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lammps/src/fix_rigid_nvt.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: Tony Sheh (U Michigan), Trung Dac Nguyen (U Michigan)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
Miller et al., J Chem Phys. 116, 8649-8659
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "fix_rigid_nvt.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "modify.h"
#include "group.h"
#include "comm.h"
#include "force.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
FixRigid(lmp, narg, arg)
{
// other settings are made by FixRigid parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
// error checking
// convert input period to frequency
if (tempflag == 0)
error->all("Did not set temp for fix rigid/nvt");
if (t_start < 0.0 || t_stop <= 0.0)
error->all("Target temperature for fix rigid/nvt cannot be 0.0");
if (t_period <= 0.0) error->all("Fix rigid/nvt period must be > 0.0");
t_freq = 1.0 / t_period;
if (t_chain < 1) error->all("Illegal fix_modify command");
if (t_iter < 1) error->all("Illegal fix_modify command");
if (t_order != 3 && t_order != 5)
error->all("Fix_modify order must be 3 or 5");
allocate_chain();
allocate_order();
conjqm = memory->create_2d_double_array(nbody,4,"nve_rigid:conjqm");
// one-time initialize of thermostat variables
eta_t[0] = eta_r[0] = 0.0;
eta_dot_t[0] = eta_dot_r[0] = 0.0;
f_eta_t[0] = f_eta_r[0] = 0.0;
for (int i = 1; i < t_chain; i++) {
eta_t[i] = eta_r[i] = 0.0;
eta_dot_t[i] = eta_dot_r[i] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
FixRigidNVT::~FixRigidNVT()
{
deallocate_chain();
deallocate_order();
memory->destroy_2d_double_array(conjqm);
}
/* ---------------------------------------------------------------------- */
int FixRigidNVT::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_NEIGHBOR;
mask |= THERMO_ENERGY;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::init()
{
FixRigid::init();
// initialize thermostats
// set timesteps, constants
// store Yoshida-Suzuki integrator parameters
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
boltz = force->boltz;
nf_t = nf_r = domain->dimension * nbody;
for (int ibody = 0; ibody < nbody; ibody++)
for (int k = 0; k < domain->dimension; k++)
if (fabs(inertia[ibody][k]) < 1e-6) nf_r--;
// see Table 1 in Kamberaj et al
if (t_order == 3) {
w[0] = 1.0 / (2.0 - pow(2.0, 1.0/3.0));
w[1] = 1.0 - 2.0*w[0];
w[2] = w[0];
} else if (t_order == 5) {
w[0] = 1.0 / (4.0 - pow(4.0, 1.0/3.0));
w[1] = w[0];
w[2] = 1.0 - 4.0 * w[0];
w[3] = w[0];
w[4] = w[0];
}
// initialize thermostat settings
t_target = t_start;
double kt = boltz * t_target;
double t_mass = kt / (t_freq*t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
for (int i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
// initialize thermostat chain positions, velocites, forces
for (int i = 1; i < t_chain; i++) {
f_eta_t[i] = q_t[i-1] * eta_dot_t[i-1] * eta_dot_t[i-1] - kt;
f_eta_r[i] = q_r[i-1] * eta_dot_r[i-1] * eta_dot_r[i-1] - kt;
}
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::setup(int vflag)
{
FixRigid::setup(vflag);
t_target = t_start;
double mbody[3];
for (int ibody = 0; ibody < nbody; ibody++) {
matvec_rows(ex_space[ibody],ey_space[ibody],ez_space[ibody],
angmom[ibody],mbody);
quatvec(quat[ibody],mbody,conjqm[ibody]);
conjqm[ibody][0] *= 2.0;
conjqm[ibody][1] *= 2.0;
conjqm[ibody][2] *= 2.0;
conjqm[ibody][3] *= 2.0;
}
}
/* ----------------------------------------------------------------------
perform preforce velocity Verlet integration
see Kamberaj paper for step references
------------------------------------------------------------------------- */
void FixRigidNVT::initial_integrate(int vflag)
{
double tmp,akin_t,akin_r,scale_t,scale_r;
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop - t_start);
// intialize velocity scale for translation and rotation
akin_t = akin_r = 0.0;
tmp = -1.0 * dtq * eta_dot_t[0];
scale_t = exp(tmp);
tmp = -1.0 * dtq * eta_dot_r[0];
scale_r = exp(tmp);
for (int ibody = 0; ibody < nbody; ibody++) {
// step 1.1 - update vcm by 1/2 step
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];
vcm[ibody][0] *= scale_t;
vcm[ibody][1] *= scale_t;
vcm[ibody][2] *= scale_t;
tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akin_t += masstotal[ibody]*tmp;
// step 1.2 - update xcm by full step
xcm[ibody][0] += dtv * vcm[ibody][0];
xcm[ibody][1] += dtv * vcm[ibody][1];
xcm[ibody][2] += dtv * vcm[ibody][2];
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
// step 1.3 - apply torque (body coords) to quaternion momentum
matvec_rows(ex_space[ibody],ey_space[ibody],ez_space[ibody],
