Page MenuHomec4science
Files F71741046

fix_rigid_nh_omp.cpp
No OneTemporary
Actions

File Metadata

Created
Fri, Jul 12, 21:21

fix_rigid_nh_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 "fix_rigid_nh_omp.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "force.h"
#include "kspace.h"
#include "modify.h"
#include "update.h"
#include <string.h>
#if defined(_OPENMP)
#include <omp.h>
#endif
#include "math_extra.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
typedef struct { double x,y,z; } dbl3_t;
/* ----------------------------------------------------------------------
perform preforce velocity Verlet integration
see Kamberaj paper for step references
------------------------------------------------------------------------- */
void FixRigidNHOMP::initial_integrate(int vflag)
{
double scale_r,scale_t[3],scale_v[3];
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_v[0] = scale_v[1] = scale_v[2] = 1.0;
scale_r = 1.0;
if (tstat_flag) {
akin_t = akin_r = 0.0;
double tmp = exp(-dtq * eta_dot_t[0]);
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
tmp = exp(-dtq * eta_dot_r[0]);
scale_r = tmp;
}
if (pstat_flag) {
akin_t = akin_r = 0.0;
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
scale_r *= exp(-dtq * (pdim * mtk_term2));
double tmp = dtq * epsilon_dot[0];
scale_v[0] = dtv * exp(tmp) * maclaurin_series(tmp);
tmp = dtq * epsilon_dot[1];
scale_v[1] = dtv * exp(tmp) * maclaurin_series(tmp);
tmp = dtq * epsilon_dot[2];
scale_v[2] = dtv * exp(tmp) * maclaurin_series(tmp);
}
// update xcm, vcm, quat, conjqm and angmom
double akt=0.0, akr=0.0;
int ibody;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr)
#endif
for (ibody = 0; ibody < nbody; ibody++) {
double mbody[3],tbody[3],fquat[4];
const double dtf2 = dtf * 2.0;
// step 1.1 - update vcm by 1/2 step
const double dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
double tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akt += masstotal[ibody]*tmp;
}
// step 1.2 - update xcm by full step
if (!pstat_flag) {
xcm[ibody][0] += dtv * vcm[ibody][0];
xcm[ibody][1] += dtv * vcm[ibody][1];
xcm[ibody][2] += dtv * vcm[ibody][2];
} else {
xcm[ibody][0] += scale_v[0] * vcm[ibody][0];
xcm[ibody][1] += scale_v[1] * vcm[ibody][1];
xcm[ibody][2] += scale_v[2] * vcm[ibody][2];
}
// step 1.3 - apply torque (body coords) to quaternion momentum
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] *= scale_r;
conjqm[ibody][1] *= scale_r;
conjqm[ibody][2] *= scale_r;
conjqm[ibody][3] *= scale_r;
}
// step 1.4 to 1.13 - use no_squish rotate to update p and q
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
// update exyz_space
// transform p back to angmom
// update angular velocity
MathExtra::q_to_exyz(quat[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody]);
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
if (tstat_flag || pstat_flag) {
akr += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
} // end of parallel for
if (pstat_flag || tstat_flag) {
akin_t = akt;
akin_r = akr;
}
// compute target temperature
// update thermostat chains using akin_t and akin_r
// refer to update_nhcp() in Kamberaj et al.
if (tstat_flag) {
compute_temp_target();
nhc_temp_integrate();
}
// update thermostat chains coupled with barostat
// refer to update_nhcb() in Kamberaj et al.
if (pstat_flag) {
nhc_press_integrate();
}
// virial setup before call to set_xv
if (vflag) v_setup(vflag);
else evflag = 0;
// remap simulation box by 1/2 step
if (pstat_flag) remap();
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
if (triclinic)
if (evflag)
set_xv_thr<1,1>();
else
set_xv_thr<1,0>();
else
if (evflag)
set_xv_thr<0,1>();
else
set_xv_thr<0,0>();
// remap simulation box by full step
// redo KSpace coeffs since volume has changed
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
}
}
/* ---------------------------------------------------------------------- */
void FixRigidNHOMP::final_integrate()
{
double scale_t[3],scale_r;
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_r = 1.0;
if (tstat_flag) {
double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
}
if (pstat_flag) {
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
scale_r *= exp(-dtq * (pdim * mtk_term2));
akin_t = akin_r = 0.0;
}
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const double * const * const torque_one = atom->torque;
const int nlocal = atom->nlocal;
// sum over atoms to get force and torque on rigid body
// we have 3 different strategies for multi-threading this.
