ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Fixing data compression in history, small update to model

Browse Source
This commit is contained in:
Joel Thomas Clemmer
2021-09-09 09:00:21 -06:00
parent 0e72aae0a3
commit f9a972220e
10 changed files with 1293 additions and 1250 deletions
Download Patch File Download Diff File Expand all files Collapse all files

695
src/BPM/bond_bpm.cpp
View File

@ -1,349 +1,346 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "bond_bpm.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_store_local.h"
#include "fix_update_special_bonds.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp)
{
id_fix_store_local = nullptr;
id_fix_prop_atom = nullptr;
fix_store_local = nullptr;
fix_update_special_bonds = nullptr;
prop_atom_flag = 0;
nvalues = 0;
output_data = nullptr;
pack_choice = nullptr;
r0_max_estimate = 0.0;
max_stretch = 1.0;
}
/* ---------------------------------------------------------------------- */
BondBPM::~BondBPM()
{
delete [] pack_choice;
delete [] id_fix_store_local;
delete [] id_fix_prop_atom;
memory->destroy(output_data);
}
/* ---------------------------------------------------------------------- */
void BondBPM::init_style()
{
int ifix;
if (id_fix_store_local) {
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];
fix_store_local->nvalues = nvalues;
}
ifix = modify->find_fix_by_style("update/special/bonds");
if (ifix >= 0)
fix_update_special_bonds = (FixUpdateSpecialBonds *) modify->fix[ifix];
else
fix_update_special_bonds = nullptr;
if (force->angle || force->dihedral || force->improper)
error->all(FLERR,
"Bond style bpm cannot be used with 3,4-body interactions");
if (atom->molecular == 2)
error->all(FLERR,
"Bond style bpm cannot be used with atom style template");
// special 1-3 and 1-4 weights must be 1 to prevent building 1-3 and 1-4 special bond lists
if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
error->all(FLERR,"Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
}
/* ----------------------------------------------------------------------
global settings
All args before store/local command are saved for potential args
for specific bond BPM substyles
All args after optional store/local command are variables stored
in the compute store/local
------------------------------------------------------------------------- */
void BondBPM::settings(int narg, char **arg)
{
int iarg = 0;
while (iarg < narg) {
if (id_fix_store_local) {
if (strcmp(arg[iarg], "id1") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_id1;
} else if (strcmp(arg[iarg], "id2") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_id2;
} else if (strcmp(arg[iarg], "time") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_time;
} else if (strcmp(arg[iarg], "x") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_x;
} else if (strcmp(arg[iarg], "y") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_y;
} else if (strcmp(arg[iarg], "z") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_z;
} else if (strcmp(arg[iarg], "x/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_x_ref;
prop_atom_flag = 1;
} else if (strcmp(arg[iarg], "y/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_y_ref;
prop_atom_flag = 1;
} else if (strcmp(arg[iarg], "z/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_z_ref;
prop_atom_flag = 1;
} else {
error->all(FLERR, "Illegal bond_style command");
}
} else if (strcmp(arg[iarg], "store/local") == 0) {
id_fix_store_local = utils::strdup(arg[iarg+1]);
iarg ++;
nvalues = 0;
pack_choice = new FnPtrPack[narg - iarg - 1];
}
iarg ++;
}
if (id_fix_store_local) {
if (nvalues == 0) error->all(FLERR,
"Bond style bpm/rotational must include at least one value to output");
memory->create(output_data, nvalues, "bond/bpm:output_data");
// Use store property to save reference positions as it can transfer to ghost atoms
if (prop_atom_flag == 1) {
id_fix_prop_atom = utils::strdup("BPM_PROPERTY_ATOM");
int ifix = modify->find_fix(id_fix_prop_atom);
if (ifix < 0) {
modify->add_fix(fmt::format("{} all property/atom "
"d_BPM_X_REF d_BPM_Y_REF d_BPM_Z_REF ghost yes", id_fix_prop_atom));
ifix = modify->find_fix(id_fix_prop_atom);
}
int type_flag;
int col_flag;
