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lammps/src/USER-CUDA/pppm_cuda.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
See the README file in the top-level LAMMPS directory.
-----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
Theoretical Physics II, University of Technology Ilmenau, Germany
See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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)
------------------------------------------------------------------------- */
#include "mpi.h"
#include <cstring>
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include "pppm_cuda.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_cuda.h"
#include "remap_wrap.h"
#include "memory.h"
#include "error.h"
#include <ctime> //crmadd
#include "cuda_wrapper_cu.h"
#include "pppm_cuda_cu.h"
#include "cuda.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXORDER 7
#define OFFSET 4096
#define SMALL 0.00001
#define LARGE 10000.0
#define EPS_HOC 1.0e-7
void printArray(double* data,int nx, int ny, int nz)
{
for(int i=0;i<nz;i++)
for(int j=0;j<ny;j++)
{
printf("%i %i\n",i,j);
for(int k=0;k<nx;k++)
printf("%e ",data[2*(i*ny*nx+j*nx+k)]);
printf("\n\n");
}
}
void printArray(double*** data,int nx, int ny, int nz)
{
for(int i=0;i<nx;i++)
for(int j=0;j<ny;j++)
{
printf("%i %i\n",i,j);
for(int k=0;k<nz;k++)
printf("%e ",data[i][j][k]);
printf("\n\n");
}
}
/* ---------------------------------------------------------------------- */
PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, (narg==2?1:narg), arg)
{
cuda = lmp->cuda;
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
if ((narg > 3)||(narg<1)) error->all(FLERR,"Illegal kspace_style pppm/cuda command");
#ifndef FFT_CUFFT
error->all(FLERR,"Using kspace_style pppm/cuda without cufft is not possible. Compile with cufft=1 to include cufft. Aborting.");
#endif
precision = atof(arg[0]);
if(narg>1)
precisionmodify=arg[1][0];
else precisionmodify='=';
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 = vdx_brick_tmp = NULL;
density_fft = NULL;
greensfn = NULL;
work1 = work2 = NULL;
vg = NULL;
fkx = fky = fkz = NULL;
buf1 = buf2 = NULL;
gf_b = NULL;
rho1d = rho_coeff = NULL;
fft1c = fft2c = NULL;
remap = NULL;
density_brick_int=NULL;
density_intScale=1000000;
cu_vdx_brick = cu_vdy_brick = cu_vdz_brick = NULL;
cu_density_brick = NULL;
cu_density_brick_int = NULL;
cu_density_fft = NULL;
cu_energy=NULL;
cu_greensfn = NULL;
cu_work1 = cu_work2 = cu_work3 = NULL;
cu_vg = NULL;
cu_fkx = cu_fky = cu_fkz = NULL;
cu_flag = NULL;
cu_debugdata = NULL;
cu_rho_coeff = NULL;
cu_virial = NULL;
cu_gf_b = NULL;
cu_slabbuf = NULL;
slabbuf = NULL;
nmax = 0;
part2grid = NULL;
cu_part2grid = NULL;
adev_data_array=NULL;
poissontime=0;
old_nmax=0;
cu_pppm_grid_n=NULL;
cu_pppm_grid_ids=NULL;
pppm_grid_nmax=0;
pppm2partgrid=new int[3];
pppm_grid=new int[3];
firstpass=true;
scale = 1.0;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPMCuda::~PPPMCuda()
{
delete [] slabbuf;
delete cu_slabbuf;
delete [] factors;
factors=NULL;
deallocate();
delete cu_part2grid;
cu_part2grid=NULL;
memory->destroy(part2grid);
part2grid = NULL;
}
/* ----------------------------------------------------------------------
called once before run
------------------------------------------------------------------------- */
void PPPMCuda::init()
{
cuda->shared_data.pppm.cudable_force=1;
//if(cuda->finished_run) {PPPM::init(); return;}
if (me == 0) {
if (screen) fprintf(screen,"PPPMCuda initialization ...\n");
if (logfile) fprintf(logfile,"PPPMCuda initialization ...\n");
}
// error check
if (domain->triclinic)
error->all(FLERR,"Cannot (yet) use PPPMCuda with triclinic box");
if (domain->dimension == 2) error->all(FLERR,"Cannot use PPPMCuda 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 PPPMCuda");
if (slabflag == 1) {
if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMCuda");
}
if (order > MAXORDER) {
char str[128];
sprintf(str,"PPPMCuda order cannot be greater than %d",MAXORDER);
error->all(FLERR,str);
}
// free all arrays previously allocated
