ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
31d1addfadaf2bb2fd3354089421818bc14c59ac
lammps/src/fix_deposit.cpp
Axel Kohlmeyer b508229bd2 adapt to LAMMPS programming style
2025-01-11 18:05:16 -05:00

998 lines
33 KiB
C++
Raw Blame History

// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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_deposit.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "input.h"
#include "lattice.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
#include "random_park.h"
#include "region.h"
#include "update.h"
#include "variable.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{ATOM,MOLECULE};
enum{DIST_UNIFORM,DIST_GAUSSIAN};
static constexpr double EPSILON = 1.0e6;
/* ---------------------------------------------------------------------- */
FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), idregion(nullptr), idrigid(nullptr),
idshake(nullptr), onemols(nullptr), molfrac(nullptr), coords(nullptr), imageflags(nullptr),
fixrigid(nullptr), fixshake(nullptr), random(nullptr)
{
if (narg < 7) error->all(FLERR,"Illegal fix deposit command");
scalar_flag = 1;
extscalar = 0;
restart_global = 1;
time_depend = 1;
// required args
ninsert = utils::inumeric(FLERR, arg[3], false, lmp);
ntype = utils::expand_type_int(FLERR, arg[4], Atom::ATOM, lmp);
nfreq = utils::inumeric(FLERR, arg[5], false, lmp);
seed = utils::inumeric(FLERR, arg[6], false, lmp);
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) error->all(FLERR,"Must specify a region in fix deposit");
if (iregion->bboxflag == 0)
error->all(FLERR,"Fix deposit region does not support a bounding box");
if (iregion->dynamic_check())
error->all(FLERR,"Fix deposit region cannot be dynamic");
xlo = iregion->extent_xlo;
xhi = iregion->extent_xhi;
ylo = iregion->extent_ylo;
yhi = iregion->extent_yhi;
zlo = iregion->extent_zlo;
zhi = 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) {
for (int i = 0; i < nmol; i++) {
if (onemols[i]->xflag == 0)
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix deposit 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 deposit mol command");
if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemols[i]->check_attributes();
// fix deposit uses geoemetric center of molecule for insertion
onemols[i]->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_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,3,"deposit:coords");
memory->create(imageflags,natom_max,"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;
xmid *= xscale;
ymid *= yscale;
zmid *= zscale;
sigma *= xscale; // same as in region sphere
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
// 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();
// set up reneighboring
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
nfirst = next_reneighbor-nfreq;
ninserted = 0;
}
/* ---------------------------------------------------------------------- */
FixDeposit::~FixDeposit()
{
delete random;
delete[] molfrac;
delete[] idrigid;
delete[] idshake;
delete[] idregion;
delete[] vstr;
delete[] xstr;
delete[] ystr;
delete[] zstr;
memory->destroy(coords);
memory->destroy(imageflags);
}
/* ---------------------------------------------------------------------- */
int FixDeposit::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixDeposit::init()
{
warnflag = 1;
// set index and check validity of region
iregion = domain->get_region_by_id(idregion);
if (!iregion) error->all(FLERR,"Region ID {} for fix deposit does not exist", idregion);
// if rigidflag defined, check for rigid/small fix
// its molecule template must be same as this one
fixrigid = nullptr;
if (rigidflag) {
fixrigid = modify->get_fix_by_id(idrigid);
if (!fixrigid) error->all(FLERR,"Fix deposit rigid fix ID {} does not exist", idrigid);
int tmp;
if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR, "Fix deposit and rigid fix are not using the same molecule template ID");
}
// if shakeflag defined, check for SHAKE fix
// its molecule template must be same as this one
fixshake = nullptr;
if (shakeflag) {
fixshake = modify->get_fix_by_id(idshake);
if (!fixshake) error->all(FLERR,"Fix deposit shake fix ID {} does not exist", idshake);
int tmp;
if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix deposit and fix shake are not using the same molecule template ID");
}
// for finite size spherical particles:
// warn if near < 2 * maxrad of existing and inserted particles
// since may lead to overlaps
// if inserted molecule does not define diameters,
// use AtomVecSphere::create_atom() default radius = 0.5
if (atom->radius_flag) {
double *radius = atom->radius;
int nlocal = atom->nlocal;
double maxrad = 0.0;
for (int i = 0; i < nlocal; i++)
maxrad = MAX(maxrad,radius[i]);
double maxradall;
MPI_Allreduce(&maxrad,&maxradall,1,MPI_DOUBLE,MPI_MAX,world);
double maxradinsert = 0.0;
if (mode == MOLECULE) {
for (int i = 0; i < nmol; i++) {
if (onemols[i]->radiusflag)
maxradinsert = MAX(maxradinsert,onemols[i]->maxradius);
else maxradinsert = MAX(maxradinsert,0.5);
}
} else maxradinsert = 0.5;
double separation = MAX(2.0*maxradinsert,maxradall+maxradinsert);
if (sqrt(nearsq) < separation && comm->me == 0)
error->warning(FLERR,"Fix deposit near setting < possible overlap separation {}",separation);
}
}
/* ---------------------------------------------------------------------- */
