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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@931 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-10-03 16:15:35 +00:00
parent 201466f4f1
commit bc528eda85
11 changed files with 1018 additions and 182 deletions
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4
src/KSPACE/Install.csh
View File

@ -8,6 +8,7 @@ if ($1 == 1) then
cp pppm.cpp ..
cp pppm_tip4p.cpp ..
cp pair_buck_coul_long.cpp ..
cp pair_coul_long.cpp ..
cp pair_lj_cut_coul_long.cpp ..
cp pair_lj_cut_coul_long_tip4p.cpp ..
cp pair_lj_charmm_coul_long.cpp ..
@ -20,6 +21,7 @@ if ($1 == 1) then
cp pppm.h ..
cp pppm_tip4p.h ..
cp pair_buck_coul_long.h ..
cp pair_coul_long.h ..
cp pair_lj_cut_coul_long.h ..
cp pair_lj_cut_coul_long_tip4p.h ..
cp pair_lj_charmm_coul_long.h ..
@ -37,6 +39,7 @@ else if ($1 == 0) then
rm ../pppm.cpp
rm ../pppm_tip4p.cpp
rm ../pair_buck_coul_long.cpp
rm ../pair_coul_long.cpp
rm ../pair_lj_cut_coul_long.cpp
rm ../pair_lj_cut_coul_long_tip4p.cpp
rm ../pair_lj_charmm_coul_long.cpp
@ -49,6 +52,7 @@ else if ($1 == 0) then
rm ../pppm.h
rm ../pppm_tip4p.h
rm ../pair_buck_coul_long.h
rm ../pair_coul_long.h
rm ../pair_lj_cut_coul_long.h
rm ../pair_lj_cut_coul_long_tip4p.h
rm ../pair_lj_charmm_coul_long.h

30
src/KSPACE/pair_buck_coul_long.cpp
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@ -20,9 +20,9 @@
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -66,20 +66,18 @@ PairBuckCoulLong::~PairBuckCoulLong()
void PairBuckCoulLong::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype;
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcebuck,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,phibuck,r,rexp;
int *neighs;
double **f;
int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -89,19 +87,25 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -314,6 +318,8 @@ void PairBuckCoulLong::init_style()
else if (strcmp(force->kspace_style,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------

2
src/KSPACE/pair_buck_coul_long.h
View File

@ -25,8 +25,8 @@ class PairBuckCoulLong : public Pair {
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);

578
src/KSPACE/pair_coul_long.cpp Normal file
View File

@ -0,0 +1,578 @@
/* ----------------------------------------------------------------------
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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_coul_long.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.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
/* ---------------------------------------------------------------------- */
PairCoulLong::PairCoulLong(LAMMPS *lmp) : Pair(lmp)
{
ftable = NULL;
}
/* ---------------------------------------------------------------------- */
PairCoulLong::~PairCoulLong()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
}
if (ftable) free_tables();
}
/* ---------------------------------------------------------------------- */
void PairCoulLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,forcecoul,fforce,factor_coul;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul;
int *ilist,*jlist,*numneigh,**firstneigh;
float rsq;
int *int_rsq = (int *) &rsq;
eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrtf(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
itable = *int_rsq & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
fforce = forcecoul * r2inv;
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
if (eflag) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
if (newton_pair || j < nlocal) eng_coul += phicoul;
else eng_coul += 0.5*phicoul;
}
if (vflag == 1) {
if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
virial[0] += delx*delx*fforce;
virial[1] += dely*dely*fforce;
virial[2] += delz*delz*fforce;
virial[3] += delx*dely*fforce;
virial[4] += delx*delz*fforce;
virial[5] += dely*delz*fforce;
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairCoulLong::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");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulLong::settings(int narg, char **arg)
{
if (narg != 1) error->all("Illegal pair_style command");
cut_coul = atof(arg[0]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulLong::coeff(int narg, char **arg)
{
if (narg != 2) 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);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulLong::init_style()
{
int i,j;
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/long requires atom attribute q");
int 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 (cut_coul < cut_respa[3])
error->all("Pair cutoff < Respa interior cutoff");
}
} else cut_respa = NULL;
// insure use of KSpace long-range solver, set g_ewald
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,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
// setup force tables
if (ncoultablebits) init_tables();
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulLong::init_one(int i, int j)
{
return cut_coul;
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void PairCoulLong::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 = sqrtf(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 = sqrtf(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];
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulLong::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulLong::write_restart_settings(FILE *fp)
{
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
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);
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void PairCoulLong::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 PairCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,phicoul;
int itable;
r2inv = 1.0/rsq;
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
float rsq_single = rsq;
int *int_rsq = (int *) &rsq_single;
itable = *int_rsq & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_single - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
one.fforce = forcecoul * r2inv;
if (eflag) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
one.eng_vdwl = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairCoulLong::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}

