ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
444e85d46c19bed637aad26b57e44f7f2b1e27ec
lammps/src/MISC/pair_tracker.cpp

629 lines
20 KiB
C++
Raw Blame History

/* ----------------------------------------------------------------------
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 "pair_tracker.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "fix.h"
#include "fix_dummy.h"
#include "fix_neigh_history.h"
#include "fix_store_local.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "tokenizer.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairTracker::PairTracker(LAMMPS *lmp) :
Pair(lmp), onerad_dynamic(nullptr), onerad_frozen(nullptr), maxrad_dynamic(nullptr),
maxrad_frozen(nullptr), id_fix_store_local(nullptr), fix_dummy(nullptr), fix_history(nullptr),
fix_store_local(nullptr), type_filter(nullptr), output_data(nullptr), pack_choice(nullptr)
{
single_enable = 1;
no_virial_fdotr_compute = 1;
neighprev = 0;
history = 1;
size_history = 3;
nondefault_history_transfer = 1;
finitecutflag = 0;
tmin = -1;
// create dummy fix as placeholder for FixNeighHistory
// this is so final order of Modify:fix will conform to input script
fix_dummy = dynamic_cast<FixDummy *>(modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY"));
}
/* ---------------------------------------------------------------------- */
PairTracker::~PairTracker()
{
if (!fix_history)
modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY");
else
modify->delete_fix("NEIGH_HISTORY_TRACK");
if (id_fix_store_local) modify->delete_fix(id_fix_store_local);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
delete[] onerad_dynamic;
delete[] onerad_frozen;
delete[] maxrad_dynamic;
delete[] maxrad_frozen;
}
delete[] pack_choice;
delete[] id_fix_store_local;
memory->destroy(output_data);
memory->destroy(type_filter);
}
/* ---------------------------------------------------------------------- */
void PairTracker::compute(int eflag, int vflag)
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz;
double radi, radj, radsum, rsq, r;
int *ilist, *jlist, *numneigh, **firstneigh;
int *touch, **firsttouch;
double *data, *alldata, **firstdata;
int updateflag = 1;
if (update->setupflag) updateflag = 0;
ev_init(eflag, vflag);
double **x = atom->x;
double *radius = atom->radius;
int *type = atom->type;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firsttouch = fix_history->firstflag;
firstdata = fix_history->firstvalue;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (finitecutflag) radi = radius[i];
itype = type[i];
touch = firsttouch[i];
alldata = firstdata[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
r = sqrt(rsq);
if (finitecutflag) {
radj = radius[j];
radsum = radi + radj;
if (rsq >= radsum * radsum) {
data = &alldata[size_history * jj];
if (touch[jj] == 1) process_data(i, j, data);
touch[jj] = 0;
data[0] = 0.0; // initial timestep
data[1] = 0.0; // sum of r, may be inaccurate over long times
data[2] = 0.0; // min of r
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
data[0] = (double) update->ntimestep;
data[1] = r;
data[2] = r;
} else if (updateflag) {
data[1] += r;
if (data[2] > r) data[2] = r;
}
touch[jj] = 1;
}
} else {
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) {
data = &alldata[size_history * jj];
if (touch[jj] == 1) process_data(i, j, data);
touch[jj] = 0;
data[0] = 0.0; // initial timestep
data[1] = 0.0; // sum of r, may be inaccurate over long times
data[2] = 0.0; // min of r
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
data[0] = (double) update->ntimestep;
data[1] = r;
data[2] = r;
} else if (updateflag) {
data[1] += r;
if (data[2] > r) data[2] = r;
}
touch[jj] = 1;
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairTracker::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++) setflag[i][j] = 0;
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(cut, n + 1, n + 1, "pair:cut");
onerad_dynamic = new double[n + 1];
onerad_frozen = new double[n + 1];
maxrad_dynamic = new double[n + 1];
maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairTracker::settings(int narg, char **arg)
{
if (narg < 2) error->all(FLERR, "Illegal pair_style command");
id_fix_store_local = utils::strdup(arg[0]);
store_local_freq = utils::inumeric(FLERR, arg[1], false, lmp);
// If optional arguments included, this will be oversized
pack_choice = new FnPtrPack[narg - 1];
nvalues = 0;
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg], "finite") == 0) {
finitecutflag = 1;
} else if (strcmp(arg[iarg], "id1") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_id1;
} else if (strcmp(arg[iarg], "id2") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_id2;
} else if (strcmp(arg[iarg], "time/created") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_time_created;
