From 121e237acd8f1cb8c3f6c5a7f10c4ce2e2bba479 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 15 Apr 2014 15:32:49 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11792 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/KSPACE/pppm_old.cpp | 2850 --------------------------------------- src/KSPACE/pppm_old.h | 271 ---- 2 files changed, 3121 deletions(-) delete mode 100644 src/KSPACE/pppm_old.cpp delete mode 100644 src/KSPACE/pppm_old.h diff --git a/src/KSPACE/pppm_old.cpp b/src/KSPACE/pppm_old.cpp deleted file mode 100644 index c2d1cad053..0000000000 --- a/src/KSPACE/pppm_old.cpp +++ /dev/null @@ -1,2850 +0,0 @@ -/* ---------------------------------------------------------------------- - 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 (comm->xsplit[comm->myloc[0]] * nx_pppm); - nxhi_in = static_cast (comm->xsplit[comm->myloc[0]+1] * nx_pppm) - 1; - - nylo_in = static_cast (comm->ysplit[comm->myloc[1]] * ny_pppm); - nyhi_in = static_cast (comm->ysplit[comm->myloc[1]+1] * ny_pppm) - 1; - - nzlo_in = static_cast - (comm->zsplit[comm->myloc[2]] * nz_pppm/slab_volfactor); - nzhi_in = static_cast - (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 ((sublo[0]-dist[0]-boxlo[0]) * - nx_pppm/xprd + shift) - OFFSET; - nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * - nx_pppm/xprd + shift) - OFFSET; - nxlo_out = nlo + nlower; - nxhi_out = nhi + nupper; - - nlo = static_cast ((sublo[1]-dist[1]-boxlo[1]) * - ny_pppm/yprd + shift) - OFFSET; - nhi = static_cast ((subhi[1]+dist[1]-boxlo[1]) * - ny_pppm/yprd + shift) - OFFSET; - nylo_out = nlo + nlower; - nyhi_out = nhi + nupper; - - nlo = static_cast ((sublo[2]-dist[2]-boxlo[2]) * - nz_pppm/zprd_slab + shift) - OFFSET; - nhi = static_cast ((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 ((g_ewald*xprd/(MY_PI*nx_pppm)) * - pow(-log(EPS_HOC),0.25)); - int nby = static_cast ((g_ewald*yprd/(MY_PI*ny_pppm)) * - pow(-log(EPS_HOC),0.25)); - int nbz = static_cast ((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(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 (xprd/h_x) + 1; - ny_pppm = static_cast (yprd/h_y) + 1; - nz_pppm = static_cast (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(nx_pppm); - h_y = yprd/static_cast(ny_pppm); - h_z = zprd_slab/static_cast(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(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 ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET; - ny = static_cast ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET; - nz = static_cast ((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; - } -} diff --git a/src/KSPACE/pppm_old.h b/src/KSPACE/pppm_old.h deleted file mode 100644 index f8382008f9..0000000000 --- a/src/KSPACE/pppm_old.h +++ /dev/null @@ -1,271 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#ifdef KSPACE_CLASS - -KSpaceStyle(pppm/old,PPPMOld) - -#else - -#ifndef LMP_PPPM_OLD_H -#define LMP_PPPM_OLD_H - -#include "lmptype.h" -#include "mpi.h" - -#ifdef FFT_SINGLE -typedef float FFT_SCALAR; -#define MPI_FFT_SCALAR MPI_FLOAT -#else -typedef double FFT_SCALAR; -#define MPI_FFT_SCALAR MPI_DOUBLE -#endif - -#include "kspace.h" - -namespace LAMMPS_NS { - -class PPPMOld : public KSpace { - public: - PPPMOld(class LAMMPS *, int, char **); - virtual ~PPPMOld(); - virtual void init(); - virtual void setup(); - virtual void compute(int, int); - virtual int timing_1d(int, double &); - virtual int timing_3d(int, double &); - virtual double memory_usage(); - - virtual void compute_group_group(int, int, int); - - protected: - int me,nprocs; - int nfactors; - int *factors; - double cutoff; - double volume; - double delxinv,delyinv,delzinv,delvolinv; - double shift,shiftone; - int peratom_allocate_flag; - - int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in; - int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out; - int nxlo_ghost,nxhi_ghost,nylo_ghost,nyhi_ghost,nzlo_ghost,nzhi_ghost; - int nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft; - int nlower,nupper; - int ngrid,nfft,nfft_both; - int nbuf,nbuf_peratom; - - FFT_SCALAR ***density_brick; - FFT_SCALAR ***vdx_brick,***vdy_brick,***vdz_brick; - FFT_SCALAR ***u_brick; - FFT_SCALAR ***v0_brick,***v1_brick,***v2_brick; - FFT_SCALAR ***v3_brick,***v4_brick,***v5_brick; - double *greensfn; - double **vg; - double *fkx,*fky,*fkz; - FFT_SCALAR *density_fft; - FFT_SCALAR *work1,*work2; - FFT_SCALAR *buf1,*buf2,*buf3,*buf4; - - double *gf_b; - FFT_SCALAR **rho1d,**rho_coeff; - - // group-group interactions - - int group_allocate_flag; - FFT_SCALAR ***density_A_brick,***density_B_brick; - FFT_SCALAR *density_A_fft,*density_B_fft; - - - class FFT3d *fft1,*fft2; - class Remap *remap; - - int **part2grid; // storage for particle -> grid mapping - int nmax; - - int triclinic; // domain settings, orthog or triclinic - double *boxlo; - // TIP4P settings - int typeH,typeO; // atom types of TIP4P water H and O atoms - double qdist; // distance from O site to negative charge - double alpha; // geometric factor - - void set_grid(); - virtual void allocate(); - virtual void allocate_peratom(); - virtual void deallocate(); - virtual void deallocate_peratom(); - int factorable(int); - double rms(double, double, bigint, double, double **); - double diffpr(double, double, double, double, double **); - void compute_gf_denom(); - - virtual void particle_map(); - virtual void make_rho(); - virtual void brick2fft(); - virtual void fillbrick(); - virtual void fillbrick_peratom(); - virtual void poisson(); - virtual void poisson_peratom(); - virtual void fieldforce(); - virtual void fieldforce_peratom(); - void procs2grid2d(int,int,int,int *, int*); - void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &, - const FFT_SCALAR &); - void compute_rho_coeff(); - void slabcorr(); - - // group-group interactions - - virtual void allocate_groups(); - virtual void deallocate_groups(); - virtual void make_rho_groups(int, int, int); - virtual void poisson_groups(int); - -/* ---------------------------------------------------------------------- - denominator for Hockney-Eastwood Green's function - of x,y,z = sin(kx*deltax/2), etc - - inf n-1 - S(n,k) = Sum W(k+pi*j)**2 = Sum b(l)*(z*z)**l - j=-inf l=0 - - = -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x) - gf_b = denominator expansion coeffs -------------------------------------------------------------------------- */ - - inline double gf_denom(const double &x, const double &y, - const double &z) const { - double sx,sy,sz; - sz = sy = sx = 0.0; - for (int l = order-1; l >= 0; l--) { - sx = gf_b[l] + sx*x; - sy = gf_b[l] + sy*y; - sz = gf_b[l] + sz*z; - } - double s = sx*sy*sz; - return s*s; - }; -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Cannot use PPPM with 2d simulation - -The kspace style pppm cannot be used in 2d simulations. You can use -2d PPPM in a 3d simulation; see the kspace_modify command. - -E: Kspace style requires atom attribute q - -The atom style defined does not have these attributes. - -E: Cannot use nonperiodic boundaries with PPPM - -For kspace style pppm, all 3 dimensions must have periodic boundaries -unless you use the kspace_modify command to define a 2d slab with a -non-periodic z dimension. - -E: Incorrect boundaries with slab PPPM - -Must have periodic x,y dimensions and non-periodic z dimension to use -2d slab option with PPPM. - -E: PPPM order cannot be < 2 or > than %d - -This is a limitation of the PPPM implementation in LAMMPS. - -E: KSpace style is incompatible with Pair style - -Setting a kspace style requires that a pair style with a long-range -Coulombic or dispersion component be used. - -E: Bond and angle potentials must be defined for TIP4P - -Cannot use TIP4P pair potential unless bond and angle potentials -are defined. - -E: Bad TIP4P angle type for PPPM/TIP4P - -Specified angle type is not valid. - -E: Bad TIP4P bond type for PPPM/TIP4P - -Specified bond type is not valid. - -E: Cannot use kspace solver on system with no charge - -No atoms in system have a non-zero charge. - -W: System is not charge neutral, net charge = %g - -The total charge on all atoms on the system is not 0.0, which -is not valid for the long-range Coulombic solvers. - -W: Reducing PPPM order b/c stencil extends beyond neighbor processor - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. - -E: PPPM grid is too large - -The global PPPM grid is larger than OFFSET in one or more dimensions. -OFFSET is currently set to 4096. You likely need to decrease the -requested accuracy. - -E: PPPM order has been reduced to 0 - -The auto-adjust of the order failed. You will need to -set the grid size and order directly via kspace_modify. - -E: KSpace accuracy must be > 0 - -The kspace accuracy designated in the input must be greater than zero. - -E: Cannot compute PPPM G - -The Ewald factor could not be computed for the current choice of -grid size, cutoff, accuracy. - -E: Out of range atoms - cannot compute PPPM - -One or more atoms are attempting to map their charge to a PPPM grid -point that is not owned by a processor. This is likely for one of two -reasons, both of them bad. First, it may mean that an atom near the -boundary of a processor's sub-domain has moved more than 1/2 the -"neighbor skin distance"_neighbor.html without neighbor lists being -rebuilt and atoms being migrated to new processors. This also means -you may be missing pairwise interactions that need to be computed. -The solution is to change the re-neighboring criteria via the -"neigh_modify"_neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. - -E: Cannot (yet) use K-space slab correction with compute group/group - -This option is not yet supported. - -*/