From 7ae444ccac5f3b7e6c7c953219ca898ea9509956 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 6 Dec 2017 11:04:15 -0500
Subject: [PATCH] sPuReMD: split into library and driver for optimization
integration (NSGA-II). Fix bug with interaction lists being allocated for
hydrogen bonds when no hydorgen atoms present. Fix minimum allocation size of
3-body lists (uncovered with small lithium geometries). Refactor naming of
conflicting data structures with NSGA-II. Update .gitignore.
---
.gitignore | 6 +
ar-lib | 270 +++++++++++++++++++++++++
sPuReMD/Makefile.am | 20 +-
sPuReMD/aclocal.m4 | 65 ++++++
sPuReMD/configure.ac | 5 +-
sPuReMD/src/allocate.c | 14 +-
sPuReMD/src/allocate.h | 6 +-
sPuReMD/src/analyze.c | 46 ++---
sPuReMD/src/analyze.h | 12 +-
sPuReMD/src/bond_orders.c | 66 +++---
sPuReMD/src/bond_orders.h | 22 +-
sPuReMD/src/charges.c | 22 +-
sPuReMD/src/charges.h | 2 +-
sPuReMD/src/control.c | 6 +-
sPuReMD/src/driver.c | 53 +++++
sPuReMD/src/forces.c | 30 +--
sPuReMD/src/forces.h | 4 +-
sPuReMD/src/four_body_interactions.c | 4 +-
sPuReMD/src/four_body_interactions.h | 2 +-
sPuReMD/src/geo_tools.c | 2 +-
sPuReMD/src/geo_tools.h | 2 +-
sPuReMD/src/init_md.c | 44 ++--
sPuReMD/src/init_md.h | 5 +-
sPuReMD/src/integrate.c | 24 +--
sPuReMD/src/integrate.h | 16 +-
sPuReMD/src/lin_alg.c | 2 +-
sPuReMD/src/lin_alg.h | 2 +-
sPuReMD/src/list.c | 14 +-
sPuReMD/src/list.h | 14 +-
sPuReMD/src/mytypes.h | 12 +-
sPuReMD/src/neighbors.c | 18 +-
sPuReMD/src/neighbors.h | 4 +-
sPuReMD/src/print_utils.c | 48 ++---
sPuReMD/src/print_utils.h | 34 ++--
sPuReMD/src/reset_utils.c | 8 +-
sPuReMD/src/reset_utils.h | 6 +-
sPuReMD/src/single_body_interactions.c | 4 +-
sPuReMD/src/single_body_interactions.h | 2 +-
sPuReMD/src/{testmd.c => spuremd.c} | 118 ++++++-----
sPuReMD/src/spuremd.h | 38 ++++
sPuReMD/src/three_body_interactions.c | 8 +-
sPuReMD/src/three_body_interactions.h | 4 +-
sPuReMD/src/tool_box.c | 4 +-
sPuReMD/src/traj.c | 8 +-
sPuReMD/src/traj.h | 10 +-
sPuReMD/src/two_body_interactions.c | 12 +-
sPuReMD/src/two_body_interactions.h | 6 +-
47 files changed, 793 insertions(+), 331 deletions(-)
create mode 100755 ar-lib
create mode 100644 sPuReMD/src/driver.c
rename sPuReMD/src/{testmd.c => spuremd.c} (62%)
create mode 100644 sPuReMD/src/spuremd.h
diff --git a/.gitignore b/.gitignore
index a7a8c79..0e82e4b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,9 +50,13 @@ Makefile
Makefile.in
stamp-h1
test-driver
+*.lo
+*.la
# Compiled languages (C,C++,Fortran,...)
*.o
+*.so
+*.a
# flex/bison files
*.yy.c
@@ -68,4 +72,6 @@ test-driver
*.tar.gz
*.pdf
*/bin
+*/lib
*.txt
+*.zip
diff --git a/ar-lib b/ar-lib
new file mode 100755
index 0000000..463b9ec
--- /dev/null
+++ b/ar-lib
@@ -0,0 +1,270 @@
+#! /bin/sh
+# Wrapper for Microsoft lib.exe
+
+me=ar-lib
+scriptversion=2012-03-01.08; # UTC
+
+# Copyright (C) 2010-2014 Free Software Foundation, Inc.
+# Written by Peter Rosin <peda@lysator.liu.se>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+
+# func_error message
+func_error ()
+{
+ echo "$me: $1" 1>&2
+ exit 1
+}
+
+file_conv=
+
+# func_file_conv build_file
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts.
+func_file_conv ()
+{
+ file=$1
+ case $file in
+ / | /[!/]*) # absolute file, and not a UNC file
+ if test -z "$file_conv"; then
+ # lazily determine how to convert abs files
+ case `uname -s` in
+ MINGW*)
+ file_conv=mingw
+ ;;
+ CYGWIN*)
+ file_conv=cygwin
+ ;;
+ *)
+ file_conv=wine
+ ;;
+ esac
+ fi
+ case $file_conv in
+ mingw)
+ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+ ;;
+ cygwin)
+ file=`cygpath -m "$file" || echo "$file"`
+ ;;
+ wine)
+ file=`winepath -w "$file" || echo "$file"`
+ ;;
+ esac
+ ;;
+ esac
+}
+
+# func_at_file at_file operation archive
+# Iterate over all members in AT_FILE performing OPERATION on ARCHIVE
+# for each of them.
+# When interpreting the content of the @FILE, do NOT use func_file_conv,
+# since the user would need to supply preconverted file names to
+# binutils ar, at least for MinGW.
+func_at_file ()
+{
+ operation=$2
+ archive=$3
+ at_file_contents=`cat "$1"`
+ eval set x "$at_file_contents"
+ shift
+
+ for member
+ do
+ $AR -NOLOGO $operation:"$member" "$archive" || exit $?
+ done
+}
+
+case $1 in
+ '')
+ func_error "no command. Try '$0 --help' for more information."
+ ;;
+ -h | --h*)
+ cat <<EOF
+Usage: $me [--help] [--version] PROGRAM ACTION ARCHIVE [MEMBER...]
+
+Members may be specified in a file named with @FILE.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "$me, version $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test $# -lt 3; then
+ func_error "you must specify a program, an action and an archive"
+fi
+
+AR=$1
+shift
+while :
+do
+ if test $# -lt 2; then
+ func_error "you must specify a program, an action and an archive"
+ fi
+ case $1 in
+ -lib | -LIB \
+ | -ltcg | -LTCG \
+ | -machine* | -MACHINE* \
+ | -subsystem* | -SUBSYSTEM* \
+ | -verbose | -VERBOSE \
+ | -wx* | -WX* )
+ AR="$AR $1"
+ shift
+ ;;
+ *)
+ action=$1
+ shift
+ break
+ ;;
+ esac
+done
+orig_archive=$1
+shift
+func_file_conv "$orig_archive"
+archive=$file
+
+# strip leading dash in $action
+action=${action#-}
+
+delete=
+extract=
+list=
+quick=
+replace=
+index=
+create=
+
+while test -n "$action"
+do
+ case $action in
+ d*) delete=yes ;;
+ x*) extract=yes ;;
+ t*) list=yes ;;
+ q*) quick=yes ;;
+ r*) replace=yes ;;
+ s*) index=yes ;;
+ S*) ;; # the index is always updated implicitly
+ c*) create=yes ;;
+ u*) ;; # TODO: don't ignore the update modifier
+ v*) ;; # TODO: don't ignore the verbose modifier
+ *)
+ func_error "unknown action specified"
+ ;;
+ esac
+ action=${action#?}
+done
+
+case $delete$extract$list$quick$replace,$index in
+ yes,* | ,yes)
+ ;;
+ yesyes*)
+ func_error "more than one action specified"
+ ;;
+ *)
+ func_error "no action specified"
+ ;;
+esac
+
+if test -n "$delete"; then
+ if test ! -f "$orig_archive"; then
+ func_error "archive not found"
+ fi
+ for member
+ do
+ case $1 in
+ @*)
+ func_at_file "${1#@}" -REMOVE "$archive"
+ ;;
+ *)
+ func_file_conv "$1"
+ $AR -NOLOGO -REMOVE:"$file" "$archive" || exit $?
+ ;;
+ esac
+ done
+
+elif test -n "$extract"; then
+ if test ! -f "$orig_archive"; then
+ func_error "archive not found"
+ fi
+ if test $# -gt 0; then
+ for member
+ do
+ case $1 in
+ @*)
+ func_at_file "${1#@}" -EXTRACT "$archive"
+ ;;
+ *)
+ func_file_conv "$1"
+ $AR -NOLOGO -EXTRACT:"$file" "$archive" || exit $?
+ ;;
+ esac
+ done
+ else
+ $AR -NOLOGO -LIST "$archive" | sed -e 's/\\/\\\\/g' | while read member
+ do
+ $AR -NOLOGO -EXTRACT:"$member" "$archive" || exit $?
+ done
+ fi
+
+elif test -n "$quick$replace"; then
+ if test ! -f "$orig_archive"; then
+ if test -z "$create"; then
+ echo "$me: creating $orig_archive"
+ fi
+ orig_archive=
+ else
+ orig_archive=$archive
+ fi
+
+ for member
+ do
+ case $1 in
+ @*)
+ func_file_conv "${1#@}"
+ set x "$@" "@$file"
+ ;;
+ *)
+ func_file_conv "$1"
+ set x "$@" "$file"
+ ;;
+ esac
+ shift
+ shift
+ done
+
+ if test -n "$orig_archive"; then
+ $AR -NOLOGO -OUT:"$archive" "$orig_archive" "$@" || exit $?
+ else
+ $AR -NOLOGO -OUT:"$archive" "$@" || exit $?
+ fi
+
+elif test -n "$list"; then
+ if test ! -f "$orig_archive"; then
+ func_error "archive not found"
+ fi
+ $AR -NOLOGO -LIST "$archive" || exit $?
