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lammps/src/FEP/compute_fep_ta.cpp

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Shifeng Ke (Zhejiang University)
------------------------------------------------------------------------- */
#include "compute_fep_ta.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "improper.h"
#include "kspace.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "pair.h"
#include "timer.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
enum { X, Y, Z };
/* ---------------------------------------------------------------------- */
ComputeFEPTA::ComputeFEPTA(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR, "Illegal number of arguments in compute fep/ta");
scalar_flag = 0;
vector_flag = 1;
size_vector = 3;
extvector = 0;
vector = new double[size_vector];
fepinitflag = 0; // avoid init to run entirely when called by write_data
temp_fep = utils::numeric(FLERR, arg[3], false, lmp);
if (strcmp(arg[4], "xy") == 0) {
tan_axis1 = X;
tan_axis2 = Y;
norm_axis = Z;
} else if (strcmp(arg[4], "xz") == 0) {
tan_axis1 = X;
tan_axis2 = Z;
norm_axis = Y;
} else if (strcmp(arg[4], "yz") == 0) {
tan_axis1 = Y;
tan_axis2 = Z;
norm_axis = X;
} else
error->all(FLERR, "Illegal arguments in compute fep/ta");
scale_factor = utils::numeric(FLERR, arg[5], false, lmp);
// optional keywords
tailflag = 0;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg], "tail") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal optional keyword in compute fep/ta");
tailflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else
error->all(FLERR, "Illegal optional keyword in compute fep/ta");
}
// allocate space for position, force, energy, virial arrays
x_orig = nullptr;
f_orig = nullptr;
peatom_orig = keatom_orig = nullptr;
pvatom_orig = kvatom_orig = nullptr;
allocate_storage();
fixgpu = nullptr;
}
/* ---------------------------------------------------------------------- */
ComputeFEPTA::~ComputeFEPTA()
{
delete[] vector;
deallocate_storage();
}
/* ---------------------------------------------------------------------- */
void ComputeFEPTA::init()
{
int i, j;
if (!fepinitflag) // avoid init to run entirely when called by write_data
fepinitflag = 1;
else
return;
// setup and error checks
if (domain->dimension == 2) { error->all(FLERR, "Cannot compute fep/ta in 2d simulation"); }
if (tailflag) {
if (force->pair->tail_flag == 0)
error->all(FLERR,
"Compute fep/ta 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) {
auto mesg = fmt::format("FEP/TA settings ...\n temperature = {:f}\n", temp_fep);
mesg += fmt::format(" scale factor = {:f}\n", scale_factor);
mesg += fmt::format(" tail {}\n", (tailflag ? "yes" : "no"));
utils::logmesg(lmp, mesg);
}
}
/* ---------------------------------------------------------------------- */
void ComputeFEPTA::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_xfev(); // backup position, force, energy, virial array values
backup_box(); // backup box size
timer->stamp();
if (force->pair && force->pair->compute_flag) {
force->pair->compute(eflag, vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular != Atom::ATOMIC) {
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 (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);
pe0 = compute_pe();
change_box();
timer->stamp();
if (force->pair && force->pair->compute_flag) {
force->pair->compute(eflag, vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular != Atom::ATOMIC) {
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 (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_pe();
restore_xfev(); // restore position, force, energy, virial array values
restore_box(); // restore box size
vector[0] = pe1 - pe0;
vector[1] = exp(-(pe1 - pe0) / (force->boltz * temp_fep));
vector[2] = area_orig * (scale_factor - 1.0);
}
/* ----------------------------------------------------------------------
obtain potential energy from lammps accumulators
------------------------------------------------------------------------- */
double ComputeFEPTA::compute_pe()
{
double eng, eng_potential;
eng = 0.0;
if (force->pair) eng = force->pair->eng_vdwl + force->pair->eng_coul;
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) eng += force->bond->energy;
if (force->angle) eng += force->angle->energy;
if (force->dihedral) eng += force->dihedral->energy;
if (force->improper) eng += force->improper->energy;