} else if (strcmp(arg[iarg], "time/broken") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_time_broken;
} else if (strcmp(arg[iarg], "time/total") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_time_total;
} else if (strcmp(arg[iarg], "x") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_x;
} else if (strcmp(arg[iarg], "y") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_y;
} else if (strcmp(arg[iarg], "z") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_z;
} else if (strcmp(arg[iarg], "r/min") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_rmin;
} else if (strcmp(arg[iarg], "r/ave") == 0) {
pack_choice[nvalues++] = &PairTracker::pack_rave;
} else if (strcmp(arg[iarg], "time/min") == 0) {
if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in pair tracker command");
tmin = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg++;
} else if (strcmp(arg[iarg], "type/include") == 0) {
if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in pair tracker command");
int ntypes = atom->ntypes;
int i, j, itype, jtype;
int inlo, inhi, jnlo, jnhi;
if (!type_filter) {
memory->create(type_filter, ntypes + 1, ntypes + 1, "pair/tracker:type_filter");
for (i = 0; i <= ntypes; i++) {
for (j = 0; j <= ntypes; j++) type_filter[i][j] = 0;
}
}
auto iwords = Tokenizer(arg[iarg + 1], ",").as_vector();
auto jwords = Tokenizer(arg[iarg + 2], ",").as_vector();
for (const auto &ifield : iwords) {
utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error);
for (const auto &jfield : jwords) {
utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error);
for (itype = inlo; itype <= inhi; itype++) {
for (jtype = jnlo; jtype <= jnhi; jtype++) {
type_filter[itype][jtype] = 1;
type_filter[jtype][itype] = 1;
}
}
}
}
iarg += 2;
} else {
error->all(FLERR, "Illegal pair_style command");
}
iarg++;
}
if (nvalues == 0) error->all(FLERR, "Must request at least one value to output");
memory->create(output_data, nvalues, "pair/tracker:output_data");
fix_store_local = dynamic_cast<FixStoreLocal *>(modify->get_fix_by_id(id_fix_store_local));
if (!fix_store_local)
fix_store_local = dynamic_cast<FixStoreLocal *>(modify->add_fix(
fmt::format("{} all STORE/LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues)));
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairTracker::coeff(int narg, char **arg)
{
if (narg > 2 && finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients");
if (narg != 3 && !finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double cut_one = 0.0;
if (!finitecutflag) cut_one = utils::numeric(FLERR, arg[2], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
setflag[i][j] = 1;
cut[i][j] = cut_one;
count++;
}
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairTracker::init_style()
{
// error and warning checks
if (!atom->radius_flag && finitecutflag)
error->all(FLERR, "Pair tracker requires atom attribute radius for finite cutoffs");
int neigh_flags = NeighConst::REQ_DEFAULT;
// history flag won't affect results, but match granular pairstyles
// so neighborlist can be copied to reduce overhead
if (finitecutflag) neigh_flags |= NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY;
neighbor->add_request(this, neigh_flags);
// if history is stored and first init, create Fix to store history
// it replaces FixDummy, created in the constructor
// this is so its order in the fix list is preserved
if (fix_history == nullptr) {
modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY",
fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1);
fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
fix_history->pair = this;
fix_history->use_bit_flag = 0;
} else {
fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
if (!fix_history) error->all(FLERR, "Could not find pair fix neigh history ID");
}
if (finitecutflag) {
if (force->pair->beyond_contact)
error->all(FLERR,
"Pair tracker incompatible with granular pairstyles that extend beyond contact");
// check for FixFreeze and set freeze_group_bit
auto fixlist = modify->get_fix_by_style("^freeze");
if (fixlist.size() == 0)
freeze_group_bit = 0;
else if (fixlist.size() > 1)
error->all(FLERR, "Only one fix freeze command at a time allowed");
else
freeze_group_bit = fixlist.front()->groupbit;
// check for FixPour and FixDeposit so can extract particle radii
auto pours = modify->get_fix_by_style("^pour");
auto deps = modify->get_fix_by_style("^deposit");
// set maxrad_dynamic and maxrad_frozen for each type
// include future FixPour and FixDeposit particles as dynamic
int itype = 0;
for (int i = 1; i <= atom->ntypes; i++) {
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
for (auto &ipour : pours) {
itype = i;
double maxrad = *((double *) ipour->extract("radius", itype));