+fi
diff --git a/sPuReMD/Makefile.am b/sPuReMD/Makefile.am
index a31309c..2531185 100644
--- a/sPuReMD/Makefile.am
+++ b/sPuReMD/Makefile.am
@@ -1,22 +1,20 @@
ACLOCAL_AMFLAGS = -I ../m4
-bin_PROGRAMS = bin/spuremd
-
-bin_spuremd_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_utils.c \
+lib_LTLIBRARIES = lib/libspuremd.la
+lib_libspuremd_la_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_utils.c \
src/reset_utils.c src/restart.c src/random.c src/tool_box.c src/traj.c \
src/vector.c src/allocate.c src/analyze.c src/box.c src/system_props.c src/control.c \
src/geo_tools.c src/neighbors.c src/lin_alg.c src/charges.c src/bond_orders.c \
src/single_body_interactions.c src/two_body_interactions.c \
src/three_body_interactions.c src/four_body_interactions.c src/forces.c \
- src/integrate.c src/init_md.c src/testmd.c
+ src/integrate.c src/init_md.c src/spuremd.c
+lib_libspuremd_la_CFLAGS = -I src
+lib_libspuremd_la_LDFLAGS = -version-info 1:0:0
-include_HEADERS = src/mytypes.h src/ffield.h src/grid.h src/list.h src/lookup.h src/print_utils.h \
- src/reset_utils.h src/restart.h src/random.h src/tool_box.h src/traj.h \
- src/vector.h src/allocate.h src/analyze.h src/box.h src/system_props.h src/control.h \
- src/geo_tools.h src/neighbors.h src/lin_alg.h src/charges.h src/bond_orders.h \
- src/single_body_interactions.h src/two_body_interactions.h \
- src/three_body_interactions.h src/four_body_interactions.h src/forces.h \
- src/integrate.h src/init_md.h
+bin_PROGRAMS = bin/spuremd
+bin_spuremd_SOURCES = src/driver.c
+bin_spuremd_CPPFLAGS = -I src
+bin_spuremd_LDADD = lib/libspuremd.la
check_PROGRAMS =
TESTS =
diff --git a/sPuReMD/aclocal.m4 b/sPuReMD/aclocal.m4
index 48e9bea..df75c6a 100644
--- a/sPuReMD/aclocal.m4
+++ b/sPuReMD/aclocal.m4
@@ -56,6 +56,66 @@ m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
+# Copyright (C) 2011-2014 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_AR([ACT-IF-FAIL])
+# -------------------------
+# Try to determine the archiver interface, and trigger the ar-lib wrapper
+# if it is needed. If the detection of archiver interface fails, run
+# ACT-IF-FAIL (default is to abort configure with a proper error message).
+AC_DEFUN([AM_PROG_AR],
+[AC_BEFORE([$0], [LT_INIT])dnl
+AC_BEFORE([$0], [AC_PROG_LIBTOOL])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([ar-lib])dnl
+AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
+: ${AR=ar}
+
+AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
+ [AC_LANG_PUSH([C])
+ am_cv_ar_interface=ar
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
+ [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+ AC_TRY_EVAL([am_ar_try])
+ if test "$ac_status" -eq 0; then
+ am_cv_ar_interface=ar
+ else
+ am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+ AC_TRY_EVAL([am_ar_try])
+ if test "$ac_status" -eq 0; then
+ am_cv_ar_interface=lib
+ else
+ am_cv_ar_interface=unknown
+ fi
+ fi
+ rm -f conftest.lib libconftest.a
+ ])
+ AC_LANG_POP([C])])
+
+case $am_cv_ar_interface in
+ar)
+ ;;
+lib)
+ # Microsoft lib, so override with the ar-lib wrapper script.
+ # FIXME: It is wrong to rewrite AR.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__AR in this case,
+ # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
+ # similar.
+ AR="$am_aux_dir/ar-lib $AR"
+ ;;
+unknown)
+ m4_default([$1],
+ [AC_MSG_ERROR([could not determine $AR interface])])
+ ;;
+esac
+AC_SUBST([AR])dnl
+])
+
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
# Copyright (C) 2001-2014 Free Software Foundation, Inc.
@@ -1152,3 +1212,8 @@ AC_SUBST([am__untar])
m4_include([../m4/acx_pthread.m4])
m4_include([../m4/ax_compiler_vendor.m4])
+m4_include([../m4/libtool.m4])
+m4_include([../m4/ltoptions.m4])
+m4_include([../m4/ltsugar.m4])
+m4_include([../m4/ltversion.m4])
+m4_include([../m4/lt~obsolete.m4])
diff --git a/sPuReMD/configure.ac b/sPuReMD/configure.ac
index 312fa80..1a59944 100644
--- a/sPuReMD/configure.ac
+++ b/sPuReMD/configure.ac
@@ -8,8 +8,9 @@ AC_INIT([sPuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
# Enable silent build rules by default.
m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
-#LT_PREREQ([2.2])
-#LT_INIT([dlopen])
+AM_PROG_AR
+LT_PREREQ([2.2])
+LT_INIT([dlopen])
AC_LANG([C])
diff --git a/sPuReMD/src/allocate.c b/sPuReMD/src/allocate.c
index 8035410..15f4256 100644
--- a/sPuReMD/src/allocate.c
+++ b/sPuReMD/src/allocate.c
@@ -55,7 +55,7 @@ int PreAllocate_Space( reax_system *system, control_params *control,
}
-void Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
+void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, int num_intrs )
{
Delete_List( TYP_FAR_NEIGHBOR, far_nbrs );
@@ -131,7 +131,7 @@ int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name )
int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
- list *hbonds )
+ reax_list *hbonds )
{
int i, num_hbonds;
@@ -168,7 +168,7 @@ int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
}
-int Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
+int Reallocate_HBonds_List( int n, int num_h, int *h_index, reax_list *hbonds )
{
int i;
int *hb_top;
@@ -196,7 +196,7 @@ int Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
}
-int Allocate_Bond_List( int n, int *bond_top, list *bonds )
+int Allocate_Bond_List( int n, int *bond_top, reax_list *bonds )
{
int i, num_bonds;
@@ -227,7 +227,7 @@ int Allocate_Bond_List( int n, int *bond_top, list *bonds )
}
-int Reallocate_Bonds_List( int n, list *bonds, int *num_bonds, int *est_3body )
+int Reallocate_Bonds_List( int n, reax_list *bonds, int *num_bonds, int *est_3body )
{
int i;
int *bond_top;
@@ -256,7 +256,7 @@ int Reallocate_Bonds_List( int n, list *bonds, int *num_bonds, int *est_3body )
}
-void Reallocate( reax_system *system, static_storage *workspace, list **lists,
+void Reallocate( reax_system *system, control_params *control, static_storage *workspace, reax_list **lists,
int nbr_flag )
{
int i, j, k;
@@ -285,7 +285,7 @@ void Reallocate( reax_system *system, static_storage *workspace, list **lists,
workspace->U = NULL;
}
- if ( realloc->hbonds > 0 )
+ if ( control->hb_cut > 0.0 && realloc->hbonds > 0 )
{
Reallocate_HBonds_List(system->N, workspace->num_H, workspace->hbond_index,
(*lists) + HBONDS );
diff --git a/sPuReMD/src/allocate.h b/sPuReMD/src/allocate.h
index e8fdc4d..b961521 100644
--- a/sPuReMD/src/allocate.h
+++ b/sPuReMD/src/allocate.h
@@ -26,14 +26,14 @@
int PreAllocate_Space( reax_system*, control_params*, static_storage* );
-void Reallocate( reax_system*, static_storage*, list**, int );
+void Reallocate( reax_system*, control_params*, static_storage*, reax_list**, int );
int Allocate_Matrix( sparse_matrix**, int, int );
void Deallocate_Matrix( sparse_matrix* );
-int Allocate_HBond_List( int, int, int*, int*, list* );
+int Allocate_HBond_List( int, int, int*, int*, reax_list* );
-int Allocate_Bond_List( int, int*, list* );
+int Allocate_Bond_List( int, int*, reax_list* );
#endif
diff --git a/sPuReMD/src/analyze.c b/sPuReMD/src/analyze.c
index d3582fe..4e2cbe2 100644
--- a/sPuReMD/src/analyze.c
+++ b/sPuReMD/src/analyze.c
@@ -59,11 +59,11 @@ typedef struct
// copy bond list into old bond list
void Copy_Bond_List( reax_system *system, control_params *control,
- list **lists )
+ reax_list **lists )
{
int i, j, top_old;
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
+ reax_list *new_bonds = (*lists) + BONDS;
+ reax_list *old_bonds = (*lists) + OLD_BONDS;
for ( top_old = 0, i = 0; i < system->N; ++i )
{
@@ -89,11 +89,11 @@ void Copy_Bond_List( reax_system *system, control_params *control,
// ASSUMPTION: Bond lists are sorted
-int Compare_Bond_Lists( int atom, control_params *control, list **lists )
+int Compare_Bond_Lists( int atom, control_params *control, reax_list **lists )
{
int oldp, newp;
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
+ reax_list *new_bonds = (*lists) + BONDS;
+ reax_list *old_bonds = (*lists) + OLD_BONDS;
/*fprintf( stdout, "\n%d\nold_bonds:", atom );
for( oldp = Start_Index( atom, old_bonds );
@@ -168,7 +168,7 @@ int Compare_Bond_Lists( int atom, control_params *control, list **lists )
void Get_Molecule( int atom, molecule *m, int *mark, reax_system *system,
- control_params *control, list *bonds, int print,
+ control_params *control, reax_list *bonds, int print,
FILE *fout )
{
int i, start, end;
@@ -219,15 +219,15 @@ void Print_Molecule( reax_system *system, molecule *m, int mode, char *s )
void Analyze_Molecules( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout )
+ reax_list **lists, FILE *fout )
{
int atom, i, j, k, l, flag;
int *mark = workspace->mark;
int *old_mark = workspace->old_mark;
int num_old, num_new;
char s[MAX_MOLECULE_SIZE * 10];
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
+ reax_list *new_bonds = (*lists) + BONDS;
+ reax_list *old_bonds = (*lists) + OLD_BONDS;
molecule old_molecules[20], new_molecules[20];
fprintf( fout, "molecular analysis @ %d\n", data->step );
@@ -314,8 +314,8 @@ void Analyze_Molecules( reax_system *system, control_params *control,
void Report_Bond_Change( reax_system *system, control_params *control,
- static_storage *workspace, list *old_bonds,
- list *new_bonds, int a1, int a2, int flag,
+ static_storage *workspace, reax_list *old_bonds,
+ reax_list *new_bonds, int a1, int a2, int flag,
FILE *fout )
{
int i;
@@ -385,8 +385,8 @@ void Report_Bond_Change( reax_system *system, control_params *control,
/* ASSUMPTION: Bond lists are sorted */
void Compare_Bonding( int atom, reax_system *system, control_params *control,
- static_storage *workspace, list *old_bonds,
- list *new_bonds, FILE *fout )
+ static_storage *workspace, reax_list *old_bonds,
+ reax_list *new_bonds, FILE *fout )
{
int oldp, newp;
@@ -503,7 +503,7 @@ void Compare_Bonding( int atom, reax_system *system, control_params *control,
void Visit_Bonds( int atom, int *mark, int *type, reax_system *system,
- control_params *control, list *bonds, int ignore )
+ control_params *control, reax_list *bonds, int ignore )
{
int i, t, start, end, nbr;
real bo;
@@ -529,7 +529,7 @@ void Visit_Bonds( int atom, int *mark, int *type, reax_system *system,
void Analyze_Fragments( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout, int ignore )
+ reax_list **lists, FILE *fout, int ignore )
{
int atom, i, flag;
int *mark = workspace->mark;
@@ -538,8 +538,8 @@ void Analyze_Fragments( reax_system *system, control_params *control,
char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
int fragment_count[MAX_FRAGMENT_TYPES];
molecule m;
- list *new_bonds = (*lists) + BONDS;
- //list *old_bonds = (*lists) + OLD_BONDS;
+ reax_list *new_bonds = (*lists) + BONDS;
+ //reax_list *old_bonds = (*lists) + OLD_BONDS;
/* fragment analysis */
fprintf( fout, "step%d fragments\n", data->step );
@@ -594,14 +594,14 @@ void Analyze_Fragments( reax_system *system, control_params *control,
void Analyze_Silica( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout )
+ reax_list **lists, FILE *fout )
{
int atom, i, j, k, pi, pk, pk_j, newp, coord;
int O_SI_O_count, SI_O_SI_count;
int si_coord[10], ox_coord[10];
real O_SI_O, SI_O_SI;
- list *new_bonds = (*lists) + BONDS;
- list *thb_intrs = (*lists) + THREE_BODIES;
+ reax_list *new_bonds = (*lists) + BONDS;
+ reax_list *thb_intrs = (*lists) + THREE_BODIES;
Analyze_Fragments( system, control, data, workspace, lists, fout, 0 );
@@ -721,7 +721,7 @@ int Get_Type_of_Molecule( molecule *m )
void Calculate_Dipole_Moment( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list *bonds, FILE *fout )
+ reax_list *bonds, FILE *fout )
{
int i, atom, count;
molecule m;
@@ -936,7 +936,7 @@ void Calculate_Density_Slice( reax_system *system, simulation_data *data,
void Analysis( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int steps;
diff --git a/sPuReMD/src/analyze.h b/sPuReMD/src/analyze.h
index e296e57..af2b056 100644
--- a/sPuReMD/src/analyze.h
+++ b/sPuReMD/src/analyze.h
@@ -25,21 +25,21 @@
#include "mytypes.h"
void Analysis( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
-//void Copy_Bond_List( reax_system*, control_params*, list** );
+//void Copy_Bond_List( reax_system*, control_params*, reax_list** );
//void Analyze_Molecules( reax_system*, control_params*, simulation_data*,
-// static_storage*, list**, FILE* );
+// static_storage*, reax_list**, FILE* );
//void Analyze_Bonding( reax_system*, control_params*, simulation_data*,
-// static_storage*, list**, FILE* );
+// static_storage*, reax_list**, FILE* );
//void Analyze_Silica( reax_system*, control_params*, simulation_data*,
-// static_storage*, list**, FILE* );
+// static_storage*, reax_list**, FILE* );
//void Calculate_Dipole_Moment( reax_system*, control_params*, simulation_data*,
-// static_storage *, list*, FILE* );
+// static_storage *, reax_list*, FILE* );
//void Copy_Positions( reax_system*, static_storage* );
diff --git a/sPuReMD/src/bond_orders.c b/sPuReMD/src/bond_orders.c
index 7a0358e..52d5ad6 100644
--- a/sPuReMD/src/bond_orders.c
+++ b/sPuReMD/src/bond_orders.c
@@ -34,11 +34,11 @@ static inline real Cf45( real p1, real p2 )
#ifdef TEST_FORCES
-void Get_dBO( reax_system *system, list **lists,
+void Get_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
@@ -53,11 +53,11 @@ void Get_dBO( reax_system *system, list **lists,
}
-void Get_dBOpinpi2( reax_system *system, list **lists,
+void Get_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -74,11 +74,11 @@ void Get_dBOpinpi2( reax_system *system, list **lists,
}
-void Add_dBO( reax_system *system, list **lists,
+void Add_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
@@ -95,11 +95,11 @@ void Add_dBO( reax_system *system, list **lists,
}
-void Add_dBOpinpi2( reax_system *system, list **lists,
+void Add_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -116,11 +116,11 @@ void Add_dBOpinpi2( reax_system *system, list **lists,
}
-void Add_dBO_to_Forces( reax_system *system, list **lists,
+void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real C )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
@@ -135,11 +135,11 @@ void Add_dBO_to_Forces( reax_system *system, list **lists,
}
-void Add_dBOpinpi2_to_Forces( reax_system *system, list **lists,
+void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
dbond_data *dbo_k;
int start_pj, end_pj, k;
@@ -156,9 +156,9 @@ void Add_dBOpinpi2_to_Forces( reax_system *system, list **lists,
}
-void Add_dDelta( reax_system *system, list **lists, int i, real C, rvec *v )
+void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v )
{
- list *dDeltas;
+ reax_list *dDeltas;
int start, end, k;
dDeltas = &((*lists)[DDELTA]);
@@ -173,9 +173,9 @@ void Add_dDelta( reax_system *system, list **lists, int i, real C, rvec *v )
}
-void Add_dDelta_to_Forces( reax_system *system, list **lists, int i, real C )
+void Add_dDelta_to_Forces( reax_system *system, reax_list **lists, int i, real C )
{
- list *dDeltas;
+ reax_list *dDeltas;
int start, end, k;
dDeltas = &((*lists)[DDELTA]);
@@ -190,12 +190,12 @@ void Add_dDelta_to_Forces( reax_system *system, list **lists, int i, real C )
}
-void Calculate_dBO( int i, int pj, static_storage *workspace, list **lists,
+void Calculate_dBO( int i, int pj, static_storage *workspace, reax_list **lists,
int *top )
{
int j, k, l, start_i, end_i, end_j;
rvec dDeltap_self, dBOp;
- list *bonds, *dBOs;
+ reax_list *bonds, *dBOs;
bond_data *nbr_l, *nbr_k;
bond_order_data *bo_ij;
dbond_data *top_dbo;
@@ -331,9 +331,9 @@ void Calculate_dBO( int i, int pj, static_storage *workspace, list **lists,
void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
- simulation_data *data, static_storage *workspace, list **lists )
+ simulation_data *data, static_storage *workspace, reax_list **lists )
{
- list *bonds = (*lists) + BONDS;
+ reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
@@ -521,9 +521,9 @@ void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
void Add_dBond_to_Forces( int i, int pj, reax_system *system,
- simulation_data *data, static_storage *workspace, list **lists )
+ simulation_data *data, static_storage *workspace, reax_list **lists )
{
- list *bonds = (*lists) + BONDS;
+ reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
@@ -657,7 +657,7 @@ void Add_dBond_to_Forces( int i, int pj, reax_system *system,
/* Locate j on i's list.
This function assumes that j is there for sure!