deallocate();
// extract short-range Coulombic cutoff from pair style
qqrd2e = force->qqrd2e;
if (force->pair == NULL)
error->all(FLERR,"KSpace style is incompatible with Pair style");
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
qdist = 0.0;
if (strcmp(force->kspace_style,"pppm/tip4p") == 0) {
if (force->pair == NULL)
error->all(FLERR,"KSpace style is incompatible with Pair style");
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");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (2.0 * cos(0.5*theta) * blen);
}
// compute qsum & qsqsum and warn if not charge-neutral
qsum = qsqsum = 0.0;
for (int i = 0; i < atom->nlocal; i++) {
qsum += atom->q[i];
qsqsum += atom->q[i]*atom->q[i];
}
double tmp;
MPI_Allreduce(&qsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum = tmp;
MPI_Allreduce(&qsqsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum = tmp;
if (qsqsum == 0.0)
error->all(FLERR,"Cannot use kspace solver on system with no charge");
if (fabs(qsum) > SMALL && me == 0) {
char str[128];
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
error->warning(FLERR,str);
}
// 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 > 0) {
if (iteration && me == 0)
error->warning(FLERR,"Reducing PPPMCuda order b/c stencil extends "
"beyond neighbor processor");
iteration++;
set_grid();
if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET)
error->all(FLERR,"PPPMCuda grid is too large");
// global indices of PPPMCuda grid range from 0 to N-1
// nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of
// global PPPMCuda grid that I own without ghost cells
// for slab PPPMCuda, assign z grid as if it were not extended
nxlo_in = comm->myloc[0]*nx_pppm / comm->procgrid[0];
nxhi_in = (comm->myloc[0]+1)*nx_pppm / comm->procgrid[0] - 1;
nylo_in = comm->myloc[1]*ny_pppm / comm->procgrid[1];
nyhi_in = (comm->myloc[1]+1)*ny_pppm / comm->procgrid[1] - 1;
nzlo_in = comm->myloc[2] *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2];
nzhi_in = (comm->myloc[2]+1) *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2] - 1;
// nlower,nupper = stencil size for mapping particles to PPPMCuda 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 PPPMCuda 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 PPPMCuda, 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 PPPMCuda, change the grid boundary for processors at +z end
// to include the empty volume between periodically repeating slabs
// for slab PPPMCuda, 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 && ((comm->myloc[2]+1) == (comm->procgrid[2]))) {
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,"PPPMCuda order has been reduced to 0");
//printf("PPPMCuda: order is %i\n");
// 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;
// PPPMCuda 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 *= 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);
}
cuda_shared_pppm* ap=&(cuda->shared_data.pppm);
ap->density_intScale=density_intScale;
ap->nxlo_in=nxlo_in;
ap->nxhi_in=nxhi_in;
ap->nxlo_out=nxlo_out;
ap->nxhi_out=nxhi_out;
ap->nylo_in=nylo_in;
ap->nyhi_in=nyhi_in;
ap->nylo_out=nylo_out;
ap->nyhi_out=nyhi_out;
ap->nzlo_in=nzlo_in;
ap->nzhi_in=nzhi_in;
ap->nzlo_out=nzlo_out;
ap->nzhi_out=nzhi_out;
ap->nxlo_in=nxlo_fft;
ap->nxhi_in=nxhi_fft;
ap->nylo_in=nylo_fft;
ap->nyhi_in=nyhi_fft;
ap->nzlo_in=nzlo_fft;
ap->nzhi_in=nzhi_fft;
ap->nx_pppm=nx_pppm;
ap->ny_pppm=ny_pppm;
ap->nz_pppm=nz_pppm;
ap->qqrd2e=qqrd2e;
ap->order=order;
ap->nmax=nmax;
ap->nlocal=atom->nlocal;
ap->delxinv=delxinv;
ap->delyinv=delyinv;
ap->delzinv=delzinv;
ap->nlower=nlower;
ap->nupper=nupper;
ap->shiftone=shiftone;
// allocate K-space dependent memory
allocate();
// pre-compute Green's function denomiator expansion
// pre-compute 1d charge distribution coefficients
compute_gf_denom();
compute_rho_coeff();
}
/* ----------------------------------------------------------------------
adjust PPPMCuda coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMCuda::setup()
{
int i,j,k,l,m,n;
double *prd;
