Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/KSPACE/pair_lj_long_coul_long.cpp
354e20f43157efficient_neuronet

Last Change
Raw File

pair_lj_long_coul_long.cpp
View Options

/* ----------------------------------------------------------------------
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: Pieter J. in 't Veld (SNL)
Tabulation for long-range dispersion added by Wayne Mitchell (Loyola
University New Orleans)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "math_vector.h"
#include "pair_lj_long_coul_long.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJLongCoulLong::PairLJLongCoulLong(LAMMPS *lmp) : Pair(lmp)
{
dispersionflag = ewaldflag = pppmflag = 1;
respa_enable = 1;
writedata = 1;
ftable = NULL;
fdisptable = NULL;
qdist = 0.0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJLongCoulLong::options(char **arg, int order)
{
const char *option[] = {"long", "cut", "off", NULL};
int i;
if (!*arg) error->all(FLERR,"Illegal pair_style lj/long/coul/long command");
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(FLERR,"Illegal pair_style lj/long/coul/long command");
case 0: ewald_order |= 1<<order; break;
case 2: ewald_off |= 1<<order;
case 1: break;
}
}
void PairLJLongCoulLong::settings(int narg, char **arg)
{
if (narg != 3 && narg != 4) error->all(FLERR,"Illegal pair_style command");
ewald_off = 0;
ewald_order = 0;
options(arg, 6);
options(++arg, 1);
if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
error->warning(FLERR,"Using largest cutoff for lj/long/coul/long");
if (!*(++arg))
error->all(FLERR,"Cutoffs missing in pair_style lj/long/coul/long");
if (!((ewald_order^ewald_off) & (1<<1)))
error->all(FLERR,
"Coulomb cut not supported in pair_style lj/long/coul/long");
cut_lj_global = force->numeric(FLERR,*(arg++));
if (narg == 4 && ((ewald_order & 0x42) == 0x42))
error->all(FLERR,"Only one cutoff allowed when requesting all long");
if (narg == 4) cut_coul = force->numeric(FLERR,*arg);
else cut_coul = cut_lj_global;
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJLongCoulLong::~PairLJLongCoulLong()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_lj_read);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
memory->destroy(epsilon_read);
memory->destroy(epsilon);
memory->destroy(sigma_read);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
}
if (ftable) free_tables();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJLongCoulLong::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut_lj_read,n+1,n+1,"pair:cut_lj_read");
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memory->create(epsilon_read,n+1,n+1,"pair:epsilon_read");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma_read,n+1,n+1,"pair:sigma_read");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
extract protected data from object
------------------------------------------------------------------------- */
void *PairLJLongCoulLong::extract(const char *id, int &dim)
{
const char *ids[] = {
"B", "sigma", "epsilon", "ewald_order", "ewald_cut", "ewald_mix",
"cut_coul", "cut_LJ", NULL};
void *ptrs[] = {
lj4, sigma, epsilon, &ewald_order, &cut_coul, &mix_flag,
&cut_coul, &cut_lj_global, NULL};
int i;
for (i=0; ids[i]&&strcmp(ids[i], id); ++i);
if (i <= 2) dim = 2;
else dim = 0;
return ptrs[i];
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJLongCoulLong::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_lj_one = cut_lj_global;
if (narg == 5) cut_lj_one = force->numeric(FLERR,arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon_read[i][j] = epsilon_one;
sigma_read[i][j] = sigma_one;
cut_lj_read[i][j] = cut_lj_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJLongCoulLong::init_style()
{
// require an atom style with charge defined
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(FLERR,
"Invoking coulombic in pair style lj/coul requires atom attribute q");
// request regular or rRESPA neighbor lists if neighrequest_flag != 0
if (force->kspace->neighrequest_flag) {
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else irequest = neighbor->request(this,instance_me);
}
cut_coulsq = cut_coul * cut_coul;
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;
// ensure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
if (force->kspace) g_ewald = force->kspace->g_ewald;
if (force->kspace) g_ewald_6 = force->kspace->g_ewald_6;
// setup force tables
if (ncoultablebits) init_tables(cut_coul,cut_respa);
if (ndisptablebits) init_tables_disp(cut_lj_global);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJLongCoulLong::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
else if (id == 1) listinner = ptr;
else if (id == 2) listmiddle = ptr;
else if (id == 3) listouter = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJLongCoulLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon_read[i][i],epsilon_read[j][j],
sigma_read[i][i],sigma_read[j][j]);
sigma[i][j] = mix_distance(sigma_read[i][i],sigma_read[j][j]);
if (ewald_order&(1<<6))
cut_lj[i][j] = cut_lj_global;
else
cut_lj[i][j] = mix_distance(cut_lj_read[i][i],cut_lj_read[j][j]);
}
else {
sigma[i][j] = sigma_read[i][j];
epsilon[i][j] = epsilon_read[i][j];
cut_lj[i][j] = cut_lj_read[i][j];
}
double cut = MAX(cut_lj[i][j], cut_coul + 2.0*qdist);
cutsq[i][j] = cut*cut;
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
// check interior rRESPA cutoff
if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
cutsq[j][i] = cutsq[i][j];
cut_ljsq[j][i] = cut_ljsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJLongCoulLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon_read[i][j],sizeof(double),1,fp);
