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sync with SVN

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This commit is contained in:
Steve Plimpton
2016-08-31 13:28:26 -06:00
parent 62b7b69a87
commit ec8b9e21db
6 changed files with 40 additions and 35 deletions
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4
doc/src/Section_howto.txt
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@ -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 compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1[2]) variable xave equal ave(f_1\[2\])
variable xmax equal max(f_1[2]) variable xmax equal max(f_1\[2\])
thermo 1000 thermo 1000
thermo_style custom step temp v_xave v_xmax :pre thermo_style custom step temp v_xave v_xmax :pre

2
lib/kokkos/Makefile.kokkos
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@ -16,7 +16,7 @@ KOKKOS_USE_TPLS ?= ""
#Options: c++11 #Options: c++11
KOKKOS_CXX_STANDARD ?= "c++11" KOKKOS_CXX_STANDARD ?= "c++11"
#Options: aggressive_vectorization,disable_profiling #Options: aggressive_vectorization,disable_profiling
KOKKOS_OPTIONS ?= "aggressive_vectorization" KOKKOS_OPTIONS ?= ""
#Default settings specific options #Default settings specific options
#Options: force_uvm,use_ldg,rdc,enable_lambda #Options: force_uvm,use_ldg,rdc,enable_lambda

14
src/KOKKOS/pair_reax_c_kokkos.cpp
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@ -3878,14 +3878,16 @@ void PairReaxCKokkos<DeviceType>::ev_setup(int eflag, int vflag)
// reallocate per-atom arrays if necessary // reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) { if (eflag_atom && atom->nmax > maxeatom) {
memory->destroy_kokkos(k_eatom,eatom); maxeatom = atom->nmax;
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); memory->destroy_kokkos(k_eatom,eatom);
v_eatom = k_eatom.view<DeviceType>(); memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
v_eatom = k_eatom.view<DeviceType>();
} }
if (vflag_atom && atom->nmax > maxvatom) { if (vflag_atom && atom->nmax > maxvatom) {
memory->destroy_kokkos(k_vatom,vatom); maxvatom = atom->nmax;
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom"); memory->destroy_kokkos(k_vatom,vatom);
v_vatom = k_vatom.view<DeviceType>(); memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
v_vatom = k_vatom.view<DeviceType>();
} }
// zero accumulators // zero accumulators

31
src/compute_omega_chunk.cpp
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@ -27,7 +27,8 @@ using namespace LAMMPS_NS;
ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) : ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, 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"); 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]; double ione[3][3],inverse[3][3];
for (i = 0; i < nchunk; i++) { for (m = 0; m < nchunk; m++) {
ione[0][0] = inertiaall[i][0]; ione[0][0] = inertiaall[m][0];
ione[1][1] = inertiaall[i][1]; ione[1][1] = inertiaall[m][1];
ione[2][2] = inertiaall[i][2]; ione[2][2] = inertiaall[m][2];
ione[0][1] = inertiaall[i][3]; ione[0][1] = inertiaall[m][3];
ione[1][2] = inertiaall[i][4]; ione[1][2] = inertiaall[m][4];
ione[0][2] = inertiaall[i][5]; ione[0][2] = inertiaall[m][5];
ione[1][0] = ione[0][1]; ione[1][0] = ione[0][1];
ione[2][1] = ione[1][2]; ione[2][1] = ione[1][2];
ione[2][0] = ione[0][2]; ione[2][0] = ione[0][2];
@ -221,15 +222,15 @@ void ComputeOmegaChunk::compute_array()
ione[2][0]*ione[1][1]*ione[0][2]; ione[2][0]*ione[1][1]*ione[0][2];
if (determinant > 0.0) if (determinant > 0.0)
for (int i = 0; i < 3; i++) for (i = 0; i < 3; i++)
for (int j = 0; j < 3; j++) for (j = 0; j < 3; j++)
inverse[i][j] /= determinant; inverse[i][j] /= determinant;
omega[i][0] = inverse[0][0]*angmom[i][0] + inverse[0][1]*angmom[i][1] + omega[m][0] = inverse[0][0]*angmom[m][0] + inverse[0][1]*angmom[m][1] +
inverse[0][2]*angmom[i][2]; inverse[0][2]*angmom[m][2];
omega[i][1] = inverse[1][0]*angmom[i][0] + inverse[1][1]*angmom[i][1] + omega[m][1] = inverse[1][0]*angmom[m][0] + inverse[1][1]*angmom[m][1] +
inverse[1][2]*angmom[i][2]; inverse[1][2]*angmom[m][2];
omega[i][2] = inverse[2][0]*angmom[i][0] + inverse[2][1]*angmom[i][1] + omega[m][2] = inverse[2][0]*angmom[m][0] + inverse[2][1]*angmom[m][1] +
inverse[2][2]*angmom[i][2]; inverse[2][2]*angmom[i][2];
} }
} }

3
src/fix_balance.cpp
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@ -35,8 +35,7 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), Fix(lmp, narg, arg), fp(NULL)
fp(NULL), nimbalance(0), imbalance(NULL), imb_fix(NULL), balance(NULL), irregular(NULL)
{ {
if (narg < 6) error->all(FLERR,"Illegal fix balance command"); if (narg < 6) error->all(FLERR,"Illegal fix balance command");

21
src/math_extra.h
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@ -35,7 +35,8 @@ namespace MathExtra {
inline void negate3(double *v); inline void negate3(double *v);
inline void scale3(double s, double *v); inline void scale3(double s, double *v);
inline void add3(const double *v1, const double *v2, double *ans); 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 void sub3(const double *v1, const double *v2, double *ans);
inline double len3(const double *v); inline double len3(const double *v);
inline double lensq3(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 multiply the transpose of mat1 times mat2
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
inline void MathExtra::transpose_times3(const double m[3][3], const double m2[3][3], inline void MathExtra::transpose_times3(const double m[3][3],
double ans[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][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]; 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 multiply mat1 times transpose of mat2
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
inline void MathExtra::times3_transpose(const double m[3][3], const double m2[3][3], inline void MathExtra::times3_transpose(const double m[3][3],
double ans[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][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]; 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 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]) 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, inline void MathExtra::axisangle_to_quat(const double *v, const double angle,
double *quat) double *quat)
{ {
double halfa = 0.5*angle; double halfa = 0.5*angle;
double sina = sin(halfa); 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 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][0] = m[0][2];
ans[0][1] = 0; 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 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][0] = -m[0][1];
ans[0][1] = m[0][0]; ans[0][1] = m[0][0];