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lammps/src/USER-OMP/fix_nve_sphere_omp.cpp
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fix_nve_sphere_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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "fix_nve_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "respa.h"
#include "force.h"
#include "error.h"
#include "math_vector.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathExtra;
#define INERTIA 0.4 // moment of inertia prefactor for sphere
enum{NONE,DIPOLE};
enum{NODLM,DLM};
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void FixNVESphereOMP::initial_integrate(int vflag)
{
double * const * const x = atom->x;
double * const * const v = atom->v;
const double * const * const f = atom->f;
double * const * const omega = atom->omega;
const double * const * const torque = atom->torque;
const double * const radius = atom->radius;
const double * const rmass = atom->rmass;
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
// set timestep here since dt may have changed or come via rRESPA
const double dtfrotate = dtf / INERTIA;
// update v,x,omega for all particles
// d_omega/dt = torque / inertia
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
const double dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
// update mu for dipoles
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
if (extra == DIPOLE) {
double * const * const mu = atom->mu;
if (dlm == NODLM) {
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
for (i = 0; i < nlocal; i++) {
double g0,g1,g2,msq,scale;
if (mask[i] & groupbit) {
if (mu[i][3] > 0.0) {
g0 = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g1 = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g2 = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g0*g0 + g1*g1 + g2*g2;
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g0*scale;
mu[i][1] = g1*scale;
mu[i][2] = g2*scale;
}
}
}
} else {
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
for (i = 0; i < nlocal; i++) {
vector w, w_temp, a;
matrix Q, Q_temp, R;
if (mask[i] & groupbit && mu[i][3] > 0.0) {
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
// Define mu to lie along the z axis in the body frame
// We take the unit dipole to avoid getting a scaling matrix
const double inv_len_mu = 1.0/mu[i][3];
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
// vx = [ 0 -v[2] v[1]
// v[2] 0 -v[0]
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
const double s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
const double scale = (1.0 - a[2])/s2;
Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
} else { // if parallel then we just have I or -I
Q[0][0] = 1.0/a[2]; Q[0][1] = 0.0; Q[0][2] = 0.0;
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
mu[i][2] = Q_temp[2][2] * mu[i][3];
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVESphereOMP::final_integrate()
{
double * const * const v = atom->v;
const double * const * const f = atom->f;
double * const * const omega = atom->omega;
const double * const * const torque = atom->torque;
const double * const rmass = atom->rmass;
const double * const radius = atom->radius;
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
// set timestep here since dt may have changed or come via rRESPA
const double dtfrotate = dtf / INERTIA;
// update v,omega for all particles
// d_omega/dt = torque / inertia
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
const double dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
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