ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Updating to master, misc style changes

Browse Source
This commit is contained in:
Joel Clemmer
2021-04-07 17:21:16 -06:00
parent d54384dd91
commit bd6dd658d6
17 changed files with 112 additions and 112 deletions
Download Patch File Download Diff File Expand all files Collapse all files

98
src/neighbor.cpp
View File

@ -359,16 +359,16 @@ void Neighbor::init()
cutneighmaxsq = cutneighmax * cutneighmax;
// Define cutoffs for multi
if(style == Neighbor::MULTI){
if (style == Neighbor::MULTI) {
int icollection, jcollection;
// If collections not yet defined, create default map using types
if(not custom_collection_flag) {
if (not custom_collection_flag) {
ncollections = n;
interval_collection_flag = 0;
if(not type2collection)
if (not type2collection)
memory->create(type2collection,n+1,"neigh:type2collection");
for(i = 1; i <= n; i++)
for (i = 1; i <= n; i++)
type2collection[i] = i-1;
}
@ -384,30 +384,30 @@ void Neighbor::init()
//
// Define collection cutoffs
for(i = 0; i < ncollections; i++)
for(j = 0; j < ncollections; j++)
for (i = 0; i < ncollections; i++)
for (j = 0; j < ncollections; j++)
cutcollectionsq[i][j] = 0.0;
if(not interval_collection_flag){
if (not interval_collection_flag) {
finite_cut_flag = 0;
for(i = 1; i <= n; i++){
for (i = 1; i <= n; i++){
icollection = type2collection[i];
for(j = 1; j <= n; j++){
for (j = 1; j <= n; j++){
jcollection = type2collection[j];
if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
cutcollectionsq[icollection][jcollection] = cutneighsq[i][j];
cutcollectionsq[jcollection][icollection] = cutneighsq[i][j];
}
}
}
} else {
if(force->pair->finitecutflag){
if (force->pair->finitecutflag) {
finite_cut_flag = 1;
// If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs
double ri, rj, tmp;
for(i = 0; i < ncollections; i++){
for (i = 0; i < ncollections; i++){
ri = collection2cut[i]*0.5;
for(j = 0; j < ncollections; j++){
for (j = 0; j < ncollections; j++){
rj = collection2cut[j]*0.5;
tmp = force->pair->radii2cut(ri, rj) + skin;
cutcollectionsq[i][j] = tmp*tmp;
@ -417,33 +417,33 @@ void Neighbor::init()
finite_cut_flag = 0;
// Map types to collections
if(not type2collection)
if (not type2collection)
memory->create(type2collection,n+1,"neigh:type2collection");
for(i = 1; i <= n; i++)
for (i = 1; i <= n; i++)
type2collection[i] = -1;
double cuttmp;
for(i = 1; i <= n; i++){
for (i = 1; i <= n; i++){
// Remove skin added to cutneighsq
cuttmp = sqrt(cutneighsq[i][i]) - skin;
for(icollection = 0; icollection < ncollections; icollection ++){
if(collection2cut[icollection] >= cuttmp) {
for (icollection = 0; icollection < ncollections; icollection ++){
if (collection2cut[icollection] >= cuttmp) {
type2collection[i] = icollection;
break;
}
}
if(type2collection[i] == -1)
if (type2collection[i] == -1)
error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi");
}
// Define cutoffs
for(i = 1; i <= n; i++){
for (i = 1; i <= n; i++){
icollection = type2collection[i];
for(j = 1; j <= n; j++){
for (j = 1; j <= n; j++){
jcollection = type2collection[j];
if(cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
cutcollectionsq[icollection][jcollection] = cutneighsq[i][j];
cutcollectionsq[jcollection][icollection] = cutneighsq[i][j];
}
@ -2175,7 +2175,7 @@ void Neighbor::build(int topoflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
// rebuild collection array from scratch
if(style == Neighbor::MULTI) build_collection(0);
if (style == Neighbor::MULTI) build_collection(0);
// check that using special bond flags will not overflow neigh lists
@ -2500,15 +2500,15 @@ void Neighbor::modify_params(int narg, char **arg)
} else error->all(FLERR,"Illegal neigh_modify command");
} else if (strcmp(arg[iarg],"collection/interval") == 0) {
if(style != Neighbor::MULTI)
if (style != Neighbor::MULTI)
error->all(FLERR,"Cannot use collection/interval command without multi setting");
if(iarg+2 > narg)
if (iarg+2 > narg)
error->all(FLERR,"Invalid collection/interval command");
ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if(ncollections < 1)
if (ncollections < 1)
error->all(FLERR,"Invalid collection/interval command");
if(iarg+1+ncollections > narg)
if (iarg+1+ncollections > narg)
error->all(FLERR,"Invalid collection/interval command");
int ntypes = atom->ntypes;
@ -2521,26 +2521,26 @@ void Neighbor::modify_params(int narg, char **arg)
// Set upper cutoff for each collection
char *id;
double cut_interval;
for(i = 0; i < ncollections; i++){
for (i = 0; i < ncollections; i++){
cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp);
collection2cut[i] = cut_interval;
if(i != 0)
if(collection2cut[i-1] >= collection2cut[i])
if (i != 0)
if (collection2cut[i-1] >= collection2cut[i])
error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting");
}
iarg += 2 + ncollections;
} else if (strcmp(arg[iarg],"collection/type") == 0) {
if(style != Neighbor::MULTI)
if (style != Neighbor::MULTI)
error->all(FLERR,"Cannot use collection/type command without multi setting");
if(iarg+2 > narg)
if (iarg+2 > narg)
error->all(FLERR,"Invalid collection/type command");
ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if(ncollections < 1)
if (ncollections < 1)
error->all(FLERR,"Invalid collection/interval command");
if(iarg+1+ncollections > narg)
if (iarg+1+ncollections > narg)
error->all(FLERR,"Invalid collection/type command");
int ntypes = atom->ntypes;
@ -2548,17 +2548,17 @@ void Neighbor::modify_params(int narg, char **arg)
interval_collection_flag = 0;
custom_collection_flag = 1;
if(not type2collection)
if (not type2collection)
memory->create(type2collection,ntypes+1,"neigh:type2collection");
// Erase previous mapping
for(i = 1; i <= ntypes; i++)
for (i = 1; i <= ntypes; i++)
type2collection[i] = -1;
// For each custom range, define mapping for types in interval
int nfield;
char *str;
for(i = 0; i < ncollections; i++){
for (i = 0; i < ncollections; i++){
n = strlen(arg[iarg+2+i]) + 1;
str = new char[n];
strcpy(str,arg[iarg+2+i]);
@ -2570,7 +2570,7 @@ void Neighbor::modify_params(int narg, char **arg)
utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error);
for (k = nlo; k <= nhi; k++) {
if(type2collection[k] != -1)
if (type2collection[k] != -1)
error->all(FLERR,"Type specified more than once in collection/type commnd");
type2collection[k] = i;
}
@ -2580,8 +2580,8 @@ void Neighbor::modify_params(int narg, char **arg)
}
// Check for undefined atom type
for(i = 1; i <= ntypes; i++){
if(type2collection[i] == -1){
for (i = 1; i <= ntypes; i++){
if (type2collection[i] == -1) {
error->all(FLERR,"Type missing in collection/type commnd");
}
}
@ -2632,8 +2632,8 @@ int Neighbor::exclude_setting()
int Neighbor::any_full()
{
int any_full = 0;
for(int i = 0; i < old_nrequest; i++) {
if(old_requests[i]->full) any_full = 1;
for (int i = 0; i < old_nrequest; i++) {
if (old_requests[i]->full) any_full = 1;
}
return any_full;
}
@ -2648,31 +2648,31 @@ void Neighbor::build_collection(int istart)
error->all(FLERR, "Cannot define atom collections without neighbor style multi");
int nmax = atom->nlocal+atom->nghost;
if(nmax > nmax_collection){
if (nmax > nmax_collection) {
nmax_collection = nmax+DELTA_PERATOM;
memory->grow(collection, nmax_collection, "neigh:collection");
}
if(finite_cut_flag){
if (finite_cut_flag) {
double cut;
int icollection;
for(int i = istart; i < nmax; i++){
for (int i = istart; i < nmax; i++){
cut = force->pair->atom2cut(i);
collection[i] = -1;
for(icollection = 0; icollection < ncollections; icollection++){
if(collection2cut[icollection] >= cut) {
for (icollection = 0; icollection < ncollections; icollection++){
if (collection2cut[icollection] >= cut) {
collection[i] = icollection;
break;
}
}
if(collection[i] == -1)
if (collection[i] == -1)
error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi");
}
} else {
int *type = atom->type;
for(int i = istart; i < nmax; i++){
for (int i = istart; i < nmax; i++){
collection[i] = type2collection[type[i]];
}
}