diff --git a/src/USER-EWALDN/pair_buck_coul.cpp b/src/USER-EWALDN/pair_buck_coul.cpp
index 123f02d54..3c96de104 100644
--- a/src/USER-EWALDN/pair_buck_coul.cpp
+++ b/src/USER-EWALDN/pair_buck_coul.cpp
@@ -1,1176 +1,1223 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
module: pair_buck_coul.cpp
author: Pieter J. in 't Veld for SNL
date: October 2, 2006.
purpose: definition of short and long range buckingham and coulombic
pair potentials.
usage: pair_style buck/coul
long|cut|off control r^-6 contribution
long|cut|off control r^-1 contribution
rcut6 set r^-6 cut off
[rcut1] set r^-1 cut off
remarks: rcut1 cannot be set when both contributions are set to long,
rcut1 = rcut6 when ommited.
* ---------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "math_vector.h"
#include "pair_buck_coul.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.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 MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#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
/* ---------------------------------------------------------------------- */
PairBuckCoul::PairBuckCoul(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ftable = NULL;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
#define PAIR_ILLEGAL "Illegal pair_style buck/coul command"
#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
#define PAIR_MISSING "Cut-offs missing in pair_style buck/coul"
#define PAIR_LJ_OFF "LJ6 off not supported in pair_style buck/coul"
#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style buck/coul"
#define PAIR_MANY "Too many pair_style buck/coul commands"
#define PAIR_LARGEST "Using largest cut-off for buck/coul long long"
#define PAIR_MIX "Geometric mixing assumed for 1/r^6 coefficients"
void PairBuckCoul::options(char **arg, int order)
{
char *option[] = {"long", "cut", "off", NULL};
int i;
if (!*arg) error->all(PAIR_ILLEGAL);
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(PAIR_ILLEGAL);
case 0: ewald_order |= 1<<order; break; // set kspace r^-order
case 2: ewald_off |= 1<<order; // turn r^-order off
case 1: break;
}
}
void PairBuckCoul::settings(int narg, char **arg)
{
ewald_order = 0;
ewald_off = 0;
options(arg, 6);
options(++arg, 1);
if (!comm->me && ewald_order&(1<<6)) error->warning(PAIR_MIX);
if (!comm->me && ewald_order==((1<<1)|(1<<6))) error->warning(PAIR_LARGEST);
if (!*(++arg)) error->all(PAIR_MISSING);
if (ewald_off&(1<<6)) error->all(PAIR_LJ_OFF);
if (!((ewald_order^ewald_off)&(1<<1))) error->all(PAIR_COUL_CUT);
cut_buck_global = atof(*(arg++));
if (*arg&&(ewald_order&0x42==0x42)) error->all(PAIR_CUTOFF);
cut_coul = *arg ? atof(*(arg++)) : cut_buck_global;
if (*arg) error->all(PAIR_MANY);
if (allocated) { // reset explicit cuts
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_buck[i][j] = cut_buck_global;
}
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairBuckCoul::~PairBuckCoul()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut_buck_read);
memory->destroy_2d_double_array(cut_buck);
memory->destroy_2d_double_array(cut_bucksq);
memory->destroy_2d_double_array(buck_a_read);
memory->destroy_2d_double_array(buck_a);
memory->destroy_2d_double_array(buck_c_read);
memory->destroy_2d_double_array(buck_c);
memory->destroy_2d_double_array(buck_rho_read);
memory->destroy_2d_double_array(buck_rho);
memory->destroy_2d_double_array(buck1);
memory->destroy_2d_double_array(buck2);
memory->destroy_2d_double_array(rhoinv);
memory->destroy_2d_double_array(offset);
}
if (ftable) free_tables();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBuckCoul::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cut_buck_read = memory->create_2d_double_array(n+1,n+1,"pair:cut_buck_read");
cut_buck = memory->create_2d_double_array(n+1,n+1,"pair:cut_buck");
cut_bucksq = memory->create_2d_double_array(n+1,n+1,"pair:cut_bucksq");
buck_a_read = memory->create_2d_double_array(n+1,n+1,"pair:buck_a_read");
buck_a = memory->create_2d_double_array(n+1,n+1,"pair:buck_a");
buck_c_read = memory->create_2d_double_array(n+1,n+1,"pair:buck_c_read");
buck_c = memory->create_2d_double_array(n+1,n+1,"pair:buck_c");
buck_rho_read = memory->create_2d_double_array(n+1,n+1,"pair:buck_rho_read");
buck_rho = memory->create_2d_double_array(n+1,n+1,"pair:buck_rho");
buck1 = memory->create_2d_double_array(n+1,n+1,"pair:buck1");
buck2 = memory->create_2d_double_array(n+1,n+1,"pair:buck2");
rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
extract protected data from object
------------------------------------------------------------------------- */
void *PairBuckCoul::extract_ptr(char *id)
{
char *ids[] = {
"B", "sigma", "epsilon", "ewald_order", "ewald_cut", "ewald_mix", NULL};
void *ptrs[] = {
buck_c, NULL, NULL, &ewald_order, &cut_coul, &mix_flag, NULL};
int i;
for (i=0; ids[i]&&strcmp(ids[i], id); ++i);
return ptrs[i];
}
/* ---------------------------------------------------------------------- */
void PairBuckCoul::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBuckCoul::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6) error->all("Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(*(arg++),atom->ntypes,ilo,ihi);
force->bounds(*(arg++),atom->ntypes,jlo,jhi);
double buck_a_one = atof(*(arg++));
double buck_rho_one = atof(*(arg++));
double buck_c_one = atof(*(arg++));
double cut_buck_one = cut_buck_global;
if (narg == 6) cut_buck_one = atof(*(arg++));
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
buck_a_read[i][j] = buck_a_one;
buck_c_read[i][j] = buck_c_one;
