Homec4science
Diffusion lammps (master) Browse

lammps/src/RIGID/fix_rigid_small.cpp
bc446bb8b01bmaster

Last Change
Raw File

fix_rigid_small.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_rigid_small.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "molecule.h"
#include "domain.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "group.h"
#include "comm.h"
#include "force.h"
#include "output.h"
#include "random_mars.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include <map>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define MAXLINE 1024
#define CHUNK 1024
#define ATTRIBUTE_PERBODY 20
#define TOLERANCE 1.0e-6
#define EPSILON 1.0e-7
#define BIG 1.0e20
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
#define LINERTIA (1.0/12.0) // moment of inertia prefactor for line segment
#define DELTA_BODY 10000
enum{NONE,XYZ,XY,YZ,XZ}; // same as in FixRigid
enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
/* ---------------------------------------------------------------------- */
FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), step_respa(NULL),
infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL), id_dilate(NULL),
onemols(NULL), hash(NULL), bbox(NULL), ctr(NULL), idclose(NULL), rsqclose(NULL)
{
int i;
scalar_flag = 1;
extscalar = 0;
global_freq = 1;
time_integrate = 1;
rigid_flag = 1;
virial_flag = 1;
create_attribute = 1;
dof_flag = 1;
enforce2d_flag = 1;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// perform initial allocation of atom-based arrays
// register with Atom class
extended = orientflag = dorientflag = 0;
bodyown = NULL;
bodytag = NULL;
atom2body = NULL;
xcmimage = NULL;
displace = NULL;
eflags = NULL;
orient = NULL;
dorient = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// parse args for rigid body specification
if (narg < 4) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(arg[3],"molecule") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix rigid/small requires atom attribute molecule");
if (atom->map_style == 0)
error->all(FLERR,"Fix rigid/small requires an atom map, see atom_modify");
// maxmol = largest molecule #
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
maxmol = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
tagint itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol = itmp;
// number of linear molecules is counted later
nlinear = 0;
// parse optional args
int seed;
langflag = 0;
infile = NULL;
onemols = NULL;
reinitflag = 1;
tstat_flag = 0;
pstat_flag = 0;
allremap = 1;
id_dilate = NULL;
t_chain = 10;
t_iter = 1;
t_order = 3;
p_chain = 10;
pcouple = NONE;
pstyle = ANISO;
for (int i = 0; i < 3; i++) {
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
}
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"langevin") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if ((strcmp(style,"rigid/small") != 0) &&
(strcmp(style,"rigid/nve/small") != 0) &&
(strcmp(style,"rigid/nph/small") != 0))
error->all(FLERR,"Illegal fix rigid/small command");
langflag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
t_stop = force->numeric(FLERR,arg[iarg+2]);
t_period = force->numeric(FLERR,arg[iarg+3]);
seed = force->inumeric(FLERR,arg[iarg+4]);
if (t_period <= 0.0)
error->all(FLERR,"Fix rigid/small langevin period must be > 0.0");
if (seed <= 0) error->all(FLERR,"Illegal fix rigid/small command");
iarg += 5;
} else if (strcmp(arg[iarg],"infile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
delete [] infile;
int n = strlen(arg[iarg+1]) + 1;
infile = new char[n];
strcpy(infile,arg[iarg+1]);
restart_file = 1;
reinitflag = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"reinit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
else if (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
else error->all(FLERR,"Illegal fix rigid/small command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for "
"fix rigid/small does not exist");
onemols = &atom->molecules[imol];
nmol = onemols[0]->nset;
restart_file = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
t_stop = force->numeric(FLERR,arg[iarg+2]);
t_period = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
p_period[1] = force->numeric(FLERR,arg[iarg+3]);
p_flag[1] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[2] = force->numeric(FLERR,arg[iarg+3]);
p_flag[2] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
else error->all(FLERR,"Illegal fix rigid/small command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix rigid/small nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
allremap = 0;
delete [] id_dilate;
int n = strlen(arg[iarg+1]) + 1;
id_dilate = new char[n];
strcpy(id_dilate,arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix rigid/small nvt/npt/nph dilate group ID "
"does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
t_chain = force->numeric(FLERR,arg[iarg+1]);
t_iter = force->numeric(FLERR,arg[iarg+2]);
t_order = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_chain = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid/small command");
}
// error check and further setup for Molecule template
if (onemols) {
for (int i = 0; i < nmol; i++) {
if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix rigid/small molecule must have atom types");
// fix rigid/small uses center, masstotal, COM, inertia of molecule
onemols[i]->compute_center();
onemols[i]->compute_mass();
onemols[i]->compute_com();
onemols[i]->compute_inertia();
}
}
// set pstat_flag
pstat_flag = 0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) pstat_flag = 1;
if (pcouple == XYZ || (domain->dimension == 2 && pcouple == XY)) pstyle = ISO;
else pstyle = ANISO;
// create rigid bodies based on molecule ID
// sets bodytag for owned atoms
// body attributes are computed later by setup_bodies()
create_bodies();
// set nlocal_body and allocate bodies I own
tagint *tag = atom->tag;
nlocal_body = nghost_body = 0;
for (i = 0; i < nlocal; i++)
if (bodytag[i] == tag[i]) nlocal_body++;
nmax_body = 0;
while (nmax_body < nlocal_body) nmax_body += DELTA_BODY;
body = (Body *) memory->smalloc(nmax_body*sizeof(Body),
"rigid/small:body");
// set bodyown for owned atoms
nlocal_body = 0;
for (i = 0; i < nlocal; i++)
if (bodytag[i] == tag[i]) {
body[nlocal_body].ilocal = i;
bodyown[i] = nlocal_body++;
} else bodyown[i] = -1;
// bodysize = sizeof(Body) in doubles
bodysize = sizeof(Body)/sizeof(double);
if (bodysize*sizeof(double) != sizeof(Body)) bodysize++;
// set max comm sizes needed by this fix
comm_forward = 1 + bodysize;
comm_reverse = 6;
// bitmasks for properties of extended particles
POINT = 1;
SPHERE = 2;
ELLIPSOID = 4;
LINE = 8;
TRIANGLE = 16;
DIPOLE = 32;
OMEGA = 64;
ANGMOM = 128;
TORQUE = 256;
MINUSPI = -MY_PI;
TWOPI = 2.0*MY_PI;
// atom style pointers to particles that store extra info
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
// print statistics
int one = 0;
bigint atomone = 0;
for (int i = 0; i < nlocal; i++) {
if (bodyown[i] >= 0) one++;
if (bodytag[i] > 0) atomone++;
}
MPI_Allreduce(&one,&nbody,1,MPI_INT,MPI_SUM,world);
bigint atomall;
MPI_Allreduce(&atomone,&atomall,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen,"%d rigid bodies with " BIGINT_FORMAT " atoms\n",
nbody,atomall);
fprintf(screen," %g = max distance from body owner to body atom\n",
maxextent);
}
if (logfile) {
fprintf(logfile,"%d rigid bodies with " BIGINT_FORMAT " atoms\n",
nbody,atomall);
fprintf(logfile," %g = max distance from body owner to body atom\n",
maxextent);
}
}
// initialize Marsaglia RNG with processor-unique seed
maxlang = 0;
langextra = NULL;
random = NULL;
if (langflag) random = new RanMars(lmp,seed + comm->me);
// mass vector for granular pair styles
mass_body = NULL;
nmax_mass = 0;
// wait to setup bodies until comm stencils are defined
setupflag = 0;
}
/* ---------------------------------------------------------------------- */
FixRigidSmall::~FixRigidSmall()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// delete locally stored arrays
memory->sfree(body);
memory->destroy(bodyown);
memory->destroy(bodytag);
memory->destroy(atom2body);
memory->destroy(xcmimage);
memory->destroy(displace);
memory->destroy(eflags);
memory->destroy(orient);
memory->destroy(dorient);
delete random;
delete [] infile;
memory->destroy(langextra);
memory->destroy(mass_body);
}
/* ---------------------------------------------------------------------- */
int FixRigidSmall::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 FixRigidSmall::init()
{
int i;
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(FLERR,"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(FLERR,"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;
}
/* ----------------------------------------------------------------------
setup static/dynamic properties of rigid bodies, using current atom info.
if reinitflag is not set, do the initialization only once, b/c properties
may not be re-computable especially if overlapping particles or bodies
are inserted from mol template.
do not do dynamic init if read body properties from infile. this
is b/c the infile defines the static and dynamic properties and may not
be computable if contain overlapping particles setup_bodies_static()
reads infile itself.
cannot do this until now, b/c requires comm->setup() to have setup stencil
invoke pre_neighbor() to insure body xcmimage flags are reset
needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run
setup_bodies_static() invokes pre_neighbor itself
------------------------------------------------------------------------- */
void FixRigidSmall::setup_pre_neighbor()
{
if (reinitflag || !setupflag)
setup_bodies_static();
else pre_neighbor();
if ((reinitflag || !setupflag) && !infile)
setup_bodies_dynamic();
setupflag = 1;
}
/* ----------------------------------------------------------------------
compute initial fcm and torque on bodies, also initial virial
reset all particle velocities to be consistent with vcm and omega
------------------------------------------------------------------------- */
void FixRigidSmall::setup(int vflag)
{
int i,n,ibody;
//check(1);
// sum fcm, torque across all rigid bodies
// fcm = force on COM
// torque = torque around COM
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
double *xcm,*fcm,*tcm;
double dx,dy,dz;
double unwrap[3];
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
fcm = body[ibody].fcm;
fcm[0] = fcm[1] = fcm[2] = 0.0;
tcm = body[ibody].torque;
tcm[0] = tcm[1] = tcm[2] = 0.0;
}
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
fcm = b->fcm;
fcm[0] += f[i][0];
fcm[1] += f[i][1];
fcm[2] += f[i][2];
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
tcm = b->torque;
tcm[0] += dy * f[i][2] - dz * f[i][1];
tcm[1] += dz * f[i][0] - dx * f[i][2];
tcm[2] += dx * f[i][1] - dy * f[i][0];
}
// extended particles add their rotation/torque to angmom/torque of body
if (extended) {
double **torque = atom->torque;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (eflags[i] & TORQUE) {
tcm = b->torque;
tcm[0] += torque[i][0];
tcm[1] += torque[i][1];
tcm[2] += torque[i][2];
}
}
}
// reverse communicate fcm, torque of all bodies
commflag = FORCE_TORQUE;
comm->reverse_comm_fix(this,6);
// virial setup before call to set_v
if (vflag) v_setup(vflag);
else evflag = 0;
// compute and forward communicate vcm and omega of all bodies
for (ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space,
b->ez_space,b->inertia,b->omega);
}
commflag = FINAL;
comm->forward_comm_fix(this,10);
// set velocity/rotation of atoms in rigid bodues
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 FixRigidSmall::initial_integrate(int vflag)
{
double dtfm;
//check(2);
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
// update vcm by 1/2 step
dtfm = dtf / b->mass;
b->vcm[0] += dtfm * b->fcm[0];
b->vcm[1] += dtfm * b->fcm[1];
b->vcm[2] += dtfm * b->fcm[2];
// update xcm by full step
b->xcm[0] += dtv * b->vcm[0];
b->xcm[1] += dtv * b->vcm[1];
b->xcm[2] += dtv * b->vcm[2];
// update angular momentum by 1/2 step
b->angmom[0] += dtf * b->torque[0];
b->angmom[1] += dtf * b->torque[1];
b->angmom[2] += dtf * b->torque[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(b->angmom,b->ex_space,b->ey_space,
b->ez_space,b->inertia,b->omega);
MathExtra::richardson(b->quat,b->angmom,b->omega,b->inertia,dtq);
MathExtra::q_to_exyz(b->quat,b->ex_space,b->ey_space,b->ez_space);
}
// virial setup before call to set_xv
if (vflag) v_setup(vflag);
else evflag = 0;
// forward communicate updated info of all bodies
commflag = INITIAL;
comm->forward_comm_fix(this,26);
// set coords/orient and velocity/rotation of atoms in rigid bodies
set_xv();
}
/* ----------------------------------------------------------------------
apply Langevin thermostat to all 6 DOF of rigid bodies I own
unlike fix langevin, this stores extra force in extra arrays,
which are added in when final_integrate() calculates a new fcm/torque
------------------------------------------------------------------------- */
void FixRigidSmall::post_force(int vflag)
{
double gamma1,gamma2;
// grow langextra if needed
if (nlocal_body > maxlang) {
memory->destroy(langextra);
maxlang = nlocal_body + nghost_body;
memory->create(langextra,maxlang,6,"rigid/small:langextra");
}
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;
double *vcm,*omega,*inertia;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
vcm = body[ibody].vcm;
omega = body[ibody].omega;
inertia = body[ibody].inertia;
gamma1 = -body[ibody].mass / t_period / ftm2v;
gamma2 = sqrt(body[ibody].mass) * tsqrt *
sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[ibody][0] = gamma1*vcm[0] + gamma2*(random->uniform()-0.5);
langextra[ibody][1] = gamma1*vcm[1] + gamma2*(random->uniform()-0.5);
langextra[ibody][2] = gamma1*vcm[2] + gamma2*(random->uniform()-0.5);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[ibody][3] = inertia[0]*gamma1*omega[0] +
sqrt(inertia[0])*gamma2*(random->uniform()-0.5);
langextra[ibody][4] = inertia[1]*gamma1*omega[1] +
sqrt(inertia[1])*gamma2*(random->uniform()-0.5);
langextra[ibody][5] = inertia[2]*gamma1*omega[2] +
sqrt(inertia[2])*gamma2*(random->uniform()-0.5);
}
}
/* ----------------------------------------------------------------------
called from FixEnforce post_force() for 2d problems
zero all body values that should be zero for 2d model
------------------------------------------------------------------------- */
void FixRigidSmall::enforce2d()
{
Body *b;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
b = &body[ibody];
b->xcm[2] = 0.0;
b->vcm[2] = 0.0;
b->fcm[2] = 0.0;
b->torque[0] = 0.0;
b->torque[1] = 0.0;
b->angmom[0] = 0.0;
b->angmom[1] = 0.0;
b->omega[0] = 0.0;
b->omega[1] = 0.0;
if (langflag && langextra) {
langextra[ibody][2] = 0.0;
langextra[ibody][3] = 0.0;
langextra[ibody][4] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixRigidSmall::final_integrate()
{
int i,ibody;
double dtfm;
//check(3);
// sum over atoms to get force and torque on rigid body
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
double dx,dy,dz;
double unwrap[3];
double *xcm,*fcm,*tcm;
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
fcm = body[ibody].fcm;
fcm[0] = fcm[1] = fcm[2] = 0.0;
tcm = body[ibody].torque;
tcm[0] = tcm[1] = tcm[2] = 0.0;
}
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
fcm = b->fcm;
fcm[0] += f[i][0];
fcm[1] += f[i][1];
fcm[2] += f[i][2];
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
tcm = b->torque;
tcm[0] += dy*f[i][2] - dz*f[i][1];
tcm[1] += dz*f[i][0] - dx*f[i][2];
tcm[2] += dx*f[i][1] - dy*f[i][0];
}
// extended particles add their torque to torque of body
if (extended) {
double **torque = atom->torque;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
if (eflags[i] & TORQUE) {
tcm = body[atom2body[i]].torque;
tcm[0] += torque[i][0];
tcm[1] += torque[i][1];
tcm[2] += torque[i][2];
}
}
}
// reverse communicate fcm, torque of all bodies
commflag = FORCE_TORQUE;
comm->reverse_comm_fix(this,6);
// include Langevin thermostat forces and torques
if (langflag) {
for (int ibody = 0; ibody < nlocal_body; ibody++) {
fcm = body[ibody].fcm;
fcm[0] += langextra[ibody][0];
fcm[1] += langextra[ibody][1];
fcm[2] += langextra[ibody][2];
tcm = body[ibody].torque;
tcm[0] += langextra[ibody][3];
tcm[1] += langextra[ibody][4];
tcm[2] += langextra[ibody][5];
}
}
// update vcm and angmom, recompute omega
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
// update vcm by 1/2 step
dtfm = dtf / b->mass;
b->vcm[0] += dtfm * b->fcm[0];
b->vcm[1] += dtfm * b->fcm[1];
b->vcm[2] += dtfm * b->fcm[2];
// update angular momentum by 1/2 step
b->angmom[0] += dtf * b->torque[0];
b->angmom[1] += dtf * b->torque[1];
b->angmom[2] += dtf * b->torque[2];
MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space,
b->ez_space,b->inertia,b->omega);
}
// forward communicate updated info of all bodies
commflag = FINAL;
comm->forward_comm_fix(this,10);
// set velocity/rotation of atoms in rigid bodies
// virial is already setup from initial_integrate
set_v();
}
/* ---------------------------------------------------------------------- */
void FixRigidSmall::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 FixRigidSmall::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 first-time definition of rigid body in setup_bodies_static()
or due to box flip
also adjust imagebody = rigid body image flags, due to xcm remap
then communicate bodies so other procs will know of changes to body xcm
then adjust xcmimage flags of all atoms in bodies via image_shift()
for two effects
(1) change in true image flags due to pbc() call during exchange
(2) change in imagebody due to xcm remap
xcmimage flags are always -1,0,-1 so that body can be unwrapped
around in-box xcm and stay close to simulation box
if just inferred unwrapped from atom image flags,
then a body could end up very far away
when unwrapped by true image flags
then set_xv() will compute huge displacements every step to reset coords of
all the body atoms to be back inside the box, ditto for triclinic box flip
note: so just want to avoid that numeric probem?
