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lammps/src/USER-MEAMC/pair_meamc.cpp
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pair_meamc.cpp
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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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Greg Wagner (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "meam.h"
#include "pair_meamc.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
static const int nkeywords = 21;
static const char *keywords[] = {
"Ec","alpha","rho0","delta","lattce",
"attrac","repuls","nn2","Cmin","Cmax","rc","delr",
"augt1","gsmooth_factor","re","ialloy",
"mixture_ref_t","erose_form","zbl",
"emb_lin_neg","bkgd_dyn"};
/* ---------------------------------------------------------------------- */
PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
allocated = 0;
nelements = 0;
elements = NULL;
mass = NULL;
meam_inst = new MEAM(memory);
// set comm size needed by this Pair
comm_forward = 38;
comm_reverse = 30;
}
/* ----------------------------------------------------------------------
free all arrays
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairMEAMC::~PairMEAMC()
{
delete meam_inst;
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
}
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::compute(int eflag, int vflag)
{
int i,ii,n,inum_half,errorflag;
int *ilist_half,*numneigh_half,**firstneigh_half;
int *numneigh_full,**firstneigh_full;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
// neighbor list info
inum_half = listhalf->inum;
ilist_half = listhalf->ilist;
numneigh_half = listhalf->numneigh;
firstneigh_half = listhalf->firstneigh;
numneigh_full = listfull->numneigh;
firstneigh_full = listfull->firstneigh;
// strip neighbor lists of any special bond flags before using with MEAM
// necessary before doing neigh_f2c and neigh_c2f conversions each step
if (neighbor->ago == 0) {
neigh_strip(inum_half,ilist_half,numneigh_half,firstneigh_half);
neigh_strip(inum_half,ilist_half,numneigh_full,firstneigh_full);
}
// check size of scrfcn based on half neighbor list
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
n = 0;
for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];
meam_inst->meam_dens_setup(atom->nmax, nall, n);
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int ntype = atom->ntypes;
// 3 stages of MEAM calculation
// loop over my atoms followed by communication
int offset = 0;
errorflag = 0;
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
meam_inst->meam_dens_init(i,ntype,type,map,x,
numneigh_half[i],firstneigh_half[i],
numneigh_full[i],firstneigh_full[i],
offset);
offset += numneigh_half[i];
}
comm->reverse_comm_pair(this);
meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,
&eng_vdwl,eatom,ntype,type,map,errorflag);
if (errorflag) {
char str[128];
sprintf(str,"MEAM library error %d",errorflag);
error->one(FLERR,str);
}
comm->forward_comm_pair(this);
offset = 0;
// vptr is first value in vatom if it will be used by meam_force()
// else vatom may not exist, so pass dummy ptr
double **vptr;
if (vflag_atom) vptr = vatom;
else vptr = NULL;
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom,
vflag_atom,&eng_vdwl,eatom,ntype,type,map,x,
numneigh_half[i],firstneigh_half[i],
numneigh_full[i],firstneigh_full[i],
offset,f,vptr);
offset += numneigh_half[i];
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMEAMC::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMEAMC::coeff(int narg, char **arg)
{
int i,j,m,n;
if (!allocated) allocate();
if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read MEAM element names between 2 filenames
// nelements = # of MEAM elements
// elements = list of unique element names
if (nelements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
}
nelements = narg - 4 - atom->ntypes;
if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
elements = new char*[nelements];
mass = new double[nelements];
for (i = 0; i < nelements; i++) {
n = strlen(arg[i+3]) + 1;
elements[i] = new char[n];
strcpy(elements[i],arg[i+3]);
}
// read MEAM library and parameter files
// pass all parameters to MEAM package
// tell MEAM package that setup is done
read_files(arg[2],arg[2+nelements+1]);
meam_inst->meam_setup_done(&cutmax);
// read args that map atom types to MEAM elements
// map[i] = which element the Ith atom type is, -1 if not mapped
for (i = 4 + nelements; i < narg; i++) {
m = i - (4+nelements) + 1;
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
if (j < nelements) map[m] = j;
else if (strcmp(arg[i],"NULL") == 0) map[m] = -1;
else error->all(FLERR,"Incorrect args for pair coefficients");
}
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
// set mass for i,i in atom class
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(FLERR,i,mass[map[i]]);
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMEAMC::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style MEAM requires newton pair on");
// need full and half neighbor list
int irequest_full = neighbor->request(this,instance_me);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
int irequest_half = neighbor->request(this,instance_me);
neighbor->requests[irequest_half]->id = 2;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
half or full
------------------------------------------------------------------------- */
void PairMEAMC::init_list(int id, NeighList *ptr)
{
if (id == 1) listfull = ptr;
else if (id == 2) listhalf = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMEAMC::init_one(int i, int j)
{
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::read_files(char *globalfile, char *userfile)
{
// open global meamf file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(globalfile);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open MEAM potential file %s",globalfile);
error->one(FLERR,str);
}
}
// allocate parameter arrays
int params_per_line = 19;
lattice_t *lat = new lattice_t[nelements];
int *ielement = new int[nelements];
int *ibar = new int[nelements];
double *z = new double[nelements];
double *atwt = new double[nelements];
double *alpha = new double[nelements];
double *b0 = new double[nelements];
double *b1 = new double[nelements];
double *b2 = new double[nelements];
double *b3 = new double[nelements];
double *alat = new double[nelements];
double *esub = new double[nelements];
double *asub = new double[nelements];
double *t0 = new double[nelements];
double *t1 = new double[nelements];
double *t2 = new double[nelements];
double *t3 = new double[nelements];
double *rozero = new double[nelements];
bool *found = new bool[nelements];
for (int i = 0; i < nelements; i++) found[i] = false;
// read each set of params from global MEAM file
// one set of params can span multiple lines
// store params if element name is in element list
// if element name appears multiple times, only store 1st entry
int i,n,nwords;
char **words = new char*[params_per_line+1];
char line[MAXLINE],*ptr;
int eof = 0;
int nset = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in MEAM potential file");
// words = ptrs to all words in line
// strip single and double quotes from words
nwords = 0;
words[nwords++] = strtok(line,"' \t\n\r\f");
while ((words[nwords++] = strtok(NULL,"' \t\n\r\f"))) continue;
// skip if element name isn't in element list
for (i = 0; i < nelements; i++)
if (strcmp(words[0],elements[i]) == 0) break;
if (i >= nelements) continue;
// skip if element already appeared
if (found[i] == true) continue;
found[i] = true;
// map lat string to an integer
if (strcmp(words[1],"fcc") == 0) lat[i] = FCC;
else if (strcmp(words[1],"bcc") == 0) lat[i] = BCC;
else if (strcmp(words[1],"hcp") == 0) lat[i] = HCP;
else if (strcmp(words[1],"dim") == 0) lat[i] = DIM;
else if (strcmp(words[1],"dia") == 0) lat[i] = DIA;
else error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
// store parameters
z[i] = atof(words[2]);
ielement[i] = atoi(words[3]);
atwt[i] = atof(words[4]);
alpha[i] = atof(words[5]);
b0[i] = atof(words[6]);
