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lammps/src/POEMS/fix_poems.cpp
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fix_poems.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
FixPOEMS is a LAMMPS interface to the POEMS coupled multi-body simulator
POEMS authors: Rudranarayan Mukherjee (mukher@rpi.edu)
Kurt Anderson (anderk5@rpi.edu)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "workspace.h"
#include "fix_poems.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "force.h"
#include "output.h"
#include "group.h"
#include "comm.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define MAXBODY 2 // currently 2 since only linear chains allowed
#define DELTA 128
#define TOLERANCE 1.0e-6
#define EPSILON 1.0e-7
#define MAXJACOBI 50
static const char cite_fix_poems[] =
"fix poems command:\n\n"
"@Article{Mukherjee08,\n"
" author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},\n"
" title = {Substructured molecular dynamics using multibody dynamics algorithms},\n"
" journal = {Intl.~J.~Non-linear Mechanics},\n"
" year = 2008,\n"
" volume = 43,\n"
" pages = {1045--1055}\n"
"}\n\n";
/* ----------------------------------------------------------------------
define rigid bodies and joints, initiate POEMS
------------------------------------------------------------------------- */
FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), step_respa(NULL), natom2body(NULL),
atom2body(NULL), displace(NULL), nrigid(NULL), masstotal(NULL),
xcm(NULL), vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
torque(NULL), sum(NULL), all(NULL), jointbody(NULL),
xjoint(NULL), freelist(NULL), poems(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_poems);
int i,j,ibody;
time_integrate = 1;
rigid_flag = 1;
virial_flag = 1;
thermo_virial = 1;
dof_flag = 1;
MPI_Comm_rank(world,&me);
// perform initial allocation of atom-based arrays
// register with atom class
natom2body = NULL;
atom2body = NULL;
displace = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// initialize each atom to belong to no rigid bodies
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) natom2body[i] = 0;
// create an atom map if one doesn't exist already
// readfile() and jointbuild() use global atom IDs
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_init();
atom->map_set();
}
// parse command-line args
// set natom2body, atom2body for all atoms and nbody = # of rigid bodies
// atoms must also be in fix group to be in a body
if (narg < 4) error->all(FLERR,"Illegal fix poems command");
// group = arg has list of groups
if (strcmp(arg[3],"group") == 0) {
nbody = narg-4;
if (nbody <= 0) error->all(FLERR,"Illegal fix poems command");
int *igroups = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) {
igroups[ibody] = group->find(arg[ibody+4]);
if (igroups[ibody] == -1)
error->all(FLERR,"Could not find fix poems group ID");
}
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
for (ibody = 0; ibody < nbody; ibody++)
if (mask[i] & group->bitmask[igroups[ibody]]) {
if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = ibody;
natom2body[i]++;
}
}
delete [] igroups;
// file = read bodies from file
// file read doesn't pay attention to fix group,
// so after read, reset natom2body = 0 if atom is not in fix group
} else if (strcmp(arg[3],"file") == 0) {
readfile(arg[4]);
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) natom2body[i] = 0;
// each molecule in fix group is a rigid body
// maxmol = largest molecule ID
// ncount = # of atoms in each molecule (have to sum across procs)
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set atom2body[] values for each atom
} else if (strcmp(arg[3],"molecule") == 0) {
if (narg != 4) error->all(FLERR,"Illegal fix poems command");
if (atom->molecular == 0)
error->all(FLERR,
"Must use a molecular atom style with fix poems molecule");
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag,molecule[i]);
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix poems");
int maxmol = (int) itmp;
int *ncount;
memory->create(ncount,maxmol+1,"rigid:ncount");
for (i = 0; i <= maxmol; i++) ncount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount[molecule[i]]++;
int *nall;
memory->create(nall,maxmol+1,"rigid:ncount");
MPI_Allreduce(ncount,nall,maxmol+1,MPI_INT,MPI_SUM,world);
nbody = 0;
for (i = 0; i <= maxmol; i++)
if (nall[i]) nall[i] = nbody++;
else nall[i] = -1;
for (i = 0; i < nlocal; i++) {
natom2body[i] = 0;
if (mask[i] & groupbit) {
natom2body[i] = 1;
atom2body[i][0] = nall[molecule[i]];
}
}
memory->destroy(ncount);
memory->destroy(nall);
} else error->all(FLERR,"Illegal fix poems command");
// error if no bodies
