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lammps/src/KSPACE/pppm_stagger.cpp
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pppm_stagger.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: Stan Moore (Sandia)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "pppm_stagger.h"
#include "atom.h"
#include "gridcomm.h"
#include "force.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define OFFSET 16384
#define EPS_HOC 1.0e-7
enum{REVERSE_RHO};
enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#define ONEF 1.0f
#else
#define ZEROF 0.0
#define ONEF 1.0
#endif
/* ---------------------------------------------------------------------- */
PPPMStagger::PPPMStagger(LAMMPS *lmp, int narg, char **arg) :
PPPM(lmp, narg, arg),
gf_b2(NULL)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/stagger command");
stagger_flag = 1;
group_group_enable = 0;
memory->create(gf_b2,8,7,"pppm_stagger:gf_b2");
gf_b2[1][0] = 1.0;
gf_b2[2][0] = 5.0 / 6.0;
gf_b2[2][1] = 1.0 / 6.0;
gf_b2[3][0] = 61.0 / 120.0;
gf_b2[3][1] = 29.0 / 60.0;
gf_b2[3][2] = 1.0 / 120.0;
gf_b2[4][0] = 277.0 / 1008.0;
gf_b2[4][1] = 1037.0 / 1680.0;
gf_b2[4][2] = 181.0 / 1680.00;
gf_b2[4][3] = 1.0 / 5040.0;
gf_b2[5][0] = 50521.0 / 362880.0;
gf_b2[5][1] = 7367.0 / 12960.0;
gf_b2[5][2] = 16861.0 / 60480.0;
gf_b2[5][3] = 1229.0 / 90720.0;
gf_b2[5][4] = 1.0 / 362880.0;
gf_b2[6][0] = 540553.0 / 7983360.0;
gf_b2[6][1] = 17460701.0 / 39916800.0;
gf_b2[6][2] = 8444893.0 / 19958400.0;
gf_b2[6][3] = 1409633.0 / 19958400.0;
gf_b2[6][4] = 44281.0 / 39916800.0;
gf_b2[6][5] = 1.0 / 39916800.0;
gf_b2[7][0] = 199360981.0 / 6227020800.0;
gf_b2[7][1] = 103867703.0 / 345945600.0;
gf_b2[7][2] = 66714163.0 / 138378240.0;
gf_b2[7][3] = 54085121.0 / 311351040.0;
gf_b2[7][4] = 1640063.0 / 138378240.0;
gf_b2[7][5] = 671.0 / 10483200.0;
gf_b2[7][6] = 1.0 / 6227020800.0;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPMStagger::~PPPMStagger()
{
memory->destroy(gf_b2);
}
/* ----------------------------------------------------------------------
called once before run
------------------------------------------------------------------------- */
void PPPMStagger::init()
{
// error check
if (domain->triclinic)
error->all(FLERR,"Cannot (yet) use kspace_style pppm/stagger "
"with triclinic systems");
PPPM::init();
}
/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMStagger::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();
cg_peratom->ghost_notify();
cg_peratom->setup();
}
// 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->nmax > nmax) {
memory->destroy(part2grid);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"pppm:part2grid");
}
nstagger = 2;
stagger = 0.0;
for (int n=0; n<nstagger; n++) {
// 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
cg->reverse_comm(this,REVERSE_RHO);
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
if (differentiation_flag == 1) cg->forward_comm(this,FORWARD_AD);
else cg->forward_comm(this,FORWARD_IK);
// extra per-atom energy/virial communication
if (evflag_atom) {
if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
}
// calculate the force on my particles
fieldforce();
// extra per-atom energy/virial communication
if (evflag_atom) fieldforce_peratom();
stagger += 1.0/float(nstagger);
}
// update qsum and qsqsum, if atom count has changed and energy needed
if ((eflag_global || eflag_atom) && atom->natoms != natoms_original) {
qsum_qsq();
natoms_original = atom->natoms;
}
// sum global energy across procs and add in volume-dependent term
const double qscale = 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/float(nstagger);
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]/float(nstagger);
}
// per-atom energy/virial
// energy includes self-energy correction
// ntotal accounts for TIP4P tallying eatom/vatom for ghost atoms
if (evflag_atom) {
double *q = atom->q;
int nlocal = atom->nlocal;
int ntotal = nlocal;
if (tip4pflag) ntotal += atom->nghost;
if (eflag_atom) {
for (i = 0; i < nlocal; i++) {
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;
}
