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lammps/src/KSPACE/pppm_tip4p.cpp
Axel Kohlmeyer 09c19a936b update URLs in source code and manual
2021-05-24 14:18:20 -04:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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: Amalie Frischknecht and Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
#include "pppm_tip4p.h"
#include <mpi.h>
#include <cmath>
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define OFFSET 16384
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#define ONEF 1.0f
#else
#define ZEROF 0.0
#define ONEF 1.0
#endif
/* ---------------------------------------------------------------------- */
PPPMTIP4P::PPPMTIP4P(LAMMPS *lmp) : PPPM(lmp)
{
triclinic_support = 1;
tip4pflag = 1;
}
/* ---------------------------------------------------------------------- */
void PPPMTIP4P::init()
{
// TIP4P PPPM requires newton on, b/c it computes forces on ghost atoms
if (force->newton == 0)
error->all(FLERR,"Kspace style pppm/tip4p requires newton on");
PPPM::init();
}
/* ----------------------------------------------------------------------
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 PPPMTIP4P::particle_map()
{
int nx,ny,nz,iH1,iH2;
double *xi,xM[3];
int *type = atom->type;
double **x = atom->x;
int nlocal = atom->nlocal;
if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx = static_cast<int> ((xi[0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((xi[1]-boxlo[1])*delyinv+shift) - OFFSET;
nz = static_cast<int> ((xi[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++;
}
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Out of range atoms - cannot compute 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 PPPMTIP4P::make_rho()
{
int i,l,m,n,nx,ny,nz,mx,my,mz,iH1,iH2;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
double *xi,xM[3];
// clear 3d density array
FFT_SCALAR *vec = &density_brick[nzlo_out][nylo_out][nxlo_out];
for (i = 0; i < ngrid; i++) vec[i] = ZEROF;
// 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
int *type = atom->type;
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[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];
}
}
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ik
------------------------------------------------------------------------- */
void PPPMTIP4P::fieldforce_ik()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR ekx,eky,ekz;
double *xi;
int iH1,iH2;
double xM[3];
double fx,fy,fz;
// 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 *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[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];
if (type[i] != typeO) {
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
if (slabflag != 2) f[i][2] += qfactor*ekz;
} else {
fx = qfactor * ekx;
fy = qfactor * eky;
fz = qfactor * ekz;
find_M(i,iH1,iH2,xM);
f[i][0] += fx*(1 - alpha);
f[i][1] += fy*(1 - alpha);
if (slabflag != 2) f[i][2] += fz*(1 - alpha);
f[iH1][0] += 0.5*alpha*fx;
f[iH1][1] += 0.5*alpha*fy;
if (slabflag != 2) f[iH1][2] += 0.5*alpha*fz;
f[iH2][0] += 0.5*alpha*fx;
f[iH2][1] += 0.5*alpha*fy;
if (slabflag != 2) f[iH2][2] += 0.5*alpha*fz;
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ad
------------------------------------------------------------------------- */
void PPPMTIP4P::fieldforce_ad()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz;
FFT_SCALAR ekx,eky,ekz;
double *xi;
int iH1,iH2;
double xM[3];
double s1,s2,s3;
double sf;
double *prd;
double fx,fy,fz;
if (triclinic == 0) prd = domain->prd;
else prd = domain->prd_lamda;
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double hx_inv = nx_pppm/xprd;
double hy_inv = ny_pppm/yprd;
double hz_inv = nz_pppm/zprd;
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
// ek = 3 components of E-field on particle
double *q = atom->q;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
compute_drho1d(dx,dy,dz);
ekx = eky = ekz = ZEROF;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
for (m = nlower; m <= nupper; m++) {
my = m+ny;
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
ekx += drho1d[0][l]*rho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx];
eky += rho1d[0][l]*drho1d[1][m]*rho1d[2][n]*u_brick[mz][my][mx];
ekz += rho1d[0][l]*rho1d[1][m]*drho1d[2][n]*u_brick[mz][my][mx];
}
}
}
ekx *= hx_inv;
eky *= hy_inv;
ekz *= hz_inv;
// convert E-field to force and subtract self forces
const double qfactor = qqrd2e * scale;
s1 = xi[0]*hx_inv;
s2 = xi[1]*hy_inv;
s3 = xi[2]*hz_inv;
sf = sf_coeff[0]*sin(2*MY_PI*s1);
sf += sf_coeff[1]*sin(4*MY_PI*s1);
sf *= 2.0*q[i]*q[i];
fx = qfactor*(ekx*q[i] - sf);
