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lammps/src/USER-FEP/compute_fep.cpp
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compute_fep.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: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <mpi.h>
#include "comm.h"
#include "update.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "kspace.h"
#include "input.h"
#include "fix.h"
#include "modify.h"
#include "variable.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
#include "compute_fep.h"
using namespace LAMMPS_NS;
enum{PAIR,ATOM};
enum{CHARGE};
/* ---------------------------------------------------------------------- */
ComputeFEP::ComputeFEP(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal number of arguments in compute fep");
scalar_flag = 0;
vector_flag = 1;
size_vector = 3;
extvector = 0;
vector = new double[3];
fepinitflag = 0; // avoid init to run entirely when called by write_data
temp_fep = force->numeric(FLERR,arg[3]);
// count # of perturbations
npert = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,
"Illegal pair attribute in compute fep");
npert++;
iarg += 6;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+4 > narg) error->all(FLERR,
"Illegal atom attribute in compute fep");
npert++;
iarg += 4;
} else break;
}
if (npert == 0) error->all(FLERR,"Illegal syntax in compute fep");
perturb = new Perturb[npert];
// parse keywords
npert = 0;
chgflag = 0;
iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
perturb[npert].which = PAIR;
int n = strlen(arg[iarg+1]) + 1;
perturb[npert].pstyle = new char[n];
strcpy(perturb[npert].pstyle,arg[iarg+1]);
n = strlen(arg[iarg+2]) + 1;
perturb[npert].pparam = new char[n];
strcpy(perturb[npert].pparam,arg[iarg+2]);
force->bounds(arg[iarg+3],atom->ntypes,
perturb[npert].ilo,perturb[npert].ihi);
force->bounds(arg[iarg+4],atom->ntypes,
perturb[npert].jlo,perturb[npert].jhi);
if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
n = strlen(&arg[iarg+5][2]) + 1;
perturb[npert].var = new char[n];
strcpy(perturb[npert].var,&arg[iarg+5][2]);
} else error->all(FLERR,"Illegal variable in compute fep");
npert++;
iarg += 6;
} else if (strcmp(arg[iarg],"atom") == 0) {
perturb[npert].which = ATOM;
if (strcmp(arg[iarg+1],"charge") == 0) {
perturb[npert].aparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal atom argument in compute fep");
force->bounds(arg[iarg+2],atom->ntypes,
perturb[npert].ilo,perturb[npert].ihi);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
perturb[npert].var = new char[n];
strcpy(perturb[npert].var,&arg[iarg+3][2]);
} else error->all(FLERR,"Illegal variable in compute fep");
npert++;
iarg += 4;
} else break;
}
// optional keywords
tailflag = 0;
volumeflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"tail") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal optional keyword "
"in compute fep");
if (strcmp(arg[iarg+1],"no") == 0) tailflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) tailflag = 1;
else error->all(FLERR,"Illegal optional keyword in compute fep");
iarg += 2;
} else if (strcmp(arg[iarg],"volume") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal optional keyword "
"in compute fep");
if (strcmp(arg[iarg+1],"no") == 0) volumeflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) volumeflag = 1;
else error->all(FLERR,"Illegal optional keyword in compute fep");
iarg += 2;
} else
error->all(FLERR,"Illegal optional keyword in compute fep");
}
// allocate pair style arrays
int ntype = atom->ntypes;
for (int m = 0; m < npert; m++) {
if (perturb[m].which == PAIR)
memory->create(perturb[m].array_orig,ntype+1,ntype+1,"fep:array_orig");
}
// allocate space for charge, force, energy, virial arrays
f_orig = NULL;
q_orig = NULL;
peatom_orig = keatom_orig = NULL;
pvatom_orig = kvatom_orig = NULL;
allocate_storage();
fixgpu = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeFEP::~ComputeFEP()
{
delete [] vector;
for (int m = 0; m < npert; m++) {
