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lammps/src/bond.cpp

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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 "bond.h"
#include <mpi.h>
#include <ctime>
#include <string>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "suffix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include "utils.h"
#include "fmt/format.h"
using namespace LAMMPS_NS;
enum{NONE,LINEAR,SPLINE};
/* -----------------------------------------------------------------------
set bond contribution to Vdwl energy to 0.0
a particular bond style can override this
------------------------------------------------------------------------- */
Bond::Bond(LAMMPS *lmp) : Pointers(lmp)
{
energy = 0.0;
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
writedata = 1;
allocated = 0;
suffix_flag = Suffix::NONE;
maxeatom = maxvatom = 0;
eatom = NULL;
vatom = NULL;
setflag = NULL;
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
copymode = 0;
}
/* ---------------------------------------------------------------------- */
Bond::~Bond()
{
if (copymode) return;
memory->destroy(eatom);
memory->destroy(vatom);
}
/* ----------------------------------------------------------------------
check if all coeffs are set
------------------------------------------------------------------------- */
void Bond::init()
{
if (!allocated && atom->nbondtypes)
error->all(FLERR,"Bond coeffs are not set");
for (int i = 1; i <= atom->nbondtypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All bond coeffs are not set");
init_style();
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
void Bond::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
evflag = 1;
eflag_either = eflag;
eflag_global = eflag % 2;
eflag_atom = eflag / 2;
vflag_either = vflag;
vflag_global = vflag % 4;
// per-atom virial and per-atom centroid virial are the same for bonds
vflag_atom = vflag / 4;
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
if (alloc) {
memory->destroy(eatom);
memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom");
}
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
if (alloc) {
memory->destroy(vatom);
memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom");
}
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
if (vflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
for (i = 0; i < n; i++) {
vatom[i][0] = 0.0;
vatom[i][1] = 0.0;
vatom[i][2] = 0.0;
vatom[i][3] = 0.0;
vatom[i][4] = 0.0;
vatom[i][5] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */
void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
double ebond, double fbond,
double delx, double dely, double delz)
{
double ebondhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) energy += ebond;
else {
ebondhalf = 0.5*ebond;
if (i < nlocal) energy += ebondhalf;
if (j < nlocal) energy += ebondhalf;
}
}
if (eflag_atom) {
ebondhalf = 0.5*ebond;
if (newton_bond || i < nlocal) eatom[i] += ebondhalf;
if (newton_bond || j < nlocal) eatom[j] += ebondhalf;
}
}
if (vflag_either) {
v[0] = delx*delx*fbond;
v[1] = dely*dely*fbond;
v[2] = delz*delz*fbond;
v[3] = delx*dely*fbond;
v[4] = delx*delz*fbond;
v[5] = dely*delz*fbond;
if (vflag_global) {
if (newton_bond) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ----------------------------------------------------------------------
write a table of bond potential energy/force vs distance to a file
------------------------------------------------------------------------- */
void Bond::write_file(int narg, char **arg)
{
if (narg != 6 && narg !=8) error->all(FLERR,"Illegal bond_write command");
// parse optional arguments
int itype = 0;
int jtype = 0;
if (narg == 8) {
itype = force->inumeric(FLERR,arg[6]);
jtype = force->inumeric(FLERR,arg[7]);
if (itype < 1 || itype > atom->ntypes || jtype < 1 || jtype > atom->ntypes)
error->all(FLERR,"Invalid atom types in bond_write command");
}
int btype = force->inumeric(FLERR,arg[0]);
int n = force->inumeric(FLERR,arg[1]);
double inner = force->numeric(FLERR,arg[2]);
double outer = force->numeric(FLERR,arg[3]);
if (inner <= 0.0 || inner >= outer)
error->all(FLERR,"Invalid rlo/rhi values in bond_write command");
double r0 = equilibrium_distance(btype);
// open file in append mode if exists
// add line with DATE: and UNITS: tag when creating new file
// print header in format used by bond_style table
FILE *fp = nullptr;
if (comm->me == 0) {
std::string table_file = arg[4];
// units sanity check:
// - if this is the first time we write to this potential file,
// write out a line with "DATE:" and "UNITS:" tags
// - if the file already exists, print a message about appending
// while printing the date and check that units are consistent.
if (utils::file_is_readable(table_file)) {
std::string units = utils::get_potential_units(table_file,"table");
if (!units.empty() && (units != update->unit_style)) {
error->one(FLERR,fmt::format("Trying to append to a table file "
"with UNITS: {} while units are {}",
units, update->unit_style));
}
std::string date = utils::get_potential_date(table_file,"table");
utils::logmesg(lmp,fmt::format("Appending to table file {} with "
"DATE: {}\n", table_file, date));
fp = fopen(table_file.c_str(),"a");
} else {
char datebuf[16];
time_t tv = time(NULL);
strftime(datebuf,15,"%Y-%m-%d",localtime(&tv));
utils::logmesg(lmp,fmt::format("Creating table file {} with "
"DATE: {}\n", table_file, datebuf));
fp = fopen(table_file.c_str(),"w");
if (fp) fmt::print(fp,"# DATE: {} UNITS: {} Created by bond_write\n",
datebuf, update->unit_style);
}
if (fp == NULL)
error->one(FLERR,fmt::format("Cannot open bond_write file {}: {}",
arg[4], utils::getsyserror()));
}
// initialize potentials before evaluating bond potential
// insures all bond coeffs are set and force constants
// also initialize neighbor so that neighbor requests are processed
// NOTE: might be safest to just do lmp->init()
force->init();
neighbor->init();
if (comm->me == 0) {
double r,e,f;
// evaluate energy and force at each of N distances
// note that Bond::single() takes r**2 and returns f/r.
fprintf(fp,"# Bond potential %s for bond type %d: i,r,energy,force\n",
force->bond_style,btype);
fprintf(fp,"\n%s\nN %d EQ %.15g\n\n",arg[5],n,r0);
const double dr = (outer-inner) / static_cast<double>(n-1);
for (int i = 0; i < n; i++) {
r = inner + dr * static_cast<double>(i);
e = single(btype,r*r,itype,jtype,f);
fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f*r);
}
fclose(fp);
}
}
/* ---------------------------------------------------------------------- */
double Bond::memory_usage()
{
double bytes = comm->nthreads*maxeatom * sizeof(double);
bytes += comm->nthreads*maxvatom*6 * sizeof(double);
return bytes;
}
/* -----------------------------------------------------------------------
Reset all type-based bond params via init.
-------------------------------------------------------------------------- */
void Bond::reinit()
{
if (!reinitflag)
error->all(FLERR,"Fix adapt interface to this bond style not supported");
init();
}
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