buck_rho_read[i][j] = buck_rho_one;
cut_buck_read[i][j] = cut_buck_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
-/* ----------------------------------------------------------------------
- init for one type pair i,j and corresponding j,i
-------------------------------------------------------------------------- */
-
-double PairBuckCoul::init_one(int i, int j)
-{
- if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
-
- cut_buck[i][j] = cut_buck_read[i][j];
- buck_a[i][j] = buck_a_read[i][j];
- buck_c[i][j] = buck_c_read[i][j];
- buck_rho[i][j] = buck_rho_read[i][j];
-
- double cut = MAX(cut_buck[i][j], cut_coul);
- cutsq[i][j] = cut*cut;
- cut_bucksq[i][j] = cut_buck[i][j] * cut_buck[i][j];
-
- buck1[i][j] = buck_a[i][j]/buck_rho[i][j];
- buck2[i][j] = 6.0*buck_c[i][j];
- rhoinv[i][j] = 1.0/buck_rho[i][j];
-
- if (offset_flag) {
- double rexp = exp(-cut_buck[i][j]/buck_rho[i][j]);
- offset[i][j] = buck_a[i][j]*rexp - buck_c[i][j]/pow(cut_buck[i][j],6.0);
- } else offset[i][j] = 0.0;
-
- cutsq[j][i] = cutsq[i][j];
- cut_bucksq[j][i] = cut_bucksq[i][j];
- buck_a[j][i] = buck_a[i][j];
- buck_c[j][i] = buck_c[i][j];
- rhoinv[j][i] = rhoinv[i][j];
- buck1[j][i] = buck1[i][j];
- buck2[j][i] = buck2[i][j];
- offset[j][i] = offset[i][j];
-
- return cut;
-}
-
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBuckCoul::init_style()
{
int i,j;
// require an atom style with charge defined
- //if (atom->charge_allow == 0)
- //error->all("Must use charged atom style with this pair style");
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(
"Invoking coulombic in pair style lj/coul requires atom attribute q");
+ // request regular or rRESPA neighbor lists
+
+ int irequest;
+
+ if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
+ 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);
+ else if (respa == 1) {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ } else {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 2;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respamiddle = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ }
+
+ } else irequest = neighbor->request(this);
+
cut_coulsq = cut_coul * cut_coul;
// set & error check interior rRESPA cutoffs
if (strcmp(update->integrate_style,"respa") == 0) {
if (((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (MIN(cut_buck[i][j],cut_coul) < cut_respa[3])
error->all("Pair cutoff < Respa interior cutoff");
}
} else cut_respa = NULL;
// ensure use of KSpace long-range solver, set g_ewald
if (ewald_order&(1<<1)) { // r^-1 kspace
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
else if (strcmp(force->kspace_style,"ewald") == 0)
g_ewald = force->kspace->g_ewald;
else if (strcmp(force->kspace_style,"ewald/n") == 0)
g_ewald = force->kspace->g_ewald;
else if (strcmp(force->kspace_style,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
}
if (ewald_order&(1<<6)) { // r^-6 kspace
if (!force->kspace && strcmp(force->kspace_style,"ewald/n"))
error->all("Pair style is incompatible with KSpace style");
else g_ewald = force->kspace->g_ewald;
}
// setup force tables
if (ncoultablebits) init_tables();
}
+/* ----------------------------------------------------------------------
+ neighbor callback to inform pair style of neighbor list to use
+ regular or rRESPA
+------------------------------------------------------------------------- */
+
+void PairBuckCoul::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 PairBuckCoul::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
+
+ cut_buck[i][j] = cut_buck_read[i][j];
+ buck_a[i][j] = buck_a_read[i][j];
+ buck_c[i][j] = buck_c_read[i][j];
+ buck_rho[i][j] = buck_rho_read[i][j];
+
+ double cut = MAX(cut_buck[i][j], cut_coul);
+ cutsq[i][j] = cut*cut;
+ cut_bucksq[i][j] = cut_buck[i][j] * cut_buck[i][j];
+
+ buck1[i][j] = buck_a[i][j]/buck_rho[i][j];
+ buck2[i][j] = 6.0*buck_c[i][j];
+ rhoinv[i][j] = 1.0/buck_rho[i][j];
+
+ if (offset_flag) {
+ double rexp = exp(-cut_buck[i][j]/buck_rho[i][j]);
+ offset[i][j] = buck_a[i][j]*rexp - buck_c[i][j]/pow(cut_buck[i][j],6.0);
+ } else offset[i][j] = 0.0;
+
+ cutsq[j][i] = cutsq[i][j];
+ cut_bucksq[j][i] = cut_bucksq[i][j];
+ buck_a[j][i] = buck_a[i][j];
+ buck_c[j][i] = buck_c[i][j];
+ rhoinv[j][i] = rhoinv[i][j];
+ buck1[j][i] = buck1[i][j];
+ buck2[j][i] = buck2[i][j];
+ offset[j][i] = offset[i][j];
+
+ return cut;
+}
+
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBuckCoul::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(&buck_a_read[i][j],sizeof(double),1,fp);
fwrite(&buck_c_read[i][j],sizeof(double),1,fp);
fwrite(&buck_rho_read[i][j],sizeof(double),1,fp);
fwrite(&cut_buck_read[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBuckCoul::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(&buck_a_read[i][j],sizeof(double),1,fp);
fread(&buck_c_read[i][j],sizeof(double),1,fp);
fread(&buck_rho_read[i][j],sizeof(double),1,fp);
fread(&cut_buck_read[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&buck_c_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_buck_read[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBuckCoul::write_restart_settings(FILE *fp)
{
fwrite(&cut_buck_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(&ewald_order,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBuckCoul::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_buck_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(&ewald_order,sizeof(int),1,fp);
}
MPI_Bcast(&cut_buck_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(&ewald_order,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
compute pair interactions
------------------------------------------------------------------------- */
void PairBuckCoul::compute(int eflag, int vflag)
{
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;
int nall = atom->nlocal + atom->nghost;
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, qri, *cutsqi, *cut_bucksqi,
*buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
double r, rsq, r2inv, force_coul, force_buck, fforce, factor;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
eng_vdwl = eng_coul = 0.0; // reset energy&virial
if (vflag) memset(virial, 0, sizeof(shape));
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]];
buck1i = buck1[typei]; buck2i = buck2[typei];
buckai = buck_a[typei]; buckci = buck_c[typei], rhoinvi = rhoinv[typei];
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
{ 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;
r = sqrt(rsq);
factor = newton_pair || j<nlocal ? 1.0 : 0.5;
if (order1 && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double 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) eng_coul += factor*t;
}
else { // special case
register double f = 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-f;
if (eflag) eng_coul += factor*(t-f);
}
} // table real space
else {
register float t = rsq;
register int k = (((int *) &t)[0] & 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) eng_coul += factor*qiqj*(etable[k]+f*detable[k]);
}
else { // special case
t = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) eng_coul += factor*qiqj*(etable[k]+f*detable[k]-t);
}
}
}
else force_coul = 0.0;
if (rsq < cut_bucksqi[typej]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
if (order6) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*buckci[typej];
if (ni < 0) {
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag) eng_vdwl +=
factor*(expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2);
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_buck = f*r*expr*buck1i[typej]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
if (eflag) eng_vdwl += factor*(
f*expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej]);
}
}
else { // cut
if (ni < 0) {
force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
if (eflag) eng_vdwl += factor*(
expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
}
else { // special case
register double f = special_lj[ni];
force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
if (eflag) eng_vdwl += f*factor*(
expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
}
}
}
else force_buck = 0.0;
fforce = (force_coul+force_buck)*r2inv; // force and virial
if (vflag==1) {
if (newton_pair || j < nlocal) {
register double f = d[0]*fforce, *fj = f0+(j+(j<<1));
fi[0] += f; fj[0] -= f;
virial[0] += f*d[0]; virial[3] += f*d[1];
fi[1] += f = d[1]*fforce; fj[1] -= f;
virial[1] += f*d[1]; virial[5] += f*d[2];
fi[2] += f = d[2]*fforce; fj[2] -= f;
virial[2] += f*d[2]; virial[4] += f*d[0];
}
else {
register double f = d[0]*fforce;
fi[0] += f; virial[0] += (f *= 0.5)*d[0]; virial[3] += f*d[1];
fi[1] += f = d[1]*fforce; virial[1] += 0.5*f*d[1];
fi[2] += f = d[2]*fforce; virial[2] += (f *= 0.5)*d[2];
virial[4] += f*d[0]; virial[5] += f*d[1];
}
}
else if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
if (vflag == 2) virial_compute();
}
/* ---------------------------------------------------------------------- */
void PairBuckCoul::compute_inner()
{
double r, rsq, r2inv, force_coul, force_buck, fforce;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
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_bucksqi, *buck1i, *buck2i, *rhoinvi, *offseti;
vector xi, d;
- ineighn = (ineigh = list->ilist)+list->inum;
+ ineighn = (ineigh = listinner->ilist)+listinner->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
offseti = offset[typei = type[i]];
cut_bucksqi = cut_bucksq[typei];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
- jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
+ jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
{ 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;
r = sqrt(r);
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
qri*q[j]/r : qri*q[j]/r*special_coul[ni];
if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
force_buck = ni<0 ?
(r*expr*buck1i[typej]-rn*buck2i[typej]) :
(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
else force_buck = 0.0;
fforce = (force_coul + force_buck) * r2inv;
if (rsq > cut_out_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 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]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairBuckCoul::compute_middle()
{
double r, rsq, r2inv, force_coul, force_buck, fforce;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
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_bucksqi, *buck1i, *buck2i, *rhoinvi, *offseti;
vector xi, d;
- ineighn = (ineigh = list->ilist)+list->inum;
+ ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
offseti = offset[typei = type[i]];
cut_bucksqi = cut_bucksq[typei];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
- jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
+ jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
{ 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;
r = sqrt(rsq);
if (order1 && (rsq < cut_coulsq)) // coulombic
force_coul = ni<0 ?
qri*q[j]/r : qri*q[j]/r*special_coul[ni];
if (rsq < cut_bucksqi[typej = type[j]]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
force_buck = ni<0 ?
(r*expr*buck1i[typej]-rn*buck2i[typej]) :
(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
}
else force_buck = 0.0;
fforce = (force_coul + force_buck) * r2inv;
if (rsq < cut_in_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fforce *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 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]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairBuckCoul::compute_outer(int eflag, int vflag)
{
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;
int nall = atom->nlocal + atom->nghost;
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, qri, *cutsqi, *cut_bucksqi,
*buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
double r, rsq, r2inv, force_coul, force_buck, fforce, factor;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
double respa_buck, respa_coul, frespa;
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;
eng_vdwl = eng_coul = 0.0; // reset energy&virial
if (vflag) memset(virial, 0, sizeof(shape));
- ineighn = (ineigh = list->ilist)+list->inum;
+ 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]];
buck1i = buck1[typei]; buck2i = buck2[typei];
buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
- jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
+ jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
{ 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;
r = sqrt(rsq);
factor = newton_pair || j<nlocal ? 1.0 : 0.5;
if ((respa_flag = (rsq>cut_in_off_sq)&&(rsq<cut_in_on_sq))) {
register double rsw = (r-cut_in_off)/cut_in_diff;
frespa = rsw*rsw*(3.0-2.0*rsw);
}
if (order1 && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double 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;
if (eflag) eng_coul += factor*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;
if (eflag) eng_coul += factor*(t-r);
}
} // table real space
else {
if (respa_flag) respa_coul = ni<0 ? // correct for respa
frespa*qri*q[j]/r :
frespa*qri*q[j]/r*special_coul[ni];
register float t = rsq;
register int k = (((int *) &t)[0] & 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) eng_coul += factor*qiqj*(etable[k]+f*detable[k]);
}
else { // correct for special
t = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) eng_coul += factor*qiqj*(etable[k]+f*detable[k]-t);
}
}
}
else force_coul = respa_coul = 0.0;
if (rsq < cut_bucksqi[typej]) { // buckingham
register double rn = r2inv*r2inv*r2inv,
expr = exp(-r*rhoinvi[typej]);
if (respa_flag) respa_buck = ni<0 ? // correct for respa
frespa*(r*expr*buck1i[typej]-rn*buck2i[typej]) :
frespa*(r*expr*buck1i[typej]-rn*buck2i[typej])*special_lj[ni];
if (order6) { // long-range form
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*buckci[typej];
if (ni < 0) {
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag) eng_vdwl +=
factor*(expr*buckai[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_buck = f*r*expr*buck1i[typej]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
if (eflag) eng_vdwl += factor*(
f*expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej]);
}
}
else { // cut form
if (ni < 0) {
force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
if (eflag) eng_vdwl += factor*(
expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
}
else { // correct for special
register double f = special_lj[ni];
force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
if (eflag) eng_vdwl += f*factor*(
expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
}
}
}
else force_buck = respa_buck = 0.0;
fforce = (force_coul+force_buck)*r2inv; // force and virial
frespa = fforce-(respa_coul+respa_buck)*r2inv;
if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*frespa; fj[0] -= f;
fi[1] += f = d[1]*frespa; fj[1] -= f;
fi[2] += f = d[2]*frespa; fj[2] -= f;
if (vflag==1) {
virial[0] += (f = d[0]*fforce)*d[0]; virial[3] += f*d[1];
virial[1] += (f = d[1]*fforce)*d[1]; virial[5] += f*d[2];
virial[2] += (f = d[2]*fforce)*d[2]; virial[4] += f*d[0];
}
}
else {
fi[0] += d[0]*frespa;
fi[1] += d[1]*frespa;
fi[2] += d[2]*frespa;
if (vflag==1) {
register double f;
virial[0] += (f = 0.5*d[0]*fforce)*d[0]; virial[3] += f*d[1];
virial[1] += (f = 0.5*d[1]*fforce)*d[1]; virial[5] += f*d[2];
virial[2] += (f = 0.5*d[2]*fforce)*d[2]; virial[4] += f*d[0];
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void PairBuckCoul::init_tables()
{
int masklo,maskhi;
double r,grij,expm2,derfc,rsw;
double qqrd2e = force->qqrd2e;
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
masklo,maskhi,ncoulmask,ncoulshiftbits);
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
rtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:rtable");
ftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ftable");
ctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ctable");
etable = (double *) memory->smalloc(ntable*sizeof(double),"pair:etable");
drtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:drtable");
dftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dftable");
dctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dctable");
detable = (double *) memory->smalloc(ntable*sizeof(double),"pair:detable");
if (cut_respa == NULL) {
vtable = ptable = dvtable = dptable = NULL;
} else {
vtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:vtable");
ptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ptable");
dvtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dvtable");
dptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dptable");
}
float rsq;
int *int_rsq = (int *) &rsq;
float minrsq;
int *int_minrsq = (int *) &minrsq;
int itablemin;
*int_minrsq = 0 << ncoulshiftbits;
*int_minrsq = *int_minrsq | maskhi;
for (int i = 0; i < ntable; i++) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | masklo;
if (rsq < tabinnersq) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
}
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
etable[i] = qqrd2e/r * derfc;
} else {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
ctable[i] = 0.0;
etable[i] = qqrd2e/r * derfc;
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
}
}
}
minrsq = MIN(minrsq,rsq);
}
tabinnersq = minrsq;
int ntablem1 = ntable - 1;
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
dctable[i] = ctable[i+1] - ctable[i];
detable[i] = etable[i+1] - etable[i];
}
if (cut_respa) {
for (int i = 0; i < ntablem1; i++) {
dvtable[i] = vtable[i+1] - vtable[i];
dptable[i] = ptable[i+1] - ptable[i];
}
}
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
detable[ntablem1] = etable[0] - etable[ntablem1];
if (cut_respa) {
dvtable[ntablem1] = vtable[0] - vtable[ntablem1];
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = *int_minrsq & ncoulmask;
itablemin >>= ncoulshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
*int_rsq = itablemax << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
if (rsq < cut_coulsq) {
rsq = cut_coulsq;
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
e_tmp = qqrd2e/r * derfc;
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
c_tmp = 0.0;
e_tmp = qqrd2e/r * derfc;
p_tmp = qqrd2e/r;
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
}
}
}
drtable[itablemax] = 1.0/(rsq - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
}
}
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void PairBuckCoul::free_tables()
{
memory->sfree(rtable);
memory->sfree(drtable);
memory->sfree(ftable);
memory->sfree(dftable);
memory->sfree(ctable);
memory->sfree(dctable);
memory->sfree(etable);
memory->sfree(detable);
memory->sfree(vtable);
memory->sfree(dvtable);
memory->sfree(ptable);
memory->sfree(dptable);
}
/* ---------------------------------------------------------------------- */
void PairBuckCoul::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_buck,
int eflag, One &one)
{
double f, r, r2inv, r6inv, force_coul, force_buck;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
r = sqrt(rsq);
r2inv = 1.0/rsq;
one.eng_coul = 0.0;
if ((ewald_order&2) && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double x = g_ewald*r;
register double s = force->qqrd2e*q[i]*q[j], t = 1.0/(1.0+EWALD_P*x);
f = 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-f;
if (eflag) one.eng_coul = t-f;
}
else { // table real space
register float t = rsq;
register int k = (((int *) &t)[0] & ncoulmask)>>ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = q[i]*q[j];
t = (1.0-factor_coul)*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) one.eng_coul = qiqj*(etable[k]+f*detable[k]-t);
}
}
else force_coul = 0.0;
one.eng_vdwl = 0.0;
if (rsq < cut_bucksq[itype][jtype]) { // buckingham
register double expr = factor_buck*exp(-sqrt(rsq)*rhoinv[itype][jtype]);
r6inv = r2inv*r2inv*r2inv;
if (ewald_order&64) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2, t = r6inv*(1.0-factor_buck);
x2 = a2*exp(-x2)*buck_c[itype][jtype];
force_buck = buck1[itype][jtype]*r*expr-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*buck2[itype][jtype];
if (eflag) one.eng_vdwl = buck_a[itype][jtype]*expr-
g6*((a2+1.0)*a2+0.5)*x2+t*buck_c[itype][jtype];
}
else { // cut
force_buck =
buck1[itype][jtype]*r*expr-factor_buck*buck_c[itype][jtype]*r6inv;
if (eflag) one.eng_vdwl = buck_a[itype][jtype]*expr-
factor_buck*(buck_c[itype][jtype]*r6inv-offset[itype][jtype]);
}
}
else force_buck = 0.0;
one.fforce = (force_coul+force_buck)*r2inv;
}
diff --git a/src/USER-EWALDN/pair_buck_coul.h b/src/USER-EWALDN/pair_buck_coul.h
index 0b6fc7920..3be521219 100644
--- a/src/USER-EWALDN/pair_buck_coul.h
+++ b/src/USER-EWALDN/pair_buck_coul.h
@@ -1,69 +1,70 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
#ifndef PAIR_BUCK_COUL_H
#define PAIR_BUCK_COUL_H
#include "pair.h"
namespace LAMMPS_NS {
class PairBuckCoul : public Pair {
public:
double cut_coul;
PairBuckCoul(class LAMMPS *);
~PairBuckCoul();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
+ void init_style();
+ void init_list(int, class NeighList *);
double init_one(int, int);
- virtual void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
- virtual void write_restart_settings(FILE *);
- virtual void read_restart_settings(FILE *);
- virtual void single(int, int, int, int, double, double, double, int, One &);
- virtual void *extract_ptr(char *);
- virtual void extract_long(double *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void single(int, int, int, int, double, double, double, int, One &);
+ void *extract_ptr(char *);
+ void extract_long(double *);
void compute_inner();
void compute_middle();
void compute_outer(int, int);
protected:
double cut_buck_global;
double **cut_buck, **cut_buck_read, **cut_bucksq;
double cut_coulsq;
double **buck_a_read, **buck_a, **buck_c_read, **buck_c;
double **buck1, **buck2, **buck_rho_read, **buck_rho, **rhoinv, **offset;
double *cut_respa;
double g_ewald;
int ewald_order, ewald_off;
double tabinnersq;
double *rtable, *drtable, *ftable, *dftable, *ctable, *dctable;
double *etable, *detable, *ptable, *dptable, *vtable, *dvtable;
int ncoulshiftbits, ncoulmask;
void options(char **arg, int order);
void allocate();
void init_tables();
void free_tables();
};
}
#endif
diff --git a/src/USER-EWALDN/pair_lj_coul.cpp b/src/USER-EWALDN/pair_lj_coul.cpp
index 1ce093e57..077a25c91 100644
--- a/src/USER-EWALDN/pair_lj_coul.cpp
+++ b/src/USER-EWALDN/pair_lj_coul.cpp
@@ -1,1159 +1,1206 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
module: pair_lj_coul.cpp
author: Pieter J. in 't Veld for SNL
date: September 21, 2006.
purpose: definition of short and long range lj and coulombic pair
potentials.