if (rstyle == SINGLE) {
// we have just one rigid body. use OpenMP reduction to get sum[]
double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
int i;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) reduction(+:s0,s1,s2,s3,s4,s5)
#endif
for (i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody < 0) continue;
double unwrap[3];
domain->unmap(x[i],xcmimage[i],unwrap);
const double dx = unwrap[0] - xcm[0][0];
const double dy = unwrap[1] - xcm[0][1];
const double dz = unwrap[2] - xcm[0][2];
s0 += f[i].x;
s1 += f[i].y;
s2 += f[i].z;
s3 += dy*f[i].z - dz*f[i].y;
s4 += dz*f[i].x - dx*f[i].z;
s5 += dx*f[i].y - dy*f[i].x;
if (extended && (eflags[i] & TORQUE)) {
s3 += torque_one[i][0];
s4 += torque_one[i][1];
s5 += torque_one[i][2];
}
}
sum[0][0]=s0; sum[0][1]=s1; sum[0][2]=s2;
sum[0][3]=s3; sum[0][4]=s4; sum[0][5]=s5;
} else if (rstyle == GROUP) {
// we likely have only a rather number of groups so we loops
// over bodies and thread over all atoms for each of them.
for (int ib = 0; ib < nbody; ++ib) {
double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
int i;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5)
#endif
for (i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody != ib) continue;
s0 += f[i].x;
s1 += f[i].y;
s2 += f[i].z;
double unwrap[3];
domain->unmap(x[i],xcmimage[i],unwrap);
const double dx = unwrap[0] - xcm[ibody][0];
const double dy = unwrap[1] - xcm[ibody][1];
const double dz = unwrap[2] - xcm[ibody][2];
s3 += dy*f[i].z - dz*f[i].y;
s4 += dz*f[i].x - dx*f[i].z;
s5 += dx*f[i].y - dy*f[i].x;
if (extended && (eflags[i] & TORQUE)) {
s3 += torque_one[i][0];
s4 += torque_one[i][1];
s5 += torque_one[i][2];
}
}
sum[ib][0]=s0; sum[ib][1]=s1; sum[ib][2]=s2;
sum[ib][3]=s3; sum[ib][4]=s4; sum[ib][5]=s5;
}
} else if (rstyle == MOLECULE) {
// we likely have a large number of rigid objects with only a
// a few atoms each. so we loop over all atoms for all threads
// and then each thread only processes some bodies.
const int nthreads=comm->nthreads;
memset(&sum[0][0],0,6*nbody*sizeof(double));
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
const int tid = 0;
#endif
for (int i = 0; i < nlocal; i++) {
const int ibody = body[i];
if ((ibody < 0) || (ibody % nthreads != tid)) continue;
double unwrap[3];
domain->unmap(x[i],xcmimage[i],unwrap);
const double dx = unwrap[0] - xcm[ibody][0];
const double dy = unwrap[1] - xcm[ibody][1];
const double dz = unwrap[2] - xcm[ibody][2];
const double s0 = f[i].x;
const double s1 = f[i].y;
const double s2 = f[i].z;
double s3 = dy*s2 - dz*s1;
double s4 = dz*s0 - dx*s2;
double s5 = dx*s1 - dy*s0;
if (extended && (eflags[i] & TORQUE)) {
s3 += torque_one[i][0];
s4 += torque_one[i][1];
s5 += torque_one[i][2];
}
sum[ibody][0] += s0; sum[ibody][1] += s1; sum[ibody][2] += s2;
sum[ibody][3] += s3; sum[ibody][4] += s4; sum[ibody][5] += s5;
}
}
} else
error->all(FLERR,"rigid style is unsupported by fix rigid/omp");
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
double akt=0.0,akr=0.0;
const double dtf2 = dtf * 2.0;
int ibody;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr)
#endif
for (ibody = 0; ibody < nbody; ibody++) {
double mbody[3],tbody[3],fquat[4];
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
const double dtfm = dtf / masstotal[ibody];
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
}
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
if (pstat_flag) {
double tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akt += masstotal[ibody]*tmp;
}
// update conjqm, then transform to angmom, set velocity again
// virial is already setup from initial_integrate
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] = scale_r * conjqm[ibody][0] + dtf2 * fquat[0];
conjqm[ibody][1] = scale_r * conjqm[ibody][1] + dtf2 * fquat[1];
conjqm[ibody][2] = scale_r * conjqm[ibody][2] + dtf2 * fquat[2];
conjqm[ibody][3] = scale_r * conjqm[ibody][3] + dtf2 * fquat[3];
} else {
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
}
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
if (pstat_flag) {
akr += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] +
angmom[ibody][2]*omega[ibody][2];
}
} // end of parallel for
if (pstat_flag) {
akin_t += akt;
akin_r += akr;
}
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
// triclinic only matters for virial calculation.