for (i = nlocal; i < ntotal; i++) eatom[i] *= 0.5*qscale;
}
if (vflag_atom) {
for (i = 0; i < ntotal; i++)
for (j = 0; j < 6; j++) vatom[i][j] *= 0.5*qscale;
}
}
// 2d slab correction
if (slabflag == 1) slabcorr();
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
compute qopt
------------------------------------------------------------------------- */
double PPPMStagger::compute_qopt()
{
if (differentiation_flag == 1)
return compute_qopt_ad();
double qopt = 0.0;
const double * const prd = domain->prd;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
double snx,sny,snz;
double cnx,cny,cnz;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,sum2,dot1,dot2;
double numerator,denominator;
double u1,u2,u3,sqk;
int k,l,m,nx,ny,nz,kper,lper,mper;
const int nbx = 2;
const int nby = 2;
const int nbz = 2;
const int twoorder = 2*order;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm));
cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm);
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
sny = square(sin(0.5*unitky*lper*yprd/ny_pppm));
cny = cos(0.5*unitky*lper*yprd/ny_pppm);
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm));
cnx = cos(0.5*unitkx*kper*xprd/nx_pppm);
sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
if (sqk != 0.0) {
numerator = MY_4PI/sqk;
denominator = 0.5*(gf_denom(snx,sny,snz) + gf_denom2(cnx,cny,cnz));
sum1 = 0.0;
sum2 = 0.0;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
dot2 = qx*qx + qy*qy + qz*qz;
u1 = sx*sy*sz;
u2 = wx*wy*wz;
u3 = numerator*u1*u2*dot1;
sum1 += u1*u1*MY_4PI*MY_4PI/dot2;
sum2 += u3*u3/dot2;
}
}
}
qopt += sum1 - sum2/denominator;
}
}
}
}
double qopt_all;
MPI_Allreduce(&qopt,&qopt_all,1,MPI_DOUBLE,MPI_SUM,world);
return qopt_all;
}
/* ----------------------------------------------------------------------
compute qopt_ad
------------------------------------------------------------------------- */
double PPPMStagger::compute_qopt_ad()
{
double qopt = 0.0;
const double * const prd = domain->prd;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,sum2,sum3,sum4,sum5,sum6,dot2;
double u1,u2,sqk;
int k,l,m,nx,ny,nz,kper,lper,mper;
const int nbx = 2;
const int nby = 2;
const int nbz = 2;
const int twoorder = 2*order;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
if (sqk != 0.0) {
sum1 = 0.0;
sum2 = 0.0;
sum3 = 0.0;
sum4 = 0.0;
sum5 = 0.0;
sum6 = 0.0;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
dot2 = qx*qx + qy*qy + qz*qz;
u1 = sx*sy*sz;
u2 = wx*wy*wz;
sum1 += u1*u1/dot2*MY_4PI*MY_4PI;
sum2 += u1*u1*u2*u2*MY_4PI*MY_4PI;
sum3 += u2;
sum4 += dot2*u2;
sum5 += u2*powint(-1.0,nx+ny+nz);
sum6 += dot2*u2*powint(-1.0,nx+ny+nz);
}
}
}
qopt += sum1 - sum2/(0.5*(sum3*sum4 + sum5*sum6));
}
}
}
}
double qopt_all;
MPI_Allreduce(&qopt,&qopt_all,1,MPI_DOUBLE,MPI_SUM,world);
return qopt_all;
}
/* ----------------------------------------------------------------------
pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPMStagger::compute_gf_denom()
{
if (gf_b) memory->destroy(gf_b);
memory->create(gf_b,order,"pppm:gf_b");
int k,l,m;
for (l = 1; l < order; l++) gf_b[l] = 0.0;
gf_b[0] = 1.0;
for (m = 1; m < order; m++) {
for (l = m; l > 0; l--)
gf_b[l] = 4.0 * (gf_b[l]*(l-m)*(l-m-0.5)-gf_b[l-1]*(l-m-1)*(l-m-1));
gf_b[0] = 4.0 * (gf_b[0]*(l-m)*(l-m-0.5));
}
bigint ifact = 1;
for (k = 1; k < 2*order; k++) ifact *= k;
double gaminv = 1.0/ifact;
for (l = 0; l < order; l++) gf_b[l] *= gaminv;
}
/* ----------------------------------------------------------------------
pre-compute modified (Hockney-Eastwood) Coulomb Green's function
------------------------------------------------------------------------- */
void PPPMStagger::compute_gf_ik()
{
const double * const prd = domain->prd;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
double snx,sny,snz;
double cnx,cny,cnz;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,dot1,dot2;
double numerator,denominator;
double sqk;
int k,l,m,n,nx,ny,nz,kper,lper,mper;
const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
pow(-log(EPS_HOC),0.25));
const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
pow(-log(EPS_HOC),0.25));
const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
pow(-log(EPS_HOC),0.25));
const int twoorder = 2*order;
n = 0;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm));
cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm);
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
sny = square(sin(0.5*unitky*lper*yprd/ny_pppm));
cny = cos(0.5*unitky*lper*yprd/ny_pppm);
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm));
cnx = cos(0.5*unitkx*kper*xprd/nx_pppm);
sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
if (sqk != 0.0) {
numerator = MY_4PI/sqk;
denominator = 0.5*(gf_denom(snx,sny,snz) + gf_denom2(cnx,cny,cnz));
sum1 = 0.0;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
dot2 = qx*qx+qy*qy+qz*qz;
sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
}
}
}
greensfn[n++] = numerator*sum1/denominator;
} else greensfn[n++] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
compute optimized Green's function for energy calculation
------------------------------------------------------------------------- */
void PPPMStagger::compute_gf_ad()
{
const double * const prd = domain->prd;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
double snx,sny,snz,sqk;
double cnx,cny,cnz;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double numerator,denominator;
int k,l,m,n,kper,lper,mper;
const int twoorder = 2*order;
for (int i = 0; i < 6; i++) sf_coeff[i] = 0.0;
n = 0;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
qz = unitkz*mper;
snz = square(sin(0.5*qz*zprd_slab/nz_pppm));
cnz = cos(0.5*qz*zprd_slab/nz_pppm);
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
qy = unitky*lper;
sny = square(sin(0.5*qy*yprd/ny_pppm));
cny = cos(0.5*qy*yprd/ny_pppm);
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
qx = unitkx*kper;
snx = square(sin(0.5*qx*xprd/nx_pppm));
cnx = cos(0.5*qx*xprd/nx_pppm);
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
sqk = qx*qx + qy*qy + qz*qz;
if (sqk != 0.0) {
numerator = MY_4PI/sqk;
denominator = 0.5*(gf_denom(snx,sny,snz) + gf_denom2(cnx,cny,cnz));
greensfn[n] = numerator*sx*sy*sz*wx*wy*wz/denominator;
sf_coeff[0] += sf_precoeff1[n]*greensfn[n];
sf_coeff[1] += sf_precoeff2[n]*greensfn[n];
sf_coeff[2] += sf_precoeff3[n]*greensfn[n];
sf_coeff[3] += sf_precoeff4[n]*greensfn[n];
sf_coeff[4] += sf_precoeff5[n]*greensfn[n];
sf_coeff[5] += sf_precoeff6[n]*greensfn[n];
n++;
} else {
greensfn[n] = 0.0;
sf_coeff[0] += sf_precoeff1[n]*greensfn[n];
sf_coeff[1] += sf_precoeff2[n]*greensfn[n];
sf_coeff[2] += sf_precoeff3[n]*greensfn[n];
sf_coeff[3] += sf_precoeff4[n]*greensfn[n];
sf_coeff[4] += sf_precoeff5[n]*greensfn[n];
sf_coeff[5] += sf_precoeff6[n]*greensfn[n];
n++;
}
}
}
}
// compute the coefficients for the self-force correction
double prex, prey, prez;
prex = prey = prez = MY_PI/volume;
prex *= nx_pppm/xprd;
prey *= ny_pppm/yprd;
prez *= nz_pppm/zprd_slab;
sf_coeff[0] *= prex;
sf_coeff[1] *= prex*2;
sf_coeff[2] *= prey;
sf_coeff[3] *= prey*2;
sf_coeff[4] *= prez;
sf_coeff[5] *= prez*2;
// communicate values with other procs
double tmp[6];
MPI_Allreduce(sf_coeff,tmp,6,MPI_DOUBLE,MPI_SUM,world);
for (n = 0; n < 6; n++) sf_coeff[n] = tmp[n];
}
/* ----------------------------------------------------------------------
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 PPPMStagger::particle_map()
{
int nx,ny,nz;
double **x = atom->x;
int nlocal = atom->nlocal;
if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {
// (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 + stagger) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxlo[1])*delyinv+shift + stagger) - OFFSET;
nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift + stagger) - 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 PPPMStagger::make_rho()
{
int l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
// clear 3d density array
memset(&(density_brick[nzlo_out][nylo_out][nxlo_out]),0,
ngrid*sizeof(FFT_SCALAR));
