void Velocity::create(double t_desired, int seed)
{
int i;
if (seed <= 0) error->all(FLERR,"Illegal velocity create command");
// if temperature = NULL, create a new ComputeTemp with the velocity group
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning(FLERR,"Mismatch between velocity and compute groups");
temperature->init();
temperature->setup();
// store a copy of current velocities
double **v = atom->v;
int nlocal = atom->nlocal;
double **vhold;
memory->create(vhold,nlocal,3,"velocity:vnew");
for (i = 0; i < nlocal; i++) {
vhold[i][0] = v[i][0];
vhold[i][1] = v[i][1];
vhold[i][2] = v[i][2];
}
// create new velocities, in uniform or gaussian distribution
// loop option determines looping style, ALL is default
// ALL = loop over all natoms, only set those I own via atom->map
// cannot do this if atom IDs do not span 1-Natoms (some were deleted)
// will produce same V, independent of P, if atoms were read-in
// will NOT produce same V, independent of P, if used create_atoms
// LOCAL = only loop over my atoms, adjust RNG to be proc-specific
// will never produce same V, independent of P
// GEOM = only loop over my atoms
// choose RNG for each atom based on its xyz coord (geometry)
// via random->reset()
// will always produce same V, independent of P
// adjust by factor for atom mass
// for 2d, set Vz to 0.0
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int dimension = domain->dimension;
int m;
double vx,vy,vz,factor;
RanPark *random;
if (loop_flag == ALL) {
// create an atom map if one doesn't exist already
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_style = 1;
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// error check
if (atom->natoms > MAXSMALLINT)
error->all(FLERR,"Too big a problem to use velocity create loop all");
if (atom->tag_enable == 0)
error->all(FLERR,
"Cannot use velocity create loop all unless atoms have IDs");
if (atom->tag_consecutive() == 0)
error->all(FLERR,
"Atom IDs must be consecutive for velocity create loop all");
// loop over all atoms in system
// generate RNGs for all atoms, only assign to ones I own
// use either per-type mass or per-atom rmass
random = new RanPark(lmp,seed);
int natoms = static_cast<int> (atom->natoms);
for (i = 1; i <= natoms; i++) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
m = atom->map(i);
if (m >= 0 && m < nlocal) {
if (mask[m] & groupbit) {
if (rmass) factor = 1.0/sqrt(rmass[m]);
else factor = 1.0/sqrt(mass[type[m]]);
v[m][0] = vx * factor;
v[m][1] = vy * factor;
if (dimension == 3) v[m][2] = vz * factor;
else v[m][2] = 0.0;
}
}
}
// delete temporary atom map
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
} else if (loop_flag == LOCAL) {
random = new RanPark(lmp,seed + comm->me);
for (i = 0; i < WARMUP; i++) random->uniform();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
} else if (loop_flag == GEOM) {
random = new RanPark(lmp,1);
double **x = atom->x;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
}
// apply momentum and rotation zeroing
if (momentum_flag) zero_momentum();
if (rotation_flag) zero_rotation();
// scale temp to desired value
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if sum_flag set, add back in previous velocities
if (sum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] += vhold[i][0];
v[i][1] += vhold[i][1];
v[i][2] += vhold[i][2];
}
}
}
// free local memory
// if temperature was created, delete it
memory->destroy(vhold);
delete random;
if (tflag) delete temperature;
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
int style;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of displace_atoms with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
if (style == MOVE) {
double delx = xscale*atof(arg[2]);
double dely = yscale*atof(arg[3]);
double delz = zscale*atof(arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*atof(arg[3]);
d_hi = xscale*atof(arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*atof(arg[3]);
d_hi = yscale*atof(arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*atof(arg[3]);
d_hi = zscale*atof(arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[6]);
coord_hi = xscale*atof(arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[6]);
coord_hi = yscale*atof(arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[6]);
coord_hi = zscale*atof(arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*atof(arg[2]);