cu_gf_b->upload();
// volume-dependent factors
// adjust z dimension for 2d slab PPPMCuda
// z dimension for 3d PPPMCuda 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
Cuda_PPPM_Setup_fkxyz_vg(nx_pppm, ny_pppm,nz_pppm,unitkx,unitky,unitkz,g_ewald);
/* cu_vg->download();
int offset=8100-2;//10*(nxhi_fft-nxlo_fft+1)*(nyhi_fft-nylo_fft+1)+10*(nyhi_fft-nylo_fft+1);
for (int i=nxlo_fft; i <= nxhi_fft+1;i++) printf("%e ",vg[i-nxlo_fft+offset][0]);
printf("\n\n");
double per;
#ifndef FFT_CUFFT
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;
}
#endif
#ifdef FFT_CUFFT
for (i = 0; i < nx_pppm; i++) {
per = i - nx_pppm*(2*i/nx_pppm);
fkx[i] = unitkx*per;
}
for (i = 0; i < ny_pppm; i++) {
per = i - ny_pppm*(2*i/ny_pppm);
fky[i] = unitky*per;
}
for (i = 0; i < nz_pppm; i++) {
per = i - nz_pppm*(2*i/nz_pppm);
fkz[i] = unitkz*per;
}
#endif
// virial coefficients
double sqk,vterm;
int save_n=0;
int s_i,s_j,s_k;
double max=0.0;
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(n==8100) printf("%lf\n",sqk);
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));
double tmp=vg[n][0];
vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
if(((vg[n][0]-tmp)*(vg[n][0]-tmp)>1e-6)&&(save_n==0)) {save_n=n;s_k=k;s_j=j;s_i=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];
//if(vg[n][0]>max) {max=vg[n][0]; save_n=n;}
}
n++;
}
}
}
printf("%lf %i %i %i %i\n",max,save_n,s_k,s_j,s_i);
for (int i=nxlo_fft; i <= nxhi_fft;i++) printf("%e ",vg[i-nxlo_fft+offset][0]);
printf("\n\n");
//cu_fkx->upload();
//cu_fky->upload();
// cu_fkz->upload();
//cu_vg->upload(); */
// modified (Hockney-Eastwood) Coulomb Green's function
double sqk;
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));
Cuda_PPPM_setup_greensfn(nx_pppm,ny_pppm,nz_pppm,unitkx,unitky,unitkz,g_ewald,
nbx,nby,nbz,xprd,yprd,zprd_slab);
/*
double form = 1.0;
n = 0;
#ifndef FFT_CUFFT
for (m = nzlo_fft; m <= nzhi_fft; m++) {
#endif
#ifdef FFT_CUFFT
for (m = 0; m < nz_pppm; m++) {
#endif
mper = m - nz_pppm*(2*m/nz_pppm);
snz = sin(0.5*unitkz*mper*zprd_slab/nz_pppm);
snz2 = snz*snz;
#ifndef FFT_CUFFT
for (l = nylo_fft; l <= nyhi_fft; l++) {
#endif
#ifdef FFT_CUFFT
for (l = 0; l < ny_pppm; l++) {
#endif
lper = l - ny_pppm*(2*l/ny_pppm);
sny = sin(0.5*unitky*lper*yprd/ny_pppm);
sny2 = sny*sny;
#ifndef FFT_CUFFT
for (k = nxlo_fft; k <= nxhi_fft; k++) {
#endif
#ifdef FFT_CUFFT
for (k = 0; k < nx_pppm; k++) {
#endif
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;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-.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,order);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-.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,order);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-.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,order);
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;
}
}
}*/
#ifdef FFT_CUFFT
//cu_greensfn->upload();
//cu_fkx->upload();
//cu_fky->upload();
//cu_fkz->upload();
//cu_vg->upload();
cu_vdx_brick->upload();
cu_vdy_brick->upload();
cu_vdz_brick->upload();
#endif
cu_rho_coeff->upload();
cu_density_brick->memset_device(0);
pppm_device_init_setup(&cuda->shared_data,shiftone,delxinv,delyinv,delzinv,nlower,nupper);
}
/* ----------------------------------------------------------------------
compute the PPPMCuda long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMCuda::compute(int eflag, int vflag)
{
// printf("PPPMCuda::compute START\n");
cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
int i;
timespec starttime;
timespec endtime;
timespec starttotal;
timespec endtotal;
// 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 ((cu_atom->update_nmax)||(old_nmax==0)) {
memory->destroy(part2grid);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"pppm:part2grid");
delete cu_part2grid;
delete [] adev_data_array;
adev_data_array=new dev_array[1];
cu_part2grid = new cCudaData<int , int , yx > ((int*)part2grid,adev_data_array, nmax,3);
pppm_device_update(&cuda->shared_data,cu_part2grid->dev_data(),atom->nlocal,atom->nmax);