55
src/KSPACE/pair_coul_long.h Normal file
View File

@ -0,0 +1,55 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef PAIR_COUL_LONG_H
#define PAIR_COUL_LONG_H
#include "pair.h"
namespace LAMMPS_NS {
class PairCoulLong : public Pair {
public:
PairCoulLong(class LAMMPS *);
~PairCoulLong();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
void extract_long(double *);
private:
double cut_coul,cut_coulsq;
double *cut_respa;
double g_ewald;
double tabinnersq;
double *rtable,*drtable,*ftable,*dftable,*ctable,*dctable;
double *etable,*detable,*ptable,*dptable,*vtable,*dvtable;
int ncoulshiftbits,ncoulmask;
void allocate();
void init_tables();
void free_tables();
};
}
#endif

222
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -27,8 +27,10 @@
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -80,22 +82,20 @@ PairLJCharmmCoulLong::~PairLJCharmmCoulLong()
void PairLJCharmmCoulLong::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj,switch1,switch2;
int *neighs;
double **f;
int *ilist,*jlist,*numneigh,**firstneigh;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -105,19 +105,25 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -226,14 +232,14 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
void PairLJCharmmCoulLong::compute_inner()
{
int i,j,k,numneigh,itype,jtype;
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -243,6 +249,11 @@ void PairLJCharmmCoulLong::compute_inner()
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
@ -252,17 +263,18 @@ void PairLJCharmmCoulLong::compute_inner()
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_inner[i];
numneigh = neighbor->numneigh_inner[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -309,15 +321,15 @@ void PairLJCharmmCoulLong::compute_inner()
void PairLJCharmmCoulLong::compute_middle()
{
int i,j,k,numneigh,itype,jtype;
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double philj,switch1,switch2;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -327,6 +339,11 @@ void PairLJCharmmCoulLong::compute_middle()
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listmiddle->inum;
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
@ -341,18 +358,19 @@ void PairLJCharmmCoulLong::compute_middle()
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_middle[i];
numneigh = neighbor->numneigh_middle[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -410,21 +428,21 @@ void PairLJCharmmCoulLong::compute_middle()
void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj,switch1,switch2;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -434,6 +452,11 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listouter->inum;
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
@ -443,18 +466,18 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -703,44 +726,6 @@ void PairLJCharmmCoulLong::coeff(int narg, char **arg)
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCharmmCoulLong::init_one(int i, int j)
{
// always mix arithmetically
if (setflag[i][j] == 0) {
epsilon[i][j] = sqrt(epsilon[i][i]*epsilon[j][j]);
sigma[i][j] = 0.5 * (sigma[i][i] + sigma[j][j]);
eps14[i][j] = sqrt(eps14[i][i]*eps14[j][j]);
sigma14[i][j] = 0.5 * (sigma14[i][i] + sigma14[j][j]);
}
double cut = MAX(cut_lj,cut_coul);
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);
lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
lj14_1[j][i] = lj14_1[i][j];
lj14_2[j][i] = lj14_2[i][j];
lj14_3[j][i] = lj14_3[i][j];
lj14_4[j][i] = lj14_4[i][j];
return cut;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
@ -750,6 +735,42 @@ void PairLJCharmmCoulLong::init_style()
if (!atom->q_flag)
error->all("Pair style lj/charmm/coul/long 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);
// require cut_lj_inner < cut_lj
if (cut_lj_inner >= cut_lj)
@ -793,6 +814,57 @@ void PairLJCharmmCoulLong::init_style()
if (ncoultablebits) init_tables();
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::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 PairLJCharmmCoulLong::init_one(int i, int j)
{
// always mix arithmetically
if (setflag[i][j] == 0) {
epsilon[i][j] = sqrt(epsilon[i][i]*epsilon[j][j]);
sigma[i][j] = 0.5 * (sigma[i][i] + sigma[j][j]);
eps14[i][j] = sqrt(eps14[i][i]*eps14[j][j]);
sigma14[i][j] = 0.5 * (sigma14[i][i] + sigma14[j][j]);
}
double cut = MAX(cut_lj,cut_coul);
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);
lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
lj14_1[j][i] = lj14_1[i][j];
lj14_2[j][i] = lj14_2[i][j];
lj14_3[j][i] = lj14_3[i][j];
lj14_4[j][i] = lj14_4[i][j];
return cut;
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */

3
src/KSPACE/pair_lj_charmm_coul_long.h
View File

@ -25,8 +25,9 @@ class PairLJCharmmCoulLong : public Pair {
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);

