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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3682 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-01-14 19:44:09 +00:00
parent cab0846444
commit 9cecf81520
3 changed files with 22 additions and 14 deletions
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30
src/atom.cpp
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@ -53,7 +53,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
extra_bond_per_atom = 0; extra_bond_per_atom = 0;
firstgroupname = NULL; firstgroupname = NULL;
sortfreq = 1000; sortfreq = 0;
//sortfreq = 1000;
userbinsize = 0.0; userbinsize = 0.0;
maxbin = maxnext = 0; maxbin = maxnext = 0;
binhead = NULL; binhead = NULL;
@ -353,13 +354,15 @@ void Atom::modify_params(int narg, char **arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) { } else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command"); if (iarg+2 > narg) error->all("Illegal atom_modify command");
if (strcmp(arg[iarg+1],"all") == 0) delete [] firstgroupname; if (strcmp(arg[iarg+1],"all") == 0) {
else { delete [] firstgroupname;
firstgroupname = NULL;
} else {
int n = strlen(arg[iarg+1]) + 1; int n = strlen(arg[iarg+1]) + 1;
firstgroupname = new char[n]; firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]); strcpy(firstgroupname,arg[iarg+1]);
sortfreq = 0;
} }
sortfreq = 0;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) { } else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+3 > narg) error->all("Illegal atom_modify command"); if (iarg+3 > narg) error->all("Illegal atom_modify command");
@ -1360,9 +1363,9 @@ void Atom::sort()
for (i = 0; i < nbins; i++) binhead[i] = -1; for (i = 0; i < nbins; i++) binhead[i] = -1;
for (i = nlocal-1; i >= 0; i--) { for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininv); ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininv); iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininv); iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininvz);
ix = MAX(ix,0); ix = MAX(ix,0);
iy = MAX(iy,0); iy = MAX(iy,0);
iz = MAX(iz,0); iz = MAX(iz,0);
@ -1439,7 +1442,7 @@ void Atom::setup_sort_bins()
else binsize = 0.5 * neighbor->cutneighmax; else binsize = 0.5 * neighbor->cutneighmax;
if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0"); if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0");
bininv = 1.0/binsize; double bininv = 1.0/binsize;
// nbin xyz = local bins // nbin xyz = local bins
// bbox lo/hi = bounding box of my sub-domain // bbox lo/hi = bounding box of my sub-domain
@ -1458,10 +1461,15 @@ void Atom::setup_sort_bins()
nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv); nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv); nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv); nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
if (domain->dimension == 2) nbinz = 1;
nbinx = MAX(nbinx,1); if (nbinx == 0) nbinx = 1;
nbinx = MAX(nbiny,1); if (nbiny == 0) nbiny = 1;
nbinx = MAX(nbinz,1); if (nbinz == 0) nbinz = 1;
bininvx = nbinx / (bboxhi[0]-bboxlo[0]);
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
if (1.0*nbinx*nbiny*nbinz > INT_MAX) if (1.0*nbinx*nbiny*nbinz > INT_MAX)
error->one("Too many atom sorting bins"); error->one("Too many atom sorting bins");

4
src/atom.h
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@ -203,8 +203,8 @@ class Atom : protected Pointers {
int *binhead; // 1st atom in each bin int *binhead; // 1st atom in each bin
int *next; // next atom in bin int *next; // next atom in bin
int *permute; // permutation vector int *permute; // permutation vector
double userbinsize; // sorting bin size double userbinsize; // requested sort bin size
double bininv; double bininvx,bininvy,bininvz; // inverse actual bin sizes
double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain
int memlength; // allocated size of memstr int memlength; // allocated size of memstr

2
src/universe.cpp
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@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp) Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
{ {
version = (char *) "7 Jul 2009"; version = (char *) "15 Jan 2010";
uworld = communicator; uworld = communicator;
MPI_Comm_rank(uworld,&me); MPI_Comm_rank(uworld,&me);