git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5792 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -138,26 +138,26 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
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Neighbor::~Neighbor()
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{
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memory->destroy_2d_double_array(cutneighsq);
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memory->destroy(cutneighsq);
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delete [] cuttype;
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delete [] cuttypesq;
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delete [] fixchecklist;
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memory->destroy_2d_double_array(xhold);
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memory->destroy(xhold);
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memory->sfree(binhead);
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memory->sfree(bins);
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memory->destroy(binhead);
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memory->destroy(bins);
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memory->sfree(ex1_type);
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memory->sfree(ex2_type);
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memory->destroy_2d_int_array(ex_type);
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memory->destroy(ex1_type);
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memory->destroy(ex2_type);
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memory->destroy(ex_type);
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memory->sfree(ex1_group);
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memory->sfree(ex2_group);
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memory->destroy(ex1_group);
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memory->destroy(ex2_group);
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delete [] ex1_bit;
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delete [] ex2_bit;
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memory->sfree(ex_mol_group);
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memory->destroy(ex_mol_group);
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delete [] ex_mol_bit;
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for (int i = 0; i < nlist; i++) delete lists[i];
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@ -173,10 +173,10 @@ Neighbor::~Neighbor()
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for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
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memory->sfree(old_requests);
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memory->destroy_2d_int_array(bondlist);
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memory->destroy_2d_int_array(anglelist);
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memory->destroy_2d_int_array(dihedrallist);
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memory->destroy_2d_int_array(improperlist);
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memory->destroy(bondlist);
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memory->destroy(anglelist);
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memory->destroy(dihedrallist);
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memory->destroy(improperlist);
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}
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/* ---------------------------------------------------------------------- */
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@ -225,7 +225,7 @@ void Neighbor::init()
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n = atom->ntypes;
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if (cutneighsq == NULL) {
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cutneighsq = memory->create_2d_double_array(n+1,n+1,"neigh:cutneighsq");
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memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
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cuttype = new double[n+1];
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cuttypesq = new double[n+1];
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}
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@ -326,14 +326,14 @@ void Neighbor::init()
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// free xhold and bins if not needed for this run
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if (dist_check == 0) {
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memory->destroy_2d_double_array(xhold);
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memory->destroy(xhold);
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maxhold = 0;
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xhold = NULL;
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}
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if (style == NSQ) {
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memory->sfree(bins);
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memory->sfree(binhead);
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memory->destroy(bins);
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memory->destroy(binhead);
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maxbin = maxhead = 0;
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binhead = NULL;
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bins = NULL;
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@ -344,14 +344,14 @@ void Neighbor::init()
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if (dist_check) {
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if (maxhold == 0) {
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maxhold = atom->nmax;
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xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
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memory->create(xhold,maxhold,3,"neigh:xhold");
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}
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}
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if (style != NSQ) {
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if (maxbin == 0) {
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maxbin = atom->nmax;
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bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
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memory->create(bins,maxbin,"bins");
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}
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}
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@ -363,8 +363,8 @@ void Neighbor::init()
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else exclude = 1;
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if (nex_type) {
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memory->destroy_2d_int_array(ex_type);
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ex_type = (int **) memory->create_2d_int_array(n+1,n+1,"neigh:ex_type");
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memory->destroy(ex_type);
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memory->create(ex_type,n+1,n+1,"neigh:ex_type");
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for (i = 1; i <= n; i++)
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for (j = 1; j <= n; j++)
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@ -647,7 +647,7 @@ void Neighbor::init()
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// copy current requests and style to old for next run
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for (i = 0; i < old_nrequest; i++) delete old_requests[i];
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memory->sfree(old_requests);
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memory->destroy(old_requests);
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old_nrequest = nrequest;
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old_requests = requests;
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nrequest = maxrequest = 0;
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@ -663,29 +663,27 @@ void Neighbor::init()
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if (atom->molecular && atom->nbonds && maxbond == 0) {
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if (nprocs == 1) maxbond = atom->nbonds;
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else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
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bondlist = memory->create_2d_int_array(maxbond,3,"neigh:bondlist");
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memory->create(bondlist,maxbond,3,"neigh:bondlist");
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}
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if (atom->molecular && atom->nangles && maxangle == 0) {