And this is the case given our method of neighbor generation*/
-int Locate_Symmetric_Bond( list *bonds, int i, int j )
+int Locate_Symmetric_Bond( reax_list *bonds, int i, int j )
{
int start = Start_Index(i, bonds);
int end = End_Index(i, bonds);
@@ -719,11 +719,11 @@ int compare_bonds( const void *p1, const void *p2 )
This can either be done in the general coordinator function or here */
void Calculate_Bond_Orders( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
real p_lp1;
real p_boc1, p_boc2;
- list *bonds;
+ reax_list *bonds;
p_lp1 = system->reaxprm.gp.l[15];
p_boc1 = system->reaxprm.gp.l[0];
@@ -753,8 +753,8 @@ void Calculate_Bond_Orders( reax_system *system, control_params *control,
int top_dbo, top_dDelta;
dbond_data *pdbo;
dDelta_data *ptop_dDelta;
- list *dDeltas;
- list *dBOs;
+ reax_list *dDeltas;
+ reax_list *dBOs;
top_dbo = 0;
top_dDelta = 0;
diff --git a/sPuReMD/src/bond_orders.h b/sPuReMD/src/bond_orders.h
index b6ca199..67592ed 100644
--- a/sPuReMD/src/bond_orders.h
+++ b/sPuReMD/src/bond_orders.h
@@ -33,23 +33,23 @@ typedef struct
} dbond_coefficients;
#ifdef TEST_FORCES
-void Get_dBO( reax_system*, list**, int, int, real, rvec* );
-void Get_dBOpinpi2( reax_system*, list**, int, int, real, real, rvec*, rvec* );
+void Get_dBO( reax_system*, reax_list**, int, int, real, rvec* );
+void Get_dBOpinpi2( reax_system*, reax_list**, int, int, real, real, rvec*, rvec* );
-void Add_dBO( reax_system*, list**, int, int, real, rvec* );
-void Add_dBOpinpi2( reax_system*, list**, int, int, real, real, rvec*, rvec* );
+void Add_dBO( reax_system*, reax_list**, int, int, real, rvec* );
+void Add_dBOpinpi2( reax_system*, reax_list**, int, int, real, real, rvec*, rvec* );
-void Add_dBO_to_Forces( reax_system*, list**, int, int, real );
-void Add_dBOpinpi2_to_Forces( reax_system*, list**, int, int, real, real );
+void Add_dBO_to_Forces( reax_system*, reax_list**, int, int, real );
+void Add_dBOpinpi2_to_Forces( reax_system*, reax_list**, int, int, real, real );
-void Add_dDelta( reax_system*, list**, int, real, rvec* );
-void Add_dDelta_to_Forces( reax_system *, list**, int, real );
+void Add_dDelta( reax_system*, reax_list**, int, real, rvec* );
+void Add_dDelta_to_Forces( reax_system *, reax_list**, int, real );
#endif
void Add_dBond_to_Forces( int, int, reax_system*, simulation_data*,
- static_storage*, list** );
+ static_storage*, reax_list** );
void Add_dBond_to_Forces_NPT( int, int, reax_system*, simulation_data*,
- static_storage*, list** );
+ static_storage*, reax_list** );
void Calculate_Bond_Orders( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
#endif
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index 63ed940..5003d28 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -1514,7 +1514,7 @@ static void Extrapolate_Charges_EE( const reax_system * const system,
static void Compute_Preconditioner_QEq( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
real time;
sparse_matrix *Hptr;
@@ -1612,7 +1612,7 @@ static void Compute_Preconditioner_QEq( const reax_system * const system,
//static void Compute_Preconditioner_EE( const reax_system * const system,
// const control_params * const control,
// simulation_data * const data, static_storage * const workspace,
-// const list * const far_nbrs )
+// const reax_list * const far_nbrs )
//{
// int i, top;
// static real * ones = NULL, * x = NULL, * y = NULL;
@@ -1856,7 +1856,7 @@ static void Compute_Preconditioner_QEq( const reax_system * const system,
static void Compute_Preconditioner_EE( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
real time;
sparse_matrix *Hptr;
@@ -1958,7 +1958,7 @@ static void Compute_Preconditioner_EE( const reax_system * const system,
static void Compute_Preconditioner_ACKS2( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
real time;
sparse_matrix *Hptr;
@@ -2062,7 +2062,7 @@ static void Compute_Preconditioner_ACKS2( const reax_system * const system,
static void Setup_Preconditioner_QEq( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
int fillin;
real time;
@@ -2207,7 +2207,7 @@ static void Setup_Preconditioner_QEq( const reax_system * const system,
static void Setup_Preconditioner_EE( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
int fillin;
real time;
@@ -2356,7 +2356,7 @@ static void Setup_Preconditioner_EE( const reax_system * const system,
static void Setup_Preconditioner_ACKS2( const reax_system * const system,
const control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs )
+ const reax_list * const far_nbrs )
{
int fillin;
real time;
@@ -2561,7 +2561,7 @@ static void Calculate_Charges_EE( const reax_system * const system,
*/
static void QEq( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs, const output_controls * const out_control )
+ const reax_list * const far_nbrs, const output_controls * const out_control )
{
int iters;
@@ -2650,7 +2650,7 @@ static void QEq( reax_system * const system, control_params * const control,
*/
static void EE( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs, const output_controls * const out_control )
+ const reax_list * const far_nbrs, const output_controls * const out_control )
{
int iters;
@@ -2722,7 +2722,7 @@ static void EE( reax_system * const system, control_params * const control,
*/
static void ACKS2( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs, const output_controls * const out_control )
+ const reax_list * const far_nbrs, const output_controls * const out_control )
{
int iters;
@@ -2784,7 +2784,7 @@ static void ACKS2( reax_system * const system, control_params * const control,
void Compute_Charges( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- const list * const far_nbrs, const output_controls * const out_control )
+ const reax_list * const far_nbrs, const output_controls * const out_control )
{
#if defined(DEBUG_FOCUS)
char fname[200];
diff --git a/sPuReMD/src/charges.h b/sPuReMD/src/charges.h
index 50f563c..e0520fc 100644
--- a/sPuReMD/src/charges.h
+++ b/sPuReMD/src/charges.h
@@ -25,7 +25,7 @@
#include "mytypes.h"
void Compute_Charges( reax_system* const, control_params* const, simulation_data* const,
- static_storage* const, const list* const,
+ static_storage* const, const reax_list* const,
const output_controls* const );
#endif
diff --git a/sPuReMD/src/control.c b/sPuReMD/src/control.c
index 127543e..ead9035 100644
--- a/sPuReMD/src/control.c
+++ b/sPuReMD/src/control.c
@@ -115,7 +115,7 @@ char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
static_storage*, void* )) Write_Custom_Header;
out_control->append_traj_frame =
(int (*)( reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void* )) Append_Custom_Frame;
+ static_storage*, reax_list **, void* )) Append_Custom_Frame;
strcpy( out_control->traj_title, "default_title" );
out_control->atom_format = 0;
@@ -450,7 +450,7 @@ char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
static_storage*, void* )) Write_Custom_Header;
out_control->append_traj_frame =
(int (*)(reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void*)) Append_Custom_Frame;
+ static_storage*, reax_list **, void*)) Append_Custom_Frame;
}
else if ( out_control->traj_format == 1 )
{
@@ -459,7 +459,7 @@ char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
static_storage*, void* )) Write_xyz_Header;
out_control->append_traj_frame =
(int (*)( reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void* )) Append_xyz_Frame;
+ static_storage*, reax_list **, void* )) Append_xyz_Frame;
}
}
else if ( strcmp(tmp[0], "traj_title") == 0 )
diff --git a/sPuReMD/src/driver.c b/sPuReMD/src/driver.c
new file mode 100644
index 0000000..6d2ff6a
--- /dev/null
+++ b/sPuReMD/src/driver.c
@@ -0,0 +1,53 @@
+
+/*----------------------------------------------------------------------
+ SerialReax - Reax Force Field Simulator
+
+ Copyright (2010) Purdue University
+ Hasan Metin Aktulga, haktulga@cs.purdue.edu
+ Joseph Fogarty, jcfogart@mail.usf.edu
+ Sagar Pandit, pandit@usf.edu
+ Ananth Y Grama, ayg@cs.purdue.edu
+
+ 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:
+ <http://www.gnu.org/licenses/>.
+ ----------------------------------------------------------------------*/
+
+#include "mytypes.h"
+
+#include "spuremd.h"
+
+
+static void usage( char * argv[] )
+{
+ fprintf( stderr, "usage: ./%s geometry ffield control\n", argv[0] );
+}
+
+
+int main( int argc, char* argv[] )
+{
+ reax_system system;
+ control_params control;
+ simulation_data data;
+
+ if ( argc != 4 )
+ {
+ usage( argv );
+ exit( INVALID_INPUT );
+ }
+
+ Setup( argv + 1, &system, &control, &data );
+
+ Run( &system, &control, &data, TRUE );
+
+ Cleanup( &system, &control, &data, TRUE );
+
+ return 0;
+}
diff --git a/sPuReMD/src/forces.c b/sPuReMD/src/forces.c
index 4ae2acc..10e31fd 100644
--- a/sPuReMD/src/forces.c
+++ b/sPuReMD/src/forces.c
@@ -47,7 +47,7 @@ typedef enum
void Dummy_Interaction( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
}
@@ -77,7 +77,7 @@ void Init_Bonded_Force_Functions( control_params *control )
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -133,7 +133,7 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list** lists, output_controls *out_control )
+ reax_list** lists, output_controls *out_control )
{
real t_start, t_elapsed;
@@ -177,10 +177,10 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
/* This version of Compute_Total_Force computes forces from coefficients
accumulated by all interaction functions. Saves enormous time & space! */
void Compute_Total_Force( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists )
+ simulation_data *data, static_storage *workspace, reax_list **lists )
{
int i;
- list *bonds;
+ reax_list *bonds;
bonds = (*lists) + BONDS;
@@ -230,11 +230,11 @@ void Compute_Total_Force( reax_system *system, control_params *control,
}
-void Validate_Lists( static_storage *workspace, list **lists, int step, int n,
+void Validate_Lists( static_storage *workspace, reax_list **lists, int step, int n,
int Hmax, int Htop, int num_bonds, int num_hbonds )
{
int i, flag;
- list *bonds, *hbonds;
+ reax_list *bonds, *hbonds;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
@@ -439,7 +439,7 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
- control_params *control, list *far_nbrs,
+ control_params *control, reax_list *far_nbrs,
sparse_matrix * H, sparse_matrix * H_sp,
int * Htop, int * H_sp_top )
{
@@ -610,7 +610,7 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, pj;
int start_i, end_i;
@@ -623,7 +623,7 @@ void Init_Forces( reax_system *system, control_params *control,
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
real BO, BO_s, BO_pi, BO_pi2;
sparse_matrix *H, *H_sp;
- list *far_nbrs, *bonds, *hbonds;
+ reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
@@ -922,7 +922,7 @@ void Init_Forces( reax_system *system, control_params *control,
void Init_Forces_Tab( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, pj;
int start_i, end_i;
@@ -935,7 +935,7 @@ void Init_Forces_Tab( reax_system *system, control_params *control,
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
real BO, BO_s, BO_pi, BO_pi2;
sparse_matrix *H, *H_sp;
- list *far_nbrs, *bonds, *hbonds;
+ reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
@@ -1201,7 +1201,7 @@ void Init_Forces_Tab( reax_system *system, control_params *control,
void Estimate_Storage_Sizes( reax_system *system, control_params *control,
- list **lists, int *Htop, int *hb_top, int *bond_top, int *num_3body )
+ reax_list **lists, int *Htop, int *hb_top, int *bond_top, int *num_3body )
{
int i, j, pj;
int start_i, end_i;
@@ -1210,7 +1210,7 @@ void Estimate_Storage_Sizes( reax_system *system, control_params *control,
real r_ij;
real C12, C34, C56;
real BO, BO_s, BO_pi, BO_pi2;
- list *far_nbrs;
+ reax_list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
@@ -1304,7 +1304,7 @@ void Estimate_Storage_Sizes( reax_system *system, control_params *control,
void Compute_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list** lists, output_controls *out_control )
+ reax_list** lists, output_controls *out_control )
{
real t_start, t_elapsed;
diff --git a/sPuReMD/src/forces.h b/sPuReMD/src/forces.h
index c57aa15..4777325 100644
--- a/sPuReMD/src/forces.h
+++ b/sPuReMD/src/forces.h
@@ -27,8 +27,8 @@
void Init_Bonded_Force_Functions( control_params* );
void Compute_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
-void Estimate_Storage_Sizes( reax_system*, control_params*, list**,
+void Estimate_Storage_Sizes( reax_system*, control_params*, reax_list**,
int*, int*, int*, int* );
#endif
diff --git a/sPuReMD/src/four_body_interactions.c b/sPuReMD/src/four_body_interactions.c
index e0010e8..26a15b7 100644
--- a/sPuReMD/src/four_body_interactions.c
+++ b/sPuReMD/src/four_body_interactions.c
@@ -154,10 +154,10 @@ real Calculate_Omega( rvec dvec_ij, real r_ij, rvec dvec_jk, real r_jk,
void Four_Body_Interactions( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
real p_tor2, p_tor3, p_tor4, p_cot2;
- list *bonds, *thb_intrs;
+ reax_list *bonds, *thb_intrs;
real e_tor_total, e_con_total;
p_tor2 = system->reaxprm.gp.l[23];
diff --git a/sPuReMD/src/four_body_interactions.h b/sPuReMD/src/four_body_interactions.h
index 37136cd..88261c5 100644
--- a/sPuReMD/src/four_body_interactions.h
+++ b/sPuReMD/src/four_body_interactions.h
@@ -25,6 +25,6 @@
#include "mytypes.h"
void Four_Body_Interactions( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
#endif
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index dbcb9ab..48eb0db 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -444,7 +444,7 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
cause trouble, if so we'll have to rethink this approach
Also, we do not write connect lines yet.
