// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories LAMMPS development team: developers@lammps.org 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 author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ #include "pppm_cg.h" #include "atom.h" #include "domain.h" #include "error.h" #include "force.h" #include "grid3d.h" #include "math_const.h" #include "memory.h" #include "neighbor.h" #include #include using namespace LAMMPS_NS; using namespace MathConst; static constexpr int OFFSET = 16384; static constexpr double SMALLQ = 0.00001; static constexpr FFT_SCALAR ZEROF = 0.0; /* ---------------------------------------------------------------------- */ PPPMCG::PPPMCG(LAMMPS *lmp) : PPPM(lmp), is_charged(nullptr) { num_charged = -1; group_group_enable = 1; } /* ---------------------------------------------------------------------- */ void PPPMCG::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); // first argument is processed in parent class PPPM::settings(narg,arg); if (narg == 2) smallq = fabs(utils::numeric(FLERR,arg[1],false,lmp)); else smallq = SMALLQ; } /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ PPPMCG::~PPPMCG() { memory->destroy(is_charged); } /* ---------------------------------------------------------------------- compute the PPPM long-range force, energy, virial ------------------------------------------------------------------------- */ void PPPMCG::compute(int eflag, int vflag) { // set energy/virial flags // invoke allocate_peratom() if needed for first time ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) allocate_peratom(); // if atom count has changed, update qsum and qsqsum if (atom->natoms != natoms_original) { qsum_qsq(); natoms_original = atom->natoms; } // return if there are no charges if (qsqsum == 0.0) return; // 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->nmax > nmax) { memory->destroy(part2grid); memory->destroy(is_charged); nmax = atom->nmax; memory->create(part2grid,nmax,3,"pppm:part2grid"); memory->create(is_charged,nmax,"pppm/cg:is_charged"); } // one time setup message if (num_charged < 0) { bigint charged_all, charged_num; double charged_frac, charged_fmax, charged_fmin; num_charged=0; for (int i=0; i < atom->nlocal; ++i) if (fabs(atom->q[i]) > smallq) ++num_charged; // get fraction of charged particles per domain if (atom->nlocal > 0) charged_frac = static_cast(num_charged) * 100.0 / static_cast(atom->nlocal); else charged_frac = 0.0; MPI_Reduce(&charged_frac,&charged_fmax,1,MPI_DOUBLE,MPI_MAX,0,world); MPI_Reduce(&charged_frac,&charged_fmin,1,MPI_DOUBLE,MPI_MIN,0,world); // get fraction of charged particles overall charged_num = num_charged; MPI_Reduce(&charged_num,&charged_all,1,MPI_LMP_BIGINT,MPI_SUM,0,world); charged_frac = static_cast(charged_all) * 100.0 / static_cast(atom->natoms); if (me == 0) utils::logmesg(lmp," PPPM/cg optimization cutoff: {:.8g}\n" " Total charged atoms: {:.1f}%\n" " Min/max charged atoms/proc: {:.1f}% {:.1f}%\n", smallq,charged_frac,charged_fmin,charged_fmax); } // only need to rebuild this list after a neighbor list update if (neighbor->ago == 0) { num_charged = 0; for (int i = 0; i < atom->nlocal; ++i) { if (fabs(atom->q[i]) > smallq) { is_charged[num_charged] = i; ++num_charged; } } } // 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 gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); 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 if (differentiation_flag == 1) gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); else gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); } // 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 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; 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 (int 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) { const double * const q = atom->q; if (eflag_atom) { for (int j = 0; j < num_charged; j++) { const int i = is_charged[j]; 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 (int n = 0; n < num_charged; n++) { const int i = is_charged[n]; for (int j = 0; j < 6; j++) vatom[i][j] *= 0.5*qscale; } } } // 2d slab correction if (slabflag == 1) slabcorr(); // convert atoms back from lamda to box coords if (triclinic) domain->lamda2x(atom->nlocal); } /* ---------------------------------------------------------------------- 