------------------------------------------------------------------------- */
void FixRigidSmall::pre_neighbor()
{
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
domain->remap(b->xcm,b->image);
}
nghost_body = 0;
commflag = FULL_BODY;
comm->forward_comm_fix(this);
reset_atom2body();
//check(4);
image_shift();
}
/* ----------------------------------------------------------------------
reset body xcmimage flags of atoms in bodies
xcmimage flags are relative to xcm so that body can be unwrapped
xcmimage = true image flag - imagebody flag
------------------------------------------------------------------------- */
void FixRigidSmall::image_shift()
{
imageint tdim,bdim,xdim[3];
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
tdim = image[i] & IMGMASK;
bdim = b->image & IMGMASK;
xdim[0] = IMGMAX + tdim - bdim;
tdim = (image[i] >> IMGBITS) & IMGMASK;
bdim = (b->image >> IMGBITS) & IMGMASK;
xdim[1] = IMGMAX + tdim - bdim;
tdim = image[i] >> IMG2BITS;
bdim = b->image >> IMG2BITS;
xdim[2] = IMGMAX + tdim - bdim;
xcmimage[i] = (xdim[2] << IMG2BITS) | (xdim[1] << IMGBITS) | xdim[0];
}
}
/* ----------------------------------------------------------------------
count # of DOF removed by rigid bodies for atoms in igroup
return total count of DOF
------------------------------------------------------------------------- */
int FixRigidSmall::dof(int tgroup)
{
int i,j;
// cannot count DOF correctly unless setup_bodies_static() has been called
if (!setupflag) {
if (comm->me == 0)
error->warning(FLERR,"Cannot count rigid body degrees-of-freedom "
"before bodies are fully initialized");
return 0;
}
int tgroupbit = group->bitmask[tgroup];
// counts = 3 values per rigid body I own
// 0 = # of point particles in rigid body and in temperature group
// 1 = # of finite-size particles in rigid body and in temperature group
// 2 = # of particles in rigid body, disregarding temperature group
memory->create(counts,nlocal_body+nghost_body,3,"rigid/small:counts");
for (int i = 0; i < nlocal_body+nghost_body; i++)
counts[i][0] = counts[i][1] = counts[i][2] = 0;
// tally counts from my owned atoms
// 0 = # of point particles in rigid body and in temperature group
// 1 = # of finite-size particles in rigid body and in temperature group
// 2 = # of particles in rigid body, disregarding temperature group
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
j = atom2body[i];
counts[j][2]++;
if (mask[i] & tgroupbit) {
if (extended && (eflags[i] & ~(POINT | DIPOLE))) counts[j][1]++;
else counts[j][0]++;
}
}
commflag = DOF;
comm->reverse_comm_fix(this,3);
// nall = count0 = # of point particles in each rigid body
// mall = count1 = # of finite-size particles in each rigid body
// warn if nall+mall != nrigid for any body included in temperature group
int flag = 0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
if (counts[ibody][0]+counts[ibody][1] > 0 &&
counts[ibody][0]+counts[ibody][1] != counts[ibody][2]) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall && me == 0)
error->warning(FLERR,"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
double *inertia;
int n = 0;
nlinear = 0;
if (domain->dimension == 3) {
for (int ibody = 0; ibody < nlocal_body; ibody++) {
if (counts[ibody][0]+counts[ibody][1] == counts[ibody][2]) {
n += 3*counts[ibody][0] + 6*counts[ibody][1] - 6;
inertia = body[ibody].inertia;
if (inertia[0] == 0.0 || inertia[1] == 0.0 || inertia[2] == 0.0) {
n++;
nlinear++;
}
}
}
} else if (domain->dimension == 2) {
for (int ibody = 0; ibody < nlocal_body; ibody++)
if (counts[ibody][0]+counts[ibody][1] == counts[ibody][2])
n += 2*counts[ibody][0] + 3*counts[ibody][1] - 3;
}
memory->destroy(counts);
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
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 FixRigidSmall::deform(int flag)
{
if (flag == 0)
for (int ibody = 0; ibody < nlocal_body; ibody++)
domain->x2lamda(body[ibody].xcm,body[ibody].xcm);
else
for (int ibody = 0; ibody < nlocal_body; ibody++)
domain->lamda2x(body[ibody].xcm,body[ibody].xcm);
}
/* ----------------------------------------------------------------------
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 FixRigidSmall::set_xv()
{
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double ione[3],exone[3],eyone[3],ezone[3],vr[6],p[3][3];
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
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;
// set x and v of each atom
for (int i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
// 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(b->ex_space,b->ey_space,b->ez_space,displace[i],x[i]);
v[i][0] = b->omega[1]*x[i][2] - b->omega[2]*x[i][1] + b->vcm[0];
v[i][1] = b->omega[2]*x[i][0] - b->omega[0]*x[i][2] + b->vcm[1];
v[i][2] = b->omega[0]*x[i][1] - b->omega[1]*x[i][0] + b->vcm[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] += b->xcm[0] - xbox*xprd;
x[i][1] += b->xcm[1] - ybox*yprd;
x[i][2] += b->xcm[2] - zbox*zprd;
} else {
x[i][0] += b->xcm[0] - xbox*xprd - ybox*xy - zbox*xz;
x[i][1] += b->xcm[1] - ybox*yprd - zbox*yz;
x[i][2] += b->xcm[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 theta_body,theta;
double *shape,*quatatom,*inertiaatom;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecLine::Bonus *lbonus;
if (avec_line) lbonus = avec_line->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
double **omega = atom->omega;
double **angmom = atom->angmom;
double **mu = atom->mu;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
for (int i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (eflags[i] & SPHERE) {
omega[i][0] = b->omega[0];
omega[i][1] = b->omega[1];
omega[i][2] = b->omega[2];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::quatquat(b->quat,orient[i],quatatom);
MathExtra::qnormalize(quatatom);
ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(b->omega,exone,eyone,ezone,ione,angmom[i]);
} else if (eflags[i] & LINE) {
if (b->quat[3] >= 0.0) theta_body = 2.0*acos(b->quat[0]);
else theta_body = -2.0*acos(b->quat[0]);
theta = orient[i][0] + theta_body;
while (theta <= MINUSPI) theta += TWOPI;
while (theta > MY_PI) theta -= TWOPI;
lbonus[line[i]].theta = theta;
omega[i][0] = b->omega[0];
omega[i][1] = b->omega[1];
omega[i][2] = b->omega[2];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
quatatom = tbonus[tri[i]].quat;
MathExtra::quatquat(b->quat,orient[i],quatatom);
MathExtra::qnormalize(quatatom);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(b->omega,exone,eyone,ezone,
inertiaatom,angmom[i]);
}
if (eflags[i] & DIPOLE) {
MathExtra::quat_to_mat(b->quat,p);
MathExtra::matvec(p,dorient[i],mu[i]);
MathExtra::snormalize3(mu[i][3],mu[i],mu[i]);
}
}
}
}
/* ----------------------------------------------------------------------
set space-frame velocity of each atom in a rigid body
set omega and angmom of extended particles
v = Vcm + (W cross (x - Xcm))
------------------------------------------------------------------------- */
void FixRigidSmall::set_v()
{
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double ione[3],exone[3],eyone[3],ezone[3],delta[3],vr[6];
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
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;
// set v of each atom
for (int i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
MathExtra::matvec(b->ex_space,b->ey_space,b->ez_space,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] = b->omega[1]*delta[2] - b->omega[2]*delta[1] + b->vcm[0];
v[i][1] = b->omega[2]*delta[0] - b->omega[0]*delta[2] + b->vcm[1];
v[i][2] = b->omega[0]*delta[1] - b->omega[1]*delta[0] + b->vcm[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 = (xcmimage[i] & IMGMASK) - IMGMAX;
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
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,*inertiaatom;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
double **omega = atom->omega;
double **angmom = atom->angmom;
int *ellipsoid = atom->ellipsoid;
int *tri = atom->tri;
for (int i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (eflags[i] & SPHERE) {
omega[i][0] = b->omega[0];
omega[i][1] = b->omega[1];
omega[i][2] = b->omega[2];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
ione[0] = EINERTIA*rmass[i] * (shape[1]*shape[1] + shape[2]*shape[2]);
ione[1] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[2]*shape[2]);
ione[2] = EINERTIA*rmass[i] * (shape[0]*shape[0] + shape[1]*shape[1]);
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(b->omega,exone,eyone,ezone,ione,
angmom[i]);
} else if (eflags[i] & LINE) {
omega[i][0] = b->omega[0];
omega[i][1] = b->omega[1];
omega[i][2] = b->omega[2];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
quatatom = tbonus[tri[i]].quat;
MathExtra::q_to_exyz(quatatom,exone,eyone,ezone);
MathExtra::omega_to_angmom(b->omega,exone,eyone,ezone,
inertiaatom,angmom[i]);
}
}
}
}
/* ----------------------------------------------------------------------
one-time identification of which atoms are in which rigid bodies
set bodytag for all owned atoms
------------------------------------------------------------------------- */
void FixRigidSmall::create_bodies()
{
int i,m,n;
double unwrap[3];
// error check on image flags of atoms in rigid bodies
imageint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *periodicity = domain->periodicity;
int xbox,ybox,zbox;
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
if ((xbox && !periodicity[0]) || (ybox && !periodicity[1]) ||
(zbox && !periodicity[2])) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Fix rigid/small atom has non-zero image flag "
"in a non-periodic dimension");
// allocate buffer for passing messages around ring of procs
// percount = max number of values to put in buffer for each of ncount
int ncount = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount++;
int percount = 5;
double *buf;
memory->create(buf,ncount*percount,"rigid/small:buf");