// error if any atom in too many bodies
if (nbody == 0) error->all(FLERR,"No rigid bodies defined");
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (natom2body[i] > MAXBODY) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY");
// create all nbody-length arrays
nrigid = new int[nbody];
masstotal = new double[nbody];
memory->create(xcm,nbody,3,"poems:xcm");
memory->create(vcm,nbody,3,"poems:vcm");
memory->create(fcm,nbody,3,"poems:fcm");
memory->create(inertia,nbody,3,"poems:inertia");
memory->create(ex_space,nbody,3,"poems:ex_space");
memory->create(ey_space,nbody,3,"poems:ey_space");
memory->create(ez_space,nbody,3,"poems:ez_space");
memory->create(angmom,nbody,3,"poems:angmom");
memory->create(omega,nbody,3,"poems:omega");
memory->create(torque,nbody,3,"poems:torque");
memory->create(sum,nbody,6,"poems:sum");
memory->create(all,nbody,6,"poems:all");
// nrigid[n] = # of atoms in Nth rigid body
// double count joint atoms as being in multiple bodies
// error if one or zero atoms
int *ncount = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < natom2body[i]; j++)
ncount[atom2body[i][j]]++;
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
delete [] ncount;
for (ibody = 0; ibody < nbody; ibody++)
if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body");
// build list of joint connections and check for cycles and trees
jointbuild();
// delete temporary atom map
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
// create POEMS instance
poems = new Workspace;
// print statistics
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
nsum -= njoint;
if (me == 0) {
if (screen)
fprintf(screen,"%d clusters, %d bodies, %d joints, %d atoms\n",
ncluster,nbody,njoint,nsum);
if (logfile)
fprintf(logfile,"%d clusters, %d bodies, %d joints, %d atoms\n",
ncluster,nbody,njoint,nsum);
}
}
/* ----------------------------------------------------------------------
free all memory for rigid bodies, joints, and POEMS
------------------------------------------------------------------------- */
FixPOEMS::~FixPOEMS()
{
// if atom class still exists:
// unregister this fix so atom class doesn't invoke it any more
if (atom) atom->delete_callback(id,0);
// delete locally stored arrays
memory->destroy(natom2body);
memory->destroy(atom2body);
memory->destroy(displace);
// delete nbody-length arrays
delete [] nrigid;
delete [] masstotal;
memory->destroy(xcm);
memory->destroy(vcm);
memory->destroy(fcm);
memory->destroy(inertia);
memory->destroy(ex_space);
memory->destroy(ey_space);
memory->destroy(ez_space);
memory->destroy(angmom);
memory->destroy(omega);
memory->destroy(torque);
memory->destroy(sum);
memory->destroy(all);
// delete joint arrays
memory->destroy(jointbody);
memory->destroy(xjoint);
delete [] freelist;
// delete POEMS object
delete poems;
}
/* ---------------------------------------------------------------------- */
int FixPOEMS::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_NEIGHBOR;
mask |= POST_FORCE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::init()
{
int i,ibody;
// warn if more than one POEMS fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"poems") == 0)
error->all(FLERR,"POEMS fix must come before NPT/NPH fix");
}
// timestep info
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
// rRESPA info
if (strstr(update->integrate_style,"respa")) {
step_respa = ((Respa *) update->integrate)->step;
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
// compute masstotal & center-of-mass xcm of each rigid body
// only count joint atoms in 1st body
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double **x = atom->x;
double **v = atom->v;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double massone;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
for (i = 0; i < nlocal; i++) {
if (natom2body[i]) {
ibody = atom2body[i][0];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
massone = mass[type[i]];
sum[ibody][0] += (x[i][0] + xbox*xprd) * massone;
sum[ibody][1] += (x[i][1] + ybox*yprd) * massone;
sum[ibody][2] += (x[i][2] + zbox*zprd) * massone;
sum[ibody][3] += massone;
sum[ibody][4] += massone *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
total_ke = 0.0;
for (ibody = 0; ibody < nbody; ibody++) {
masstotal[ibody] = all[ibody][3];
xcm[ibody][0] = all[ibody][0]/masstotal[ibody];
xcm[ibody][1] = all[ibody][1]/masstotal[ibody];
xcm[ibody][2] = all[ibody][2]/masstotal[ibody];
total_ke += 0.5 * all[ibody][4];
}
// compute 6 moments of inertia of each body
// only count joint atoms in 1st body
// dx,dy,dz = coords relative to center-of-mass
double 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 (natom2body[i]) {
