Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/MOLECULE/pair_hbond_dreiding_lj.cpp
dadf60427b97lammm-master-deprecated

Last Change
Raw File

pair_hbond_dreiding_lj.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 author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_hbond_dreiding_lj.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "domain.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define SMALL 0.001
#define CHUNK 8
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJ::PairHbondDreidingLJ(LAMMPS *lmp) : Pair(lmp)
{
// hbond cannot compute virial as F dot r
// due to using map() to find bonded H atoms which are not near donor atom
no_virial_fdotr_compute = 1;
restartinfo = 0;
nparams = maxparam = 0;
params = NULL;
nextra = 2;
pvector = new double[2];
}
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJ::~PairHbondDreidingLJ()
{
memory->sfree(params);
delete [] pvector;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] donor;
delete [] acceptor;
memory->destroy(type2param);
}
}
/* ---------------------------------------------------------------------- */
void PairHbondDreidingLJ::compute(int eflag, int vflag)
{
int i,j,k,m,ii,jj,kk,inum,jnum,knum,itype,jtype,ktype,iatom,imol;
tagint tagprev;
double delx,dely,delz,rsq,rsq1,rsq2,r1,r2;
double factor_hb,force_angle,force_kernel,evdwl,eng_lj,ehbond,force_switch;
double c,s,a,b,ac,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2,d;
double fi[3],fj[3],delr1[3],delr2[3];
double r2inv,r10inv;
double switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
tagint *klist;
evdwl = ehbond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int *type = atom->type;
double *special_lj = force->special_lj;
int molecular = atom->molecular;
Molecule **onemols = atom->avec->onemols;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
int hbcount = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
if (!donor[itype]) continue;
if (molecular == 1) {
klist = special[i];
knum = nspecial[i][0];
} else {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = tag[i] - iatom - 1;
}
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_hb = special_lj[sbmask(j)];
j &= NEIGHMASK;
jtype = type[j];
if (!acceptor[jtype]) continue;
delx = x[i][0] - x[j][0];
dely = x[i][1] - x[j][1];
delz = x[i][2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
if (m < 0) continue;
const Param &pm = params[m];
if (rsq < pm.cut_outersq) {
delr1[0] = x[i][0] - x[k][0];
delr1[1] = x[i][1] - x[k][1];
delr1[2] = x[i][2] - x[k][2];
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
ac = acos(c);
if (ac > pm.cut_angle && ac < (2.0*MY_PI - pm.cut_angle)) {
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
// LJ-specific kernel
r2inv = 1.0/rsq;
r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
force_kernel = r10inv*(pm.lj1*r2inv - pm.lj2)*r2inv *
powint(c,pm.ap);
force_angle = pm.ap * r10inv*(pm.lj3*r2inv - pm.lj4) *
powint(c,pm.ap-1)*s;
eng_lj = r10inv*(pm.lj3*r2inv - pm.lj4);
force_switch=0.0;
if (rsq > pm.cut_innersq) {
switch1 = (pm.cut_outersq-rsq) * (pm.cut_outersq-rsq) *
(pm.cut_outersq + 2.0*rsq - 3.0*pm.cut_innersq) /
pm.denom_vdw;
switch2 = 12.0*rsq * (pm.cut_outersq-rsq) *
(rsq-pm.cut_innersq) / pm.denom_vdw;
force_kernel *= switch1;
force_angle *= switch1;
force_switch = eng_lj*switch2/rsq;
eng_lj *= switch1;
}
if (eflag) {
evdwl = eng_lj * powint(c,pm.ap);
evdwl *= factor_hb;
ehbond += evdwl;
}
a = factor_hb*force_angle/s;
b = factor_hb*force_kernel;
d = factor_hb*force_switch;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
vx1 = a11*delr1[0] + a12*delr2[0];
vx2 = a22*delr2[0] + a12*delr1[0];
vy1 = a11*delr1[1] + a12*delr2[1];
vy2 = a22*delr2[1] + a12*delr1[1];
vz1 = a11*delr1[2] + a12*delr2[2];
vz2 = a22*delr2[2] + a12*delr1[2];
