git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/KSPACE/pppm_tip4p.cpp
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src/KSPACE/pppm_tip4p.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "pppm_tip4p.h"
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#include "atom.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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#define OFFSET 4096
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/* ---------------------------------------------------------------------- */
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PPPMTIP4P::PPPMTIP4P(int narg, char **arg) : PPPM(narg, arg) {}
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/* ----------------------------------------------------------------------
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find center grid pt for each of my particles
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check that full stencil for the particle will fit in my 3d brick
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store central grid pt indices in part2grid array
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------------------------------------------------------------------------- */
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void PPPMTIP4P::particle_map()
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{
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int nx,ny,nz,iH1,iH2;
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double *xi,xM[3];
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int *type = atom->type;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double boxxlo = domain->boxxlo;
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double boxylo = domain->boxylo;
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double boxzlo = domain->boxzlo;
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int flag = 0;
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for (int i = 0; i < nlocal; i++) {
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if (type[i] == typeO) {
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find_M(i,iH1,iH2,xM);
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xi = xM;
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} else xi = x[i];
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// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
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// current particle coord can be outside global and local box
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// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
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nx = static_cast<int> ((xi[0]-boxxlo)*delxinv+shift) - OFFSET;
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ny = static_cast<int> ((xi[1]-boxylo)*delyinv+shift) - OFFSET;
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nz = static_cast<int> ((xi[2]-boxzlo)*delzinv+shift) - OFFSET;
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part2grid[i][0] = nx;
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part2grid[i][1] = ny;
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part2grid[i][2] = nz;
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// check that entire stencil around nx,ny,nz will fit in my 3d brick
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if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
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ny+nlower < nylo_out || ny+nupper > nyhi_out ||
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nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
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}
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int flag_all;
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MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
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if (flag_all) error->all("Out of range atoms - cannot compute PPPM");
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}
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/* ----------------------------------------------------------------------
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create discretized "density" on section of global grid due to my particles
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density(x,y,z) = charge "density" at grid points of my 3d brick
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(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
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in global grid
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------------------------------------------------------------------------- */
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void PPPMTIP4P::make_rho()
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{
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int i,l,m,n,nx,ny,nz,mx,my,mz,iH1,iH2;
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double dx,dy,dz,x0,y0,z0;
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double *xi,xM[3];
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// clear 3d density array
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double *vec = &density_brick[nzlo_out][nylo_out][nxlo_out];
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for (i = 0; i < ngrid; i++) vec[i] = 0.0;
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// loop over my charges, add their contribution to nearby grid points
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// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
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// (dx,dy,dz) = distance to "lower left" grid pt
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// (mx,my,mz) = global coords of moving stencil pt
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int *type = atom->type;
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double *q = atom->q;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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double boxxlo = domain->boxxlo;
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double boxylo = domain->boxylo;
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double boxzlo = domain->boxzlo;
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for (int i = 0; i < nlocal; i++) {
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if (type[i] == typeO) {
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find_M(i,iH1,iH2,xM);
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xi = xM;
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} else xi = x[i];
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nx = part2grid[i][0];
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ny = part2grid[i][1];
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nz = part2grid[i][2];
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dx = nx+shiftone - (xi[0]-boxxlo)*delxinv;
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dy = ny+shiftone - (xi[1]-boxylo)*delyinv;
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dz = nz+shiftone - (xi[2]-boxzlo)*delzinv;
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compute_rho1d(dx,dy,dz);
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z0 = delvolinv * q[i];
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for (n = nlower; n <= nupper; n++) {
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mz = n+nz;
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y0 = z0*rho1d[2][n];
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for (m = nlower; m <= nupper; m++) {
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my = m+ny;
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x0 = y0*rho1d[1][m];
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for (l = nlower; l <= nupper; l++) {
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mx = l+nx;
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density_brick[mz][my][mx] += x0*rho1d[0][l];
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}