ibody = atom2body[i][0];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
massone = mass[type[i]];
sum[ibody][0] += massone * (dy*dy + dz*dz);
sum[ibody][1] += massone * (dx*dx + dz*dz);
sum[ibody][2] += massone * (dx*dx + dy*dy);
sum[ibody][3] -= massone * dx*dy;
sum[ibody][4] -= massone * dy*dz;
sum[ibody][5] -= massone * dx*dz;
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
// inertia = 3 eigenvalues = principal moments of inertia
// ex_space,ey_space,ez_space = 3 eigenvectors = principal axes of rigid body
double **tensor,**evectors;
memory->create(tensor,3,3,"fix_rigid:tensor");
memory->create(evectors,3,3,"fix_rigid:evectors");
int ierror;
double ez0,ez1,ez2;
for (ibody = 0; ibody < nbody; ibody++) {
tensor[0][0] = all[ibody][0];
tensor[1][1] = all[ibody][1];
tensor[2][2] = all[ibody][2];
tensor[0][1] = tensor[1][0] = all[ibody][3];
tensor[1][2] = tensor[2][1] = all[ibody][4];
tensor[0][2] = tensor[2][0] = all[ibody][5];
ierror = jacobi(tensor,inertia[ibody],evectors);
if (ierror) error->all(FLERR,"Insufficient Jacobi rotations for POEMS body");
ex_space[ibody][0] = evectors[0][0];
ex_space[ibody][1] = evectors[1][0];
ex_space[ibody][2] = evectors[2][0];
ey_space[ibody][0] = evectors[0][1];
ey_space[ibody][1] = evectors[1][1];
ey_space[ibody][2] = evectors[2][1];
ez_space[ibody][0] = evectors[0][2];
ez_space[ibody][1] = evectors[1][2];
ez_space[ibody][2] = evectors[2][2];
// if any principal moment < scaled EPSILON, error
// this is b/c POEMS cannot yet handle degenerate bodies
double max;
max = MAX(inertia[ibody][0],inertia[ibody][1]);
max = MAX(max,inertia[ibody][2]);
if (inertia[ibody][0] < EPSILON*max ||
inertia[ibody][1] < EPSILON*max ||
inertia[ibody][2] < EPSILON*max)
error->all(FLERR,"Rigid body has degenerate moment of inertia");
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd evector if needed
ez0 = ex_space[ibody][1]*ey_space[ibody][2] -
ex_space[ibody][2]*ey_space[ibody][1];
ez1 = ex_space[ibody][2]*ey_space[ibody][0] -
ex_space[ibody][0]*ey_space[ibody][2];
ez2 = ex_space[ibody][0]*ey_space[ibody][1] -
ex_space[ibody][1]*ey_space[ibody][0];
if (ez0*ez_space[ibody][0] + ez1*ez_space[ibody][1] +
ez2*ez_space[ibody][2] < 0.0) {
ez_space[ibody][0] = -ez_space[ibody][0];
ez_space[ibody][1] = -ez_space[ibody][1];
ez_space[ibody][2] = -ez_space[ibody][2];
}
}
// free temporary memory
memory->destroy(tensor);
memory->destroy(evectors);
// displace = initial atom coords in basis of principal axes
// only set joint atoms relative to 1st body
// set displace = 0.0 for atoms not in any rigid body
for (i = 0; i < nlocal; i++) {
if (natom2body[i]) {
ibody = atom2body[i][0];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
displace[i][0] = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
dz*ex_space[ibody][2];
displace[i][1] = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
dz*ey_space[ibody][2];
displace[i][2] = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
dz*ez_space[ibody][2];
} else displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
}
// test for valid principal moments & axes
// recompute moments of inertia around new axes
// only count joint atoms in 1st body
// 3 diagonal moments should equal principal moments
// 3 off-diagonal moments should be 0.0
// (ddx,ddy,ddz) is projection of atom within rigid body onto principal axes
// 6 moments use (ddx,ddy,ddz) displacements from principal axes
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
double ddx,ddy,ddz;
for (i = 0; i < nlocal; i++) {
if (natom2body[i]) {
ibody = atom2body[i][0];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
massone = mass[type[i]];
ddx = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
dz*ex_space[ibody][2];
ddy = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
dz*ey_space[ibody][2];
ddz = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
dz*ez_space[ibody][2];
sum[ibody][0] += massone * (ddy*ddy + ddz*ddz);
sum[ibody][1] += massone * (ddx*ddx + ddz*ddz);
sum[ibody][2] += massone * (ddx*ddx + ddy*ddy);
sum[ibody][3] -= massone * ddx*ddy;
sum[ibody][4] -= massone * ddy*ddz;
sum[ibody][5] -= massone * ddx*ddz;
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
if (fabs(all[ibody][0]-inertia[ibody][0]) > TOLERANCE ||
fabs(all[ibody][1]-inertia[ibody][1]) > TOLERANCE ||
fabs(all[ibody][2]-inertia[ibody][2]) > TOLERANCE)
error->all(FLERR,"Bad principal moments");
if (fabs(all[ibody][3]) > TOLERANCE ||
fabs(all[ibody][4]) > TOLERANCE ||
fabs(all[ibody][5]) > TOLERANCE)
error->all(FLERR,"Bad principal moments");
}
}
/* ----------------------------------------------------------------------
compute initial rigid body info
make setup call to POEMS
------------------------------------------------------------------------- */
void FixPOEMS::setup(int vflag)
{
int i,n,ibody;
// vcm = velocity of center-of-mass of each rigid body
// angmom = angular momentum of each rigid body
// only count joint atoms in 1st body
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double **x = atom->x;
double **v = atom->v;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double massone,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 (natom2body[i]) {
ibody = atom2body[i][0];
massone = mass[type[i]];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - xcm[ibody][2];
sum[ibody][0] += v[i][0] * massone;
sum[ibody][1] += v[i][1] * massone;
sum[ibody][2] += v[i][2] * massone;
sum[ibody][3] += dy * massone*v[i][2] - dz * massone*v[i][1];
sum[ibody][4] += dz * massone*v[i][0] - dx * massone*v[i][2];
sum[ibody][5] += dx * massone*v[i][1] - dy * massone*v[i][0];
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
vcm[ibody][0] = all[ibody][0]/masstotal[ibody];
vcm[ibody][1] = all[ibody][1]/masstotal[ibody];
vcm[ibody][2] = all[ibody][2]/masstotal[ibody];
angmom[ibody][0] = all[ibody][3];
angmom[ibody][1] = all[ibody][4];
angmom[ibody][2] = all[ibody][5];
}
// virial setup before call to set_v
if (vflag) v_setup(vflag);
else evflag = 0;
// set velocities from angmom & omega
for (ibody = 0; ibody < nbody; ibody++)
omega_from_mq(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
set_v();
// guestimate virial as 2x the set_v contribution
if (evflag) {
if (vflag_global)
for (n = 0; n < 6; n++) virial[n] *= 2.0;
if (vflag_atom) {
for (i = 0; i < nlocal; i++)
for (n = 0; n < 6; n++)
vatom[i][n] *= 2.0;
}
}
// use post_force() to compute initial fcm & torque
post_force(vflag);
// setup for POEMS
poems->MakeSystem(nbody,masstotal,inertia,xcm,vcm,omega,
ex_space,ey_space,ez_space,
njoint,jointbody,xjoint,nfree,freelist,
dthalf,dtv,force->ftm2v,total_ke);
}
/* ----------------------------------------------------------------------
update vcm,omega by 1/2 step and xcm,orientation by full step
set x,v of body atoms accordingly
---------------------------------------------------------------------- */
void FixPOEMS::initial_integrate(int vflag)
{
// perform POEMS integration
poems->LobattoOne(xcm,vcm,omega,torque,fcm,ex_space,ey_space,ez_space);
// virial setup before call to set_xv
if (vflag) v_setup(vflag);
else evflag = 0;
// set coords and velocities of atoms in rigid bodies
set_xv();
}
/* ----------------------------------------------------------------------
compute fcm,torque on each rigid body
only count joint atoms in 1st body
------------------------------------------------------------------------- */
void FixPOEMS::post_force(int vflag)
{
int i,ibody;
int xbox,ybox,zbox;
double dx,dy,dz;
imageint *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;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
for (i = 0; i < nlocal; i++) {
if (natom2body[i]) {
ibody = atom2body[i][0];
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xcm[ibody][0];
dy = x[i][1] + ybox*yprd - xcm[ibody][1];
dz = x[i][2] + zbox*zprd - 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];
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
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];
}
}
/* ----------------------------------------------------------------------
update vcm,omega by last 1/2 step
set v of body atoms accordingly
------------------------------------------------------------------------- */
void FixPOEMS::final_integrate()
{
// perform POEMS integration
poems->LobattoTwo(vcm,omega,torque,fcm);
// set velocities of atoms in rigid bodies
// virial is already setup from initial_integrate
set_v();
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
if (ilevel == 0) initial_integrate(vflag);
else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::final_integrate_respa(int ilevel, int iloop)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
}
/* ----------------------------------------------------------------------
remap xcm of each rigid body back into periodic simulation box
done during pre_neighbor so will be after call to pbc()
and after fix_deform::pre_exchange() may have flipped box
if don't do this, then atoms of a body which drifts far away
from a triclinic box will be remapped back into box
with huge displacements when the box tilt changes via set_x()
NOTE: cannot do this by changing xcm of each body in cluster
or even 1st body in cluster
b/c POEMS library does not see xcm but only sets xcm
so remap needs to be coordinated with POEMS library
thus this routine does nothing for now
------------------------------------------------------------------------- */
void FixPOEMS::pre_neighbor() {}
/* ----------------------------------------------------------------------
count # of degrees-of-freedom removed by fix_poems for atoms in igroup
------------------------------------------------------------------------- */
int FixPOEMS::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
// ncount = # of atoms in each rigid body that are also in group
// only count joint atoms as part of first body
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *ncount = new int[nbody];
for (int ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (natom2body[i]) ncount[atom2body[i][0]]++;
int *nall = new int[nbody];
MPI_Allreduce(ncount,nall,nbody,MPI_INT,MPI_SUM,world);
// remove 3N - 6 dof for each rigid body if at least 2 atoms are in igroup
int n = 0;
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody] > 2) n += 3*nall[ibody] - 6;
// subtract 3 additional dof for each joint if atom is also in igroup
int m = 0;
for (int i = 0; i < nlocal; i++)
if (natom2body[i] > 1 && (mask[i] & groupbit)) m += 3*(natom2body[i]-1);
int mall;
MPI_Allreduce(&m,&mall,1,MPI_INT,MPI_SUM,world);
n += mall;
// delete local memory
delete [] ncount;
delete [] nall;
return n;
}
/* ----------------------------------------------------------------------
adjust xcm of each cluster due to box deformation
called by various fixes that change box size/shape
flag = 0/1 means map from box to lamda coords or vice versa
NOTE: cannot do this by changing xcm of each body in cluster
or even 1st body in cluster
b/c POEMS library does not see xcm but only sets xcm
so deform needs to be coordinated with POEMS library
thus this routine does nothing for now
------------------------------------------------------------------------- */
void FixPOEMS::deform(int flag) {}
/* ---------------------------------------------------------------------- */
void FixPOEMS::readfile(char *file)
{
FILE *fp;
if (me == 0) {
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix poems file %s",file);
error->one(FLERR,str);
}
}
nbody = 0;
char *line = NULL;
int maxline = 0;
char *ptr;
int nlocal = atom->nlocal;
int i,id,nlen;
while (1) {
if (me == 0) nlen = readline(fp,&line,&maxline);
MPI_Bcast(&nlen,1,MPI_INT,0,world);
if (nlen == 0) break;
MPI_Bcast(line,nlen,MPI_CHAR,0,world);
ptr = strtok(line," ,\t\n\0");
if (ptr == NULL || ptr[0] == '#') continue;
ptr = strtok(NULL," ,\t\n\0");
while ((ptr = strtok(NULL," ,\t\n\0"))) {
id = atoi(ptr);
i = atom->map(id);
if (i < 0 || i >= nlocal) continue;
if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = nbody;
natom2body[i]++;
}
nbody++;
}
memory->destroy(line);
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixPOEMS::readline(FILE *fp, char **pline, int *pmaxline)
{
int n = 0;
char *line = *pline;
int maxline = *pmaxline;
while (1) {
if (n+1 >= maxline) {
maxline += DELTA;
memory->grow(line,maxline,"fix_poems:line");
}
if (fgets(&line[n],maxline-n,fp) == NULL) {
n = 0;
break;
}
n = strlen(line);
if (n < maxline-1 || line[n-1] == '\n') break;
}
*pmaxline = maxline;
*pline = line;
return n;
}
/* ----------------------------------------------------------------------
build list of joints and error check for cycles and trees
------------------------------------------------------------------------- */
void FixPOEMS::jointbuild()
{
int i,j;
// convert atom2body into list of joint atoms on this proc
// mjoint = # of joint atoms in this proc
// an atom in N rigid bodies, infers N-1 joints between 1st body and others
// mylist = [0],[1] = 2 body indices, [2] = global ID of joint atom
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int mjoint = 0;
for (i = 0; i < nlocal; i++) {
if (natom2body[i] <= 1) continue;
mjoint += natom2body[i]-1;
}
tagint **mylist = NULL;
if (mjoint) memory->create(mylist,mjoint,3,"poems:mylist");
mjoint = 0;
for (i = 0; i < nlocal; i++) {
if (natom2body[i] <= 1) continue;
for (j = 1; j < natom2body[i]; j++) {
mylist[mjoint][0] = atom2body[i][0];
mylist[mjoint][1] = atom2body[i][j];
mylist[mjoint][2] = tag[i];
mjoint++;
}
}
// jlist = mylist concatenated across all procs via MPI_Allgatherv
MPI_Allreduce(&mjoint,&njoint,1,MPI_INT,MPI_SUM,world);
tagint **jlist = NULL;
if (njoint) memory->create(jlist,njoint,3,"poems:jlist");
int nprocs;
MPI_Comm_size(world,&nprocs);
int *recvcounts = new int[nprocs];
int tmp = 3*mjoint;
MPI_Allgather(&tmp,1,MPI_INT,recvcounts,1,MPI_INT,world);
int *displs = new int[nprocs];
displs[0] = 0;
for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1];
// allgather the local joint lists