*/
-char Write_PDB( reax_system* system, list* bonds, simulation_data *data,
+char Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
control_params *control, static_storage *workspace, output_controls *out_control )
{
int i, buffer_req, buffer_len;
diff --git a/sPuReMD/src/geo_tools.h b/sPuReMD/src/geo_tools.h
index 4c44e30..0339a16 100644
--- a/sPuReMD/src/geo_tools.h
+++ b/sPuReMD/src/geo_tools.h
@@ -123,7 +123,7 @@ char Read_PDB( char*, reax_system*, control_params*,
char Read_BGF( char*, reax_system*, control_params*,
simulation_data*, static_storage* );
-char Write_PDB( reax_system*, list*, simulation_data*,
+char Write_PDB( reax_system*, reax_list*, simulation_data*,
control_params*, static_storage*, output_controls* );
#endif
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 850c044..d4175d4 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -507,7 +507,7 @@ void Init_Workspace( reax_system *system, control_params *control,
void Init_Lists( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, num_nbrs, num_bonds, num_3body, Htop, max_nnz;
int *hb_top, *bond_top;
@@ -531,6 +531,7 @@ void Init_Lists( reax_system *system, control_params *control,
num_3body = 0;
Estimate_Storage_Sizes( system, control, lists, &Htop,
hb_top, bond_top, &num_3body );
+ num_3body = MAX( num_3body, MIN_BONDS );
switch ( control->charge_method )
{
@@ -570,7 +571,7 @@ void Init_Lists( reax_system *system, control_params *control,
#endif
workspace->num_H = 0;
- if ( control->hb_cut > 0 )
+ if ( control->hb_cut > 0.0 )
{
/* init H indexes */
for ( i = 0; i < system->N; ++i )
@@ -586,8 +587,15 @@ void Init_Lists( reax_system *system, control_params *control,
}
}
- Allocate_HBond_List( system->N, workspace->num_H, workspace->hbond_index,
- hb_top, (*lists) + HBONDS );
+ if ( workspace->num_H == 0 )
+ {
+ control->hb_cut = 0.0;
+ }
+ else
+ {
+ Allocate_HBond_List( system->N, workspace->num_H, workspace->hbond_index,
+ hb_top, (*lists) + HBONDS );
+ }
#if defined(DEBUG_FOCUS)
num_hbonds = hb_top[system->N - 1];
@@ -854,8 +862,9 @@ void Init_Out_Controls( reax_system *system, control_params *control,
void Initialize( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
- output_controls *out_control, evolve_function *Evolve )
+ simulation_data *data, static_storage *workspace, reax_list **lists,
+ output_controls *out_control, evolve_function *Evolve,
+ const int output_enabled )
{
#if defined(DEBUG)
real start, end;
@@ -879,7 +888,10 @@ void Initialize( reax_system *system, control_params *control,
Init_Lists( system, control, data, workspace, lists, out_control );
- Init_Out_Controls( system, control, workspace, out_control );
+ if ( output_enabled == TRUE )
+ {
+ Init_Out_Controls( system, control, workspace, out_control );
+ }
/* These are done in forces.c, only forces.c can see all those functions */
Init_Bonded_Force_Functions( control );
@@ -1118,10 +1130,13 @@ void Finalize_Workspace( reax_system *system, control_params *control,
}
-void Finalize_Lists( list **lists )
+void Finalize_Lists( control_params *control, reax_list **lists )
{
Delete_List( TYP_FAR_NEIGHBOR, (*lists) + FAR_NBRS );
- Delete_List( TYP_HBOND, (*lists) + HBONDS );
+ if ( control->hb_cut > 0.0 )
+ {
+ Delete_List( TYP_HBOND, (*lists) + HBONDS );
+ }
Delete_List( TYP_BOND, (*lists) + BONDS );
Delete_List( TYP_THREE_BODY, (*lists) + THREE_BODIES );
@@ -1341,17 +1356,20 @@ void Finalize_Out_Controls( reax_system *system, control_params *control,
void Finalize( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
- output_controls *out_control )
+ simulation_data *data, static_storage *workspace, reax_list **lists,
+ output_controls *out_control, const int output_enabled )
{
if ( control->tabulate )
{
Finalize_LR_Lookup_Table( system, control );
}
- Finalize_Out_Controls( system, control, workspace, out_control );
+ if ( output_enabled == TRUE )
+ {
+ Finalize_Out_Controls( system, control, workspace, out_control );
+ }
- Finalize_Lists( lists );
+ Finalize_Lists( control, lists );
Finalize_Workspace( system, control, workspace );
diff --git a/sPuReMD/src/init_md.h b/sPuReMD/src/init_md.h
index 3d31189..0643e0d 100644
--- a/sPuReMD/src/init_md.h
+++ b/sPuReMD/src/init_md.h
@@ -26,10 +26,11 @@
void Initialize( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*, evolve_function* );
+ static_storage*, reax_list**, output_controls*, evolve_function*,
+ const int );
void Finalize( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls*, const int );
#endif
diff --git a/sPuReMD/src/integrate.c b/sPuReMD/src/integrate.c
index 7f42a36..567e96a 100644
--- a/sPuReMD/src/integrate.c
+++ b/sPuReMD/src/integrate.c
@@ -37,7 +37,7 @@
void Velocity_Verlet_NVE(reax_system* system, control_params* control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, steps, renbr;
real inv_m, dt, dt_sqr;
@@ -68,7 +68,7 @@ void Velocity_Verlet_NVE(reax_system* system, control_params* control,
fprintf( stderr, "verlet1 - ");
#endif
- Reallocate( system, workspace, lists, renbr );
+ Reallocate( system, control, workspace, lists, renbr );
Reset( system, control, data, workspace, lists );
if ( renbr )
{
@@ -92,7 +92,7 @@ void Velocity_Verlet_NVE(reax_system* system, control_params* control,
void Velocity_Verlet_Nose_Hoover_NVT_Klein(reax_system* system, control_params* control,
- simulation_data *data, static_storage *workspace, list **lists,
+ simulation_data *data, static_storage *workspace, reax_list **lists,
output_controls *out_control )
{
int i, itr, steps, renbr;
@@ -130,7 +130,7 @@ void Velocity_Verlet_Nose_Hoover_NVT_Klein(reax_system* system, control_params*
fprintf( stderr, "verlet1 - " );
#endif
- Reallocate( system, workspace, lists, renbr );
+ Reallocate( system, control, workspace, lists, renbr );
Reset( system, control, data, workspace, lists );
if ( renbr )
{
@@ -209,7 +209,7 @@ void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system* system,
control_params* control,
simulation_data *data,
static_storage *workspace,
- list **lists,
+ reax_list **lists,
output_controls *out_control )
{
int i, steps, renbr;
@@ -248,7 +248,7 @@ void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system* system,
fprintf( stderr, "verlet1 - " );
#endif
- Reallocate( system, workspace, lists, renbr );
+ Reallocate( system, control, workspace, lists, renbr );
Reset( system, control, data, workspace, lists );
if ( renbr )
{
@@ -324,7 +324,7 @@ void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system* system,
control_params* control,
simulation_data *data,
static_storage *workspace,
- list **lists,
+ reax_list **lists,
output_controls *out_control )
{
int i, d, steps, renbr;
@@ -363,7 +363,7 @@ void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system* system,
fprintf( stderr, "verlet1 - " );
#endif
- Reallocate( system, workspace, lists, renbr );
+ Reallocate( system, control, workspace, lists, renbr );
Reset( system, control, data, workspace, lists );
if ( renbr )
{
@@ -450,7 +450,7 @@ void Velocity_Verlet_Nose_Hoover_NVT(reax_system* system,
control_params* control,
simulation_data *data,
static_storage *workspace,
- list **lists,
+ reax_list **lists,
output_controls *out_control )
{
int i;
@@ -524,7 +524,7 @@ void Velocity_Verlet_Isotropic_NPT( reax_system* system,
control_params* control,
simulation_data *data,
static_storage *workspace,
- list **lists,
+ reax_list **lists,
output_controls *out_control )
{
int i, itr;
@@ -701,7 +701,7 @@ void Velocity_Verlet_Berendsen_NVT( reax_system* system,
control_params* control,
simulation_data *data,
static_storage *workspace,
- list **lists,
+ reax_list **lists,
output_controls *out_control
)
{
@@ -739,7 +739,7 @@ void Velocity_Verlet_Berendsen_NVT( reax_system* system,
fprintf(stderr, "step%d: verlet1 done\n", data->step);
#endif
- Reallocate( system, workspace, lists, renbr );
+ Reallocate( system, control, workspace, lists, renbr );
Reset( system, control, data, workspace, lists );
if ( renbr )
diff --git a/sPuReMD/src/integrate.h b/sPuReMD/src/integrate.h
index 55d9878..1a821fe 100644
--- a/sPuReMD/src/integrate.h
+++ b/sPuReMD/src/integrate.h
@@ -25,25 +25,25 @@
#include "mytypes.h"
void Velocity_Verlet_NVE( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Velocity_Verlet_Nose_Hoover_NVT( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
void Velocity_Verlet_Nose_Hoover_NVT_Klein( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
void Velocity_Verlet_Flexible_NPT( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
void Velocity_Verlet_Isotropic_NPT( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system*, control_params*,
simulation_data*,
- static_storage*, list**,
+ static_storage*, reax_list**,
output_controls* );
//upon Adri's request moved from parallel code to serial code
@@ -51,7 +51,7 @@ void Velocity_Verlet_Berendsen_NVT( reax_system* ,
control_params* ,
simulation_data *,
static_storage *,
- list **,
+ reax_list **,
output_controls *
);
#endif
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 576c01b..2094d4f 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -142,7 +142,7 @@ static void Sparse_MatVec( const sparse_matrix * const A,
* A: stored in CSR
* A_t: stored in CSR
*/
-void Transpose( const sparse_matrix * const A, sparse_matrix const *A_t )
+void Transpose( const sparse_matrix * const A, sparse_matrix * const A_t )
{