old_nmax=nmax;
}
if(cu_atom->update_nlocal) {pppm_update_nlocal(cu_atom->nlocal);}
energy = 0.0;
if (vflag)
{
for (i = 0; i < 6; i++) virial[i] = 0.0;
cu_virial->memset_device(0);
}
if(eflag) cu_energy->memset_device(0);
clock_gettime(CLOCK_REALTIME,&starttotal);
// find grid points for all my particles
// map my particle charge onto my local 3d density grid
clock_gettime(CLOCK_REALTIME,&starttime);
particle_map();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pppm_particle_map+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
//cu_part2grid->download();
clock_gettime(CLOCK_REALTIME,&starttime);
make_rho();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pppm_make_rho+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
int nprocs=comm->nprocs;
clock_gettime(CLOCK_REALTIME,&starttime);
if(nprocs>1)
{
cu_density_brick->download();
brick2fft();
}
else
{
#ifdef FFT_CUFFT
pppm_initfftdata(&cuda->shared_data,(PPPM_FLOAT*)cu_density_brick->dev_data(),(FFT_FLOAT*)cu_work2->dev_data());
#endif
}
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pppm_brick2fft+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
// 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
clock_gettime(CLOCK_REALTIME,&starttime);
poisson(eflag,vflag);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pppm_poisson+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
// all procs communicate E-field values to fill ghost cells
// surrounding their 3d bricks
// not necessary since all the calculations are done on one proc
// calculate the force on my particles
//cu_vdx_brick->download();
//cu_vdy_brick->download();
//cu_vdz_brick->download();
clock_gettime(CLOCK_REALTIME,&starttime);
fieldforce();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pppm_fieldforce+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
// sum energy across procs and add in volume-dependent term
clock_gettime(CLOCK_REALTIME,&endtotal);
cuda->shared_data.cuda_timings.pppm_compute+=(endtotal.tv_sec-starttotal.tv_sec+1.0*(endtotal.tv_nsec-starttotal.tv_nsec)/1000000000);
if (eflag) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/1.772453851 +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qqrd2e;
}
// sum virial across procs
if (vflag) {
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*qqrd2e*volume*virial_all[i];
}
// 2d slab correction
if (slabflag) slabcorr(eflag);
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
if(firstpass) firstpass=false;
}
/* ----------------------------------------------------------------------
allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMCuda::allocate()
{
//printf("PPPMCuda::allocate START Mem: %i\n",CudaWrapper_CheckMemUseage());
/*if(sizeof(CUDA_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision\n");
#ifdef PPPM_PRECISION
if(sizeof(PPPM_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision for pppm core\n");
if(sizeof(PPPM_FLOAT)==sizeof(double)) printf("PPPMCuda: Using double precision for pppm core\n");
#endif
#ifdef ENERGY_PRECISION
if(sizeof(ENERGY_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision for energy\n");
if(sizeof(ENERGY_FLOAT)==sizeof(double)) printf("PPPMCuda: Using double precision for energy\n");
#endif
#ifdef ENERGY_PRECISION
if(sizeof(FFT_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision for fft\n");
if(sizeof(FFT_FLOAT)==sizeof(double)) printf("PPPMCuda: Using double precision for fft\n");
#endif
#ifdef X_PRECISION
if(sizeof(X_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision for positions\n");
if(sizeof(X_FLOAT)==sizeof(double)) printf("PPPMCuda: Using double precision for positions\n");
#endif
#ifdef F_PRECISION
if(sizeof(F_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision for forces\n");
if(sizeof(F_FLOAT)==sizeof(double)) printf("PPPMCuda: Using double precision for forces\n");
#endif*/
//if(sizeof(PPPM_FLOAT)==sizeof(float)) printf("PPPMCuda: Using single precision\n");
struct dev_array* dev_tmp=new struct dev_array[20];
int n_cudata=0;
