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Adding files for BPM

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This commit is contained in:
Joel Thomas Clemmer
2021-08-27 09:22:56 -06:00
parent 3404920e98
commit bb720626e3
87 changed files with 5392 additions and 905 deletions
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245
src/MISC/pair_tracker.cpp
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@ -19,20 +19,23 @@
#include "fix.h"
#include "fix_dummy.h"
#include "fix_neigh_history.h"
#include "fix_pair_tracker.h"
#include "fix_store_local.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "tokenizer.h"
#include "utils.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
PairTracker::PairTracker(LAMMPS *lmp) :
Pair(lmp), pack_choice(NULL)
{
single_enable = 1;
no_virial_fdotr_compute = 1;
@ -43,6 +46,7 @@ PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
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
@ -50,6 +54,12 @@ PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
fix_history = nullptr;
modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY");
fix_dummy = (FixDummy *) modify->fix[modify->nfix - 1];
fix_store_local = nullptr;
output_data = nullptr;
pack_choice = nullptr;
type_filter = nullptr;
}
/* ---------------------------------------------------------------------- */
@ -71,6 +81,12 @@ PairTracker::~PairTracker()
delete[] maxrad_dynamic;
delete[] maxrad_frozen;
}
delete[] pack_choice;
delete [] id_fix_store_local;
memory->destroy(output_data);
memory->destroy(type_filter);
}
/* ---------------------------------------------------------------------- */
@ -130,8 +146,9 @@ void PairTracker::compute(int eflag, int vflag)
data = &alldata[size_history * jj];
if (touch[jj] == 1) {
fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
process_data(i, j, data);
}
touch[jj] = 0;
data[0] = 0.0; // initial time
data[1] = 0.0; // initial timestep
@ -159,7 +176,7 @@ void PairTracker::compute(int eflag, int vflag)
data = &alldata[size_history * jj];
if (touch[jj] == 1) {
fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
process_data(i, j, data);
}
touch[jj] = 0;
@ -216,14 +233,98 @@ void PairTracker::allocate()
void PairTracker::settings(int narg, char **arg)
{
if (narg != 0 && narg != 1) error->all(FLERR, "Illegal pair_style command");
if (narg < 1) error->all(FLERR, "Illegal pair_style command");
if (narg == 1) {
if (strcmp(arg[0], "finite") == 0)
id_fix_store_local = utils::strdup(arg[0]);
// If optional arguments included, this will be oversized
pack_choice = new FnPtrPack[narg - 1];
nvalues = 0;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg], "finite") == 0) {
finitecutflag = 1;
else
} 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, in, jn, infield, jnfield;
int inlo, inhi, jnlo, jnhi;
char *istr, *jstr;
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;
}
}
in = strlen(arg[iarg + 1]) + 1;
istr = new char[in];
strcpy(istr, arg[iarg + 1]);
std::vector<std::string> iwords = Tokenizer(istr, ",").as_vector();
infield = iwords.size();
jn = strlen(arg[iarg + 2]) + 1;
jstr = new char[jn];
strcpy(jstr, arg[iarg + 2]);
std::vector<std::string> jwords = Tokenizer(jstr, ",").as_vector();
jnfield = jwords.size();
for (i = 0; i < infield; i++) {
const char *ifield = iwords[i].c_str();
utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error);
for (j = 0; j < jnfield; j++) {
const char *jfield = jwords[j].c_str();
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;
}
}
}
}
delete[] istr;
delete[] jstr;
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");
}
/* ----------------------------------------------------------------------
@ -262,7 +363,6 @@ void PairTracker::coeff(int narg, char **arg)
void PairTracker::init_style()
{
int i;
// error and warning checks
if (!atom->radius_flag && finitecutflag)
@ -275,7 +375,7 @@ void PairTracker::init_style()
neighbor->requests[irequest]->size = 1;
neighbor->requests[irequest]->history = 1;
// history flag won't affect results, but match granular pairstyles
// so neighborlist can be copied to reduce overhead
// to copy neighbor list and reduce overhead
}
// if history is stored and first init, create Fix to store history
@ -284,7 +384,7 @@ void PairTracker::init_style()
