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fix_nh_intel.cpp
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Tue, May 28, 11:01

fix_nh_intel.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: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "fix_nh_intel.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "update.h"
#include <cstring>
#include <math.h>
#include <stdio.h>
using namespace LAMMPS_NS;
using namespace FixConst;
#define TILTMAX 1.5
enum{NOBIAS,BIAS};
enum{ISO,ANISO,TRICLINIC};
typedef struct { double x,y,z; } dbl3_t;
/* ----------------------------------------------------------------------
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
FixNHIntel::FixNHIntel(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
_dtfm = 0;
_nlocal3 = 0;
_nlocal_max = 0;
}
/* ---------------------------------------------------------------------- */
FixNHIntel::~FixNHIntel()
{
}
/* ---------------------------------------------------------------------- */
void FixNHIntel::setup(int vflag)
{
FixNH::setup(vflag);
reset_dt();
}
/* ----------------------------------------------------------------------
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 FixNHIntel::remap()
{
double oldlo,oldhi;
double expfac;
dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *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
const double hi0 = domain->h_inv[0];
const double hi1 = domain->h_inv[1];
const double hi2 = domain->h_inv[2];
const double hi3 = domain->h_inv[3];
const double hi4 = domain->h_inv[4];
const double hi5 = domain->h_inv[5];
const double b0 = domain->boxlo[0];
const double b1 = domain->boxlo[1];
const double b2 = domain->boxlo[2];
if (allremap) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
const double d0 = x[i].x - b0;
const double d1 = x[i].y - b1;
const double d2 = x[i].z - b2;
x[i].x = hi0*d0 + hi5*d1 + hi4*d2;
x[i].y = hi1*d1 + hi3*d2;
x[i].z = hi2*d2;
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
if (mask[i] & dilate_group_bit) {
const double d0 = x[i].x - b0;
const double d1 = x[i].y - b1;
const double d2 = x[i].z - b2;
x[i].x = hi0*d0 + hi5*d1 + hi4*d2;
x[i].y = hi1*d1 + hi3*d2;
x[i].z = hi2*d2;
}
}
}
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.
double dto2 = dto/2.0;
double dto4 = dto/4.0;
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
const double h0 = domain->h[0];
const double h1 = domain->h[1];
const double h2 = domain->h[2];
const double h3 = domain->h[3];
const double h4 = domain->h[4];
const double h5 = domain->h[5];
const double nb0 = domain->boxlo[0];
const double nb1 = domain->boxlo[1];
const double nb2 = domain->boxlo[2];
if (allremap) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
x[i].x = h0*x[i].x + h5*x[i].y + h4*x[i].z + nb0;
x[i].y = h1*x[i].y + h3*x[i].z + nb1;
x[i].z = h2*x[i].z + nb2;
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
if (mask[i] & dilate_group_bit) {
x[i].x = h0*x[i].x + h5*x[i].y + h4*x[i].z + nb0;
x[i].y = h1*x[i].y + h3*x[i].z + nb1;
x[i].z = h2*x[i].z + nb2;
}
}
}
if (nrigid)
for (int i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ---------------------------------------------------------------------- */
void FixNHIntel::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
dt4 = 0.25 * update->dt;
dt8 = 0.125 * update->dt;
dto = dthalf;
// If using respa, then remap is performed in innermost level
if (strstr(update->integrate_style,"respa"))
dto = 0.5*step_respa[0];
if (pstat_flag)
pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
if (tstat_flag)
tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst :
atom->nlocal;
if (nlocal > _nlocal_max) {
if (_nlocal_max) memory->destroy(_dtfm);
_nlocal_max = static_cast<int>(1.20 * nlocal);
memory->create(_dtfm, _nlocal_max * 3, "fix_nve_intel:dtfm");
}
_nlocal3 = nlocal * 3;
if (igroup == 0) {
if (atom->rmass) {
const double * const rmass = atom->rmass;
int n = 0;
for (int i = 0; i < nlocal; i++) {
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
}
} else {
const double * const mass = atom->mass;
const int * const type = atom->type;
int n = 0;
for (int i = 0; i < nlocal; i++) {
_dtfm[n++] = dtf / mass[type[i]];
_dtfm[n++] = dtf / mass[type[i]];
_dtfm[n++] = dtf / mass[type[i]];
}
}
} else {
if (atom->rmass) {
const double * const rmass = atom->rmass;
int n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
} else {
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
}
} else {
const double * const mass = atom->mass;
const int * const type = atom->type;
int n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
_dtfm[n++] = dtf / mass[type[i]];
_dtfm[n++] = dtf / mass[type[i]];
_dtfm[n++] = dtf / mass[type[i]];
} else {
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
perform half-step barostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNHIntel::nh_v_press()
{
if (pstyle == TRICLINIC || which == BIAS) {
FixNH::nh_v_press();
return;
}
dbl3_t * _noalias const v = (dbl3_t *)atom->v[0];
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double f0 = exp(-dt4*(omega_dot[0]+mtk_term2));
double f1 = exp(-dt4*(omega_dot[1]+mtk_term2));
double f2 = exp(-dt4*(omega_dot[2]+mtk_term2));
f0 *= f0;
f1 *= f1;
f2 *= f2;
if (igroup == 0) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
v[i].x *= f0;
v[i].y *= f1;
v[i].z *= f2;
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i].x *= f0;
v[i].y *= f1;
v[i].z *= f2;
}
}
}
}
/* ----------------------------------------------------------------------
perform half-step update of velocities
-----------------------------------------------------------------------*/
void FixNHIntel::nve_v()
{
if (neighbor->ago == 0) reset_dt();
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++)
v[i] += _dtfm[i] * f[i];
}
/* ----------------------------------------------------------------------
perform full-step update of positions
-----------------------------------------------------------------------*/
void FixNHIntel::nve_x()
{
double * _noalias const x = atom->x[0];
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
// x update by full step only for atoms in group
if (igroup == 0) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++)
x[i] += dtv * v[i];
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++) {
if (_dtfm[i] != 0.0)
x[i] += dtv * v[i];
}
}
}
/* ----------------------------------------------------------------------
perform half-step thermostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNHIntel::nh_v_temp()
{
if (which == BIAS) {
FixNH::nh_v_temp();
return;
}
double * _noalias const v = atom->v[0];
if (igroup == 0) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++)
v[i] *= factor_eta;
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++) {
if (_dtfm[i] != 0.0)
v[i] *= factor_eta;
}
}
}
double FixNHIntel::memory_usage()
{
return FixNH::memory_usage() + _nlocal_max * 3 * sizeof(double);
}

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