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lammps/src/GRANULAR/fix_pour.cpp
jrgissing 73186e4d26 correction to molecule-ID-increment logic
2020-03-08 16:06:49 -06:00

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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 "fix_pour.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "molecule.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 "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{ATOM,MOLECULE};
enum{ONE,RANGE,POLY};
#define EPSILON 0.001
#define SMALL 1.0e-10
/* ---------------------------------------------------------------------- */
FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), radius_poly(NULL), frac_poly(NULL),
idrigid(NULL), idshake(NULL), onemols(NULL), molfrac(NULL), coords(NULL),
imageflags(NULL), fixrigid(NULL), fixshake(NULL), recvcounts(NULL),
displs(NULL), random(NULL), random2(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal fix pour command");
if (lmp->kokkos)
error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package");
time_depend = 1;
if (!atom->radius_flag || !atom->rmass_flag)
error->all(FLERR,"Fix pour requires atom attributes radius, rmass");
// required args
ninsert = force->inumeric(FLERR,arg[3]);
ntype = force->inumeric(FLERR,arg[4]);
seed = force->inumeric(FLERR,arg[5]);
if (seed <= 0) error->all(FLERR,"Illegal fix pour command");
// read options from end of input line
options(narg-6,&arg[6]);
// error check on type
if (mode == ATOM && (ntype <= 0 || ntype > atom->ntypes))
error->all(FLERR,"Invalid atom type in 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 region 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");
// error check and further setup for mode = MOLECULE
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix_pour unless atoms have IDs");
if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) {
if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix pour molecule must have atom types");
if (ntype+onemols[i]->ntypes <= 0 ||
ntype+onemols[i]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix pour mol command");
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix pour molecule template ID must be same "
"as atom style template ID");
onemols[i]->check_attributes(0);
// fix pour uses geoemetric center of molecule for insertion
onemols[i]->compute_center();
}
}
if (rigidflag && mode == ATOM)
error->all(FLERR,"Cannot use fix pour rigid and not molecule");
if (shakeflag && mode == ATOM)
error->all(FLERR,"Cannot use fix pour shake and not molecule");
if (rigidflag && shakeflag)
error->all(FLERR,"Cannot use fix pour rigid and shake");
// setup of coords and imageflags array
if (mode == ATOM) natom_max = 1;
else {
natom_max = 0;
for (int i = 0; i < nmol; i++)
natom_max = MAX(natom_max,onemols[i]->natoms);
}
memory->create(coords,natom_max,4,"pour:coords");
memory->create(imageflags,natom_max,"pour:imageflags");
// find max atom and molecule IDs just once
if (idnext) find_maxid();
// random number generator, same for all procs
// warm up the generator 30x to avoid correlations in first-particle
// positions if runs are repeated with consecutive seeds
random = new RanPark(lmp,seed);
for (int ii=0; ii < 30; ii++) random->uniform();
// 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 = modify->find_fix_by_style("^gravity");
if (ifix == -1)
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=1.0;
molradius_max = 0.0;
if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++)
molradius_max = MAX(molradius_max,onemols[i]->molradius);
}
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 = MY_PI*rc*rc * (zhi-zlo);
if (mode == MOLECULE) {
volume_one = 4.0/3.0 * MY_PI * molradius_max*molradius_max*molradius_max;
} else if (dstyle == ONE || dstyle == RANGE) {
volume_one = 4.0/3.0 * MY_PI * radius_max*radius_max*radius_max;
} else if (dstyle == POLY) {
volume_one = 0.0;
for (int i = 0; i < npoly; i++)
volume_one += (4.0/3.0 * MY_PI *