torque[ibody],tbody);
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];
conjqm[ibody][0] *= scale_r;
conjqm[ibody][1] *= scale_r;
conjqm[ibody][2] *= scale_r;
conjqm[ibody][3] *= scale_r;
// step 1.4 to 1.8 - use no_squish rotate to update p (i.e. conjqm) and q
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
// update the exyz_space from new quaternion
// transform p back to angmom
// update angular velocity
exyz_from_q(quat[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody]);
invquatvec(quat[ibody],conjqm[ibody],mbody);
matvec_cols(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;
omega_from_angmom(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
// update thermostat chains
update_nhcp(akin_t,akin_r);
// virial setup before call to set_xv
if (vflag) v_setup(vflag);
else evflag = 0;
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
set_xv();
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::final_integrate()
{
int i,ibody;
double tmp,scale_t,scale_r,akin_t,akin_r;
double dtfm,xy,xz,yz;
// compute velocity scales for translation and rotation
tmp = -1.0 * dtq * eta_dot_t[0];
scale_t = exp(tmp);
tmp = -1.0 * dtq * eta_dot_r[0];
scale_r = exp(tmp);
// sum over atoms to get force and torque on rigid body
int *image = atom->image;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
if (triclinic) {
xy = domain->xy;
xz = domain->xz;
yz = domain->yz;
}
int xbox,ybox,zbox;
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (triclinic == 0) {
xunwrap = x[i][0] + xbox*xprd;
yunwrap = x[i][1] + ybox*yprd;
zunwrap = x[i][2] + zbox*zprd;
} else {
xunwrap = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
yunwrap = x[i][1] + ybox*yprd + zbox*yz;
zunwrap = x[i][2] + zbox*zprd;
}
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
}
// extended particles add their torque to torque of body
if (extended) {
double **torque_one = atom->torque;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (eflags[i] & TORQUE) {
sum[ibody][3] += torque_one[i][0];
sum[ibody][4] += torque_one[i][1];
sum[ibody][5] += torque_one[i][2];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
double mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0];
fcm[ibody][1] = all[ibody][1];
fcm[ibody][2] = all[ibody][2];
torque[ibody][0] = all[ibody][3];
torque[ibody][1] = all[ibody][4];
torque[ibody][2] = all[ibody][5];
// 2.5-2.6 update vcm by 1/2 step
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] *= scale_t;
vcm[ibody][1] *= scale_t;
vcm[ibody][2] *= scale_t;
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];
// 2.1-2.4 update conjqm, angular momentum and angular velocity
// apply body torque flags
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
// convert torque to the body frame
matvec_rows(ex_space[ibody],ey_space[ibody],ez_space[ibody],
torque[ibody],tbody);
// compute "force" for quaternion
quatvec(quat[ibody],tbody,fquat);
// update the conjugate quaternion momentum (conjqm)
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];
// compute angular momentum in the body frame then convert to the space-fixed frame
invquatvec(quat[ibody],conjqm[ibody],mbody);
matvec_cols(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;
// compute new angular velocity
omega_from_angmom(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
}
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
set_v();
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::update_nhcp(double akin_t, double akin_r)
{
int i,j,k;
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
kt = boltz * t_target;
gfkt_t = nf_t * kt;
gfkt_r = nf_r * kt;
akin_t *= force->mvv2e;
akin_r *= force->mvv2e;
// update thermostat masses
double t_mass = boltz * t_target / (t_freq * t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
for (i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
// update order/timestep dependent coefficients
for (i = 0; i < t_order; i++) {
wdti1[i] = w[i] * dtv / t_iter;
wdti2[i] = wdti1[i] / 2.0;
wdti4[i] = wdti1[i] / 4.0;
}
// update force of thermostats coupled to particles
f_eta_t[0] = (akin_t - gfkt_t) / q_t[0];
f_eta_r[0] = (akin_r - gfkt_r) / q_r[0];
// multiple timestep iteration
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
// update thermostat velocities half step
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
for (k = 1; k < t_chain; k++) {
tmp = wdti4[j] * eta_dot_t[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
wdti2[j] * f_eta_t[t_chain-k-1] * s * ms;
tmp = wdti4[j] * eta_dot_r[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
wdti2[j] * f_eta_r[t_chain-k-1] * s * ms;
}