// 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;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv - stagger;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv - stagger;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv - stagger;
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 for ik
------------------------------------------------------------------------- */
void PPPMStagger::fieldforce_ik()
{
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;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv - stagger;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv - stagger;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv - stagger;
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 = qqrd2e * scale * q[i] / float(nstagger);
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
if (slabflag != 2) f[i][2] += qfactor*ekz;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ad
------------------------------------------------------------------------- */
void PPPMStagger::fieldforce_ad()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz;
FFT_SCALAR ekx,eky,ekz;
double s1,s2,s3;
double sf = 0.0;
double *prd;
prd = domain->prd;
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double hx_inv = nx_pppm/xprd;
double hy_inv = ny_pppm/yprd;
double hz_inv = nz_pppm/zprd;
// 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;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv - stagger;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv - stagger;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv - stagger;
compute_rho1d(dx,dy,dz);
compute_drho1d(dx,dy,dz);
ekx = eky = ekz = ZEROF;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
for (m = nlower; m <= nupper; m++) {
my = m+ny;
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
ekx += drho1d[0][l]*rho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx];
eky += rho1d[0][l]*drho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx];
ekz += rho1d[0][l]*rho1d[1][m]*drho1d[2][n]*u_brick[mz][my][mx];
}
}
}
ekx *= hx_inv;
eky *= hy_inv;
ekz *= hz_inv;
// convert E-field to force and substract self forces
const double qfactor = qqrd2e * scale / float(nstagger);
s1 = x[i][0]*hx_inv + stagger;
s2 = x[i][1]*hy_inv + stagger;
s3 = x[i][2]*hz_inv + stagger;
sf = sf_coeff[0]*sin(2*MY_PI*s1);
sf += sf_coeff[1]*sin(4*MY_PI*s1);
sf *= 2*q[i]*q[i];
f[i][0] += qfactor*(ekx*q[i] - sf);
sf = sf_coeff[2]*sin(2*MY_PI*s2);
sf += sf_coeff[3]*sin(4*MY_PI*s2);
sf *= 2*q[i]*q[i];
f[i][1] += qfactor*(eky*q[i] - sf);
sf = sf_coeff[4]*sin(2*MY_PI*s3);
sf += sf_coeff[5]*sin(4*MY_PI*s3);
sf *= 2*q[i]*q[i];
if (slabflag != 2) f[i][2] += qfactor*(ekz*q[i] - sf);
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get per-atom energy/virial
------------------------------------------------------------------------- */
void PPPMStagger::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;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv - stagger;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv - stagger;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv - stagger;
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/float(nstagger);
if (vflag_atom) {
vatom[i][0] += q[i]*v0/float(nstagger);
vatom[i][1] += q[i]*v1/float(nstagger);
vatom[i][2] += q[i]*v2/float(nstagger);
vatom[i][3] += q[i]*v3/float(nstagger);
vatom[i][4] += q[i]*v4/float(nstagger);
vatom[i][5] += q[i]*v5/float(nstagger);
}
}
}
/* ----------------------------------------------------------------------
perform and time the 1d FFTs required for N timesteps
------------------------------------------------------------------------- */
int PPPMStagger::timing_1d(int n, double &time1d)
{
PPPM::timing_1d(n,time1d);
time1d *= 2.0;
if (differentiation_flag) return 2;
return 4;
}
/* ----------------------------------------------------------------------
perform and time the 3d FFTs required for N timesteps
------------------------------------------------------------------------- */
int PPPMStagger::timing_3d(int n, double &time3d)
{
PPPM::timing_3d(n,time3d);
time3d *= 2.0;
if (differentiation_flag) return 2;
return 4;
}
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