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domain_omp.cpp
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Tue, Jun 25, 01:09

domain_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author : Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "domain.h"
#include "accelerator_omp.h"
#include "atom.h"
using namespace LAMMPS_NS;
typedef struct { double x,y,z; } dbl3_t;
/* ----------------------------------------------------------------------
enforce PBC and modify box image flags for each atom
called every reneighboring and by other commands that change atoms
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
if fix deform, remap velocity of fix group atoms by box edge velocities
for triclinic, atoms must be in lamda coords (0-1) before pbc is called
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */
void DomainOMP::pbc()
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
dbl3_t * _noalias const v = (dbl3_t *)&atom->v[0][0];
const double * _noalias const lo = (triclinic == 0) ? boxlo : boxlo_lamda;
const double * _noalias const hi = (triclinic == 0) ? boxhi : boxhi_lamda;
const double * _noalias const period = (triclinic == 0) ? prd : prd_lamda;
const int * _noalias const mask = atom->mask;
imageint * _noalias const image = atom->image;
const int nlocal = atom->nlocal;
int i;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
imageint idim,otherdims;
if (xperiodic) {
if (x[i].x < lo[0]) {
x[i].x += period[0];
if (deform_vremap && mask[i] & deform_groupbit) v[i].x += h_rate[0];
idim = image[i] & IMGMASK;
otherdims = image[i] ^ idim;
idim--;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
if (x[i].x >= hi[0]) {
x[i].x -= period[0];
x[i].x = MAX(x[i].x,lo[0]);
if (deform_vremap && mask[i] & deform_groupbit) v[i].x -= h_rate[0];
idim = image[i] & IMGMASK;
otherdims = image[i] ^ idim;
idim++;
idim &= IMGMASK;
image[i] = otherdims | idim;
}
}
if (yperiodic) {
if (x[i].y < lo[1]) {
x[i].y += period[1];
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x += h_rate[5];
v[i].y += h_rate[1];
}
idim = (image[i] >> IMGBITS) & IMGMASK;
otherdims = image[i] ^ (idim << IMGBITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
if (x[i].y >= hi[1]) {
x[i].y -= period[1];
x[i].y = MAX(x[i].y,lo[1]);
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x -= h_rate[5];
v[i].y -= h_rate[1];
}
idim = (image[i] >> IMGBITS) & IMGMASK;
otherdims = image[i] ^ (idim << IMGBITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMGBITS);
}
}
if (zperiodic) {
if (x[i].z < lo[2]) {
x[i].z += period[2];
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x += h_rate[4];
v[i].y += h_rate[3];
v[i].z += h_rate[2];
}
idim = image[i] >> IMG2BITS;
otherdims = image[i] ^ (idim << IMG2BITS);
idim--;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
if (x[i].z >= hi[2]) {
x[i].z -= period[2];
x[i].z = MAX(x[i].z,lo[2]);
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x -= h_rate[4];
v[i].y -= h_rate[3];
v[i].z -= h_rate[2];
}
idim = image[i] >> IMG2BITS;
otherdims = image[i] ^ (idim << IMG2BITS);
idim++;
idim &= IMGMASK;
image[i] = otherdims | (idim << IMG2BITS);
}
}
}
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for all N atoms
x = H lamda + x0;
------------------------------------------------------------------------- */
void DomainOMP::lamda2x(int n)
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
int i;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for (i = 0; i < num; i++) {
x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0];
x[i].y = h[1]*x[i].y + h[3]*x[i].z + boxlo[1];
x[i].z = h[2]*x[i].z + boxlo[2];
}
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for all N atoms
lamda = H^-1 (x - x0)
------------------------------------------------------------------------- */
void DomainOMP::x2lamda(int n)
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
int i;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for (i = 0; i < num; i++) {
double delta0 = x[i].x - boxlo[0];
double delta1 = x[i].y - boxlo[1];
double delta2 = x[i].z - boxlo[2];
x[i].x = h_inv[0]*delta0 + h_inv[5]*delta1 + h_inv[4]*delta2;
x[i].y = h_inv[1]*delta1 + h_inv[3]*delta2;
x[i].z = h_inv[2]*delta2;
}
}

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