index_x_ref = atom->find_custom("BPM_X_REF", type_flag, col_flag);
index_y_ref = atom->find_custom("BPM_Y_REF", type_flag, col_flag);
index_z_ref = atom->find_custom("BPM_Z_REF", type_flag, col_flag);
if (modify->fix[ifix]->restart_reset) {
modify->fix[ifix]->restart_reset = 0;
} else {
double *x_ref = atom->dvector[index_x_ref];
double *y_ref = atom->dvector[index_y_ref];
double *z_ref = atom->dvector[index_z_ref];
double **x = atom->x;
for (int i = 0; i < atom->nlocal; i++) {
x_ref[i] = x[i][0];
y_ref[i] = x[i][1];
z_ref[i] = x[i][2];
}
}
}
}
}
/* ----------------------------------------------------------------------
used to check bond communiction cutoff - not perfect, estimates based on local-local only
------------------------------------------------------------------------- */
double BondBPM::equilibrium_distance(int i)
{
// Ghost atoms may not yet be communicated, this may only be an estimate
if (r0_max_estimate == 0) {
int type, j;
double delx, dely, delz, r;
double **x = atom->x;
for (int i = 0; i < atom->nlocal; i ++) {
for (int m = 0; m < atom->num_bond[i]; m ++) {
type = atom->bond_type[i][m];
if (type == 0) continue;
j = atom->map(atom->bond_atom[i][m]);
if(j == -1) continue;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
domain->minimum_image(delx, dely, delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if(r > r0_max_estimate) r0_max_estimate = r;
}
}
double temp;
MPI_Allreduce(&r0_max_estimate,&temp,1,MPI_DOUBLE,MPI_MAX,world);
r0_max_estimate = temp;
//if (comm->me == 0)
// utils::logmesg(lmp,fmt::format("Estimating longest bond = {}\n",r0_max_estimate));
}
// Divide out heuristic prefactor added in comm class
return max_stretch*r0_max_estimate/1.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::process_broken(int i, int j)
{
if (fix_store_local) {
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n, i, j);
fix_store_local->add_data(output_data, i, j);
}
if (fix_update_special_bonds)
fix_update_special_bonds->add_broken_bond(i, j);
// Manually search and remove from atom arrays
// need to remove in case special bonds arrays rebuilt
int m, n;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
if (i < nlocal) {
for (m = 0; m < num_bond[i]; m++) {
// if(tag[i] == 25 or tag[j] == 25) printf("\t 1 ATOM LOOP %d-%d, %d/%d \n", tag[i], bond_atom[i][m], m, num_bond[i]);
if (bond_atom[i][m] == tag[j]) {
// if(tag[i] == 25 or tag[j] == 25) printf("\t DELETED\n");
bond_type[i][m] = 0;
n = num_bond[i];
bond_type[i][m] = bond_type[i][n-1];
bond_atom[i][m] = bond_atom[i][n-1];
num_bond[i]--;
break;
}
}
}
if (j < nlocal) {
for (m = 0; m < num_bond[j]; m++) {
// if(tag[i] == 25 or tag[j] == 25) printf("\t 2 ATOM LOOP %d-%d, %d/%d \n", tag[j], bond_atom[j][m], m, num_bond[j]);
if (bond_atom[j][m] == tag[i]) {
// if(tag[j] == 25 or tag[j] == 25) printf("\t DELETED\n");
bond_type[j][m] = 0;
n = num_bond[j];
bond_type[j][m] = bond_type[j][n-1];
bond_atom[j][m] = bond_atom[j][n-1];
num_bond[j]--;
break;
}
}
}
// if((tag[i] == 10 and tag[j] == 23)or (tag[i] == 23 and tag[j] == 10)) printf("Broken bond %d-%d (%d %d/%d)\n", tag[i], tag[j], i, j, nlocal);
}
/* ----------------------------------------------------------------------
one method for every keyword bond bpm can output
the atom property is packed into array or vector
------------------------------------------------------------------------- */
void BondBPM::pack_id1(int n, int i, int j)
{
tagint *tag = atom->tag;
output_data[n] = tag[i];
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_id2(int n, int i, int j)
{
tagint *tag = atom->tag;
output_data[n] = tag[j];
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_time(int n, int i, int j)
{
bigint time = update->ntimestep;
output_data[n] = time;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_x(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][0] + x[j][0])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_y(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][1] + x[j][1])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_z(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][2] + x[j][2])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_x_ref(int n, int i, int j)
{