sf = sf_coeff[2]*sin(2*MY_PI*s2);
sf += sf_coeff[3]*sin(4*MY_PI*s2);
sf *= 2.0*q[i]*q[i];
fy = qfactor*(eky*q[i] - sf);
sf = sf_coeff[4]*sin(2*MY_PI*s3);
sf += sf_coeff[5]*sin(4*MY_PI*s3);
sf *= 2.0*q[i]*q[i];
fz = qfactor*(ekz*q[i] - sf);
if (type[i] != typeO) {
f[i][0] += fx;
f[i][1] += fy;
if (slabflag != 2) f[i][2] += fz;
} else {
find_M(i,iH1,iH2,xM);
f[i][0] += fx*(1 - alpha);
f[i][1] += fy*(1 - alpha);
if (slabflag != 2) f[i][2] += fz*(1 - alpha);
f[iH1][0] += 0.5*alpha*fx;
f[iH1][1] += 0.5*alpha*fy;
if (slabflag != 2) f[iH1][2] += 0.5*alpha*fz;
f[iH2][0] += 0.5*alpha*fx;
f[iH2][1] += 0.5*alpha*fy;
if (slabflag != 2) f[iH2][2] += 0.5*alpha*fz;
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMTIP4P::fieldforce_peratom()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
double *xi;
int iH1,iH2;
double xM[3];
FFT_SCALAR u_pa,v0,v1,v2,v3,v4,v5;
// 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;
int *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
u_pa = 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_pa += 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) {
if (type[i] != typeO) {
eatom[i] += q[i]*u_pa;
} else {
eatom[i] += q[i]*u_pa*(1-alpha);
eatom[iH1] += q[i]*u_pa*alpha*0.5;
eatom[iH2] += q[i]*u_pa*alpha*0.5;
}
}
if (vflag_atom) {
if (type[i] != typeO) {
vatom[i][0] += v0*q[i];
vatom[i][1] += v1*q[i];
vatom[i][2] += v2*q[i];
vatom[i][3] += v3*q[i];
vatom[i][4] += v4*q[i];
vatom[i][5] += v5*q[i];
} else {
vatom[i][0] += v0*(1-alpha)*q[i];
vatom[i][1] += v1*(1-alpha)*q[i];
vatom[i][2] += v2*(1-alpha)*q[i];
vatom[i][3] += v3*(1-alpha)*q[i];
vatom[i][4] += v4*(1-alpha)*q[i];
vatom[i][5] += v5*(1-alpha)*q[i];
vatom[iH1][0] += v0*alpha*0.5*q[i];
vatom[iH1][1] += v1*alpha*0.5*q[i];
vatom[iH1][2] += v2*alpha*0.5*q[i];
vatom[iH1][3] += v3*alpha*0.5*q[i];
vatom[iH1][4] += v4*alpha*0.5*q[i];
vatom[iH1][5] += v5*alpha*0.5*q[i];
vatom[iH2][0] += v0*alpha*0.5*q[i];
vatom[iH2][1] += v1*alpha*0.5*q[i];
vatom[iH2][2] += v2*alpha*0.5*q[i];
vatom[iH2][3] += v3*alpha*0.5*q[i];
vatom[iH2][4] += v4*alpha*0.5*q[i];
vatom[iH2][5] += v5*alpha*0.5*q[i];
}
}
}
}
/* ----------------------------------------------------------------------
find 2 H atoms bonded to O atom i
compute position xM of fictitious charge site for O atom
also return local indices iH1,iH2 of H atoms
------------------------------------------------------------------------- */
void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
{
double **x = atom->x;
iH1 = atom->map(atom->tag[i] + 1);
iH2 = atom->map(atom->tag[i] + 2);
if (iH1 == -1 || iH2 == -1) error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
if (triclinic) {
// need to use custom code to find the closest image for triclinic,
// since local atoms are in lambda coordinates, but ghosts are not.
int *sametag = atom->sametag;
double xo[3],xh1[3],xh2[3],xm[3];
const int nlocal = atom->nlocal;
for (int ii = 0; ii < 3; ++ii) {
xo[ii] = x[i][ii];
xh1[ii] = x[iH1][ii];
xh2[ii] = x[iH2][ii];
}
if (i < nlocal) domain->lamda2x(x[i],xo);
if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1);
if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2);
double delx = xo[0] - xh1[0];
double dely = xo[1] - xh1[1];
double delz = xo[2] - xh1[2];
double rsqmin = delx*delx + dely*dely + delz*delz;
double rsq;
int closest = iH1;
// no need to run lamda2x() here -> ghost atoms
while (sametag[iH1] >= 0) {
iH1 = sametag[iH1];
delx = xo[0] - x[iH1][0];
dely = xo[1] - x[iH1][1];
delz = xo[2] - x[iH1][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH1;
xh1[0] = x[iH1][0];
xh1[1] = x[iH1][1];
xh1[2] = x[iH1][2];
}
}
iH1 = closest;
closest = iH2;
delx = xo[0] - xh2[0];
dely = xo[1] - xh2[1];
delz = xo[2] - xh2[2];
rsqmin = delx*delx + dely*dely + delz*delz;
while (sametag[iH2] >= 0) {
iH2 = sametag[iH2];
delx = xo[0] - x[iH2][0];
dely = xo[1] - x[iH2][1];
delz = xo[2] - x[iH2][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH2;
xh2[0] = x[iH2][0];
xh2[1] = x[iH2][1];
xh2[2] = x[iH2][2];
}
}
iH2 = closest;
// finally compute M in real coordinates ...
double delx1 = xh1[0] - xo[0];
double dely1 = xh1[1] - xo[1];
double delz1 = xh1[2] - xo[2];
double delx2 = xh2[0] - xo[0];
double dely2 = xh2[1] - xo[1];
double delz2 = xh2[2] - xo[2];
xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
// ... and convert M to lamda space for PPPM
domain->x2lamda(xm,xM);
} else {
// set iH1,iH2 to index of closest image to O
iH1 = domain->closest_image(i,iH1);
iH2 = domain->closest_image(i,iH2);
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
}
}
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