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fix_pour.cpp
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Mon, Sep 30, 06:24

fix_pour.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_pour.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "modify.h"
#include "fix_gravity.h"
#include "domain.h"
#include "region.h"
#include "region_block.h"
#include "region_cylinder.h"
#include "random_park.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EPSILON 0.001
/* ---------------------------------------------------------------------- */
FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix pour command");
time_depend = 1;
if (!atom->radius_flag || !atom->rmass_flag)
error->all(FLERR,"Fix pour requires atom attributes radius, rmass");
// required args
ninsert = atoi(arg[3]);
ntype = atoi(arg[4]);
seed = atoi(arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal fix pour command");
PI = 4.0*atan(1.0);
// option defaults
int iregion = -1;
radius_lo = radius_hi = 0.5;
density_lo = density_hi = 1.0;
volfrac = 0.25;
maxattempt = 50;
rate = 0.0;
vxlo = vxhi = vylo = vyhi = vy = vz = 0.0;
// optional args
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1) error->all(FLERR,"Fix pour region ID does not exist");
iarg += 2;
} else if (strcmp(arg[iarg],"diam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
radius_lo = 0.5 * atof(arg[iarg+1]);
radius_hi = 0.5 * atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"dens") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
density_lo = atof(arg[iarg+1]);
density_hi = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"vol") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
volfrac = atof(arg[iarg+1]);
maxattempt = atoi(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"rate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
rate = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (domain->dimension == 3) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix pour command");
vxlo = atof(arg[iarg+1]);
vxhi = atof(arg[iarg+2]);
vylo = atof(arg[iarg+3]);
vyhi = atof(arg[iarg+4]);
vz = atof(arg[iarg+5]);
iarg += 6;
} else {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix pour command");
vxlo = atof(arg[iarg+1]);
vxhi = atof(arg[iarg+2]);
vy = atof(arg[iarg+3]);
vz = 0.0;
iarg += 4;
}
} else error->all(FLERR,"Illegal fix pour command");
}
// error checks on region and its extent being inside simulation box
if (iregion == -1) error->all(FLERR,"Must specify a region in fix pour");
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix pour region does not support a bounding box");
if (domain->regions[iregion]->dynamic_check())
error->all(FLERR,"Fix pour region cannot be dynamic");
if (strcmp(domain->regions[iregion]->style,"block") == 0) {
region_style = 1;
xlo = ((RegBlock *) domain->regions[iregion])->xlo;
xhi = ((RegBlock *) domain->regions[iregion])->xhi;
ylo = ((RegBlock *) domain->regions[iregion])->ylo;
yhi = ((RegBlock *) domain->regions[iregion])->yhi;
zlo = ((RegBlock *) domain->regions[iregion])->zlo;
zhi = ((RegBlock *) domain->regions[iregion])->zhi;
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,"Insertion region extends outside simulation box");
} else if (strcmp(domain->regions[iregion]->style,"cylinder") == 0) {
region_style = 2;
char axis = ((RegCylinder *) domain->regions[iregion])->axis;
xc = ((RegCylinder *) domain->regions[iregion])->c1;
yc = ((RegCylinder *) domain->regions[iregion])->c2;
rc = ((RegCylinder *) domain->regions[iregion])->radius;
zlo = ((RegCylinder *) domain->regions[iregion])->lo;
zhi = ((RegCylinder *) domain->regions[iregion])->hi;
if (axis != 'z')
error->all(FLERR,"Must use a z-axis cylinder with fix pour");
if (xc-rc < domain->boxlo[0] || xc+rc > domain->boxhi[0] ||