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 PPPMCG::particle_map() { int nx,ny,nz; double **x = atom->x; 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 j = 0; j < num_charged; j++) { int i = is_charged[j]; // (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 PPPMCG::make_rho() { int i,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; for (int j = 0; j < num_charged; j++) { i = is_charged[j]; 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]; } } } } } /* ---------------------------------------------------------------------- interpolate from grid to get electric field & force on my particles for ik ------------------------------------------------------------------------- */ void PPPMCG::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; // 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; for (int j = 0; j < num_charged; j++) { i = is_charged[j]; 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 electric field & force on my particles for ad ------------------------------------------------------------------------- */ void PPPMCG::fieldforce_ad() { int i,l,m,n,nx,ny,nz,mx,my,mz; FFT_SCALAR dx,dy,dz; FFT_SCALAR ekx,eky,ekz; double s1,s2,s3; double sf = 0.0; double *prd; 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; for (int j = 0; j < num_charged; j++) { i = is_charged[j]; 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); 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 = x[i][0]*hx_inv; s2 = x[i][1]*hy_inv; s3 = x[i][2]*hz_inv; sf = sf_coeff[0]*sin(2*MY_PI*s1); sf += sf_coeff[1]*sin(4*MY_PI*s1); sf *= 2*q[i]*q[i]; f[i][0] += 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*q[i]*q[i]; f[i][1] += 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*q[i]*q[i]; if (slabflag != 2) f[i][2] += qfactor*(ekz*q[i] - sf); } } /* ---------------------------------------------------------------------- interpolate from grid to get per-atom energy/virial ------------------------------------------------------------------------- */ void PPPMCG::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; for (int j = 0; j < num_charged; j++) { i = is_charged[j]; 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] += q[i]*v0; vatom[i][1] += q[i]*v1; vatom[i][2] += q[i]*v2; vatom[i][3] += q[i]*v3; vatom[i][4] += q[i]*v4; vatom[i][5] += q[i]*v5; } } } /* ---------------------------------------------------------------------- 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 PPPMCG::slabcorr() { int i,j; // compute local contribution to global dipole moment const double * const q = atom->q; const double * const * const x = atom->x; const double zprd_slab = domain->zprd*slab_volfactor; double dipole = 0.0; for (j = 0; j < num_charged; j++) { i = is_charged[j]; 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) > SMALLQ) { for (j = 0; j < num_charged; j++) { i = is_charged[j]; 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_slab*zprd_slab/12.0)/volume; const double qscale = qqrd2e * scale; if (eflag_global) energy += qscale * e_slabcorr; // per-atom energy if (eflag_atom) { const double efact = qscale * MY_2PI/volume; for (j = 0; j < num_charged; j++) { i = is_charged[j]; eatom[i] += efact * q[i]*(x[i][2]*dipole_all - 0.5*(dipole_r2 + qsum*x[i][2]*x[i][2]) - qsum*zprd_slab*zprd_slab/12.0); } } // add on force corrections const double ffact = qscale * (-MY_4PI/volume); double * const * const f = atom->f; for (j = 0; j < num_charged; j++) { i = is_charged[j]; f[i][2] += ffact * q[i]*(dipole_all - qsum*x[i][2]); } } /* ---------------------------------------------------------------------- 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 PPPMCG::make_rho_groups(int groupbit_A, int groupbit_B, int BA_flag) { int i,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 const double * const q = atom->q; const double * const * const x = atom->x; const int * const mask = atom->mask; for (int j = 0; j < num_charged; j++) { i = is_charged[j]; 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]; } } } } } } /* ---------------------------------------------------------------------- memory usage of local arrays ------------------------------------------------------------------------- */ double PPPMCG::memory_usage() { double bytes = PPPM::memory_usage(); bytes += (double)nmax * sizeof(int); return bytes; }