From ec8b9e21dbb40c81d0ba94e730db192136daf595 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Wed, 31 Aug 2016 13:28:26 -0600
Subject: [PATCH] sync with SVN
---
doc/src/Section_howto.txt | 4 ++--
lib/kokkos/Makefile.kokkos | 2 +-
src/KOKKOS/pair_reax_c_kokkos.cpp | 14 ++++++++------
src/compute_omega_chunk.cpp | 31 ++++++++++++++++---------------
src/fix_balance.cpp | 3 +--
src/math_extra.h | 21 ++++++++++++---------
6 files changed, 40 insertions(+), 35 deletions(-)
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 8bd9ef805d..d88ab0c2de 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -2303,8 +2303,8 @@ fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_1[2])
-variable xmax equal max(f_1[2])
+variable xave equal ave(f_1\[2\])
+variable xmax equal max(f_1\[2\])
thermo 1000
thermo_style custom step temp v_xave v_xmax :pre
diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos
index af2a617752..c01ceaf64d 100644
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@@ -16,7 +16,7 @@ KOKKOS_USE_TPLS ?= ""
#Options: c++11
KOKKOS_CXX_STANDARD ?= "c++11"
#Options: aggressive_vectorization,disable_profiling
-KOKKOS_OPTIONS ?= "aggressive_vectorization"
+KOKKOS_OPTIONS ?= ""
#Default settings specific options
#Options: force_uvm,use_ldg,rdc,enable_lambda
diff --git a/src/KOKKOS/pair_reax_c_kokkos.cpp b/src/KOKKOS/pair_reax_c_kokkos.cpp
index 9e0f06ef30..eba6fbb0b5 100644
--- a/src/KOKKOS/pair_reax_c_kokkos.cpp
+++ b/src/KOKKOS/pair_reax_c_kokkos.cpp
@@ -3878,14 +3878,16 @@ void PairReaxCKokkos<DeviceType>::ev_setup(int eflag, int vflag)
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
- memory->destroy_kokkos(k_eatom,eatom);
- memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
- v_eatom = k_eatom.view<DeviceType>();
+ maxeatom = atom->nmax;
+ memory->destroy_kokkos(k_eatom,eatom);
+ memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+ v_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom && atom->nmax > maxvatom) {
- memory->destroy_kokkos(k_vatom,vatom);
- memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
- v_vatom = k_vatom.view<DeviceType>();
+ maxvatom = atom->nmax;
+ memory->destroy_kokkos(k_vatom,vatom);
+ memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
+ v_vatom = k_vatom.view<DeviceType>();
}
// zero accumulators
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index 58acc19c37..50f7db7aa7 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -27,7 +27,8 @@ using namespace LAMMPS_NS;
ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), angmom(NULL), angmomall(NULL)
+ idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL),
+ angmom(NULL), angmomall(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
@@ -192,13 +193,13 @@ void ComputeOmegaChunk::compute_array()
double ione[3][3],inverse[3][3];
- for (i = 0; i < nchunk; i++) {
- ione[0][0] = inertiaall[i][0];
- ione[1][1] = inertiaall[i][1];
- ione[2][2] = inertiaall[i][2];
- ione[0][1] = inertiaall[i][3];
- ione[1][2] = inertiaall[i][4];
- ione[0][2] = inertiaall[i][5];
+ for (m = 0; m < nchunk; m++) {
+ ione[0][0] = inertiaall[m][0];
+ ione[1][1] = inertiaall[m][1];
+ ione[2][2] = inertiaall[m][2];
+ ione[0][1] = inertiaall[m][3];
+ ione[1][2] = inertiaall[m][4];
+ ione[0][2] = inertiaall[m][5];
ione[1][0] = ione[0][1];
ione[2][1] = ione[1][2];
ione[2][0] = ione[0][2];
@@ -221,15 +222,15 @@ void ComputeOmegaChunk::compute_array()
ione[2][0]*ione[1][1]*ione[0][2];
if (determinant > 0.0)
- for (int i = 0; i < 3; i++)
- for (int j = 0; j < 3; j++)
+ for (i = 0; i < 3; i++)
+ for (j = 0; j < 3; j++)
inverse[i][j] /= determinant;
- omega[i][0] = inverse[0][0]*angmom[i][0] + inverse[0][1]*angmom[i][1] +
- inverse[0][2]*angmom[i][2];
- omega[i][1] = inverse[1][0]*angmom[i][0] + inverse[1][1]*angmom[i][1] +
- inverse[1][2]*angmom[i][2];
- omega[i][2] = inverse[2][0]*angmom[i][0] + inverse[2][1]*angmom[i][1] +
+ omega[m][0] = inverse[0][0]*angmom[m][0] + inverse[0][1]*angmom[m][1] +
+ inverse[0][2]*angmom[m][2];
+ omega[m][1] = inverse[1][0]*angmom[m][0] + inverse[1][1]*angmom[m][1] +