usage: pair_style lj/coul
long|cut|off control r^-6 contribution
long|cut|off control r^-1 contribution
rcut6 set r^-6 cut off
[rcut1] set r^-1 cut off
remarks: - rcut1 cannot be set when both contributions are set to long,
rcut1 = rcut6 when ommited
- coulombics from Macromolecules 1989, 93, 7320
* ---------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "math_vector.h"
#include "pair_lj_coul.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.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 MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#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
/* ---------------------------------------------------------------------- */
PairLJCoul::PairLJCoul(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ftable = NULL;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
#define PAIR_ILLEGAL "Illegal pair_style lj/coul command"
#define PAIR_CUTOFF "Only one cut-off allowed when requesting all long"
#define PAIR_MISSING "Cut-offs missing in pair_style lj/coul"
#define PAIR_COUL_CUT "Coulombic cut not supported in pair_style lj/coul"
#define PAIR_MANY "Too many pair_style lj/coul commands"
#define PAIR_LARGEST "Using largest cut-off for lj/coul long long"
#define PAIR_MIX "Mixing forced for lj coefficients"
void PairLJCoul::options(char **arg, int order)
{
char *option[] = {"long", "cut", "off", NULL};
int i;
if (!*arg) error->all(PAIR_ILLEGAL);
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(PAIR_ILLEGAL);
case 0: ewald_order |= 1<<order; break; // set kspace r^-order
case 2: ewald_off |= 1<<order; // turn r^-order off
case 1: break;
}
}
void PairLJCoul::settings(int narg, char **arg)
{
ewald_off = 0;
ewald_order = 0;
options(arg, 6);
options(++arg, 1);
if (!comm->me && ewald_order&(1<<6)) error->warning(PAIR_MIX);
if (!comm->me && ewald_order==((1<<1)|(1<<6))) error->warning(PAIR_LARGEST);
if (!*(++arg)) error->all(PAIR_MISSING);
if (!((ewald_order^ewald_off)&(1<<1))) error->all(PAIR_COUL_CUT);
cut_lj_global = atof(*(arg++));
if (*arg&&(ewald_order&0x42==0x42)) error->all(PAIR_CUTOFF);
cut_coul = *arg ? atof(*(arg++)) : cut_lj_global;
if (*arg) error->all(PAIR_MANY);
if (allocated) { // reset explicit cuts
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
------------------------------------------------------------------------- */
PairLJCoul::~PairLJCoul()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut_lj_read);
memory->destroy_2d_double_array(cut_lj);
memory->destroy_2d_double_array(cut_ljsq);
memory->destroy_2d_double_array(epsilon_read);
memory->destroy_2d_double_array(epsilon);
memory->destroy_2d_double_array(sigma_read);
memory->destroy_2d_double_array(sigma);
memory->destroy_2d_double_array(lj1);
memory->destroy_2d_double_array(lj2);
memory->destroy_2d_double_array(lj3);
memory->destroy_2d_double_array(lj4);
memory->destroy_2d_double_array(offset);
}
if (ftable) free_tables();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCoul::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cut_lj_read = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj_read");
cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj");
cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq");
epsilon_read = memory->create_2d_double_array(n+1,n+1,"pair:epsilon_read");
epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");
sigma_read = memory->create_2d_double_array(n+1,n+1,"pair:sigma_read");
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
extract protected data from object
------------------------------------------------------------------------- */
void *PairLJCoul::extract_ptr(char *id)
{
char *ids[] = {
"B", "sigma", "epsilon", "ewald_order", "ewald_cut", "ewald_mix", NULL};
void *ptrs[] = {
lj4, sigma, epsilon, &ewald_order, &cut_coul, &mix_flag, NULL};
int i;
for (i=0; ids[i]&&strcmp(ids[i], id); ++i);
return ptrs[i];
}
/* ---------------------------------------------------------------------- */
void PairLJCoul::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCoul::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) error->all("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 = atof(arg[2]);
double sigma_one = atof(arg[3]);
double cut_lj_one = cut_lj_global;
if (narg == 5) cut_lj_one = atof(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("Incorrect args for pair coefficients");
}
-/* ----------------------------------------------------------------------
- init for one type pair i,j and corresponding j,i
-------------------------------------------------------------------------- */
-
-double PairLJCoul::init_one(int i, int j)
-{
- if ((ewald_order&(1<<6))||(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);
- 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);
-
- 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;
-}
-
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCoul::init_style()
{
char *style1[] = {"ewald", "ewald/n", "pppm", NULL};
char *style6[] = {"ewald/n", NULL};
int i,j;
// require an atom style with charge defined
- //if (atom->charge_allow == 0)
- //error->all("Must use charged atom style with this pair style");
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(
"Invoking coulombic in pair style lj/coul requires atom attribute q");
+ // request regular or rRESPA neighbor lists
+
+ int irequest;
+
+ if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
+ 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);
+ else if (respa == 1) {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ } else {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 2;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respamiddle = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ }
+
+ } else irequest = neighbor->request(this);
+
cut_coulsq = cut_coul * cut_coul;
// set & error check interior rRESPA cutoffs
if (strcmp(update->integrate_style,"respa") == 0) {
if (((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
error->all("Pair cutoff < Respa interior cutoff");
}
} else cut_respa = NULL;
// ensure use of KSpace long-range solver, set g_ewald
if (ewald_order&(1<<1)) { // r^-1 kspace
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
for (i=0; style1[i]&&strcmp(force->kspace_style, style1[i]); ++i);
if (!style1[i]) error->all("Pair style is incompatible with KSpace style");
}
if (ewald_order&(1<<6)) { // r^-6 kspace
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
for (i=0; style6[i]&&strcmp(force->kspace_style, style6[i]); ++i);
if (!style6[i]) error->all("Pair style is incompatible with KSpace style");
}
if (force->kspace) g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables();
}
+/* ----------------------------------------------------------------------
+ neighbor callback to inform pair style of neighbor list to use
+ regular or rRESPA
+------------------------------------------------------------------------- */
+
+void PairLJCoul::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 PairLJCoul::init_one(int i, int j)