// 2 versions in case mjoint is 0 on this proc
if (njoint) {
if (mjoint)
MPI_Allgatherv(mylist[0],3*mjoint,MPI_LMP_TAGINT,jlist[0],
recvcounts,displs,MPI_LMP_TAGINT,world);
else
MPI_Allgatherv(NULL,3*mjoint,MPI_LMP_TAGINT,jlist[0],
recvcounts,displs,MPI_LMP_TAGINT,world);
}
delete [] recvcounts;
delete [] displs;
// warning if no joints
if (njoint == 0 && me == 0)
error->warning(FLERR,
"No joints between rigid bodies, use fix rigid instead");
// sort joint list in ascending order by body indices
// check for loops in joint connections between rigid bodies
// check for trees = same body in more than 2 joints
sortlist(njoint,jlist);
if (loopcheck(nbody,njoint,jlist))
error->all(FLERR,"Cyclic loop in joint connections");
int *bodyflag = new int[nbody];
for (i = 0; i < nbody; i++) bodyflag[i] = 0;
for (i = 0; i < njoint; i++) {
bodyflag[jlist[i][0]]++;
bodyflag[jlist[i][1]]++;
}
for (i = 0; i < nbody; i++)
if (bodyflag[i] > 2)
error->all(FLERR,"Tree structure in joint connections");
delete [] bodyflag;
// allocate and setup joint arrays
// jointbody stores body indices from 1 to Nbody to pass to POEMS
// each proc sets myjoint if it owns joint atom
// MPI_Allreduce gives all procs the xjoint coords
jointbody = NULL;
xjoint = NULL;
double **myjoint = NULL;
if (njoint) {
memory->create(jointbody,njoint,2,"poems:jointbody");
memory->create(xjoint,njoint,3,"poems:xjoint");
memory->create(myjoint,njoint,3,"poems:myjoint");
}
double **x = atom->x;
for (i = 0; i < njoint; i++) {
jointbody[i][0] = jlist[i][0] + 1;
jointbody[i][1] = jlist[i][1] + 1;
j = atom->map(jlist[i][2]);
if (j >= 0 && j < nlocal) {
myjoint[i][0] = x[j][0];
myjoint[i][1] = x[j][1];
myjoint[i][2] = x[j][2];
} else myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0;
}
if (njoint)
MPI_Allreduce(myjoint[0],xjoint[0],3*njoint,MPI_DOUBLE,MPI_SUM,world);
// compute freelist of nfree single unconnected bodies
// POEMS could do this itself
int *mark = new int[nbody];
for (i = 0; i < nbody; i++) mark[i] = 1;
for (i = 0; i < njoint; i++) {
mark[jointbody[i][0]-1] = 0;
mark[jointbody[i][1]-1] = 0;
}
nfree = 0;
for (i = 0; i < nbody; i++)
if (mark[i]) nfree++;
if (nfree) freelist = new int[nfree];
else freelist = NULL;
nfree = 0;
for (i = 0; i < nbody; i++)
if (mark[i]) freelist[nfree++] = i + 1;
delete [] mark;
// free memory local to this routine
memory->destroy(mylist);
memory->destroy(jlist);
memory->destroy(myjoint);
}
/* ----------------------------------------------------------------------
sort joint list (Numerical Recipes shell sort)
sort criterion: sort on 1st body, if equal sort on 2nd body
------------------------------------------------------------------------- */
void FixPOEMS::sortlist(int n, tagint **list)
{
int i,j,flag;
tagint v0,v1,v2;
int inc = 1;
while (inc <= n) inc = 3*inc + 1;
do {
inc /= 3;
for (i = inc+1; i <= n; i++) {
v0 = list[i-1][0];
v1 = list[i-1][1];
v2 = list[i-1][2];
j = i;
flag = 0;
if (list[j-inc-1][0] > v0 ||
(list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
while (flag) {
list[j-1][0] = list[j-inc-1][0];
list[j-1][1] = list[j-inc-1][1];
list[j-1][2] = list[j-inc-1][2];
j -= inc;
if (j <= inc) break;
flag = 0;
if (list[j-inc-1][0] > v0 ||
(list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
}
list[j-1][0] = v0;
list[j-1][1] = v1;
list[j-1][2] = v2;
}
} while (inc > 1);
}
/* ----------------------------------------------------------------------
check for cycles in list of joint connections between rigid bodies
treat as graph: vertex = body, edge = joint between 2 bodies
------------------------------------------------------------------------- */
int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist)
{
int i,j,k;
// ecount[i] = # of vertices connected to vertex i via edge
// elistfull[i][*] = list of vertices connected to vertex i
int *ecount = new int[nvert];
for (i = 0; i < nvert; i++) ecount[i] = 0;
for (i = 0; i < nedge; i++) {
ecount[elist[i][0]]++;
ecount[elist[i][1]]++;
}
int emax = 0;
for (i = 0; i < nvert; i++) emax = MAX(emax,ecount[i]);
int **elistfull;
memory->create(elistfull,nvert,emax,"poems:elistfull");
for (i = 0; i < nvert; i++) ecount[i] = 0;
for (i = 0; i < nedge; i++) {
elistfull[elist[i][0]][ecount[elist[i][0]]++] = elist[i][1];
elistfull[elist[i][1]][ecount[elist[i][1]]++] = elist[i][0];
}
// cycle detection algorithm
// mark = 0/1 marking of each vertex, all initially unmarked
// outer while loop:
// if all vertices are marked, no cycles, exit loop
// push an unmarked vertex on stack and mark it, parent is -1
// while stack is not empty:
// pop vertex I from stack
// loop over vertices J connected to I via edge