double dy = yscale*atof(arg[3]);
double dz = zscale*atof(arg[4]);
int seed = atoi(arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(FLERR,str);
}
}
void CreateAtoms::add_random()
{
double xlo,ylo,zlo,xhi,yhi,zhi,zmid;
double lamda[3],*coord;
double *boxlo,*boxhi;
// random number generator, same for all procs
RanPark *random = new RanPark(lmp,seed);
// bounding box for atom creation
// in real units, even if triclinic
// only limit bbox by region if its bboxflag is set (interior region)
if (triclinic == 0) {
xlo = domain->boxlo[0]; xhi = domain->boxhi[0];
ylo = domain->boxlo[1]; yhi = domain->boxhi[1];
zlo = domain->boxlo[2]; zhi = domain->boxhi[2];
zmid = zlo + 0.5*(zhi-zlo);
} else {
xlo = domain->boxlo_bound[0]; xhi = domain->boxhi_bound[0];
ylo = domain->boxlo_bound[1]; yhi = domain->boxhi_bound[1];
zlo = domain->boxlo_bound[2]; zhi = domain->boxhi_bound[2];
zmid = zlo + 0.5*(zhi-zlo);
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
}
if (nregion >= 0 && domain->regions[nregion]->bboxflag) {
xlo = MAX(xlo,domain->regions[nregion]->extent_xlo);
xhi = MIN(xhi,domain->regions[nregion]->extent_xhi);
ylo = MAX(ylo,domain->regions[nregion]->extent_ylo);
yhi = MIN(yhi,domain->regions[nregion]->extent_yhi);
zlo = MAX(zlo,domain->regions[nregion]->extent_zlo);
zhi = MIN(zhi,domain->regions[nregion]->extent_zhi);
}
// generate random positions for each new atom/molecule within bounding box
// iterate until atom is within region, variable, and triclinic simulation box
// if final atom position is in my subbox, create it
if (xlo > xhi || ylo > yhi || zlo > zhi)
error->all(FLERR,"No overlap of box and region for create_atoms");
int valid;
for (int i = 0; i < nrandom; i++) {
while (1) {
xone[0] = xlo + random->uniform() * (xhi-xlo);
xone[1] = ylo + random->uniform() * (yhi-ylo);
xone[2] = zlo + random->uniform() * (zhi-zlo);
if (domain->dimension == 2) xone[2] = zmid;
valid = 1;
if (nregion >= 0 &&
domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
valid = 0;
if (varflag && vartest(xone) == 0) valid = 0;
if (triclinic) {
domain->x2lamda(xone,lamda);
coord = lamda;
if (coord[0] < boxlo[0] || coord[0] >= boxhi[0] ||
coord[1] < boxlo[1] || coord[1] >= boxhi[1] ||
coord[2] < boxlo[2] || coord[2] >= boxhi[2]) valid = 0;
} else coord = xone;
if (valid) break;
}
// if triclinic, coord is now in lamda units
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
if (mode == ATOM) atom->avec->create_atom(ntype,xone);
else add_molecule(xone);
}
}
// clean-up
delete random;
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
groupbit = group->bitmask[igroup];
int style = -1;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else if (strcmp(arg[1],"rotate") == 0) style = ROTATE;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
else if (style == ROTATE) options(narg-9,&arg[9]);
// setup scaling
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector or specified variable(s)
if (style == MOVE) {
move(0,arg[2],xscale);
move(1,arg[3],yscale);
move(2,arg[4],zscale);
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*force->numeric(FLERR,arg[3]);
d_hi = xscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*force->numeric(FLERR,arg[3]);
d_hi = yscale*force->numeric(FLERR,arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*force->numeric(FLERR,arg[3]);
d_hi = zscale*force->numeric(FLERR,arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*force->numeric(FLERR,arg[6]);
coord_hi = xscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*force->numeric(FLERR,arg[6]);
coord_hi = yscale*force->numeric(FLERR,arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*force->numeric(FLERR,arg[6]);
coord_hi = zscale*force->numeric(FLERR,arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*force->numeric(FLERR,arg[2]);
double dy = yscale*force->numeric(FLERR,arg[3]);
double dz = zscale*force->numeric(FLERR,arg[4]);
int seed = force->inumeric(FLERR,arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if (style == ROTATE) {
double theta_new;
double axis[3],point[3],qrotate[4],qnew[4];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
double *quat;
int dim = domain->dimension;
point[0] = xscale*force->numeric(FLERR,arg[2]);
point[1] = yscale*force->numeric(FLERR,arg[3]);
point[2] = zscale*force->numeric(FLERR,arg[4]);
