forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9402 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
0beb95626f
commit
31dea6d086
|
|
@ -18,6 +18,11 @@ if (test $1 = 1) then
|
|||
cp pair_cg_cmm_coul_long.h ..
|
||||
fi
|
||||
|
||||
if (test -e ../msm.cpp) then
|
||||
cp pair_lj_sdk_coul_msm.cpp ..
|
||||
cp pair_lj_sdk_coul_msm.h ..
|
||||
fi
|
||||
|
||||
cp cg_cmm_parms.h ..
|
||||
cp cg_cmm_parms.cpp ..
|
||||
|
||||
|
|
@ -59,4 +64,6 @@ elif (test $1 = 0) then
|
|||
rm -f ../pair_lj_sdk.h
|
||||
rm -f ../pair_lj_sdk_coul_long.cpp
|
||||
rm -f ../pair_lj_sdk_coul_long.h
|
||||
rm -f ../pair_lj_sdk_coul_msm.cpp
|
||||
rm -f ../pair_lj_sdk_coul_msm.h
|
||||
fi
|
||||
|
|
|
|||
|
|
@ -27,6 +27,12 @@ for file in *.cpp *.h; do
|
|||
if (test $file = pair_lj_sdk_coul_long.h -a ! -e ../pair_lj_cut_coul_long.h) then
|
||||
continue
|
||||
fi
|
||||
if (test $file = pair_lj_sdk_coul_msm.cpp -a ! -e ../pair_lj_cut_coul_msm.cpp) then
|
||||
continue
|
||||
fi
|
||||
if (test $file = pair_lj_sdk_coul_msm.h -a ! -e ../pair_lj_cut_coul_msm.h) then
|
||||
continue
|
||||
fi
|
||||
|
||||
if (test ! -e ../$file) then
|
||||
echo " creating src/$file"
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@ class PairLJSDKCoulLong : public Pair {
|
|||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
virtual void *extract(const char *, int &);
|
||||
virtual double memory_usage();
|
||||
|
||||
protected:
|
||||
|
|
|
|||
|
|
@ -0,0 +1,307 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Axel Kohlmeyer (Temple U)
|
||||
This style is a simplified re-implementation of the CG/CMM pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_lj_sdk_coul_msm.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "kspace.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "lj_sdk_common.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using namespace LJSDKParms;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJSDKCoulMSM::PairLJSDKCoulMSM(LAMMPS *lmp) : PairLJSDKCoulLong(lmp)
|
||||
{
|
||||
ewaldflag = pppmflag = 0;
|
||||
msmflag = 1;
|
||||
respa_enable = 0;
|
||||
ftable = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSDKCoulMSM::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) {
|
||||
ev_setup(eflag,vflag);
|
||||
} else evflag = vflag_fdotr = 0;
|
||||
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (force->newton_pair) eval_msm<1,1,1>();
|
||||
else eval_msm<1,1,0>();
|
||||
} else {
|
||||
if (force->newton_pair) eval_msm<1,0,1>();
|
||||
else eval_msm<1,0,0>();
|
||||
}
|
||||
} else {
|
||||
if (force->newton_pair) eval_msm<0,0,1>();
|
||||
else eval_msm<0,0,0>();
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJSDKCoulMSM::eval_msm()
|
||||
{
|
||||
int i,ii,j,jj,jtype,itable;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction,table;
|
||||
double r,rsq,r2inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double egamma,fgamma,prefactor;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * 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_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
const int inum = list->inum;
|
||||
const int * const ilist = list->ilist;
|
||||
const int * const numneigh = list->numneigh;
|
||||
const int * const * const 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];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
const int itype = type[i];
|
||||
const int * const jlist = firstneigh[i];
|
||||
const int jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
forcecoul = forcelj = evdwl = ecoul = 0.0;
|
||||
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
const int ljt = lj_type[itype][jtype];
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
|
||||
forcecoul = prefactor * fgamma;
|
||||
if (EFLAG) {
|
||||
egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
|
||||
ecoul = prefactor*egamma;
|
||||
}
|
||||
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;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (EFLAG) ecoul = qtmp*q[j] *
|
||||
