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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
Download Patch File Download Diff File Expand all files Collapse all files

98
src/compute_centro_atom.cpp
View File

@ -5,7 +5,7 @@
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
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.
@ -38,7 +38,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute centro/atom command");
if (strcmp(arg[3],"fcc") == 0) nnn = 12;
else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
else nnn = atoi(arg[3]);
@ -69,7 +69,7 @@ ComputeCentroAtom::~ComputeCentroAtom()
void ComputeCentroAtom::init()
{
if (force->pair == NULL)
if (force->pair == NULL)
error->all(FLERR,"Compute centro/atom requires a pair style be defined");
int count = 0;
@ -148,11 +148,11 @@ void ComputeCentroAtom::compute_peratom()
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
memory->destroy(distsq);
memory->destroy(nearest);
maxneigh = jnum;
memory->create(distsq,maxneigh,"centro/atom:distsq");
memory->create(nearest,maxneigh,"centro/atom:nearest");
memory->destroy(distsq);
memory->destroy(nearest);
maxneigh = jnum;
memory->create(distsq,maxneigh,"centro/atom:distsq");
memory->create(nearest,maxneigh,"centro/atom:nearest");
}
// loop over list of all neighbors within force cutoff
@ -161,24 +161,24 @@ void ComputeCentroAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
}
// if not nnn neighbors, centro = 0.0
if (n < nnn) {
centro[i] = 0.0;
continue;
centro[i] = 0.0;
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
@ -190,14 +190,14 @@ void ComputeCentroAtom::compute_peratom()
n = 0;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
pairs[n++] = delx*delx + dely*dely + delz*delz;
}
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
pairs[n++] = delx*delx + dely*dely + delz*delz;
}
}
// store nhalf smallest pair distances in 1st nhalf locations of pairs
@ -235,29 +235,29 @@ void ComputeCentroAtom::select(int k, int n, double *arr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
@ -281,8 +281,8 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
return;
} else {
@ -290,27 +290,27 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
ISWAP(iarr[l+1],iarr[ir])
SWAP(arr[l+1],arr[ir])
ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
ISWAP(iarr[l],iarr[l+1])
SWAP(arr[l],arr[l+1])
ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
ISWAP(iarr[i],iarr[j])
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;