// create map hash for storing unique molecule IDs of my atoms
// key = molecule ID
// value = index into per-body data structure
// n = # of entries in hash
hash = new std::map<tagint,int>();
hash->clear();
// setup hash
// key = body ID
// value = index into N-length data structure
// n = count of unique bodies my atoms are part of
tagint *molecule = atom->molecule;
n = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (hash->find(molecule[i]) == hash->end()) (*hash)[molecule[i]] = n++;
}
// bbox = bounding box of each rigid body my atoms are part of
memory->create(bbox,n,6,"rigid/small:bbox");
for (i = 0; i < n; i++) {
bbox[i][0] = bbox[i][2] = bbox[i][4] = BIG;
bbox[i][1] = bbox[i][3] = bbox[i][5] = -BIG;
}
// pack my atoms into buffer as molecule ID, unwrapped coords
double **x = atom->x;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = molecule[i];
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
}
// pass buffer around ring of procs
// func = update bbox with atom coords from every proc
// when done, have full bbox for every rigid body my atoms are part of
comm->ring(m,sizeof(double),buf,1,ring_bbox,NULL,(void *)this);
// check if any bbox is size 0.0, meaning rigid body is a single particle
flag = 0;
for (i = 0; i < n; i++)
if (bbox[i][0] == bbox[i][1] && bbox[i][2] == bbox[i][3] &&
bbox[i][4] == bbox[i][5]) flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"One or more rigid bodies are a single particle");
// ctr = center pt of each rigid body my atoms are part of
memory->create(ctr,n,6,"rigid/small:bbox");
for (i = 0; i < n; i++) {
ctr[i][0] = 0.5 * (bbox[i][0] + bbox[i][1]);
ctr[i][1] = 0.5 * (bbox[i][2] + bbox[i][3]);
ctr[i][2] = 0.5 * (bbox[i][4] + bbox[i][5]);
}
// idclose = ID of atom in body closest to center pt (smaller ID if tied)
// rsqclose = distance squared from idclose to center pt
memory->create(idclose,n,"rigid/small:idclose");
memory->create(rsqclose,n,"rigid/small:rsqclose");
for (i = 0; i < n; i++) rsqclose[i] = BIG;
// pack my atoms into buffer as molecule ID, atom ID, unwrapped coords
tagint *tag = atom->tag;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = molecule[i];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
}
// pass buffer around ring of procs
// func = update idclose,rsqclose with atom IDs from every proc
// when done, have idclose for every rigid body my atoms are part of
comm->ring(m,sizeof(double),buf,2,ring_nearest,NULL,(void *)this);
// set bodytag of all owned atoms, based on idclose
// find max value of rsqclose across all procs
double rsqmax = 0.0;
for (i = 0; i < nlocal; i++) {
bodytag[i] = 0;
if (!(mask[i] & groupbit)) continue;
m = hash->find(molecule[i])->second;
bodytag[i] = idclose[m];
rsqmax = MAX(rsqmax,rsqclose[m]);
}
// pack my atoms into buffer as bodytag of owning atom, unwrapped coords
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = ubuf(bodytag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
}
// pass buffer around ring of procs
// func = update rsqfar for atoms belonging to bodies I own
// when done, have rsqfar for all atoms in bodies I own
rsqfar = 0.0;
comm->ring(m,sizeof(double),buf,3,ring_farthest,NULL,(void *)this);
// find maxextent of rsqfar across all procs
// if defined, include molecule->maxextent
MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world);
maxextent = sqrt(maxextent);
if (onemols) {
for (int i = 0; i < nmol; i++)
maxextent = MAX(maxextent,onemols[i]->maxextent);
}
// clean up
delete hash;
memory->destroy(buf);
memory->destroy(bbox);
memory->destroy(ctr);
memory->destroy(idclose);
memory->destroy(rsqclose);
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update bounding box for rigid bodies my atoms are part of
------------------------------------------------------------------------- */
void FixRigidSmall::ring_bbox(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
std::map<tagint,int> *hash = frsptr->hash;
double **bbox = frsptr->bbox;
double *buf = (double *) cbuf;
int ndatums = n/4;
int j,imol;
double *x;
int m = 0;
for (int i = 0; i < ndatums; i++, m += 4) {
imol = static_cast<int> (buf[m]);
if (hash->find(imol) != hash->end()) {
j = hash->find(imol)->second;
x = &buf[m+1];
bbox[j][0] = MIN(bbox[j][0],x[0]);
bbox[j][1] = MAX(bbox[j][1],x[0]);
bbox[j][2] = MIN(bbox[j][2],x[1]);
bbox[j][3] = MAX(bbox[j][3],x[1]);
bbox[j][4] = MIN(bbox[j][4],x[2]);
bbox[j][5] = MAX(bbox[j][5],x[2]);
}
}
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update nearest atom to body center for rigid bodies my atoms are part of
------------------------------------------------------------------------- */
void FixRigidSmall::ring_nearest(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
std::map<tagint,int> *hash = frsptr->hash;
double **ctr = frsptr->ctr;
tagint *idclose = frsptr->idclose;
double *rsqclose = frsptr->rsqclose;
double *buf = (double *) cbuf;
int ndatums = n/5;
int j,imol;
tagint tag;
double delx,dely,delz,rsq;
double *x;
int m = 0;
for (int i = 0; i < ndatums; i++, m += 5) {
imol = static_cast<int> (buf[m]);
if (hash->find(imol) != hash->end()) {
j = hash->find(imol)->second;
tag = (tagint) ubuf(buf[m+1]).i;
x = &buf[m+2];
delx = x[0] - ctr[j][0];
dely = x[1] - ctr[j][1];
delz = x[2] - ctr[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= rsqclose[j]) {
if (rsq == rsqclose[j] && tag > idclose[j]) continue;
idclose[j] = tag;
rsqclose[j] = rsq;
}
}
}
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update rsqfar = distance from owning atom to other atom
------------------------------------------------------------------------- */
void FixRigidSmall::ring_farthest(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
double **x = frsptr->atom->x;
imageint *image = frsptr->atom->image;
int nlocal = frsptr->atom->nlocal;
double *buf = (double *) cbuf;
int ndatums = n/4;
int iowner;
tagint tag;
double delx,dely,delz,rsq;
double *xx;
double unwrap[3];
int m = 0;
for (int i = 0; i < ndatums; i++, m += 4) {
tag = (tagint) ubuf(buf[m]).i;
iowner = frsptr->atom->map(tag);
if (iowner < 0 || iowner >= nlocal) continue;
frsptr->domain->unmap(x[iowner],image[iowner],unwrap);
xx = &buf[m+1];
delx = xx[0] - unwrap[0];
dely = xx[1] - unwrap[1];
delz = xx[2] - unwrap[2];
rsq = delx*delx + dely*dely + delz*delz;
frsptr->rsqfar = MAX(frsptr->rsqfar,rsq);
}
}
/* ----------------------------------------------------------------------
one-time initialization of rigid body attributes
sets extended flags, masstotal, center-of-mass
sets Cartesian and diagonalized inertia tensor
sets body image flags
may read some properties from infile
------------------------------------------------------------------------- */
void FixRigidSmall::setup_bodies_static()
{
int i,ibody;
// extended = 1 if any particle in a rigid body is finite size
// or has a dipole moment
extended = orientflag = dorientflag = 0;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecLine::Bonus *lbonus;
if (avec_line) lbonus = avec_line->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
double **mu = atom->mu;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *type = atom->type;
int nlocal = atom->nlocal;
if (atom->radius_flag || atom->ellipsoid_flag || atom->line_flag ||
atom->tri_flag || atom->mu_flag) {
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (bodytag[i] == 0) continue;
if (radius && radius[i] > 0.0) flag = 1;
if (ellipsoid && ellipsoid[i] >= 0) flag = 1;
if (line && line[i] >= 0) flag = 1;
if (tri && tri[i] >= 0) flag = 1;
if (mu && mu[i][3] > 0.0) flag = 1;
}
MPI_Allreduce(&flag,&extended,1,MPI_INT,MPI_MAX,world);
}
// extended = 1 if using molecule template with finite-size particles
// require all molecules in template to have consistent radiusflag
if (onemols) {
int radiusflag = onemols[0]->radiusflag;
for (i = 1; i < nmol; i++) {
if (onemols[i]->radiusflag != radiusflag)
error->all(FLERR,"Inconsistent use of finite-size particles "
"by molecule template molecules");
}
if (radiusflag) extended = 1;
}
// grow extended arrays and set extended flags for each particle
// orientflag = 4 if any particle stores ellipsoid or tri orientation
// orientflag = 1 if any particle stores line orientation
// dorientflag = 1 if any particle stores dipole orientation
if (extended) {
if (atom->ellipsoid_flag) orientflag = 4;
if (atom->line_flag) orientflag = 1;
if (atom->tri_flag) orientflag = 4;
if (atom->mu_flag) dorientflag = 1;
grow_arrays(atom->nmax);
for (i = 0; i < nlocal; i++) {
eflags[i] = 0;
if (bodytag[i] == 0) continue;
// set to POINT or SPHERE or ELLIPSOID or LINE
if (radius && radius[i] > 0.0) {
eflags[i] |= SPHERE;
eflags[i] |= OMEGA;
eflags[i] |= TORQUE;
} else if (ellipsoid && ellipsoid[i] >= 0) {
eflags[i] |= ELLIPSOID;
eflags[i] |= ANGMOM;
eflags[i] |= TORQUE;
} else if (line && line[i] >= 0) {
eflags[i] |= LINE;
eflags[i] |= OMEGA;
eflags[i] |= TORQUE;
} else if (tri && tri[i] >= 0) {
eflags[i] |= TRIANGLE;
eflags[i] |= ANGMOM;
eflags[i] |= TORQUE;
} else eflags[i] |= POINT;
// set DIPOLE if atom->mu and mu[3] > 0.0
if (atom->mu_flag && mu[i][3] > 0.0)
eflags[i] |= DIPOLE;
}
}
// set body xcmimage flags = true image flags
imageint *image = atom->image;
for (i = 0; i < nlocal; i++)
if (bodytag[i] >= 0) xcmimage[i] = image[i];
else xcmimage[i] = 0;
// acquire ghost bodies via forward comm
// set atom2body for ghost atoms via forward comm
// set atom2body for other owned atoms via reset_atom2body()
nghost_body = 0;
commflag = FULL_BODY;
comm->forward_comm_fix(this);
reset_atom2body();
// compute mass & center-of-mass of each rigid body
double **x = atom->x;
double *xcm;
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
xcm = body[ibody].xcm;
xcm[0] = xcm[1] = xcm[2] = 0.0;
body[ibody].mass = 0.0;
}
double unwrap[3];
double massone;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
xcm[0] += unwrap[0] * massone;
xcm[1] += unwrap[1] * massone;
xcm[2] += unwrap[2] * massone;
b->mass += massone;
