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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12069 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-06-04 20:52:04 +00:00
parent 88a3f9d326
commit 1f667449d1
15 changed files with 172 additions and 159 deletions
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100
src/verlet.cpp
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@ -17,6 +17,7 @@
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
@ -69,17 +70,11 @@ void Verlet::init()
int ifix = modify->find_fix("package_omp");
if (ifix >= 0) external_force_clear = 1;
// set flags for what arrays to clear in force_clear()
// need to clear additionals arrays if they exist
// set flags for arrays to clear in force_clear()
torqueflag = 0;
torqueflag = extraflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
e_flag = 0;
if (atom->e_flag) e_flag = 1;
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
if (atom->avec->forceclearflag) extraflag = 1;
// orthogonal vs triclinic simulation box
@ -330,6 +325,7 @@ void Verlet::cleanup()
void Verlet::force_clear()
{
int i;
size_t nbytes;
if (external_force_clear) return;
@ -337,19 +333,16 @@ void Verlet::force_clear()
// if either newton flag is set, also include ghosts
// when using threads always clear all forces.
if (neighbor->includegroup == 0) {
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
int nlocal = atom->nlocal;
size_t nbytes = sizeof(double) * nall;
if (neighbor->includegroup == 0) {
nbytes = sizeof(double) * nlocal;
if (force->newton) nbytes += sizeof(double) * atom->nghost;
if (nbytes) {
memset(&(atom->f[0][0]),0,3*nbytes);
if (torqueflag) memset(&(atom->torque[0][0]),0,3*nbytes);
if (erforceflag) memset(&(atom->erforce[0]), 0, nbytes);
if (e_flag) memset(&(atom->de[0]), 0, nbytes);
if (rho_flag) memset(&(atom->drho[0]), 0, nbytes);
memset(&atom->f[0][0],0,3*nbytes);
if (torqueflag) memset(&atom->torque[0][0],0,3*nbytes);
if (extraflag) atom->avec->force_clear(0,nbytes);
}
// neighbor includegroup flag is set
@ -357,70 +350,21 @@ void Verlet::force_clear()
// if either newton flag is set, also include ghosts
} else {
int nall = atom->nfirst;
nbytes = sizeof(double) * atom->nfirst;
double **f = atom->f;
for (i = 0; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
if (nbytes) {
memset(&atom->f[0][0],0,3*nbytes);
if (torqueflag) memset(&atom->torque[0][0],0,3*nbytes);
if (extraflag) atom->avec->force_clear(0,nbytes);
}
if (force->newton) {
nall = atom->nlocal + atom->nghost;
nbytes = sizeof(double) * atom->nghost;
for (i = atom->nlocal; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = atom->nlocal; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
if (nbytes) {
memset(&atom->f[nlocal][0],0,3*nbytes);
if (torqueflag) memset(&atom->torque[nlocal][0],0,3*nbytes);
if (extraflag) atom->avec->force_clear(nlocal,nbytes);
}
}
}