b1[i] = atof(words[7]);
b2[i] = atof(words[8]);
b3[i] = atof(words[9]);
alat[i] = atof(words[10]);
esub[i] = atof(words[11]);
asub[i] = atof(words[12]);
t0[i] = atof(words[13]);
t1[i] = atof(words[14]);
t2[i] = atof(words[15]);
t3[i] = atof(words[16]);
rozero[i] = atof(words[17]);
ibar[i] = atoi(words[18]);
nset++;
}
// error if didn't find all elements in file
if (nset != nelements)
error->all(FLERR,"Did not find all elements in MEAM library file");
// pass element parameters to MEAM package
meam_inst->meam_setup_global(nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
// set element masses
for (i = 0; i < nelements; i++) mass[i] = atwt[i];
// clean-up memory
delete [] words;
delete [] lat;
delete [] ielement;
delete [] ibar;
delete [] z;
delete [] atwt;
delete [] alpha;
delete [] b0;
delete [] b1;
delete [] b2;
delete [] b3;
delete [] alat;
delete [] esub;
delete [] asub;
delete [] t0;
delete [] t1;
delete [] t2;
delete [] t3;
delete [] rozero;
delete [] found;
// done if user param file is NULL
if (strcmp(userfile,"NULL") == 0) return;
// open user param file on proc 0
if (comm->me == 0) {
fp = force->open_potential(userfile);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open MEAM potential file %s",userfile);
error->one(FLERR,str);
}
}
// read settings
// pass them one at a time to MEAM package
// match strings to list of corresponding ints
int which;
double value;
int nindex,index[3];
int maxparams = 6;
char **params = new char*[maxparams];
int nparams;
eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nparams = atom->count_words(line);
if (nparams == 0) continue;
// words = ptrs to all words in line
nparams = 0;
params[nparams++] = strtok(line,"=(), '\t\n\r\f");
while (nparams < maxparams &&
(params[nparams++] = strtok(NULL,"=(), '\t\n\r\f")))
continue;
nparams--;
for (which = 0; which < nkeywords; which++)
if (strcmp(params[0],keywords[which]) == 0) break;
if (which == nkeywords) {
char str[128];
sprintf(str,"Keyword %s in MEAM parameter file not recognized",
params[0]);
error->all(FLERR,str);
}
nindex = nparams - 2;
for (i = 0; i < nindex; i++) index[i] = atoi(params[i+1]) - 1;
// map lattce_meam value to an integer
if (which == 4) {
if (strcmp(params[nparams-1],"fcc") == 0) value = FCC;
else if (strcmp(params[nparams-1],"bcc") == 0) value = BCC;
else if (strcmp(params[nparams-1],"hcp") == 0) value = HCP;
else if (strcmp(params[nparams-1],"dim") == 0) value = DIM;
else if (strcmp(params[nparams-1],"dia") == 0) value = DIA;
else if (strcmp(params[nparams-1],"b1") == 0) value = B1;
else if (strcmp(params[nparams-1],"c11") == 0) value = C11;
else if (strcmp(params[nparams-1],"l12") == 0) value = L12;
else if (strcmp(params[nparams-1],"b2") == 0) value = B2;
else error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
}
else value = atof(params[nparams-1]);
// pass single setting to MEAM package
int errorflag = 0;
meam_inst->meam_setup_param(which,value,nindex,index,&errorflag);
if (errorflag) {
char str[128];
sprintf(str,"MEAM library error %d",errorflag);
error->all(FLERR,str);
}
}
delete [] params;
}
/* ---------------------------------------------------------------------- */
int PairMEAMC::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = meam_inst->rho0[j];
buf[m++] = meam_inst->rho1[j];
buf[m++] = meam_inst->rho2[j];
buf[m++] = meam_inst->rho3[j];
buf[m++] = meam_inst->frhop[j];
buf[m++] = meam_inst->gamma[j];
buf[m++] = meam_inst->dgamma1[j];
buf[m++] = meam_inst->dgamma2[j];
buf[m++] = meam_inst->dgamma3[j];
buf[m++] = meam_inst->arho2b[j];
buf[m++] = meam_inst->arho1[j][0];
buf[m++] = meam_inst->arho1[j][1];
buf[m++] = meam_inst->arho1[j][2];
buf[m++] = meam_inst->arho2[j][0];
buf[m++] = meam_inst->arho2[j][1];
buf[m++] = meam_inst->arho2[j][2];
buf[m++] = meam_inst->arho2[j][3];
buf[m++] = meam_inst->arho2[j][4];
buf[m++] = meam_inst->arho2[j][5];
for (k = 0; k < 10; k++) buf[m++] = meam_inst->arho3[j][k];
buf[m++] = meam_inst->arho3b[j][0];
buf[m++] = meam_inst->arho3b[j][1];
