From 44c9e8135353fa44992e241bed9474b703382dae Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Wed, 7 Sep 2016 11:13:49 -0400
Subject: [PATCH] sPuReMD: fix incorrect thread parallelism inside bonded force
routines. Update default value of CFLAGS in autotools.
---
PG-PuReMD/configure.ac | 1 +
PuReMD-GPU/configure.ac | 1 +
PuReMD/configure.ac | 1 +
configure.ac | 1 +
sPuReMD/configure.ac | 1 +
sPuReMD/src/three_body_interactions.c | 4 ++--
6 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/PG-PuReMD/configure.ac b/PG-PuReMD/configure.ac
index 8b29f9ab..68be6a51 100644
--- a/PG-PuReMD/configure.ac
+++ b/PG-PuReMD/configure.ac
@@ -4,6 +4,7 @@
AC_PREREQ([2.69])
AC_INIT([PG-PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
+: ${CFLAGS=""}
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])])
diff --git a/PuReMD-GPU/configure.ac b/PuReMD-GPU/configure.ac
index 11ed3370..c947ed02 100644
--- a/PuReMD-GPU/configure.ac
+++ b/PuReMD-GPU/configure.ac
@@ -4,6 +4,7 @@
AC_PREREQ([2.69])
AC_INIT([PuReMD-GPU], [1.0], [ohearnku@msu.edu hma@msu.edu])
+: ${CFLAGS=""}
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])])
diff --git a/PuReMD/configure.ac b/PuReMD/configure.ac
index 213b239f..28e6d7df 100644
--- a/PuReMD/configure.ac
+++ b/PuReMD/configure.ac
@@ -4,6 +4,7 @@
AC_PREREQ([2.69])
AC_INIT([PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
+: ${CFLAGS=""}
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])])
diff --git a/configure.ac b/configure.ac
index 11130d74..7081dd34 100644
--- a/configure.ac
+++ b/configure.ac
@@ -4,6 +4,7 @@
AC_PREREQ([2.69])
AC_INIT([Purdue Molecular Dynamics Suite], [1.0], [ohearnku@msu.edu hma@msu.edu])
+: ${CFLAGS=""}
AM_INIT_AUTOMAKE([1.15 -Wall -Werror])
# Enable silent build rules by default.
m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
diff --git a/sPuReMD/configure.ac b/sPuReMD/configure.ac
index 358dfe7e..1ffd7f0a 100644
--- a/sPuReMD/configure.ac
+++ b/sPuReMD/configure.ac
@@ -4,6 +4,7 @@
AC_PREREQ([2.69])
AC_INIT([sPuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
+: ${CFLAGS=""}
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])])
diff --git a/sPuReMD/src/three_body_interactions.c b/sPuReMD/src/three_body_interactions.c
index d12ab80f..078d951a 100644
--- a/sPuReMD/src/three_body_interactions.c
+++ b/sPuReMD/src/three_body_interactions.c
@@ -30,7 +30,7 @@
void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
real *theta, real *cos_theta )
{
- (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk );
+ (*cos_theta) = rvec_Dot( dvec_ji, dvec_jk ) / ( d_ji * d_jk );
if ( *cos_theta > 1. ) *cos_theta = 1.0;
if ( *cos_theta < -1. ) *cos_theta = -1.0;
@@ -48,7 +48,7 @@ void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
real sqr_d_jk = SQR(d_jk);
real inv_dists = 1.0 / (d_ji * d_jk);
real inv_dists3 = POW( inv_dists, 3 );
- real dot_dvecs = Dot( dvec_ji, dvec_jk, 3 );
+ real dot_dvecs = rvec_Dot( dvec_ji, dvec_jk );
real Cdot_inv3 = dot_dvecs * inv_dists3;
for ( t = 0; t < 3; ++t )
--
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