radius_poly[i]*radius_poly[i]*radius_poly[i]) * frac_poly[i];
}
} else {
volume = (xhi-xlo) * (yhi-ylo);
if (mode == MOLECULE) {
volume_one = MY_PI * molradius_max*molradius_max;
} else if (dstyle == ONE || dstyle == RANGE) {
volume_one = MY_PI * radius_max*radius_max;
} else if (dstyle == POLY) {
volume_one = 0.0;
for (int i = 0; i < npoly; i++)
volume_one += (MY_PI * radius_poly[i]*radius_poly[i]) * frac_poly[i];
}
}
nper = static_cast<int> (volfrac*volume/volume_one);
if (nper == 0) error->all(FLERR,"Fix pour insertion count per timestep is 0");
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 [] molfrac;
delete [] idrigid;
delete [] idshake;
delete [] radius_poly;
delete [] frac_poly;
memory->destroy(coords);
memory->destroy(imageflags);
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 (still) exists
// for 3d must point in -z, for 2d must point in -y
// else insertion cannot work
int ifix = modify->find_fix_by_style("^gravity");
if (ifix == -1)
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");
// 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 (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix pour and fix rigid/small not using "
"same molecule template 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 pour shake fix does not exist");
fixshake = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix pour and fix shake not using "
"same molecule template ID");
}
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixPour::pre_exchange()
{
int i,m,flag,nlocalprev,imol,natom;
double r[3],rotmat[3][3],quat[4],vnew[3];
double *newcoord;
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c inserting atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// find current max atom and molecule IDs on every insertion step
if (!idnext) find_maxid();
// nnew = # of particles (atoms or molecules) 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
int dimension = domain->dimension;
if (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*natom_max,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 particles 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
// for MOLECULE mode:
// coords = coords of all atoms in particle
// perform random rotation around center pt
// apply PBC so final coords are inside box
// store image flag modified due to PBC
int success;
double radtmp,delx,dely,delz,rsq,radsum,rn,h;
double coord[3];
double denstmp;
double *sublo = domain->sublo;
double *subhi = domain->subhi;
int nsuccess = 0;
int attempt = 0;
int maxiter = nnew * maxattempt;
while (nsuccess < nnew) {
rn = random->uniform();
h = hi_current - rn*rn * (hi_current-lo_current);
if (mode == ATOM) radtmp = radius_sample();
success = 0;
while (attempt < maxiter) {
attempt++;
xyz_random(h,coord);
if (mode == ATOM) {
natom = 1;
coords[0][0] = coord[0];
coords[0][1] = coord[1];
coords[0][2] = coord[2];
coords[0][3] = radtmp;
imageflags[0] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
} else {
double rng = random->uniform();
imol = 0;
while (rng > molfrac[imol]) imol++;
natom = onemols[imol]->natoms;
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,onemols[imol]->dx[i],coords[i]);
coords[i][0] += coord[0];
coords[i][1] += coord[1];
coords[i][2] += coord[2];
// coords[3] = particle radius
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked below
if (onemols[imol]->radiusflag)
coords[i][3] = onemols[imol]->radius[i];
else coords[i][3] = 0.5;
imageflags[i] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
domain->remap(coords[i],imageflags[i]);
}
}
// if any pair of atoms overlap, try again
// use minimum_image() to account for PBC
for (m = 0; m < natom; m++) {
for (i = 0; i < nnear; i++) {
delx = coords[m][0] - xnear[i][0];
dely = coords[m][1] - xnear[i][1];
delz = coords[m][2] - xnear[i][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
radsum = coords[m][3] + xnear[i][3];
if (rsq <= radsum*radsum) break;
}
if (i < nnear) break;
}
if (m == natom) {
success = 1;
break;
}
}
if (!success) break;
// proceed with insertion
