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fix_rigid_nh.cpp
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fix_rigid_nh.cpp
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// 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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 (2002)
------------------------------------------------------------------------- */
#include "fix_rigid_nh.h"
#include "atom.h"
#include "molecule.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix_deform.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "rigid_const.h"
#include "update.h"
#include <cmath>
#include <cstring>
#include "math_const.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "pair.h"
#include <iomanip>
#include <iostream>
#include <sstream>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace RigidConst;
using namespace std;
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
/* ---------------------------------------------------------------------- */
FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
FixRigid(lmp, narg, arg), conjqm(nullptr), w(nullptr),
wdti1(nullptr), wdti2(nullptr), wdti4(nullptr), q_t(nullptr), q_r(nullptr),
eta_t(nullptr), eta_r(nullptr), eta_dot_t(nullptr), eta_dot_r(nullptr),
f_eta_t(nullptr), f_eta_r(nullptr), q_b(nullptr), eta_b(nullptr),
eta_dot_b(nullptr), f_eta_b(nullptr), rfix(nullptr), id_temp(nullptr),
id_press(nullptr), temperature(nullptr), pressure(nullptr)
{
if (tstat_flag || pstat_flag) ecouple_flag = 1;
// error checks: could be moved up to FixRigid
if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
(p_flag[1] == 1 && p_period[1] <= 0.0) ||
(p_flag[2] == 1 && p_period[2] <= 0.0))
error->all(FLERR,"Fix rigid npt/nph period must be > 0.0");
if (dimension == 2 && p_flag[2])
error->all(FLERR,"Invalid fix rigid npt/nph command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all(FLERR,"Invalid fix rigid npt/nph command for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
// require periodicity in tensile dimension
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,
"Cannot use fix rigid npt/nph on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,
"Cannot use fix rigid npt/nph on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix rigid npt/nph on a non-periodic dimension");
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XYZ && dimension == 2 &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix rigid npt/nph command pressure settings");
if (p_flag[0]) box_change |= BOX_CHANGE_X;
if (p_flag[1]) box_change |= BOX_CHANGE_Y;
if (p_flag[2]) box_change |= BOX_CHANGE_Z;
if ((tstat_flag && t_period <= 0.0) ||
(p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0))
error->all(FLERR,"Fix rigid nvt/npt/nph damping parameters must be > 0.0");
// memory allocation and initialization
memory->create(conjqm,nbody,4,"rigid_nh:conjqm");
// memory allocation and initialization
// CS modified
memory->create(total_torque,nbody,3,"rigid_nh:total_torque"); //total torque of each particle
memory->create(pair_torque, nbody, nbody,3,"rigid_nh:pair_torque");
memory->create(final_torque, nbody, nbody,3,"rigid_nh:final_torque");
memory->create(total_force,nbody,3,"rigid_nh:total_force"); //total torque of each particle
memory->create(pair_force, nbody, nbody,3,"rigid_nh:pair_force");
memory->create(final_force, nbody, nbody,3,"rigid_nh:final_force");
natoms = atom->natoms;
memory->create(cs_pe, natoms, "rigid_nh:cs_pe");
memory->create(cs_pe_final, natoms,"rigid_nh:cs_pe_final");
memory->create(body_pe, nbody, "rigid_nh:body_pe");
memory->create(body_mass, nbody, "rigid_nh:body_mass");
memory->create(flux, 15, "rigid_nh:flux");
memory->create(flux_na, 15, "rigid_nh:flux");
memory->create(flux_oxy, 15, "rigid_nh:flux");
// open the data file
std::ostringstream fname;
fname<<"flux_data_"<<id<<".txt";
mydata.open(fname.str());
std::ostringstream fname3;
fname3<<"flux_na_data_"<<id<<".txt";
nadata.open(fname3.str());
std::ostringstream fname4;
fname4<<"flux_oxy_data_"<<id<<".txt";
oxydata.open(fname4.str());
std::ostringstream fname2;
fname2<<"body_properties_"<<id<<".txt";
body_properties.open(fname2.str());
// set the initial value for count
ncount=0;
never=2;
dump_flag=0;
nbody_count=0;
nbody_ever=50000;