if (evflag)
if (triclinic)
set_v_thr<1,1>();
else
set_v_thr<0,1>();
else
set_v_thr<0,0>();
// compute current temperature
if (tcomputeflag) t_current = temperature->compute_scalar();
// compute current and target pressures
// update epsilon dot using akin_t and akin_r
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
pressure->addstep(update->ntimestep+1);
compute_press_target();
nh_epsilon_dot();
}
}
/* ---------------------------------------------------------------------- */
void FixRigidNHOMP::remap()
{
double * const * _noalias const x = atom->x;
const int * _noalias const mask = atom->mask;
const int nlocal = atom->nlocal;
// epsilon is not used, except for book-keeping
for (int i = 0; i < 3; i++) epsilon[i] += dtq * epsilon_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 < nrigidfix; i++)
modify->fix[rfix[i]]->deform(0);
// reset global and local box to new size/shape
for (int i = 0; i < 3; i++) {
if (p_flag[i]) {
const double oldlo = domain->boxlo[i];
const double oldhi = domain->boxhi[i];
const double ctr = 0.5 * (oldlo + oldhi);
const double expfac = exp(dtq * epsilon_dot[i]);
domain->boxlo[i] = (oldlo-ctr)*expfac + ctr;
domain->boxhi[i] = (oldhi-ctr)*expfac + ctr;
}
}
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< nrigidfix; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ----------------------------------------------------------------------
set space-frame coords and velocity of each atom in each rigid body
set orientation and rotation of extended particles
x = Q displace + Xcm, mapped back to periodic box
v = Vcm + (W cross (x - Xcm))
NOTE: this needs to be kept in sync with FixRigidOMP
------------------------------------------------------------------------- */
template <int TRICLINIC, int EVFLAG>
void FixRigidNHOMP::set_xv_thr()
{
dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const double * _noalias const rmass = atom->rmass;
const double * _noalias const mass = atom->mass;
const int * _noalias const type = atom->type;
double v0=0.0,v1=0.0,v2=0.0,v3=0.0,v4=0.0,v5=0.0;
const double xprd = domain->xprd;
const double yprd = domain->yprd;
const double zprd = domain->zprd;
const double xy = domain->xy;
const double xz = domain->xz;
const double yz = domain->yz;
// set x and v of each atom
const int nlocal = atom->nlocal;
int i;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
#endif
for (i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody < 0) continue;
const dbl3_t &xcmi = * ((dbl3_t *) xcm[ibody]);
const dbl3_t &vcmi = * ((dbl3_t *) vcm[ibody]);
const dbl3_t &omegai = * ((dbl3_t *) omega[ibody]);
const int xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
const int ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
const int zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
const double deltax = xbox*xprd + (TRICLINIC ? ybox*xy + zbox*xz : 0.0);
const double deltay = ybox*yprd + (TRICLINIC ? zbox*yz : 0.0);
const double deltaz = zbox*zprd;
// save old positions and velocities for virial
double x0,x1,x2,vx,vy,vz;
if (EVFLAG) {
x0 = x[i].x + deltax;
x1 = x[i].y + deltay;
x2 = x[i].z + deltaz;
vx = v[i].x;
vy = v[i].y;
vz = v[i].z;
}
// x = displacement from center-of-mass, based on body orientation
// v = vcm + omega around center-of-mass
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],displace[i],&x[i].x);
v[i].x = omegai.y*x[i].z - omegai.z*x[i].y + vcmi.x;
v[i].y = omegai.z*x[i].x - omegai.x*x[i].z + vcmi.y;
v[i].z = omegai.x*x[i].y - omegai.y*x[i].x + vcmi.z;
// add center of mass to displacement
// map back into periodic box via xbox,ybox,zbox
// for triclinic, add in box tilt factors as well
x[i].x += xcmi.x - deltax;
x[i].y += xcmi.y - deltay;
x[i].z += xcmi.z - deltaz;
// virial = unwrapped coords dotted into body constraint force
// body constraint force = implied force due to v change minus f external
// assume f does not include forces internal to body
// 1/2 factor b/c final_integrate contributes other half
// assume per-atom contribution is due to constraint force on that atom
if (EVFLAG) {
double massone,vr[6];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
const double fc0 = 0.5*(massone*(v[i].x - vx)/dtf - f[i].x);
const double fc1 = 0.5*(massone*(v[i].y - vy)/dtf - f[i].y);
const double fc2 = 0.5*(massone*(v[i].z - vz)/dtf - f[i].z);
vr[0] = x0*fc0; vr[1] = x1*fc1; vr[2] = x2*fc2;
vr[3] = x0*fc1; vr[4] = x0*fc2; vr[5] = x1*fc2;
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables for reduction
if (vflag_global) {
v0 += vr[0];
v1 += vr[1];
v2 += vr[2];
v3 += vr[3];
v4 += vr[4];
v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
vatom[i][0] += vr[0];
vatom[i][1] += vr[1];
vatom[i][2] += vr[2];
vatom[i][3] += vr[3];
vatom[i][4] += vr[4];
vatom[i][5] += vr[5];
}
}
}
// second part of thread safe virial accumulation
// add global virial component after it was reduced across all threads
if (EVFLAG) {
if (vflag_global) {
virial[0] += v0;
virial[1] += v1;
virial[2] += v2;
virial[3] += v3;
virial[4] += v4;
virial[5] += v5;
}
}
// set orientation, omega, angmom of each extended particle
// XXX: extended particle info not yet multi-threaded
if (extended) {
double *shape,*quatatom,*inertiaatom;
double theta_body,theta;
double ione[3],exone[3],eyone[3],ezone[3],p[3][3];
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecLine::Bonus *lbonus;
if (avec_line) lbonus = avec_line->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
double **omega_one = atom->omega;
double **angmom_one = atom->angmom;
double **mu = atom->mu;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
for (int i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody < 0) continue;
if (eflags[i] & SPHERE) {
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::quatquat(quat[ibody],orient[i],quatatom);
MathExtra::qnormalize(quatatom);
ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
angmom_one[i]);
} else if (eflags[i] & LINE) {
if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]);
else theta_body = -2.0*acos(quat[ibody][0]);
theta = orient[i][0] + theta_body;
while (theta <= MINUSPI) theta += TWOPI;
while (theta > MY_PI) theta -= TWOPI;
lbonus[line[i]].theta = theta;
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
quatatom = tbonus[tri[i]].quat;
MathExtra::quatquat(quat[ibody],orient[i],quatatom);
MathExtra::qnormalize(quatatom);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
inertiaatom,angmom_one[i]);
}
if (eflags[i] & DIPOLE) {
MathExtra::quat_to_mat(quat[ibody],p);
MathExtra::matvec(p,dorient[i],mu[i]);
MathExtra::snormalize3(mu[i][3],mu[i],mu[i]);
}
}
}
}
/* ----------------------------------------------------------------------
set space-frame velocity of each atom in a rigid body
set omega and angmom of extended particles
v = Vcm + (W cross (x - Xcm))
NOTE: this needs to be kept in sync with FixRigidOMP
------------------------------------------------------------------------- */
template <int TRICLINIC, int EVFLAG>
void FixRigidNHOMP::set_v_thr()
{
dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const double * _noalias const rmass = atom->rmass;
const double * _noalias const mass = atom->mass;