+{
+ if ((ewald_order&(1<<6))||(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);
+ 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);
+
+ 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 PairLJCoul::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 PairLJCoul::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 PairLJCoul::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(&ewald_order,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCoul::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(&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(&ewald_order,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
compute pair interactions
------------------------------------------------------------------------- */
void PairLJCoul::compute(int eflag, int vflag)
{
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;
int nall = atom->nlocal + atom->nghost;
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, qri, *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double rsq, r2inv, force_coul, force_lj, fforce, factor;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
eng_vdwl = eng_coul = 0.0; // reset energy&virial
if (vflag) memset(virial, 0, sizeof(shape));
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
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
{ 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;
factor = newton_pair || j<nlocal ? 1.0 : 0.5;
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) eng_coul += factor*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) eng_coul += factor*(t-r);
}
} // table real space
else {
register float t = rsq;
register int k = (((int *) &t)[0] & 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) eng_coul += factor*qiqj*(etable[k]+f*detable[k]);
}
else { // special case
t = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) eng_coul += factor*qiqj*(etable[k]+f*detable[k]-t);
}
}
}
else force_coul = 0.0;
if (rsq < cut_ljsqi[typej]) { // lj
if (order6) { // long-range lj
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) eng_vdwl +=
factor*(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) eng_vdwl += factor*(
f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+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) eng_vdwl += factor*(
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) eng_vdwl += f*factor*(
rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
}
}
}
else force_lj = 0.0;
fforce = (force_coul+force_lj)*r2inv; // force and virial
if (vflag==1) {
if (newton_pair || j < nlocal) {
register double f = d[0]*fforce, *fj = f0+(j+(j<<1));
fi[0] += f; fj[0] -= f;
virial[0] += f*d[0]; virial[3] += f*d[1];
fi[1] += f = d[1]*fforce; fj[1] -= f;
virial[1] += f*d[1]; virial[5] += f*d[2];
fi[2] += f = d[2]*fforce; fj[2] -= f;
virial[2] += f*d[2]; virial[4] += f*d[0];
}
else {
register double f = d[0]*fforce;
fi[0] += f; virial[0] += (f *= 0.5)*d[0]; virial[3] += f*d[1];
fi[1] += f = d[1]*fforce; virial[1] += 0.5*f*d[1];
fi[2] += f = d[2]*fforce; virial[2] += (f *= 0.5)*d[2];
virial[4] += f*d[0]; virial[5] += f*d[1];
}
}
else if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
if (vflag == 2) virial_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCoul::compute_inner()
{
double rsq, r2inv, force_coul, force_lj, fforce;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
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, *offseti;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
offseti = offset[typei = type[i]];
cut_ljsqi = cut_ljsq[typei];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
{ 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
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;
fforce = (force_coul + force_lj) * r2inv;
if (rsq > cut_out_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 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]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCoul::compute_middle()
{
double rsq, r2inv, force_coul, force_lj, fforce;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
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, *offseti;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
offseti = offset[typei = type[i]];
cut_ljsqi = cut_ljsq[typei];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) {
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; }
{ 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;
fforce = (force_coul + force_lj) * r2inv;
if (rsq < cut_in_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fforce *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 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]*fforce; fj[0] -= f;
fi[1] += f = d[1]*fforce; fj[1] -= f;
fi[2] += f = d[2]*fforce; fj[2] -= f;
}
else {
fi[0] += d[0]*fforce;
fi[1] += d[1]*fforce;
fi[2] += d[2]*fforce;
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCoul::compute_outer(int eflag, int vflag)
{
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;
int nall = atom->nlocal + atom->nghost;
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, qri, *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double rsq, r2inv, force_coul, force_lj, fforce, factor;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
double respa_lj, respa_coul, frespa;
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;
eng_vdwl = eng_coul = 0.0; // reset energy&virial
if (vflag) memset(virial, 0, sizeof(shape));
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
if ((j = *jneigh) < nall) ni = -1;
else { ni = j/nall; j %= nall; } // special index
{ 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;
factor = newton_pair || j<nlocal ? 1.0 : 0.5;
if ((respa_flag = (rsq>cut_in_off_sq)&&(rsq<cut_in_on_sq))) {
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 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;
if (eflag) eng_coul += factor*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;
if (eflag) eng_coul += factor*(t-r);
}
} // table real space
else {
if (respa_flag) respa_coul = ni<0 ? // correct for respa
frespa*qri*q[j]/sqrt(rsq) :
frespa*qri*q[j]/sqrt(rsq)*special_coul[ni];
register float t = rsq;
register int k = (((int *) &t)[0] & 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) eng_coul += factor*qiqj*(etable[k]+f*detable[k]);
}
else { // correct for special
t = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) eng_coul += factor*qiqj*(etable[k]+f*detable[k]-t);
}
}
}
else force_coul = respa_coul = 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
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) eng_vdwl +=
factor*(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];
if (eflag) eng_vdwl += factor*(
f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej]);
}
}
else { // cut form
if (ni < 0) {
force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
if (eflag) eng_vdwl += factor*(
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]);