}
// reverse communicate xcm, mass of all bodies
commflag = XCM_MASS;
comm->reverse_comm_fix(this,4);
for (ibody = 0; ibody < nlocal_body; ibody++) {
xcm = body[ibody].xcm;
xcm[0] /= body[ibody].mass;
xcm[1] /= body[ibody].mass;
xcm[2] /= body[ibody].mass;
}
// set vcm, angmom = 0.0 in case infile is used
// and doesn't overwrite all body's values
// since setup_bodies_dynamic() will not be called
double *vcm,*angmom;
for (ibody = 0; ibody < nlocal_body; ibody++) {
vcm = body[ibody].vcm;
vcm[0] = vcm[1] = vcm[2] = 0.0;
angmom = body[ibody].angmom;
angmom[0] = angmom[1] = angmom[2] = 0.0;
}
// set rigid body image flags to default values
for (ibody = 0; ibody < nlocal_body; ibody++)
body[ibody].image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// overwrite masstotal, center-of-mass, image flags with file values
// inbody[i] = 0/1 if Ith rigid body is initialized by file
int *inbody;
if (infile) {
memory->create(inbody,nlocal_body,"rigid/small:inbody");
for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0;
readfile(0,NULL,inbody);
}
// remap the xcm of each body back into simulation box
// and reset body and atom xcmimage flags via pre_neighbor()
pre_neighbor();
// compute 6 moments of inertia of each body in Cartesian reference frame
// dx,dy,dz = coords relative to center-of-mass
// symmetric 3x3 inertia tensor stored in Voigt notation as 6-vector
memory->create(itensor,nlocal_body+nghost_body,6,"rigid/small:itensor");
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++)
for (i = 0; i < 6; i++) itensor[ibody][i] = 0.0;
double dx,dy,dz;
double *inertia;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
inertia = itensor[atom2body[i]];
inertia[0] += massone * (dy*dy + dz*dz);
inertia[1] += massone * (dx*dx + dz*dz);
inertia[2] += massone * (dx*dx + dy*dy);
inertia[3] -= massone * dy*dz;
inertia[4] -= massone * dx*dz;
inertia[5] -= massone * dx*dy;
}
// extended particles may contribute extra terms to moments of inertia
if (extended) {
double ivec[6];
double *shape,*quatatom,*inertiaatom;
double length,theta;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
inertia = itensor[atom2body[i]];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (eflags[i] & SPHERE) {
inertia[0] += SINERTIA*massone * radius[i]*radius[i];
inertia[1] += SINERTIA*massone * radius[i]*radius[i];
inertia[2] += SINERTIA*massone * radius[i]*radius[i];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::inertia_ellipsoid(shape,quatatom,massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
} else if (eflags[i] & LINE) {
length = lbonus[line[i]].length;
theta = lbonus[line[i]].theta;
MathExtra::inertia_line(length,theta,massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
quatatom = tbonus[tri[i]].quat;
MathExtra::inertia_triangle(inertiaatom,quatatom,massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
}
}
}
// reverse communicate inertia tensor of all bodies
commflag = ITENSOR;
comm->reverse_comm_fix(this,6);
// overwrite Cartesian inertia tensor with file values
if (infile) readfile(1,itensor,inbody);
// 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];
double *ex,*ey,*ez;
for (ibody = 0; ibody < nlocal_body; ibody++) {
tensor[0][0] = itensor[ibody][0];
tensor[1][1] = itensor[ibody][1];
tensor[2][2] = itensor[ibody][2];
tensor[1][2] = tensor[2][1] = itensor[ibody][3];
tensor[0][2] = tensor[2][0] = itensor[ibody][4];
tensor[0][1] = tensor[1][0] = itensor[ibody][5];
inertia = body[ibody].inertia;
ierror = MathExtra::jacobi(tensor,inertia,evectors);
if (ierror) error->all(FLERR,
"Insufficient Jacobi rotations for rigid body");
ex = body[ibody].ex_space;
ex[0] = evectors[0][0];
ex[1] = evectors[1][0];
ex[2] = evectors[2][0];
ey = body[ibody].ey_space;
ey[0] = evectors[0][1];
ey[1] = evectors[1][1];
ey[2] = evectors[2][1];
ez = body[ibody].ez_space;
ez[0] = evectors[0][2];
ez[1] = evectors[1][2];
ez[2] = evectors[2][2];
// if any principal moment < scaled EPSILON, set to 0.0
double max;
max = MAX(inertia[0],inertia[1]);
max = MAX(max,inertia[2]);
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
// create initial quaternion
MathExtra::exyz_to_q(ex,ey,ez,body[ibody].quat);
}
// forward communicate updated info of all bodies
commflag = INITIAL;
comm->forward_comm_fix(this,26);
// 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;
double theta_body;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) {
displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
continue;
}
Body *b = &body[atom2body[i]];
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
delta[0] = unwrap[0] - xcm[0];
delta[1] = unwrap[1] - xcm[1];
delta[2] = unwrap[2] - xcm[2];
MathExtra::transpose_matvec(b->ex_space,b->ey_space,b->ez_space,
delta,displace[i]);
if (extended) {
if (eflags[i] & ELLIPSOID) {
quatatom = ebonus[ellipsoid[i]].quat;
MathExtra::qconjugate(b->quat,qc);
MathExtra::quatquat(qc,quatatom,orient[i]);
MathExtra::qnormalize(orient[i]);
} else if (eflags[i] & LINE) {
if (b->quat[3] >= 0.0) theta_body = 2.0*acos(b->quat[0]);
else theta_body = -2.0*acos(b->quat[0]);
orient[i][0] = lbonus[line[i]].theta - theta_body;
while (orient[i][0] <= MINUSPI) orient[i][0] += TWOPI;
while (orient[i][0] > MY_PI) orient[i][0] -= TWOPI;
if (orientflag == 4) orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
} else if (eflags[i] & TRIANGLE) {
quatatom = tbonus[tri[i]].quat;
MathExtra::qconjugate(b->quat,qc);
MathExtra::quatquat(qc,quatatom,orient[i]);
MathExtra::qnormalize(orient[i]);
} else if (orientflag == 4) {
orient[i][0] = orient[i][1] = orient[i][2] = orient[i][3] = 0.0;
} else if (orientflag == 1)
orient[i][0] = 0.0;
if (eflags[i] & DIPOLE) {
MathExtra::transpose_matvec(b->ex_space,b->ey_space,b->ez_space,
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;
}
}
// 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 < nlocal_body+nghost_body; ibody++)
for (i = 0; i < 6; i++) itensor[ibody][i] = 0.0;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
inertia = itensor[atom2body[i]];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
inertia[0] += massone *
(displace[i][1]*displace[i][1] + displace[i][2]*displace[i][2]);
inertia[1] += massone *
(displace[i][0]*displace[i][0] + displace[i][2]*displace[i][2]);
inertia[2] += massone *
(displace[i][0]*displace[i][0] + displace[i][1]*displace[i][1]);
inertia[3] -= massone * displace[i][1]*displace[i][2];
inertia[4] -= massone * displace[i][0]*displace[i][2];
inertia[5] -= massone * displace[i][0]*displace[i][1];
}
if (extended) {
double ivec[6];
double *shape,*inertiaatom;
double length;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
inertia = itensor[atom2body[i]];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (eflags[i] & SPHERE) {
inertia[0] += SINERTIA*massone * radius[i]*radius[i];
inertia[1] += SINERTIA*massone * radius[i]*radius[i];
inertia[2] += SINERTIA*massone * radius[i]*radius[i];
} else if (eflags[i] & ELLIPSOID) {
shape = ebonus[ellipsoid[i]].shape;
MathExtra::inertia_ellipsoid(shape,orient[i],massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
} else if (eflags[i] & LINE) {
length = lbonus[line[i]].length;
MathExtra::inertia_line(length,orient[i][0],massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
} else if (eflags[i] & TRIANGLE) {
inertiaatom = tbonus[tri[i]].inertia;
MathExtra::inertia_triangle(inertiaatom,orient[i],massone,ivec);
inertia[0] += ivec[0];
inertia[1] += ivec[1];
inertia[2] += ivec[2];
inertia[3] += ivec[3];
inertia[4] += ivec[4];
inertia[5] += ivec[5];
}
}
}
// reverse communicate inertia tensor of all bodies
commflag = ITENSOR;
comm->reverse_comm_fix(this,6);
// error check that re-computed moments of inertia match diagonalized ones
// do not do test for bodies with params read from infile
double norm;
for (ibody = 0; ibody < nlocal_body; ibody++) {
if (infile && inbody[ibody]) continue;
inertia = body[ibody].inertia;
if (inertia[0] == 0.0) {
if (fabs(itensor[ibody][0]) > TOLERANCE)
error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
if (fabs((itensor[ibody][0]-inertia[0])/inertia[0]) >
TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
if (inertia[1] == 0.0) {
if (fabs(itensor[ibody][1]) > TOLERANCE)
error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
if (fabs((itensor[ibody][1]-inertia[1])/inertia[1]) >
TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
if (inertia[2] == 0.0) {
if (fabs(itensor[ibody][2]) > TOLERANCE)
error->all(FLERR,"Fix rigid: Bad principal moments");
} else {
if (fabs((itensor[ibody][2]-inertia[2])/inertia[2]) >
TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments");
}
norm = (inertia[0] + inertia[1] + inertia[2]) / 3.0;
if (fabs(itensor[ibody][3]/norm) > TOLERANCE ||
fabs(itensor[ibody][4]/norm) > TOLERANCE ||
fabs(itensor[ibody][5]/norm) > TOLERANCE)
error->all(FLERR,"Fix rigid: Bad principal moments");
}
// clean up
memory->destroy(itensor);
if (infile) memory->destroy(inbody);
}
/* ----------------------------------------------------------------------
one-time initialization of dynamic rigid body attributes
vcm and angmom, computed explicitly from constituent particles
not done if body properites read from file, e.g. for overlapping particles
------------------------------------------------------------------------- */
void FixRigidSmall::setup_bodies_dynamic()
{
int i,ibody;
double massone,radone;
// sum vcm, angmom across all rigid bodies
// vcm = velocity of COM
// angmom = angular momentum around COM
double **x = atom->x;
double **v = atom->v;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
double *xcm,*vcm,*acm;
double dx,dy,dz;
double unwrap[3];
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
vcm = body[ibody].vcm;
vcm[0] = vcm[1] = vcm[2] = 0.0;
acm = body[ibody].angmom;
acm[0] = acm[1] = acm[2] = 0.0;
}
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vcm = b->vcm;
vcm[0] += v[i][0] * massone;
vcm[1] += v[i][1] * massone;