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if (nprocs == 1) maxangle = atom->nangles;
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else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
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anglelist = memory->create_2d_int_array(maxangle,4,"neigh:anglelist");
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memory->create(anglelist,maxangle,4,"neigh:anglelist");
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}
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if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
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if (nprocs == 1) maxdihedral = atom->ndihedrals;
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else maxdihedral = static_cast<int>
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(LB_FACTOR * atom->ndihedrals / nprocs);
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dihedrallist =
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memory->create_2d_int_array(maxdihedral,5,"neigh:dihedrallist");
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memory->create(dihedrallist,maxdihedral,5,"neigh:dihedrallist");
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}
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if (atom->molecular && atom->nimpropers && maximproper == 0) {
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if (nprocs == 1) maximproper = atom->nimpropers;
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else maximproper = static_cast<int>
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(LB_FACTOR * atom->nimpropers / nprocs);
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improperlist =
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memory->create_2d_int_array(maximproper,5,"neigh:improperlist");
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memory->create(improperlist,maximproper,5,"neigh:improperlist");
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}
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// set flags that determine which topology neighboring routines to use
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@ -1093,8 +1091,8 @@ void Neighbor::build()
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if (includegroup) nlocal = atom->nfirst;
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if (nlocal > maxhold) {
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maxhold = atom->nmax;
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memory->destroy_2d_double_array(xhold);
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xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
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memory->destroy(xhold);
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memory->create(xhold,maxhold,3,"neigh:xhold");
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}
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for (i = 0; i < nlocal; i++) {
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xhold[i][0] = x[i][0];
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@ -1133,8 +1131,8 @@ void Neighbor::build()
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if (style != NSQ && atom->nmax > maxbin) {
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maxbin = atom->nmax;
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memory->sfree(bins);
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bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
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memory->destroy(bins);
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memory->create(bins,maxbin,"bins");
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}
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// check that pairwise lists with special bond weighting will not overflow
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@ -1179,8 +1177,8 @@ void Neighbor::build_one(int i)
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if (style != NSQ && atom->nmax > maxbin) {
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maxbin = atom->nmax;
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memory->sfree(bins);
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bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
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memory->destroy(bins);
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memory->create(bins,maxbin,"bins");
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}
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// this condition can cause LAMMPS to crash
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@ -1354,8 +1352,8 @@ void Neighbor::setup_bins()
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mbins = bbin;
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if (mbins > maxhead) {
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maxhead = mbins;
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memory->sfree(binhead);
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binhead = (int *) memory->smalloc(maxhead*sizeof(int),"neigh:binhead");
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memory->destroy(binhead);
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memory->create(binhead,maxhead,"neigh:binhead");
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}
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// create stencil of bins to search over in neighbor list construction
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@ -1481,10 +1479,8 @@ void Neighbor::modify_params(int narg, char **arg)
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if (iarg+4 > narg) error->all("Illegal neigh_modify command");
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if (nex_type == maxex_type) {
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maxex_type += EXDELTA;
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ex1_type = (int *) memory->srealloc(ex1_type,maxex_type*sizeof(int),
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"neigh:ex1_type");
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ex2_type = (int *) memory->srealloc(ex2_type,maxex_type*sizeof(int),
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"neigh:ex2_type");
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memory->grow(ex1_type,maxex_type,"neigh:ex1_type");
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memory->grow(ex2_type,maxex_type,"neigh:ex2_type");
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}
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ex1_type[nex_type] = atoi(arg[iarg+2]);
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ex2_type[nex_type] = atoi(arg[iarg+3]);
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@ -1495,12 +1491,8 @@ void Neighbor::modify_params(int narg, char **arg)
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if (iarg+4 > narg) error->all("Illegal neigh_modify command");
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if (nex_group == maxex_group) {
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maxex_group += EXDELTA;
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ex1_group =
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(int *) memory->srealloc(ex1_group,maxex_group*sizeof(int),
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"neigh:ex1_group");
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ex2_group =
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(int *) memory->srealloc(ex2_group,maxex_group*sizeof(int),
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"neigh:ex2_group");
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memory->grow(ex1_group,maxex_group,"neigh:ex1_group");
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memory->grow(ex2_group,maxex_group,"neigh:ex2_group");
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}
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ex1_group[nex_group] = group->find(arg[iarg+2]);
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ex2_group[nex_group] = group->find(arg[iarg+3]);
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@ -1518,9 +1510,7 @@ void Neighbor::modify_params(int narg, char **arg)
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}
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if (nex_mol == maxex_mol) {
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maxex_mol += EXDELTA;
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ex_mol_group =
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(int *) memory->srealloc(ex_mol_group,maxex_mol*sizeof(int),
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"neigh:ex_mol_group");
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memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
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}
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ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
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if (ex_mol_group[nex_mol] == -1)
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