224
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -27,8 +27,10 @@
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -77,22 +79,20 @@ PairLJCutCoulLong::~PairLJCutCoulLong()
void PairLJCutCoulLong::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj;
int *neighs;
double **f;
int *ilist,*jlist,*numneigh,**firstneigh;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -102,19 +102,25 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -211,14 +217,14 @@ void PairLJCutCoulLong::compute(int eflag, int vflag)
void PairLJCutCoulLong::compute_inner()
{
int i,j,k,numneigh,itype,jtype;
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -228,6 +234,11 @@ void PairLJCutCoulLong::compute_inner()
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
@ -237,17 +248,18 @@ void PairLJCutCoulLong::compute_inner()
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_inner[i];
numneigh = neighbor->numneigh_inner[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -295,14 +307,14 @@ void PairLJCutCoulLong::compute_inner()
void PairLJCutCoulLong::compute_middle()
{
int i,j,k,numneigh,itype,jtype;
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -312,6 +324,11 @@ void PairLJCutCoulLong::compute_middle()
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listmiddle->inum;
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
@ -326,17 +343,18 @@ void PairLJCutCoulLong::compute_middle()
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_middle[i];
numneigh = neighbor->numneigh_middle[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -388,21 +406,21 @@ void PairLJCutCoulLong::compute_middle()
void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj;
double rsw;
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
double **f = atom->f;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@ -412,6 +430,11 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = listouter->inum;
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
@ -421,18 +444,18 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -650,6 +673,95 @@ void PairLJCutCoulLong::coeff(int narg, char **arg)
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLong::init_style()
{
int i,j;
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/long 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;
// insure use of KSpace long-range solver, set g_ewald
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,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
// setup force tables
if (ncoultablebits) init_tables();
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJCutCoulLong::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
------------------------------------------------------------------------- */
@ -713,46 +825,6 @@ double PairLJCutCoulLong::init_one(int i, int j)
return cut;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLong::init_style()
{
int i,j;
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/long requires atom attribute q");
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;
// insure use of KSpace long-range solver, set g_ewald
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,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
// setup force tables
if (ncoultablebits) init_tables();
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */

3
src/KSPACE/pair_lj_cut_coul_long.h
View File

@ -25,8 +25,9 @@ class PairLJCutCoulLong : public Pair {
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
virtual void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);

75
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
View File

@ -29,8 +29,10 @@
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -58,7 +60,7 @@ PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3;
double r,r2inv,r6inv,forcecoul,forcelj,cforce,negforce;
@ -69,7 +71,7 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
double xiM[3],xjM[3];
double *x1,*x2;
double fO[3],fH[3];
int *neighs;
int *ilist,*jlist,*numneigh,**firstneigh;
double **f;
float rsq;
int *int_rsq = (int *) &rsq;
@ -78,7 +80,8 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
if (vflag) for (i = 0; i < 6; i++) virial[i] = tvirial[i] = 0.0;
if (vflag == 2) {
f = update->f_pair;
//f = update->f_pair;
f = atom->f;
tf = atom->f;
}
else f = atom->f;
@ -91,9 +94,15 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
@ -103,11 +112,11 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
find_M(i,iH1,iH2,xiM);
x1 = xiM;
} else x1 = x[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@ -281,12 +290,12 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
tf[j][1] -= dely * cforce;
tf[j][2] -= delz * cforce;
tvirial[0] += 0.5 * (delx * delx * cforce);
tvirial[1] += 0.5 * (dely * dely * cforce);
tvirial[2] += 0.5 * (delz * delz * cforce);
tvirial[3] += 0.5 * (dely * delx * cforce);
tvirial[4] += 0.5 * (delz * delx * cforce);
tvirial[5] += 0.5 * (delz * dely * cforce);
tvirial[0] += 0.5 * delx * delx * cforce;
tvirial[1] += 0.5 * dely * dely * cforce;
tvirial[2] += 0.5 * delz * delz * cforce;
tvirial[3] += 0.5 * dely * delx * cforce;
tvirial[4] += 0.5 * delz * delx * cforce;
tvirial[5] += 0.5 * delz * dely * cforce;
}
} else {
@ -413,6 +422,42 @@ void PairLJCutCoulLongTIP4P::init_style()
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/long/tip4p 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

2
src/KSPACE/style_kspace.h
View File

@ -25,6 +25,7 @@ KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#ifdef PairInclude
#include "pair_buck_coul_long.h"
#include "pair_coul_long.h"
#include "pair_lj_cut_coul_long.h"
#include "pair_lj_cut_coul_long_tip4p.h"
#include "pair_lj_charmm_coul_long.h"
@ -32,6 +33,7 @@ KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#ifdef PairClass
PairStyle(buck/coul/long,PairBuckCoulLong)
PairStyle(coul/long,PairCoulLong)
PairStyle(lj/cut/coul/long,PairLJCutCoulLong)
PairStyle(lj/cut/coul/long/tip4p,PairLJCutCoulLongTIP4P)
PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong)