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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11394 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-01-30 18:36:07 +00:00
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479
src/USER-CG-CMM/pair_cmm_common.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Common functionality for the CMM coarse grained MD potentials.
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
------------------------------------------------------------------------- */
#include "pair_cmm_common.h"
#include "memory.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "math.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 1.0e-6
/* ---------------------------------------------------------------------- */
PairCMMCommon::PairCMMCommon(class LAMMPS *lmp) : Pair(lmp)
{
ftable = NULL;
allocated_coul = 0;
kappa = 0.0;
respa_enable = 0;
single_enable = 0;
}
/* ---------------------------------------------------------------------- *
* clean up common arrays *
* ---------------------------------------------------------------------- */
PairCMMCommon::~PairCMMCommon() {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cg_type);
memory->destroy(cut);
memory->destroy(cutsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(offset);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
allocated = 0;
}
}
/* ---------------------------------------------------------------------- *
* allocate common arrays *
* ---------------------------------------------------------------------- */
void PairCMMCommon::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"paircg:setflag");
memory->create(cg_type,n+1,n+1,"paircg:cg_type");
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
setflag[i][j] = 0;
cg_type[i][j] = CG_NOT_SET;
}
}
memory->create(cut,n+1,n+1,"paircg:cut");
memory->create(cutsq,n+1,n+1,"paircg:cutsq");
memory->create(epsilon,n+1,n+1,"paircg:epsilon");
memory->create(sigma,n+1,n+1,"paircg:sigma");
memory->create(offset,n+1,n+1,"paircg:offset");
memory->create(lj1,n+1,n+1,"paircg:lj1");
memory->create(lj2,n+1,n+1,"paircg:lj2");
memory->create(lj3,n+1,n+1,"paircg:lj3");
memory->create(lj4,n+1,n+1,"paircg:lj4");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
// arguments to the pair_style command (global version)
// args = cutoff (cutoff2 (kappa))
void PairCMMCommon::settings(int narg, char **arg)
{
if ((narg < 1) || (narg > 3)) error->all(FLERR,"Illegal pair_style command");
cut_lj_global = force->numeric(FLERR,arg[0]);
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = force->numeric(FLERR,arg[1]);
cut_coulsq_global = cut_coul_global*cut_coul_global;
// exponential coulomb screening (optional)
if (narg == 3) kappa = force->numeric(FLERR,arg[2]);
if (fabs(kappa) < SMALL) kappa=0.0;
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i+1; j <= atom->ntypes; j++) {
if (setflag[i][j]) {
cut[i][j] = cut_lj_global;
if (allocated_coul) {
cut[i][j] = MAX(cut_lj_global,cut_coul_global);
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCMMCommon::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
int cg_type_one=find_cg_type(arg[2]);
if (cg_type_one == CG_NOT_SET) error->all(FLERR,"Error reading CG type flag.");
double epsilon_one = force->numeric(FLERR,arg[3]);
double sigma_one = force->numeric(FLERR,arg[4]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
if (narg >= 6) cut_lj_one = force->numeric(FLERR,arg[5]);
if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cg_type[i][j] = cg_type_one;
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
setflag[i][j] = 1;
if (allocated_coul) {
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
} else {
cut[i][j] = cut_lj_one;
}
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCMMCommon::init_style()
{
// request regular or rRESPA neighbor lists
int irequest;
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this);
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);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairCMMCommon::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 PairCMMCommon::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all(FLERR,"for CG styles, epsilon and sigma need to be set explicitly for all pairs.");
}
const int cgt = cg_type[i][j];
if (cgt == CG_NOT_SET)
error->all(FLERR,"unrecognized LJ parameter flag");
lj1[i][j] = cg_prefact[cgt] * cg_pow1[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
lj2[i][j] = cg_prefact[cgt] * cg_pow2[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow2[cgt]);
lj3[i][j] = cg_prefact[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow1[cgt]);
lj4[i][j] = cg_prefact[cgt] * epsilon[i][j] * pow(sigma[i][j],cg_pow2[cgt]);
double mycut = cut[i][j];
if (offset_flag) {
double ratio = sigma[i][j] / mycut;
offset[i][j] = cg_prefact[cgt] * epsilon[i][j] * (pow(ratio,cg_pow1[cgt]) - pow(ratio,cg_pow2[cgt]));
} else offset[i][j] = 0.0;
if (allocated_coul) {
mycut = MAX(cut_lj[i][j],cut_coul[i][j]);
cut[i][j] = mycut;
cut_ljsq[i][j]=cut_lj[i][j]*cut_lj[i][j];
cut_coulsq[i][j]=cut_coul[i][j]*cut_coul[i][j];
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = cg_prefact[cgt] * epsilon[i][j] * (pow(ratio,cg_pow1[cgt]) - pow(ratio,cg_pow2[cgt]));
} else offset[i][j] = 0.0;
}
// make sure data is stored symmetrically
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];
cg_type[j][i] = cg_type[i][j];
cut[j][i] = mycut;
if (allocated_coul) {
cut_lj[j][i]=cut_lj[i][j];
cut_ljsq[j][i]=cut_ljsq[i][j];
cut_coul[j][i]=cut_coul[i][j];
cut_coulsq[j][i]=cut_coulsq[i][j];
}
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
#if 1
error->all(FLERR,"tail correction not (yet) supported by CG potentials.");
#else
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
#endif
}
return mycut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCMMCommon::write_restart(FILE *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(&cg_type[i][j],sizeof(int),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
if (allocated_coul) {
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCMMCommon::read_restart(FILE *fp)
{
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(&cg_type[i][j],sizeof(int),1,fp);
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
if(allocated_coul) {
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
}
MPI_Bcast(&cg_type[i][j],1,MPI_INT,0,world);
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (allocated_coul) {
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCMMCommon::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&kappa,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCMMCommon::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&kappa,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&kappa,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(&tail_flag,1,MPI_INT,0,world);
cut_coulsq_global = cut_coul_global*cut_coul_global;
}
/* ---------------------------------------------------------------------- */
double PairCMMCommon::memory_usage()
{
double bytes=Pair::memory_usage();
int n = atom->ntypes;
// setflag/cg_type
bytes += (n+1)*(n+1)*sizeof(int)*2;
// cut/cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4
bytes += (n+1)*(n+1)*sizeof(double)*9;
return bytes;
}
/* ------------------------------------------------------------------------ */
double PairCMMCommon::eval_single(int coul_type, int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double lj_force, lj_erg, coul_force, coul_erg;
lj_force=lj_erg=coul_force=coul_erg=0.0;
if (rsq < cut_ljsq[itype][jtype]) {
const int cgt = cg_type[itype][jtype];
const double cgpow1 = cg_pow1[cgt];
const double cgpow2 = cg_pow2[cgt];
const double cgpref = cg_prefact[cgt];
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
lj_force = cgpref*eps * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2))/rsq;
lj_erg = cgpref*eps * (pow(ratio,cgpow1) - pow(ratio,cgpow2));
}
if (rsq < cut_coul[itype][jtype]) {
if(coul_type == CG_COUL_LONG) {
error->all(FLERR,"single energy computation with long-range coulomb not supported by CG potentials.");
} else if ((coul_type == CG_COUL_CUT) || (coul_type == CG_COUL_DEBYE)) {
const double r2inv = 1.0/rsq;
const double rinv = sqrt(r2inv);
const double qscreen=exp(-kappa*sqrt(rsq));
coul_force = force->qqrd2e * atom->q[i]*atom->q[j]*rinv * qscreen * (kappa + rinv);
coul_erg = force->qqrd2e * atom->q[i]*atom->q[j]*rinv * qscreen;
// error->all(FLERR,"single energy computation with coulomb not supported by CG potentials.");
} else if (coul_type == CG_COUL_NONE) {
; // do nothing
} else {
error->all(FLERR,"unknown coulomb type with CG potentials.");
}
}
fforce = factor_lj*lj_force + factor_coul*coul_force;
return factor_lj*lj_erg + factor_coul*coul_erg;
}

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src/USER-CG-CMM/pair_cmm_common.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Common functionality for the CMM coarse grained MD potentials.
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_CMM_COMMON_H
#define LMP_PAIR_CMM_COMMON_H
#include "pair.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "respa.h"
#include "update.h"
#include "cg_cmm_parms.h"
#include "math.h"
namespace LAMMPS_NS {
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define EWALD_A1 0.254829592
#define EWALD_A2 -0.284496736
#define EWALD_A3 1.421413741
#define EWALD_A4 -1.453152027
#define EWALD_A5 1.061405429
class PairCMMCommon : public Pair , public CGCMMParms {
public:
PairCMMCommon(class LAMMPS *);
virtual ~PairCMMCommon();
virtual void settings(int, char **);
virtual void coeff(int, char **);
virtual void init_style();
virtual void init_list(int, class NeighList *);
virtual double init_one(int, int);
virtual void write_restart(FILE *);
virtual void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
virtual double memory_usage();
protected:
// coarse grain flags
int **cg_type;
// lennard jones parameters
double cut_lj_global, **cut, **cut_lj, **cut_ljsq;
double **epsilon, **sigma;
double **lj1, **lj2, **lj3, **lj4, **offset;
// coulomb parameters
int allocated_coul; // 0/1 = whether coulomb arrays are allocated
double cut_coul_global, cut_coulsq_global, kappa, g_ewald;
double **cut_coul, **cut_coulsq;
// r-RESPA parameters
double *cut_respa;
// methods
virtual void allocate();
private:
// disable default constructor
PairCMMCommon();
protected:
// general optimizeable real space loops
template < const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int COUL_TYPE >
void eval_verlet();
template < const int NEWTON_PAIR, const int COUL_TYPE >
void eval_inner();
template < const int NEWTON_PAIR, const int COUL_TYPE >
void eval_middle();
template < const int EVFLAG, const int EFLAG, const int VFLAG,
const int NEWTON_PAIR, const int COUL_TYPE >
void eval_outer();
// this one is not performance critical... no template needed.
double eval_single(int, int, int, int, int,
double, double, double, double &);
};
/* ---------------------------------------------------------------------- */
/* this is the inner heart of the CG potentials. */
#define CG_LJ_INNER(eflag,fvar) \
fvar=factor_lj; \
if (eflag) evdwl=factor_lj; \
\
if (cgt == CG_LJ12_4) { \
const double r4inv=r2inv*r2inv; \
\
fvar *= r4inv*(lj1[itype][jtype]*r4inv*r4inv \
- lj2[itype][jtype]); \
\
if (eflag) { \
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} \
} else if (cgt == CG_LJ9_6) { \
const double r3inv = r2inv*sqrt(r2inv); \
const double r6inv = r3inv*r3inv; \
fvar *= r6inv*(lj1[itype][jtype]*r3inv \
- lj2[itype][jtype]); \
if (eflag) { \
evdwl *= r6inv*(lj3[itype][jtype]*r3inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} \
} else if (cgt == CG_LJ12_6) { \
const double r6inv = r2inv*r2inv*r2inv; \
fvar *= r6inv*(lj1[itype][jtype]*r6inv \
- lj2[itype][jtype]); \
if (eflag) { \
evdwl *= r6inv*(lj3[itype][jtype]*r6inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} \
} else { \
/* do nothing. this is a "cannot happen(TM)" case */ \
; \
}
#define CG_LJ_ENERGY(eflag) \
if (eflag) { \
evdwl=factor_lj; \
\
if (cgt == CG_LJ12_4) { \
const double r4inv=r2inv*r2inv; \
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} else if (cgt == CG_LJ9_6) { \
const double r3inv = r2inv*sqrt(r2inv); \
const double r6inv = r3inv*r3inv; \
evdwl *= r6inv*(lj3[itype][jtype]*r3inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} else if (cgt == CG_LJ12_6) { \
const double r6inv = r2inv*r2inv*r2inv; \
evdwl *= r6inv*(lj3[itype][jtype]*r6inv \
- lj4[itype][jtype]) - offset[itype][jtype]; \
} else { \
/* do nothing. this is a "cannot happen(TM)" case */ \
; \
} \
} \
template < const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_verlet()
{
double ** const x = atom->x;
double ** const f = atom->f;
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = list->inum;
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
int * const * const firstneigh = list->firstneigh;
// loop over neighbors of my atoms
int ii,jj;
for (ii = 0; ii < inum; ii++) {
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double qtmp = (COUL_TYPE != CG_COUL_NONE) ? q[i] : 0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
if (rsq < cutsq[itype][jtype]) {
if (COUL_TYPE == CG_COUL_NONE) {
CG_LJ_INNER(EFLAG,fpair);
fpair *= r2inv;
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(EFLAG,forcelj);
}
// coulomb with cutoff and screening
if ((COUL_TYPE == CG_COUL_CUT) || (COUL_TYPE == CG_COUL_DEBYE)) {
if (rsq < cut_coulsq[itype][jtype]) {
double r=sqrt(rsq);
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * qscreen / r;
}
}
if (COUL_TYPE == CG_COUL_LONG) {
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
const double erfc = t * (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (EFLAG) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (EFLAG) {
const double table2 = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table2;
}
if (factor_coul < 1.0) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
}
fpair = (forcecoul + forcelj) * r2inv;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
template < const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_inner()
{
double ** const x = atom->x;
double ** const f = atom->f;
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listinner->inum;
const int * const ilist = listinner->ilist;
const int * const numneigh = listinner->numneigh;
int * const * const firstneigh = listinner->firstneigh;
const double cut_out_on = cut_respa[0];
const double cut_out_off = cut_respa[1];
const double cut_out_diff = cut_out_off - cut_out_on;
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
int ii,jj;
for (ii = 0; ii < inum; ii++) {
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double qtmp = (COUL_TYPE != CG_COUL_NONE) ? q[i] : 0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
if (rsq < cut_out_off_sq) {
if (COUL_TYPE == CG_COUL_NONE) {
CG_LJ_INNER(0,fpair);
fpair *= r2inv;
if (rsq > cut_out_on_sq) {
const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
}
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(0,forcelj);
}
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0 -factor_coul)*forcecoul;
fpair = (forcecoul + forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
}
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
template < const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_middle()
{
double ** const x = atom->x;
double ** const f = atom->f;
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listmiddle->inum;
const int * const ilist = listmiddle->ilist;
const int * const numneigh = listmiddle->numneigh;
int * const * const firstneigh = listmiddle->firstneigh;
const double cut_in_off = cut_respa[0];
const double cut_in_on = cut_respa[1];
const double cut_out_on = cut_respa[2];
const double cut_out_off = cut_respa[3];
const double cut_in_diff = cut_in_on - cut_in_off;
const double cut_out_diff = cut_out_off - cut_out_on;
const double cut_in_off_sq = cut_in_off*cut_in_off;
const double cut_in_on_sq = cut_in_on*cut_in_on;
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
int ii,jj;
for (ii = 0; ii < inum; ii++) {
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double qtmp = (COUL_TYPE != CG_COUL_NONE) ? q[i] : 0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
if (COUL_TYPE == CG_COUL_NONE) {
CG_LJ_INNER(0,fpair);
fpair *= r2inv;
if (rsq < cut_in_on_sq) {
const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(0,forcelj);
}
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0 -factor_coul)*forcecoul;
fpair = (forcecoul + forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
const double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
template < const int EVFLAG, const int EFLAG, const int VFLAG,
const int NEWTON_PAIR, const int COUL_TYPE >
void PairCMMCommon::eval_outer()
{
double ** const x = atom->x;
double ** const f = atom->f;
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double factor_lj,factor_coul;
const int inum = listouter->inum;
const int * const ilist = listouter->ilist;
const int * const numneigh = listouter->numneigh;
int * const * const firstneigh = listouter->firstneigh;
const double cut_in_off = cut_respa[2];
const double cut_in_on = cut_respa[3];
const double cut_in_diff = cut_in_on - cut_in_off;
const double cut_in_off_sq = cut_in_off*cut_in_off;
const double cut_in_on_sq = cut_in_on*cut_in_on;
// loop over neighbors of my atoms
int ii,jj;
for (ii = 0; ii < inum; ii++) {
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double qtmp = (COUL_TYPE != CG_COUL_NONE) ? q[i] : 0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
int j2 = jlist[jj];
factor_lj = special_lj[sbmask(j2)];
factor_coul = special_coul[sbmask(j2)];
const int j = j2 & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
if (rsq < cutsq[itype][jtype]) {
if (COUL_TYPE == CG_COUL_NONE) {
double forcelj=0.0;
if (rsq > cut_in_off_sq) {
CG_LJ_INNER(0,forcelj);
fpair = forcelj*r2inv;
if (rsq < cut_in_on_sq) {
const double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
CG_LJ_ENERGY(EFLAG);
if (VFLAG) {
if (rsq <= cut_in_off_sq) {
CG_LJ_INNER(0,fpair);
fpair *= r2inv;
} else if (rsq < cut_in_on_sq) {
fpair = forcelj*r2inv;
}
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
} else {
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
CG_LJ_INNER(EFLAG,forcelj);
}
// coulomb with cutoff and screening
if ((COUL_TYPE == CG_COUL_CUT) || (COUL_TYPE == CG_COUL_DEBYE)) {
if (rsq < cut_coulsq[itype][jtype]) {
double r=sqrt(rsq);
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * qscreen / r;
}
}
if (COUL_TYPE == CG_COUL_LONG) {
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
const double erfc = t * (EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (EFLAG) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (EFLAG) {
const double table2 = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table2;
}
if (factor_coul < 1.0) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
}
fpair = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
}
/* ------------------------------------------------------------------------ */
}
#undef EWALD_F
#undef EWALD_P
#undef EWALD_A1
#undef EWALD_A2
#undef EWALD_A3
#undef EWALD_A4
#undef EWALD_A5
#endif