Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/compute_group_group.cpp
2fe1d1b90451lammm-devel

Last Change
Raw File

compute_group_group.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: Naveen Michaud-Agrawal (Johns Hopkins U)
K-space terms added by Stan Moore (BYU)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include "compute_group_group.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "kspace.h"
#include "error.h"
#include <math.h>
#include "comm.h"
#include "domain.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.00001
enum{OFF,INTER,INTRA};
/* ---------------------------------------------------------------------- */
ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
group2(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute group/group command");
scalar_flag = vector_flag = 1;
size_vector = 3;
extscalar = 1;
extvector = 1;
int n = strlen(arg[3]) + 1;
group2 = new char[n];
strcpy(group2,arg[3]);
jgroup = group->find(group2);
if (jgroup == -1)
error->all(FLERR,"Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
pairflag = 1;
kspaceflag = 0;
boundaryflag = 1;
molflag = OFF;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) pairflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) pairflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
iarg += 2;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) kspaceflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
iarg += 2;
} else if (strcmp(arg[iarg],"boundary") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"yes") == 0) boundaryflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) boundaryflag = 0;
else error->all(FLERR,"Illegal compute group/group command");
iarg += 2;
} else if (strcmp(arg[iarg],"molecule") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute group/group command");
if (strcmp(arg[iarg+1],"off") == 0) molflag = OFF;
else if (strcmp(arg[iarg+1],"inter") == 0) molflag = INTER;
else if (strcmp(arg[iarg+1],"intra") == 0) molflag = INTRA;
else error->all(FLERR,"Illegal compute group/group command");
if (molflag != OFF && atom->molecule_flag == 0)
error->all(FLERR,"Compute group/group molecule requires molecule IDs");
iarg += 2;
} else error->all(FLERR,"Illegal compute group/group command");
}
vector = new double[3];
}
/* ---------------------------------------------------------------------- */
ComputeGroupGroup::~ComputeGroupGroup()
{
delete [] group2;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::init()
{
// if non-hybrid, then error if single_enable = 0
// if hybrid, let hybrid determine if sub-style sets single_enable = 0
if (pairflag && force->pair == NULL)
error->all(FLERR,"No pair style defined for compute group/group");
if (force->pair_match("hybrid",0) == NULL && force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute group/group");
// error if Kspace style does not compute group/group interactions
if (kspaceflag && force->kspace == NULL)
error->all(FLERR,"No Kspace style defined for compute group/group");
if (kspaceflag && force->kspace->group_group_enable == 0)
error->all(FLERR,"Kspace style does not support compute group/group");
if (pairflag) {
pair = force->pair;
cutsq = force->pair->cutsq;
} else pair = NULL;
if (kspaceflag) kspace = force->kspace;
else kspace = NULL;
// compute Kspace correction terms
if (kspaceflag) {
kspace_correction();
if (fabs(e_correction) > SMALL && comm->me == 0) {
char str[128];
sprintf(str,"Both groups in compute group/group have a net charge; "
"the Kspace boundary correction to energy will be non-zero");
error->warning(FLERR,str);
}
}
// recheck that group 2 has not been deleted
jgroup = group->find(group2);
if (jgroup == -1)
error->all(FLERR,"Compute group/group group ID does not exist");
jgroupbit = group->bitmask[jgroup];
// need an occasional half neighbor list
if (pairflag) {
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
double ComputeGroupGroup::compute_scalar()
{
invoked_scalar = invoked_vector = update->ntimestep;
scalar = 0.0;
vector[0] = vector[1] = vector[2] = 0.0;
if (pairflag) pair_contribution();
if (kspaceflag) kspace_contribution();
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::compute_vector()
{
invoked_scalar = invoked_vector = update->ntimestep;
scalar = 0.0;
vector[0] = vector[1] = vector[2] = 0.0;
if (pairflag) pair_contribution();
if (kspaceflag) kspace_contribution();