const int * _noalias const type = atom->type;
const double xprd = domain->xprd;
const double yprd = domain->yprd;
const double zprd = domain->zprd;
const double xy = domain->xy;
const double xz = domain->xz;
const double yz = domain->yz;
double v0=0.0,v1=0.0,v2=0.0,v3=0.0,v4=0.0,v5=0.0;
// set v of each atom
const int nlocal = atom->nlocal;
int i;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5)
#endif
for (i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody < 0) continue;
const dbl3_t &vcmi = * ((dbl3_t *) vcm[ibody]);
const dbl3_t &omegai = * ((dbl3_t *) omega[ibody]);
double delta[3],vx,vy,vz;
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],displace[i],delta);
// save old velocities for virial
if (EVFLAG) {
vx = v[i].x;
vy = v[i].y;
vz = v[i].z;
}
v[i].x = omegai.y*delta[2] - omegai.z*delta[1] + vcmi.x;
v[i].y = omegai.z*delta[0] - omegai.x*delta[2] + vcmi.y;
v[i].z = omegai.x*delta[1] - omegai.y*delta[0] + vcmi.z;
// virial = unwrapped coords dotted into body constraint force
// body constraint force = implied force due to v change minus f external
// assume f does not include forces internal to body
// 1/2 factor b/c initial_integrate contributes other half
// assume per-atom contribution is due to constraint force on that atom
if (EVFLAG) {
double massone, vr[6];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
const int xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
const int ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
const int zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
const double deltax = xbox*xprd + (TRICLINIC ? ybox*xy + zbox*xz : 0.0);
const double deltay = ybox*yprd + (TRICLINIC ? zbox*yz : 0.0);
const double deltaz = zbox*zprd;
const double fc0 = 0.5*(massone*(v[i].x - vx)/dtf - f[i].x);
const double fc1 = 0.5*(massone*(v[i].y - vy)/dtf - f[i].y);
const double fc2 = 0.5*(massone*(v[i].z - vz)/dtf - f[i].z);
const double x0 = x[i].x + deltax;
const double x1 = x[i].y + deltay;
const double x2 = x[i].z + deltaz;
vr[0] = x0*fc0; vr[1] = x1*fc1; vr[2] = x2*fc2;
vr[3] = x0*fc1; vr[4] = x0*fc2; vr[5] = x1*fc2;
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables and reduce them later
if (vflag_global) {
v0 += vr[0];
v1 += vr[1];
v2 += vr[2];
v3 += vr[3];
v4 += vr[4];
v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
vatom[i][0] += vr[0];
vatom[i][1] += vr[1];
vatom[i][2] += vr[2];
vatom[i][3] += vr[3];
vatom[i][4] += vr[4];
vatom[i][5] += vr[5];
}
}
} // end of parallel for
// second part of thread safe virial accumulation
// add global virial component after it was reduced across all threads
if (EVFLAG) {
if (vflag_global) {
virial[0] += v0;
virial[1] += v1;
virial[2] += v2;
virial[3] += v3;
virial[4] += v4;
virial[5] += v5;
}
}
// set omega, angmom of each extended particle
// XXX: extended particle info not yet multi-threaded
if (extended) {
double *shape,*quatatom,*inertiaatom;
double ione[3],exone[3],eyone[3],ezone[3];
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
double **omega_one = atom->omega;
double **angmom_one = atom->angmom;
int *ellipsoid = atom->ellipsoid;
int *tri = atom->tri;
for (int i = 0; i < nlocal; i++) {
const int ibody = body[i];
if (ibody < 0) continue;
if (eflags[i] & SPHERE) {
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,ione,
angmom_one[i]);
} else if (eflags[i] & LINE) {
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
quatatom = tbonus[tri[i]].quat;
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(omega[ibody],exone,eyone,ezone,
inertiaatom,angmom_one[i]);
}
}
}
}

Event Timeline

c4science · Help