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fix_nh_omp.cpp
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Sat, Nov 2, 01:15

fix_nh_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 authors: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "fix_nh_omp.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "modify.h"
#include <math.h>
#include <stdio.h>
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{ISO,ANISO,TRICLINIC};
#define TILTMAX 1.5
typedef struct { double x,y,z; } dbl3_t;
/* ----------------------------------------------------------------------
change box size
remap all atoms or dilate group atoms depending on allremap flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void FixNHOMP::remap()
{
double oldlo,oldhi,expfac;
double * const * _noalias const x = atom->x;
const int * _noalias const mask = atom->mask;
const int nlocal = atom->nlocal;
double * _noalias const h = domain->h;
// omega is not used, except for book-keeping
for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i];
// convert pertinent atoms and rigid bodies to lamda coords
if (allremap) domain->x2lamda(nlocal);
else {
int i;
#if defined (_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->x2lamda(x[i],x[i]);
}
if (nrigid)
for (int i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(0);
// reset global and local box to new size/shape
// this operation corresponds to applying the
// translate and scale operations
// corresponding to the solution of the following ODE:
//
// h_dot = omega_dot * h
//
// where h_dot, omega_dot and h are all upper-triangular
// 3x3 tensors. In Voigt notation, the elements of the
// RHS product tensor are:
// h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
//
// Ordering of operations preserves time symmetry.
const double dto2 = dto/2.0;
const double dto4 = dto/4.0;
const double dto8 = dto/8.0;
// off-diagonal components, first half
if (pstyle == TRICLINIC) {
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
}
// scale diagonal components
// scale tilt factors with cell, if set
if (p_flag[0]) {
oldlo = domain->boxlo[0];
oldhi = domain->boxhi[0];
expfac = exp(dto*omega_dot[0]);
domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
}
if (p_flag[1]) {
oldlo = domain->boxlo[1];
oldhi = domain->boxhi[1];
expfac = exp(dto*omega_dot[1]);
domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
if (scalexy) h[5] *= expfac;
}
if (p_flag[2]) {
oldlo = domain->boxlo[2];
oldhi = domain->boxhi[2];
expfac = exp(dto*omega_dot[2]);
domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
if (scalexz) h[4] *= expfac;
if (scaleyz) h[3] *= expfac;
}
// off-diagonal components, second half
if (pstyle == TRICLINIC) {
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
}
domain->yz = h[3];
domain->xz = h[4];
domain->xy = h[5];
// tilt factor to cell length ratio can not exceed TILTMAX in one step
if (domain->yz < -TILTMAX*domain->yprd ||
domain->yz > TILTMAX*domain->yprd ||
domain->xz < -TILTMAX*domain->xprd ||
domain->xz > TILTMAX*domain->xprd ||
domain->xy < -TILTMAX*domain->xprd ||
domain->xy > TILTMAX*domain->xprd)
error->all(FLERR,"Fix npt/nph has tilted box too far in one step - "
"periodic cell is too far from equilibrium state");
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
if (allremap) domain->lamda2x(nlocal);
else {
int i;
#if defined (_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->lamda2x(x[i],x[i]);
}
if (nrigid)
for (int i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ----------------------------------------------------------------------
perform half-step barostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNHOMP::nh_v_press()
{
const double factor0 = exp(-dt4*(omega_dot[0]+mtk_term2));
const double factor1 = exp(-dt4*(omega_dot[1]+mtk_term2));
const double factor2 = exp(-dt4*(omega_dot[2]+mtk_term2));
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
if (which == NOBIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i].x *= factor0;
v[i].y *= factor1;
v[i].z *= factor2;
if (pstyle == TRICLINIC) {
v[i].x += -dthalf*(v[i].y*omega_dot[5] + v[i].z*omega_dot[4]);
v[i].y += -dthalf*v[i].z*omega_dot[3];
}
v[i].x *= factor0;
v[i].y *= factor1;
v[i].z *= factor2;
}
}
} else if (which == BIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
double buf[3];
if (mask[i] & groupbit) {
temperature->remove_bias(i,&v[i].x);
v[i].x *= factor0;
v[i].y *= factor1;
v[i].z *= factor2;
if (pstyle == TRICLINIC) {
v[i].x += -dthalf*(v[i].y*omega_dot[5] + v[i].z*omega_dot[4]);
v[i].y += -dthalf*v[i].z*omega_dot[3];
}
v[i].x *= factor0;
v[i].y *= factor1;
v[i].z *= factor2;
temperature->restore_bias(i,&v[i].x);
}
}
}
}
/* ----------------------------------------------------------------------
perform half-step update of velocities
-----------------------------------------------------------------------*/
void FixNHOMP::nve_v()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
if (atom->rmass) {
const double * _noalias const rmass = atom->rmass;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
const double dtfm = dtf / rmass[i];
v[i].x += dtfm*f[i].x;
v[i].y += dtfm*f[i].y;
v[i].z += dtfm*f[i].z;
}
}
} else {
const double *_noalias const mass = atom->mass;
const int * _noalias const type = atom->type;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
const double dtfm = dtf / mass[type[i]];
v[i].x += dtfm*f[i].x;
v[i].y += dtfm*f[i].y;
v[i].z += dtfm*f[i].z;
}
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of positions
-----------------------------------------------------------------------*/
void FixNHOMP::nve_x()
{
dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
// x update by full step only for atoms in group
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i].x += dtv * v[i].x;
x[i].y += dtv * v[i].y;
x[i].z += dtv * v[i].z;
}
}
}
/* ----------------------------------------------------------------------
perform half-step thermostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNHOMP::nh_v_temp()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
if (which == NOBIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i].x *= factor_eta;
v[i].y *= factor_eta;
v[i].z *= factor_eta;
}
}
} else if (which == BIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
double buf[3];
if (mask[i] & groupbit) {
temperature->remove_bias(i,&v[i].x);
v[i].x *= factor_eta;
v[i].y *= factor_eta;
v[i].z *= factor_eta;
temperature->restore_bias(i,&v[i].x);
}
}
}
}

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