244 lines
8.0 KiB
C++
244 lines
8.0 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, 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 "omp_compat.h"
|
|
#include "fix_nve_sphere_omp.h"
|
|
|
|
#include "atom.h"
|
|
#include "force.h"
|
|
#include "math_extra.h"
|
|
|
|
#include <cmath>
|
|
|
|
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;
|
|
|
|
// 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 LMP_DEFAULT_NONE
|
|
#endif
|
|
for (int 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 LMP_DEFAULT_NONE
|
|
#endif
|
|
for (int 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 LMP_DEFAULT_NONE
|
|
#endif
|
|
// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
|
|
for (int i = 0; i < nlocal; i++) {
|
|
double w[3], w_temp[3], a[3];
|
|
double Q[3][3], Q_temp[3][3], R[3][3];
|
|
|
|
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;
|
|
|
|
// 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 LMP_DEFAULT_NONE
|
|
#endif
|
|
for (int 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];
|
|
}
|
|
}
|