// update thermostat positions a full step
for (k = 0; k < t_chain; k++) {
eta_t[k] += wdti1[j] * eta_dot_t[k];
eta_r[k] += wdti1[j] * eta_dot_r[k];
}
// update thermostat forces
for (k = 1; k < t_chain; k++) {
f_eta_t[k] = q_t[k-1] * eta_dot_t[k-1] * eta_dot_t[k-1] - kt;
f_eta_t[k] /= q_t[k];
f_eta_r[k] = q_r[k-1] * eta_dot_r[k-1] * eta_dot_r[k-1] - kt;
f_eta_r[k] /= q_r[k];
}
// update thermostat velocities a full step
for (k = 0; k < t_chain-1; k++) {
tmp = wdti4[j] * eta_dot_t[k+1];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
eta_dot_t[k] = eta_dot_t[k] * s2 + wdti2[j] * f_eta_t[k] * s * ms;
tmp = q_t[k] * eta_dot_t[k] * eta_dot_t[k] - kt;
f_eta_t[k+1] = tmp / q_t[k+1];
tmp = wdti4[j] * eta_dot_r[k+1];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
eta_dot_r[k] = eta_dot_r[k] * s2 + wdti2[j] * f_eta_r[k] * s * ms;
tmp = q_r[k] * eta_dot_r[k] * eta_dot_r[k] - kt;
f_eta_r[k+1] = tmp / q_r[k+1];
}
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
}
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixRigidNVT::write_restart(FILE *fp)
{
int n = 0;
double *list = new double[1+6*t_chain];
list[n++] = t_chain;
for (int i = 0; i < t_chain; i++) {
list[n++] = eta_t[i];
list[n++] = eta_r[i];
list[n++] = eta_dot_t[i];
list[n++] = eta_dot_r[i];
list[n++] = f_eta_t[i];
list[n++] = f_eta_r[i];
}
if (comm->me == 0) {
int size = (1 + 6*t_chain)*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),1+6*t_chain,fp);
}
delete list;
}
/* ----------------------------------------------------------------------
compute kinetic energy in the extended Hamiltonian
conserved quantity = sum of returned energy and potential energy
-----------------------------------------------------------------------*/
double FixRigidNVT::compute_scalar()
{
int i,k,ibody;
double kt = boltz * t_target;
double energy,ke_t,ke_q,tmp,Pkq[4];
// compute the kinetic parts of H_NVE in Kameraj et al (JCP 2005, pp 224114)
// translational kinetic energy
ke_t = 0.0;
for (ibody = 0; ibody < nbody; ibody++)
ke_t += 0.5 * masstotal[ibody] * (vcm[ibody][0]*vcm[ibody][0] +
vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2]);
// rotational kinetic energy
ke_q = 0.0;
for (ibody = 0; ibody < nbody; ibody++) {
for (k = 1; k < 4; k++) {
if (k == 1) {
Pkq[0] = -quat[ibody][1];
Pkq[1] = quat[ibody][0];
Pkq[2] = quat[ibody][3];
Pkq[3] = -quat[ibody][2];
} else if (k == 2) {
Pkq[0] = -quat[ibody][2];
Pkq[1] = -quat[ibody][3];
Pkq[2] = quat[ibody][0];
Pkq[3] = quat[ibody][1];
} else if (k == 3) {
Pkq[0] = -quat[ibody][3];
Pkq[1] = quat[ibody][2];
Pkq[2] = -quat[ibody][1];
Pkq[3] = quat[ibody][0];
}
tmp = conjqm[ibody][0]*Pkq[0] + conjqm[ibody][1]*Pkq[1] +
conjqm[ibody][2]*Pkq[2] + conjqm[ibody][3]*Pkq[3];
tmp *= tmp;
if (fabs(inertia[ibody][k-1]) < 1e-6) tmp = 0.0;
else tmp /= (8.0 * inertia[ibody][k-1]);
ke_q += tmp;
}
}
energy = ke_t + ke_q;
// thermostat chain energy: from equation 12 in Kameraj et al (JCP 2005)
energy += kt * (nf_t * eta_t[0] + nf_r * eta_r[0]);
for (i = 1; i < t_chain; i++)
energy += kt * (eta_t[i] + eta_r[i]);
for (i = 0; i < t_chain; i++) {
energy += 0.5 * q_t[i] * (eta_dot_t[i] * eta_dot_t[i]);
energy += 0.5 * q_r[i] * (eta_dot_r[i] * eta_dot_r[i]);
}
return energy;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixRigidNVT::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
int t_chain_prev = static_cast<int> (list[n++]);
if (t_chain_prev != t_chain)
error->all("Cannot restart fix rigid/nvt with different # of chains");
for (int i = 0; i < t_chain; i++) {
eta_t[i] = list[n++];
eta_r[i] = list[n++];
eta_dot_t[i] = list[n++];
eta_dot_r[i] = list[n++];
f_eta_t[i] = list[n++];
f_eta_r[i] = list[n++];
}
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::allocate_chain()
{
q_t = new double[t_chain];
q_r = new double[t_chain];
eta_t = new double[t_chain];
eta_r = new double[t_chain];
eta_dot_t = new double[t_chain];
eta_dot_r = new double[t_chain];
f_eta_t = new double[t_chain];
f_eta_r = new double[t_chain];
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::allocate_order()
{
w = new double[t_order];
wdti1 = new double[t_order];
wdti2 = new double[t_order];
wdti4 = new double[t_order];
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::deallocate_chain()
{
delete [] q_t;
delete [] q_r;
delete [] eta_t;
delete [] eta_r;
delete [] eta_dot_t;
delete [] eta_dot_r;
delete [] f_eta_t;
delete [] f_eta_r;
}
/* ---------------------------------------------------------------------- */
void FixRigidNVT::deallocate_order()
{
delete [] w;
delete [] wdti1;
delete [] wdti2;
delete [] wdti4;
}
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