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fix_deposit.cpp
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Tue, Jul 2, 08:02

fix_deposit.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_deposit.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "random_park.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{ATOM,MOLECULE};
/* ---------------------------------------------------------------------- */
FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix deposit command");
restart_global = 1;
time_depend = 1;
// required args
ninsert = force->inumeric(FLERR,arg[3]);
ntype = force->inumeric(FLERR,arg[4]);
nfreq = force->inumeric(FLERR,arg[5]);
seed = force->inumeric(FLERR,arg[6]);
if (seed <= 0) error->all(FLERR,"Illegal fix deposit command");
// read options from end of input line
options(narg-7,&arg[7]);
// error check on type
if (mode == ATOM && (ntype <= 0 || ntype > atom->ntypes))
error->all(FLERR,"Invalid atom type in fix deposit command");
// error checks on region and its extent being inside simulation box
if (iregion == -1) error->all(FLERR,"Must specify a region in fix deposit");
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix deposit region does not support a bounding box");
if (domain->regions[iregion]->dynamic_check())
error->all(FLERR,"Fix deposit region cannot be dynamic");
xlo = domain->regions[iregion]->extent_xlo;
xhi = domain->regions[iregion]->extent_xhi;
ylo = domain->regions[iregion]->extent_ylo;
yhi = domain->regions[iregion]->extent_yhi;
zlo = domain->regions[iregion]->extent_zlo;
zhi = domain->regions[iregion]->extent_zhi;
if (domain->triclinic == 0) {
if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
error->all(FLERR,"Deposition region extends outside simulation box");
} else {
if (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])
error->all(FLERR,"Deposition region extends outside simulation box");
}
// error check and further setup for mode = MOLECULE
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix_deposit unless atoms have IDs");
if (mode == MOLECULE) {
if (onemol->xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Fix deposit molecule must have atom types");
if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
// fix deposit uses geoemetric center of molecule for insertion
onemol->compute_center();
}
if (rigidflag && mode == ATOM)
error->all(FLERR,"Cannot use fix deposit rigid and not molecule");
if (shakeflag && mode == ATOM)
error->all(FLERR,"Cannot use fix deposit shake and not molecule");
if (rigidflag && shakeflag)
error->all(FLERR,"Cannot use fix deposit rigid and shake");
// setup of coords and imageflags array
if (mode == ATOM) natom = 1;
else natom = onemol->natoms;
memory->create(coords,natom,3,"deposit:coords");
memory->create(imageflags,natom,"deposit:imageflags");
// 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;
// apply scaling to all input parameters with dist/vel units
if (domain->dimension == 2) {
lo *= yscale;
hi *= yscale;
rate *= yscale;
} else {
lo *= zscale;
hi *= zscale;
rate *= zscale;
}
deltasq *= xscale*xscale;
nearsq *= xscale*xscale;
vxlo *= xscale;
vxhi *= xscale;
vylo *= yscale;
vyhi *= yscale;
vzlo *= zscale;
vzhi *= zscale;
tx *= xscale;
ty *= yscale;
tz *= zscale;
// find current max atom and molecule IDs if necessary
if (idnext) find_maxid();
// random number generator, same for all procs
random = new RanPark(lmp,seed);
// set up reneighboring
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
nfirst = next_reneighbor;
ninserted = 0;
}
/* ---------------------------------------------------------------------- */
FixDeposit::~FixDeposit()
{
delete random;
delete [] idrigid;
delete [] idshake;
delete [] idregion;
memory->destroy(coords);
memory->destroy(imageflags);
}
/* ---------------------------------------------------------------------- */
int FixDeposit::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixDeposit::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix deposit does not exist");
// if rigidflag defined, check for rigid/small fix
// its molecule template must be same as this one
fixrigid = NULL;
if (rigidflag) {
int ifix = modify->find_fix(idrigid);
if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
fixrigid = modify->fix[ifix];
int tmp;
if (onemol != (Molecule *) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix deposit and fix rigid/small not using same molecule ID");
}
// if shakeflag defined, check for SHAKE fix
// its molecule template must be same as this one
fixshake = NULL;
if (shakeflag) {
int ifix = modify->find_fix(idshake);
if (ifix < 0) error->all(FLERR,"Fix deposit shake fix does not exist");
fixshake = modify->fix[ifix];
int tmp;
if (onemol != (Molecule *) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix deposit and fix shake not using same molecule ID");
}
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixDeposit::pre_exchange()
{
int i,j,m,n,nlocalprev,flag,flagall;
double coord[3],lamda[3],delx,dely,delz,rsq;
double alpha,beta,gamma;
double r[3],vnew[3],rotmat[3][3],quat[4];
double *newcoord;
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
// compute current offset = bottom of insertion volume
double offset = 0.0;
if (rateflag) offset = (update->ntimestep - nfirst) * update->dt * rate;
double *sublo,*subhi;
if (domain->triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
// find current max atom and molecule IDs if necessary
if (!idnext) find_maxid();
// attempt an insertion until successful
int dimension = domain->dimension;
int nfix = modify->nfix;
Fix **fix = modify->fix;
int success = 0;
int attempt = 0;
while (attempt < maxattempt) {
attempt++;
// choose random position for new particle within region
coord[0] = xlo + random->uniform() * (xhi-xlo);
coord[1] = ylo + random->uniform() * (yhi-ylo);
coord[2] = zlo + random->uniform() * (zhi-zlo);
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
coord[0] = xlo + random->uniform() * (xhi-xlo);
coord[1] = ylo + random->uniform() * (yhi-ylo);
coord[2] = zlo + random->uniform() * (zhi-zlo);
}
// adjust vertical coord by offset
if (dimension == 2) coord[1] += offset;
else coord[2] += offset;
// if global, reset vertical coord to be lo-hi above highest atom
// if local, reset vertical coord to be lo-hi above highest "nearby" atom
// local computation computes lateral distance between 2 particles w/ PBC
// when done, have final coord of atom or center pt of molecule
if (globalflag || localflag) {
int dim;
double max,maxall,delx,dely,delz,rsq;
if (dimension == 2) {
dim = 1;
max = domain->boxlo[1];
} else {
dim = 2;
max = domain->boxlo[2];
}
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (localflag) {
delx = coord[0] - x[i][0];
dely = coord[1] - x[i][1];
delz = 0.0;
domain->minimum_image(delx,dely,delz);
if (dimension == 2) rsq = delx*delx;
else rsq = delx*delx + dely*dely;
if (rsq > deltasq) continue;
}
if (x[i][dim] > max) max = x[i][dim];
}
MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
if (dimension == 2)
coord[1] = maxall + lo + random->uniform()*(hi-lo);
else
coord[2] = maxall + lo + random->uniform()*(hi-lo);
}
// coords = coords of all atoms
// for molecule, perform random rotation around center pt
// apply PBC so final coords are inside box
// also store image flag modified due to PBC
if (mode == ATOM) {
coords[0][0] = coord[0];
coords[0][1] = coord[1];
coords[0][2] = coord[2];
} else {
if (dimension == 3) {
r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5;
r[2] = random->uniform() - 0.5;
} else {
r[0] = r[1] = 0.0;
r[2] = 1.0;
}
double theta = random->uniform() * MY_2PI;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
for (i = 0; i < natom; i++) {
MathExtra::matvec(rotmat,onemol->dx[i],coords[i]);
coords[i][0] += coord[0];
coords[i][1] += coord[1];
coords[i][2] += coord[2];
imageflags[i] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
domain->remap(coords[i],imageflags[i]);
}
}
// if distance to any inserted atom is less than near, try again
// use minimum_image() to account for PBC
double **x = atom->x;
int nlocal = atom->nlocal;
flag = 0;
for (m = 0; m < natom; m++) {
for (i = 0; i < nlocal; i++) {
delx = coords[m][0] - x[i][0];
dely = coords[m][1] - x[i][1];
delz = coords[m][2] - x[i][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < nearsq) flag = 1;
}
}
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall) continue;
// proceed with insertion
nlocalprev = atom->nlocal;
// choose random velocity for new particle
// used for every atom in molecule
vnew[0] = vxlo + random->uniform() * (vxhi-vxlo);
vnew[1] = vylo + random->uniform() * (vyhi-vylo);
vnew[2] = vzlo + random->uniform() * (vzhi-vzlo);
// if target specified, change velocity vector accordingly
if (targetflag) {
double vel = sqrt(vnew[0]*vnew[0] + vnew[1]*vnew[1] + vnew[2]*vnew[2]);
delx = tx - coord[0];
dely = ty - coord[1];
delz = tz - coord[2];
double rsq = delx*delx + dely*dely + delz*delz;
if (rsq > 0.0) {
double rinv = sqrt(1.0/rsq);
vnew[0] = delx*rinv*vel;
vnew[1] = dely*rinv*vel;
vnew[2] = delz*rinv*vel;
}
}
// check if new atoms are in my sub-box or above it if I am highest proc
// if so, add atom to my list via create_atom()
// initialize additional info about the atoms
// set group mask to "all" plus fix group
for (m = 0; m < natom; m++) {
if (domain->triclinic) {
domain->x2lamda(coords[m],lamda);
newcoord = lamda;
} else newcoord = coords[m];
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
comm->myloc[2] == comm->procgrid[2]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
else if (dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
comm->myloc[1] == comm->procgrid[1]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
if (flag) {
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]);
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE && atom->molecule_flag)
atom->molecule[n] = maxmol_all+1;
atom->mask[n] = 1 | groupbit;
atom->image[n] = imageflags[m];
atom->v[n][0] = vnew[0];
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE) atom->add_molecule_atom(onemol,m,n,maxtag_all);
for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(n);
}
// FixRigidSmall::set_molecule stores rigid body attributes
// coord is new position of geometric center of mol, not COM
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
}