(etable[itable] + fraction*detable[itable]);
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
|
||||
if (ljt == LJ12_4) {
|
||||
const double r4inv=r2inv*r2inv;
|
||||
forcelj = 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 (ljt == LJ9_6) {
|
||||
const double r3inv = r2inv*sqrt(r2inv);
|
||||
const double r6inv = r3inv*r3inv;
|
||||
forcelj = r6inv*(lj1[itype][jtype]*r3inv
|
||||
- lj2[itype][jtype]);
|
||||
if (EFLAG)
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r3inv
|
||||
- lj4[itype][jtype]) - offset[itype][jtype];
|
||||
|
||||
} else if (ljt == LJ12_6) {
|
||||
const double r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv*(lj1[itype][jtype]*r6inv
|
||||
- lj2[itype][jtype]);
|
||||
if (EFLAG)
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv
|
||||
- lj4[itype][jtype]) - offset[itype][jtype];
|
||||
}
|
||||
forcelj *= factor_lj;
|
||||
if (EFLAG) evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += 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);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJSDKCoulMSM::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r,fgamma,egamma,prefactor;
|
||||
double fraction,table,forcecoul,forcelj,phicoul,philj;
|
||||
int itable;
|
||||
|
||||
forcecoul = forcelj = phicoul = philj = 0.0;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
|
||||
egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
|
||||
fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
|
||||
forcecoul = prefactor * fgamma;
|
||||
phicoul = prefactor * egamma;
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
phicoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
} else {
|
||||
union_int_float_t rsq_lookup_single;
|
||||
rsq_lookup_single.f = rsq;
|
||||
itable = rsq_lookup_single.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = atom->q[i]*atom->q[j] * table;
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
phicoul = 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;
|
||||
phicoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
const int ljt = lj_type[itype][jtype];
|
||||
const double ljpow1 = lj_pow1[ljt];
|
||||
const double ljpow2 = lj_pow2[ljt];
|
||||
const double ljpref = lj_prefact[ljt];
|
||||
|
||||
const double ratio = sigma[itype][jtype]/sqrt(rsq);
|
||||
const double eps = epsilon[itype][jtype];
|
||||
|
||||
forcelj = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
|
||||
- ljpow2*pow(ratio,ljpow2))/rsq;
|
||||
philj = factor_lj * (ljpref*eps * (pow(ratio,ljpow1) - pow(ratio,ljpow2))
|
||||
- offset[itype][jtype]);
|
||||
}
|
||||
|
||||
fforce = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
return phicoul + philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJSDKCoulMSM::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"lj_type") == 0) return (void *) lj_type;
|
||||
if (strcmp(str,"lj1") == 0) return (void *) lj1;
|
||||
if (strcmp(str,"lj2") == 0) return (void *) lj2;
|
||||
if (strcmp(str,"lj3") == 0) return (void *) lj3;
|
||||
if (strcmp(str,"lj4") == 0) return (void *) lj4;
|
||||
if (strcmp(str,"rminsq") == 0) return (void *) rminsq;
|
||||
if (strcmp(str,"emin") == 0) return (void *) emin;
|
||||
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
if (strcmp(str,"cut_msm") == 0) return (void *) &cut_coul;
|
||||
return NULL;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/sdk/coul/msm,PairLJSDKCoulMSM)
|
||||
PairStyle(cg/cmm/coul/msm,PairLJSDKCoulMSM)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_SDK_COUL_MSM_H
|
||||
#define LMP_PAIR_LJ_SDK_COUL_MSM_H
|
||||
|
||||
#include "pair_lj_sdk_coul_long.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJSDKCoulMSM : public PairLJSDKCoulLong {
|
||||
public:
|
||||
PairLJSDKCoulMSM(class LAMMPS *);
|
||||
virtual ~PairLJSDKCoulMSM() {};
|
||||
virtual void compute(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
virtual void *extract(const char *, int &);
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void eval_msm();
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue