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b2005b3fb4511a276bd219903eccf70f454e2bc7
lammps/src/fix_rigid.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.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "fix_rigid.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "group.h"
#include "comm.h"
#include "random_mars.h"
#include "force.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 1.0e-6
#define EPSILON 1.0e-7
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
int i,ibody;
scalar_flag = 1;
extscalar = 0;
time_integrate = 1;
rigid_flag = 1;
virial_flag = 1;
create_attribute = 1;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// perform initial allocation of atom-based arrays
// register with Atom class
extended = dorientflag = qorientflag = 0;
body = NULL;
displace = NULL;
eflags = NULL;
dorient = NULL;
qorient = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// parse args for rigid body specification
// set nbody and body[i] for each atom
if (narg < 4) error->all("Illegal fix rigid command");
int iarg;
// single rigid body
// nbody = 1
// all atoms in fix group are part of body
if (strcmp(arg[3],"single") == 0) {
iarg = 4;
nbody = 1;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
body[i] = -1;
if (mask[i] & groupbit) body[i] = 0;
}
// each molecule in fix group is a rigid body
// maxmol = largest molecule #
// ncount = # of atoms in each molecule (have to sum across procs)
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set body[] values for each atom
} else if (strcmp(arg[3],"molecule") == 0) {
iarg = 4;
if (atom->molecule_flag == 0)
error->all("Fix rigid molecule requires atom attribute molecule");
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int maxmol = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
int itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_INT,MPI_MAX,world);
maxmol = itmp + 1;
int *ncount = new int[maxmol];
for (i = 0; i < maxmol; i++) ncount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount[molecule[i]]++;
int *nall = new int[maxmol];
MPI_Allreduce(ncount,nall,maxmol,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++) {
body[i] = -1;
if (mask[i] & groupbit) body[i] = nall[molecule[i]];
}
delete [] ncount;
delete [] nall;
// each listed group is a rigid body
// check if all listed groups exist
// an atom must belong to fix group and listed group to be in rigid body
// error if atom belongs to more than 1 rigid body
} else if (strcmp(arg[3],"group") == 0) {
if (narg < 5) error->all("Illegal fix rigid command");
nbody = atoi(arg[4]);
if (nbody <= 0) error->all("Illegal fix rigid command");
if (narg < 5+nbody) error->all("Illegal fix rigid command");
iarg = 5+nbody;
int *igroups = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) {
igroups[ibody] = group->find(arg[5+ibody]);
if (igroups[ibody] == -1)
error->all("Could not find fix rigid group ID");
}
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
for (i = 0; i < nlocal; i++) {
body[i] = -1;
if (mask[i] & groupbit)
for (ibody = 0; ibody < nbody; ibody++)
if (mask[i] & group->bitmask[igroups[ibody]]) {
if (body[i] >= 0) flag = 1;
body[i] = ibody;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all("One or more atoms belong to multiple rigid bodies");
delete [] igroups;
} else error->all("Illegal fix rigid command");
// error check on nbody
if (nbody == 0) error->all("No rigid bodies defined");
// create all nbody-length arrays
memory->create(nrigid,nbody,"rigid:nrigid");
memory->create(masstotal,nbody,"rigid:masstotal");
memory->create(xcm,nbody,3,"rigid:xcm");
memory->create(vcm,nbody,3,"rigid:vcm");
memory->create(fcm,nbody,3,"rigid:fcm");
memory->create(inertia,nbody,3,"rigid:inertia");
memory->create(ex_space,nbody,3,"rigid:ex_space");
memory->create(ey_space,nbody,3,"rigid:ey_space");
memory->create(ez_space,nbody,3,"rigid:ez_space");
memory->create(angmom,nbody,3,"rigid:angmom");
memory->create(omega,nbody,3,"rigid:omega");
memory->create(torque,nbody,3,"rigid:torque");
memory->create(quat,nbody,4,"rigid:quat");
memory->create(imagebody,nbody,"rigid:imagebody");
memory->create(fflag,nbody,3,"rigid:fflag");
memory->create(tflag,nbody,3,"rigid:tflag");
memory->create(langextra,nbody,6,"rigid:langextra");
memory->create(sum,nbody,6,"rigid:sum");
memory->create(all,nbody,6,"rigid:all");
memory->create(remapflag,nbody,4,"rigid:remapflag");
// initialize force/torque flags to default = 1.0
// for 2d: fz, tx, ty = 0.0
array_flag = 1;
size_array_rows = nbody;
size_array_cols = 15;
global_freq = 1;
extarray = 0;
for (i = 0; i < nbody; i++) {
fflag[i][0] = fflag[i][1] = fflag[i][2] = 1.0;
tflag[i][0] = tflag[i][1] = tflag[i][2] = 1.0;
if (domain->dimension == 2) fflag[i][2] = tflag[i][0] = tflag[i][1] = 0.0;
}
// parse optional args
int seed;
langflag = 0;
tempflag = 0;
pressflag = 0;
t_chain = 10;
t_iter = 1;
t_order = 3;
p_chain = 10;
while (iarg < narg) {
if (strcmp(arg[iarg],"force") == 0) {
if (iarg+5 > narg) error->all("Illegal fix rigid command");
int mlo,mhi;
force->bounds(arg[iarg+1],nbody,mlo,mhi);
double xflag,yflag,zflag;
if (strcmp(arg[iarg+2],"off") == 0) xflag = 0.0;
else if (strcmp(arg[iarg+2],"on") == 0) xflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+3],"off") == 0) yflag = 0.0;
else if (strcmp(arg[iarg+3],"on") == 0) yflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+4],"off") == 0) zflag = 0.0;
else if (strcmp(arg[iarg+4],"on") == 0) zflag = 1.0;
else error->all("Illegal fix rigid command");
if (domain->dimension == 2 && zflag == 1.0)
error->all("Fix rigid z force cannot be on for 2d simulation");
int count = 0;
for (int m = mlo; m <= mhi; m++) {
fflag[m-1][0] = xflag;
fflag[m-1][1] = yflag;
fflag[m-1][2] = zflag;
count++;
}
if (count == 0) error->all("Illegal fix rigid command");
iarg += 5;
} else if (strcmp(arg[iarg],"torque") == 0) {
if (iarg+5 > narg) error->all("Illegal fix rigid command");
int mlo,mhi;
force->bounds(arg[iarg+1],nbody,mlo,mhi);
double xflag,yflag,zflag;
if (strcmp(arg[iarg+2],"off") == 0) xflag = 0.0;
else if (strcmp(arg[iarg+2],"on") == 0) xflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+3],"off") == 0) yflag = 0.0;
else if (strcmp(arg[iarg+3],"on") == 0) yflag = 1.0;
else error->all("Illegal fix rigid command");
if (strcmp(arg[iarg+4],"off") == 0) zflag = 0.0;
else if (strcmp(arg[iarg+4],"on") == 0) zflag = 1.0;
else error->all("Illegal fix rigid command");
if (domain->dimension == 2 && (xflag == 1.0 || yflag == 1.0))
error->all("Fix rigid xy torque cannot be on for 2d simulation");
int count = 0;
for (int m = mlo; m <= mhi; m++) {
tflag[m-1][0] = xflag;
tflag[m-1][1] = yflag;
tflag[m-1][2] = zflag;
count++;
}
if (count == 0) error->all("Illegal fix rigid command");
iarg += 5;
} else if (strcmp(arg[iarg],"langevin") == 0) {
if (iarg+5 > narg) error->all("Illegal fix rigid command");
if (strcmp(style,"rigid") != 0 && strcmp(style,"rigid/nve") != 0)
error->all("Illegal fix rigid command");
langflag = 1;
t_start = atof(arg[iarg+1]);
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
seed = atoi(arg[iarg+4]);
if (t_period <= 0.0)
error->all("Fix rigid langevin period must be > 0.0");
if (seed <= 0) error->all("Illegal fix rigid command");
iarg += 5;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all("Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0)
error->all("Illegal fix rigid command");
tempflag = 1;
t_start = atof(arg[iarg+1]);
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"press") == 0) {
if (iarg+4 > narg) error->all("Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0)
error->all("Illegal fix rigid command");
pressflag = 1;
p_start = atof(arg[iarg+1]);
p_stop = atof(arg[iarg+2]);
p_period = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all("Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0)
error->all("Illegal fix rigid command");
t_chain = atoi(arg[iarg+1]);
t_iter = atoi(arg[iarg+2]);
t_order = atoi(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"pparam") == 0) {
if (iarg+2 > narg) error->all("Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0)
error->all("Illegal fix rigid command");
p_chain = atoi(arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix rigid command");
}
// initialize Marsaglia RNG with processor-unique seed
if (langflag) random = new RanMars(lmp,seed + me);
else random = NULL;
// initialize vector output quantities in case accessed before run
for (i = 0; i < nbody; i++) {
xcm[i][0] = xcm[i][1] = xcm[i][2] = 0.0;
vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
fcm[i][0] = fcm[i][1] = fcm[i][2] = 0.0;
torque[i][0] = torque[i][1] = torque[i][2] = 0.0;
}
// nrigid[n] = # of atoms in Nth rigid body
// error if one or zero atoms
int *ncount = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) ncount[body[i]]++;
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
delete [] ncount;
for (ibody = 0; ibody < nbody; ibody++)
if (nrigid[ibody] <= 1) error->all("One or zero atoms in rigid body");
// set image flags for each rigid body to default values
// will be reset during init() based on xcm and then by pre_neighbor()
// set here, so image value will persist from run to run
for (ibody = 0; ibody < nbody; ibody++)
imagebody[ibody] = (512 << 20) | (512 << 10) | 512;
// bitmasks for properties of extended particles
INERTIA_POINT = 1;
INERTIA_SPHERE = 2;
INERTIA_ELLIPSOID = 4;
ORIENT_DIPOLE = 8;
ORIENT_QUAT = 16;
OMEGA = 32;
ANGMOM = 64;
TORQUE = 128;
// atom style pointers to particles that store extra info
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
// print statistics
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
if (me == 0) {
if (screen) fprintf(screen,"%d rigid bodies with %d atoms\n",nbody,nsum);
if (logfile) fprintf(logfile,"%d rigid bodies with %d atoms\n",nbody,nsum);
}
}
/* ---------------------------------------------------------------------- */
FixRigid::~FixRigid()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
delete random;
// delete locally stored arrays
memory->destroy(body);
memory->destroy(displace);
memory->destroy(eflags);
memory->destroy(dorient);
memory->destroy(qorient);
// delete nbody-length arrays
memory->destroy(nrigid);
memory->destroy(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(quat);
memory->destroy(imagebody);
memory->destroy(fflag);
memory->destroy(tflag);
memory->destroy(langextra);
memory->destroy(sum);
memory->destroy(all);
memory->destroy(remapflag);
}
/* ---------------------------------------------------------------------- */
int FixRigid::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
if (langflag) mask |= POST_FORCE;
mask |= PRE_NEIGHBOR;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixRigid::init()
{
int i,ibody;
triclinic = domain->triclinic;
// warn if more than one rigid fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
if (count > 1 && me == 0) error->warning("More than one fix rigid");
// 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,"rigid") == 0)
error->all("Rigid fix must come before NPT/NPH fix");
}
// timestep info
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
if (strstr(update->integrate_style,"respa"))
step_respa = ((Respa *) update->integrate)->step;
// extended = 1 if any particle in a rigid body is finite size
// or has a dipole moment
extended = dorientflag = qorientflag = 0;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
double **mu = atom->mu;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *ellipsoid = atom->ellipsoid;
int *type = atom->type;
int nlocal = atom->nlocal;
if (atom->radius_flag || atom->ellipsoid_flag || atom->mu_flag) {
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
if (radius && radius[i] > 0.0) flag = 1;
if (ellipsoid && ellipsoid[i] >= 0) flag = 1;
if (mu && mu[i][3] > 0.0) flag = 1;
}
MPI_Allreduce(&flag,&extended,1,MPI_INT,MPI_MAX,world);
}
// grow extended arrays and set extended flags for each particle
// qorientflag = 1 if any particle stores quat orientation
// dorientflag = 1 if any particle stores dipole orientation
if (extended) {
if (atom->mu_flag) dorientflag = 1;
if (atom->ellipsoid_flag) qorientflag = 1;
grow_arrays(atom->nmax);
for (i = 0; i < nlocal; i++) {
eflags[i] = 0;
if (body[i] < 0) continue;
// set INERTIA to POINT or SPHERE or ELLIPSOID
if (radius && radius[i] > 0.0) {
eflags[i] |= INERTIA_SPHERE;
eflags[i] |= OMEGA;
eflags[i] |= TORQUE;
} else if (ellipsoid && ellipsoid[i] >= 0) {
eflags[i] |= INERTIA_ELLIPSOID;
eflags[i] |= ORIENT_QUAT;
eflags[i] |= ANGMOM;
eflags[i] |= TORQUE;
} else eflags[i] |= INERTIA_POINT;
// set DIPOLE if atom->mu and mu[3] > 0.0
if (atom->mu_flag && mu[i][3] > 0.0)
eflags[i] |= ORIENT_DIPOLE;
}
}
// compute masstotal & center-of-mass of each rigid body
// error if image flag is not 0 in a non-periodic dim
double **x = atom->x;
int *image = atom->image;
int *periodicity = domain->periodicity;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
int xbox,ybox,zbox;
double massone,xunwrap,yunwrap,zunwrap;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if ((xbox && !periodicity[0]) || (ybox && !periodicity[1]) ||
(zbox && !periodicity[2]))
error->one("Fix rigid atom has non-zero image flag "
"in a non-periodic dimension");
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;
}
sum[ibody][0] += xunwrap * massone;
sum[ibody][1] += yunwrap * massone;
sum[ibody][2] += zunwrap * massone;
sum[ibody][3] += massone;
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
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];
}
// remap the xcm of each body back into simulation box if needed
// only really necessary the 1st time a run is performed
pre_neighbor();
// compute 6 moments of inertia of each body
// dx,dy,dz = coords relative to center-of-mass
// symmetric 3x3 inertia tensor stored in Voigt notation as 6-vector
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 (body[i] < 0) continue;
ibody = body[i];
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];
if (rmass) massone = rmass[i];
else 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 * dy*dz;
sum[ibody][4] -= massone * dx*dz;
sum[ibody][5] -= massone * dx*dy;
}
// extended particles may contribute extra terms to moments of inertia
if (extended) {
double ivec[6];
double *shape,*quatatom;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
massone = rmass[i];
if (eflags[i] & INERTIA_SPHERE) {
sum[ibody][0] += 0.4 * massone * radius[i]*radius[i];
sum[ibody][1] += 0.4 * massone * radius[i]*radius[i];
sum[ibody][2] += 0.4 * massone * radius[i]*radius[i];
} else if (eflags[i] & INERTIA_ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::inertia_ellipsoid(shape,quatatom,massone,ivec);
sum[ibody][0] += ivec[0];
sum[ibody][1] += ivec[1];
sum[ibody][2] += ivec[2];
sum[ibody][3] += ivec[3];
sum[ibody][4] += ivec[4];
sum[ibody][5] += ivec[5];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
// diagonalize inertia tensor for each body via Jacobi rotations
// inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy_space = 3 evectors = principal axes of rigid body
int ierror;
double cross[3];
double tensor[3][3],evectors[3][3];
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[1][2] = tensor[2][1] = all[ibody][3];
tensor[0][2] = tensor[2][0] = all[ibody][4];
tensor[0][1] = tensor[1][0] = all[ibody][5];
ierror = MathExtra::jacobi(tensor,inertia[ibody],evectors);
if (ierror) error->all("Insufficient Jacobi rotations for rigid 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, set to 0.0
double max;
max = MAX(inertia[ibody][0],inertia[ibody][1]);
max = MAX(max,inertia[ibody][2]);
if (inertia[ibody][0] < EPSILON*max) inertia[ibody][0] = 0.0;
if (inertia[ibody][1] < EPSILON*max) inertia[ibody][1] = 0.0;
if (inertia[ibody][2] < EPSILON*max) inertia[ibody][2] = 0.0;
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex_space[ibody],ey_space[ibody],cross);
if (MathExtra::dot3(cross,ez_space[ibody]) < 0.0)
MathExtra::negate3(ez_space[ibody]);
// create initial quaternion
MathExtra::exyz_to_q(ex_space[ibody],ey_space[ibody],ez_space[ibody],
quat[ibody]);
}
// displace = initial atom coords in basis of principal axes
// set displace = 0.0 for atoms not in any rigid body
// for extended particles, set their orientation wrt to rigid body
double qc[4],delta[3];
double *quatatom;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) {
displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
continue;
}
ibody = body[i];
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;
}
delta[0] = xunwrap - xcm[ibody][0];
delta[1] = yunwrap - xcm[ibody][1];
delta[2] = zunwrap - xcm[ibody][2];
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],delta,displace[i]);
if (extended) {
if (eflags[i] & ORIENT_DIPOLE) {
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],mu[i],dorient[i]);
MathExtra::snormalize3(mu[i][3],dorient[i],dorient[i]);
} else if (dorientflag)
dorient[i][0] = dorient[i][1] = dorient[i][2] = 0.0;
if (eflags[i] & ORIENT_QUAT) {
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::qconjugate(quat[ibody],qc);
MathExtra::quatquat(qc,quatatom,qorient[i]);
MathExtra::qnormalize(qorient[i]);
} else if (qorientflag)
qorient[i][0] = qorient[i][1] = qorient[i][2] = qorient[i][3] = 0.0;
}
}
// test for valid principal moments & axes
// recompute moments of inertia around new axes
// 3 diagonal moments should equal principal moments
// 3 off-diagonal moments should be 0.0
// extended particles may contribute extra terms to moments of inertia
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];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
sum[ibody][0] += massone *
(displace[i][1]*displace[i][1] + displace[i][2]*displace[i][2]);
sum[ibody][1] += massone *
(displace[i][0]*displace[i][0] + displace[i][2]*displace[i][2]);
sum[ibody][2] += massone *
(displace[i][0]*displace[i][0] + displace[i][1]*displace[i][1]);
sum[ibody][3] -= massone * displace[i][1]*displace[i][2];
sum[ibody][4] -= massone * displace[i][0]*displace[i][2];
sum[ibody][5] -= massone * displace[i][0]*displace[i][1];
}
if (extended) {
double ivec[6];
double *shape;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
massone = rmass[i];
if (eflags[i] & INERTIA_SPHERE) {
sum[ibody][0] += 0.4 * massone * radius[i]*radius[i];
sum[ibody][1] += 0.4 * massone * radius[i]*radius[i];
sum[ibody][2] += 0.4 * massone * radius[i]*radius[i];
} else if (eflags[i] & INERTIA_ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
MathExtra::inertia_ellipsoid(shape,qorient[i],massone,ivec);
sum[ibody][0] += ivec[0];
sum[ibody][1] += ivec[1];
sum[ibody][2] += ivec[2];
sum[ibody][3] += ivec[3];
sum[ibody][4] += ivec[4];
sum[ibody][5] += ivec[5];
}
}
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
double norm;
for (ibody = 0; ibody < nbody; ibody++) {
if (inertia[ibody][0] == 0.0) {
if (fabs(all[ibody][0]) > TOLERANCE)
error->all("Fix rigid: Bad principal moments");
} else {
if (fabs((all[ibody][0]-inertia[ibody][0])/inertia[ibody][0]) >
TOLERANCE) error->all("Fix rigid: Bad principal moments");
}
if (inertia[ibody][1] == 0.0) {
if (fabs(all[ibody][1]) > TOLERANCE)
error->all("Fix rigid: Bad principal moments");
} else {
if (fabs((all[ibody][1]-inertia[ibody][1])/inertia[ibody][1]) >
TOLERANCE) error->all("Fix rigid: Bad principal moments");
}
if (inertia[ibody][2] == 0.0) {
if (fabs(all[ibody][2]) > TOLERANCE)
error->all("Fix rigid: Bad principal moments");
} else {
if (fabs((all[ibody][2]-inertia[ibody][2])/inertia[ibody][2]) >
TOLERANCE) error->all("Fix rigid: Bad principal moments");
}
norm = (inertia[ibody][0] + inertia[ibody][1] + inertia[ibody][2]) / 3.0;
if (fabs(all[ibody][3]/norm) > TOLERANCE ||
fabs(all[ibody][4]/norm) > TOLERANCE ||
fabs(all[ibody][5]/norm) > TOLERANCE)
error->all("Fix rigid: Bad principal moments");
}
// temperature scale factor
double ndof = 0.0;
for (ibody = 0; ibody < nbody; ibody++) {
ndof += fflag[ibody][0] + fflag[ibody][1] + fflag[ibody][2];
ndof += tflag[ibody][0] + tflag[ibody][1] + tflag[ibody][2];
}
tfactor = force->mvv2e / (ndof * force->boltz);
}
/* ---------------------------------------------------------------------- */
void FixRigid::setup(int vflag)
{
int i,n,ibody;
double massone,radone;
// vcm = velocity of center-of-mass of each rigid body
// fcm = force on center-of-mass of each rigid body
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
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];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
sum[ibody][0] += v[i][0] * massone;
sum[ibody][1] += v[i][1] * massone;