fwrite(&sigma_read[i][j],sizeof(double),1,fp);
fwrite(&cut_lj_read[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJLongCoulLong::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon_read[i][j],sizeof(double),1,fp);
fread(&sigma_read[i][j],sizeof(double),1,fp);
fread(&cut_lj_read[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj_read[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJLongCoulLong::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&ncoultablebits,sizeof(int),1,fp);
fwrite(&tabinner,sizeof(double),1,fp);
fwrite(&ewald_order,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJLongCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
fread(&ewald_order,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&ewald_order,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJLongCoulLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon_read[i][i],sigma_read[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJLongCoulLong::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g\n",i,j,
epsilon_read[i][j],sigma_read[i][j],cut_lj_read[i][j]);
}
/* ----------------------------------------------------------------------
compute pair interactions
------------------------------------------------------------------------- */
void PairLJLongCoulLong::compute(int eflag, int vflag)
{
double evdwl,ecoul,fpair;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni;
double qi = 0.0, qri = 0.0;
double *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double rsq, r2inv, force_coul, force_lj;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
if (order1 && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
if (eflag) ecoul = t;
}
else { // special case
r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
if (eflag) ecoul = t-r;
}
} // table real space
else {
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
else { // special case
t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
}
}
}
else force_coul = ecoul = 0.0;
if (rsq < cut_ljsqi[typej]) { // lj
if (order6) { // long-range lj
if(!ndisptablebits || rsq <= tabinnerdispsq) { // series real space
register double rn = r2inv*r2inv*r2inv;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[typej];
if (ni == 0) {
force_lj =
(rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag)
evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
if (eflag)
evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
}
}
else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
register double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k];
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) {
force_lj = (rn*=rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej];
if (eflag) evdwl = rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej];
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]+t*lj2i[typej];
if (eflag) evdwl = f*rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej]+t*lj4i[typej];
}
}
}
else { // cut lj
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) {
force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
}
else { // special case
register double f = special_lj[ni];
force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
if (eflag)
evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
}
}
}
else force_lj = evdwl = 0.0;
fpair = (force_coul+force_lj)*r2inv;
if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
fi[1] += f = d[1]*fpair; fj[1] -= f;
fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
fi[0] += d[0]*fpair;
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJLongCoulLong::compute_inner()
{
double rsq, r2inv, force_coul = 0.0, force_lj, fpair;
int *type = atom->type;
int nlocal = atom->nlocal;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni;
int i, j, order1 = (ewald_order|(ewald_off^-1))&(1<<1);
double qri, *cut_ljsqi, *lj1i, *lj2i;
vector xi, d;
ineighn = (ineigh = listinner->ilist)+listinner->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_ljsqi = cut_ljsq[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
r2inv = 1.0/rsq;
if (order1 && (rsq < cut_coulsq)) { // coulombic
qri = qqrd2e*q[i];
force_coul = ni == 0 ?
qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
}
if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
force_lj = ni == 0 ?
rn*(rn*lj1i[typej]-lj2i[typej]) :
rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
else force_lj = 0.0;
fpair = (force_coul + force_lj) * r2inv;
if (rsq > cut_out_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
if (newton_pair || j < nlocal) { // force update
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
fi[1] += f = d[1]*fpair; fj[1] -= f;
fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
fi[0] += d[0]*fpair;
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJLongCoulLong::compute_middle()
{
double rsq, r2inv, force_coul = 0.0, force_lj, fpair;
int *type = atom->type;
int nlocal = atom->nlocal;
double *x0 = atom->x[0], *f0 = atom->f[0], *fi = f0, *q = atom->q;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni;
int i, j, order1 = (ewald_order|(ewald_off^-1))&(1<<1);
double qri, *cut_ljsqi, *lj1i, *lj2i;
vector xi, d;
ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (order1) qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_ljsqi = cut_ljsq[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) {
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cut_out_off_sq) continue;
if (rsq <= cut_in_off_sq) continue;
r2inv = 1.0/rsq;
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni == 0 ?