vcm[2] += v[i][2] * massone;
domain->unmap(x[i],xcmimage[i],unwrap);
xcm = b->xcm;
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
acm = b->angmom;
acm[0] += dy * massone*v[i][2] - dz * massone*v[i][1];
acm[1] += dz * massone*v[i][0] - dx * massone*v[i][2];
acm[2] += dx * massone*v[i][1] - dy * massone*v[i][0];
}
// extended particles add their rotation to angmom of body
if (extended) {
AtomVecLine::Bonus *lbonus;
if (avec_line) lbonus = avec_line->bonus;
double **omega = atom->omega;
double **angmom = atom->angmom;
double *radius = atom->radius;
int *line = atom->line;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
Body *b = &body[atom2body[i]];
if (eflags[i] & OMEGA) {
if (eflags[i] & SPHERE) {
radone = radius[i];
acm = b->angmom;
acm[0] += SINERTIA*rmass[i] * radone*radone * omega[i][0];
acm[1] += SINERTIA*rmass[i] * radone*radone * omega[i][1];
acm[2] += SINERTIA*rmass[i] * radone*radone * omega[i][2];
} else if (eflags[i] & LINE) {
radone = lbonus[line[i]].length;
b->angmom[2] += LINERTIA*rmass[i] * radone*radone * omega[i][2];
}
}
if (eflags[i] & ANGMOM) {
acm = b->angmom;
acm[0] += angmom[i][0];
acm[1] += angmom[i][1];
acm[2] += angmom[i][2];
}
}
}
// reverse communicate vcm, angmom of all bodies
commflag = VCM_ANGMOM;
comm->reverse_comm_fix(this,6);
// normalize velocity of COM
for (ibody = 0; ibody < nlocal_body; ibody++) {
vcm = body[ibody].vcm;
vcm[0] /= body[ibody].mass;
vcm[1] /= body[ibody].mass;
vcm[2] /= body[ibody].mass;
}
}
/* ----------------------------------------------------------------------
read per rigid body info from user-provided file
which = 0 to read everthing except 6 moments of inertia
which = 1 to read just 6 moments of inertia
flag inbody = 0 for local bodies this proc initializes from file
nlines = # of lines of rigid body info, 0 is OK
one line = rigid-ID mass xcm ycm zcm ixx iyy izz ixy ixz iyz
vxcm vycm vzcm lx ly lz
where rigid-ID = mol-ID for fix rigid/small
------------------------------------------------------------------------- */
void FixRigidSmall::readfile(int which, double **array, int *inbody)
{
int i,j,m,nchunk,eofflag,nlines,xbox,ybox,zbox;
tagint id;
FILE *fp;
char *eof,*start,*next,*buf;
char line[MAXLINE];
// create local hash with key/value pairs
// key = mol ID of bodies my atoms own
// value = index into local body array
int nlocal = atom->nlocal;
hash = new std::map<tagint,int>();
for (i = 0; i < nlocal; i++)
if (bodyown[i] >= 0) (*hash)[atom->molecule[i]] = bodyown[i];
// open file and read header
if (me == 0) {
fp = fopen(infile,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix rigid/small infile %s",infile);
error->one(FLERR,str);
}
while (1) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL)
error->one(FLERR,"Unexpected end of fix rigid/small file");
start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break;
}
sscanf(line,"%d",&nlines);
}
MPI_Bcast(&nlines,1,MPI_INT,0,world);
char *buffer = new char[CHUNK*MAXLINE];
char **values = new char*[ATTRIBUTE_PERBODY];
int nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid/small file");
buf = buffer;
next = strchr(buf,'\n');
*next = '\0';
int nwords = atom->count_words(buf);
*next = '\n';
if (nwords != ATTRIBUTE_PERBODY)
error->all(FLERR,"Incorrect rigid body format in fix rigid/small file");
// loop over lines of rigid body attributes
// tokenize the line into values
// id = rigid body ID = mol-ID
// for which = 0, store all but inertia directly in body struct
// for which = 1, store inertia tensor array, invert 3,4,5 values to Voigt
for (int i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
id = ATOTAGINT(values[0]);
if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
if (hash->find(id) == hash->end()) {
buf = next + 1;
continue;
}
m = (*hash)[id];
inbody[m] = 1;
if (which == 0) {
body[m].mass = atof(values[1]);
body[m].xcm[0] = atof(values[2]);
body[m].xcm[1] = atof(values[3]);
body[m].xcm[2] = atof(values[4]);
body[m].vcm[0] = atof(values[11]);
body[m].vcm[1] = atof(values[12]);
body[m].vcm[2] = atof(values[13]);
body[m].angmom[0] = atof(values[14]);
body[m].angmom[1] = atof(values[15]);
body[m].angmom[2] = atof(values[16]);
xbox = atoi(values[17]);
ybox = atoi(values[18]);
zbox = atoi(values[19]);
body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
array[m][0] = atof(values[5]);
array[m][1] = atof(values[6]);
array[m][2] = atof(values[7]);
array[m][3] = atof(values[10]);
array[m][4] = atof(values[9]);
array[m][5] = atof(values[8]);
}
buf = next + 1;
}
nread += nchunk;
}
if (me == 0) fclose(fp);
delete [] buffer;
delete [] values;
delete hash;
}
/* ----------------------------------------------------------------------
write out restart info for mass, COM, inertia tensor to file
identical format to infile option, so info can be read in when restarting
each proc contributes info for rigid bodies it owns
------------------------------------------------------------------------- */
void FixRigidSmall::write_restart_file(char *file)
{
FILE *fp;
// do not write file if bodies have not yet been initialized
if (!setupflag) return;
// proc 0 opens file and writes header
if (me == 0) {
char outfile[128];
sprintf(outfile,"%s.rigid",file);
fp = fopen(outfile,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
fprintf(fp,"# fix rigid mass, COM, inertia tensor info for "
"%d bodies on timestep " BIGINT_FORMAT "\n\n",
nbody,update->ntimestep);
fprintf(fp,"%d\n",nbody);
}
// communication buffer for all my rigid body info
// max_size = largest buffer needed by any proc
// ncol = # of values per line in output file
int ncol = ATTRIBUTE_PERBODY;
int sendrow = nlocal_body;
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
double **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"rigid/small:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"rigid/small:buf");
// pack my rigid body info into buf
// compute I tensor against xyz axes from diagonalized I and current quat
// Ispace = P Idiag P_transpose
// P is stored column-wise in exyz_space
double p[3][3],pdiag[3][3],ispace[3][3];
for (int i = 0; i < nlocal_body; i++) {
MathExtra::col2mat(body[i].ex_space,body[i].ey_space,body[i].ez_space,p);
MathExtra::times3_diag(p,body[i].inertia,pdiag);
MathExtra::times3_transpose(pdiag,p,ispace);
buf[i][0] = atom->molecule[body[i].ilocal];
buf[i][1] = body[i].mass;
buf[i][2] = body[i].xcm[0];
buf[i][3] = body[i].xcm[1];
buf[i][4] = body[i].xcm[2];
buf[i][5] = ispace[0][0];
buf[i][6] = ispace[1][1];
buf[i][7] = ispace[2][2];
buf[i][8] = ispace[0][1];
buf[i][9] = ispace[0][2];
buf[i][10] = ispace[1][2];
buf[i][11] = body[i].vcm[0];
buf[i][12] = body[i].vcm[1];
buf[i][13] = body[i].vcm[2];
buf[i][14] = body[i].angmom[0];
buf[i][15] = body[i].angmom[1];
buf[i][16] = body[i].angmom[2];
buf[i][17] = (body[i].image & IMGMASK) - IMGMAX;
buf[i][18] = (body[i].image >> IMGBITS & IMGMASK) - IMGMAX;
buf[i][19] = (body[i].image >> IMG2BITS) - IMGMAX;
}
// write one chunk of rigid body info per proc to file
// proc 0 pings each proc, receives its chunk, writes to file
// all other procs wait for ping, send their chunk to proc 0
int tmp,recvrow;
if (me == 0) {
MPI_Status status;
MPI_Request request;
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
for (int i = 0; i < recvrow; i++)
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
static_cast<int> (buf[i][0]),buf[i][1],
buf[i][2],buf[i][3],buf[i][4],
buf[i][5],buf[i][6],buf[i][7],
buf[i][8],buf[i][9],buf[i][10],
buf[i][11],buf[i][12],buf[i][13],
buf[i][14],buf[i][15],buf[i][16],
static_cast<int> (buf[i][17]),
static_cast<int> (buf[i][18]),
static_cast<int> (buf[i][19]));
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
}
// clean up and close file
memory->destroy(buf);
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixRigidSmall::grow_arrays(int nmax)
{
memory->grow(bodyown,nmax,"rigid/small:bodyown");
memory->grow(bodytag,nmax,"rigid/small:bodytag");
memory->grow(atom2body,nmax,"rigid/small:atom2body");
memory->grow(xcmimage,nmax,"rigid/small:xcmimage");
memory->grow(displace,nmax,3,"rigid/small:displace");
if (extended) {
memory->grow(eflags,nmax,"rigid/small:eflags");
if (orientflag) memory->grow(orient,nmax,orientflag,"rigid/small:orient");
if (dorientflag) memory->grow(dorient,nmax,3,"rigid/small:dorient");
}
// check for regrow of vatom
// must be done whether per-atom virial is accumulated on this step or not
// b/c this is only time grow_array() may be called
// need to regrow b/c vatom is calculated before and after atom migration
if (nmax > maxvatom) {
maxvatom = atom->nmax;
memory->grow(vatom,maxvatom,6,"fix:vatom");
}
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixRigidSmall::copy_arrays(int i, int j, int delflag)
{
bodytag[j] = bodytag[i];
xcmimage[j] = xcmimage[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];
for (int k = 0; k < orientflag; k++)
orient[j][k] = orient[i][k];
if (dorientflag) {
dorient[j][0] = dorient[i][0];
dorient[j][1] = dorient[i][1];
dorient[j][2] = dorient[i][2];
}
}
// must also copy vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
vatom[j][k] = vatom[i][k];
// if deleting atom J via delflag and J owns a body, then delete it
if (delflag && bodyown[j] >= 0) {
bodyown[body[nlocal_body-1].ilocal] = bodyown[j];
memcpy(&body[bodyown[j]],&body[nlocal_body-1],sizeof(Body));
nlocal_body--;
}
// if atom I owns a body, reset I's body.ilocal to loc J
// do NOT do this if self-copy (I=J) since I's body is already deleted
if (bodyown[i] >= 0 && i != j) body[bodyown[i]].ilocal = j;
bodyown[j] = bodyown[i];
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixRigidSmall::set_arrays(int i)
{
bodyown[i] = -1;
bodytag[i] = 0;
atom2body[i] = -1;
xcmimage[i] = 0;
displace[i][0] = 0.0;
displace[i][1] = 0.0;
displace[i][2] = 0.0;
// must also zero vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
vatom[i][k] = 0.0;
}
/* ----------------------------------------------------------------------
