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lammps/src/USER-CUDA/pppm_old.cpp
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pppm_old.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 authors: Roy Pollock (LLNL), Paul Crozier (SNL)
per-atom energy/virial & group/group energy/force added by Stan Moore (BYU)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "stdio.h"
#include "stdlib.h"
#include "math.h"
#include "pppm_old.h"
#include "math_const.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "domain.h"
#include "fft3d_wrap.h"
#include "remap_wrap.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXORDER 7
#define OFFSET 16384
#define SMALL 0.00001
#define LARGE 10000.0
#define EPS_HOC 1.0e-7
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#define ONEF 1.0f
#else
#define ZEROF 0.0
#define ONEF 1.0
#endif
/* ---------------------------------------------------------------------- */
PPPMOld::PPPMOld(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command");
triclinic_support = 0;
pppmflag = 1;
group_group_enable = 0;
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
nfactors = 3;
factors = new int[nfactors];
factors[0] = 2;
factors[1] = 3;
factors[2] = 5;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
density_brick = vdx_brick = vdy_brick = vdz_brick = NULL;
density_fft = NULL;
u_brick = NULL;
v0_brick = v1_brick = v2_brick = v3_brick = v4_brick = v5_brick = NULL;
greensfn = NULL;
work1 = work2 = NULL;
vg = NULL;
fkx = fky = fkz = NULL;
buf1 = buf2 = buf3 = buf4 = NULL;
density_A_brick = density_B_brick = NULL;
density_A_fft = density_B_fft = NULL;
gf_b = NULL;
rho1d = rho_coeff = NULL;
fft1 = fft2 = NULL;
remap = NULL;
nmax = 0;
part2grid = NULL;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPMOld::~PPPMOld()
{
delete [] factors;
deallocate();
deallocate_peratom();
deallocate_groups();
memory->destroy(part2grid);
}
/* ----------------------------------------------------------------------
called once before run
------------------------------------------------------------------------- */
void PPPMOld::init()
{
if (me == 0) {
if (screen) fprintf(screen,"PPPM initialization ...\n");
if (logfile) fprintf(logfile,"PPPM initialization ...\n");
}
// error check
triclinic_check();
if (domain->dimension == 2) error->all(FLERR,
"Cannot use PPPM with 2d simulation");
if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM");
if (slabflag) {
if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPM");
}
if (order < 2 || order > MAXORDER) {
char str[128];
sprintf(str,"PPPM order cannot be < 2 or > than %d",MAXORDER);
error->all(FLERR,str);
}
// free all arrays previously allocated
deallocate();
deallocate_peratom();
peratom_allocate_flag = 0;
deallocate_groups();
group_allocate_flag = 0;
// extract short-range Coulombic cutoff from pair style
pair_check();
int itmp=0;
double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
if (p_cutoff == NULL)
error->all(FLERR,"KSpace style is incompatible with Pair style");
cutoff = *p_cutoff;
// if kspace is TIP4P, extract TIP4P params from pair style
// bond/angle are not yet init(), so insure equilibrium request is valid
qdist = 0.0;
if (tip4pflag) {
double *p_qdist = (double *) force->pair->extract("qdist",itmp);
int *p_typeO = (int *) force->pair->extract("typeO",itmp);
int *p_typeH = (int *) force->pair->extract("typeH",itmp);
int *p_typeA = (int *) force->pair->extract("typeA",itmp);
int *p_typeB = (int *) force->pair->extract("typeB",itmp);
if (!p_qdist || !p_typeO || !p_typeH || !p_typeA || !p_typeB)
error->all(FLERR,"KSpace style is incompatible with Pair style");
qdist = *p_qdist;
typeO = *p_typeO;
typeH = *p_typeH;
int typeA = *p_typeA;
int typeB = *p_typeB;
if (force->angle == NULL || force->bond == NULL)
error->all(FLERR,"Bond and angle potentials must be defined for TIP4P");
if (typeA < 1 || typeA > atom->nangletypes ||
force->angle->setflag[typeA] == 0)
error->all(FLERR,"Bad TIP4P angle type for PPPM/TIP4P");
if (typeB < 1 || typeB > atom->nbondtypes ||
force->bond->setflag[typeB] == 0)
error->all(FLERR,"Bad TIP4P bond type for PPPM/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (cos(0.5*theta) * blen);
}
// compute qsum & qsqsum and warn if not charge-neutral
scale = 1.0;
qqrd2e = force->qqrd2e;
qsum_qsq(0);
natoms_original = atom->natoms;
// set accuracy (force units) from accuracy_relative or accuracy_absolute
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
// setup FFT grid resolution and g_ewald
// normally one iteration thru while loop is all that is required
// if grid stencil extends beyond neighbor proc, reduce order and try again
int iteration = 0;
while (order > 1) {
if (iteration && me == 0)
error->warning(FLERR,"Reducing PPPM order b/c stencil extends "
"beyond neighbor processor");
iteration++;
set_grid();
if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET)
error->all(FLERR,"PPPM grid is too large");
// global indices of PPPM grid range from 0 to N-1
// nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of
// global PPPM grid that I own without ghost cells
// for slab PPPM, assign z grid as if it were not extended
nxlo_in = static_cast<int> (comm->xsplit[comm->myloc[0]] * nx_pppm);
nxhi_in = static_cast<int> (comm->xsplit[comm->myloc[0]+1] * nx_pppm) - 1;
nylo_in = static_cast<int> (comm->ysplit[comm->myloc[1]] * ny_pppm);
nyhi_in = static_cast<int> (comm->ysplit[comm->myloc[1]+1] * ny_pppm) - 1;
nzlo_in = static_cast<int>
(comm->zsplit[comm->myloc[2]] * nz_pppm/slab_volfactor);
nzhi_in = static_cast<int>
(comm->zsplit[comm->myloc[2]+1] * nz_pppm/slab_volfactor) - 1;
// nlower,nupper = stencil size for mapping particles to PPPM grid
nlower = -(order-1)/2;
nupper = order/2;
// shift values for particle <-> grid mapping
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
if (order % 2) shift = OFFSET + 0.5;
else shift = OFFSET;
if (order % 2) shiftone = 0.0;
else shiftone = 0.5;
// nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of
// global PPPM grid that my particles can contribute charge to