sum[ibody][2] += v[i][2] * massone;
sum[ibody][3] += f[i][0];
sum[ibody][4] += f[i][1];
sum[ibody][5] += f[i][2];
}
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];
fcm[ibody][0] = all[ibody][3];
fcm[ibody][1] = all[ibody][4];
fcm[ibody][2] = all[ibody][5];
}
// angmom = angular momentum of each rigid body
// torque = torque on each rigid body
int *image = atom->image;
double **x = atom->x;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
int xbox,ybox,zbox;
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
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];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
sum[ibody][0] += dy * massone*v[i][2] - dz * massone*v[i][1];
sum[ibody][1] += dz * massone*v[i][0] - dx * massone*v[i][2];
sum[ibody][2] += dx * massone*v[i][1] - dy * massone*v[i][0];
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 rotation/torque to angmom/torque of body
if (extended) {
double **omega_one = atom->omega;
double **angmom_one = atom->angmom;
double **torque_one = atom->torque;
double *radius = atom->radius;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (eflags[i] & OMEGA) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
radone = radius[i];
sum[ibody][0] += 0.4 * massone * radone*radone * omega_one[i][0];
sum[ibody][1] += 0.4 * massone * radone*radone * omega_one[i][1];
sum[ibody][2] += 0.4 * massone * radone*radone * omega_one[i][2];
}
if (eflags[i] & ANGMOM) {
sum[ibody][0] += angmom_one[i][0];
sum[ibody][1] += angmom_one[i][1];
sum[ibody][2] += angmom_one[i][2];
}
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);
for (ibody = 0; ibody < nbody; ibody++) {
angmom[ibody][0] = all[ibody][0];
angmom[ibody][1] = all[ibody][1];
angmom[ibody][2] = all[ibody][2];
torque[ibody][0] = all[ibody][3];
torque[ibody][1] = all[ibody][4];
torque[ibody][2] = all[ibody][5];
}
// zero langextra in case Langevin thermostat not used
// no point to calling post_force() here since langextra
// is only added to fcm/torque in final_integrate()
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) langextra[ibody][i] = 0.0;
// 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++)
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
set_v();
// guesstimate virial as 2x the set_v contribution
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;
}
}
/* ---------------------------------------------------------------------- */
void FixRigid::initial_integrate(int vflag)
{
double dtfm;
for (int ibody = 0; ibody < nbody; ibody++) {
// 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];
// 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];
// update angular momentum by 1/2 step
angmom[ibody][0] += dtf * torque[ibody][0] * tflag[ibody][0];
angmom[ibody][1] += dtf * torque[ibody][1] * tflag[ibody][1];
angmom[ibody][2] += dtf * torque[ibody][2] * tflag[ibody][2];
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion, also updated omega at 1/2 step
// update ex,ey,ez to reflect new quaternion
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody],
inertia[ibody],dtq);
MathExtra::q_to_exyz(quat[ibody],
ex_space[ibody],ey_space[ibody],ez_space[ibody]);
}
// 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();
}
/* ----------------------------------------------------------------------
apply Langevin thermostat to all 6 DOF of rigid bodies
computed by proc 0, broadcast to other procs
unlike fix langevin, this stores extra force in extra arrays,
which are added in when final_integrate() calculates a new fcm/torque
------------------------------------------------------------------------- */
void FixRigid::post_force(int vflag)
{
if (me == 0) {
double gamma1,gamma2;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double t_target = t_start + delta * (t_stop-t_start);
double tsqrt = sqrt(t_target);
double boltz = force->boltz;
double dt = update->dt;
double mvv2e = force->mvv2e;
double ftm2v = force->ftm2v;
for (int i = 0; i < nbody; i++) {
gamma1 = -masstotal[i] / t_period / ftm2v;
gamma2 = sqrt(masstotal[i]) * tsqrt *
sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[i][0] = gamma1*vcm[i][0] + gamma2*(random->uniform()-0.5);
langextra[i][1] = gamma1*vcm[i][1] + gamma2*(random->uniform()-0.5);
langextra[i][2] = gamma1*vcm[i][2] + gamma2*(random->uniform()-0.5);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[i][3] = inertia[i][0]*gamma1*omega[i][0] +
sqrt(inertia[i][0])*gamma2*(random->uniform()-0.5);
langextra[i][4] = inertia[i][1]*gamma1*omega[i][1] +
sqrt(inertia[i][1])*gamma2*(random->uniform()-0.5);
langextra[i][5] = inertia[i][2]*gamma1*omega[i][2] +
sqrt(inertia[i][2])*gamma2*(random->uniform()-0.5);
}
}
MPI_Bcast(&langextra[0][0],6*nbody,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
void FixRigid::final_integrate()
{
int i,ibody;
double dtfm,xy,xz,yz;
// 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);
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
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
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];
// update angular momentum by 1/2 step
angmom[ibody][0] += dtf * torque[ibody][0] * tflag[ibody][0];