nsuccess++;
nlocalprev = atom->nlocal;
// add all atoms in particle to xnear
for (m = 0; m < natom; m++) {
xnear[nnear][0] = coords[m][0];
xnear[nnear][1] = coords[m][1];
xnear[nnear][2] = coords[m][2];
xnear[nnear][3] = coords[m][3];
nnear++;
}
// choose random velocity for new particle
// used for every atom in molecule
// 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
if (dimension == 3) {
vnew[0] = vxlo + random->uniform() * (vxhi-vxlo);
vnew[1] = vylo + random->uniform() * (vyhi-vylo);
vnew[2] = -sqrt(vz*vz + 2.0*grav*(coord[2]-hi_current));
} else {
vnew[0] = vxlo + random->uniform() * (vxhi-vxlo);
vnew[1] = -sqrt(vy*vy + 2.0*grav*(coord[1]-hi_current));
vnew[2] = 0.0;
}
// 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 (mode == ATOM)
denstmp = density_lo + random->uniform() * (density_hi-density_lo);
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]) {
if (comm->layout != Comm::LAYOUT_TILED) {
if (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 (comm->mysplit[2][1] == 1.0 &&
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]) {
if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
} else {
if (comm->mysplit[1][1] == 1.0 &&
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+onemols[imol]->type[m],coords[m]);
int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + m+1;
if (mode == MOLECULE) {
if (atom->molecule_flag) {
if (onemols[imol]->moleculeflag) {
atom->molecule[n] = maxmol_all + onemols[imol]->molecule[m];
} else {
atom->molecule[n] = maxmol_all+1;
}
}
if (atom->molecular == 2) {
atom->molindex[n] = 0;
atom->molatom[n] = m;
}
}
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 == ATOM) {
radtmp = newcoord[3];
atom->radius[n] = radtmp;
atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp;
} else {
onemols[imol]->quat_external = quat;
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
}
modify->create_attribute(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,imol,coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
maxtag_all += natom;
if (mode == MOLECULE && atom->molecule_flag) {
if (onemols[imol]->moleculeflag) {
maxmol_all += onemols[imol]->nmolecules;
} else {
maxmol_all++;
}
}
}
// warn if not successful with all insertions b/c too many attempts
int ninserted_atoms = nnear - nprevious;
int ninserted_mols = ninserted_atoms / natom;
ninserted += ninserted_mols;
if (ninserted_mols < nnew && me == 0)
error->warning(FLERR,"Less insertions than requested",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 other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
if (ninserted_atoms) {
atom->natoms += ninserted_atoms;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds * ninserted_mols;
atom->nangles += onemols[imol]->nangles * ninserted_mols;
atom->ndihedrals += onemols[imol]->ndihedrals * ninserted_mols;
atom->nimpropers += onemols[imol]->nimpropers * ninserted_mols;
}
if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (atom->map_style) {
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;
}
/* ----------------------------------------------------------------------
maxtag_all = current max atom ID for all atoms
maxmol_all = current max molecule ID for all atoms
------------------------------------------------------------------------- */
void FixPour::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);
}
}
/* ----------------------------------------------------------------------
check if particle i could overlap with a particle inserted into region
return 1 if yes, 0 if no
for ATOM mode, use delta with maximum size for inserted atoms
for MOLECULE mode, use delta with max radius of inserted molecules
if ignore line/tri set, ignore line or tri particles
account for PBC in overlap decision via outside() and minimum_image()
------------------------------------------------------------------------- */
int FixPour::overlap(int i)
{
double delta;
if (ignoreflag) {
if (ignoreline && atom->line[i] >= 0) return 0;
if (ignoretri && atom->tri[i] >= 0) return 0;