// effectively nlo_in,nhi_in + ghost cells
// nlo,nhi = global coords of grid pt to "lower left" of smallest/largest
// position a particle in my box can be at
// dist[3] = particle position bound = subbox + skin/2.0 + qdist
// qdist = offset due to TIP4P fictitious charge
// convert to triclinic if necessary
// nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping
// for slab PPPM, assign z grid as if it were not extended
triclinic = domain->triclinic;
double *prd,*sublo,*subhi;
if (triclinic == 0) {
prd = domain->prd;
boxlo = domain->boxlo;
sublo = domain->sublo;
subhi = domain->subhi;
} else {
prd = domain->prd_lamda;
boxlo = domain->boxlo_lamda;
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
double dist[3];
double cuthalf = 0.5*neighbor->skin + qdist;
if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf;
else {
dist[0] = cuthalf/domain->prd[0];
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
int nlo,nhi;
nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nxlo_out = nlo + nlower;
nxhi_out = nhi + nupper;
nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nylo_out = nlo + nlower;
nyhi_out = nhi + nupper;
nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nzlo_out = nlo + nlower;
nzhi_out = nhi + nupper;
// for slab PPPM, change the grid boundary for processors at +z end
// to include the empty volume between periodically repeating slabs
// for slab PPPM, want charge data communicated from -z proc to +z proc,
// but not vice versa, also want field data communicated from +z proc to
// -z proc, but not vice versa
// this is accomplished by nzhi_in = nzhi_out on +z end (no ghost cells)
if (slabflag == 1 && (comm->myloc[2] == comm->procgrid[2]-1)) {
nzhi_in = nz_pppm - 1;
nzhi_out = nz_pppm - 1;
}
// nlo_ghost,nhi_ghost = # of planes I will recv from 6 directions
// that overlay domain I own
// proc in that direction tells me via sendrecv()
// if no neighbor proc, value is from self since I have ghosts regardless
int nplanes;
MPI_Status status;
nplanes = nxlo_in - nxlo_out;
if (comm->procneigh[0][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][0],0,
&nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
world,&status);
else nxhi_ghost = nplanes;
nplanes = nxhi_out - nxhi_in;
if (comm->procneigh[0][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][1],0,
&nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
0,world,&status);
else nxlo_ghost = nplanes;
nplanes = nylo_in - nylo_out;
if (comm->procneigh[1][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][0],0,
&nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
world,&status);
else nyhi_ghost = nplanes;
nplanes = nyhi_out - nyhi_in;
if (comm->procneigh[1][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][1],0,
&nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
world,&status);
else nylo_ghost = nplanes;
nplanes = nzlo_in - nzlo_out;
if (comm->procneigh[2][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][0],0,
&nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
world,&status);
else nzhi_ghost = nplanes;
nplanes = nzhi_out - nzhi_in;
if (comm->procneigh[2][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][1],0,
&nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
world,&status);
else nzlo_ghost = nplanes;
// test that ghost overlap is not bigger than my sub-domain
int flag = 0;
if (nxlo_ghost > nxhi_in-nxlo_in+1) flag = 1;
if (nxhi_ghost > nxhi_in-nxlo_in+1) flag = 1;
if (nylo_ghost > nyhi_in-nylo_in+1) flag = 1;
if (nyhi_ghost > nyhi_in-nylo_in+1) flag = 1;
if (nzlo_ghost > nzhi_in-nzlo_in+1) flag = 1;
if (nzhi_ghost > nzhi_in-nzlo_in+1) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all == 0) break;
order--;
}
if (order == 0) error->all(FLERR,"PPPM order has been reduced to 0");
// decomposition of FFT mesh
// global indices range from 0 to N-1
// proc owns entire x-dimension, clump of columns in y,z dimensions
// npey_fft,npez_fft = # of procs in y,z dims
// if nprocs is small enough, proc can own 1 or more entire xy planes,
// else proc owns 2d sub-blocks of yz plane
// me_y,me_z = which proc (0-npe_fft-1) I am in y,z dimensions
// nlo_fft,nhi_fft = lower/upper limit of the section
// of the global FFT mesh that I own
int npey_fft,npez_fft;
if (nz_pppm >= nprocs) {
npey_fft = 1;
npez_fft = nprocs;
} else procs2grid2d(nprocs,ny_pppm,nz_pppm,&npey_fft,&npez_fft);
int me_y = me % npey_fft;
int me_z = me / npey_fft;
nxlo_fft = 0;
nxhi_fft = nx_pppm - 1;
nylo_fft = me_y*ny_pppm/npey_fft;
nyhi_fft = (me_y+1)*ny_pppm/npey_fft - 1;
nzlo_fft = me_z*nz_pppm/npez_fft;
nzhi_fft = (me_z+1)*nz_pppm/npez_fft - 1;
// PPPM grid for this proc, including ghosts
ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
// FFT arrays on this proc, without ghosts
// nfft = FFT points in FFT decomposition on this proc
// nfft_brick = FFT points in 3d brick-decomposition on this proc
// nfft_both = greater of 2 values
nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) *
(nzhi_fft-nzlo_fft+1);
int nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) *
(nzhi_in-nzlo_in+1);
nfft_both = MAX(nfft,nfft_brick);
// buffer space for use in brick2fft and fillbrick
// idel = max # of ghost planes to send or recv in +/- dir of each dim
// nx,ny,nz = owned planes (including ghosts) in each dim
// nxx,nyy,nzz = max # of grid cells to send in each dim
// nbuf = max in any dim, augment by 3x for components of vd_xyz in fillbrick
int idelx,idely,idelz,nx,ny,nz,nxx,nyy,nzz;
idelx = MAX(nxlo_ghost,nxhi_ghost);
idelx = MAX(idelx,nxhi_out-nxhi_in);
idelx = MAX(idelx,nxlo_in-nxlo_out);
idely = MAX(nylo_ghost,nyhi_ghost);
idely = MAX(idely,nyhi_out-nyhi_in);
idely = MAX(idely,nylo_in-nylo_out);
idelz = MAX(nzlo_ghost,nzhi_ghost);
idelz = MAX(idelz,nzhi_out-nzhi_in);
idelz = MAX(idelz,nzlo_in-nzlo_out);
nx = nxhi_out - nxlo_out + 1;
ny = nyhi_out - nylo_out + 1;
nz = nzhi_out - nzlo_out + 1;
nxx = idelx * ny * nz;
nyy = idely * nx * nz;
nzz = idelz * nx * ny;
nbuf = MAX(nxx,nyy);
nbuf = MAX(nbuf,nzz);