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_brick");
memory->create3d_offset(density_brick_int,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_brick_int");
cu_density_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(density_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
(nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
cu_density_brick_int = new cCudaData<int, int, x> ((int*) &(density_brick_int[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
(nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdx_brick");
memory->create3d_offset(vdx_brick_tmp,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdx_brick_tmp");
cu_vdx_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdx_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
(nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdy_brick");
cu_vdy_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdy_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
(nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdz_brick");
cu_vdz_brick = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(vdz_brick[nzlo_out][nylo_out][nxlo_out]), & (dev_tmp[n_cudata++]),
(nzhi_out-nzlo_out+1)*(nyhi_out-nylo_out+1)*(nxhi_out-nxlo_out+1));
memory->create(density_fft,nfft_both,"pppm:density_fft");
cu_density_fft = new cCudaData<double, PPPM_FLOAT, x> (density_fft, & (dev_tmp[n_cudata++]),nfft_both);
cu_energy = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm);
cu_virial = new cCudaData<double, ENERGY_FLOAT, x> (NULL, &(dev_tmp[n_cudata++]),ny_pppm*nz_pppm*6);
memory->create(greensfn,nfft_both,"pppm:greensfn");
cu_greensfn = new cCudaData<double, PPPM_FLOAT, x> (greensfn, & (dev_tmp[n_cudata++]) , nx_pppm*ny_pppm*nz_pppm);
memory->create(work1,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work1");
memory->create(work2,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work2");
memory->create(work3,2*nx_pppm*ny_pppm*nz_pppm,"pppm:work3");
cu_work1 = new cCudaData<double, FFT_FLOAT, x> (work1, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
cu_work2 = new cCudaData<double, FFT_FLOAT, x> (work2, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
cu_work3 = new cCudaData<double, FFT_FLOAT, x> (work3, & (dev_tmp[n_cudata++]) , 2*nx_pppm*ny_pppm*nz_pppm);
memory->create(fkx,nx_pppm,"pppmcuda:fkx");
cu_fkx = new cCudaData<double, PPPM_FLOAT, x> (fkx, & (dev_tmp[n_cudata++]) , nx_pppm);
memory->create(fky,ny_pppm,"pppmcuda:fky");
cu_fky = new cCudaData<double, PPPM_FLOAT, x> (fky, & (dev_tmp[n_cudata++]) , ny_pppm);
memory->create(fkz,nz_pppm,"pppmcuda:fkz");
cu_fkz = new cCudaData<double, PPPM_FLOAT, x> (fkz, & (dev_tmp[n_cudata++]) , nz_pppm);
memory->create(vg,nfft_both,6,"pppm:vg");
cu_vg = new cCudaData<double, PPPM_FLOAT, xy> ((double*)vg, & (dev_tmp[n_cudata++]) , nfft_both,6);
memory->create(buf1,nbuf,"pppm:buf1");
memory->create(buf2,nbuf,"pppm:buf2");
// summation coeffs
gf_b = new double[order];
cu_gf_b = new cCudaData<double,PPPM_FLOAT,x> (gf_b, &(dev_tmp[n_cudata++]) , order);
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");
cu_rho_coeff = new cCudaData<double, PPPM_FLOAT, x> ((double*) &(rho_coeff[0][(1-order)/2]), & (dev_tmp[n_cudata++]) , order*(order/2-(1-order)/2+1));
debugdata=new PPPM_FLOAT[100];
cu_debugdata = new cCudaData<PPPM_FLOAT, PPPM_FLOAT, x> (debugdata,& (dev_tmp[n_cudata++]),100);
cu_flag = new cCudaData<int, int, x> (&global_flag,& (dev_tmp[n_cudata++]),3);
// 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;
fft1c = new FFT3dCuda(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,true);
fft2c = new FFT3dCuda(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,false);
#ifdef FFT_CUFFT
fft1c->set_cudata(cu_work2->dev_data(),cu_work1->dev_data());
fft2c->set_cudata(cu_work2->dev_data(),cu_work3->dev_data());
#endif
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,
1,0,0,2);
pppm_device_init(cu_density_brick->dev_data(), cu_vdx_brick->dev_data(), cu_vdy_brick->dev_data(), cu_vdz_brick->dev_data(), cu_density_fft->dev_data(),cu_energy->dev_data(),cu_virial->dev_data()