dump_body_flag=0;
// CS end
if (tstat_flag || pstat_flag) {
allocate_chain();
allocate_order();
}
if (tstat_flag) {
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;
}
}
if (pstat_flag) {
epsilon_dot[0] = epsilon_dot[1] = epsilon_dot[2] = 0.0;
eta_b[0] = eta_dot_b[0] = f_eta_b[0] = 0.0;
for (int i = 1; i < p_chain; i++)
eta_b[i] = eta_dot_b[i] = 0.0;
}
// rigid body pointers
nrigidfix = 0;
rfix = nullptr;
vol0 = 0.0;
t0 = 1.0;
tcomputeflag = 0;
pcomputeflag = 0;
id_temp = nullptr;
id_press = nullptr;
}
/* ---------------------------------------------------------------------- */
FixRigidNH::~FixRigidNH()
{
memory->destroy(conjqm);
if (tstat_flag || pstat_flag) {
deallocate_chain();
deallocate_order();
}
if (rfix) delete [] rfix;
if (tcomputeflag) modify->delete_compute(id_temp);
delete [] id_temp;
// delete pressure if fix created it
if (pstat_flag) {
if (pcomputeflag) modify->delete_compute(id_press);
delete [] id_press;
}
// CS: start modification
memory->destroy(pair_torque);
memory->destroy(final_torque);
memory->destroy(total_torque);
memory->destroy(pair_force);
memory->destroy(final_force);
memory->destroy(total_force);
// CS modified
memory->destroy(cs_pe);
memory->destroy(cs_pe_final);
memory->destroy(body_pe);
memory->destroy(body_mass);
memory->destroy(flux);
memory->destroy(flux_na);
memory->destroy(flux_oxy);
mydata.close();
nadata.close();
oxydata.close();
body_properties.close();
// CS end
}
void FixRigidNH::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
int FixRigidNH::setmask()
{
int mask = 0;
mask = FixRigid::setmask();
return mask;
}
/* ---------------------------------------------------------------------- */
void FixRigidNH::init()
{
FixRigid::init();
int *type = atom->type;
double *mass = atom->mass; // mass for each type
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
// recheck that dilate group has not been deleted
if (allremap == 0) {
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix rigid npt/nph dilate group ID does not exist");
dilate_group_bit = group->bitmask[idilate];
}
// 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;
nktv2p = force->nktv2p;
mvv2e = force->mvv2e;
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
nf_t = dimension * nbody;
if (dimension == 3) {
nf_r = dimension * nbody;
for (int ibody = 0; ibody < nbody; ibody++)
for (int k = 0; k < domain->dimension; k++)
if (fabs(inertia[ibody][k]) < EPSILON) nf_r--;
} else if (dimension == 2) {
nf_r = nbody;
for (int ibody = 0; ibody < nbody; ibody++)
if (fabs(inertia[ibody][2]) < EPSILON) nf_r--;
}
g_f = nf_t + nf_r;
// see Table 1 in Kamberaj et al
if (tstat_flag || pstat_flag) {
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];
}
}
int icompute;
if (tcomputeflag) {
icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix rigid nvt/npt/nph does not exist");
temperature = modify->compute[icompute];
}
if (pstat_flag) {
if (domain->triclinic)
error->all(FLERR,"Fix rigid npt/nph does not yet allow triclinic box");
// ensure no conflict with fix deform
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
error->all(FLERR,"Cannot use fix rigid npt/nph and fix deform on "
"same component of stress tensor");
}
// set frequency
p_freq_max = 0.0;
p_freq_max = MAX(p_freq[0],p_freq[1]);
p_freq_max = MAX(p_freq_max,p_freq[2]);
// tally the number of dimensions that are barostatted
// set initial volume and reference cell, if not already done
pdim = p_flag[0] + p_flag[1] + p_flag[2];
if (vol0 == 0.0) {
if (dimension == 2) vol0 = domain->xprd * domain->yprd;
else vol0 = domain->xprd * domain->yprd * domain->zprd;
}
// set pressure compute ptr
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix rigid npt/nph does not exist");
pressure = modify->compute[icompute];
// detect if any rigid fixes exist so rigid bodies move on remap
// rfix[] = indices to each fix rigid
// this will include self
if (rfix) delete [] rfix;
nrigidfix = 0;
rfix = nullptr;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) nrigidfix++;
if (nrigidfix) {
rfix = new int[nrigidfix];
nrigidfix = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) rfix[nrigidfix++] = i;
}
}
// CS: need a full neighbor list once
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// CS: calc the mass for each rigid body