// old code: unsuccessful if no proc performed insertion of an atom
// don't think that check is necessary
// if get this far, should always be succesful
// would be hard to undo partial insertion for a molecule
// better to check how many atoms could be inserted (w/out inserting)
// then sum to insure all are inserted, before doing actual insertion
// MPI_Allreduce(&flag,&success,1,MPI_INT,MPI_MAX,world);
success = 1;
break;
}
// warn if not successful b/c too many attempts
if (!success && comm->me == 0)
error->warning(FLERR,"Particle deposition was unsuccessful",0);
// reset global natoms,nbonds,etc
// increment maxtag_all and maxmol_all if necessary
// if global map exists, reset it now instead of waiting for comm
// since adding atoms messes up ghosts
if (success) {
atom->natoms += natom;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol->nbonds;
atom->nangles += onemol->nangles;
atom->ndihedrals += onemol->ndihedrals;
atom->nimpropers += onemol->nimpropers;
}
maxtag_all += natom;
if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
}
// next timestep to insert
// next_reneighbor = 0 if done
if (success) ninserted++;
if (ninserted < ninsert) next_reneighbor += nfreq;
else next_reneighbor = 0;
}
/* ----------------------------------------------------------------------
maxtag_all = current max atom ID for all atoms
maxmol_all = current max molecule ID for all atoms
------------------------------------------------------------------------- */
void FixDeposit::find_maxid()
{
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (mode == MOLECULE && molecule) {
max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixDeposit::options(int narg, char **arg)
{
// defaults
iregion = -1;
idregion = NULL;
mode = ATOM;
rigidflag = 0;
idrigid = NULL;
shakeflag = 0;
idshake = NULL;
idnext = 0;
globalflag = localflag = 0;
lo = hi = deltasq = 0.0;
nearsq = 0.0;
maxattempt = 10;
rateflag = 0;
vxlo = vxhi = vylo = vyhi = vzlo = vzhi = 0.0;
scaleflag = 1;
targetflag = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix deposit does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix deposit does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix deposit has multiple molecules");
mode = MOLECULE;
onemol = atom->molecules[imol];
iarg += 2;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int n = strlen(arg[iarg+1]) + 1;
delete [] idrigid;
idrigid = new char[n];
strcpy(idrigid,arg[iarg+1]);
rigidflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"shake") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int n = strlen(arg[iarg+1]) + 1;
delete [] idshake;
idshake = new char[n];
strcpy(idshake,arg[iarg+1]);
shakeflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"id") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
if (strcmp(arg[iarg+1],"max") == 0) idnext = 0;
else if (strcmp(arg[iarg+1],"next") == 0) idnext = 1;
else error->all(FLERR,"Illegal fix deposit command");
iarg += 2;
} else if (strcmp(arg[iarg],"global") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
globalflag = 1;
localflag = 0;
lo = force->numeric(FLERR,arg[iarg+1]);
hi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"local") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
localflag = 1;
globalflag = 0;
lo = force->numeric(FLERR,arg[iarg+1]);
hi = force->numeric(FLERR,arg[iarg+2]);
deltasq = force->numeric(FLERR,arg[iarg+3]) *
force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"near") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
nearsq = force->numeric(FLERR,arg[iarg+1]) *
force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"attempt") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
maxattempt = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"rate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
rateflag = 1;
rate = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vxlo = force->numeric(FLERR,arg[iarg+1]);
vxhi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"vy") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vylo = force->numeric(FLERR,arg[iarg+1]);
vyhi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"vz") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vzlo = force->numeric(FLERR,arg[iarg+1]);
vzhi = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix deposit command");
iarg += 2;
} else if (strcmp(arg[iarg],"target") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
tx = force->numeric(FLERR,arg[iarg+1]);
ty = force->numeric(FLERR,arg[iarg+2]);
tz = force->numeric(FLERR,arg[iarg+3]);
targetflag = 1;
iarg += 4;
} else error->all(FLERR,"Illegal fix deposit command");
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixDeposit::write_restart(FILE *fp)
{
int n = 0;
double list[4];
list[n++] = random->state();
list[n++] = ninserted;
list[n++] = nfirst;
list[n++] = next_reneighbor;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixDeposit::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
seed = static_cast<int> (list[n++]);
ninserted = static_cast<int> (list[n++]);
nfirst = static_cast<int> (list[n++]);
next_reneighbor = static_cast<int> (list[n++]);
random->reset(seed);
}

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