initialize a molecule inserted by another fix, e.g. deposit or pour
called when molecule is created
nlocalprev = # of atoms on this proc before molecule inserted
tagprev = atom ID previous to new atoms in the molecule
xgeom = geometric center of new molecule
vcm = COM velocity of new molecule
quat = rotation of new molecule (around geometric center)
relative to template in Molecule class
------------------------------------------------------------------------- */
void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev, int imol,
double *xgeom, double *vcm, double *quat)
{
int m;
double ctr2com[3],ctr2com_rotate[3];
double rotmat[3][3];
// increment total # of rigid bodies
nbody++;
// loop over atoms I added for the new body
int nlocal = atom->nlocal;
if (nlocalprev == nlocal) return;
tagint *tag = atom->tag;
for (int i = nlocalprev; i < nlocal; i++) {
bodytag[i] = tagprev + onemols[imol]->comatom;
if (tag[i]-tagprev == onemols[imol]->comatom) bodyown[i] = nlocal_body;
m = tag[i] - tagprev-1;
displace[i][0] = onemols[imol]->dxbody[m][0];
displace[i][1] = onemols[imol]->dxbody[m][1];
displace[i][2] = onemols[imol]->dxbody[m][2];
if (extended) {
eflags[i] = 0;
if (onemols[imol]->radiusflag) {
eflags[i] |= SPHERE;
eflags[i] |= OMEGA;
eflags[i] |= TORQUE;
}
}
if (bodyown[i] >= 0) {
if (nlocal_body == nmax_body) grow_body();
Body *b = &body[nlocal_body];
b->mass = onemols[imol]->masstotal;
// new COM = Q (onemols[imol]->xcm - onemols[imol]->center) + xgeom
// Q = rotation matrix associated with quat
MathExtra::quat_to_mat(quat,rotmat);
MathExtra::sub3(onemols[imol]->com,onemols[imol]->center,ctr2com);
MathExtra::matvec(rotmat,ctr2com,ctr2com_rotate);
MathExtra::add3(ctr2com_rotate,xgeom,b->xcm);
b->vcm[0] = vcm[0];
b->vcm[1] = vcm[1];
b->vcm[2] = vcm[2];
b->inertia[0] = onemols[imol]->inertia[0];
b->inertia[1] = onemols[imol]->inertia[1];
b->inertia[2] = onemols[imol]->inertia[2];
// final quat is product of insertion quat and original quat
// true even if insertion rotation was not around COM
MathExtra::quatquat(quat,onemols[imol]->quat,b->quat);
MathExtra::q_to_exyz(b->quat,b->ex_space,b->ey_space,b->ez_space);
b->angmom[0] = b->angmom[1] = b->angmom[2] = 0.0;
b->omega[0] = b->omega[1] = b->omega[2] = 0.0;
b->conjqm[0] = b->conjqm[1] = b->conjqm[2] = b->conjqm[3] = 0.0;
b->image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
b->ilocal = i;
nlocal_body++;
}
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixRigidSmall::pack_exchange(int i, double *buf)
{
buf[0] = ubuf(bodytag[i]).d;
buf[1] = ubuf(xcmimage[i]).d;
buf[2] = displace[i][0];
buf[3] = displace[i][1];
buf[4] = displace[i][2];
// extended attribute info
int m = 5;
if (extended) {
buf[m++] = eflags[i];
for (int j = 0; j < orientflag; j++)
buf[m++] = orient[i][j];
if (dorientflag) {
buf[m++] = dorient[i][0];
buf[m++] = dorient[i][1];
buf[m++] = dorient[i][2];
}
}
// atom not in a rigid body
if (!bodytag[i]) return m;
// must also pack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
buf[m++] = vatom[i][k];
// atom does not own its rigid body
if (bodyown[i] < 0) {
buf[m++] = 0;
return m;
}
// body info for atom that owns a rigid body
buf[m++] = 1;
memcpy(&buf[m],&body[bodyown[i]],sizeof(Body));
m += bodysize;
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixRigidSmall::unpack_exchange(int nlocal, double *buf)
{
bodytag[nlocal] = (tagint) ubuf(buf[0]).i;
xcmimage[nlocal] = (imageint) ubuf(buf[1]).i;
displace[nlocal][0] = buf[2];
displace[nlocal][1] = buf[3];
displace[nlocal][2] = buf[4];
// extended attribute info
int m = 5;
if (extended) {
eflags[nlocal] = static_cast<int> (buf[m++]);
for (int j = 0; j < orientflag; j++)
orient[nlocal][j] = buf[m++];
if (dorientflag) {
dorient[nlocal][0] = buf[m++];
dorient[nlocal][1] = buf[m++];
dorient[nlocal][2] = buf[m++];
}
}
// atom not in a rigid body
if (!bodytag[nlocal]) {
bodyown[nlocal] = -1;
return m;
}
// must also unpack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
vatom[nlocal][k] = buf[m++];
// atom does not own its rigid body
bodyown[nlocal] = static_cast<int> (buf[m++]);
if (bodyown[nlocal] == 0) {
bodyown[nlocal] = -1;
return m;
}
// body info for atom that owns a rigid body
if (nlocal_body == nmax_body) grow_body();
memcpy(&body[nlocal_body],&buf[m],sizeof(Body));
m += bodysize;
body[nlocal_body].ilocal = nlocal;
bodyown[nlocal] = nlocal_body++;
return m;
}
/* ----------------------------------------------------------------------
only pack body info if own or ghost atom owns the body
for FULL_BODY, send 0/1 flag with every atom
------------------------------------------------------------------------- */
int FixRigidSmall::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm;
int m = 0;
if (commflag == INITIAL) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
xcm = body[bodyown[j]].xcm;
buf[m++] = xcm[0];
buf[m++] = xcm[1];
buf[m++] = xcm[2];
vcm = body[bodyown[j]].vcm;
buf[m++] = vcm[0];
buf[m++] = vcm[1];
buf[m++] = vcm[2];
quat = body[bodyown[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
omega = body[bodyown[j]].omega;
buf[m++] = omega[0];
buf[m++] = omega[1];
buf[m++] = omega[2];
ex_space = body[bodyown[j]].ex_space;
buf[m++] = ex_space[0];
buf[m++] = ex_space[1];
buf[m++] = ex_space[2];
ey_space = body[bodyown[j]].ey_space;
buf[m++] = ey_space[0];
buf[m++] = ey_space[1];
buf[m++] = ey_space[2];
ez_space = body[bodyown[j]].ez_space;
buf[m++] = ez_space[0];
buf[m++] = ez_space[1];
buf[m++] = ez_space[2];
conjqm = body[bodyown[j]].conjqm;
buf[m++] = conjqm[0];
buf[m++] = conjqm[1];
buf[m++] = conjqm[2];
buf[m++] = conjqm[3];
}
} else if (commflag == FINAL) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
vcm = body[bodyown[j]].vcm;
buf[m++] = vcm[0];
buf[m++] = vcm[1];
buf[m++] = vcm[2];
omega = body[bodyown[j]].omega;
buf[m++] = omega[0];
buf[m++] = omega[1];
buf[m++] = omega[2];
conjqm = body[bodyown[j]].conjqm;
buf[m++] = conjqm[0];
buf[m++] = conjqm[1];
buf[m++] = conjqm[2];
buf[m++] = conjqm[3];
}
} else if (commflag == FULL_BODY) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
memcpy(&buf[m],&body[bodyown[j]],sizeof(Body));
m += bodysize;
}
}
}
return m;
}
/* ----------------------------------------------------------------------
only ghost atoms are looped over
for FULL_BODY, store a new ghost body if this atom owns it
for other commflag values, only unpack body info if atom owns it
------------------------------------------------------------------------- */
void FixRigidSmall::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,last;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm;
int m = 0;
last = first + n;
if (commflag == INITIAL) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
xcm = body[bodyown[i]].xcm;
xcm[0] = buf[m++];
xcm[1] = buf[m++];
xcm[2] = buf[m++];
vcm = body[bodyown[i]].vcm;
vcm[0] = buf[m++];
vcm[1] = buf[m++];
vcm[2] = buf[m++];
quat = body[bodyown[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
omega = body[bodyown[i]].omega;
omega[0] = buf[m++];
omega[1] = buf[m++];
omega[2] = buf[m++];
ex_space = body[bodyown[i]].ex_space;
ex_space[0] = buf[m++];
ex_space[1] = buf[m++];
ex_space[2] = buf[m++];
ey_space = body[bodyown[i]].ey_space;
ey_space[0] = buf[m++];
ey_space[1] = buf[m++];
ey_space[2] = buf[m++];
ez_space = body[bodyown[i]].ez_space;
ez_space[0] = buf[m++];
ez_space[1] = buf[m++];
ez_space[2] = buf[m++];
conjqm = body[bodyown[i]].conjqm;
conjqm[0] = buf[m++];
conjqm[1] = buf[m++];
conjqm[2] = buf[m++];
conjqm[3] = buf[m++];
}
} else if (commflag == FINAL) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
vcm = body[bodyown[i]].vcm;
vcm[0] = buf[m++];
vcm[1] = buf[m++];
vcm[2] = buf[m++];
omega = body[bodyown[i]].omega;
omega[0] = buf[m++];
omega[1] = buf[m++];
omega[2] = buf[m++];
conjqm = body[bodyown[i]].conjqm;
conjqm[0] = buf[m++];
conjqm[1] = buf[m++];
conjqm[2] = buf[m++];
conjqm[3] = buf[m++];
}
} else if (commflag == FULL_BODY) {
for (i = first; i < last; i++) {
bodyown[i] = static_cast<int> (buf[m++]);
if (bodyown[i] == 0) bodyown[i] = -1;
else {
j = nlocal_body + nghost_body;
if (j == nmax_body) grow_body();
memcpy(&body[j],&buf[m],sizeof(Body));
m += bodysize;
body[j].ilocal = i;
bodyown[i] = j;
nghost_body++;
}
}
}
}
/* ----------------------------------------------------------------------
only ghost atoms are looped over
only pack body info if atom owns it
------------------------------------------------------------------------- */
int FixRigidSmall::pack_reverse_comm(int n, int first, double *buf)
{
int i,j,m,last;
double *fcm,*torque,*vcm,*angmom,*xcm;
m = 0;
last = first + n;
if (commflag == FORCE_TORQUE) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
fcm = body[bodyown[i]].fcm;
buf[m++] = fcm[0];
buf[m++] = fcm[1];
buf[m++] = fcm[2];
torque = body[bodyown[i]].torque;
buf[m++] = torque[0];
buf[m++] = torque[1];
buf[m++] = torque[2];
}
} else if (commflag == VCM_ANGMOM) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
vcm = body[bodyown[i]].vcm;
buf[m++] = vcm[0];
buf[m++] = vcm[1];
buf[m++] = vcm[2];
angmom = body[bodyown[i]].angmom;
buf[m++] = angmom[0];
buf[m++] = angmom[1];
buf[m++] = angmom[2];
}
} else if (commflag == XCM_MASS) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
xcm = body[bodyown[i]].xcm;
buf[m++] = xcm[0];
buf[m++] = xcm[1];
buf[m++] = xcm[2];
buf[m++] = body[bodyown[i]].mass;
}
} else if (commflag == ITENSOR) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
j = bodyown[i];
buf[m++] = itensor[j][0];
buf[m++] = itensor[j][1];
buf[m++] = itensor[j][2];
buf[m++] = itensor[j][3];
buf[m++] = itensor[j][4];
buf[m++] = itensor[j][5];
}
} else if (commflag == DOF) {
for (i = first; i < last; i++) {
if (bodyown[i] < 0) continue;
j = bodyown[i];
buf[m++] = counts[j][0];
buf[m++] = counts[j][1];
buf[m++] = counts[j][2];
}
}
return m;
}
/* ----------------------------------------------------------------------
only unpack body info if own or ghost atom owns the body
------------------------------------------------------------------------- */
void FixRigidSmall::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,k;
double *fcm,*torque,*vcm,*angmom,*xcm;
int m = 0;
if (commflag == FORCE_TORQUE) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
fcm = body[bodyown[j]].fcm;
fcm[0] += buf[m++];
fcm[1] += buf[m++];
fcm[2] += buf[m++];
torque = body[bodyown[j]].torque;
torque[0] += buf[m++];
torque[1] += buf[m++];
torque[2] += buf[m++];
}
} else if (commflag == VCM_ANGMOM) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
vcm = body[bodyown[j]].vcm;
vcm[0] += buf[m++];
vcm[1] += buf[m++];
vcm[2] += buf[m++];
angmom = body[bodyown[j]].angmom;
angmom[0] += buf[m++];
angmom[1] += buf[m++];
angmom[2] += buf[m++];
}
} else if (commflag == XCM_MASS) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
xcm = body[bodyown[j]].xcm;
xcm[0] += buf[m++];
xcm[1] += buf[m++];
xcm[2] += buf[m++];
body[bodyown[j]].mass += buf[m++];
}
} else if (commflag == ITENSOR) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
k = bodyown[j];
itensor[k][0] += buf[m++];
itensor[k][1] += buf[m++];
itensor[k][2] += buf[m++];
itensor[k][3] += buf[m++];
itensor[k][4] += buf[m++];
itensor[k][5] += buf[m++];
}
} else if (commflag == DOF) {
for (i = 0; i < n; i++) {
j = list[i];
if (bodyown[j] < 0) continue;
k = bodyown[j];
counts[k][0] += static_cast<int> (buf[m++]);
counts[k][1] += static_cast<int> (buf[m++]);
counts[k][2] += static_cast<int> (buf[m++]);
}
}
}
/* ----------------------------------------------------------------------
grow body data structure
------------------------------------------------------------------------- */
void FixRigidSmall::grow_body()
{
nmax_body += DELTA_BODY;
body = (Body *) memory->srealloc(body,nmax_body*sizeof(Body),
"rigid/small:body");
}
/* ----------------------------------------------------------------------
reset atom2body for all owned atoms
do this via bodyown of atom that owns the body the owned atom is in
atom2body values can point to original body or any image of the body
------------------------------------------------------------------------- */
void FixRigidSmall::reset_atom2body()
{
int iowner;
// iowner = index of atom that owns the body that atom I is in
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
atom2body[i] = -1;
if (bodytag[i]) {
iowner = atom->map(bodytag[i]);
if (iowner == -1) {
char str[128];
sprintf(str,
"Rigid body atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
atom->tag[i],bodytag[i],comm->me,update->ntimestep);
error->one(FLERR,str);
}
atom2body[i] = bodyown[iowner];
}
}
}
/* ---------------------------------------------------------------------- */
void FixRigidSmall::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
}
/* ----------------------------------------------------------------------
zero linear momentum of each rigid body
set Vcm to 0.0, then reset velocities of particles via set_v()
------------------------------------------------------------------------- */
void FixRigidSmall::zero_momentum()
{
double *vcm;
for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
vcm = body[ibody].vcm;
vcm[0] = vcm[1] = vcm[2] = 0.0;
}
// forward communicate of vcm to all ghost copies
commflag = FINAL;
comm->forward_comm_fix(this,10);
// set velocity of atoms in rigid bodues
evflag = 0;
set_v();
}
/* ----------------------------------------------------------------------
zero angular momentum of each rigid body
set angmom/omega to 0.0, then reset velocities of particles via set_v()
------------------------------------------------------------------------- */
void FixRigidSmall::zero_rotation()
{
double *angmom,*omega;
for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
angmom = body[ibody].angmom;
angmom[0] = angmom[1] = angmom[2] = 0.0;
omega = body[ibody].omega;
omega[0] = omega[1] = omega[2] = 0.0;
}
// forward communicate of omega to all ghost copies
commflag = FINAL;
comm->forward_comm_fix(this,10);
// set velocity of atoms in rigid bodues
evflag = 0;
set_v();
}
/* ---------------------------------------------------------------------- */
void *FixRigidSmall::extract(const char *str, int &dim)
{
if (strcmp(str,"body") == 0) {
dim = 1;
return atom2body;
}
if (strcmp(str,"onemol") == 0) {
dim = 0;
return onemols;
}
// return vector of rigid body masses, for owned+ghost bodies
// used by granular pair styles, indexed by atom2body
if (strcmp(str,"masstotal") == 0) {
dim = 1;
if (nmax_mass < nmax_body) {
memory->destroy(mass_body);
nmax_mass = nmax_body;
memory->create(mass_body,nmax_mass,"rigid:mass_body");
}
int n = nlocal_body + nghost_body;
for (int i = 0; i < n; i++)
mass_body[i] = body[i].mass;
return mass_body;
}
return NULL;
}
/* ----------------------------------------------------------------------
return translational KE for all rigid bodies
KE = 1/2 M Vcm^2
sum local body results across procs
------------------------------------------------------------------------- */
double FixRigidSmall::extract_ke()
{
double *vcm;
double ke = 0.0;
for (int i = 0; i < nlocal_body; i++) {
vcm = body[i].vcm;
ke += body[i].mass * (vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2]);
}
double keall;
MPI_Allreduce(&ke,&keall,1,MPI_DOUBLE,MPI_SUM,world);
return 0.5*keall;
}
/* ----------------------------------------------------------------------
return rotational KE for all rigid bodies
Erotational = 1/2 I wbody^2
------------------------------------------------------------------------- */
double FixRigidSmall::extract_erotational()
{
double wbody[3],rot[3][3];
double *inertia;
double erotate = 0.0;
for (int i = 0; i < nlocal_body; i++) {
// for Iw^2 rotational term, need wbody = angular velocity in body frame
// not omega = angular velocity in space frame
inertia = body[i].inertia;
MathExtra::quat_to_mat(body[i].quat,rot);
MathExtra::transpose_matvec(rot,body[i].angmom,wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] + inertia[1]*wbody[1]*wbody[1] +
inertia[2]*wbody[2]*wbody[2];
}
double erotateall;
MPI_Allreduce(&erotate,&erotateall,1,MPI_DOUBLE,MPI_SUM,world);
return 0.5*erotateall;
}
/* ----------------------------------------------------------------------
return temperature of collection of rigid bodies
non-active DOF are removed by fflag/tflag and in tfactor
------------------------------------------------------------------------- */
double FixRigidSmall::compute_scalar()
{
double wbody[3],rot[3][3];
double *vcm,*inertia;
double t = 0.0;
for (int i = 0; i < nlocal_body; i++) {
vcm = body[i].vcm;
t += body[i].mass * (vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2]);
// for Iw^2 rotational term, need wbody = angular velocity in body frame
// not omega = angular velocity in space frame
inertia = body[i].inertia;
MathExtra::quat_to_mat(body[i].quat,rot);
MathExtra::transpose_matvec(rot,body[i].angmom,wbody);
if (inertia[0] == 0.0) wbody[0] = 0.0;
else wbody[0] /= inertia[0];
if (inertia[1] == 0.0) wbody[1] = 0.0;
else wbody[1] /= inertia[1];
if (inertia[2] == 0.0) wbody[2] = 0.0;
else wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] + inertia[1]*wbody[1]*wbody[1] +
inertia[2]*wbody[2]*wbody[2];
}
double tall;
MPI_Allreduce(&t,&tall,1,MPI_DOUBLE,MPI_SUM,world);
double tfactor = force->mvv2e / ((6.0*nbody - nlinear) * force->boltz);
tall *= tfactor;
return tall;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixRigidSmall::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax*2 * sizeof(int);
bytes += nmax * sizeof(imageint);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double); // vatom
if (extended) {
bytes += nmax * sizeof(int);
if (orientflag) bytes = nmax*orientflag * sizeof(double);
if (dorientflag) bytes = nmax*3 * sizeof(double);
}
bytes += nmax_body * sizeof(Body);
return bytes;
}
/* ----------------------------------------------------------------------
debug method for sanity checking of atom/body data pointers
------------------------------------------------------------------------- */
/*
void FixRigidSmall::check(int flag)
{
for (int i = 0; i < atom->nlocal; i++) {
if (bodyown[i] >= 0) {
if (bodytag[i] != atom->tag[i]) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD AAA");
}
if (bodyown[i] < 0 || bodyown[i] >= nlocal_body) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD BBB");
}
if (atom2body[i] != bodyown[i]) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD CCC");
}
if (body[bodyown[i]].ilocal != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD DDD");
}
}
}
for (int i = 0; i < atom->nlocal; i++) {
if (bodyown[i] < 0 && bodytag[i] > 0) {
if (atom2body[i] < 0 || atom2body[i] >= nlocal_body+nghost_body) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD EEE");
}
if (bodytag[i] != atom->tag[body[atom2body[i]].ilocal]) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD FFF");
}
}
}
for (int i = atom->nlocal; i < atom->nlocal + atom->nghost; i++) {
if (bodyown[i] >= 0) {
if (bodyown[i] < nlocal_body ||
bodyown[i] >= nlocal_body+nghost_body) {
printf("Values %d %d: %d %d %d\n",
i,atom->tag[i],bodyown[i],nlocal_body,nghost_body);
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD GGG");
}
if (body[bodyown[i]].ilocal != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD HHH");
}
}
}
for (int i = 0; i < nlocal_body; i++) {
if (body[i].ilocal < 0 || body[i].ilocal >= atom->nlocal) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD III");
}
if (bodytag[body[i].ilocal] != atom->tag[body[i].ilocal] ||
bodyown[body[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD JJJ");
}
}
for (int i = nlocal_body; i < nlocal_body + nghost_body; i++) {
if (body[i].ilocal < atom->nlocal ||
body[i].ilocal >= atom->nlocal + atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD KKK");
}
if (bodyown[body[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD LLL");
}
}
}
*/
c4science · Help