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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3674 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-01-13 20:55:06 +00:00
parent 363e6c371f
commit 1dbad849b7
7 changed files with 39 additions and 29 deletions
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35
src/atom.cpp
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@ -52,6 +52,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
extra_bond_per_atom = 0;
firstgroupname = NULL;
sortfreq = 0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// initialize atom arrays
// customize by adding new array
@ -110,13 +114,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nextra_store = 0;
extra = NULL;
// sorting
sortflag = 0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// default mapping values and hash table primes
tag_enable = 1;
@ -146,7 +143,11 @@ Atom::~Atom()
{
delete [] atom_style;
delete avec;
delete [] firstgroupname;
memory->sfree(binhead);
memory->sfree(next);
memory->sfree(permute);
// delete atom arrays
// customize by adding new array
@ -211,12 +212,6 @@ Atom::~Atom()
delete [] dipole;
delete [] dipole_setflag;
// delete sorting arrays
memory->sfree(binhead);
memory->sfree(next);
memory->sfree(permute);
// delete extra arrays
memory->sfree(extra_grow);
@ -315,7 +310,7 @@ void Atom::setup()
// setup for sorting
// binsize = user setting or 1/2 of neighbor cutoff
if (sortflag) {
if (sortfreq > 0) {
double binsize;
if (userbinsize > 0.0) binsize = userbinsize;
else binsize = 0.5 * neighbor->cutneighmax;
@ -341,6 +336,8 @@ int Atom::style_match(const char *style)
/* ----------------------------------------------------------------------
modify parameters of the atom style
some options can only be invoked before simulation box is defined
first and sort options cannot be used together
------------------------------------------------------------------------- */
void Atom::modify_params(int narg, char **arg)
@ -354,6 +351,8 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all("Illegal atom_modify command");
if (domain->box_exist)
error->all("Atom_modify map command after simulation box is defined");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
@ -363,6 +362,7 @@ void Atom::modify_params(int narg, char **arg)
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
}
sortfreq = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+3 > narg) error->all("Illegal atom_modify command");
@ -370,8 +370,9 @@ void Atom::modify_params(int narg, char **arg)
userbinsize = atof(arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
error->all("Illegal atom_modify command");
if (sortfreq == 0) sortflag = 0;
else sortflag = 1;
if (sortfreq >= 0 && firstgroupname)
error->all("Atom_modify sort and first options "
"cannot be used together");
iarg += 3;
} else error->all("Illegal atom_modify command");
}
@ -1370,7 +1371,7 @@ void Atom::sort()
permute = (int *) memory->smalloc(maxnext*sizeof(int),"atom:permute");
}
// insure one extra location at end of atom arrays
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);