delete [] perturb[m].var;
if (perturb[m].which == PAIR) {
delete [] perturb[m].pstyle;
delete [] perturb[m].pparam;
memory->destroy(perturb[m].array_orig);
}
}
delete [] perturb;
deallocate_storage();
}
/* ---------------------------------------------------------------------- */
void ComputeFEP::init()
{
int i,j;
if (!fepinitflag) // avoid init to run entirely when called by write_data
fepinitflag = 1;
else return;
// setup and error checks
pairflag = 0;
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
pert->ivar = input->variable->find(pert->var);
if (pert->ivar < 0)
error->all(FLERR,"Variable name for compute fep does not exist");
if (!input->variable->equalstyle(pert->ivar))
error->all(FLERR,"Variable for compute fep is of invalid style");
if (force->pair == NULL)
error->all(FLERR,"compute fep pair requires pair interactions");
if (pert->which == PAIR) {
pairflag = 1;
Pair *pair = force->pair_match(pert->pstyle,1);
if (pair == NULL) error->all(FLERR,"compute fep pair style "
"does not exist");
void *ptr = pair->extract(pert->pparam,pert->pdim);
if (ptr == NULL)
error->all(FLERR,"compute fep pair style param not supported");
pert->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if ((strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = pert->ilo; i <= pert->ihi; i++)
for (j = MAX(pert->jlo,i); j <= pert->jhi; j++)
if (!pair->check_ijtype(i,j,pert->pstyle))
error->all(FLERR,"compute fep type pair range is not valid for "
"pair hybrid sub-style");
}
} else if (pert->which == ATOM) {
if (pert->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"compute fep requires atom attribute charge");
}
}
}
if (tailflag) {
if (force->pair->tail_flag == 0)
error->all(FLERR,"Compute fep tail when pair style does not "
"compute tail corrections");
}
// detect if package gpu is present
int ifixgpu = modify->find_fix("package_gpu");
if (ifixgpu >= 0) fixgpu = modify->fix[ifixgpu];
if (comm->me == 0) {
if (screen) {
fprintf(screen, "FEP settings ...\n");
fprintf(screen, " temperature = %f\n", temp_fep);
fprintf(screen, " tail %s\n", (tailflag ? "yes":"no"));
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR)
fprintf(screen, " %s %s %d-%d %d-%d\n", pert->pstyle, pert->pparam,
pert->ilo, pert->ihi, pert->jlo, pert->jhi);
else if (pert->which == ATOM)
fprintf(screen, " %d-%d charge\n", pert->ilo, pert->ihi);
}
}
if (logfile) {
fprintf(logfile, "FEP settings ...\n");
fprintf(logfile, " temperature = %f\n", temp_fep);
fprintf(logfile, " tail %s\n", (tailflag ? "yes":"no"));
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR)
fprintf(logfile, " %s %s %d-%d %d-%d\n", pert->pstyle, pert->pparam,
pert->ilo, pert->ihi, pert->jlo, pert->jhi);
else if (pert->which == ATOM)
fprintf(logfile, " %d-%d charge\n", pert->ilo, pert->ihi);
}
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeFEP::compute_vector()
{
double pe0,pe1;
eflag = 1;
vflag = 0;
invoked_vector = update->ntimestep;
if (atom->nmax > nmax) { // reallocate working arrays if necessary
deallocate_storage();
allocate_storage();
}
backup_qfev(); // backup charge, force, energy, virial array values
backup_params(); // backup pair parameters
timer->stamp();
if (force->pair && force->pair->compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (chgflag && force->kspace && force->kspace->compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
// accumulate force/energy/virial from /gpu pair styles
if (fixgpu) fixgpu->post_force(vflag);
pe0 = compute_epair();
perturb_params();
timer->stamp();
if (force->pair && force->pair->compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (chgflag && force->kspace && force->kspace->compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
// accumulate force/energy/virial from /gpu pair styles
// this is required as to empty the answer queue,
// otherwise the force compute on the GPU in the next step would be incorrect
if (fixgpu) fixgpu->post_force(vflag);
pe1 = compute_epair();