nbuf_peratom = 7*nbuf;
nbuf *= 3;
// print stats
int ngrid_max,nfft_both_max,nbuf_max;
MPI_Allreduce(&ngrid,&ngrid_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nbuf,&nbuf_max,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) fprintf(screen," brick FFT buffer size/proc = %d %d %d\n",
ngrid_max,nfft_both_max,nbuf_max);
if (logfile) fprintf(logfile," brick FFT buffer size/proc = %d %d %d\n",
ngrid_max,nfft_both_max,nbuf_max);
}
// allocate K-space dependent memory
// don't invoke allocate_peratom() here, wait to see if needed
allocate();
// pre-compute Green's function denomiator expansion
// pre-compute 1d charge distribution coefficients
compute_gf_denom();
compute_rho_coeff();
}
/* ----------------------------------------------------------------------
adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMOld::setup()
{
int i,j,k,l,m,n;
double *prd;
// volume-dependent factors
// adjust z dimension for 2d slab PPPM
// z dimension for 3d PPPM is zprd since slab_volfactor = 1.0
if (triclinic == 0) prd = domain->prd;
else prd = domain->prd_lamda;
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
delvolinv = delxinv*delyinv*delzinv;
double unitkx = (2.0*MY_PI/xprd);
double unitky = (2.0*MY_PI/yprd);
double unitkz = (2.0*MY_PI/zprd_slab);
// fkx,fky,fkz for my FFT grid pts
double per;
for (i = nxlo_fft; i <= nxhi_fft; i++) {
per = i - nx_pppm*(2*i/nx_pppm);
fkx[i] = unitkx*per;
}
for (i = nylo_fft; i <= nyhi_fft; i++) {
per = i - ny_pppm*(2*i/ny_pppm);
fky[i] = unitky*per;
}
for (i = nzlo_fft; i <= nzhi_fft; i++) {
per = i - nz_pppm*(2*i/nz_pppm);
fkz[i] = unitkz*per;
}
// virial coefficients
double sqk,vterm;
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
if (sqk == 0.0) {
vg[n][0] = 0.0;
vg[n][1] = 0.0;
vg[n][2] = 0.0;
vg[n][3] = 0.0;
vg[n][4] = 0.0;
vg[n][5] = 0.0;
} else {
vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
vg[n][3] = vterm*fkx[i]*fky[j];
vg[n][4] = vterm*fkx[i]*fkz[k];
vg[n][5] = vterm*fky[j]*fkz[k];
}
n++;
}
}
}
// modified (Hockney-Eastwood) Coulomb Green's function
int nx,ny,nz,kper,lper,mper;
double snx,sny,snz,snx2,sny2,snz2;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,dot1,dot2;
double numerator,denominator;
int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
pow(-log(EPS_HOC),0.25));
int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
pow(-log(EPS_HOC),0.25));
int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
pow(-log(EPS_HOC),0.25));
double form = 1.0;
n = 0;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
snz = sin(0.5*unitkz*mper*zprd_slab/nz_pppm);
snz2 = snz*snz;
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
sny = sin(0.5*unitky*lper*yprd/ny_pppm);
sny2 = sny*sny;
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
snx = sin(0.5*unitkx*kper*xprd/nx_pppm);
snx2 = snx*snx;
sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
numerator = form*12.5663706/sqk;
denominator = gf_denom(snx2,sny2,snz2);
sum1 = 0.0;
const double dorder = static_cast<double>(order);
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-0.25*pow(qx/g_ewald,2.0));
wx = 1.0;
argx = 0.5*qx*xprd/nx_pppm;
if (argx != 0.0) wx = pow(sin(argx)/argx,dorder);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-0.25*pow(qy/g_ewald,2.0));
wy = 1.0;
argy = 0.5*qy*yprd/ny_pppm;
if (argy != 0.0) wy = pow(sin(argy)/argy,dorder);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-0.25*pow(qz/g_ewald,2.0));
wz = 1.0;
argz = 0.5*qz*zprd_slab/nz_pppm;
if (argz != 0.0) wz = pow(sin(argz)/argz,dorder);
dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
dot2 = qx*qx+qy*qy+qz*qz;
sum1 += (dot1/dot2) * sx*sy*sz * pow(wx*wy*wz,2.0);
}
}
}
greensfn[n++] = numerator*sum1/denominator;
} else greensfn[n++] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMOld::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);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"pppm:part2grid");
}
// 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
// reset qsum and qsqsum if atom count has changed
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;
if (atom->natoms != natoms_original) {
qsum_qsq(0);
natoms_original = atom->natoms;
}
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 (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;
}
}
if (vflag_atom) {
for (i = 0; i < nlocal; i++)
for (j = 0; j < 6; j++) vatom[i][j] *= 0.5*q[i]*qscale;
}
}
// 2d slab correction
if (slabflag == 1) slabcorr();
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::allocate()
{
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_brick");
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdx_brick");
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdy_brick");
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdz_brick");
memory->create(density_fft,nfft_both,"pppm:density_fft");
memory->create(greensfn,nfft_both,"pppm:greensfn");
memory->create(work1,2*nfft_both,"pppm:work1");
memory->create(work2,2*nfft_both,"pppm:work2");
memory->create(vg,nfft_both,6,"pppm:vg");
memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx");
memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky");
memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz");
memory->create(buf1,nbuf,"pppm:buf1");
memory->create(buf2,nbuf,"pppm:buf2");
// summation coeffs
memory->create(gf_b,order,"pppm:gf_b");
memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm:rho1d");
memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm:rho_coeff");
// create 2 FFTs and a Remap
// 1st FFT keeps data in FFT decompostion
// 2nd FFT returns data in 3d brick decomposition
// remap takes data from 3d brick to FFT decomposition
int tmp;
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
0,0,&tmp,collective_flag);
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
0,0,&tmp,collective_flag);
remap = new Remap(lmp,world,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
1,0,0,FFT_PRECISION,collective_flag);
}
/* ----------------------------------------------------------------------
allocate per-atom memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::allocate_peratom()
{
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:u_brick");
memory->create3d_offset(v0_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v0_brick");
memory->create3d_offset(v1_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v1_brick");
memory->create3d_offset(v2_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v2_brick");
memory->create3d_offset(v3_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v3_brick");
memory->create3d_offset(v4_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v4_brick");
memory->create3d_offset(v5_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:v5_brick");
memory->create(buf3,nbuf_peratom,"pppm:buf3");
memory->create(buf4,nbuf_peratom,"pppm:buf4");
}
/* ----------------------------------------------------------------------
deallocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::deallocate()
{
memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdx_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdy_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdz_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy(density_fft);
memory->destroy(greensfn);
memory->destroy(work1);
memory->destroy(work2);
memory->destroy(vg);
memory->destroy1d_offset(fkx,nxlo_fft);
memory->destroy1d_offset(fky,nylo_fft);
memory->destroy1d_offset(fkz,nzlo_fft);
memory->destroy(buf1);
memory->destroy(buf2);
memory->destroy(gf_b);
memory->destroy2d_offset(rho1d,-order/2);
memory->destroy2d_offset(rho_coeff,(1-order)/2);
delete fft1;
delete fft2;
delete remap;
}
/* ----------------------------------------------------------------------
deallocate per-atom memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::deallocate_peratom()
{
memory->destroy3d_offset(u_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v0_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v1_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v2_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v3_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v4_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(v5_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy(buf3);
memory->destroy(buf4);
}
/* ----------------------------------------------------------------------
set size of FFT grid (nx,ny,nz_pppm) and g_ewald
------------------------------------------------------------------------- */
void PPPMOld::set_grid()
{
// see JCP 109, pg 7698 for derivation of coefficients
// higher order coefficients may be computed if needed
double **acons;
memory->create(acons,8,7,"pppm:acons");
acons[1][0] = 2.0 / 3.0;
acons[2][0] = 1.0 / 50.0;
acons[2][1] = 5.0 / 294.0;
acons[3][0] = 1.0 / 588.0;
acons[3][1] = 7.0 / 1440.0;
acons[3][2] = 21.0 / 3872.0;
acons[4][0] = 1.0 / 4320.0;
acons[4][1] = 3.0 / 1936.0;
acons[4][2] = 7601.0 / 2271360.0;
acons[4][3] = 143.0 / 28800.0;
acons[5][0] = 1.0 / 23232.0;
acons[5][1] = 7601.0 / 13628160.0;
acons[5][2] = 143.0 / 69120.0;
acons[5][3] = 517231.0 / 106536960.0;
acons[5][4] = 106640677.0 / 11737571328.0;
acons[6][0] = 691.0 / 68140800.0;
acons[6][1] = 13.0 / 57600.0;
acons[6][2] = 47021.0 / 35512320.0;
acons[6][3] = 9694607.0 / 2095994880.0;
acons[6][4] = 733191589.0 / 59609088000.0;
acons[6][5] = 326190917.0 / 11700633600.0;
acons[7][0] = 1.0 / 345600.0;
acons[7][1] = 3617.0 / 35512320.0;
acons[7][2] = 745739.0 / 838397952.0;
acons[7][3] = 56399353.0 / 12773376000.0;
acons[7][4] = 25091609.0 / 1560084480.0;
acons[7][5] = 1755948832039.0 / 36229939200000.0;
acons[7][6] = 4887769399.0 / 37838389248.0;
// use xprd,yprd,zprd even if triclinic so grid size is the same
// adjust z dimension for 2d slab PPPM
// 3d PPPM just uses zprd since slab_volfactor = 1.0
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
// make initial g_ewald estimate
// based on desired accuracy and real space cutoff
// fluid-occupied volume used to estimate real-space error
// zprd used rather than zprd_slab
double h_x,h_y,h_z;
bigint natoms = atom->natoms;
if (!gewaldflag) {
if (accuracy <= 0.0)
error->all(FLERR,"KSpace accuracy must be > 0");
g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2);
if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff;
else g_ewald = sqrt(-log(g_ewald)) / cutoff;
}
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and accuracy
// nz_pppm uses extended zprd_slab instead of zprd
// h = 1/g_ewald is upper bound on h such that h*g_ewald <= 1
// reduce it until accuracy target is met
if (!gridflag) {
double err;
h_x = h_y = h_z = 1.0/g_ewald;
nx_pppm = static_cast<int> (xprd/h_x) + 1;
ny_pppm = static_cast<int> (yprd/h_y) + 1;
nz_pppm = static_cast<int> (zprd_slab/h_z) + 1;
err = rms(h_x,xprd,natoms,q2,acons);
while (err > accuracy) {
err = rms(h_x,xprd,natoms,q2,acons);
nx_pppm++;
h_x = xprd/nx_pppm;
}
err = rms(h_y,yprd,natoms,q2,acons);
while (err > accuracy) {
err = rms(h_y,yprd,natoms,q2,acons);
ny_pppm++;
h_y = yprd/ny_pppm;
}
err = rms(h_z,zprd_slab,natoms,q2,acons);
while (err > accuracy) {
err = rms(h_z,zprd_slab,natoms,q2,acons);
nz_pppm++;
h_z = zprd_slab/nz_pppm;
}
}
// boost grid size until it is factorable
while (!factorable(nx_pppm)) nx_pppm++;
while (!factorable(ny_pppm)) ny_pppm++;
while (!factorable(nz_pppm)) nz_pppm++;
// adjust g_ewald for new grid size
h_x = xprd/static_cast<double>(nx_pppm);
h_y = yprd/static_cast<double>(ny_pppm);
h_z = zprd_slab/static_cast<double>(nz_pppm);
if (!gewaldflag) {
double gew1,gew2,dgew,f,fmid,hmin,rtb;
int ncount;
gew1 = 0.0;
g_ewald = gew1;
f = diffpr(h_x,h_y,h_z,q2,acons);
hmin = MIN(h_x,MIN(h_y,h_z));
gew2 = 10.0/hmin;
g_ewald = gew2;
fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (f*fmid >= 0.0) error->all(FLERR,"Cannot compute PPPM G");
rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2);
ncount = 0;
while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5;
g_ewald = rtb + dgew;
fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (fmid <= 0.0) rtb = g_ewald;
ncount++;