fi[0] = vx1 + b*delx + d*delx;
fi[1] = vy1 + b*dely + d*dely;
fi[2] = vz1 + b*delz + d*delz;
fj[0] = vx2 - b*delx - d*delx;
fj[1] = vy2 - b*dely - d*dely;
fj[2] = vz2 - b*delz - d*delz;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] -= vx1 + vx2;
f[k][1] -= vy1 + vy2;
f[k][2] -= vz1 + vz2;
// KIJ instead of IJK b/c delr1/delr2 are both with respect to k
if (evflag) ev_tally3(k,i,j,evdwl,0.0,fi,fj,delr1,delr2);
hbcount++;
}
}
}
}
}
if (eflag_global) {
pvector[0] = hbcount;
pvector[1] = ehbond;
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::allocate()
{
allocated = 1;
int n = atom->ntypes;
// mark all setflag as set, since don't require pair_coeff of all I,J
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] = 1;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
donor = new int[n+1];
acceptor = new int[n+1];
memory->create(type2param,n+1,n+1,n+1,"pair:type2param");
int i,j,k;
for (i = 1; i <= n; i++)
for (j = 1; j <= n; j++)
for (k = 1; k <= n; k++)
type2param[i][j][k] = -1;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::settings(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Illegal pair_style command");
ap_global = force->inumeric(FLERR,arg[0]);
cut_inner_global = force->numeric(FLERR,arg[1]);
cut_outer_global = force->numeric(FLERR,arg[2]);
cut_angle_global = force->numeric(FLERR,arg[3]) * MY_PI/180.0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::coeff(int narg, char **arg)
{
if (narg < 6 || narg > 10)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi,klo,khi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
force->bounds(arg[2],atom->ntypes,klo,khi);
int donor_flag;
if (strcmp(arg[3],"i") == 0) donor_flag = 0;
else if (strcmp(arg[3],"j") == 0) donor_flag = 1;
else error->all(FLERR,"Incorrect args for pair coefficients");
double epsilon_one = force->numeric(FLERR,arg[4]);
double sigma_one = force->numeric(FLERR,arg[5]);
int ap_one = ap_global;
if (narg > 6) ap_one = force->inumeric(FLERR,arg[6]);
double cut_inner_one = cut_inner_global;
double cut_outer_one = cut_outer_global;
if (narg > 8) {
cut_inner_one = force->numeric(FLERR,arg[7]);
cut_outer_one = force->numeric(FLERR,arg[8]);
}
if (cut_inner_one>cut_outer_one)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
double cut_angle_one = cut_angle_global;
if (narg == 10) cut_angle_one = force->numeric(FLERR,arg[9]) * MY_PI/180.0;
// grow params array if necessary
if (nparams == maxparam) {
maxparam += CHUNK;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].epsilon = epsilon_one;
params[nparams].sigma = sigma_one;
params[nparams].ap = ap_one;
params[nparams].cut_inner = cut_inner_one;
params[nparams].cut_outer = cut_outer_one;
params[nparams].cut_innersq = cut_inner_one*cut_inner_one;
params[nparams].cut_outersq = cut_outer_one*cut_outer_one;
params[nparams].cut_angle = cut_angle_one;
params[nparams].denom_vdw =
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
(params[nparams].cut_outersq-params[nparams].cut_innersq) *
(params[nparams].cut_outersq-params[nparams].cut_innersq);
// flag type2param with either i,j = D,A or j,i = D,A
int count = 0;
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++)
for (int k = klo; k <= khi; k++) {
if (donor_flag == 0) type2param[i][j][k] = nparams;
else type2param[j][i][k] = nparams;
count++;
}
nparams++;
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairHbondDreidingLJ::init_style()
{
// molecular system required to use special list to find H atoms
// tags required to use special list
// pair newton on required since are looping over D atoms
// and computing forces on A,H which may be on different procs
if (atom->molecular == 0)
error->all(FLERR,"Pair style hbond/dreiding requires molecular system");