restore_qfev(); // restore charge, force, energy, virial array values
restore_params(); // restore pair parameters
vector[0] = pe1-pe0;
vector[1] = exp(-(pe1-pe0)/(force->boltz*temp_fep));
vector[2] = domain->xprd * domain->yprd * domain->zprd;
if (volumeflag)
vector[1] *= vector[2];
}
/* ----------------------------------------------------------------------
obtain pair energy from lammps accumulators
------------------------------------------------------------------------- */
double ComputeFEP::compute_epair()
{
double eng, eng_pair;
eng = 0.0;
if (force->pair)
eng = force->pair->eng_vdwl + force->pair->eng_coul;
MPI_Allreduce(&eng,&eng_pair,1,MPI_DOUBLE,MPI_SUM,world);
if (tailflag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
eng_pair += force->pair->etail / volume;
}
if (chgflag && force->kspace) eng_pair += force->kspace->energy;
return eng_pair;
}
/* ----------------------------------------------------------------------
apply perturbation to pair, atom parameters based on variable evaluation
------------------------------------------------------------------------- */
void ComputeFEP::perturb_params()
{
int i,j;
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
double delta = input->variable->compute_equal(pert->ivar);
if (pert->which == PAIR) { // modify pair parameters
for (i = pert->ilo; i <= pert->ihi; i++)
for (j = MAX(pert->jlo,i); j <= pert->jhi; j++)
pert->array[i][j] = pert->array_orig[i][j] + delta;
} else if (pert->which == ATOM) {
if (pert->aparam == CHARGE) { // modify charges
int *atype = atom->type;
double *q = atom->q;
int *mask = atom->mask;
int natom = atom->nlocal + atom->nghost;
for (i = 0; i < natom; i++)
if (atype[i] >= pert->ilo && atype[i] <= pert->ihi)
if (mask[i] & groupbit)
q[i] += delta;
}
}
}
// re-initialize pair styles if any PAIR settings were changed
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections
if (pairflag) force->pair->reinit();
// reset KSpace charges if charges have changed
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
backup pair parameters
------------------------------------------------------------------------- */
void ComputeFEP::backup_params()
{
int i,j;
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR) {
for (i = pert->ilo; i <= pert->ihi; i++)
for (j = MAX(pert->jlo,i); j <= pert->jhi; j++)
pert->array_orig[i][j] = pert->array[i][j];
}
}
}
/* ----------------------------------------------------------------------
restore pair parameters to original values
------------------------------------------------------------------------- */
void ComputeFEP::restore_params()
{
int i,j;
for (int m = 0; m < npert; m++) {
Perturb *pert = &perturb[m];
if (pert->which == PAIR) {
for (i = pert->ilo; i <= pert->ihi; i++)
for (j = MAX(pert->jlo,i); j <= pert->jhi; j++)
pert->array[i][j] = pert->array_orig[i][j];
}
}
if (pairflag) force->pair->reinit();
// reset KSpace charges if charges have changed
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
manage storage for charge, force, energy, virial arrays
------------------------------------------------------------------------- */
void ComputeFEP::allocate_storage()
{
nmax = atom->nmax;
memory->create(f_orig,nmax,3,"fep:f_orig");
memory->create(peatom_orig,nmax,"fep:peatom_orig");
memory->create(pvatom_orig,nmax,6,"fep:pvatom_orig");
if (chgflag) {
memory->create(q_orig,nmax,"fep:q_orig");
if (force->kspace) {
memory->create(keatom_orig,nmax,"fep:keatom_orig");
memory->create(kvatom_orig,nmax,6,"fep:kvatom_orig");
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeFEP::deallocate_storage()
{
memory->destroy(f_orig);
memory->destroy(peatom_orig);
memory->destroy(pvatom_orig);
memory->destroy(q_orig);
memory->destroy(keatom_orig);
memory->destroy(kvatom_orig);
f_orig = NULL;
q_orig = NULL;
peatom_orig = keatom_orig = NULL;
pvatom_orig = kvatom_orig = NULL;
}
/* ----------------------------------------------------------------------
backup and restore arrays with charge, force, energy, virial