unsigned int i, j, pj, *A_t_top;
diff --git a/sPuReMD/src/lin_alg.h b/sPuReMD/src/lin_alg.h
index a314851..3946f60 100644
--- a/sPuReMD/src/lin_alg.h
+++ b/sPuReMD/src/lin_alg.h
@@ -31,7 +31,7 @@ typedef enum
} TRIANGULARITY;
-void Transpose( const sparse_matrix * const, sparse_matrix const * );
+void Transpose( const sparse_matrix * const, sparse_matrix * const );
void Transpose_I( sparse_matrix * const );
diff --git a/sPuReMD/src/list.c b/sPuReMD/src/list.c
index 351ee88..e6fbd2f 100644
--- a/sPuReMD/src/list.c
+++ b/sPuReMD/src/list.c
@@ -24,7 +24,7 @@
#include "tool_box.h"
-void Make_List( int n, int total_intrs, int type, list* l )
+void Make_List( int n, int total_intrs, int type, reax_list* l )
{
l->n = n;
l->total_intrs = total_intrs;
@@ -89,16 +89,10 @@ void Make_List( int n, int total_intrs, int type, list* l )
}
-void Delete_List( int type, list* l )
+void Delete_List( int type, reax_list* l )
{
- if ( l->index != NULL )
- {
- sfree( l->index, "Delete_List::l->index" );
- }
- if ( l->end_index != NULL )
- {
- sfree( l->end_index, "Delete_List::l->end_index" );
- }
+ sfree( l->index, "Delete_List::l->index" );
+ sfree( l->end_index, "Delete_List::l->end_index" );
switch ( type )
{
diff --git a/sPuReMD/src/list.h b/sPuReMD/src/list.h
index a270158..9cd53cb 100644
--- a/sPuReMD/src/list.h
+++ b/sPuReMD/src/list.h
@@ -25,36 +25,36 @@
#include "mytypes.h"
-void Make_List( int, int, int, list* );
+void Make_List( int, int, int, reax_list* );
-void Delete_List( int, list* );
+void Delete_List( int, reax_list* );
-static inline int Num_Entries( int i, list* l )
+static inline int Num_Entries( int i, reax_list* l )
{
return l->end_index[i] - l->index[i];
}
-static inline int Start_Index( int i, list *l )
+static inline int Start_Index( int i, reax_list *l )
{
return l->index[i];
}
-static inline int End_Index( int i, list *l )
+static inline int End_Index( int i, reax_list *l )
{
return l->end_index[i];
}
-static inline void Set_Start_Index( int i, int val, list *l )
+static inline void Set_Start_Index( int i, int val, reax_list *l )
{
l->index[i] = val;
}
-static inline void Set_End_Index( int i, int val, list *l )
+static inline void Set_End_Index( int i, int val, reax_list *l )
{
l->end_index[i] = val;
}
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index ccc54b8..f75ad16 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -80,7 +80,9 @@
#define NAN_REAL(a) (0)
#endif
-#define PI 3.14159265
+#if !defined(PI)
+ #define PI 3.14159265
+#endif
#define C_ele 332.06371
//#define K_B 503.398008 // kcal/mol/K
#define K_B 0.831687 // amu A^2 / ps^2 / K
@@ -993,7 +995,7 @@ typedef struct
/* hydrogen bond interaction list */
hbond_data *hbond_list;
} select;
-} list;
+} reax_list;
typedef struct
@@ -1025,7 +1027,7 @@ typedef struct
/* trajectory output function pointer definitions */
int (* write_header)( reax_system*, control_params*, static_storage*, void* );
int (* append_traj_frame)(reax_system*, control_params*,
- simulation_data*, static_storage*, list **, void* );
+ simulation_data*, static_storage*, reax_list **, void* );
int (* write)( FILE *, const char *, ... );
#ifdef TEST_ENERGY
@@ -1116,11 +1118,11 @@ typedef struct
/* Function pointer definitions */
typedef void (*interaction_function)(reax_system*, control_params*,
- simulation_data*, static_storage*, list**, output_controls*);
+ simulation_data*, static_storage*, reax_list**, output_controls*);
typedef void (*evolve_function)(reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls*);
+ reax_list**, output_controls*);
/* Global variables */
diff --git a/sPuReMD/src/neighbors.c b/sPuReMD/src/neighbors.c
index 5e23558..c0351c8 100644
--- a/sPuReMD/src/neighbors.c
+++ b/sPuReMD/src/neighbors.c
@@ -54,7 +54,7 @@ static inline real DistSqr_to_CP( rvec cp, rvec x )
void Generate_Neighbor_Lists( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, k, l, m, itr;
int x, y, z;
@@ -64,7 +64,7 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
ivec *nbrs;
rvec *nbrs_cp;
grid *g;
- list *far_nbrs;
+ reax_list *far_nbrs;
far_neighbor_data *nbr_data;
real t_start, t_elapsed;
@@ -174,7 +174,7 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
int Estimate_NumNeighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, j, k, l, m, itr;
int x, y, z;
@@ -349,7 +349,7 @@ static inline int can_Bond( static_storage *workspace, int atom1, int atom2 )
/* check if atom2 is on atom1's near neighbor list */
-static inline int is_Near_Neighbor( list *near_nbrs, int atom1, int atom2 )
+static inline int is_Near_Neighbor( reax_list *near_nbrs, int atom1, int atom2 )
{
int i;
@@ -367,7 +367,7 @@ static inline int is_Near_Neighbor( list *near_nbrs, int atom1, int atom2 )
void Generate_Neighbor_Lists( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, k;
int x, y, z;
@@ -377,9 +377,9 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
int c, count;
int grid_top;
grid *g = &( system->g );
- list *far_nbrs = (*lists) + FAR_NBRS;
+ reax_list *far_nbrs = (*lists) + FAR_NBRS;
//int hb_type1, hb_type2;
- //list *hbonds = (*lists) + HBOND;
+ //reax_list *hbonds = (*lists) + HBOND;
//int top_hbond1, top_hbond2;
get_far_neighbors_function Get_Far_Neighbors;
far_neighbor_data new_nbrs[125];
@@ -617,7 +617,7 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
void Generate_Neighbor_Lists( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, k, l, m, itr;
int x, y, z;
@@ -627,7 +627,7 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
ivec *nbrs;
rvec *nbrs_cp;
grid *g;
- list *far_nbrs;
+ reax_list *far_nbrs;
get_far_neighbors_function Get_Far_Neighbors;
far_neighbor_data new_nbrs[125];
diff --git a/sPuReMD/src/neighbors.h b/sPuReMD/src/neighbors.h
index e849b1e..fde27eb 100644
--- a/sPuReMD/src/neighbors.h
+++ b/sPuReMD/src/neighbors.h
@@ -25,8 +25,8 @@
#include "mytypes.h"
void Generate_Neighbor_Lists( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
int Estimate_NumNeighbors( reax_system*, control_params*,
- static_storage*, list** );
+ static_storage*, reax_list** );
#endif
diff --git a/sPuReMD/src/print_utils.c b/sPuReMD/src/print_utils.c
index 684c2cb..1ef0a52 100644
--- a/sPuReMD/src/print_utils.c
+++ b/sPuReMD/src/print_utils.c
@@ -31,19 +31,19 @@
#ifdef TEST_FORCES
void Dummy_Printer( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
}
void Print_Bond_Orders( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, pj, pk;
bond_order_data *bo_ij;
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *dBOs = (*lists) + DBO;
dbond_data *dbo_k;
/* bond orders */
@@ -110,7 +110,7 @@ void Print_Bond_Orders( reax_system *system, control_params *control,
void Print_Bond_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -128,7 +128,7 @@ void Print_Bond_Forces( reax_system *system, control_params *control,
void Print_LonePair_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -147,7 +147,7 @@ void Print_LonePair_Forces( reax_system *system, control_params *control,
void Print_OverUnderCoor_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
+ simulation_data *data, static_storage *workspace, reax_list **lists,
output_controls *out_control )
{
int i;
@@ -187,7 +187,7 @@ void Print_OverUnderCoor_Forces( reax_system *system, control_params *control,
void Print_Three_Body_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int j;
@@ -245,7 +245,7 @@ void Print_Three_Body_Forces( reax_system *system, control_params *control,
void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
+ simulation_data *data, static_storage *workspace, reax_list **lists,
output_controls *out_control )
{
int j;
@@ -266,7 +266,7 @@ void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
void Print_Four_Body_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int j;
@@ -304,7 +304,7 @@ void Print_Four_Body_Forces( reax_system *system, control_params *control,
void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -343,7 +343,7 @@ void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
void Compare_Total_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
@@ -399,12 +399,12 @@ void Init_Force_Test_Functions( )
/* near nbrs contain both i-j, j-i nbrhood info */
void Print_Near_Neighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, j, id_i, id_j;
char fname[MAX_STR];
FILE *fout;
- list *near_nbrs = &((*lists)[NEAR_NBRS]);
+ reax_list *near_nbrs = &((*lists)[NEAR_NBRS]);
sprintf( fname, "%s.near_nbrs", control->sim_name );
fout = fopen( fname, "w" );
@@ -433,12 +433,12 @@ void Print_Near_Neighbors( reax_system *system, control_params *control,
/* near nbrs contain both i-j, j-i nbrhood info */
void Print_Near_Neighbors2( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, j, id_i, id_j;
char fname[MAX_STR];
FILE *fout;
- list *near_nbrs = &((*lists)[NEAR_NBRS]);
+ reax_list *near_nbrs = &((*lists)[NEAR_NBRS]);
sprintf( fname, "%s.near_nbrs_lgj", control->sim_name );
fout = fopen( fname, "w" );
@@ -468,12 +468,12 @@ void Print_Near_Neighbors2( reax_system *system, control_params *control,
/* far nbrs contain only i-j nbrhood info, no j-i. */
void Print_Far_Neighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, j, id_i, id_j;
char fname[MAX_STR];
FILE *fout;
- list *far_nbrs = &((*lists)[FAR_NBRS]);
+ reax_list *far_nbrs = &((*lists)[FAR_NBRS]);
sprintf( fname, "%s.far_nbrs", control->sim_name );
fout = fopen( fname, "w" );
@@ -513,12 +513,12 @@ int fn_qsort_intcmp( const void *a, const void *b )
void Print_Far_Neighbors2( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, j, id_i, id_j;
char fname[MAX_STR];
FILE *fout;
- list *far_nbrs = &((*lists)[FAR_NBRS]);
+ reax_list *far_nbrs = &((*lists)[FAR_NBRS]);
sprintf( fname, "%s.far_nbrs_lgj", control->sim_name );
fout = fopen( fname, "w" );
@@ -548,7 +548,7 @@ void Print_Far_Neighbors2( reax_system *system, control_params *control,
void Print_Total_Force( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
#if !defined(TEST_FORCES)
@@ -575,7 +575,7 @@ void Print_Total_Force( reax_system *system, control_params *control,
void Output_Results( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, type_i;
real e_pol, q, f_update;
@@ -937,7 +937,7 @@ void Print_Sparse_Matrix_Binary( sparse_matrix *A, char *fname )
}
-void Print_Bonds( reax_system *system, list *bonds, char *fname )
+void Print_Bonds( reax_system *system, reax_list *bonds, char *fname )
{
int i, pj;
bond_data *pbond;
@@ -962,7 +962,7 @@ void Print_Bonds( reax_system *system, list *bonds, char *fname )
}
-void Print_Bond_List2( reax_system *system, list *bonds, char *fname )
+void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
{
int i, j, id_i, id_j, nbr, pj;
FILE *f = fopen( fname, "w" );
diff --git a/sPuReMD/src/print_utils.h b/sPuReMD/src/print_utils.h
index 8c15ebb..fe75d19 100644
--- a/sPuReMD/src/print_utils.h
+++ b/sPuReMD/src/print_utils.h
@@ -25,7 +25,7 @@
#include "mytypes.h"
typedef void (*print_interaction)(reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*);
+ static_storage*, reax_list**, output_controls*);
print_interaction Print_Interactions[NO_OF_INTERACTIONS];
char *Get_Element( reax_system*, int );
@@ -33,19 +33,19 @@ char *Get_Element( reax_system*, int );
char *Get_Atom_Name( reax_system*, int );
void Print_Near_Neighbors( reax_system*, control_params*, static_storage*,
- list** );
+ reax_list** );
void Print_Far_Neighbors( reax_system*, control_params*, static_storage*,
- list** );
+ reax_list** );
void Print_Total_Force( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Output_Results( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_Bond_Orders( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_Linear_System( reax_system*, control_params*, static_storage*, int );
@@ -59,28 +59,28 @@ void Print_Sparse_Matrix2( sparse_matrix*, char*, char* );
void Print_Sparse_Matrix_Binary( sparse_matrix*, char* );
-void Print_Bonds( reax_system*, list*, char* );
-void Print_Bond_List2( reax_system*, list*, char* );
+void Print_Bonds( reax_system*, reax_list*, char* );
+void Print_Bond_List2( reax_system*, reax_list*, char* );
#ifdef TEST_FORCES
void Dummy_Printer( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_Bond_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_OverUnderCoor_Forces(reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*);
+ static_storage*, reax_list**, output_controls*);
void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_Hydrogen_Bond_Forces(reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*);
+ static_storage*, reax_list**, output_controls*);
void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Print_vdW_Coulomb_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Compare_Total_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Init_Force_Test_Functions( );
#endif
diff --git a/sPuReMD/src/reset_utils.c b/sPuReMD/src/reset_utils.c
index bf5330d..0aed2a9 100644
--- a/sPuReMD/src/reset_utils.c
+++ b/sPuReMD/src/reset_utils.c
@@ -115,11 +115,11 @@ void Reset_Workspace( reax_system *system, static_storage *workspace )
void Reset_Neighbor_Lists( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+ static_storage *workspace, reax_list **lists )
{
int i, tmp;
- list *bonds = (*lists) + BONDS;
- list *hbonds = (*lists) + HBONDS;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *hbonds = (*lists) + HBONDS;
for ( i = 0; i < system->N; ++i )
{
@@ -145,7 +145,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control,
void Reset( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists )
+ simulation_data *data, static_storage *workspace, reax_list **lists )
{
Reset_Atoms( system );
diff --git a/sPuReMD/src/reset_utils.h b/sPuReMD/src/reset_utils.h
index aadfe73..4355460 100644
--- a/sPuReMD/src/reset_utils.h
+++ b/sPuReMD/src/reset_utils.h
@@ -37,12 +37,12 @@ void Reset_Test_Forces( reax_system*, static_storage* );
void Reset_Workspace( reax_system*, static_storage* );
void Reset_Neighbor_Lists( reax_system*, control_params*,
- static_storage*, list** );
+ static_storage*, reax_list** );
void Reset( reax_system*, control_params*, simulation_data*,
- static_storage*, list** );
+ static_storage*, reax_list** );
-//void Reset_Neighbor_Lists( reax_system*, static_storage*, list** );
+//void Reset_Neighbor_Lists( reax_system*, static_storage*, reax_list** );
void Reset_Grid( grid* );
diff --git a/sPuReMD/src/single_body_interactions.c b/sPuReMD/src/single_body_interactions.c
index 9da3e21..b6edce1 100644
--- a/sPuReMD/src/single_body_interactions.c
+++ b/sPuReMD/src/single_body_interactions.c
@@ -27,7 +27,7 @@
void LonePair_OverUnder_Coordination_Energy( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
+ simulation_data *data, static_storage *workspace, reax_list **lists,
output_controls *out_control )
{
int i, j, pj, type_i, type_j;
@@ -45,7 +45,7 @@ void LonePair_OverUnder_Coordination_Energy( reax_system *system, control_params
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
- list *bonds = (*lists) + BONDS;
+ reax_list *bonds = (*lists) + BONDS;
/* Initialize parameters */
p_lp1 = system->reaxprm.gp.l[15];
diff --git a/sPuReMD/src/single_body_interactions.h b/sPuReMD/src/single_body_interactions.h
index 41cc649..8283c62 100644
--- a/sPuReMD/src/single_body_interactions.h
+++ b/sPuReMD/src/single_body_interactions.h
@@ -26,5 +26,5 @@
void LonePair_OverUnder_Coordination_Energy( reax_system*, control_params*,
simulation_data*, static_storage*,
- list**, output_controls* );
+ reax_list**, output_controls* );
#endif
diff --git a/sPuReMD/src/testmd.c b/sPuReMD/src/spuremd.c
similarity index 62%
rename from sPuReMD/src/testmd.c
rename to sPuReMD/src/spuremd.c
index 9ef2774..2e791a3 100644
--- a/sPuReMD/src/testmd.c
+++ b/sPuReMD/src/spuremd.c
@@ -36,9 +36,14 @@
#include "vector.h"
+static static_storage workspace;
+static reax_list *lists;
+static output_controls out_control;
+
+
static void Post_Evolve( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- list ** const lists, output_controls * const out_control )
+ reax_list ** const lists, output_controls * const out_control )
{
int i;
rvec diff, cross;
@@ -90,12 +95,14 @@ void static Read_System( char * const geo_file,
if ( (ffield = fopen( ffield_file, "r" )) == NULL )
{
- fprintf( stderr, "Error opening the ffield file!\n" );
+ fprintf( stderr, "[ERROR] Error opening the ffield file!\n" );
+ fprintf( stderr, " [INFO] (%s)\n", ffield_file );
exit( FILE_NOT_FOUND );
}
if ( (ctrl = fopen( control_file, "r" )) == NULL )
{
- fprintf( stderr, "Error opening the ffield file!\n" );
+ fprintf( stderr, "[ERROR] Error opening the ffield file!\n" );
+ fprintf( stderr, " [INFO] (%s)\n", control_file );
exit( FILE_NOT_FOUND );
}
@@ -130,7 +137,7 @@ void static Read_System( char * const geo_file,
}
else
{
- fprintf( stderr, "unknown geo file format. terminating!\n" );
+ fprintf( stderr, "[ERROR] unknown geo file format. terminating!\n" );
exit( INVALID_GEO );
}
@@ -144,84 +151,93 @@ void static Read_System( char * const geo_file,
}
-static void usage( char* argv[] )
+int Setup( char ** args, reax_system * const system, control_params * const control,
+ simulation_data * const data )
{
- fprintf(stderr, "usage: ./%s geometry ffield control\n", argv[0]);
+ lists = (reax_list*) malloc( sizeof(reax_list) * LIST_N );
+
+ Read_System( args[0], args[1], args[2], system, control,
+ data, &workspace, &out_control );
+
+ return SUCCESS;
}
-int main( int argc, char* argv[] )
+int Run( reax_system * const system, control_params * const control, simulation_data * const data,
+ const int output_enabled )
{
- reax_system system;
- control_params control;
- simulation_data data;
- static_storage workspace;
- list *lists;
- output_controls out_control;
- evolve_function Evolve;
int steps;
+ evolve_function Evolve;
- if ( argc != 4 )
- {
- usage(argv);
- exit( INVALID_INPUT );
- }
-
- lists = (list*) malloc( sizeof(list) * LIST_N );
-
- Read_System( argv[1], argv[2], argv[3], &system, &control,
- &data, &workspace, &out_control );
-
- Initialize( &system, &control, &data, &workspace, &lists,
- &out_control, &Evolve );
+ Initialize( system, control, data, &workspace, &lists,
+ &out_control, &Evolve, output_enabled );
/* compute f_0 */
//if( control.restart == 0 ) {
- Reset( &system, &control, &data, &workspace, &lists );
- Generate_Neighbor_Lists( &system, &control, &data, &workspace,
+ Reset( system, control, data, &workspace, &lists );
+ Generate_Neighbor_Lists( system, control, data, &workspace,
&lists, &out_control );
//fprintf( stderr, "total: %.2f secs\n", data.timing.nbrs);
- Compute_Forces(&system, &control, &data, &workspace, &lists, &out_control);
- Compute_Kinetic_Energy( &system, &data );
- Output_Results(&system, &control, &data, &workspace, &lists, &out_control);