double *x = atom->dvector[index_x_ref];
output_data[n] = (x[i] + x[j])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_y_ref(int n, int i, int j)
{
double *y = atom->dvector[index_y_ref];
output_data[n] = (y[i] + y[j])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_z_ref(int n, int i, int j)
{
double *z = atom->dvector[index_z_ref];
output_data[n] = (z[i] + z[j])*0.5;
}
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "bond_bpm.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_bond_history.h"
#include "fix_store_local.h"
#include "fix_update_special_bonds.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp)
{
id_fix_store_local = nullptr;
id_fix_prop_atom = nullptr;
fix_store_local = nullptr;
fix_update_special_bonds = nullptr;
fix_bond_history = nullptr;
prop_atom_flag = 0;
nvalues = 0;
output_data = nullptr;
pack_choice = nullptr;
r0_max_estimate = 0.0;
max_stretch = 1.0;
}
/* ---------------------------------------------------------------------- */
BondBPM::~BondBPM()
{
delete [] pack_choice;
delete [] id_fix_store_local;
delete [] id_fix_prop_atom;
memory->destroy(output_data);
}
/* ---------------------------------------------------------------------- */
void BondBPM::init_style()
{
int ifix;
if (id_fix_store_local) {
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];
fix_store_local->nvalues = nvalues;
}
ifix = modify->find_fix_by_style("update/special/bonds");
if (ifix >= 0)
fix_update_special_bonds = (FixUpdateSpecialBonds *) modify->fix[ifix];
else
fix_update_special_bonds = nullptr;
if (force->angle || force->dihedral || force->improper)
error->all(FLERR,
"Bond style bpm cannot be used with 3,4-body interactions");
if (atom->molecular == 2)
error->all(FLERR,
"Bond style bpm cannot be used with atom style template");
// special 1-3 and 1-4 weights must be 1 to prevent building 1-3 and 1-4 special bond lists
if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
error->all(FLERR,"Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
}
/* ----------------------------------------------------------------------
global settings
All args before store/local command are saved for potential args
for specific bond BPM substyles
All args after optional store/local command are variables stored
in the compute store/local
------------------------------------------------------------------------- */
void BondBPM::settings(int narg, char **arg)
{
int iarg = 0;
while (iarg < narg) {
if (id_fix_store_local) {
if (strcmp(arg[iarg], "id1") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_id1;
} else if (strcmp(arg[iarg], "id2") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_id2;
} else if (strcmp(arg[iarg], "time") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_time;
} else if (strcmp(arg[iarg], "x") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_x;
} else if (strcmp(arg[iarg], "y") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_y;
} else if (strcmp(arg[iarg], "z") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_z;
} else if (strcmp(arg[iarg], "x/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_x_ref;
prop_atom_flag = 1;
} else if (strcmp(arg[iarg], "y/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_y_ref;
prop_atom_flag = 1;
} else if (strcmp(arg[iarg], "z/ref") == 0) {
pack_choice[nvalues++] = &BondBPM::pack_z_ref;
prop_atom_flag = 1;
} else {
error->all(FLERR, "Illegal bond_style command");
}
} else if (strcmp(arg[iarg], "store/local") == 0) {
id_fix_store_local = utils::strdup(arg[iarg+1]);
iarg ++;
nvalues = 0;
pack_choice = new FnPtrPack[narg - iarg - 1];
}
iarg ++;
}
if (id_fix_store_local) {
if (nvalues == 0) error->all(FLERR,
"Bond style bpm/rotational must include at least one value to output");
memory->create(output_data, nvalues, "bond/bpm:output_data");
// Use store property to save reference positions as it can transfer to ghost atoms
if (prop_atom_flag == 1) {
id_fix_prop_atom = utils::strdup("BPM_PROPERTY_ATOM");
int ifix = modify->find_fix(id_fix_prop_atom);
if (ifix < 0) {
modify->add_fix(fmt::format("{} all property/atom "
"d_BPM_X_REF d_BPM_Y_REF d_BPM_Z_REF ghost yes", id_fix_prop_atom));
ifix = modify->find_fix(id_fix_prop_atom);
}
int type_flag;
int col_flag;