angmom[ibody][1] += dtf * torque[ibody][1] * tflag[ibody][1];
angmom[ibody][2] += dtf * torque[ibody][2] * tflag[ibody][2];
MathExtra::angmom_to_omega(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();
}
/* ----------------------------------------------------------------------
apply evolution operators to quat, quat momentum
see Miller paper cited in fix rigid/nvt and fix rigid/npt
------------------------------------------------------------------------- */
void FixRigid::no_squish_rotate(int k, double *p, double *q,
double *inertia, double dt)
{
double phi,c_phi,s_phi,kp[4],kq[4];
// apply permuation operator on p and q, get kp and kq
if (k == 1) {
kq[0] = -q[1]; kp[0] = -p[1];
kq[1] = q[0]; kp[1] = p[0];
kq[2] = q[3]; kp[2] = p[3];
kq[3] = -q[2]; kp[3] = -p[2];
} else if (k == 2) {
kq[0] = -q[2]; kp[0] = -p[2];
kq[1] = -q[3]; kp[1] = -p[3];
kq[2] = q[0]; kp[2] = p[0];
kq[3] = q[1]; kp[3] = p[1];
} else if (k == 3) {
kq[0] = -q[3]; kp[0] = -p[3];
kq[1] = q[2]; kp[1] = p[2];
kq[2] = -q[1]; kp[2] = -p[1];
kq[3] = q[0]; kp[3] = p[0];
}
// obtain phi, cosines and sines
phi = p[0]*kq[0] + p[1]*kq[1] + p[2]*kq[2] + p[3]*kq[3];
if (fabs(inertia[k-1]) < 1e-6) phi *= 0.0;
else phi /= 4.0 * inertia[k-1];
c_phi = cos(dt * phi);
s_phi = sin(dt * phi);
// advance p and q
p[0] = c_phi*p[0] + s_phi*kp[0];
p[1] = c_phi*p[1] + s_phi*kp[1];
p[2] = c_phi*p[2] + s_phi*kp[2];
p[3] = c_phi*p[3] + s_phi*kp[3];
q[0] = c_phi*q[0] + s_phi*kq[0];
q[1] = c_phi*q[1] + s_phi*kq[1];
q[2] = c_phi*q[2] + s_phi*kq[2];
q[3] = c_phi*q[3] + s_phi*kq[3];
}
/* ---------------------------------------------------------------------- */
void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dtq = 0.5 * step_respa[ilevel];
if (ilevel == 0) initial_integrate(vflag);
else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixRigid::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
use domain->remap() in case xcm is far away from box
due to 1st definition of rigid body or due to box flip
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()
adjust image flag of body and image flags of all atoms in body
------------------------------------------------------------------------- */
void FixRigid::pre_neighbor()
{
int original,oldimage,newimage;
for (int ibody = 0; ibody < nbody; ibody++) {
original = imagebody[ibody];
domain->remap(xcm[ibody],imagebody[ibody]);
if (original == imagebody[ibody]) remapflag[ibody][3] = 0;
else {
oldimage = original & 1023;
newimage = imagebody[ibody] & 1023;
remapflag[ibody][0] = newimage - oldimage;
oldimage = (original >> 10) & 1023;
newimage = (imagebody[ibody] >> 10) & 1023;
remapflag[ibody][1] = newimage - oldimage;
oldimage = original >> 20;
newimage = imagebody[ibody] >> 20;
remapflag[ibody][2] = newimage - oldimage;
remapflag[ibody][3] = 1;
}
}
// adjust image flags of any atom in a rigid body whose xcm was remapped
int *image = atom->image;
int nlocal = atom->nlocal;
int ibody,idim,otherdims;
for (int i = 0; i < nlocal; i++) {
if (body[i] == -1) continue;
if (remapflag[body[i]][3] == 0) continue;
ibody = body[i];
if (remapflag[ibody][0]) {
idim = image[i] & 1023;
otherdims = image[i] ^ idim;
idim -= remapflag[ibody][0];
idim &= 1023;
image[i] = otherdims | idim;
}
if (remapflag[ibody][1]) {
idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
idim -= remapflag[ibody][1];
idim &= 1023;
image[i] = otherdims | (idim << 10);
}
if (remapflag[ibody][2]) {
idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
idim -= remapflag[ibody][2];
idim &= 1023;
image[i] = otherdims | (idim << 20);
}
}
}
/* ----------------------------------------------------------------------
count # of degrees-of-freedom removed by fix_rigid for atoms in igroup
------------------------------------------------------------------------- */
int FixRigid::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
// nall = # of point particles in each rigid body
// mall = # of finite-size particles in each rigid body
// particles must also be in temperature group
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *ncount = new int[nbody];
int *mcount = new int[nbody];
for (int ibody = 0; ibody < nbody; ibody++)
ncount[ibody] = mcount[ibody] = 0;
for (int i = 0; i < nlocal; i++)
if (body[i] >= 0 && mask[i] & groupbit) {
if (extended && eflags[i]) mcount[body[i]]++;
else ncount[body[i]]++;
}
int *nall = new int[nbody];
int *mall = new int[nbody];
MPI_Allreduce(ncount,nall,nbody,MPI_INT,MPI_SUM,world);
MPI_Allreduce(mcount,mall,nbody,MPI_INT,MPI_SUM,world);
// warn if nall+mall != nrigid for any body included in temperature group
int flag = 0;
for (int ibody = 0; ibody < nbody; ibody++) {
if (nall[ibody]+mall[ibody] > 0 &&
nall[ibody]+mall[ibody] != nrigid[ibody]) flag = 1;
}
if (flag && me == 0)
error->warning("Computing temperature of portions of rigid bodies");
// remove appropriate DOFs for each rigid body wholly in temperature group
// N = # of point particles in body
// M = # of finite-size particles in body
// 3d body has 3N + 6M dof to start with
// 2d body has 2N + 3M dof to start with
// 3d point-particle body with all non-zero I should have 6 dof, remove 3N-6