if (ncount > LARGE) error->all(FLERR,"Cannot compute PPPM G");
}
}
// final RMS accuracy
double lprx = rms(h_x,xprd,natoms,q2,acons);
double lpry = rms(h_y,yprd,natoms,q2,acons);
double lprz = rms(h_z,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
double q2_over_sqrt = q2 / sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
double spr = 2.0 *q2_over_sqrt * exp(-g_ewald*g_ewald*cutoff*cutoff);
double tpr = estimate_table_accuracy(q2_over_sqrt,spr);
double accuracy = sqrt(lpr*lpr + spr*spr + tpr*tpr);
// free local memory
memory->destroy(acons);
// print info
if (me == 0) {
#ifdef FFT_SINGLE
const char fft_prec[] = "single";
#else
const char fft_prec[] = "double";
#endif
if (screen) {
fprintf(screen," G vector (1/distance)= %g\n",g_ewald);
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(screen," stencil order = %d\n",order);
fprintf(screen," estimated absolute RMS force accuracy = %g\n",
accuracy);
fprintf(screen," estimated relative force accuracy = %g\n",
accuracy/two_charge_force);
fprintf(screen," using %s precision FFTs\n",fft_prec);
}
if (logfile) {
fprintf(logfile," G vector (1/distance) = %g\n",g_ewald);
fprintf(logfile," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(logfile," stencil order = %d\n",order);
fprintf(logfile," estimated absolute RMS force accuracy = %g\n",
accuracy);
fprintf(logfile," estimated relative force accuracy = %g\n",
accuracy/two_charge_force);
fprintf(logfile," using %s precision FFTs\n",fft_prec);
}
}
}
/* ----------------------------------------------------------------------
check if all factors of n are in list of factors
return 1 if yes, 0 if no
------------------------------------------------------------------------- */
int PPPMOld::factorable(int n)
{
int i;
while (n > 1) {
for (i = 0; i < nfactors; i++) {
if (n % factors[i] == 0) {
n /= factors[i];
break;
}
}
if (i == nfactors) return 0;
}
return 1;
}
/* ----------------------------------------------------------------------
compute RMS accuracy for a dimension
------------------------------------------------------------------------- */
double PPPMOld::rms(double h, double prd, bigint natoms,
double q2, double **acons)
{
double sum = 0.0;
for (int m = 0; m < order; m++)
sum += acons[order][m] * pow(h*g_ewald,2.0*m);
double value = q2 * pow(h*g_ewald,(double)order) *
sqrt(g_ewald*prd*sqrt(2.0*MY_PI)*sum/natoms) / (prd*prd);
return value;
}
/* ----------------------------------------------------------------------
compute difference in real-space and KSpace RMS accuracy
------------------------------------------------------------------------- */
double PPPMOld::diffpr(double h_x, double h_y, double h_z, double q2,
double **acons)
{
double lprx,lpry,lprz,kspace_prec,real_prec;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
bigint natoms = atom->natoms;
lprx = rms(h_x,xprd,natoms,q2,acons);
lpry = rms(h_y,yprd,natoms,q2,acons);
lprz = rms(h_z,zprd*slab_volfactor,natoms,q2,acons);
kspace_prec = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(static_cast<double>(natoms)*cutoff*xprd*yprd*zprd);
double value = kspace_prec - real_prec;
return value;
}
/* ----------------------------------------------------------------------
pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPMOld::compute_gf_denom()
{
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;
}
/* ----------------------------------------------------------------------
ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFT decomposition
------------------------------------------------------------------------- */
void PPPMOld::brick2fft()
{
int i,n,ix,iy,iz;
MPI_Request request;
MPI_Status status;
// pack my ghosts for +x processor
// pass data to self or +x processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -x processor
// pass data to self or -x processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +y processor
// pass data to self or +y processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -y processor
// pass data to self or -y processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +z processor
// pass data to self or +z processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -z processor
// pass data to self or -z processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// remap from 3d brick decomposition to FFT decomposition
// copy grabs inner portion of density from 3d brick
// remap could be done as pre-stage of FFT,
// but this works optimally on only double values, not complex values
n = 0;
for (iz = nzlo_in; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_fft[n++] = density_brick[iz][iy][ix];
remap->perform(density_fft,density_fft,work1);
}
/* ----------------------------------------------------------------------
ghost-swap to fill ghost cells of my brick with field values
------------------------------------------------------------------------- */
void PPPMOld::fillbrick()
{
int i,n,ix,iy,iz;
MPI_Request request;
MPI_Status status;
// pack my real cells for +z processor
// pass data to self or +z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -z processor
// pass data to self or -z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +y processor
// pass data to self or +y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -y processor
// pass data to self or -y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +x processor
// pass data to self or +x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -x processor
// pass data to self or -x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world,&request);
MPI_Send(buf1,n,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
}
/* ----------------------------------------------------------------------
ghost-swap to fill ghost cells of my brick with per-atom field values
------------------------------------------------------------------------- */
void PPPMOld::fillbrick_peratom()
{
int i,n,ix,iy,iz;
MPI_Request request;
MPI_Status status;
// pack my real cells for +z processor
// pass data to self or +z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[2][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[n++];