if (eflag) eng_vdwl += f*factor*(
rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
}
}
}
else force_lj = respa_lj = 0.0;
fforce = (force_coul+force_lj)*r2inv; // force and virial
frespa = fforce-(respa_coul+respa_lj)*r2inv;
if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*frespa; fj[0] -= f;
fi[1] += f = d[1]*frespa; fj[1] -= f;
fi[2] += f = d[2]*frespa; fj[2] -= f;
if (vflag==1) {
virial[0] += (f = d[0]*fforce)*d[0]; virial[3] += f*d[1];
virial[1] += (f = d[1]*fforce)*d[1]; virial[5] += f*d[2];
virial[2] += (f = d[2]*fforce)*d[2]; virial[4] += f*d[0];
}
}
else {
fi[0] += d[0]*frespa;
fi[1] += d[1]*frespa;
fi[2] += d[2]*frespa;
if (vflag==1) {
register double f;
virial[0] += (f = 0.5*d[0]*fforce)*d[0]; virial[3] += f*d[1];
virial[1] += (f = 0.5*d[1]*fforce)*d[1]; virial[5] += f*d[2];
virial[2] += (f = 0.5*d[2]*fforce)*d[2]; virial[4] += f*d[0];
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void PairLJCoul::init_tables()
{
int masklo,maskhi;
double r,grij,expm2,derfc,rsw;
double qqrd2e = force->qqrd2e;
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
masklo,maskhi,ncoulmask,ncoulshiftbits);
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
rtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:rtable");
ftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ftable");
ctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ctable");
etable = (double *) memory->smalloc(ntable*sizeof(double),"pair:etable");
drtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:drtable");
dftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dftable");
dctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dctable");
detable = (double *) memory->smalloc(ntable*sizeof(double),"pair:detable");
if (cut_respa == NULL) {
vtable = ptable = dvtable = dptable = NULL;
} else {
vtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:vtable");
ptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ptable");
dvtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dvtable");
dptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dptable");
}
float rsq;
int *int_rsq = (int *) &rsq;
float minrsq;
int *int_minrsq = (int *) &minrsq;
int itablemin;
*int_minrsq = 0 << ncoulshiftbits;
*int_minrsq = *int_minrsq | maskhi;
for (int i = 0; i < ntable; i++) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | masklo;
if (rsq < tabinnersq) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
}
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
etable[i] = qqrd2e/r * derfc;
} else {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
ctable[i] = 0.0;
etable[i] = qqrd2e/r * derfc;
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
}
}
}
minrsq = MIN(minrsq,rsq);
}
tabinnersq = minrsq;
int ntablem1 = ntable - 1;
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
dctable[i] = ctable[i+1] - ctable[i];
detable[i] = etable[i+1] - etable[i];
}
if (cut_respa) {
for (int i = 0; i < ntablem1; i++) {
dvtable[i] = vtable[i+1] - vtable[i];
dptable[i] = ptable[i+1] - ptable[i];
}
}
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
detable[ntablem1] = etable[0] - etable[ntablem1];
if (cut_respa) {
dvtable[ntablem1] = vtable[0] - vtable[ntablem1];
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = *int_minrsq & ncoulmask;
itablemin >>= ncoulshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
*int_rsq = itablemax << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
if (rsq < cut_coulsq) {
rsq = cut_coulsq;
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
e_tmp = qqrd2e/r * derfc;
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
c_tmp = 0.0;
e_tmp = qqrd2e/r * derfc;
p_tmp = qqrd2e/r;
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
}
}
}
drtable[itablemax] = 1.0/(rsq - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
}
}
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void PairLJCoul::free_tables()
{
memory->sfree(rtable);
memory->sfree(drtable);
memory->sfree(ftable);
memory->sfree(dftable);
memory->sfree(ctable);
memory->sfree(dctable);
memory->sfree(etable);
memory->sfree(detable);
memory->sfree(vtable);
memory->sfree(dvtable);
memory->sfree(ptable);
memory->sfree(dptable);
}
/* ---------------------------------------------------------------------- */
void PairLJCoul::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
{
double r2inv, r6inv, force_coul, force_lj;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
r2inv = 1.0/rsq;
one.eng_coul = 0.0;
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;
if (eflag) one.eng_coul = t-r;
}
else { // table real space
register float t = rsq;
register int k = (((int *) &t)[0] & ncoulmask)>>ncoulshiftbits;
register double f = (rsq-rtable[k])*drtable[k], qiqj = q[i]*q[j];
t = (1.0-factor_coul)*(ctable[k]+f*dctable[k]);
force_coul = qiqj*(ftable[k]+f*dftable[k]-t);
if (eflag) one.eng_coul = qiqj*(etable[k]+f*detable[k]-t);
}
}
else force_coul = 0.0;
one.eng_vdwl = 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];
if (eflag) one.eng_vdwl = 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]);
if (eflag) one.eng_vdwl = factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
lj4[itype][jtype])-offset[itype][jtype]);
}
}
else force_lj = 0.0;
one.fforce = (force_coul+force_lj)*r2inv;
}
diff --git a/src/USER-EWALDN/pair_lj_coul.h b/src/USER-EWALDN/pair_lj_coul.h
index 01b43623e..694ea8aa5 100644
--- a/src/USER-EWALDN/pair_lj_coul.h
+++ b/src/USER-EWALDN/pair_lj_coul.h
@@ -1,68 +1,69 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
#ifndef PAIR_LJ_COUL_H
#define PAIR_LJ_COUL_H
#include "pair.h"
namespace LAMMPS_NS {
class PairLJCoul : public Pair {
public:
double cut_coul;
PairLJCoul(class LAMMPS *);
virtual ~PairLJCoul();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
+ void init_style();
+ void init_list(int, class NeighList *);
double init_one(int, int);
- virtual void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
- virtual void write_restart_settings(FILE *);
- virtual void read_restart_settings(FILE *);
- virtual void single(int, int, int, int, double, double, double, int, One &);
- virtual void *extract_ptr(char *);
- virtual void extract_long(double *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void single(int, int, int, int, double, double, double, int, One &);
+ void *extract_ptr(char *);
+ void extract_long(double *);
void compute_inner();
void compute_middle();
void compute_outer(int, int);
protected:
double cut_lj_global;
double **cut_lj, **cut_lj_read, **cut_ljsq;
double cut_coulsq;
double **epsilon_read, **epsilon, **sigma_read, **sigma;
double **lj1, **lj2, **lj3, **lj4, **offset;
double *cut_respa;
double g_ewald;
int ewald_order, ewald_off;
double tabinnersq;
double *rtable, *drtable, *ftable, *dftable, *ctable, *dctable;
double *etable, *detable, *ptable, *dptable, *vtable, *dvtable;
int ncoulshiftbits, ncoulmask;
void options(char **arg, int order);
void allocate();
void init_tables();
void free_tables();
};
}
#endif