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style hbond/dreiding requires atom IDs");
if (atom->map_style == 0)
error->all(FLERR,"Pair style hbond/dreiding requires an atom map, "
"see atom_modify");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style hbond/dreiding requires newton pair on");
// set donor[M]/acceptor[M] if any atom of type M is a donor/acceptor
int anyflag = 0;
int n = atom->ntypes;
for (int m = 1; m <= n; m++) donor[m] = acceptor[m] = 0;
for (int i = 1; i <= n; i++)
for (int j = 1; j <= n; j++)
for (int k = 1; k <= n; k++)
if (type2param[i][j][k] >= 0) {
anyflag = 1;
donor[i] = 1;
acceptor[j] = 1;
}
if (!anyflag) error->all(FLERR,"No pair hbond/dreiding coefficients set");
// set additional param values
// offset is for LJ only, angle term is not included
for (int m = 0; m < nparams; m++) {
params[m].lj1 = 60.0*params[m].epsilon*pow(params[m].sigma,12.0);
params[m].lj2 = 60.0*params[m].epsilon*pow(params[m].sigma,10.0);
params[m].lj3 = 5.0*params[m].epsilon*pow(params[m].sigma,12.0);
params[m].lj4 = 6.0*params[m].epsilon*pow(params[m].sigma,10.0);
/*
if (offset_flag) {
double ratio = params[m].sigma / params[m].cut_outer;
params[m].offset = params[m].epsilon *
((2.0*pow(ratio,9.0)) - (3.0*pow(ratio,6.0)));
} else params[m].offset = 0.0;
*/
}
// full neighbor list request
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairHbondDreidingLJ::init_one(int i, int j)
{
int m;
// return maximum cutoff for any K with I,J = D,A or J,I = D,A
// donor/acceptor is not symmetric, IJ interaction != JI interaction
double cut = 0.0;
for (int k = 1; k <= atom->ntypes; k++) {
m = type2param[i][j][k];
if (m >= 0) cut = MAX(cut,params[m].cut_outer);
m = type2param[j][i][k];
if (m >= 0) cut = MAX(cut,params[m].cut_outer);
}
return cut;
}
/* ---------------------------------------------------------------------- */
double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
int k,kk,ktype,knum,m;
tagint tagprev;
double eng,eng_lj,force_kernel,force_angle;
double rsq1,rsq2,r1,r2,c,s,ac,r2inv,r10inv,factor_hb;
double switch1,switch2;
double delr1[3],delr2[3];
tagint *klist;
double **x = atom->x;
int *type = atom->type;
double *special_lj = force->special_lj;
eng = 0.0;
fforce = 0;
// sanity check
if (!donor[itype]) return 0.0;
if (!acceptor[jtype]) return 0.0;
int molecular = atom->molecular;
if (molecular == 1) {
klist = atom->special[i];
knum = atom->nspecial[i][0];
} else {
if (atom->molindex[i] < 0) return 0.0;
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
Molecule **onemols = atom->avec->onemols;
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = atom->tag[i] - iatom - 1;
}
factor_hb = special_lj[sbmask(j)];
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
if (m < 0) continue;
const Param &pm = params[m];
delr1[0] = x[i][0] - x[k][0];
delr1[1] = x[i][1] - x[k][1];
delr1[2] = x[i][2] - x[k][2];
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
ac = acos(c);
if (ac < pm.cut_angle || ac > (2.0*MY_PI - pm.cut_angle)) return 0.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
// LJ-specific kernel
r2inv = 1.0/rsq;
r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
force_kernel = r10inv*(pm.lj1*r2inv - pm.lj2)*r2inv * powint(c,pm.ap);
force_angle = pm.ap * r10inv*(pm.lj3*r2inv - pm.lj4) *
powint(c,pm.ap-1)*s;
// only lj part for now
eng_lj = r10inv*(pm.lj3*r2inv - pm.lj4);
if (rsq > pm.cut_innersq) {
switch1 = (pm.cut_outersq-rsq) * (pm.cut_outersq-rsq) *
(pm.cut_outersq + 2.0*rsq - 3.0*pm.cut_innersq) / pm.denom_vdw;
switch2 = 12.0*rsq * (pm.cut_outersq-rsq) *
(rsq-pm.cut_innersq) / pm.denom_vdw;
force_kernel = force_kernel*switch1 + eng_lj*switch2;
eng_lj *= switch1;
}
fforce += force_kernel*powint(c,pm.ap) + eng_lj*force_angle;
eng += eng_lj * powint(c,pm.ap) * factor_hb;
}
return eng;
}
c4science · Help