}
}
// pack my real cells for -z processor
// pass data to self or -z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[2][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[n++];
}
}
// pack my real cells for +y processor
// pass data to self or +y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[1][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[n++];
}
}
// pack my real cells for -y processor
// pass data to self or -y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[1][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[n++];
}
}
// pack my real cells for +x processor
// pass data to self or +x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[0][0],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[n++];
}
}
// pack my real cells for -x processor
// pass data to self or -x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++) {
if (eflag_atom) buf3[n++] = u_brick[iz][iy][ix];
if (vflag_atom) {
buf3[n++] = v0_brick[iz][iy][ix];
buf3[n++] = v1_brick[iz][iy][ix];
buf3[n++] = v2_brick[iz][iy][ix];
buf3[n++] = v3_brick[iz][iy][ix];
buf3[n++] = v4_brick[iz][iy][ix];
buf3[n++] = v5_brick[iz][iy][ix];
}
}
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf4[i] = buf3[i];
else {
MPI_Irecv(buf4,nbuf_peratom,MPI_FFT_SCALAR,
comm->procneigh[0][1],0,world,&request);
MPI_Send(buf3,n,MPI_FFT_SCALAR,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++) {
if (eflag_atom) u_brick[iz][iy][ix] = buf4[n++];
if (vflag_atom) {
v0_brick[iz][iy][ix] = buf4[n++];
v1_brick[iz][iy][ix] = buf4[n++];
v2_brick[iz][iy][ix] = buf4[n++];
v3_brick[iz][iy][ix] = buf4[n++];
v4_brick[iz][iy][ix] = buf4[n++];
v5_brick[iz][iy][ix] = buf4[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 PPPMOld::particle_map()
{
int nx,ny,nz;
double **x = atom->x;
int nlocal = atom->nlocal;
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) - 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 PPPMOld::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;
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];
}
}
}
}
}
/* ----------------------------------------------------------------------
FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPMOld::poisson()
{
int i,j,k,n;
double eng;
// transform charge density (r -> k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] = density_fft[i];
work1[n++] = ZEROF;
}
fft1->compute(work1,work1,1);
// global energy and virial contribution
double scaleinv = 1.0/(nx_pppm*ny_pppm*nz_pppm);
double s2 = scaleinv*scaleinv;
if (eflag_global || vflag_global) {
if (vflag_global) {
n = 0;
for (i = 0; i < nfft; i++) {
eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
if (eflag_global) energy += eng;
n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft; i++) {
energy +=
s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
n += 2;
}
}
}
// scale by 1/total-grid-pts to get rho(k)
// multiply by Green's function to get V(k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] *= scaleinv * greensfn[i];
work1[n++] *= scaleinv * greensfn[i];
}
// extra FFTs for per-atom energy/virial
if (evflag_atom) poisson_peratom();
// compute gradients of V(r) in each of 3 dims by transformimg -ik*V(k)
// FFT leaves data in 3d brick decomposition
// copy it into inner portion of vdx,vdy,vdz arrays
// x direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fkx[i]*work1[n+1];
work2[n+1] = -fkx[i]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdx_brick[k][j][i] = work2[n];
n += 2;
}
// y direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fky[j]*work1[n+1];
work2[n+1] = -fky[j]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdy_brick[k][j][i] = work2[n];
n += 2;
}
// z direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fkz[k]*work1[n+1];
work2[n+1] = -fkz[k]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdz_brick[k][j][i] = work2[n];
n += 2;
}
}
/* ----------------------------------------------------------------------
FFT-based Poisson solver for per-atom energy/virial
------------------------------------------------------------------------- */
void PPPMOld::poisson_peratom()
{
int i,j,k,n;
// energy
if (eflag_atom) {
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n];
work2[n+1] = work1[n+1];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
u_brick[k][j][i] = work2[n];
n += 2;
}
}
// 6 components of virial in v0 thru v5
if (!vflag_atom) return;
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][0];
work2[n+1] = work1[n+1]*vg[i][0];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v0_brick[k][j][i] = work2[n];
n += 2;
}
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][1];
work2[n+1] = work1[n+1]*vg[i][1];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v1_brick[k][j][i] = work2[n];
n += 2;
}
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][2];
work2[n+1] = work1[n+1]*vg[i][2];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v2_brick[k][j][i] = work2[n];
n += 2;
}
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][3];
work2[n+1] = work1[n+1]*vg[i][3];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v3_brick[k][j][i] = work2[n];
n += 2;
}
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][4];
work2[n+1] = work1[n+1]*vg[i][4];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v4_brick[k][j][i] = work2[n];
n += 2;
}
n = 0;
for (i = 0; i < nfft; i++) {
work2[n] = work1[n]*vg[i][5];
work2[n+1] = work1[n+1]*vg[i][5];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
v5_brick[k][j][i] = work2[n];
n += 2;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMOld::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;
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;
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 = qqrd2e * scale * q[i];
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
if (slabflag != 2) f[i][2] += qfactor*ekz;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get per-atom energy/virial
------------------------------------------------------------------------- */
void PPPMOld::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;
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;
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;
}
}
}
/* ----------------------------------------------------------------------
map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
------------------------------------------------------------------------- */
void PPPMOld::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
{
// loop thru all possible factorizations of nprocs
// surf = surface area of largest proc sub-domain
// innermost if test minimizes surface area and surface/volume ratio
int bestsurf = 2 * (nx + ny);
int bestboxx = 0;
int bestboxy = 0;
int boxx,boxy,surf,ipx,ipy;
ipx = 1;
while (ipx <= nprocs) {
if (nprocs % ipx == 0) {
ipy = nprocs/ipx;
boxx = nx/ipx;
if (nx % ipx) boxx++;
boxy = ny/ipy;
if (ny % ipy) boxy++;
surf = boxx + boxy;
if (surf < bestsurf ||
(surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
bestsurf = surf;
bestboxx = boxx;
bestboxy = boxy;
*px = ipx;
*py = ipy;
}
}
ipx++;
}
}
/* ----------------------------------------------------------------------
charge assignment into rho1d
dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMOld::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
for (k = (1-order)/2; k <= order/2; k++) {
r1 = r2 = r3 = ZEROF;
for (l = order-1; l >= 0; l--) {
r1 = rho_coeff[l][k] + r1*dx;
r2 = rho_coeff[l][k] + r2*dy;
r3 = rho_coeff[l][k] + r3*dz;
}
rho1d[0][k] = r1;
rho1d[1][k] = r2;
rho1d[2][k] = r3;
}
}
/* ----------------------------------------------------------------------
generate coeffients for the weight function of order n
(n-1)
Wn(x) = Sum wn(k,x) , Sum is over every other integer
k=-(n-1)
For k=-(n-1),-(n-1)+2, ....., (n-1)-2,n-1
k is odd integers if n is even and even integers if n is odd
---
| n-1
| Sum a(l,j)*(x-k/2)**l if abs(x-k/2) < 1/2
wn(k,x) = < l=0
|
| 0 otherwise
---
a coeffients are packed into the array rho_coeff to eliminate zeros
rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
------------------------------------------------------------------------- */
void PPPMOld::compute_rho_coeff()
{
int j,k,l,m;
FFT_SCALAR s;
FFT_SCALAR **a;
memory->create2d_offset(a,order,-order,order,"pppm:a");
for (k = -order; k <= order; k++)
for (l = 0; l < order; l++)
a[l][k] = 0.0;
a[0][0] = 1.0;
for (j = 1; j < order; j++) {
for (k = -j; k <= j; k += 2) {
s = 0.0;
for (l = 0; l < j; l++) {
a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
#ifdef FFT_SINGLE
s += powf(0.5,(float) l+1) *
(a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1);
#else
s += pow(0.5,(double) l+1) *
(a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1);
#endif
}
a[0][k] = s;
}
}
m = (1-order)/2;
for (k = -(order-1); k < order; k += 2) {
for (l = 0; l < order; l++)
rho_coeff[l][m] = a[l][k];
m++;
}
memory->destroy2d_offset(a,-order);
}
/* ----------------------------------------------------------------------
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. Also
extended to non-neutral systems (J. Chem. Phys. 131, 094107).
------------------------------------------------------------------------- */
void PPPMOld::slabcorr()
{
// compute local contribution to global dipole moment
double *q = atom->q;
double **x = atom->x;
double zprd = domain->zprd;
int nlocal = atom->nlocal;
double dipole = 0.0;
for (int i = 0; i < nlocal; i++) 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);
// need to make non-neutral systems and/or
// per-atom energy translationally invariant
double dipole_r2 = 0.0;
if (eflag_atom || fabs(qsum) > SMALL) {
for (int i = 0; i < nlocal; i++)
dipole_r2 += q[i]*x[i][2]*x[i][2];
// sum local contributions
double tmp;
MPI_Allreduce(&dipole_r2,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
dipole_r2 = tmp;
}
// compute corrections
const double e_slabcorr = MY_2PI*(dipole_all*dipole_all -
qsum*dipole_r2 - qsum*qsum*zprd*zprd/12.0)/volume;
const double qscale = qqrd2e * scale;
if (eflag_global) energy += qscale * e_slabcorr;
// per-atom energy
if (eflag_atom) {
double efact = qscale * MY_2PI/volume;
for (int i = 0; i < nlocal; i++)
eatom[i] += efact * q[i]*(x[i][2]*dipole_all - 0.5*(dipole_r2 +
qsum*x[i][2]*x[i][2]) - qsum*zprd*zprd/12.0);
}
// add on force corrections
double ffact = qscale * (-4.0*MY_PI/volume);
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += ffact * q[i]*(dipole_all - qsum*x[i][2]);
}
/* ----------------------------------------------------------------------
perform and time the 1d FFTs required for N timesteps
------------------------------------------------------------------------- */
int PPPMOld::timing_1d(int n, double &time1d)
{
double time1,time2;
for (int i = 0; i < 2*nfft_both; i++) work1[i] = ZEROF;
MPI_Barrier(world);
time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1->timing1d(work1,nfft_both,1);
fft2->timing1d(work1,nfft_both,-1);
fft2->timing1d(work1,nfft_both,-1);
fft2->timing1d(work1,nfft_both,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time1d = time2 - time1;
return 4;
}
/* ----------------------------------------------------------------------
perform and time the 3d FFTs required for N timesteps
------------------------------------------------------------------------- */
int PPPMOld::timing_3d(int n, double &time3d)
{
double time1,time2;
for (int i = 0; i < 2*nfft_both; i++) work1[i] = ZEROF;
MPI_Barrier(world);
time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1->compute(work1,work1,1);
fft2->compute(work1,work1,-1);
fft2->compute(work1,work1,-1);
fft2->compute(work1,work1,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time3d = time2 - time1;
return 4;
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double PPPMOld::memory_usage()
{
double bytes = nmax*3 * sizeof(double);
int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
bytes += 4 * nbrick * sizeof(FFT_SCALAR);
bytes += 6 * nfft_both * sizeof(double);
bytes += nfft_both * sizeof(double);
bytes += nfft_both*5 * sizeof(FFT_SCALAR);
bytes += 2 * nbuf * sizeof(FFT_SCALAR);
if (peratom_allocate_flag) {
bytes += 7 * nbrick * sizeof(FFT_SCALAR);
bytes += 2 * nbuf_peratom * sizeof(FFT_SCALAR);
}
if (group_allocate_flag) {
bytes += 2 * nbrick * sizeof(FFT_SCALAR);
bytes += 2 * nfft_both * sizeof(FFT_SCALAR);;
}
return bytes;
}
/* ----------------------------------------------------------------------
group-group interactions
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
compute the PPPM total long-range force and energy for groups A and B
------------------------------------------------------------------------- */
void PPPMOld::compute_group_group(int groupbit_A, int groupbit_B, int BA_flag)
{
if (slabflag)
error->all(FLERR,"Cannot (yet) use K-space slab "
"correction with compute group/group");
int i,j;
if (!group_allocate_flag) {
allocate_groups();
group_allocate_flag = 1;
}
e2group = 0; //energy
f2group[0] = 0; //force in x-direction
f2group[1] = 0; //force in y-direction
f2group[2] = 0; //force in z-direction
double *q = atom->q;
int nlocal = atom->nlocal;
int *mask = atom->mask;
// map my particle charge onto my local 3d density grid
make_rho_groups(groupbit_A,groupbit_B,BA_flag);
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
// temporarily store and switch pointers so we can
// use brick2fft() for groups A and B (without
// writing an additional function)
FFT_SCALAR ***density_brick_real = density_brick;
FFT_SCALAR *density_fft_real = density_fft;
// group A
density_brick = density_A_brick;
density_fft = density_A_fft;
brick2fft();
// group B
density_brick = density_B_brick;
density_fft = density_B_fft;
brick2fft();
// switch back pointers
density_brick = density_brick_real;
density_fft = density_fft_real;
// compute potential gradient on my FFT grid and
// portion of group-group energy/force on this proc's FFT grid
poisson_groups(BA_flag);
const double qscale = qqrd2e * scale;
// total group A <--> group B energy
// self and boundary correction terms are in compute_group_group.cpp
double e2group_all;
MPI_Allreduce(&e2group,&e2group_all,1,MPI_DOUBLE,MPI_SUM,world);
e2group = e2group_all;
e2group *= qscale*0.5*volume;
// total group A <--> group B force
double f2group_all[3];
MPI_Allreduce(f2group,f2group_all,3,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 3; i++) f2group[i] = qscale*volume*f2group_all[i];
}
/* ----------------------------------------------------------------------
allocate group-group memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::allocate_groups()
{
memory->create3d_offset(density_A_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_A_brick");
memory->create3d_offset(density_B_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_B_brick");
memory->create(density_A_fft,nfft_both,"pppm:density_A_fft");
memory->create(density_B_fft,nfft_both,"pppm:density_B_fft");
}
/* ----------------------------------------------------------------------
deallocate group-group memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMOld::deallocate_groups()
{
memory->destroy3d_offset(density_A_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(density_B_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy(density_A_fft);
memory->destroy(density_B_fft);
}
/* ----------------------------------------------------------------------
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 for group-group interactions
------------------------------------------------------------------------- */
void PPPMOld::make_rho_groups(int groupbit_A, int groupbit_B, int BA_flag)
{
int l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
// clear 3d density arrays
memset(&(density_A_brick[nzlo_out][nylo_out][nxlo_out]),0,
ngrid*sizeof(FFT_SCALAR));
memset(&(density_B_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;
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
if (BA_flag) continue;
if ((mask[i] & groupbit_A) || (mask[i] & groupbit_B)) {
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;
// group A
if (mask[i] & groupbit_A)
density_A_brick[mz][my][mx] += x0*rho1d[0][l];
// group B
if (mask[i] & groupbit_B)
density_B_brick[mz][my][mx] += x0*rho1d[0][l];
}
}
}
}
}
}
/* ----------------------------------------------------------------------
FFT-based Poisson solver for group-group interactions
------------------------------------------------------------------------- */
void PPPMOld::poisson_groups(int BA_flag)
{
int i,j,k,n;
double eng;
// reuse memory (already declared)
FFT_SCALAR *work_A = work1;
FFT_SCALAR *work_B = work2;
// transform charge density (r -> k)
// group A
n = 0;
for (i = 0; i < nfft; i++) {
work_A[n++] = density_A_fft[i];
work_A[n++] = ZEROF;
}
fft1->compute(work_A,work_A,1);
// group B
n = 0;
for (i = 0; i < nfft; i++) {
work_B[n++] = density_B_fft[i];
work_B[n++] = ZEROF;
}
fft1->compute(work_B,work_B,1);
// group-group energy and force contribution,
// keep everything in reciprocal space so
// no inverse FFTs needed
double scaleinv = 1.0/(nx_pppm*ny_pppm*nz_pppm);
double s2 = scaleinv*scaleinv;
// energy
n = 0;
for (i = 0; i < nfft; i++) {
e2group += s2 * greensfn[i] *
(work_A[n]*work_B[n] + work_A[n+1]*work_B[n+1]);
n += 2;
}
if (BA_flag) return;
// multiply by Green's function and s2
// (only for work_A so it is not squared below)
n = 0;
for (i = 0; i < nfft; i++) {
work_A[n++] *= s2 * greensfn[i];
work_A[n++] *= s2 * greensfn[i];
}
double partial_group;
// force, x direction
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
partial_group = work_A[n+1]*work_B[n] - work_A[n]*work_B[n+1];
f2group[0] += fkx[i] * partial_group;
n += 2;
}
// force, y direction
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
partial_group = work_A[n+1]*work_B[n] - work_A[n]*work_B[n+1];
f2group[1] += fky[j] * partial_group;
n += 2;
}
// force, z direction
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
partial_group = work_A[n+1]*work_B[n] - work_A[n]*work_B[n+1];
f2group[2] += fkz[k] * partial_group;
n += 2;
}
}
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