+ inverse[1][2]*angmom[m][2];
+ omega[m][2] = inverse[2][0]*angmom[m][0] + inverse[2][1]*angmom[m][1] +
inverse[2][2]*angmom[i][2];
}
}
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index f29518515c..500498b463 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -35,8 +35,7 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg),
- fp(NULL), nimbalance(0), imbalance(NULL), imb_fix(NULL), balance(NULL), irregular(NULL)
+ Fix(lmp, narg, arg), fp(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal fix balance command");
diff --git a/src/math_extra.h b/src/math_extra.h
index 0bfc7193a4..3c00f7a4fc 100755
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -35,7 +35,8 @@ namespace MathExtra {
inline void negate3(double *v);
inline void scale3(double s, double *v);
inline void add3(const double *v1, const double *v2, double *ans);
- inline void scaleadd3(double s, const double *v1, const double *v2, double *ans);
+ inline void scaleadd3(double s, const double *v1, const double *v2,
+ double *ans);
inline void sub3(const double *v1, const double *v2, double *ans);
inline double len3(const double *v);
inline double lensq3(const double *v);
@@ -389,8 +390,8 @@ inline void MathExtra::times3(const double m[3][3], const double m2[3][3],
multiply the transpose of mat1 times mat2
------------------------------------------------------------------------- */
-inline void MathExtra::transpose_times3(const double m[3][3], const double m2[3][3],
- double ans[3][3])
+inline void MathExtra::transpose_times3(const double m[3][3],
+ const double m2[3][3],double ans[3][3])
{
ans[0][0] = m[0][0]*m2[0][0] + m[1][0]*m2[1][0] + m[2][0]*m2[2][0];
ans[0][1] = m[0][0]*m2[0][1] + m[1][0]*m2[1][1] + m[2][0]*m2[2][1];
@@ -407,8 +408,8 @@ inline void MathExtra::transpose_times3(const double m[3][3], const double m2[3]
multiply mat1 times transpose of mat2
------------------------------------------------------------------------- */
-inline void MathExtra::times3_transpose(const double m[3][3], const double m2[3][3],
- double ans[3][3])
+inline void MathExtra::times3_transpose(const double m[3][3],
+ const double m2[3][3],double ans[3][3])
{
ans[0][0] = m[0][0]*m2[0][0] + m[0][1]*m2[0][1] + m[0][2]*m2[0][2];
ans[0][1] = m[0][0]*m2[1][0] + m[0][1]*m2[1][1] + m[0][2]*m2[1][2];
@@ -423,7 +424,7 @@ inline void MathExtra::times3_transpose(const double m[3][3], const double m2[3]
/* ----------------------------------------------------------------------
invert a matrix
- does NOT checks for singular or badly scaled matrix
+ does NOT check for singular or badly scaled matrix
------------------------------------------------------------------------- */
inline void MathExtra::invert3(const double m[3][3], double ans[3][3])
@@ -631,7 +632,7 @@ inline void MathExtra::invquatvec(double *a, double *b, double *c)
------------------------------------------------------------------------- */
inline void MathExtra::axisangle_to_quat(const double *v, const double angle,
- double *quat)
+ double *quat)
{
double halfa = 0.5*angle;
double sina = sin(halfa);
@@ -663,7 +664,8 @@ inline void MathExtra::rotation_generator_x(const double m[3][3],
Apply principal rotation generator about y to rotation matrix m
------------------------------------------------------------------------- */
-inline void MathExtra::rotation_generator_y(const double m[3][3], double ans[3][3])
+inline void MathExtra::rotation_generator_y(const double m[3][3],
+ double ans[3][3])
{
ans[0][0] = m[0][2];
ans[0][1] = 0;
@@ -680,7 +682,8 @@ inline void MathExtra::rotation_generator_y(const double m[3][3], double ans[3][
Apply principal rotation generator about z to rotation matrix m
------------------------------------------------------------------------- */
-inline void MathExtra::rotation_generator_z(const double m[3][3], double ans[3][3])
+inline void MathExtra::rotation_generator_z(const double m[3][3],
+ double ans[3][3])
{
ans[0][0] = -m[0][1];
ans[0][1] = m[0][0];
--
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