void FixDeposit::setup_pre_exchange()
{
if (ninserted < ninsert) next_reneighbor = nfirst + ((update->ntimestep - nfirst)/nfreq)*nfreq + nfreq;
else next_reneighbor = 0;
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixDeposit::pre_exchange()
{
int i,m,n,nlocalprev,imol,natom,flag,flagall;
double coord[3],lamda[3],delx,dely,delz,rsq;
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;
// clear ghost count (and atom map) 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
if (atom->map_style != Atom::MAP_NONE) atom->map_clear();
atom->nghost = 0;
atom->avec->clear_bonus();
// 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 success = 0;
int attempt = 0;
while (attempt < maxattempt) {
attempt++;
// choose random position for new particle within region
if (distflag == DIST_UNIFORM) {
do {
coord[0] = xlo + random->uniform() * (xhi-xlo);
coord[1] = ylo + random->uniform() * (yhi-ylo);
coord[2] = zlo + random->uniform() * (zhi-zlo);
} while (iregion->match(coord[0],coord[1],coord[2]) == 0);
} else if (distflag == DIST_GAUSSIAN) {
do {
coord[0] = xmid + random->gaussian() * sigma;
coord[1] = ymid + random->gaussian() * sigma;
coord[2] = zmid + random->gaussian() * sigma;
} while (iregion->match(coord[0],coord[1],coord[2]) == 0);
} else error->all(FLERR,"Unknown particle distribution in fix deposit");
if (varflag && vartest(coord[0],coord[1],coord[2]) == 0) continue;
// 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 modify image flags due to PBC
if (mode == ATOM) {
natom = 1;
coords[0][0] = coord[0];
coords[0][1] = coord[1];
coords[0][2] = coord[2];
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) {
if (orientflag) {
r[0] = rx;
r[1] = ry;
r[2] = rz;
} else {
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];
imageflags[i] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
domain->remap(coords[i],imageflags[i]);
}
}
// check distance between any existing atom and any inserted atom
// if 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]) {
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]);
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 == Atom::TEMPLATE) {
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 == MOLECULE) {
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 (mode == 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);
}
success = 1;
break;
}
// warn if not successful b/c too many attempts
if (warnflag && !success && comm->me == 0) {
error->warning(FLERR,"One or more particle depositions were unsuccessful");
warnflag = 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 (success) {
atom->natoms += natom;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
atom->ndihedrals += onemols[imol]->ndihedrals;
atom->nimpropers += onemols[imol]->nimpropers;
}
maxtag_all += natom;
if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (mode == MOLECULE && atom->molecule_flag) {
if (onemols[imol]->moleculeflag) {
maxmol_all += onemols[imol]->nmolecules;
} else {
maxmol_all++;
}
}
}
// rebuild atom map
if (atom->map_style != Atom::MAP_NONE) {
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 = nullptr;
idregion = nullptr;
varflag = 0;
vstr = xstr = ystr = zstr = nullptr;
mode = ATOM;
molfrac = nullptr;
rigidflag = 0;
idrigid = nullptr;
shakeflag = 0;
idshake = nullptr;
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;
distflag = DIST_UNIFORM;
sigma = 1.0;
xmid = ymid = zmid = 0.0;
scaleflag = 1;
targetflag = 0;
orientflag = 0;
warnflag = 1;
rx = 0.0;
ry = 0.0;
rz = 0.0;
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->get_region_by_id(arg[iarg+1]);
if (!iregion) error->all(FLERR,"Region ID {} for fix deposit does not exist",arg[iarg+1]);
idregion = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg], "var") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix deposit var", error);
delete[] vstr;
vstr = utils::strdup(arg[iarg + 1]);
varflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg], "set") == 0) {
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix deposit set", error);
if (strcmp(arg[iarg + 1], "x") == 0) {
delete[] xstr;
xstr = utils::strdup(arg[iarg + 2]);
} else if (strcmp(arg[iarg + 1], "y") == 0) {
delete[] ystr;
ystr = utils::strdup(arg[iarg + 2]);
} else if (strcmp(arg[iarg + 1], "z") == 0) {
delete[] zstr;
zstr = utils::strdup(arg[iarg + 2]);
} else
error->all(FLERR, "Unknown fix deposit set option {}", arg[iarg + 2]);
iarg += 3;
} 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");
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 deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + utils::numeric(FLERR,arg[iarg+i+1],false,lmp);
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit 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 deposit command");
delete[] idrigid;
idrigid = utils::strdup(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");
delete[] idshake;
idshake = utils::strdup(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 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
hi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
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 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
hi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
deltasq = utils::numeric(FLERR,arg[iarg+3],false,lmp) *
utils::numeric(FLERR,arg[iarg+3],false,lmp);
iarg += 4;