------------------------------------------------------------------------- */
void ComputeFEP::backup_qfev()
{
int i;
int nall = atom->nlocal + atom->nghost;
int natom = atom->nlocal;
if (force->newton || force->kspace->tip4pflag)
natom += atom->nghost;
double **f = atom->f;
for (i = 0; i < natom; i++) {
f_orig[i][0] = f[i][0];
f_orig[i][1] = f[i][1];
f_orig[i][2] = f[i][2];
}
eng_vdwl_orig = force->pair->eng_vdwl;
eng_coul_orig = force->pair->eng_coul;
pvirial_orig[0] = force->pair->virial[0];
pvirial_orig[1] = force->pair->virial[1];
pvirial_orig[2] = force->pair->virial[2];
pvirial_orig[3] = force->pair->virial[3];
pvirial_orig[4] = force->pair->virial[4];
pvirial_orig[5] = force->pair->virial[5];
if (update->eflag_atom) {
double *peatom = force->pair->eatom;
for (i = 0; i < natom; i++)
peatom_orig[i] = peatom[i];
}
if (update->vflag_atom) {
double **pvatom = force->pair->vatom;
for (i = 0; i < natom; i++) {
pvatom_orig[i][0] = pvatom[i][0];
pvatom_orig[i][1] = pvatom[i][1];
pvatom_orig[i][2] = pvatom[i][2];
pvatom_orig[i][3] = pvatom[i][3];
pvatom_orig[i][4] = pvatom[i][4];
pvatom_orig[i][5] = pvatom[i][5];
}
}
if (chgflag) {
double *q = atom->q;
for (i = 0; i < nall; i++)
q_orig[i] = q[i];
if (force->kspace) {
energy_orig = force->kspace->energy;
kvirial_orig[0] = force->kspace->virial[0];
kvirial_orig[1] = force->kspace->virial[1];
kvirial_orig[2] = force->kspace->virial[2];
kvirial_orig[3] = force->kspace->virial[3];
kvirial_orig[4] = force->kspace->virial[4];
kvirial_orig[5] = force->kspace->virial[5];
if (update->eflag_atom) {
double *keatom = force->kspace->eatom;
for (i = 0; i < natom; i++)
keatom_orig[i] = keatom[i];
}
if (update->vflag_atom) {
double **kvatom = force->kspace->vatom;
for (i = 0; i < natom; i++) {
kvatom_orig[i][0] = kvatom[i][0];
kvatom_orig[i][1] = kvatom[i][1];
kvatom_orig[i][2] = kvatom[i][2];
kvatom_orig[i][3] = kvatom[i][3];
kvatom_orig[i][4] = kvatom[i][4];
kvatom_orig[i][5] = kvatom[i][5];
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeFEP::restore_qfev()
{
int i;
int nall = atom->nlocal + atom->nghost;
int natom = atom->nlocal;
if (force->newton || force->kspace->tip4pflag)
natom += atom->nghost;
double **f = atom->f;
for (i = 0; i < natom; i++) {
f[i][0] = f_orig[i][0];
f[i][1] = f_orig[i][1];
f[i][2] = f_orig[i][2];
}
force->pair->eng_vdwl = eng_vdwl_orig;
force->pair->eng_coul = eng_coul_orig;
force->pair->virial[0] = pvirial_orig[0];
force->pair->virial[1] = pvirial_orig[1];
force->pair->virial[2] = pvirial_orig[2];
force->pair->virial[3] = pvirial_orig[3];
force->pair->virial[4] = pvirial_orig[4];
force->pair->virial[5] = pvirial_orig[5];
if (update->eflag_atom) {
double *peatom = force->pair->eatom;
for (i = 0; i < natom; i++)
peatom[i] = peatom_orig[i];
}
if (update->vflag_atom) {
double **pvatom = force->pair->vatom;
for (i = 0; i < natom; i++) {
pvatom[i][0] = pvatom_orig[i][0];
pvatom[i][1] = pvatom_orig[i][1];
pvatom[i][2] = pvatom_orig[i][2];
pvatom[i][3] = pvatom_orig[i][3];
pvatom[i][4] = pvatom_orig[i][4];
pvatom[i][5] = pvatom_orig[i][5];
}
}
if (chgflag) {
double *q = atom->q;
for (i = 0; i < nall; i++)
q[i] = q_orig[i];
if (force->kspace) {
force->kspace->energy = energy_orig;
force->kspace->virial[0] = kvirial_orig[0];
force->kspace->virial[1] = kvirial_orig[1];
force->kspace->virial[2] = kvirial_orig[2];
force->kspace->virial[3] = kvirial_orig[3];
force->kspace->virial[4] = kvirial_orig[4];
force->kspace->virial[5] = kvirial_orig[5];
if (update->eflag_atom) {
double *keatom = force->kspace->eatom;
for (i = 0; i < natom; i++)
keatom[i] = keatom_orig[i];
}
if (update->vflag_atom) {
double **kvatom = force->kspace->vatom;
for (i = 0; i < natom; i++) {
kvatom[i][0] = kvatom_orig[i][0];
kvatom[i][1] = kvatom_orig[i][1];
kvatom[i][2] = kvatom_orig[i][2];
kvatom[i][3] = kvatom_orig[i][3];
kvatom[i][4] = kvatom_orig[i][4];
kvatom[i][5] = kvatom_orig[i][5];
}
}
}
}
}
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