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::pair_contribution()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
tagint *molecule = atom->molecule;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I,J are not in 2 groups
double one[4];
one[0] = one[1] = one[2] = one[3] = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
// skip if atom I is not in either group
if (!(mask[i] & groupbit || mask[i] & jgroupbit)) continue;
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];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// skip if atom J is not in either group
if (!(mask[j] & groupbit || mask[j] & jgroupbit)) continue;
// skip if atoms I,J are only in the same group
int ij_flag = 0;
int ji_flag = 0;
if (mask[i] & groupbit && mask[j] & jgroupbit) ij_flag = 1;
if (mask[j] & groupbit && mask[i] & jgroupbit) ji_flag = 1;
if (!ij_flag && !ji_flag) continue;
// skip if molecule IDs of atoms I,J do not satisfy molflag setting
if (molflag != OFF) {
if (molflag == INTER) {
if (molecule[i] == molecule[j]) continue;
} else {
if (molecule[i] != molecule[j]) continue;
}
}
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]) {
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
// energy only computed once so tally full amount
// force tally is jgroup acting on igroup
if (newton_pair || j < nlocal) {
one[0] += eng;
if (ij_flag) {
one[1] += delx*fpair;
one[2] += dely*fpair;
one[3] += delz*fpair;
}
if (ji_flag) {
one[1] -= delx*fpair;
one[2] -= dely*fpair;
one[3] -= delz*fpair;
}
// energy computed twice so tally half amount
// only tally force if I own igroup atom
} else {
one[0] += 0.5*eng;
if (ij_flag) {
one[1] += delx*fpair;
one[2] += dely*fpair;
one[3] += delz*fpair;
}
}
}
}
}
double all[4];
MPI_Allreduce(one,all,4,MPI_DOUBLE,MPI_SUM,world);
scalar += all[0];
vector[0] += all[1]; vector[1] += all[2]; vector[2] += all[3];
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::kspace_contribution()
{
double *vector_kspace = force->kspace->f2group;
force->kspace->compute_group_group(groupbit,jgroupbit,0);
scalar += 2.0*force->kspace->e2group;
vector[0] += vector_kspace[0];
vector[1] += vector_kspace[1];
vector[2] += vector_kspace[2];
// subtract extra A <--> A Kspace interaction so energy matches
// real-space style of compute group-group
// add extra Kspace term to energy
force->kspace->compute_group_group(groupbit,jgroupbit,1);
scalar -= force->kspace->e2group;
// self energy correction term
scalar -= e_self;
// k=0 boundary correction term
if (boundaryflag) {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
// adjustment of z dimension for 2d slab Ewald
// 3d Ewald just uses zprd since slab_volfactor = 1.0
double volume = xprd*yprd*zprd*force->kspace->slab_volfactor;
scalar -= e_correction/volume;
}
}
/* ---------------------------------------------------------------------- */
void ComputeGroupGroup::kspace_correction()
{
// total charge of groups A & B, needed for correction term
double qsqsum_group,qsum_A,qsum_B;
qsqsum_group = qsum_A = qsum_B = 0.0;
double *q = atom->q;
int *mask = atom->mask;
int groupbit_A = groupbit;
int groupbit_B = jgroupbit;
for (int i = 0; i < atom->nlocal; i++) {
if ((mask[i] & groupbit_A) && (mask[i] & groupbit_B))
qsqsum_group += q[i]*q[i];
if (mask[i] & groupbit_A) qsum_A += q[i];
if (mask[i] & groupbit_B) qsum_B += q[i];
}
double tmp;
MPI_Allreduce(&qsqsum_group,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum_group = tmp;
MPI_Allreduce(&qsum_A,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_A = tmp;
MPI_Allreduce(&qsum_B,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_B = tmp;
double g_ewald = force->kspace->g_ewald;
double scale = 1.0;
const double qscale = force->qqrd2e * scale;
// self-energy correction
e_self = qscale * g_ewald*qsqsum_group/MY_PIS;
e_correction = 2.0*qsum_A*qsum_B;
// subtract extra AA terms
qsum_A = qsum_B = 0.0;
for (int i = 0; i < atom->nlocal; i++) {
if (!((mask[i] & groupbit_A) && (mask[i] & groupbit_B)))
continue;
if (mask[i] & groupbit_A) qsum_A += q[i];
if (mask[i] & groupbit_B) qsum_B += q[i];
}
MPI_Allreduce(&qsum_A,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_A = tmp;
MPI_Allreduce(&qsum_B,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum_B = tmp;
// k=0 energy correction term (still need to divide by volume above)
e_correction -= qsum_A*qsum_B;
e_correction *= qscale * MY_PI2 / (g_ewald*g_ewald);
}
c4science · Help