if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
}
for (auto &idep : deps) {
itype = i;
double maxrad = *((double *) idep->extract("radius", itype));
if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
}
}
double *radius = atom->radius;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & freeze_group_bit)
onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]], radius[i]);
else
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairTracker::init_one(int i, int j)
{
if (!allocated) allocate();
// always mix prefactors geometrically
if (setflag[i][j] == 0) cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
cut[j][i] = cut[i][j];
// if finite, cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
double cutoff;
if (finitecutflag) {
cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
} else {
cutoff = cut[i][j];
}
return cutoff;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairTracker::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i, j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) fwrite(&cut[i][j], sizeof(double), 1, fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairTracker::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairTracker::write_restart_settings(FILE *fp)
{
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairTracker::read_restart_settings(FILE *fp)
{
if (comm->me == 0) { utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); }
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
double PairTracker::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
double /*factor_coul*/, double /*factor_lj*/, double & /*fforce*/)
{
return 0.0;
}
/* ----------------------------------------------------------------------
transfer history during fix/neigh/history exchange
only needed if any history entries i-j are not just negative of j-i entries
------------------------------------------------------------------------- */
void PairTracker::transfer_history(double *source, double *target, int /*itype*/, int /*jtype*/)
{
for (int i = 0; i < size_history; i++) target[i] = source[i];
}
/* ----------------------------------------------------------------------
self-interaction range of particle if finite particles
------------------------------------------------------------------------- */
double PairTracker::atom2cut(int i)
{
double cut = atom->radius[i] * 2;
return cut;
}
/* ----------------------------------------------------------------------
maximum interaction range for two finite particles
------------------------------------------------------------------------- */
double PairTracker::radii2cut(double r1, double r2)
{
double cut = r1 + r2;
return cut;
}
/* ---------------------------------------------------------------------- */
void PairTracker::process_data(int i, int j, double *input_data)
{
if ((update->ntimestep - input_data[0]) < tmin) return;
if (type_filter) {
int *type = atom->type;
if (type_filter[type[i]][type[j]] == 0) return;
}
for (int k = 0; k < nvalues; k++) (this->*pack_choice[k])(k, i, j, input_data);
fix_store_local->add_data(output_data, i, j);
}
/* ----------------------------------------------------------------------
one method for every keyword fix pair/tracker can output
the atom property is packed into a local vector or array
------------------------------------------------------------------------- */
void PairTracker::pack_time_created(int n, int /*i*/, int /*j*/, double *data)
{
output_data[n] = data[0];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_broken(int n, int /*i*/, int /*j*/, double * /*data*/)
{
output_data[n] = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_total(int n, int /*i*/, int /*j*/, double *data)
{
output_data[n] = update->ntimestep - data[0];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_id1(int n, int i, int /*j*/, double * /*data*/)
{
output_data[n] = atom->tag[i];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_id2(int n, int /*i*/, int j, double * /*data*/)
{
output_data[n] = atom->tag[j];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_x(int n, int i, int j, double * /*data*/)
{
output_data[n] = (atom->x[i][0] + atom->x[j][0]) * 0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_y(int n, int i, int j, double * /*data*/)
{
output_data[n] = (atom->x[i][1] + atom->x[j][1]) * 0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_z(int n, int i, int j, double * /*data*/)
{
output_data[n] = (atom->x[i][2] + atom->x[j][2]) * 0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_rmin(int n, int /*i*/, int /*j*/, double *data)
{
output_data[n] = data[2];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_rave(int n, int /*i*/, int /*j*/, double *data)
{
output_data[n] = data[1] / (update->ntimestep - data[0]);
}
Reference in New Issue View Git Blame Copy Permalink