if (fix_history == nullptr) {
modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY",
fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1);
fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1);
int ifix = modify->find_fix("NEIGH_HISTORY_TRACK");
fix_history = (FixNeighHistory *) modify->fix[ifix];
fix_history->pair = this;
@ -295,9 +395,14 @@ void PairTracker::init_style()
if (force->pair->beyond_contact)
error->all(FLERR,
"Pair tracker incompatible with granular pairstyles that extend beyond contact");
// check for FixPour and FixDeposit so can extract particle radii
"Pair tracker incompatible with granular pairstyles that extend beyond contact");
// check for FixFreeze and set freeze_group_bit
int ifix = modify->find_fix_by_style("^freeze");
if (ifix < 0) freeze_group_bit = 0;
else freeze_group_bit = modify->fix[ifix]->groupbit;
// check for FixPour and FixDeposit so can extract particle radii
int ipour;
for (ipour = 0; ipour < modify->nfix; ipour++)
if (strcmp(modify->fix[ipour]->style, "pour") == 0) break;
@ -310,7 +415,6 @@ void PairTracker::init_style()
// set maxrad_dynamic and maxrad_frozen for each type
// include future FixPour and FixDeposit particles as dynamic
int itype;
for (i = 1; i <= atom->ntypes; i++) {
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
@ -343,9 +447,13 @@ void PairTracker::init_style()
if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID");
fix_history = (FixNeighHistory *) modify->fix[ifix];
ifix = modify->find_fix_by_style("pair/tracker");
if (ifix < 0) error->all(FLERR, "Cannot use pair tracker without fix pair/tracker");
fix_pair_tracker = (FixPairTracker *) modify->fix[ifix];
ifix = modify->find_fix(id_fix_store_local);
if (ifix < 0) error->all(FLERR, "Cannot find fix store/local");
if (strcmp(modify->fix[ifix]->style, "store/local") != 0)
error->all(FLERR, "Incorrect fix style matched, not store/local");
fix_store_local = (FixStoreLocal *) modify->fix[ifix];
if (fix_store_local->nvalues != nvalues)
error->all(FLERR, "Inconsistent number of output variables in fix store/local");
}
/* ----------------------------------------------------------------------
@ -357,7 +465,6 @@ 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];
@ -469,3 +576,105 @@ double PairTracker::radii2cut(double r1, double r2)
double cut = r1 + r2;
return cut;
}
/* ---------------------------------------------------------------------- */
void PairTracker::process_data(int i, int j, double * input_data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
int time_initial = (int) input_data[0];
if ((time - time_initial) < 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)
{
double time_initial = data[0];
output_data[n] = time_initial;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_broken(int n, int i, int j, double * data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
output_data[n] = time;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_total(int n, int i, int j, double * data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
double time_initial = data[0];
output_data[n] = time - time_initial;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_id1(int n, int i, int j, double * data)
{
tagint *tag = atom->tag;
output_data[n] = tag[i];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_id2(int n, int i, int j, double * data)
{
tagint *tag = atom->tag;
output_data[n] = tag[j];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_x(int n, int i, int j, double * data)
{
double **x = atom->x;
output_data[n] = (x[i][0] + x[j][0])*0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_y(int n, int i, int j, double * data)
{
double **x = atom->x;
output_data[n] = (x[i][1] + x[j][1])*0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_z(int n, int i, int j, double * data)
{
double **x = atom->x;
output_data[n] = (x[i][2] + x[j][2])*0.5;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_rmin(int n, int i, int j, double * data)
{
double rmin = data[3];
output_data[n] = rmin;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_rave(int n, int i, int j, double * data)
{
double rsum = data[2];
double nstep_initial = data[1];
output_data[n] = rsum / (update->ntimestep - nstep_initial);
}