Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80464212
domain_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Aug 31, 21:12
Size
5 KB
Mime Type
text/x-c
Expires
Mon, Sep 2, 21:12 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
20059015
Attached To
rLAMMPS lammps
domain_omp.cpp
View Options
/* ----------------------------------------------------------------------
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;
}
}
Event Timeline
Log In to Comment