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msm_cg_omp.cpp
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Sat, Nov 9, 16:07

msm_cg_omp.cpp
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/* ----------------------------------------------------------------------
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 author: Axel Kohlmeyer (Temple U)
Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "gridcomm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "memory.h"
#include "msm_cg_omp.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define OFFSET 16384
#define SMALLQ 0.00001
enum{REVERSE_RHO,REVERSE_AD,REVERSE_AD_PERATOM};
enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
MSMCGOMP::MSMCGOMP(LAMMPS *lmp, int narg, char **arg) : MSMOMP(lmp, narg, arg)
{
if ((narg < 1) || (narg > 2))
error->all(FLERR,"Illegal kspace_style msm/cg/omp command");
triclinic_support = 0;
if (narg == 2) smallq = fabs(force->numeric(FLERR,arg[1]));
else smallq = SMALLQ;
num_charged = -1;
is_charged = NULL;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
MSMCGOMP::~MSMCGOMP()
{
memory->destroy(is_charged);
}
/* ----------------------------------------------------------------------
compute the MSM long-range force, energy, virial
------------------------------------------------------------------------- */
void MSMCGOMP::compute(int eflag, int vflag)
{
if (scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' "
"with kspace_style msm/cg/omp");
const double * const q = atom->q;
const int nlocal = atom->nlocal;
int i,j,n;
// set energy/virial flags
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = eflag_either = vflag_either = 0;
// invoke allocate_peratom() if needed for first time
if (vflag_atom && !peratom_allocate_flag) {
allocate_peratom();
cg_peratom_all->ghost_notify();
cg_peratom_all->setup();
for (int n=0; n<levels; n++) {
if (!active_flag[n]) continue;
cg_peratom[n]->ghost_notify();
cg_peratom[n]->setup();
}
peratom_allocate_flag = 1;
}
// 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,"msm:part2grid");
memory->create(is_charged,nmax,"msm/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 (i=0; i < nlocal; ++i)
if (fabs(q[i]) > smallq)
++num_charged;
// get fraction of charged particles per domain
if (nlocal > 0)
charged_frac = static_cast<double>(num_charged) * 100.0
/ static_cast<double>(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<double>(charged_all) * 100.0
/ static_cast<double>(atom->natoms);
if (me == 0) {
if (screen)
fprintf(screen,
" MSM/cg optimization cutoff: %g\n"
" Total charged atoms: %.1f%%\n"
" Min/max charged atoms/proc: %.1f%% %.1f%%\n",
smallq,charged_frac,charged_fmin,charged_fmax);
if (logfile)
fprintf(logfile,
" MSM/cg optimization cutoff: %g\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 (i = 0; i < nlocal; ++i) {
if (fabs(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 (aninterpolation)
particle_map();
make_rho();
// all procs reverse communicate charge density values from their ghost grid points
// to fully sum contribution in their 3d grid
current_level = 0;
cg_all->reverse_comm(this,REVERSE_RHO);
// forward communicate charge density values to fill ghost grid points
// compute direct sum interaction and then restrict to coarser grid
for (int n=0; n<=levels-2; n++) {
if (!active_flag[n]) continue;
current_level = n;
cg[n]->forward_comm(this,FORWARD_RHO);
direct(n);
restriction(n);
}
// compute direct interation for top grid level for nonperiodic
// and for second from top grid level for periodic
if (active_flag[levels-1]) {
if (domain->nonperiodic) {
current_level = levels-1;
cg[levels-1]->forward_comm(this,FORWARD_RHO);
direct_top(levels-1);
cg[levels-1]->reverse_comm(this,REVERSE_AD);
if (vflag_atom)
cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
} else {
// Here using MPI_Allreduce is cheaper than using commgrid
grid_swap_forward(levels-1,qgrid[levels-1]);
direct(levels-1);
grid_swap_reverse(levels-1,egrid[levels-1]);
current_level = levels-1;
if (vflag_atom)
cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
}
}
// prolongate energy/virial from coarser grid to finer grid
// reverse communicate from ghost grid points to get full sum
for (int n=levels-2; n>=0; n--) {
if (!active_flag[n]) continue;
prolongation(n);
current_level = n;
cg[n]->reverse_comm(this,REVERSE_AD);
// extra per-atom virial communication
if (vflag_atom)
cg_peratom[n]->reverse_comm(this,REVERSE_AD_PERATOM);
}
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks
current_level = 0;
cg_all->forward_comm(this,FORWARD_AD);
// extra per-atom energy/virial communication
if (vflag_atom)
cg_peratom_all->forward_comm(this,FORWARD_AD_PERATOM);
// calculate the force on my particles (interpolation)
fieldforce();
// calculate the per-atom energy/virial for my particles
if (evflag_atom) fieldforce_peratom();
// update qsum and qsqsum, if atom count has changed and energy needed
if ((eflag_global || eflag_atom) && atom->natoms != natoms_original) {
qsum_qsq();
natoms_original = atom->natoms;
}
// sum global energy across procs and add in self-energy term
const double qscale = force->qqrd2e * scale;
if (eflag_global) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
double e_self = qsqsum*gamma(0.0)/cutoff;
energy -= e_self;
energy *= 0.5*qscale;
}
// total long-range virial
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*virial_all[i];
}
// per-atom energy/virial
// energy includes self-energy correction
if (evflag_atom) {
const double qs = 0.5*qscale;
if (eflag_atom) {
const double sf = gamma(0.0)/cutoff;
for (j = 0; j < num_charged; j++) {
i = is_charged[j];
eatom[i] -= q[i]*q[i]*sf;
eatom[i] *= qs;
}
}
if (vflag_atom) {
for (n = 0; n < num_charged; n++) {
i = is_charged[n];
for (j = 0; j < 6; j++)
vatom[i][j] *= qs;
}
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
const int tid = 0;
#endif
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
/* ----------------------------------------------------------------------
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 MSMCGOMP::particle_map()
{
const double * const * const x = atom->x;
int flag = 0;
int i;
if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
// XXX: O(N). is it worth to add OpenMP here?
