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pppm_cg.cpp
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pppm_cg.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "pppm_cg.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define OFFSET 16384
#define SMALLQ 0.00001
#if defined(FFT_SINGLE)
#define ZEROF 0.0f
#else
#define ZEROF 0.0
#endif
/* ---------------------------------------------------------------------- */
PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPMOld(lmp, narg, arg)
{
if ((narg < 1) || (narg > 2))
error->all(FLERR,"Illegal kspace_style pppm/cg command");
if (narg == 2)
smallq = atof(arg[1]);
else
smallq = SMALLQ;
num_charged = -1;
is_charged = NULL;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPMCG::~PPPMCG()
{
memory->destroy(is_charged);
}
/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMCG::compute(int eflag, int vflag)
{
int i,j;
// set energy/virial flags
// invoke allocate_peratom() if needed for first time
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
if (evflag_atom && !peratom_allocate_flag) {
allocate_peratom();
peratom_allocate_flag = 1;
}
// convert atoms from box to lamda coords
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
domain->x2lamda(atom->nlocal);
}
// extend size of per-atom arrays if necessary
if (atom->nlocal > nmax) {
memory->destroy(part2grid);
memory->destroy(is_charged);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"pppm:part2grid");
memory->create(is_charged,nmax,"pppm/cg:is_charged");
}
// one time setup message
if (num_charged < 0) {
bigint charged_all, charged_num;
double charged_frac, charged_fmax, charged_fmin;
num_charged=0;
for (i=0; i < atom->nlocal; ++i)
if (fabs(atom->q[i]) > smallq)
++num_charged;
// get fraction of charged particles per domain
if (atom->nlocal > 0)
charged_frac = static_cast<double>(num_charged) * 100.0
/ static_cast<double>(atom->nlocal);
else
charged_frac = 0.0;
MPI_Reduce(&charged_frac,&charged_fmax,1,MPI_DOUBLE,MPI_MAX,0,world);
MPI_Reduce(&charged_frac,&charged_fmin,1,MPI_DOUBLE,MPI_MIN,0,world);
// get fraction of charged particles overall
charged_num = num_charged;
MPI_Reduce(&charged_num,&charged_all,1,MPI_LMP_BIGINT,MPI_SUM,0,world);
charged_frac = static_cast<double>(charged_all) * 100.0
/ static_cast<double>(atom->natoms);
if (me == 0) {
if (screen)
fprintf(screen,
" PPPM/cg optimization cutoff: %g\n"
" Total charged atoms: %.1f%%\n"
" Min/max charged atoms/proc: %.1f%% %.1f%%\n",
smallq,charged_frac,charged_fmin,charged_fmax);
if (logfile)
fprintf(logfile,
" PPPM/cg optimization cutoff: %g\n"
" Total charged atoms: %.1f%%\n"
" Min/max charged atoms/proc: %.1f%% %.1f%%\n",
smallq,charged_frac,charged_fmin,charged_fmax);
}
}
num_charged = 0;
for (i = 0; i < atom->nlocal; ++i)
if (fabs(atom->q[i]) > smallq) {
is_charged[num_charged] = i;
++num_charged;
}
// find grid points for all my particles
// map my particle charge onto my local 3d density grid
particle_map();
make_rho();
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
brick2fft();
// compute potential gradient on my FFT grid and
// portion of e_long on this proc's FFT grid
// return gradients (electric fields) in 3d brick decomposition
// also performs per-atom calculations via poisson_peratom()
poisson();
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks
fillbrick();
// extra per-atom energy/virial communication
if (evflag_atom) fillbrick_peratom();
// calculate the force on my particles
fieldforce();
// extra per-atom energy/virial communication
if (evflag_atom) fieldforce_peratom();
// sum global energy across procs and add in volume-dependent term
const double qscale = force->qqrd2e * scale;
if (eflag_global) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qscale;
}
// sum global virial across procs
if (vflag_global) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
}
// per-atom energy/virial
// energy includes self-energy correction
if (evflag_atom) {
double *q = atom->q;
int nlocal = atom->nlocal;
if (eflag_atom) {
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
eatom[i] *= 0.5;
eatom[i] -= g_ewald*q[i]*q[i]/MY_PIS + MY_PI2*q[i]*qsum /
(g_ewald*g_ewald*volume);
eatom[i] *= qscale;
}
}
if (vflag_atom) {
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
for (int n = 0; n < 6; n++) vatom[i][n] *= 0.5*q[i]*qscale;
}
}
}
// 2d slab correction
if (slabflag) slabcorr();
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMCG::particle_map()
{
int nx,ny,nz;
double **x = atom->x;
