Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F120135354
pair_zbl.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Jul 2, 04:38
Size
10 KB
Mime Type
text/x-c
Expires
Fri, Jul 4, 04:38 (2 d)
Engine
blob
Format
Raw Data
Handle
27145625
Attached To
rLAMMPS lammps
pair_zbl.cpp
View Options
/* ----------------------------------------------------------------------
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 authors: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_zbl.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace PairZBLConstants;
/* ---------------------------------------------------------------------- */
PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairZBL::~PairZBL()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(z);
memory->destroy(d1a);
memory->destroy(d2a);
memory->destroy(d3a);
memory->destroy(d4a);
memory->destroy(zze);
memory->destroy(sw1);
memory->destroy(sw2);
memory->destroy(sw3);
memory->destroy(sw4);
memory->destroy(sw5);
}
}
/* ---------------------------------------------------------------------- */
void PairZBL::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,t,fswitch,eswitch;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
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];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
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 < cut_globalsq) {
r = sqrt(rsq);
fpair = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fpair += fswitch;
}
fpair *= -1.0/r;
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 (eflag) {
evdwl = e_zbl(r, itype, jtype);
evdwl += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
evdwl += eswitch;
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairZBL::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(z,n+1,"pair:z");
memory->create(d1a,n+1,n+1,"pair:d1a");
memory->create(d2a,n+1,n+1,"pair:d2a");
memory->create(d3a,n+1,n+1,"pair:d3a");
memory->create(d4a,n+1,n+1,"pair:d4a");
memory->create(zze,n+1,n+1,"pair:zze");
memory->create(sw1,n+1,n+1,"pair:sw1");
memory->create(sw2,n+1,n+1,"pair:sw2");
memory->create(sw3,n+1,n+1,"pair:sw3");
memory->create(sw4,n+1,n+1,"pair:sw4");
memory->create(sw5,n+1,n+1,"pair:sw5");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairZBL::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_inner = force->numeric(FLERR,arg[0]);
cut_global = force->numeric(FLERR,arg[1]);
if (cut_inner <= 0.0 )
error->all(FLERR,"Illegal pair_style command");
if (cut_inner > cut_global)
error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairZBL::coeff(int narg, char **arg)
{
if (narg != 3)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
int jlo,jhi;
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double z_one = force->numeric(FLERR,arg[2]);
// Set flag for each i-j pair
// Set z-parameter only for i-i pairs
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (i == j) z[i] = z_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairZBL::init_style()
{
neighbor->request(this);
cut_innersq = cut_inner * cut_inner;
cut_globalsq = cut_global * cut_global;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairZBL::init_one(int i, int j)
{
double ainv = (pow(z[i],pzbl) + pow(z[j],pzbl))/(a0*force->angstrom);
d1a[i][j] = d1*ainv;
d2a[i][j] = d2*ainv;
d3a[i][j] = d3*ainv;
d4a[i][j] = d4*ainv;
zze[i][j] = z[i]*z[j]*force->qqr2e*force->qelectron*force->qelectron;
d1a[j][i] = d1a[i][j];
d2a[j][i] = d2a[i][j];
d3a[j][i] = d3a[i][j];
d4a[j][i] = d4a[i][j];
zze[j][i] = zze[i][j];
// e = t^3 (sw3 + sw4*t) + sw5
// = A/3*t^3 + B/4*t^4 + C
// sw3 = A/3
// sw4 = B/4
// sw5 = C
// dedr = t^2 (sw1 + sw2*t)
// = A*t^2 + B*t^3
// sw1 = A
// sw2 = B
// de2dr2 = 2*A*t + 3*B*t^2
// Require that at t = tc:
// e = -Fc
// dedr = -Fc'
// d2edr2 = -Fc''
// Hence:
// A = (-3Fc' + tc*Fc'')/tc^2
// B = ( 2Fc' - tc*Fc'')/tc^3
// C = -Fc + tc/2*Fc' - tc^2/12*Fc''
double tc = cut_global - cut_inner;
double fc = e_zbl(cut_global, i, j);
double fcp = dzbldr(cut_global, i, j);
double fcpp = d2zbldr2(cut_global, i, j);
double swa = (-3.0*fcp + tc*fcpp)/(tc*tc);
double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc);
double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
sw1[i][j] = swa;
sw2[i][j] = swb;
sw3[i][j] = swa/3.0;
sw4[i][j] = swb/4.0;
sw5[i][j] = swc;
sw1[j][i] = sw1[i][j];
sw2[j][i] = sw2[i][j];
sw3[j][i] = sw3[i][j];
sw4[j][i] = sw4[i][j];
sw5[j][i] = sw5[i][j];
return cut_global;
}
/* ---------------------------------------------------------------------- */
double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
double dummy1, double dummy2,
double &fforce)
{
double phi,r,t,eswitch,fswitch;
r = sqrt(rsq);
fforce = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fforce += fswitch;
}
fforce *= -1.0/r;
phi = e_zbl(r, itype, jtype);
phi += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
phi += eswitch;
}
return phi;
}
/* ----------------------------------------------------------------------
compute ZBL pair energy
------------------------------------------------------------------------- */
double PairZBL::e_zbl(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double sum = c1*exp(-d1aij*r);
sum += c2*exp(-d2aij*r);
sum += c3*exp(-d3aij*r);
sum += c4*exp(-d4aij*r);
double result = zzeij*sum*rinv;
return result;
};
/* ----------------------------------------------------------------------
compute ZBL first derivative
------------------------------------------------------------------------- */
double PairZBL::dzbldr(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum_p = -c1*d1aij*e1;
sum_p -= c2*d2aij*e2;
sum_p -= c3*d3aij*e3;
sum_p -= c4*d4aij*e4;
double result = zzeij*(sum_p - sum*rinv)*rinv;
return result;
};
/* ----------------------------------------------------------------------
compute ZBL second derivative
------------------------------------------------------------------------- */
double PairZBL::d2zbldr2(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum_p = c1*e1*d1aij;
sum_p += c2*e2*d2aij;
sum_p += c3*e3*d3aij;
sum_p += c4*e4*d4aij;
double sum_pp = c1*e1*d1aij*d1aij;
sum_pp += c2*e2*d2aij*d2aij;
sum_pp += c3*e3*d3aij*d3aij;
sum_pp += c4*e4*d4aij*d4aij;
double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
2.0*sum*rinv*rinv)*rinv;
return result;
};
Event Timeline
Log In to Comment