for (int j = 0; j < num_charged; j++) {
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
const int nx=static_cast<int>((x[i][0]-boxlo[0])*delxinv[0]+OFFSET)-OFFSET;
const int ny=static_cast<int>((x[i][1]-boxlo[1])*delyinv[0]+OFFSET)-OFFSET;
const int nz=static_cast<int>((x[i][2]-boxlo[2])*delzinv[0]+OFFSET)-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[0] || nx+nupper > nxhi_out[0] ||
ny+nlower < nylo_out[0] || ny+nupper > nyhi_out[0] ||
nz+nlower < nzlo_out[0] || nz+nupper > nzhi_out[0])
flag = 1;
}
if (flag) error->one(FLERR,"Out of range atoms - cannot compute MSM");
}
/* ----------------------------------------------------------------------
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 MSMCGOMP::make_rho()
{
const double * const q = atom->q;
const double * const * const x = atom->x;
// clear 3d density array
double * const * const * const qgridn = qgrid[0];
memset(&(qgridn[nzlo_out[0]][nylo_out[0]][nxlo_out[0]]),0,ngrid[0]*sizeof(double));
double dx,dy,dz,x0,y0,z0;
int i,j,l,m,n,nx,ny,nz,mx,my,mz;
// 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
for (j = 0; j < num_charged; j++) {
i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx - (x[i][0]-boxlo[0])*delxinv[0];
dy = ny - (x[i][1]-boxlo[1])*delyinv[0];
dz = nz - (x[i][2]-boxlo[2])*delzinv[0];
compute_phis(dx,dy,dz);
z0 = q[i];
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
y0 = z0*phi1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
x0 = y0*phi1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
qgridn[mz][my][mx] += x0*phi1d[0][l];
}
}
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get force on my particles
------------------------------------------------------------------------- */
void MSMCGOMP::fieldforce()
{
const double * const * const * const egridn = egrid[0];
const double * const * const x = atom->x;
double * const * const f = atom->f;
const double * const q = atom->q;
int i,j,l,m,n,nx,ny,nz,mx,my,mz;
double dx,dy,dz;
double phi_x,phi_y,phi_z;
double dphi_x,dphi_y,dphi_z;
double 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
for (j = 0; j < num_charged; j++) {
i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx - (x[i][0]-boxlo[0])*delxinv[0];
dy = ny - (x[i][1]-boxlo[1])*delyinv[0];
dz = nz - (x[i][2]-boxlo[2])*delzinv[0];
compute_phis_and_dphis(dx,dy,dz);
ekx = eky = ekz = 0.0;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
phi_z = phi1d[2][n];
dphi_z = dphi1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
phi_y = phi1d[1][m];
dphi_y = dphi1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
phi_x = phi1d[0][l];
dphi_x = dphi1d[0][l];
ekx += dphi_x*phi_y*phi_z*egridn[mz][my][mx];
eky += phi_x*dphi_y*phi_z*egridn[mz][my][mx];
ekz += phi_x*phi_y*dphi_z*egridn[mz][my][mx];
}
}
}
ekx *= delxinv[0];
eky *= delyinv[0];
ekz *= delzinv[0];
// convert E-field to force
const double qfactor = force->qqrd2e*scale*q[i];
f[i][0] += qfactor*ekx;
f[i][1] += qfactor*eky;
f[i][2] += qfactor*ekz;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get per-atom energy/virial
------------------------------------------------------------------------- */
void MSMCGOMP::fieldforce_peratom()
{
const double * const q = atom->q;
const double * const * const x = atom->x;
double ***egridn = egrid[0];
double ***v0gridn = v0grid[0];
double ***v1gridn = v1grid[0];
double ***v2gridn = v2grid[0];
double ***v3gridn = v3grid[0];
double ***v4gridn = v4grid[0];
double ***v5gridn = v5grid[0];
int i,j,l,m,n,nx,ny,nz,mx,my,mz;
double dx,dy,dz,x0,y0,z0;
double 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
for (j = 0; j < num_charged; j++) {
i = is_charged[j];
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx - (x[i][0]-boxlo[0])*delxinv[0];
dy = ny - (x[i][1]-boxlo[1])*delyinv[0];
dz = nz - (x[i][2]-boxlo[2])*delzinv[0];
compute_phis_and_dphis(dx,dy,dz);
u = v0 = v1 = v2 = v3 = v4 = v5 = 0.0;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
z0 = phi1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
y0 = z0*phi1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*phi1d[0][l];
if (eflag_atom) u += x0*egridn[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0gridn[mz][my][mx];
v1 += x0*v1gridn[mz][my][mx];
v2 += x0*v2gridn[mz][my][mx];
v3 += x0*v3gridn[mz][my][mx];
v4 += x0*v4gridn[mz][my][mx];
v5 += x0*v5gridn[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;
}
}
}
double MSMCGOMP::memory_usage()
{
double bytes = MSM::memory_usage();
bytes += nmax * sizeof(int);
return bytes;
}

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