}
if (mode == ATOM) delta = atom->radius[i] + radius_max;
else delta = atom->radius[i] + molradius_max;
double *x = atom->x[i];
if (domain->dimension == 3) {
if (region_style == 1) {
if (outside(0,x[0],xlo-delta,xhi+delta)) return 0;
if (outside(1,x[1],ylo-delta,yhi+delta)) return 0;
if (outside(2,x[2],lo_current-delta,hi_current+delta)) return 0;
} else {
double delx = x[0] - xc;
double dely = x[1] - yc;
double delz = 0.0;
domain->minimum_image(delx,dely,delz);
double rsq = delx*delx + dely*dely;
double r = rc + delta;
if (rsq > r*r) return 0;
if (outside(2,x[2],lo_current-delta,hi_current+delta)) return 0;
}
} else {
if (outside(0,x[0],xlo-delta,xhi+delta)) return 0;
if (outside(1,x[1],lo_current-delta,hi_current+delta)) return 0;
}
return 1;
}
/* ----------------------------------------------------------------------
check if value is inside/outside lo/hi bounds in dimension
account for PBC if needed
return 1 if value is outside, 0 if inside
------------------------------------------------------------------------- */
bool FixPour::outside(int dim, double value, double lo, double hi)
{
double boxlo = domain->boxlo[dim];
double boxhi = domain->boxhi[dim];
// check for value inside/outside range, ignoring periodicity
// if inside or dim is non-periodic, only this test is needed
bool outside_range = (value < lo || value > hi);
if (!outside_range || !domain->periodicity[dim]) return outside_range;
// for periodic dimension:
// must perform additional tests if range wraps around the periodic box
bool outside_pbc_range = true;
if ((lo < boxlo && hi > boxhi) || (hi - lo) > domain->prd[dim]) {
// value is always inside
outside_pbc_range = false;
} else if (lo < boxlo) {
// lower boundary crosses periodic boundary
outside_pbc_range = (value > hi && value < lo + domain->prd[dim]);
} else if (hi > boxhi) {
// upper boundary crosses periodic boundary
outside_pbc_range = (value < lo && value > hi - domain->prd[dim]);
}
return outside_pbc_range;
}
/* ---------------------------------------------------------------------- */
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;
}
}
/* ---------------------------------------------------------------------- */
double FixPour::radius_sample()
{
if (dstyle == ONE) return radius_one;
if (dstyle == RANGE) return radius_lo +
random->uniform()*(radius_hi-radius_lo);
double value = random->uniform();
int i = 0;
double sum = 0.0;
while (sum < value) {
sum += frac_poly[i];
i++;
}
return radius_poly[i-1];
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixPour::options(int narg, char **arg)
{
// defaults
iregion = -1;
mode = ATOM;
molfrac = NULL;
rigidflag = 0;
idrigid = NULL;
shakeflag = 0;
idshake = NULL;
idnext = 0;
ignoreflag = ignoreline = ignoretri = 0;
dstyle = ONE;
radius_max = radius_one = 0.5;
radius_poly = frac_poly = NULL;
density_lo = density_hi = 1.0;
volfrac = 0.25;
maxattempt = 50;
rate = 0.0;
vxlo = vxhi = vylo = vyhi = vy = vz = 0.0;
int iarg = 0;
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],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix pour does not exist");
mode = MOLECULE;
onemols = &atom->molecules[imol];
nmol = onemols[0]->nset;
delete [] molfrac;
molfrac = new double[nmol];
molfrac[0] = 1.0/nmol;
for (int i = 1; i < nmol-1; i++) molfrac[i] = molfrac[i-1] + 1.0/nmol;
molfrac[nmol-1] = 1.0;
iarg += 2;
} else if (strcmp(arg[iarg],"molfrac") == 0) {
if (mode != MOLECULE) error->all(FLERR,"Illegal fix pour command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix pour command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix pour command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour 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 pour 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 pour 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 pour command");
iarg += 2;
} else if (strcmp(arg[iarg],"ignore") == 0) {
if (atom->line_flag) ignoreline = 1;
if (atom->tri_flag) ignoretri = 1;