yc-rc < domain->boxlo[1] || yc+rc > domain->boxhi[1] ||
zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
error->all(FLERR,"Insertion region extends outside simulation box");
} else error->all(FLERR,"Must use a block or cylinder region with fix pour");
if (region_style == 2 && domain->dimension == 2)
error->all(FLERR,"Must use a block region with fix pour for 2d simulations");
// random number generator, same for all procs
random = new RanPark(lmp,seed);
// allgather arrays
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
recvcounts = new int[nprocs];
displs = new int[nprocs];
// grav = gravity in distance/time^2 units
// assume grav = -magnitude at this point, enforce in init()
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
if (ifix == modify->nfix)
error->all(FLERR,"No fix gravity defined for fix pour");
grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v;
// nfreq = timesteps between insertions
// should be time for a particle to fall from top of insertion region
// to bottom, taking into account that the region may be moving
// set these 2 eqs equal to each other, solve for smallest positive t
// x = zhi + vz*t + 1/2 grav t^2
// x = zlo + rate*t
// gives t = [-(vz-rate) - sqrt((vz-rate)^2 - 2*grav*(zhi-zlo))] / grav
// where zhi-zlo > 0, grav < 0, and vz & rate can be either > 0 or < 0
double v_relative,delta;
if (domain->dimension == 3) {
v_relative = vz - rate;
delta = zhi - zlo;
} else {
v_relative = vy - rate;
delta = yhi - ylo;
}
double t =
(-v_relative - sqrt(v_relative*v_relative - 2.0*grav*delta)) / grav;
nfreq = static_cast<int> (t/update->dt + 0.5);
// 1st insertion on next timestep
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
nfirst = next_reneighbor;
ninserted = 0;
// nper = # to insert each time
// depends on specified volume fraction
// volume = volume of insertion region
// volume_one = volume of inserted particle (with max possible radius)
// in 3d, insure dy >= 1, for quasi-2d simulations
double volume,volume_one;
if (domain->dimension == 3) {
if (region_style == 1) {
double dy = yhi - ylo;
if (dy < 1.0) dy = 1.0;
volume = (xhi-xlo) * dy * (zhi-zlo);
} else volume = PI*rc*rc * (zhi-zlo);
volume_one = 4.0/3.0 * PI * radius_hi*radius_hi*radius_hi;
} else {
volume = (xhi-xlo) * (yhi-ylo);
volume_one = PI * radius_hi*radius_hi;
}
nper = static_cast<int> (volfrac*volume/volume_one);
int nfinal = update->ntimestep + 1 + (ninsert-1)/nper * nfreq;
// print stats
if (me == 0) {
if (screen)
fprintf(screen,
"Particle insertion: %d every %d steps, %d by step %d\n",
nper,nfreq,ninsert,nfinal);
if (logfile)
fprintf(logfile,
"Particle insertion: %d every %d steps, %d by step %d\n",
nper,nfreq,ninsert,nfinal);
}
}
/* ---------------------------------------------------------------------- */
FixPour::~FixPour()
{
delete random;
delete [] recvcounts;
delete [] displs;
}
/* ---------------------------------------------------------------------- */
int FixPour::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPour::init()
{
if (domain->triclinic) error->all(FLERR,"Cannot use fix pour with triclinic box");
// insure gravity fix exists
// for 3d must point in -z, for 2d must point in -y
// else insertion cannot work
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
if (ifix == modify->nfix)
error->all(FLERR,"No fix gravity defined for fix pour");
double xgrav = ((FixGravity *) modify->fix[ifix])->xgrav;
double ygrav = ((FixGravity *) modify->fix[ifix])->ygrav;
double zgrav = ((FixGravity *) modify->fix[ifix])->zgrav;
if (domain->dimension == 3) {
if (fabs(xgrav) > EPSILON || fabs(ygrav) > EPSILON ||
fabs(zgrav+1.0) > EPSILON)
error->all(FLERR,"Gravity must point in -z to use with fix pour in 3d");
} else {
if (fabs(xgrav) > EPSILON || fabs(ygrav+1.0) > EPSILON ||
fabs(zgrav) > EPSILON)