// 3d point-particle body (linear) with a 0 I should have 5 dof, remove 3N-5
// 2d point-particle body should have 3 dof, remove 2N-3
// 3d body with any finite-size M should have 6 dof, remove (3N+6M) - 6
// 2d body with any finite-size M should have 3 dof, remove (2N+3M) - 3
int n = 0;
if (domain->dimension == 3) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody]+mall[ibody] == nrigid[ibody]) {
n += 3*nall[ibody] + 6*mall[ibody] - 6;
if (inertia[ibody][0] == 0.0 || inertia[ibody][1] == 0.0 ||
inertia[ibody][2] == 0.0) n++;
}
} else if (domain->dimension == 2) {
for (int ibody = 0; ibody < nbody; ibody++)
if (nall[ibody]+mall[ibody] == nrigid[ibody])
n += 2*nall[ibody] + 3*mall[ibody] - 3;
}
delete [] ncount;
delete [] mcount;
delete [] nall;
delete [] mall;
return n;
}
/* ----------------------------------------------------------------------
adjust xcm of each rigid body 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
------------------------------------------------------------------------- */
void FixRigid::deform(int flag)
{
if (flag == 0)
for (int ibody = 0; ibody < nbody; ibody++)
domain->x2lamda(xcm[ibody],xcm[ibody]);
else
for (int ibody = 0; ibody < nbody; ibody++)
domain->lamda2x(xcm[ibody],xcm[ibody]);
}
/* ----------------------------------------------------------------------
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))
------------------------------------------------------------------------- */
void FixRigid::set_xv()
{
int ibody;
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double xy,xz,yz;
double ione[3],exone[3],eyone[3],ezone[3],vr[6],p[3][3];
int *image = atom->image;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
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;
}
// set x and v of each atom
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
// save old positions and velocities for virial
if (evflag) {
if (triclinic == 0) {
x0 = x[i][0] + xbox*xprd;
x1 = x[i][1] + ybox*yprd;
x2 = x[i][2] + zbox*zprd;
} else {
x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
x1 = x[i][1] + ybox*yprd + zbox*yz;
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
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],displace[i],x[i]);
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
// for triclinic, add in box tilt factors as well
if (triclinic == 0) {
x[i][0] += xcm[ibody][0] - xbox*xprd;
x[i][1] += xcm[ibody][1] - ybox*yprd;
x[i][2] += xcm[ibody][2] - zbox*zprd;
} else {
x[i][0] += xcm[ibody][0] - xbox*xprd - ybox*xy - zbox*xz;
x[i][1] += xcm[ibody][1] - ybox*yprd - zbox*yz;
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) {
if (rmass) massone = rmass[i];
else 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*x0*fc0;
vr[1] = 0.5*x1*fc1;
vr[2] = 0.5*x2*fc2;
vr[3] = 0.5*x0*fc1;
vr[4] = 0.5*x0*fc2;
vr[5] = 0.5*x1*fc2;
v_tally(1,&i,1.0,vr);
}
}
// set orientation, omega, angmom of each extended particle
if (extended) {
double *shape,*quatatom;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
double **omega_one = atom->omega;
double **angmom_one = atom->angmom;
double **mu = atom->mu;
int *ellipsoid = atom->ellipsoid;
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (eflags[i] & ORIENT_DIPOLE) {
MathExtra::quat_to_mat(quat[ibody],p);
MathExtra::matvec(p,dorient[i],mu[i]);
MathExtra::snormalize3(mu[i][3],mu[i],mu[i]);
}
if (eflags[i] & ORIENT_QUAT) {
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::quatquat(quat[ibody],qorient[i],quatatom);
MathExtra::qnormalize(quatatom);
}
if (eflags[i] & OMEGA) {
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
}
if (eflags[i] & ANGMOM) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
ione[0] = 0.2*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = 0.2*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = 0.2*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]);
}
}
}
}
/* ----------------------------------------------------------------------
set space-frame velocity of each atom in a rigid body
set omega and angmom of extended particles
v = Vcm + (W cross (x - Xcm))
------------------------------------------------------------------------- */
void FixRigid::set_v()
{
int ibody;
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double xy,xz,yz;
double ione[3],exone[3],eyone[3],ezone[3],delta[3],vr[6];
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *image = atom->image;
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;
}
// set v of each atom
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
MathExtra::matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],displace[i],delta);
// 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]*delta[2] - omega[ibody][2]*delta[1] +
vcm[ibody][0];
v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] +
vcm[ibody][1];
v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
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) {
if (rmass) massone = rmass[i];
else 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] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (triclinic == 0) {
x0 = x[i][0] + xbox*xprd;