- ++data.step;
+ Compute_Forces( system, control, data, &workspace, &lists, &out_control );
+ Compute_Kinetic_Energy( system, data );
+ if ( output_enabled == TRUE )
+ {
+ Output_Results( system, control, data, &workspace, &lists, &out_control );
+ }
+ ++data->step;
//}
//
- for ( ; data.step <= control.nsteps; data.step++ )
+ for ( ; data->step <= control->nsteps; data->step++ )
{
- if ( control.T_mode )
+ if ( control->T_mode )
+ {
+ Temperature_Control( control, data, &out_control );
+ }
+
+ Evolve( system, control, data, &workspace, &lists, &out_control );
+ Post_Evolve( system, control, data, &workspace, &lists, &out_control );
+
+ if ( output_enabled == TRUE )
{
- Temperature_Control( &control, &data, &out_control );
+ Output_Results( system, control, data, &workspace, &lists, &out_control );
+ Analysis( system, control, data, &workspace, &lists, &out_control );
}
- Evolve( &system, &control, &data, &workspace, &lists, &out_control );
- Post_Evolve( &system, &control, &data, &workspace, &lists, &out_control );
- Output_Results( &system, &control, &data, &workspace, &lists, &out_control );
- Analysis( &system, &control, &data, &workspace, &lists, &out_control );
- steps = data.step - data.prev_steps;
+ steps = data->step - data->prev_steps;
if ( steps && out_control.restart_freq &&
- steps % out_control.restart_freq == 0 )
+ steps % out_control.restart_freq == 0 &&
+ output_enabled == TRUE )
{
- Write_Restart( &system, &control, &data, &workspace, &out_control );
+ Write_Restart( system, control, data, &workspace, &out_control );
}
}
- if ( out_control.write_steps > 0 )
+ if ( out_control.write_steps > 0 && output_enabled == TRUE )
{
fclose( out_control.trj );
- Write_PDB( &system, &(lists[BONDS]), &data, &control, &workspace, &out_control );
+ Write_PDB( system, &(lists[BONDS]), data, control, &workspace, &out_control );
}
- data.timing.end = Get_Time( );
- data.timing.elapsed = Get_Timing_Info( data.timing.start );
- fprintf( out_control.log, "total: %.2f secs\n", data.timing.elapsed );
+ data->timing.end = Get_Time( );
+ data->timing.elapsed = Get_Timing_Info( data->timing.start );
+ if ( output_enabled == TRUE )
+ {
+ fprintf( out_control.log, "total: %.2f secs\n", data->timing.elapsed );
+ }
+
+ return SUCCESS;
+}
+
- Finalize( &system, &control, &data, &workspace, &lists,
- &out_control );
+int Cleanup( reax_system * const system, control_params * const control,
+ simulation_data * const data, const int output_enabled )
+{
+ Finalize( system, control, data, &workspace, &lists, &out_control,
+ output_enabled );
sfree( lists, "main::lists" );
- return 0;
+ return SUCCESS;
}
diff --git a/sPuReMD/src/spuremd.h b/sPuReMD/src/spuremd.h
new file mode 100644
index 0000000..7cad1a6
--- /dev/null
+++ b/sPuReMD/src/spuremd.h
@@ -0,0 +1,38 @@
+/*----------------------------------------------------------------------
+ SerialReax - Reax Force Field Simulator
+
+ Copyright (2010) Purdue University
+ Hasan Metin Aktulga, haktulga@cs.purdue.edu
+ Joseph Fogarty, jcfogart@mail.usf.edu
+ Sagar Pandit, pandit@usf.edu
+ Ananth Y Grama, ayg@cs.purdue.edu
+
+ 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:
+ <http://www.gnu.org/licenses/>.
+ ----------------------------------------------------------------------*/
+
+#ifndef __SPUREMD_H_
+#define __SPUREMD_H_
+
+#include "mytypes.h"
+
+
+int Setup( char **, reax_system * const, control_params * const,
+ simulation_data * const );
+
+int Run( reax_system * const, control_params * const,
+ simulation_data * const, const int );
+
+int Cleanup( reax_system * const, control_params * const,
+ simulation_data * const, const int );
+
+
+#endif
diff --git a/sPuReMD/src/three_body_interactions.c b/sPuReMD/src/three_body_interactions.c
index 533c652..159e0cc 100644
--- a/sPuReMD/src/three_body_interactions.c
+++ b/sPuReMD/src/three_body_interactions.c
@@ -80,10 +80,10 @@ void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
played by j which sits in the middle of the other two. */
void Three_Body_Interactions( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
real *total_bo;
- list *bonds, *thb_intrs;
+ reax_list *bonds, *thb_intrs;
bond_data *bond_list;
three_body_interaction_data *thb_list;
real p_pen2, p_pen3, p_pen4;
@@ -667,7 +667,7 @@ void Three_Body_Interactions( reax_system *system, control_params *control,
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
real e_hb_total;
@@ -694,7 +694,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
bond_order_data *bo_ij;
bond_data *pbond_ij;
far_neighbor_data *nbr_jk;
- list *bonds, *hbonds;
+ reax_list *bonds, *hbonds;
bond_data *bond_list;
hbond_data *hbond_list;
rvec *f_i, *f_j, *f_k;
diff --git a/sPuReMD/src/three_body_interactions.h b/sPuReMD/src/three_body_interactions.h
index 55a1188..c654751 100644
--- a/sPuReMD/src/three_body_interactions.h
+++ b/sPuReMD/src/three_body_interactions.h
@@ -25,10 +25,10 @@
#include "mytypes.h"
void Three_Body_Interactions( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Hydrogen_Bonds( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Calculate_Theta( rvec, real, rvec, real, real*, real* );
diff --git a/sPuReMD/src/tool_box.c b/sPuReMD/src/tool_box.c
index 61ab5e7..c37ccc3 100644
--- a/sPuReMD/src/tool_box.c
+++ b/sPuReMD/src/tool_box.c
@@ -402,12 +402,12 @@ int Tokenize( char* s, char*** tok )
{
char test[MAX_LINE];
char *sep = "\t \n!=";
- char *word;
+ char *word, *saveptr;
int count = 0;
strncpy( test, s, MAX_LINE );
- for ( word = strtok(test, sep); word; word = strtok(NULL, sep) )
+ for ( word = strtok_r(test, sep, &saveptr); word; word = strtok_r(NULL, sep, &saveptr) )
{
strncpy( (*tok)[count], word, MAX_LINE );
count++;
diff --git a/sPuReMD/src/traj.c b/sPuReMD/src/traj.c
index 017d657..bfdd2fc 100644
--- a/sPuReMD/src/traj.c
+++ b/sPuReMD/src/traj.c
@@ -164,7 +164,7 @@ int Write_Custom_Header( reax_system *system, control_params *control,
int Append_Custom_Frame( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i, j, pi, pk, pk_j;
int write_atoms, write_bonds, write_angles;
@@ -172,8 +172,8 @@ int Append_Custom_Frame( reax_system *system, control_params *control,
int frame_globals_len, num_bonds, num_thb_intrs;
real P;
char buffer[2048];
- list *bonds = (*lists) + BONDS;
- list *thb_intrs = (*lists) + THREE_BODIES;
+ reax_list *bonds = (*lists) + BONDS;
+ reax_list *thb_intrs = (*lists) + THREE_BODIES;
bond_data *bo_ij;
/* IMPORTANT: This whole part will go to init_trj after finalized! */
@@ -534,7 +534,7 @@ int Write_xyz_Header( reax_system *system, control_params *control,
int Append_xyz_Frame( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
diff --git a/sPuReMD/src/traj.h b/sPuReMD/src/traj.h
index 0e75905..e45921d 100644
--- a/sPuReMD/src/traj.h
+++ b/sPuReMD/src/traj.h
@@ -164,11 +164,11 @@ char Write_Traj_Header( FILE*, int, char**, char**, control_params* );
control_params* control,
simulation_data* data,
static_storage* workspace,
- list** lists,
+ reax_list** lists,
char** various flags);
*/
int Push_Traj_Frame( /*gzfile*/ FILE*, reax_system*, control_params*,
- simulation_data*, static_storage*, list**, char** );
+ simulation_data*, static_storage*, reax_list**, char** );
/*
Append_Traj_Frame( gzfile file,
@@ -176,13 +176,13 @@ int Push_Traj_Frame( /*gzfile*/ FILE*, reax_system*, control_params*,
control_params* control,
simulation_data* data,
static_storage* workspace,
- list** lists,
+ reax_list** lists,
char** various flags);
*/
int Append_Custom_Frame( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
int Append_xyz_Frame ( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void Read_Traj( output_controls*, char * );
diff --git a/sPuReMD/src/two_body_interactions.c b/sPuReMD/src/two_body_interactions.c
index 49fa32b..e533d18 100644
--- a/sPuReMD/src/two_body_interactions.c
+++ b/sPuReMD/src/two_body_interactions.c
@@ -29,11 +29,11 @@
void Bond_Energy( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
real gp3, gp4, gp7, gp10, gp37, ebond_total;
- list *bonds;
+ reax_list *bonds;
bonds = (*lists) + BONDS;
gp3 = system->reaxprm.gp.l[3];
@@ -168,11 +168,11 @@ void Bond_Energy( reax_system *system, control_params *control,
void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+ reax_list **lists, output_controls *out_control )
{
int i;
real p_vdW1, p_vdW1i;
- list *far_nbrs;
+ reax_list *far_nbrs;
real e_vdW_total, e_ele_total;
p_vdW1 = system->reaxprm.gp.l[28];
@@ -520,11 +520,11 @@ void LR_vdW_Coulomb( reax_system *system, control_params *control,
void Tabulated_vdW_Coulomb_Energy( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
+ simulation_data *data, static_storage *workspace, reax_list **lists,
output_controls *out_control )
{
int steps, update_freq, update_energies;
- list *far_nbrs;
+ reax_list *far_nbrs;
real e_vdW_total, e_ele_total;
far_nbrs = (*lists) + FAR_NBRS;
diff --git a/sPuReMD/src/two_body_interactions.h b/sPuReMD/src/two_body_interactions.h
index bee9779..b176b5e 100644
--- a/sPuReMD/src/two_body_interactions.h
+++ b/sPuReMD/src/two_body_interactions.h
@@ -25,10 +25,10 @@
#include <mytypes.h>
void Bond_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
void LR_vdW_Coulomb( reax_system*, control_params*, int, int, real, LR_data* );
void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, reax_list**, output_controls* );
#endif
--
GitLab