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verlet.cpp
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Mon, Nov 11, 16:34

verlet.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 "string.h"
#include "verlet.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Verlet::Verlet(LAMMPS *lmp, int narg, char **arg) :
Integrate(lmp, narg, arg) {}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void Verlet::init()
{
Integrate::init();
// warn if no fixes
if (modify->nfix == 0 && comm->me == 0)
error->warning(FLERR,"No fixes defined, atoms won't move");
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_fdotr_compute via sum over ghosts
if (force->newton_pair) virial_style = 2;
else virial_style = 1;
// setup lists of computes for global and per-atom PE and pressure
ev_setup();
// detect if fix omp is present for clearing force arrays
int ifix = modify->find_fix("package_omp");
if (ifix >= 0) external_force_clear = 1;
// set flags for what arrays to clear in force_clear()
// need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
e_flag = 0;
if (atom->e_flag) e_flag = 1;
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void Verlet::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build();
neighbor->ncalls = 0;
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup();
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Verlet::setup_minimal(int flag)
{
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void Verlet::run(int n)
{
bigint ntimestep;
int nflag,sortflag;
int n_post_integrate = modify->n_post_integrate;
int n_pre_exchange = modify->n_pre_exchange;
int n_pre_neighbor = modify->n_pre_neighbor;
int n_pre_force = modify->n_pre_force;
int n_post_force = modify->n_post_force;
int n_end_of_step = modify->n_end_of_step;
if (atom->sortfreq > 0) sortflag = 1;
else sortflag = 0;
for (int i = 0; i < n; i++) {
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
// initial time integration
timer->stamp();
modify->initial_integrate(vflag);
if (n_post_integrate) modify->post_integrate();
timer->stamp(Timer::MODIFY);
// regular communication vs neighbor list rebuild
nflag = neighbor->decide();
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
} else {
if (n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (sortflag && ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
if (n_pre_neighbor) {
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
}
// force computations
force_clear();
timer->stamp();
if (n_pre_force) {
modify->pre_force(vflag);
timer->stamp(Timer::MODIFY);
}
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
// reverse communication of forces
if (force->newton) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
// force modifications, final time integration, diagnostics
if (n_post_force) modify->post_force(vflag);
modify->final_integrate();
if (n_end_of_step) modify->end_of_step();
timer->stamp(Timer::MODIFY);
// all output
if (ntimestep == output->next) {
timer->stamp();
output->write(ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
}
/* ---------------------------------------------------------------------- */
void Verlet::cleanup()
{
modify->post_run();
domain->box_too_small_check();
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
clear other arrays as needed
------------------------------------------------------------------------- */
void Verlet::force_clear()
{
int i;
if (external_force_clear) return;
// clear force on all particles
// if either newton flag is set, also include ghosts
// when using threads always clear all forces.
if (neighbor->includegroup == 0) {
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
size_t nbytes = sizeof(double) * nall;
if (nbytes > 0) {
memset(&(atom->f[0][0]),0,3*nbytes);
if (torqueflag) memset(&(atom->torque[0][0]),0,3*nbytes);
if (erforceflag) memset(&(atom->erforce[0]), 0, nbytes);
if (e_flag) memset(&(atom->de[0]), 0, nbytes);
if (rho_flag) memset(&(atom->drho[0]), 0, nbytes);
}
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
} else {
int nall = atom->nfirst;
double **f = atom->f;
for (i = 0; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
if (force->newton) {
nall = atom->nlocal + atom->nghost;
for (i = atom->nlocal; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = atom->nlocal; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
}
}
}

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