Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/fix_deposit.cpp
209f169cbc4elammm-master-deprecated

Last Change
Raw File

fix_deposit.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 "stdlib.h"
#include "string.h"
#include "fix_deposit.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "random_park.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all("Illegal fix deposit command");
// required args
ninsert = atoi(arg[3]);
ntype = atoi(arg[4]);
nfreq = atoi(arg[5]);
seed = atoi(arg[6]);
// set defaults
iregion = -1;
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;
// read options from end of input line
options(narg-7,&arg[7]);
// error check on region
if (iregion == -1) error->all("Must specify a region in fix deposit");
if (domain->regions[iregion]->interior == 0)
error->all("Must use region with side = in with fix deposit");
// store extent of region
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;
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix deposit 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;
// apply scaling to all input parameters with dist/vel units
if (force->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;
// store extent of region
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;
// 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;
}
/* ---------------------------------------------------------------------- */
int FixDeposit::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixDeposit::pre_exchange()
{
int flag,flagall;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
// 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;
// attempt an insertion until successful
int success = 0;
int attempt = 0;
while (attempt < maxattempt) {
attempt++;
// choose random position for new atom within region
xtmp = xlo + random->uniform() * (xhi-xlo);
ytmp = ylo + random->uniform() * (yhi-ylo);
ztmp = zlo + random->uniform() * (zhi-zlo);
while (domain->regions[iregion]->match(xtmp,ytmp,ztmp) == 0) {
xtmp = xlo + random->uniform() * (xhi-xlo);
ytmp = ylo + random->uniform() * (yhi-ylo);
ztmp = zlo + random->uniform() * (zhi-zlo);
}
// adjust vertical coord by offset
if (force->dimension == 2) ytmp += offset;
else ztmp += 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
if (globalflag || localflag) {
int dim;
double max,maxall,delx,dely,delz,rsq;
if (force->dimension == 2) {
dim = 1;
max = domain->boxylo;
} else {
dim = 2;
max = domain->boxzlo;
}
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (localflag) {
delx = xtmp - x[i][0];
dely = ytmp - x[i][1];
delz = 0.0;
domain->minimum_image(&delx,&dely,&delz);
if (force->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 (force->dimension == 2)
ytmp = maxall + lo + random->uniform()*(hi-lo);
else
ztmp = maxall + lo + random->uniform()*(hi-lo);
}
// now have final xtmp,ytmp,ztmp
// if distance to any atom is less than near, try again
double **x = atom->x;
int nlocal = atom->nlocal;
flag = 0;
for (int i = 0; i < nlocal; i++) {
delx = xtmp - x[i][0];
dely = ytmp - x[i][1];
delz = ztmp - 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;
// insertion will proceed
// choose random velocity for new atom
double vxtmp = vxlo + random->uniform() * (vxhi-vxlo);
double vytmp = vylo + random->uniform() * (vyhi-vylo);
double vztmp = vzlo + random->uniform() * (vzhi-vzlo);
// check if new atom is in my sub-box or above it if I'm highest proc
// if so, add to my list via create_atom()
// initialize info about the atoms
// set group mask to "all" plus fix group
flag = 0;
if (xtmp >= domain->subxlo && xtmp < domain->subxhi &&
ytmp >= domain->subylo && ytmp < domain->subyhi &&
ztmp >= domain->subzlo && ztmp < domain->subzhi) flag = 1;
else if (force->dimension == 3 && ztmp >= domain->boxzhi &&
comm->myloc[2] == comm->procgrid[2]-1 &&
xtmp >= domain->subxlo && xtmp < domain->subxhi &&
ytmp >= domain->subylo && ytmp < domain->subyhi) flag = 1;
else if (force->dimension == 2 && ytmp >= domain->boxyhi &&
comm->myloc[1] == comm->procgrid[1]-1 &&
xtmp >= domain->subxlo && xtmp < domain->subxhi) flag = 1;
if (flag) {
atom->avec->create_atom(ntype,xtmp,ytmp,ztmp,0);
int m = atom->nlocal - 1;
atom->type[m] = ntype;
atom->mask[m] = 1 | groupbit;
atom->v[m][0] = vxtmp;
atom->v[m][1] = vytmp;
atom->v[m][2] = vztmp;
}
MPI_Allreduce(&flag,&success,1,MPI_INT,MPI_MAX,world);
break;
}
// warn if not successful b/c too many attempts or no proc owned particle
if (comm->me == 0)
if (success == 0)
error->warning("Particle deposition was unsuccessful");
// set tag # of new particle beyond all previous atoms
// reset global natoms
// if global map exists, reset it
if (success && atom->tag_enable) {
atom->tag_extend();
atom->natoms += 1;
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
}
// next timestep to insert
if (ninserted < ninsert) next_reneighbor += nfreq;
else next_reneighbor = 0;
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixDeposit::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal fix indent command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all("Illegal fix deposit command");
for (iregion = 0; iregion < domain->nregion; iregion++)
if (strcmp(arg[iarg+1],domain->regions[iregion]->id) == 0) break;
if (iregion == domain->nregion)
error->all("Fix deposit region ID does not exist");
iarg += 2;
} else if (strcmp(arg[iarg],"global") == 0) {
if (iarg+3 > narg) error->all("Illegal fix deposit command");
globalflag = 1;
localflag = 0;
lo = atof(arg[iarg+1]);
hi = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"local") == 0) {
if (iarg+4 > narg) error->all("Illegal fix deposit command");
localflag = 1;
globalflag = 0;
lo = atof(arg[iarg+1]);
hi = atof(arg[iarg+2]);
deltasq = atof(arg[iarg+3])*atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"near") == 0) {
if (iarg+2 > narg) error->all("Illegal fix deposit command");
nearsq = atof(arg[iarg+1])*atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"attempt") == 0) {
if (iarg+2 > narg) error->all("Illegal fix deposit command");
maxattempt = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"rate") == 0) {
if (iarg+2 > narg) error->all("Illegal fix deposit command");
rateflag = 1;
rate = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
if (iarg+3 > narg) error->all("Illegal fix deposit command");
vxlo = atof(arg[iarg+1]);
vxhi = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"vy") == 0) {
if (iarg+3 > narg) error->all("Illegal fix deposit command");
vylo = atof(arg[iarg+1]);
vyhi = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"vz") == 0) {
if (iarg+3 > narg) error->all("Illegal fix deposit command");
vzlo = atof(arg[iarg+1]);
vzhi = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("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("Illegal fix deposit command");
iarg += 2;
} else error->all("Illegal fix deposit command");
}
}
c4science · Help