index_x_ref = atom->find_custom("BPM_X_REF", type_flag, col_flag);
index_y_ref = atom->find_custom("BPM_Y_REF", type_flag, col_flag);
index_z_ref = atom->find_custom("BPM_Z_REF", type_flag, col_flag);
if (modify->fix[ifix]->restart_reset) {
modify->fix[ifix]->restart_reset = 0;
} else {
double *x_ref = atom->dvector[index_x_ref];
double *y_ref = atom->dvector[index_y_ref];
double *z_ref = atom->dvector[index_z_ref];
double **x = atom->x;
for (int i = 0; i < atom->nlocal; i++) {
x_ref[i] = x[i][0];
y_ref[i] = x[i][1];
z_ref[i] = x[i][2];
}
}
}
}
}
/* ----------------------------------------------------------------------
used to check bond communiction cutoff - not perfect, estimates based on local-local only
------------------------------------------------------------------------- */
double BondBPM::equilibrium_distance(int i)
{
// Ghost atoms may not yet be communicated, this may only be an estimate
if (r0_max_estimate == 0) {
int type, j;
double delx, dely, delz, r;
double **x = atom->x;
for (int i = 0; i < atom->nlocal; i ++) {
for (int m = 0; m < atom->num_bond[i]; m ++) {
type = atom->bond_type[i][m];
if (type == 0) continue;
j = atom->map(atom->bond_atom[i][m]);
if(j == -1) continue;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
domain->minimum_image(delx, dely, delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if(r > r0_max_estimate) r0_max_estimate = r;
}
}
double temp;
MPI_Allreduce(&r0_max_estimate,&temp,1,MPI_DOUBLE,MPI_MAX,world);
r0_max_estimate = temp;
//if (comm->me == 0)
// utils::logmesg(lmp,fmt::format("Estimating longest bond = {}\n",r0_max_estimate));
}
// Divide out heuristic prefactor added in comm class
return max_stretch*r0_max_estimate/1.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::process_broken(int i, int j)
{
if (fix_store_local) {
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n, i, j);
fix_store_local->add_data(output_data, i, j);
}
if (fix_update_special_bonds)
fix_update_special_bonds->add_broken_bond(i, j);
// Manually search and remove from atom arrays
// need to remove in case special bonds arrays rebuilt
int m, n;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
if (i < nlocal) {
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == tag[j]) {
bond_type[i][m] = 0;
n = num_bond[i];
bond_type[i][m] = bond_type[i][n-1];
bond_atom[i][m] = bond_atom[i][n-1];
fix_bond_history->delete_bond(i, m);
num_bond[i]--;
break;
}
}
}
if (j < nlocal) {
for (m = 0; m < num_bond[j]; m++) {
if (bond_atom[j][m] == tag[i]) {
bond_type[j][m] = 0;
n = num_bond[j];
bond_type[j][m] = bond_type[j][n-1];
bond_atom[j][m] = bond_atom[j][n-1];
fix_bond_history->delete_bond(j, m);
num_bond[j]--;
break;
}
}
}
}
/* ----------------------------------------------------------------------
one method for every keyword bond bpm can output
the atom property is packed into array or vector
------------------------------------------------------------------------- */
void BondBPM::pack_id1(int n, int i, int j)
{
tagint *tag = atom->tag;
output_data[n] = tag[i];
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_id2(int n, int i, int j)
{
tagint *tag = atom->tag;
output_data[n] = tag[j];
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_time(int n, int i, int j)
{
bigint time = update->ntimestep;
output_data[n] = time;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_x(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][0] + x[j][0])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_y(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][1] + x[j][1])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_z(int n, int i, int j)
{
double **x = atom->x;
output_data[n] = (x[i][2] + x[j][2])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_x_ref(int n, int i, int j)
{
double *x = atom->dvector[index_x_ref];
output_data[n] = (x[i] + x[j])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_y_ref(int n, int i, int j)
{
double *y = atom->dvector[index_y_ref];
output_data[n] = (y[i] + y[j])*0.5;
}
/* ---------------------------------------------------------------------- */
void BondBPM::pack_z_ref(int n, int i, int j)
{
double *z = atom->dvector[index_z_ref];
output_data[n] = (z[i] + z[j])*0.5;
}