axis[0] = force->numeric(FLERR,arg[5]);
axis[1] = force->numeric(FLERR,arg[6]);
axis[2] = force->numeric(FLERR,arg[7]);
double theta = force->numeric(FLERR,arg[8]);
if (dim == 2 && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Invalid displace_atoms rotate axis for 2d");
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Zero length rotation vector with displace_atoms");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
double angle = MY_PI*theta/180.0;
double sine = sin(angle);
double cosine = cos(angle);
double ddotr;
// flags for additional orientation info stored by some atom styles
int ellipsoid_flag = atom->ellipsoid_flag;
int line_flag = atom->line_flag;
int tri_flag = atom->tri_flag;
int body_flag = atom->body_flag;
int theta_flag = 0;
int quat_flag = 0;
if (line_flag) theta_flag = 1;
if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1;
// AtomVec pointers to retrieve per-atom storage of extra quantities
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
double **x = atom->x;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
d[0] = x[i][0] - point[0];
d[1] = x[i][1] - point[1];
d[2] = x[i][2] - point[2];
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x[i][0] = point[0] + c[0] + disp[0];
x[i][1] = point[1] + c[1] + disp[1];
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
// theta for lines
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(avec_line->bonus[line[i]].theta+angle,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
// quats for ellipsoids, tris, and bodies
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
if (quat) {
qrotate[0] = cosine;
qrotate[1] = runit[0]*sine;
qrotate[2] = runit[1]*sine;
qrotate[3] = runit[2]*sine;
MathExtra::quatquat(qrotate,quat,qnew);
quat[0] = qnew[0];
quat[1] = qnew[1];
quat[2] = qnew[2];
quat[3] = qnew[3];
}
}
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Displace_atoms command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
int style;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else if (strcmp(arg[1],"rotate") == 0) style = ROTATE;
else error->all(FLERR,"Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
else if (style == ROTATE) options(narg-9,&arg[9]);
// setup scaling
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
if (style == MOVE) {
double delx = xscale*atof(arg[2]);
double dely = yscale*atof(arg[3]);
double delz = zscale*atof(arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*atof(arg[3]);
d_hi = xscale*atof(arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*atof(arg[3]);
d_hi = yscale*atof(arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*atof(arg[3]);
d_hi = zscale*atof(arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[6]);
coord_hi = xscale*atof(arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[6]);
coord_hi = yscale*atof(arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[6]);
coord_hi = zscale*atof(arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*atof(arg[2]);
double dy = yscale*atof(arg[3]);
double dz = zscale*atof(arg[4]);
int seed = atoi(arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if (style == ROTATE) {
double axis[3],point[3];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
int dim = domain->dimension;
point[0] = xscale*atof(arg[2]);
point[1] = yscale*atof(arg[3]);
point[2] = zscale*atof(arg[4]);
axis[0] = atof(arg[5]);
axis[1] = atof(arg[6]);
axis[2] = atof(arg[7]);
double theta = atof(arg[8]);
if (dim == 2 and (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Invalid displace_atoms rotate axis for 2d");
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Zero length rotation vector with displace_atoms");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
double sine = sin(MY_PI*theta/180.0);
double cosine = cos(MY_PI*theta/180.0);
double ddotr;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
d[0] = x[i][0] - point[0];
d[1] = x[i][1] - point[1];
d[2] = x[i][2] - point[2];
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = ddotr*runit[0];
c[1] = ddotr*runit[1];
c[2] = ddotr*runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x[i][0] = point[0] + c[0] + disp[0];
x[i][1] = point[1] + c[1] + disp[1];
if (dim == 3) x[i][2] = point[2] + c[2] + disp[2];
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
tagint *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