// if J is parent (vertex that pushed I on stack), skip it
// else if J is marked, a cycle is found, return 1
// else push J on stack and mark it, parent is I
// increment ncluster each time stack empties since that is new cluster
int *parent = new int[nvert];
int *mark = new int[nvert];
for (i = 0; i < nvert; i++) mark[i] = 0;
int nstack = 0;
int *stack = new int[nvert];
ncluster = 0;
while (1) {
for (i = 0; i < nvert; i++)
if (mark[i] == 0) break;
if (i == nvert) break;
stack[nstack++] = i;
mark[i] = 1;
parent[i] = -1;
while (nstack) {
i = stack[--nstack];
for (k = 0; k < ecount[i]; k++) {
j = elistfull[i][k];
if (j == parent[i]) continue;
if (mark[j]) return 1;
stack[nstack++] = j;
mark[j] = 1;
parent[j] = i;
}
}
ncluster++;
}
// free memory local to this routine
delete [] ecount;
memory->destroy(elistfull);
delete [] parent;
delete [] mark;
delete [] stack;
return 0;
}
/* ----------------------------------------------------------------------
compute evalues and evectors of 3x3 real symmetric matrix
based on Jacobi rotations
adapted from Numerical Recipes jacobi() function
------------------------------------------------------------------------- */
int FixPOEMS::jacobi(double **matrix, double *evalues, double **evectors)
{
int i,j,k;
double tresh,theta,tau,t,sm,s,h,g,c,b[3],z[3];
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) evectors[i][j] = 0.0;
evectors[i][i] = 1.0;
}
for (i = 0; i < 3; i++) {
b[i] = evalues[i] = matrix[i][i];
z[i] = 0.0;
}
for (int iter = 1; iter <= MAXJACOBI; iter++) {
sm = 0.0;
for (i = 0; i < 2; i++)
for (j = i+1; j < 3; j++)
sm += fabs(matrix[i][j]);
if (sm == 0.0) return 0;
if (iter < 4) tresh = 0.2*sm/(3*3);
else tresh = 0.0;
for (i = 0; i < 2; i++) {
for (j = i+1; j < 3; j++) {
g = 100.0*fabs(matrix[i][j]);
if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i])
&& fabs(evalues[j])+g == fabs(evalues[j]))
matrix[i][j] = 0.0;
else if (fabs(matrix[i][j]) > tresh) {
h = evalues[j]-evalues[i];
if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h;
else {
theta = 0.5*h/(matrix[i][j]);
t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta));
if (theta < 0.0) t = -t;
}
c = 1.0/sqrt(1.0+t*t);
s = t*c;
tau = s/(1.0+c);
h = t*matrix[i][j];
z[i] -= h;
z[j] += h;
evalues[i] -= h;
evalues[j] += h;
matrix[i][j] = 0.0;
for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau);
for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau);
for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau);
for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau);
}
}
}
for (i = 0; i < 3; i++) {
evalues[i] = b[i] += z[i];
z[i] = 0.0;
}
}
return 1;
}
/* ----------------------------------------------------------------------
perform a single Jacobi rotation
------------------------------------------------------------------------- */
void FixPOEMS::rotate(double **matrix, int i, int j, int k, int l,
double s, double tau)
{
double g = matrix[i][j];
double h = matrix[k][l];
matrix[i][j] = g-s*(h+g*tau);
matrix[k][l] = h+s*(g-h*tau);
}
/* ----------------------------------------------------------------------
compute omega from angular momentum
w = omega = angular velocity in space frame
wbody = angular velocity in body frame
set wbody component to 0.0 if inertia component is 0.0
otherwise body can spin easily around that axis
project space-frame angular momentum onto body axes
and divide by principal moments
------------------------------------------------------------------------- */
void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez,
double *inertia, double *w)
{
double wbody[3];
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] = (m[0]*ex[0] + m[1]*ex[1] + m[2]*ex[2]) / inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] = (m[0]*ey[0] + m[1]*ey[1] + m[2]*ey[2]) / inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] = (m[0]*ez[0] + m[1]*ez[1] + m[2]*ez[2]) / inertia[2];
w[0] = wbody[0]*ex[0] + wbody[1]*ey[0] + wbody[2]*ez[0];
w[1] = wbody[0]*ex[1] + wbody[1]*ey[1] + wbody[2]*ez[1];
w[2] = wbody[0]*ex[2] + wbody[1]*ey[2] + wbody[2]*ez[2];
}
/* ----------------------------------------------------------------------
set space-frame coords and velocity of each atom in each rigid body
x = Q displace + Xcm, mapped back to periodic box
v = Vcm + (W cross (x - Xcm))
------------------------------------------------------------------------- */
void FixPOEMS::set_xv()
{
int ibody;
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double vr[6];
imageint *image = atom->image;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
// set x and v of each atom
// only set joint atoms for 1st rigid body they belong to
for (int i = 0; i < nlocal; i++) {