181
src/BPM/bond_bpm.h
View File

@ -1,90 +1,91 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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.
------------------------------------------------------------------------- */
#ifndef LMP_BOND_BPM_H
#define LMP_BOND_BPM_H
#include "bond.h"
namespace LAMMPS_NS {
class BondBPM : public Bond {
public:
BondBPM(class LAMMPS *);
virtual ~BondBPM();
virtual void compute(int, int) = 0;
virtual void coeff(int, char **) = 0;
virtual void init_style();
void settings(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *){};
void read_restart(FILE *){};
void write_data(FILE *) {};
double single(int, double, int, int, double &) = 0;
protected:
double r0_max_estimate;
double max_stretch;
char *id_fix_store_local, *id_fix_prop_atom;
class FixStoreLocal *fix_store_local;
class FixUpdateSpecialBonds *fix_update_special_bonds;
void process_broken(int, int);
typedef void (BondBPM::*FnPtrPack)(int,int,int);
FnPtrPack *pack_choice; // ptrs to pack functions
double *output_data;
int prop_atom_flag, nvalues;
int index_x_ref, index_y_ref, index_z_ref;
void pack_id1(int,int,int);
void pack_id2(int,int,int);
void pack_time(int,int,int);
void pack_x(int,int,int);
void pack_y(int,int,int);
void pack_z(int,int,int);
void pack_x_ref(int,int,int);
void pack_y_ref(int,int,int);
void pack_z_ref(int,int,int);
};
} // namespace LAMMPS_NS
#endif
/* ERROR/WARNING messages:
E: Cannot find fix store/local
Fix id cannot be found.
E: Illegal bond_style command
Self-explanatory.
E: Bond style bpm/rotational must include at least one value to output
Must include at least one bond property to store in fix store/local
E: Bond style bpm/rotational cannot be used with 3,4-body interactions
No angle, dihedral, or improper styles can be defined when using
bond style bpm/rotational.
E: Bond style bpm/rotational cannot be used with atom style template
This bond style can change the bond topology which is not
allowed with this atom style.
*/
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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.
------------------------------------------------------------------------- */
#ifndef LMP_BOND_BPM_H
#define LMP_BOND_BPM_H
#include "bond.h"
namespace LAMMPS_NS {
class BondBPM : public Bond {
public:
BondBPM(class LAMMPS *);
virtual ~BondBPM();
virtual void compute(int, int) = 0;
virtual void coeff(int, char **) = 0;
virtual void init_style();
void settings(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *){};
void read_restart(FILE *){};
void write_data(FILE *) {};
double single(int, double, int, int, double &) = 0;
protected:
double r0_max_estimate;
double max_stretch;
char *id_fix_store_local, *id_fix_prop_atom;
class FixStoreLocal *fix_store_local;
class FixUpdateSpecialBonds *fix_update_special_bonds;
class FixBondHistory *fix_bond_history;
void process_broken(int, int);
typedef void (BondBPM::*FnPtrPack)(int,int,int);
FnPtrPack *pack_choice; // ptrs to pack functions
double *output_data;
int prop_atom_flag, nvalues;
int index_x_ref, index_y_ref, index_z_ref;
void pack_id1(int,int,int);
void pack_id2(int,int,int);
void pack_time(int,int,int);
void pack_x(int,int,int);
void pack_y(int,int,int);
void pack_z(int,int,int);
void pack_x_ref(int,int,int);
void pack_y_ref(int,int,int);
void pack_z_ref(int,int,int);
};
} // namespace LAMMPS_NS
#endif
/* ERROR/WARNING messages:
E: Cannot find fix store/local
Fix id cannot be found.
E: Illegal bond_style command
Self-explanatory.
E: Bond style bpm/rotational must include at least one value to output
Must include at least one bond property to store in fix store/local
E: Bond style bpm/rotational cannot be used with 3,4-body interactions
No angle, dihedral, or improper styles can be defined when using
bond style bpm/rotational.
E: Bond style bpm/rotational cannot be used with atom style template
This bond style can change the bond topology which is not
allowed with this atom style.
*/

1436
src/BPM/bond_bpm_rotational.cpp
View File

File diff suppressed because it is too large Load Diff

1
src/BPM/bond_bpm_rotational.h
View File

@ -44,7 +44,6 @@ class BondBPMRotational : public BondBPM {
void allocate();
void store_data();
double store_bond(int, int, int);
class FixBondHistory *fix_bond_history;
};
} // namespace LAMMPS_NS

12
src/BPM/fix_bond_history.cpp
View File

@ -291,4 +291,16 @@ void FixBondHistory::set_arrays(int i)
for (int m = 0; m < nbond; m++)
for (int idata = 0; idata < ndata; idata++)
stored[i][m*ndata+idata] = 0.0;
}
/* ----------------------------------------------------------------------
Remove all data for row by compressing data
------------------------------------------------------------------------- */
void FixBondHistory::delete_bond(int i, int m)
{
double **stored = atom->darray[index];
int n = atom->num_bond[i];
for (int idata = 0; idata < ndata; idata ++)
stored[i][m*ndata+idata] = stored[i][(n-1)*ndata+idata];
}

1
src/BPM/fix_bond_history.h
View File

@ -41,6 +41,7 @@ class FixBondHistory : public Fix {
void update_atom_value(int, int, int, double);
double get_atom_value(int, int, int);
void delete_bond(int,int);
double **bondstore;
int stored_flag;