buf[m++] = meam_inst->arho3b[j][2];
buf[m++] = meam_inst->t_ave[j][0];
buf[m++] = meam_inst->t_ave[j][1];
buf[m++] = meam_inst->t_ave[j][2];
buf[m++] = meam_inst->tsq_ave[j][0];
buf[m++] = meam_inst->tsq_ave[j][1];
buf[m++] = meam_inst->tsq_ave[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::unpack_forward_comm(int n, int first, double *buf)
{
int i,k,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
meam_inst->rho0[i] = buf[m++];
meam_inst->rho1[i] = buf[m++];
meam_inst->rho2[i] = buf[m++];
meam_inst->rho3[i] = buf[m++];
meam_inst->frhop[i] = buf[m++];
meam_inst->gamma[i] = buf[m++];
meam_inst->dgamma1[i] = buf[m++];
meam_inst->dgamma2[i] = buf[m++];
meam_inst->dgamma3[i] = buf[m++];
meam_inst->arho2b[i] = buf[m++];
meam_inst->arho1[i][0] = buf[m++];
meam_inst->arho1[i][1] = buf[m++];
meam_inst->arho1[i][2] = buf[m++];
meam_inst->arho2[i][0] = buf[m++];
meam_inst->arho2[i][1] = buf[m++];
meam_inst->arho2[i][2] = buf[m++];
meam_inst->arho2[i][3] = buf[m++];
meam_inst->arho2[i][4] = buf[m++];
meam_inst->arho2[i][5] = buf[m++];
for (k = 0; k < 10; k++) meam_inst->arho3[i][k] = buf[m++];
meam_inst->arho3b[i][0] = buf[m++];
meam_inst->arho3b[i][1] = buf[m++];
meam_inst->arho3b[i][2] = buf[m++];
meam_inst->t_ave[i][0] = buf[m++];
meam_inst->t_ave[i][1] = buf[m++];
meam_inst->t_ave[i][2] = buf[m++];
meam_inst->tsq_ave[i][0] = buf[m++];
meam_inst->tsq_ave[i][1] = buf[m++];
meam_inst->tsq_ave[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int PairMEAMC::pack_reverse_comm(int n, int first, double *buf)
{
int i,k,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = meam_inst->rho0[i];
buf[m++] = meam_inst->arho2b[i];
buf[m++] = meam_inst->arho1[i][0];
buf[m++] = meam_inst->arho1[i][1];
buf[m++] = meam_inst->arho1[i][2];
buf[m++] = meam_inst->arho2[i][0];
buf[m++] = meam_inst->arho2[i][1];
buf[m++] = meam_inst->arho2[i][2];
buf[m++] = meam_inst->arho2[i][3];
buf[m++] = meam_inst->arho2[i][4];
buf[m++] = meam_inst->arho2[i][5];
for (k = 0; k < 10; k++) buf[m++] = meam_inst->arho3[i][k];
buf[m++] = meam_inst->arho3b[i][0];
buf[m++] = meam_inst->arho3b[i][1];
buf[m++] = meam_inst->arho3b[i][2];
buf[m++] = meam_inst->t_ave[i][0];
buf[m++] = meam_inst->t_ave[i][1];
buf[m++] = meam_inst->t_ave[i][2];
buf[m++] = meam_inst->tsq_ave[i][0];
buf[m++] = meam_inst->tsq_ave[i][1];
buf[m++] = meam_inst->tsq_ave[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,k,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
meam_inst->rho0[j] += buf[m++];
meam_inst->arho2b[j] += buf[m++];
meam_inst->arho1[j][0] += buf[m++];
meam_inst->arho1[j][1] += buf[m++];
meam_inst->arho1[j][2] += buf[m++];
meam_inst->arho2[j][0] += buf[m++];
meam_inst->arho2[j][1] += buf[m++];
meam_inst->arho2[j][2] += buf[m++];
meam_inst->arho2[j][3] += buf[m++];
meam_inst->arho2[j][4] += buf[m++];
meam_inst->arho2[j][5] += buf[m++];
for (k = 0; k < 10; k++) meam_inst->arho3[j][k] += buf[m++];
meam_inst->arho3b[j][0] += buf[m++];
meam_inst->arho3b[j][1] += buf[m++];
meam_inst->arho3b[j][2] += buf[m++];
meam_inst->t_ave[j][0] += buf[m++];
meam_inst->t_ave[j][1] += buf[m++];
meam_inst->t_ave[j][2] += buf[m++];
meam_inst->tsq_ave[j][0] += buf[m++];
meam_inst->tsq_ave[j][1] += buf[m++];
meam_inst->tsq_ave[j][2] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairMEAMC::memory_usage()
{
double bytes = 11 * meam_inst->nmax * sizeof(double);
bytes += (3 + 6 + 10 + 3 + 3 + 3) * meam_inst->nmax * sizeof(double);
bytes += 3 * meam_inst->maxneigh * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
strip special bond flags from neighbor list entries
are not used with MEAM
need to do here so Fortran lib doesn't see them
done once per reneighbor so that neigh_f2c and neigh_c2f don't see them
------------------------------------------------------------------------- */
void PairMEAMC::neigh_strip(int inum, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jnum;
int *jlist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
}
}
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