error->all(FLERR,"Gravity must point in -y to use with fix pour in 2d");
}
double gnew = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v;
if (gnew != grav)
error->all(FLERR,"Gravity changed since fix pour was created");
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixPour::pre_exchange()
{
int i;
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
// nnew = # to insert this timestep
int nnew = nper;
if (ninserted + nnew > ninsert) nnew = ninsert - ninserted;
// lo/hi current = z (or y) bounds of insertion region this timestep
if (domain->dimension == 3) {
lo_current = zlo + (update->ntimestep - nfirst) * update->dt * rate;
hi_current = zhi + (update->ntimestep - nfirst) * update->dt * rate;
} else {
lo_current = ylo + (update->ntimestep - nfirst) * update->dt * rate;
hi_current = yhi + (update->ntimestep - nfirst) * update->dt * rate;
}
// ncount = # of my atoms that overlap the insertion region
// nprevious = total of ncount across all procs
int ncount = 0;
for (i = 0; i < atom->nlocal; i++)
if (overlap(i)) ncount++;
int nprevious;
MPI_Allreduce(&ncount,&nprevious,1,MPI_INT,MPI_SUM,world);
// xmine is for my atoms
// xnear is for atoms from all procs + atoms to be inserted
double **xmine,**xnear;
memory->create(xmine,ncount,4,"fix_pour:xmine");
memory->create(xnear,nprevious+nnew,4,"fix_pour:xnear");
int nnear = nprevious;
// setup for allgatherv
int n = 4*ncount;
MPI_Allgather(&n,1,MPI_INT,recvcounts,1,MPI_INT,world);
displs[0] = 0;
for (int iproc = 1; iproc < nprocs; iproc++)
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
// load up xmine array
double **x = atom->x;
double *radius = atom->radius;
ncount = 0;
for (i = 0; i < atom->nlocal; i++)
if (overlap(i)) {
xmine[ncount][0] = x[i][0];
xmine[ncount][1] = x[i][1];
xmine[ncount][2] = x[i][2];
xmine[ncount][3] = radius[i];
ncount++;
}
// perform allgatherv to acquire list of nearby particles on all procs
double *ptr = NULL;
if (ncount) ptr = xmine[0];
MPI_Allgatherv(ptr,4*ncount,MPI_DOUBLE,
xnear[0],recvcounts,displs,MPI_DOUBLE,world);
// insert new atoms into xnear list, one by one
// check against all nearby atoms and previously inserted ones
// if there is an overlap then try again at same z (3d) or y (2d) coord
// else insert by adding to xnear list
// max = maximum # of insertion attempts for all particles
// h = height, biased to give uniform distribution in time of insertion
int success;
double coord[3],radtmp,delx,dely,delz,rsq,radsum,rn,h;
int attempt = 0;
int max = nnew * maxattempt;
int ntotal = nprevious+nnew;
while (nnear < ntotal) {
rn = random->uniform();
h = hi_current - rn*rn * (hi_current-lo_current);
radtmp = radius_lo + random->uniform() * (radius_hi-radius_lo);
success = 0;
while (attempt < max) {
attempt++;
xyz_random(h,coord);
for (i = 0; i < nnear; i++) {
delx = coord[0] - xnear[i][0];
dely = coord[1] - xnear[i][1];
delz = coord[2] - xnear[i][2];
rsq = delx*delx + dely*dely + delz*delz;
radsum = radtmp + xnear[i][3];
if (rsq <= radsum*radsum) break;
}
if (i == nnear) {
success = 1;
break;
}
}
if (success) {
xnear[nnear][0] = coord[0];
xnear[nnear][1] = coord[1];
xnear[nnear][2] = coord[2];
xnear[nnear][3] = radtmp;
nnear++;
} else break;
}
// warn if not all insertions were performed
ninserted += nnear-nprevious;
if (nnear - nprevious < nnew && me == 0)
error->warning(FLERR,"Less insertions than requested",0);
// 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 atom
// type, diameter, density set from fix parameters
// group mask set to "all" plus fix group
// z velocity set to what velocity would be if particle
// had fallen from top of insertion region
// this gives continuous stream of atoms
// solution for v from these 2 eqs, after eliminate t:
// v = vz + grav*t
// coord[2] = hi_current + vz*t + 1/2 grav t^2
