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fix_latte.cpp
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rLAMMPS lammps
fix_latte.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christian Negre (LANL)
------------------------------------------------------------------------- */
#include <stdio.h>
#include <string.h>
#include "fix_latte.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "modify.h"
#include "compute.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
extern "C" {
void latte(int *, int *, double *, int *, int *,
double *, double *, double *, double *,
double *, double *, double *, int*,
double *, double *, double *, double * );
}
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (strcmp(update->unit_style,"metal") != 0)
error->all(FLERR,"Must use units metal with fix latte command");
if (comm->nprocs != 1)
error->all(FLERR,"Fix latte currently runs only in serial");
if (narg != 4) error->all(FLERR,"Illegal fix latte command");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
virial_flag = 1;
thermo_virial = 1;
// store ID of compute pe/atom used to generate Coulomb potential for LATTE
// NULL means LATTE will compute Coulombic potential
coulomb = 0;
id_pe = NULL;
if (strcmp(arg[3],"NULL") != 0) {
coulomb = 1;
error->all(FLERR,"Fix latte does not yet support a LAMMPS calculation "
"of a Coulomb potential");
int n = strlen(arg[3]) + 1;
id_pe = new char[n];
strcpy(id_pe,arg[3]);
int ipe = modify->find_compute(id_pe);
if (ipe < 0) error->all(FLERR,"Could not find fix latte compute ID");
if (modify->compute[ipe]->peatomflag == 0)
error->all(FLERR,"Fix latte compute ID does not compute pe/atom");
}
// initializations
nmax = 0;
qpotential = NULL;
flatte = NULL;
latte_energy = 0.0;
}
/* ---------------------------------------------------------------------- */
FixLatte::~FixLatte()
{
delete [] id_pe;
memory->destroy(qpotential);
memory->destroy(flatte);
}
/* ---------------------------------------------------------------------- */
int FixLatte::setmask()
{
int mask = 0;
//mask |= INITIAL_INTEGRATE;
//mask |= FINAL_INTEGRATE;
mask |= PRE_REVERSE;
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLatte::init()
{
// error checks
if (domain->dimension == 2)
error->all(FLERR,"Fix latte requires 3d problem");
if (coulomb) {
if (atom->q_flag == 0 || force->pair == NULL || force->kspace == NULL)
error->all(FLERR,"Fix latte cannot compute Coulomb potential");
int ipe = modify->find_compute(id_pe);
if (ipe < 0) error->all(FLERR,"Could not find fix latte compute ID");
c_pe = modify->compute[ipe];
}
// must be fully periodic or fully non-periodic
if (domain->nonperiodic == 0) pbcflag = 1;
else if (!domain->xperiodic && !domain->yperiodic && !domain->zperiodic)
pbcflag = 0;
else error->all(FLERR,"Fix latte requires 3d simulation");
// create qpotential & flatte if needed
// for now, assume nlocal will never change
if (coulomb && qpotential == NULL) {
memory->create(qpotential,atom->nlocal,"latte:qpotential");
memory->create(flatte,atom->nlocal,3,"latte:flatte");
}
/*
// warn if any integrate fix comes after this one
// is it actually necessary for q(n) update to come after x,v update ??
int after = 0;
int flag = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(id,modify->fix[i]->id) == 0) after = 1;
else if ((modify->fmask[i] & INITIAL_INTEGRATE) && after) flag = 1;
}
if (flag && comm->me == 0)
error->warning(FLERR,"Fix latte should come after all other "
"integration fixes");
*/
/*
// need a full neighbor list
// could we use a half list?
// perpetual list, built whenever re-neighboring occurs
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
*/
}
/* ---------------------------------------------------------------------- */
void FixLatte::init_list(int id, NeighList *ptr)
{
// list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixLatte::setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixLatte::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixLatte::setup_pre_reverse(int eflag, int vflag)
{
pre_reverse(eflag,vflag);
}
/* ----------------------------------------------------------------------
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
void FixLatte::initial_integrate(int vflag) {}
/* ----------------------------------------------------------------------
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
void FixLatte::pre_reverse(int eflag, int vflag)
{
eflag_caller = eflag;
}
/* ---------------------------------------------------------------------- */
void FixLatte::post_force(int vflag)
{
int eflag = eflag_caller;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
// compute Coulombic potential = pe[i]/q[i]
// invoke compute pe/atom
// wrap with clear/add and trigger pe/atom calculation every step
if (coulomb) {
modify->clearstep_compute();
if (!(c_pe->invoked_flag & INVOKED_PERATOM)) {
c_pe->compute_peratom();
c_pe->invoked_flag |= INVOKED_PERATOM;
}
modify->addstep_compute(update->ntimestep+1);
double *pe = c_pe->vector_atom;
double *q = atom->q;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (q[i]) qpotential[i] = pe[i]/q[i];
else qpotential[i] = 0.0;
}
// hardwire these unsupported flags for now
int coulombflag = 0;
// pe_peratom = 0;
// virial_global = 1; // set via vflag_global at some point
// virial_peratom = 0;
neighflag = 0;
// set flags used by LATTE
// NOTE: LATTE does not compute per-atom energies or virials
int flags[6];
flags[0] = pbcflag; // 1 for fully periodic, 0 for fully non-periodic
flags[1] = coulombflag; // 1 for LAMMPS computes Coulombics, 0 for LATTE
flags[2] = eflag_atom; // 1 to return per-atom energies, 0 for no
flags[3] = vflag_global && thermo_virial; // 1 to return global/per-atom
flags[4] = vflag_atom && thermo_virial; // virial, 0 for no
flags[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no
// setup LATTE arguments
int natoms = atom->nlocal;
double *coords = &atom->x[0][0];
int *type = atom->type;
int ntypes = atom->ntypes;
double *mass = &atom->mass[1];
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *forces;
if (coulomb) forces = &flatte[0][0];
else forces = &atom->f[0][0];
int maxiter = -1;
latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy,
&domain->xz,&domain->yz,
forces,&maxiter,&latte_energy,&atom->v[0][0],&update->dt,virial);
// sum LATTE forces to LAMMPS forces
// e.g. LAMMPS may compute Coulombics at some point
if (coulomb) {
double **f = atom->f;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
f[i][0] += flatte[i][0];
f[i][1] += flatte[i][1];
f[i][2] += flatte[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixLatte::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
void FixLatte::final_integrate() {}
/* ---------------------------------------------------------------------- */
void FixLatte::reset_dt()
{
//dtv = update->dt;
//dtf = 0.5 * update->dt * force->ftm2v;
}
/* ----------------------------------------------------------------------
DFTB energy from LATTE
------------------------------------------------------------------------- */
double FixLatte::compute_scalar()
{
return latte_energy;
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double FixLatte::memory_usage()
{
double bytes = 0.0;
if (coulomb) bytes += nmax * sizeof(double);
if (coulomb) bytes += nmax*3 * sizeof(double);
return bytes;
}
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