for (int ibody=0; ibody < nbody; ibody++){
body_mass[ibody] =0;
}
int ibody = 0;
for (int i=0; i<nlocal; i++){
ibody=body[i];
if (ibody >=0) body_mass[ibody] += mass[type[i]];
}
//for (int ibody=0; ibody < nbody; ibody++){
// cerr<< body_mass[ibody] << " ";
//}
//cerr<<endl;
}
/* ---------------------------------------------------------------------- */
void FixRigidNH::setup(int vflag)
{
tagint *molecule = atom->molecule;
FixRigid::setup(vflag);
double mbody[3];
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nbody; ibody++) {
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
angmom[ibody],mbody);
MathExtra::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;
if (tstat_flag || pstat_flag) {
akin_t += masstotal[ibody]*(vcm[ibody][0]*vcm[ibody][0] +
vcm[ibody][1]*vcm[ibody][1] + vcm[ibody][2]*vcm[ibody][2]);
akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
}
// compute target temperature
if (tstat_flag) compute_temp_target();
else if (pstat_flag) {
t0 = temperature->compute_scalar();
if (t0 == 0.0) {
if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
else t0 = 300.0;
}
t_target = t0;
}
// compute target pressure
// compute current pressure
// trigger virial computation on next timestep
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);
}
// initialize thermostat/barostat settings
double kt, t_mass, tb_mass;
kt = boltz * t_target;
if (tstat_flag) {
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;
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)/q_t[i];
f_eta_r[i] = (q_r[i-1] * eta_dot_r[i-1] * eta_dot_r[i-1] - kt)/q_r[i];
}
}
// initial forces on barostat thermostat variables
if (pstat_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
epsilon_mass[i] = (g_f + dimension) * kt / (p_freq[i]*p_freq[i]);
epsilon[i] = log(vol0)/dimension;
}
tb_mass = kt / (p_freq_max * p_freq_max);
q_b[0] = dimension * dimension * tb_mass;
for (int i = 1; i < p_chain; i++) {
q_b[i] = tb_mass;
f_eta_b[i] = (q_b[i] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt)/q_b[i];
}
}
// update order/timestep dependent coefficients
if (tstat_flag || pstat_flag) {
for (int 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;
}
}
if (pstat_flag) {
compute_press_target();
nh_epsilon_dot();
}
int nmolecule = -1;
for (int i = 0; i < natoms; i++){
if (molecule[i]> nmolecule) nmolecule = molecule[i];
}
// CS: start modification
for (int ibody = 0; ibody < nbody; ibody++)
for (int jbody=0; jbody < nbody; jbody++ )
for (int temp=0; temp < 3; temp++)
pair_torque[ibody][jbody][temp] = 0;
for (int ibody = 0; ibody < nbody; ibody++)
for (int jbody=0; jbody < nbody; jbody++ )
for (int temp=0; temp < 3; temp++)
final_torque[ibody][jbody][temp] = 0;
for (int ibody = 0; ibody < nbody; ibody++)
for (int jbody=0; jbody < nbody; jbody++ )
for (int temp=0; temp < 3; temp++)
pair_force[ibody][jbody][temp] = 0;
for (int ibody = 0; ibody < nbody; ibody++)
for (int jbody=0; jbody < nbody; jbody++ )
for (int temp=0; temp < 3; temp++)
final_force[ibody][jbody][temp] = 0;
// CS modified
for (int ibody = 0; ibody < nbody; ibody++)
body_pe[ibody]=0;
for (int i = 0; i < natoms; i++){
cs_pe[i] = 0;
cs_pe_final[i] = 0;
}
for(int i=0; i<15;i++){
flux[i]=0;
}
// CS end
}
/* ----------------------------------------------------------------------
perform preforce velocity Verlet integration
see Kamberaj paper for step references
------------------------------------------------------------------------- */
void FixRigidNH::initial_integrate(int vflag)
{
double tmp,scale_r,scale_t[3],scale_v[3];
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
//tagint *tag = atom->tag;
// 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;
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));
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
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];
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
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
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) {
akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
}
// 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
v_init(vflag);
// 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
set_xv();
// remap simulation box by full step
// redo KSpace coeffs since volume has changed
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
}
}
/* ---------------------------------------------------------------------- */
void FixRigidNH::final_integrate()
{
double tmp,scale_t[3],scale_r;
double dtfm;
double mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
// CS: new variables
int i;
int inum,jnum;
double ** x = atom->x;
int *ilist,*jlist,*numneigh;
int **firstneigh;
int j, itype , jtype;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint itag,jtag;
int nlocal = atom->nlocal;
// CS modified
int npair = atom->nlocal;
if (force->newton) npair += atom->nghost;
double unwrap[3];
double i_dx, i_dy, i_dz; // disp vector of atom i in body body[i]
double j_dx, j_dy, j_dz; // disp vector of atom j in body body[j]
int ibody, jbody;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// check when to dump out
ncount++;
dump_flag=0;
if (ncount== never){
ncount=0;
dump_flag=1;
}
nbody_count++;
dump_body_flag=0;
if (nbody_count==nbody_ever){
nbody_count=0;
dump_body_flag=1;
}
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
int *type = atom->type;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq, eng, fpair,factor_coul,factor_lj;
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_r = 1.0;
if (tstat_flag) {
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));
// reset akin_t and akin_r, to be accumulated for use in nh_epsilon_dot()
akin_t = akin_r = 0.0;
}
if(1==dump_flag){ // CS: start modification
for (ibody = 0; ibody < nbody; ibody++)
for (jbody = 0; jbody < nbody; jbody++){
pair_torque[ibody][jbody][0] = 0;
pair_torque[ibody][jbody][1] = 0;
pair_torque[ibody][jbody][2] = 0;
}
for (ibody = 0; ibody < nbody; ibody++)
for (jbody = 0; jbody < nbody; jbody++){
pair_force[ibody][jbody][0] = 0;
pair_force[ibody][jbody][1] = 0;
pair_force[ibody][jbody][2] = 0;
}
for (int ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itag = tag[i];
itype = type[i];
// disp vector of atom i in ibody
// body[i] or mol2body[molecule[i]]
ibody=body[i];
domain->unmap(x[i],xcmimage[i],unwrap);
i_dx = unwrap[0] - xcm[ibody][0];
i_dy = unwrap[1] - xcm[ibody][1];
i_dz = unwrap[2] - xcm[ibody][2];
if (ibody == -1) continue; // means not in a rigid body
for (int jj = 0; jj < jnum; jj++){
j = jlist[jj]; // index in the current core
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
jtag=tag[j];
jtype = type[j];
//jbody=int ((jtag-1)/60);
//CS: molecule[j]-1 is the correct molecule ID
// while body[j] is partially correct,
// body[jtag] is not correct
// more accurate: mol2body[molecule[j]]
jbody = mol2body[molecule[j]];
if (jbody == -1) continue; // means not in a rigid body
domain->unmap(x[j],xcmimage[j],unwrap);
j_dx = unwrap[0] - xcm[jbody][0];
j_dy = unwrap[1] - xcm[jbody][1];
j_dz = unwrap[2] - xcm[jbody][2];
delx = xtmp - x[j][0]; // distance between atom i and j
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
{
if (rsq >= cutsq[itype][jtype]) continue;
}
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
double i_fx=delx*fpair;
double i_fy=dely*fpair;
double i_fz=delz*fpair;
//calculate the pair_torque
pair_torque[ibody][jbody][0] += (i_dy*i_fz - i_dz*i_fy);
pair_torque[ibody][jbody][1] += (i_dz*i_fx - i_dx*i_fz);
pair_torque[ibody][jbody][2] += (i_dx*i_fy - i_dy*i_fx);
//calculate the pair_force
pair_force[ibody][jbody][0] += i_fx;
pair_force[ibody][jbody][1] += i_fy;
pair_force[ibody][jbody][2] += i_fz;
}
}
MPI_Allreduce(pair_torque[0][0],final_torque[0][0],3*nbody*nbody,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(pair_force[0][0],final_force[0][0],3*nbody*nbody,MPI_DOUBLE,MPI_SUM,world);
}
// late calculation of forces and torques (if requested)
if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom
// fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
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) {
tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akin_t += 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) {
akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] +
angmom[ibody][2]*omega[ibody][2];
}
}
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
set_v();
// post-processing for rigid-body Green-Kubo calculation
// potential energy of each atoms
double total_pe=0;