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pair_cmm_common.h
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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>
------------------------------------------------------------------------- */
#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;
// tables
double tabinnersq;
double *rtable,*drtable,*ftable,*dftable,*ctable,*dctable;
double *etable,*detable,*ptable,*dptable,*vtable,*dvtable;
int ncoulshiftbits,ncoulmask;
// 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

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