} else if (strcmp(arg[iarg],"near") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
nearsq = utils::numeric(FLERR,arg[iarg+1],false,lmp) *
utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"attempt") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
maxattempt = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"rate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
rateflag = 1;
rate = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vxlo = utils::numeric(FLERR,arg[iarg+1],false,lmp);
vxhi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
iarg += 3;
} else if (strcmp(arg[iarg],"vy") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vylo = utils::numeric(FLERR,arg[iarg+1],false,lmp);
vyhi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
iarg += 3;
} else if (strcmp(arg[iarg],"vz") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
vzlo = utils::numeric(FLERR,arg[iarg+1],false,lmp);
vzhi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
iarg += 3;
} else if (strcmp(arg[iarg],"orient") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
orientflag = 1;
rx = utils::numeric(FLERR,arg[iarg+1],false,lmp);
ry = utils::numeric(FLERR,arg[iarg+2],false,lmp);
rz = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (domain->dimension == 2 && (rx != 0.0 || ry != 0.0))
error->all(FLERR,"Illegal fix deposit orient settings");
if (rx == 0.0 && ry == 0.0 && rz == 0.0)
error->all(FLERR,"Illegal fix deposit orient settings");
iarg += 4;
} 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],"gaussian") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix deposit command");
xmid = utils::numeric(FLERR,arg[iarg+1],false,lmp);
ymid = utils::numeric(FLERR,arg[iarg+2],false,lmp);
zmid = utils::numeric(FLERR,arg[iarg+3],false,lmp);
sigma = utils::numeric(FLERR,arg[iarg+4],false,lmp);
distflag = DIST_GAUSSIAN;
iarg += 5;
} else if (strcmp(arg[iarg],"target") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
tx = utils::numeric(FLERR,arg[iarg+1],false,lmp);
ty = utils::numeric(FLERR,arg[iarg+2],false,lmp);
tz = utils::numeric(FLERR,arg[iarg+3],false,lmp);
targetflag = 1;
iarg += 4;
} else error->all(FLERR,"Illegal fix deposit command");
}
// error check and further setup for variable test
if (!vstr && (xstr || ystr || zstr))
error->all(FLERR, "Incomplete use of variables in fix deposit command");
if (vstr && (!xstr && !ystr && !zstr))
error->all(FLERR, "Incomplete use of variables in fix deposit command");
if (varflag) {
vvar = input->variable->find(vstr);
if (vvar < 0) error->all(FLERR, "Variable {} for fix deposit does not exist", vstr);
if (!input->variable->equalstyle(vvar))
error->all(FLERR, "Variable for fix deposit is invalid style");
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0) error->all(FLERR, "Variable {} for fix deposit does not exist", xstr);
if (!input->variable->internalstyle(xvar))
error->all(FLERR, "Variable for fix deposit is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0) error->all(FLERR, "Variable {} for fix deposit does not exist", ystr);
if (!input->variable->internalstyle(yvar))
error->all(FLERR, "Variable for fix deposit is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0) error->all(FLERR, "Variable {} for fix deposit does not exist", zstr);
if (!input->variable->internalstyle(zvar))
error->all(FLERR, "Variable for fix deposit is invalid style");
}
}
}
/* ----------------------------------------------------------------------
output number of successful insertions
------------------------------------------------------------------------- */
double FixDeposit::compute_scalar()
{
return ninserted;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixDeposit::write_restart(FILE *fp)
{
int n = 0;
double list[5];
list[n++] = random->state();
list[n++] = ninserted;
list[n++] = ubuf(nfirst).d;
list[n++] = ubuf(next_reneighbor).d;
list[n++] = ubuf(update->ntimestep).d;
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;
auto list = (double *) buf;
seed = static_cast<int>(list[n++]);
ninserted = static_cast<int>(list[n++]);
nfirst = static_cast<bigint>(ubuf(list[n++]).i);
next_reneighbor = static_cast<bigint>(ubuf(list[n++]).i);
bigint ntimestep_restart = static_cast<bigint>(ubuf(list[n++]).i);
if (ntimestep_restart != update->ntimestep)
error->all(FLERR,"Must not reset timestep when restarting this fix");
random->reset(seed);
}
/* ----------------------------------------------------------------------
extract particle radius for atom type = itype
------------------------------------------------------------------------- */
void *FixDeposit::extract(const char *str, int &itype)
{
if (strcmp(str,"radius") == 0) {
if (mode == ATOM) {
if (itype == ntype) oneradius = 0.5;
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 nullptr;
}
/* ----------------------------------------------------------------------
test a generated atom position against variable evaluation
first set x,y,z values in internal variables
------------------------------------------------------------------------- */
int FixDeposit::vartest(double x, double y, double z)
{
if (xstr) input->variable->internal_set(xvar, x);
if (ystr) input->variable->internal_set(yvar, y);
if (zstr) input->variable->internal_set(zvar, z);
double value = input->variable->compute_equal(vvar);
if (value == 0.0) return 0;
return 1;
}
Reference in New Issue View Git Blame Copy Permalink