if (ignoreline || ignoretri) ignoreflag = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"diam") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
if (strcmp(arg[iarg+1],"one") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
dstyle = ONE;
radius_one = 0.5 * force->numeric(FLERR,arg[iarg+2]);
radius_max = radius_one;
iarg += 3;
} else if (strcmp(arg[iarg+1],"range") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix pour command");
dstyle = RANGE;
radius_lo = 0.5 * force->numeric(FLERR,arg[iarg+2]);
radius_hi = 0.5 * force->numeric(FLERR,arg[iarg+3]);
if (radius_lo > radius_hi) error->all(FLERR,"Illegal fix pour command");
radius_max = radius_hi;
iarg += 4;
} else if (strcmp(arg[iarg+1],"poly") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
dstyle = POLY;
npoly = force->inumeric(FLERR,arg[iarg+2]);
if (npoly <= 0) error->all(FLERR,"Illegal fix pour command");
if (iarg+3 + 2*npoly > narg)
error->all(FLERR,"Illegal fix pour command");
radius_poly = new double[npoly];
frac_poly = new double[npoly];
iarg += 3;
radius_max = 0.0;
for (int i = 0; i < npoly; i++) {
radius_poly[i] = 0.5 * force->numeric(FLERR,arg[iarg++]);
frac_poly[i] = force->numeric(FLERR,arg[iarg++]);
if (radius_poly[i] <= 0.0 || frac_poly[i] < 0.0)
error->all(FLERR,"Illegal fix pour command");
radius_max = MAX(radius_max,radius_poly[i]);
}
double sum = 0.0;
for (int i = 0; i < npoly; i++) sum += frac_poly[i];
if (fabs(sum - 1.0) > SMALL)
error->all(FLERR,"Fix pour polydisperse fractions do not sum to 1.0");
} else error->all(FLERR,"Illegal fix pour command");
} else if (strcmp(arg[iarg],"dens") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
density_lo = force->numeric(FLERR,arg[iarg+1]);
density_hi = force->numeric(FLERR,arg[iarg+2]);
if (density_lo > density_hi) error->all(FLERR,"Illegal fix pour command");
iarg += 3;
} else if (strcmp(arg[iarg],"vol") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
volfrac = force->numeric(FLERR,arg[iarg+1]);
maxattempt = force->inumeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"rate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");
rate = force->numeric(FLERR,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 = force->numeric(FLERR,arg[iarg+1]);
vxhi = force->numeric(FLERR,arg[iarg+2]);
vylo = force->numeric(FLERR,arg[iarg+3]);
vyhi = force->numeric(FLERR,arg[iarg+4]);
if (vxlo > vxhi || vylo > vyhi)
error->all(FLERR,"Illegal fix pour command");
vz = force->numeric(FLERR,arg[iarg+5]);
iarg += 6;
} else {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix pour command");
vxlo = force->numeric(FLERR,arg[iarg+1]);
vxhi = force->numeric(FLERR,arg[iarg+2]);
vy = force->numeric(FLERR,arg[iarg+3]);
vz = 0.0;
if (vxlo > vxhi) error->all(FLERR,"Illegal fix pour command");
iarg += 4;
}
} else error->all(FLERR,"Illegal fix pour command");
}
}
/* ---------------------------------------------------------------------- */
void FixPour::reset_dt()
{
error->all(FLERR,"Cannot change timestep with fix pour");
}
/* ----------------------------------------------------------------------
extract particle radius for atom type = itype
------------------------------------------------------------------------- */
void *FixPour::extract(const char *str, int &itype)
{
if (strcmp(str,"radius") == 0) {
if (mode == ATOM) {
if (itype == ntype) oneradius = radius_max;
else oneradius = 0.0;
} else {
// loop over onemols molecules
// skip a molecule with no atoms as large as itype
oneradius = 0.0;
for (int i = 0; i < nmol; i++) {
if (itype > ntype+onemols[i]->ntypes) continue;
double *radius = onemols[i]->radius;
int *type = onemols[i]->type;
int natoms = onemols[i]->natoms;
// check radii of atoms in Molecule with matching types
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
for (int i = 0; i < natoms; i++)
if (type[i]+ntype == itype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = MAX(oneradius,0.5);
}
}
}
itype = 0;
return &oneradius;
}
return NULL;
}
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