// set npartner for new atom to 0 (assume not touching any others)
AtomVec *avec = atom->avec;
int j,m,flag;
double denstmp,vxtmp,vytmp,vztmp;
double *sublo = domain->sublo;
double *subhi = domain->subhi;
int nfix = modify->nfix;
Fix **fix = modify->fix;
for (i = nprevious; i < nnear; i++) {
coord[0] = xnear[i][0];
coord[1] = xnear[i][1];
coord[2] = xnear[i][2];
radtmp = xnear[i][3];
denstmp = density_lo + random->uniform() * (density_hi-density_lo);
if (domain->dimension == 3) {
vxtmp = vxlo + random->uniform() * (vxhi-vxlo);
vytmp = vylo + random->uniform() * (vyhi-vylo);
vztmp = -sqrt(vz*vz + 2.0*grav*(coord[2]-hi_current));
} else {
vxtmp = vxlo + random->uniform() * (vxhi-vxlo);
vytmp = -sqrt(vy*vy + 2.0*grav*(coord[1]-hi_current));
vztmp = 0.0;
}
flag = 0;
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]) flag = 1;
else if (domain->dimension == 3 && coord[2] >= domain->boxhi[2] &&
comm->myloc[2] == comm->procgrid[2]-1 &&
coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1]) flag = 1;
else if (domain->dimension == 2 && coord[1] >= domain->boxhi[1] &&
comm->myloc[1] == comm->procgrid[1]-1 &&
coord[0] >= sublo[0] && coord[0] < subhi[0]) flag = 1;
if (flag) {
avec->create_atom(ntype,coord);
m = atom->nlocal - 1;
atom->type[m] = ntype;
atom->radius[m] = radtmp;
atom->rmass[m] = 4.0*PI/3.0 * radtmp*radtmp*radtmp * denstmp;
atom->mask[m] = 1 | groupbit;
atom->v[m][0] = vxtmp;
atom->v[m][1] = vytmp;
atom->v[m][2] = vztmp;
for (j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(m);
}
}
// reset global natoms
// set tag # of new particles beyond all previous atoms
// if global map exists, reset it now instead of waiting for comm
// since deleting atoms messes up ghosts
if (nnear - nprevious > 0) {
atom->natoms += nnear - nprevious;
if (atom->tag_enable) {
atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
}
}
// free local memory
memory->destroy(xmine);
memory->destroy(xnear);
// next timestep to insert
if (ninserted < ninsert) next_reneighbor += nfreq;
else next_reneighbor = 0;
}
/* ----------------------------------------------------------------------
check if particle i could overlap with a particle inserted into region
return 1 if yes, 0 if no
use maximum diameter for inserted particle
------------------------------------------------------------------------- */
int FixPour::overlap(int i)
{
double delta = radius_hi + atom->radius[i];
double **x = atom->x;
if (domain->dimension == 3) {
if (region_style == 1) {
if (x[i][0] < xlo-delta || x[i][0] > xhi+delta ||
x[i][1] < ylo-delta || x[i][1] > yhi+delta ||
x[i][2] < lo_current-delta || x[i][2] > hi_current+delta) return 0;
} else {
if (x[i][2] < lo_current-delta || x[i][2] > hi_current+delta) return 0;
double delx = x[i][0] - xc;
double dely = x[i][1] - yc;
double rsq = delx*delx + dely*dely;
double r = rc + delta;
if (rsq > r*r) return 0;
}
} else {
if (x[i][0] < xlo-delta || x[i][0] > xhi+delta ||
x[i][1] < lo_current-delta || x[i][1] > hi_current+delta) return 0;
}
return 1;
}
/* ---------------------------------------------------------------------- */
void FixPour::xyz_random(double h, double *coord)
{
if (domain->dimension == 3) {
if (region_style == 1) {
coord[0] = xlo + random->uniform() * (xhi-xlo);
coord[1] = ylo + random->uniform() * (yhi-ylo);
coord[2] = h;
} else {
double r1,r2;
while (1) {
r1 = random->uniform() - 0.5;
r2 = random->uniform() - 0.5;
if (r1*r1 + r2*r2 < 0.25) break;
}
coord[0] = xc + 2.0*r1*rc;
coord[1] = yc + 2.0*r2*rc;
coord[2] = h;
}
} else {
coord[0] = xlo + random->uniform() * (xhi-xlo);
coord[1] = h;
coord[2] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void FixPour::reset_dt()
{
error->all(FLERR,"Cannot change timestep with fix pour");
}

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