x1 = x[i][1] + ybox*yprd;
x2 = x[i][2] + zbox*zprd;
} else {
x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
x1 = x[i][1] + ybox*yprd + zbox*yz;
x2 = x[i][2] + zbox*zprd;
}
vr[0] = 0.5*x0*fc0;
vr[1] = 0.5*x1*fc1;
vr[2] = 0.5*x2*fc2;
vr[3] = 0.5*x0*fc1;
vr[4] = 0.5*x0*fc2;
vr[5] = 0.5*x1*fc2;
v_tally(1,&i,1.0,vr);
}
}
// set omega, angmom of each extended particle
if (extended) {
double *shape,*quatatom;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
double **omega_one = atom->omega;
double **angmom_one = atom->angmom;
int *ellipsoid = atom->ellipsoid;
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (eflags[i] & OMEGA) {
omega_one[i][0] = omega[ibody][0];
omega_one[i][1] = omega[ibody][1];
omega_one[i][2] = omega[ibody][2];
}
if (eflags[i] & ANGMOM) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
ione[0] = 0.2*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = 0.2*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = 0.2*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]);
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixRigid::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
if (extended) {
bytes += nmax * sizeof(int);
if (dorientflag) bytes = nmax*3 * sizeof(double);
if (qorientflag) bytes = nmax*4 * sizeof(double);
}
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixRigid::grow_arrays(int nmax)
{
memory->grow(body,nmax,"rigid:body");
memory->grow(displace,nmax,3,"rigid:displace");
if (extended) {
memory->grow(eflags,nmax,"rigid:eflags");
if (dorientflag) memory->grow(dorient,nmax,3,"rigid:dorient");
if (qorientflag) memory->grow(qorient,nmax,4,"rigid:qorient");
}
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixRigid::copy_arrays(int i, int j)
{
body[j] = body[i];
displace[j][0] = displace[i][0];
displace[j][1] = displace[i][1];
displace[j][2] = displace[i][2];
if (extended) {
eflags[j] = eflags[i];
if (dorientflag) {
dorient[j][0] = dorient[i][0];
dorient[j][1] = dorient[i][1];
dorient[j][2] = dorient[i][2];
}
if (qorientflag) {
qorient[j][0] = qorient[i][0];
qorient[j][1] = qorient[i][1];
qorient[j][2] = qorient[i][2];
qorient[j][3] = qorient[i][3];
}
}
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixRigid::set_arrays(int i)
{
body[i] = -1;
displace[i][0] = 0.0;
displace[i][1] = 0.0;
displace[i][2] = 0.0;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixRigid::pack_exchange(int i, double *buf)
{
buf[0] = body[i];
buf[1] = displace[i][0];
buf[2] = displace[i][1];
buf[3] = displace[i][2];
if (!extended) return 4;
int m = 4;
buf[m++] = eflags[i];
if (dorientflag) {
buf[m++] = dorient[i][0];
buf[m++] = dorient[i][1];
buf[m++] = dorient[i][2];
}
if (qorientflag) {
buf[m++] = qorient[i][0];
buf[m++] = qorient[i][1];
buf[m++] = qorient[i][2];
buf[m++] = qorient[i][3];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixRigid::unpack_exchange(int nlocal, double *buf)
{
body[nlocal] = static_cast<int> (buf[0]);
displace[nlocal][0] = buf[1];
displace[nlocal][1] = buf[2];
displace[nlocal][2] = buf[3];
if (!extended) return 4;
int m = 4;
eflags[nlocal] = static_cast<int> (buf[m++]);
if (dorientflag) {
dorient[nlocal][0] = buf[m++];
dorient[nlocal][0] = buf[m++];
dorient[nlocal][0] = buf[m++];
}
if (qorientflag) {
qorient[nlocal][0] = buf[m++];
qorient[nlocal][0] = buf[m++];
qorient[nlocal][0] = buf[m++];
qorient[nlocal][0] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixRigid::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
}
/* ----------------------------------------------------------------------
return temperature of collection of rigid bodies
non-active DOF are removed by fflag/tflag and in tfactor
------------------------------------------------------------------------- */
double FixRigid::compute_scalar()
{
double wbody[3],rot[3][3];
double t = 0.0;
for (int i = 0; i < nbody; i++) {
t += masstotal[i] * (fflag[i][0]*vcm[i][0]*vcm[i][0] +
fflag[i][1]*vcm[i][1]*vcm[i][1] + \
fflag[i][2]*vcm[i][2]*vcm[i][2]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat[i],rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
if (inertia[i][0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[i][0];
if (inertia[i][1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[i][1];
if (inertia[i][2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[i][2];
t += tflag[i][0]*inertia[i][0]*wbody[0]*wbody[0] +
tflag[i][1]*inertia[i][1]*wbody[1]*wbody[1] +
tflag[i][2]*inertia[i][2]*wbody[2]*wbody[2];
}
t *= tfactor;
return t;
}
/* ----------------------------------------------------------------------
return attributes of a rigid body
15 values per body
xcm = 0,1,2; vcm = 3,4,5; fcm = 6,7,8; torque = 9,10,11; image = 12,13,14
------------------------------------------------------------------------- */
double FixRigid::compute_array(int i, int j)
{
if (j < 3) return xcm[i][j];
if (j < 6) return vcm[i][j-3];
if (j < 9) return fcm[i][j-6];
if (j < 12) return torque[i][j-9];
if (j == 12) return (imagebody[i] & 1023) - 512;
if (j == 13) return (imagebody[i] >> 10 & 1023) - 512;
return (imagebody[i] >> 20) - 512;
}
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