list_remove_vtx(vlist->vtx[1]->neigh,vlist->vtx[0]);
+retval=vertex_list_remove_vtx(vlist->vtx[0]->neigh,vlist->vtx[1]);
+vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
+fprintf(stderr,"Was here too!\n");
+
+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]);
+
+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");
+
+return 0; //program finished perfectly ok. We return 0.
+}
diff --git a/src/tape b/src/tape
index baaac60..620a4a3 100644
--- a/src/tape
+++ b/src/tape
@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
-nshell=5
+nshell=10
# dmax is the max. bond length (in units l_min)
dmax=1.7
# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
@@ -12,12 +12,12 @@
# Pressure calculations
# (pswitch=1: calc. p*dV energy contribution)
-pswitch = 0
+pswitch = 1
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
-pressure=0.0
+pressure=-10.0
#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
-constvolswitch=2
+constvolswitch=0
constvolprecision=1e-14
#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
@@ -25,7 +25,7 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=2
+npoly=0
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
@@ -42,7 +42,9 @@
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
R_nucleus=0
-
+R_nucleusX=2.0
+R_nucleusY=6.0
+R_nucleusZ=2.0
####### Cell definitions ############
nxmax=60
nymax=60
@@ -52,7 +54,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=20
+mcsweeps=2000
#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 b065cbb..4caa86f 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -72,10 +72,19 @@
// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
+if(vesicle->R_nucleus>0.0){
if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
+} else if(vesicle->R_nucleusX>0.0){
+// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
+ if ((vtx->x*vtx->x)/vesicle->R_nucleusX + vtx->y*vtx->y/vesicle->R_nucleusY + (vtx->z*vtx->z)/vesicle->R_nucleusZ < 1.0){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+}
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
--
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