if (natom2body[i] == 0) continue;
ibody = atom2body[i][0];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
// save old positions and velocities for virial
if (evflag) {
x0 = x[i][0] + xbox*xprd;
x1 = x[i][1] + ybox*yprd;
x2 = x[i][2] + zbox*zprd;
v0 = v[i][0];
v1 = v[i][1];
v2 = v[i][2];
}
// x = displacement from center-of-mass, based on body orientation
// v = vcm + omega around center-of-mass
x[i][0] = ex_space[ibody][0]*displace[i][0] +
ey_space[ibody][0]*displace[i][1] +
ez_space[ibody][0]*displace[i][2];
x[i][1] = ex_space[ibody][1]*displace[i][0] +
ey_space[ibody][1]*displace[i][1] +
ez_space[ibody][1]*displace[i][2];
x[i][2] = ex_space[ibody][2]*displace[i][0] +
ey_space[ibody][2]*displace[i][1] +
ez_space[ibody][2]*displace[i][2];
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
vcm[ibody][0];
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] +
vcm[ibody][1];
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
vcm[ibody][2];
// add center of mass to displacement
// map back into periodic box via xbox,ybox,zbox
x[i][0] += xcm[ibody][0] - xbox*xprd;
x[i][1] += xcm[ibody][1] - ybox*yprd;
x[i][2] += xcm[ibody][2] - zbox*zprd;
// 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) {
massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
vr[0] = 0.5*fc0*x0;
vr[1] = 0.5*fc1*x1;
vr[2] = 0.5*fc2*x2;
vr[3] = 0.5*fc1*x0;
vr[4] = 0.5*fc2*x0;
vr[5] = 0.5*fc2*x1;
v_tally(1,&i,1.0,vr);
}
}
}
/* ----------------------------------------------------------------------
set space-frame velocity of each atom in a rigid body
v = Vcm + (W cross (x - Xcm))
------------------------------------------------------------------------- */
void FixPOEMS::set_v()
{
int ibody;
int xbox,ybox,zbox;
double dx,dy,dz;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double vr[6];
double *mass = atom->mass;
double **f = atom->f;
double **x = atom->x;
double **v = atom->v;
int *type = atom->type;
imageint *image = atom->image;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
// set v of each atom
// only set joint atoms for 1st rigid body they belong to
for (int i = 0; i < nlocal; i++) {
if (natom2body[i] == 0) continue;
ibody = atom2body[i][0];
dx = ex_space[ibody][0]*displace[i][0] +
ey_space[ibody][0]*displace[i][1] +
ez_space[ibody][0]*displace[i][2];
dy = ex_space[ibody][1]*displace[i][0] +
ey_space[ibody][1]*displace[i][1] +
ez_space[ibody][1]*displace[i][2];
dz = ex_space[ibody][2]*displace[i][0] +
ey_space[ibody][2]*displace[i][1] +
ez_space[ibody][2]*displace[i][2];
// save old velocities for virial
if (evflag) {
v0 = v[i][0];
v1 = v[i][1];
v2 = v[i][2];
}
v[i][0] = omega[ibody][1]*dz - omega[ibody][2]*dy + vcm[ibody][0];
v[i][1] = omega[ibody][2]*dx - omega[ibody][0]*dz + vcm[ibody][1];
v[i][2] = omega[ibody][0]*dy - omega[ibody][1]*dx + vcm[ibody][2];
// 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) {
massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
x0 = x[i][0] + xbox*xprd;
x1 = x[i][1] + ybox*yprd;
x2 = x[i][2] + zbox*zprd;
vr[0] = 0.5*fc0*x0;
vr[1] = 0.5*fc1*x1;
vr[2] = 0.5*fc2*x2;
vr[3] = 0.5*fc1*x0;
vr[4] = 0.5*fc2*x0;
vr[5] = 0.5*fc2*x1;
v_tally(1,&i,1.0,vr);
}
}
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixPOEMS::grow_arrays(int nmax)
{
memory->grow(natom2body,nmax,"fix_poems:natom2body");
memory->grow(atom2body,nmax,MAXBODY,"fix_poems:atom2body");
memory->grow(displace,nmax,3,"fix_poems:displace");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPOEMS::copy_arrays(int i, int j, int delflag)
{
natom2body[j] = natom2body[i];
for (int k = 0; k < natom2body[j]; k++) atom2body[j][k] = atom2body[i][k];
displace[j][0] = displace[i][0];
displace[j][1] = displace[i][1];
displace[j][2] = displace[i][2];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixPOEMS::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*MAXBODY * sizeof(int);
bytes += nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixPOEMS::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = static_cast<double> (natom2body[i]);
for (int j = 0; j < natom2body[i]; j++)
buf[m++] = static_cast<double> (atom2body[i][j]);
buf[m++] = displace[i][0];
buf[m++] = displace[i][1];
buf[m++] = displace[i][2];
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixPOEMS::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
natom2body[nlocal] = static_cast<int> (buf[m++]);
for (int i = 0; i < natom2body[nlocal]; i++)
atom2body[nlocal][i] = static_cast<int> (buf[m++]);
displace[nlocal][0] = buf[m++];
displace[nlocal][1] = buf[m++];
displace[nlocal][2] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
}
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