qri*q[j]*sqrt(r2inv) : qri*q[j]*sqrt(r2inv)*special_coul[ni];
if (rsq < cut_ljsqi[typej = type[j]]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
force_lj = ni == 0 ?
rn*(rn*lj1i[typej]-lj2i[typej]) :
rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
}
else force_lj = 0.0;
fpair = (force_coul + force_lj) * r2inv;
if (rsq < cut_in_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
if (newton_pair || j < nlocal) { // force update
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
fi[1] += f = d[1]*fpair; fj[1] -= f;
fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
fi[0] += d[0]*fpair;
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
{
double evdwl,ecoul,fvirial,fpair;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni, respa_flag;
double qi = 0.0, qri = 0.0;
double *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double rsq, r2inv, force_coul, force_lj;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double respa_lj = 0.0, respa_coul = 0.0, frespa = 0.0;
vector xi, d;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
ineighn = (ineigh = listouter->ilist)+listouter->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
frespa = 1.0; // check whether and how to compute respa corrections
respa_coul = 0;
respa_lj = 0;
respa_flag = rsq < cut_in_on_sq ? 1 : 0;
if (respa_flag && (rsq > cut_in_off_sq)) {
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 1-rsw*rsw*(3.0-2.0*rsw);
}
if (order1 && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), s = qri*q[j];
if (respa_flag) // correct for respa
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
if (ni == 0) {
s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-respa_coul;
if (eflag) ecoul = t;
}
else { // correct for special
r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r-respa_coul;
if (eflag) ecoul = t-r;
}
} // table real space
else {
if (respa_flag) {
register double r = sqrt(rsq), s = qri*q[j];
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
}
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
if (ni == 0) {
force_coul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
else { // correct for special
t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
if (eflag) {
t.f = (1.0-special_coul[ni])*(ptable[k]+f*dptable[k]);
ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
}
}
}
}
else force_coul = respa_coul = ecoul = 0.0;
if (rsq < cut_ljsqi[typej]) { // lennard-jones
register double rn = r2inv*r2inv*r2inv;
if (respa_flag) respa_lj = ni == 0 ? // correct for respa
frespa*rn*(rn*lj1i[typej]-lj2i[typej]) :
frespa*rn*(rn*lj1i[typej]-lj2i[typej])*special_lj[ni];
if (order6) { // long-range form
if (!ndisptablebits || rsq <= tabinnerdispsq) {
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[typej];
if (ni == 0) {
force_lj =
(rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq-respa_lj;
if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
}
else { // correct for special
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej]-respa_lj;
if (eflag)
evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
}
}
else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
register double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k];
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) {
force_lj = (rn*=rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]-respa_lj;
if (eflag) evdwl = rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej];
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]+t*lj2i[typej]-respa_lj;
if (eflag) evdwl = f*rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej]+t*lj4i[typej];
}
}
}
else { // cut form
if (ni == 0) {
force_lj = rn*(rn*lj1i[typej]-lj2i[typej])-respa_lj;
if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
}
else { // correct for special
register double f = special_lj[ni];
force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej])-respa_lj;
if (eflag)
evdwl = f*(rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
}
}
}
else force_lj = respa_lj = evdwl = 0.0;
fpair = (force_coul+force_lj)*r2inv;
if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
fi[1] += f = d[1]*fpair; fj[1] -= f;
fi[2] += f = d[2]*fpair; fj[2] -= f;
}
else {
fi[0] += d[0]*fpair;
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
if (evflag) {
fvirial = (force_coul + force_lj + respa_coul + respa_lj)*r2inv;
ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fvirial,d[0],d[1],d[2]);
}
}
}
}
/* ---------------------------------------------------------------------- */
double PairLJLongCoulLong::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv, r6inv, force_coul, force_lj;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
double eng = 0.0;
r2inv = 1.0/rsq;
if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
r = s*(1.0-factor_coul)/r; s *= g_ewald*exp(-x*x);
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
eng += t-r;
}
else { // table real space
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = q[i]*q[j];
t.f = (1.0-factor_coul)*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
eng += qiqj*(etable[k]+f*detable[k]-t.f);
}
} else force_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
r6inv = r2inv*r2inv*r2inv;
if (ewald_order&64) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2, t = r6inv*(1.0-factor_lj);
x2 = a2*exp(-x2)*lj4[itype][jtype];
force_lj = factor_lj*(r6inv *= r6inv)*lj1[itype][jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
eng += factor_lj*r6inv*lj3[itype][jtype]-
g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
}
else { // cut
force_lj = factor_lj*r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
eng += factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
lj4[itype][jtype])-offset[itype][jtype]);
}
} else force_lj = 0.0;
fforce = (force_coul+force_lj)*r2inv;
return eng;
}
c4science · Help