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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interpolate from grid to get electric field & force on my particles
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------------------------------------------------------------------------- */
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void PPPMTIP4P::fieldforce()
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{
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int i,l,m,n,nx,ny,nz,mx,my,mz;
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double dx,dy,dz,x0,y0,z0;
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double ek[3];
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double *xi;
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int iH1,iH2;
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double xM[3];
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double fx,fy,fz;
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// loop over my charges, interpolate electric field from nearby grid points
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// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
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// (dx,dy,dz) = distance to "lower left" grid pt
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// (mx,my,mz) = global coords of moving stencil pt
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// ek = 3 components of E-field on particle
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double *q = atom->q;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double boxxlo = domain->boxxlo;
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double boxylo = domain->boxylo;
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double boxzlo = domain->boxzlo;
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for (i = 0; i < nlocal; i++) {
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if (type[i] == typeO) {
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find_M(i,iH1,iH2,xM);
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xi = xM;
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} else xi = x[i];
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nx = part2grid[i][0];
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ny = part2grid[i][1];
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nz = part2grid[i][2];
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dx = nx+shiftone - (xi[0]-boxxlo)*delxinv;
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dy = ny+shiftone - (xi[1]-boxylo)*delyinv;
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dz = nz+shiftone - (xi[2]-boxzlo)*delzinv;
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compute_rho1d(dx,dy,dz);
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ek[0] = ek[1] = ek[2] = 0.0;
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for (n = nlower; n <= nupper; n++) {
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mz = n+nz;
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z0 = rho1d[2][n];
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for (m = nlower; m <= nupper; m++) {
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my = m+ny;
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y0 = z0*rho1d[1][m];
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for (l = nlower; l <= nupper; l++) {
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mx = l+nx;
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x0 = y0*rho1d[0][l];
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ek[0] -= x0*vdx_brick[mz][my][mx];
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ek[1] -= x0*vdy_brick[mz][my][mx];
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ek[2] -= x0*vdz_brick[mz][my][mx];
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}
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}
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}
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// convert E-field to force
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if (type[i] != typeO) {
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f[i][0] += qqrd2e*q[i]*ek[0];
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f[i][1] += qqrd2e*q[i]*ek[1];
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f[i][2] += qqrd2e*q[i]*ek[2];
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} else {
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fx = qqrd2e * q[i] * ek[0];
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fy = qqrd2e * q[i] * ek[1];
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fz = qqrd2e * q[i] * ek[2];
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find_M(i,iH1,iH2,xM);
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f[i][0] += fx*(1.0-2.0*alpha);
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f[i][1] += fy*(1.0-2.0*alpha);
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f[i][2] += fz*(1.0-2.0*alpha);
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f[iH1][0] += alpha*(fx);
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f[iH1][1] += alpha*(fy);
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f[iH1][2] += alpha*(fz);
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f[iH2][0] += alpha*(fx);
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f[iH2][1] += alpha*(fy);
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f[iH2][2] += alpha*(fz);
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}
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}
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}
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/* ----------------------------------------------------------------------
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find 2 H atoms bonded to O atom i
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compute position xM of fictitious charge site for O atom
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also return local indices iH1,iH2 of H atoms
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------------------------------------------------------------------------- */
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void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
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{
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iH1 = atom->map(atom->tag[i] + 1);
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iH2 = atom->map(atom->tag[i] + 2);
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if (iH1 == -1 || iH2 == -1) error->one("TIP4P hydrogen is missing");
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if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
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error->one("TIP4P hydrogen has incorrect atom type");
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double **x = atom->x;
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double delx1 = x[iH1][0] - x[i][0];
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double dely1 = x[iH1][1] - x[i][1];
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double delz1 = x[iH1][2] - x[i][2];
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domain->minimum_image(&delx1,&dely1,&delz1);
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double delx2 = x[iH2][0] - x[i][0];
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double dely2 = x[iH2][1] - x[i][1];
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double delz2 = x[iH2][2] - x[i][2];
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domain->minimum_image(&delx2,&dely2,&delz2);
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xM[0] = x[i][0] + alpha * (delx1 + delx2);
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xM[1] = x[i][1] + alpha * (dely1 + dely2);
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xM[2] = x[i][2] + alpha * (delz1 + delz2);
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}
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