, cu_work1->dev_data(), cu_work2->dev_data(), cu_work3->dev_data(), cu_greensfn->dev_data(), cu_fkx->dev_data(), cu_fky->dev_data(), cu_fkz->dev_data(), cu_vg->dev_data()
,nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out,nx_pppm,ny_pppm,nz_pppm
,nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,cu_gf_b->dev_data()
,qqrd2e,order,cu_rho_coeff->dev_data(),cu_debugdata->dev_data(),cu_density_brick_int->dev_data(),slabflag
);
}
/* ----------------------------------------------------------------------
deallocate memory that depends on # of K-vectors and order
---------------------------------------------------------------------- */
void PPPMCuda::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);
density_brick = vdx_brick = vdy_brick = vdz_brick = NULL;
memory->destroy(density_fft);
memory->destroy(greensfn);
memory->destroy(work1);
memory->destroy(work2);
memory->destroy(vg);
density_fft = NULL;
greensfn = NULL;
work1 = NULL;
work2 = NULL;
vg = NULL;
memory->destroy(fkx);
memory->destroy(fky);
memory->destroy(fkz);
fkx = NULL;
fky = NULL;
fkz = NULL;
delete cu_density_brick;
delete cu_density_brick_int;
delete cu_vdx_brick;
delete cu_vdy_brick;
delete cu_vdz_brick;
delete cu_density_fft;
delete cu_energy;
delete cu_virial;
#ifdef FFT_CUFFT
delete cu_greensfn;
delete cu_gf_b;
delete cu_vg;
delete cu_work1;
delete cu_work2;
delete cu_work3;
delete cu_fkx;
delete cu_fky;
delete cu_fkz;
#endif
delete cu_flag;
delete cu_debugdata;
delete cu_rho_coeff;
cu_vdx_brick = cu_vdy_brick = cu_vdz_brick = NULL;
cu_density_brick = NULL;
cu_density_brick_int = NULL;
cu_density_fft = NULL;
cu_energy=NULL;
cu_virial=NULL;
#ifdef FFT_CUFFT
cu_greensfn = NULL;
cu_gf_b = NULL;
cu_work1 = cu_work2 = cu_work3 = NULL;
cu_vg = NULL;
cu_fkx = cu_fky = cu_fkz = NULL;
#endif
cu_flag = NULL;
cu_debugdata = NULL;
cu_rho_coeff = NULL;
cu_part2grid = NULL;
memory->destroy(buf1);
memory->destroy(buf2);
delete [] gf_b;
gf_b = NULL;
memory->destroy2d_offset(rho1d,-order/2); rho1d = NULL;
memory->destroy2d_offset(rho_coeff,(1-order)/2); rho_coeff = NULL;
delete fft1c;
fft1c = NULL;
double end=CudaWrapper_CheckMemUseage()/1024/1024;
delete fft2c;
fft2c = NULL;
delete remap;
remap = NULL;
buf1 = NULL;
buf2 = NULL;
}
/* ----------------------------------------------------------------------
set size of FFT grid (nx,ny,nz_pppm) and g_ewald
-------------------------------------------------------------------------*/
void PPPMCuda::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;
double q2 = qsqsum / force->dielectric;
bigint natoms = atom->natoms;
// use xprd,yprd,zprd even if triclinic so grid size is the same
// adjust z dimension for 2d slab PPPMCuda
// 3d PPPMCuda 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 error 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;
if (!gewaldflag)
g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) /
(2.0*q2))) / cutoff;
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and precision
// 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 precision target is met
if (!gridflag) {
double err;
h_x = h_y = h_z = 1/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 > precision) {
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 > precision) {
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 > precision) {
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++;
// if allowed try to change grid size until it is a power of a single prime factor
if(precisionmodify!='=')
{
if (me == 0) {
if (screen) {
fprintf(screen,"Initial grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
}
if (logfile) {
fprintf(logfile,"Initial grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
}
}
make_power_of_prime(&nx_pppm);
make_power_of_prime(&ny_pppm);
make_power_of_prime(&nz_pppm);
if (me == 0) {
if (screen) {
fprintf(screen,"Modified grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
}
if (logfile) {
fprintf(logfile,"Modified grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
}
}
}