}
MPI_Allreduce(&eng, &eng_potential, 1, MPI_DOUBLE, MPI_SUM, world);
if (tailflag) {
double volume = domain->xprd * domain->yprd * domain->zprd;
eng_potential += force->pair->etail / volume;
}
if (force->kspace) eng_potential += force->kspace->energy;
return eng_potential;
}
/* ----------------------------------------------------------------------
apply changes to box
------------------------------------------------------------------------- */
void ComputeFEPTA::change_box()
{
int i;
double **x = atom->x;
int natom = atom->nlocal + atom->nghost;
for (i = 0; i < natom; i++) domain->x2lamda(x[i], x[i]);
domain->boxhi[tan_axis1] *= sqrt(scale_factor);
domain->boxlo[tan_axis1] *= sqrt(scale_factor);
domain->boxhi[tan_axis2] *= sqrt(scale_factor);
domain->boxlo[tan_axis2] *= sqrt(scale_factor);
domain->boxhi[norm_axis] /= scale_factor;
domain->boxlo[norm_axis] /= scale_factor;
domain->set_global_box();
domain->set_local_box();
// remap atom position
for (i = 0; i < natom; i++) domain->lamda2x(x[i], x[i]);
if (force->kspace) force->kspace->setup();
}
/* ----------------------------------------------------------------------
backup box size
------------------------------------------------------------------------- */
void ComputeFEPTA::backup_box()
{
for (int i = 0; i < domain->dimension; i++) {
boxhi_orig[i] = domain->boxhi[i];
boxlo_orig[i] = domain->boxlo[i];
}
area_orig = domain->prd[tan_axis1] * domain->prd[tan_axis2];
}
/* ----------------------------------------------------------------------
restore box size to original values
------------------------------------------------------------------------- */
void ComputeFEPTA::restore_box()
{
for (int i = 0; i < domain->dimension; i++) {
domain->boxhi[i] = boxhi_orig[i];
domain->boxlo[i] = boxlo_orig[i];
}
domain->set_global_box();
domain->set_local_box();
if (force->kspace) force->kspace->setup();
}
/* ----------------------------------------------------------------------
manage storage for position, force, energy, virial arrays
------------------------------------------------------------------------- */
void ComputeFEPTA::allocate_storage()
{
nmax = atom->nmax;
memory->create(x_orig, nmax, 3, "fep:x_orig");
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 (force->kspace) {
memory->create(keatom_orig, nmax, "fep:keatom_orig");
memory->create(kvatom_orig, nmax, 6, "fep:kvatom_orig");
}
}
/* ---------------------------------------------------------------------- */
void ComputeFEPTA::deallocate_storage()
{
memory->destroy(x_orig);
memory->destroy(f_orig);
memory->destroy(peatom_orig);
memory->destroy(pvatom_orig);
memory->destroy(keatom_orig);
memory->destroy(kvatom_orig);
x_orig = nullptr;
f_orig = nullptr;
peatom_orig = keatom_orig = nullptr;
pvatom_orig = kvatom_orig = nullptr;
}
/* ----------------------------------------------------------------------
backup and restore arrays with position, force, energy, virial
------------------------------------------------------------------------- */
void ComputeFEPTA::backup_xfev()
{
int i;
int natom = atom->nlocal + atom->nghost;
double **x = atom->x;
for (i = 0; i < natom; i++) {
x_orig[i][0] = x[i][0];
x_orig[i][1] = x[i][1];
x_orig[i][2] = x[i][2];
}
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;
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) eng_bond_orig = force->bond->energy;
if (force->angle) eng_angle_orig = force->angle->energy;
if (force->dihedral) eng_dihedral_orig = force->dihedral->energy;
if (force->improper) eng_improper_orig = force->improper->energy;
}
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 (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 ComputeFEPTA::restore_xfev()
{
int i;
int natom = atom->nlocal + atom->nghost;
double **x = atom->x;
for (i = 0; i < natom; i++) {
x[i][0] = x_orig[i][0];
x[i][1] = x_orig[i][1];
x[i][2] = x_orig[i][2];
}
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;
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->energy = eng_bond_orig;
if (force->angle) force->angle->energy = eng_angle_orig;
if (force->dihedral) force->dihedral->energy = eng_dihedral_orig;
if (force->improper) force->improper->energy = eng_improper_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 (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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