int flag = 0;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx = static_cast<int> ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET;
nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET;
part2grid[i][0] = nx;
part2grid[i][1] = ny;
part2grid[i][2] = nz;
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
ny+nlower < nylo_out || ny+nupper > nyhi_out ||
nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag = 1;
}
if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM");
}
/* ----------------------------------------------------------------------
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
in global grid
------------------------------------------------------------------------- */
void PPPMCG::make_rho()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
// clear 3d density array
FFT_SCALAR *vec = &density_brick[nzlo_out][nylo_out][nxlo_out];
for (i = 0; i < ngrid; i++) vec[i] = ZEROF;
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
double *q = atom->q;
double **x = atom->x;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
z0 = delvolinv * q[i];
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
x0 = y0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
density_brick[mz][my][mx] += x0*rho1d[0][l];
}
}
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMCG::fieldforce()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR ekx,eky,ekz;
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
// ek = 3 components of E-field on particle
double *q = atom->q;
double **x = atom->x;
double **f = atom->f;
for (int j = 0; j < num_charged; j++) {
i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
ekx = eky = ekz = ZEROF;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
y0 = z0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
ekx -= x0*vdx_brick[mz][my][mx];
eky -= x0*vdy_brick[mz][my][mx];
ekz -= x0*vdz_brick[mz][my][mx];
}
}
}
// convert E-field to force
const double qfactor = force->qqrd2e * scale * q[i];
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
f[i][2] += qfactor*ekz;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get per-atom energy/virial
------------------------------------------------------------------------- */
void PPPMCG::fieldforce_peratom()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR u,v0,v1,v2,v3,v4,v5;
// loop over my charges, interpolate from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
double *q = atom->q;
double **x = atom->x;
double **f = atom->f;
for (int j = 0; j < num_charged; j++) {
i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
u = v0 = v1 = v2 = v3 = v4 = v5 = ZEROF;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
y0 = z0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
if (eflag_atom) u += x0*u_brick[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
v2 += x0*v2_brick[mz][my][mx];
v3 += x0*v3_brick[mz][my][mx];
v4 += x0*v4_brick[mz][my][mx];
v5 += x0*v5_brick[mz][my][mx];
}
}
}
}
if (eflag_atom) eatom[i] += q[i]*u;
if (vflag_atom) {
vatom[i][0] += v0;
vatom[i][1] += v1;
vatom[i][2] += v2;
vatom[i][3] += v3;
vatom[i][4] += v4;
vatom[i][5] += v5;
}
}
}
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
periodically repeating slabs. Yields good approximation to 2D Ewald if
adequate empty space is left between repeating slabs (J. Chem. Phys.
111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void PPPMCG::slabcorr()
{
// compute local contribution to global dipole moment
double *q = atom->q;
double **x = atom->x;
double dipole = 0.0;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
dipole += q[i]*x[i][2];
}
// sum local contributions to get global dipole moment
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
const double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
const double qscale = force->qqrd2e * scale;
if (eflag_global) energy += qscale * e_slabcorr;
//per-atom energy
if (eflag_atom) {
double efact = 2.0*MY_PI*dipole_all/volume;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
eatom[i] += qscale * q[i]*x[i][2]*efact;
}
}
// add on force corrections
const double ffact = -4.0*MY_PI*dipole_all/volume * qscale;
double **f = atom->f;
for (int j = 0; j < num_charged; j++) {
int i = is_charged[j];
f[i][2] += q[i]*ffact;
}
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double PPPMCG::memory_usage()
{
double bytes = PPPMOld::memory_usage();
bytes += nmax * sizeof(int);
return bytes;
}

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