// adjust g_ewald for new grid size
h_x = xprd/nx_pppm;
h_y = yprd/ny_pppm;
h_z = zprd_slab/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/hmin;
g_ewald = gew2;
fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (f*fmid >= 0.0) error->all(FLERR,"Cannot compute PPPMCuda 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 PPPMCuda G");
}
}
// final RMS precision
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 spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
// free local memory
memory->destroy(acons);
// print info
if (me == 0) {
if (screen) {
fprintf(screen," G vector = %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," RMS precision = %g\n",MAX(lpr,spr));
}
if (logfile) {
fprintf(logfile," G vector = %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," RMS precision = %g\n",MAX(lpr,spr));
}
}
}
/* ----------------------------------------------------------------------
check if all factors of n are prime
return 1 if yes, 0 if no
-------------------------------------------------------------------------*/
void PPPMCuda::make_power_of_prime(int* n)
{
if((precisionmodify!='+')&&(precisionmodify!='-')&&(precisionmodify!='c'))
{error->all(FLERR,"Unknown Option for PPPMCuda, assumeing '='");return;}
int oldn=*n;
int* primelist=new int[1000];
int count=0;
int prime=1;
while(prime<2000) primelist[count++]=prime*=2;
prime=1;
while(prime<2000) primelist[count++]=prime*=3;
prime=1;
while(prime<2000) primelist[count++]=prime*=5;
prime=1;
while(prime<2000) primelist[count++]=prime*=7;
for(int i=0;i<count-1;i++)
for(int j=0;j<count-i-1;j++)
{
if(primelist[j]>primelist[j+1])
{
int a=primelist[j+1];
primelist[j+1]=primelist[j];
primelist[j]=a;
}
}
int nextsmaller=0;
while((primelist[nextsmaller+1]<*n)&&(nextsmaller+1<count)) nextsmaller++;
int nextlarger=count-1;
while((primelist[nextlarger-1]>*n)&&(nextlarger>0)) nextlarger--;
if(precisionmodify=='-')
*n=primelist[nextsmaller];
if((precisionmodify=='+')&&
(primelist[nextlarger]*primelist[nextlarger]*primelist[nextlarger]<2*(*n)*(*n)*(*n)))
*n=primelist[nextlarger];
if(precisionmodify=='c')
{
double factorsmaller=1.0*(*n)*(*n)*(*n)/(primelist[nextsmaller]*primelist[nextsmaller]*primelist[nextsmaller]);
double factorlarger=1.0*(primelist[nextlarger]*primelist[nextlarger]*primelist[nextlarger])/((*n)*(*n)*(*n));
if((factorlarger<factorsmaller)&&(factorlarger<2)) *n=primelist[nextlarger];
else *n=primelist[nextsmaller];
}
delete [] primelist;
primelist = NULL;
if(*n<0.75*oldn)
if (me == 0) {
if (screen) {
fprintf(screen,"\n\npppm/cuda WARNING: \t\tSignificantly lower gridsize than requested.\n\t\t\t\t\tYou should most likely use '=' or '+' as precision modify option\n");
}
if (logfile) {
fprintf(logfile,"\n\npppm/cuda WARNING: \t\tSignificantly lower gridsize than requested.\n\t\t\t\t\tYou should most likely use '=' or '+' as precision modify option\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 PPPMCuda::particle_map()
{
MYDBG(printf("# CUDA PPPMCuda::particle_map() ... start\n");)
int flag = 0;
cu_flag->memset_device(0);
flag=cuda_particle_map(&cuda->shared_data,cu_flag->dev_data());
if(flag)
{
cu_debugdata->download();
printf("Out of range atom: ");
printf("ID: %i ",atom->tag[int(debugdata[0])]);
printf("x: %e ",debugdata[7]);
printf("y: %e ",debugdata[8]);
printf("z: %e ",debugdata[9]);
printf("nx: %e ",debugdata[4]);
printf("ny: %e ",debugdata[5]);
printf("\n");
//printf("debugdata: cpu: %e %e %e %i\n",boxlo[0],boxlo[1],boxlo[2],atom->nlocal);
cuda->cu_x->download();
int nx,ny,nz;
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
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;
if(i==1203)printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz);
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 || i==1203) {printf("Outside Atom: %i %e %e %e (%i %i %i)\n",i,x[i][0],x[i][1],x[i][2],nx,ny,nz); }
}
}
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute PPPMCuda!");
}
/* ----------------------------------------------------------------------
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 PPPMCuda::make_rho()
{
cuda_make_rho(&cuda->shared_data,cu_flag->dev_data(),&density_intScale,nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,cu_density_brick->dev_data(),cu_density_brick_int->dev_data());
}
/* ----------------------------------------------------------------------
FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPMCuda::poisson(int eflag, int vflag)
{
#ifndef FFT_CUFFT
PPPM::poisson(eflag,vflag);
return;
#endif
#ifdef FFT_CUFFT
timespec starttime,starttime2;
timespec endtime,endtime2;
int nprocs=comm->nprocs;
clock_gettime(CLOCK_REALTIME,&starttime);
fft1c->compute(density_fft,work1,1);
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
if (eflag || vflag) {
poisson_energy(nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,vflag);
ENERGY_FLOAT gpuvirial[6];
energy+=sum_energy(cu_virial->dev_data(),cu_energy->dev_data(),nx_pppm,ny_pppm,nz_pppm,vflag,gpuvirial);
if(vflag)
{
for(int j=0;j<6;j++) virial[j]+=gpuvirial[j];
}
}
// scale by 1/total-grid-pts to get rho(k)
// multiply by Green's function to get V(k)
poisson_scale(nx_pppm,ny_pppm,nz_pppm);
// 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
poisson_xgrad(nx_pppm,ny_pppm,nz_pppm);
clock_gettime(CLOCK_REALTIME,&starttime);
fft2c->compute(work2,work2,-1);
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
poisson_vdx_brick(nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,nx_pppm,ny_pppm,nz_pppm);
// y direction gradient
poisson_ygrad(nx_pppm,ny_pppm,nz_pppm);
clock_gettime(CLOCK_REALTIME,&starttime);
fft2c->compute(work2,work2,-1);
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
poisson_vdy_brick(nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,nx_pppm,ny_pppm,nz_pppm);
// z direction gradient
poisson_zgrad(nx_pppm,ny_pppm,nz_pppm);
clock_gettime(CLOCK_REALTIME,&starttime);
fft2c->compute(work2,work2,-1);
clock_gettime(CLOCK_REALTIME,&endtime);
poissontime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
poisson_vdz_brick(nxhi_out,nxlo_out,nyhi_out,nylo_out,nzhi_out,nzlo_out,nx_pppm,ny_pppm,nz_pppm);
#endif
}
/*----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
-------------------------------------------------------------------------*/
void PPPMCuda::fieldforce()
{
cuda_fieldforce(& cuda->shared_data,cu_flag);
return;
}
/* ----------------------------------------------------------------------
perform and time the 4 FFTs required for N timesteps
------------------------------------------------------------------------- */
void PPPMCuda::timing(int n, double &time3d, double &time1d)
{
double time1,time2;
for (int i = 0; i < 2*nfft_both; i++) work1[i] = 0.0;
MPI_Barrier(world);
time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1c->compute(work1,work1,1);
fft2c->compute(work1,work1,-1);
fft2c->compute(work1,work1,-1);
fft2c->compute(work1,work1,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time3d = time2 - time1;
MPI_Barrier(world);
/*time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1c->timing1d(work1,nfft_both,1);
fft2c->timing1d(work1,nfft_both,-1);
fft2c->timing1d(work1,nfft_both,-1);
fft2c->timing1d(work1,nfft_both,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time1d = time2 - time1;*/
}
void PPPMCuda::slabcorr(int eflag)
{
// compute local contribution to global dipole moment
if(slabbuf==NULL)
{
slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
}
if((atom->nlocal+31)/32*sizeof(ENERGY_FLOAT)>=cu_slabbuf->dev_size())
{
delete [] slabbuf;
delete cu_slabbuf;
slabbuf=new ENERGY_FLOAT[(atom->nmax+31)/32];
cu_slabbuf = new cCudaData<ENERGY_FLOAT,ENERGY_FLOAT, x> (slabbuf, (atom->nmax+31)/32);
}
double dipole = cuda_slabcorr_energy(&cuda->shared_data,slabbuf,(ENERGY_FLOAT*) cu_slabbuf->dev_data());
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
double e_slabcorr = 2.0*MY_PI*dipole_all*dipole_all/volume;
if (eflag) energy += qqrd2e*scale * e_slabcorr;
double ffact = -4.0*MY_PI*dipole_all/volume;
cuda_slabcorr_force(&cuda->shared_data,ffact);
}
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