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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
	src/MISC/fix_efield.cpp
	src/fix_addforce.cpp
	src/fix_move.cpp
	src/fix_setforce.cpp
This commit is contained in:
Axel Kohlmeyer
2014-05-08 08:49:17 -04:00
parent fc62bdc5cb cf0cd2e912
commit 4acacd8e3b
61 changed files with 224 additions and 287 deletions
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47
src/atom.cpp
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@ -330,17 +330,12 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
// create instance of AtomVec
// use grow() to initialize atom-based arrays to length 1
// so that x[0][0] can always be referenced even if proc has no atoms
// but reset nmax = 0
// so 2d arrays like bond_type will later be allocated correctly
// since currently, 2nd dimension bond_per_atom = 0
int sflag;
avec = new_avec(style,suffix,sflag);
avec->store_args(narg,arg);
avec->process_args(narg,arg);
avec->grow(1);
nmax = 0;
avec->reset();
if (sflag) {
char estyle[256];
@ -640,6 +635,48 @@ int Atom::count_words(const char *line)
return n;
}
/* ----------------------------------------------------------------------
deallocate molecular topology arrays
done before realloc with (possibly) new 2nd dimension set to
correctly initialized per-atom values, e.g. bond_per_atom
needs to be called whenever 2nd dimensions are changed
and these arrays are already pre-allocated,
e.g. due to grow(1) in create_avec()
------------------------------------------------------------------------- */
void Atom::deallocate_topology()
{
memory->destroy(atom->bond_type);
memory->destroy(atom->bond_atom);
atom->bond_type = NULL;
atom->bond_atom = NULL;
memory->destroy(atom->angle_type);
memory->destroy(atom->angle_atom1);
memory->destroy(atom->angle_atom2);
memory->destroy(atom->angle_atom3);
atom->angle_type = NULL;
atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
memory->destroy(atom->dihedral_type);
memory->destroy(atom->dihedral_atom1);
memory->destroy(atom->dihedral_atom2);
memory->destroy(atom->dihedral_atom3);
memory->destroy(atom->dihedral_atom4);
atom->dihedral_type = NULL;
atom->dihedral_atom1 = atom->dihedral_atom2 =
atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
memory->destroy(atom->improper_type);
memory->destroy(atom->improper_atom1);
memory->destroy(atom->improper_atom2);
memory->destroy(atom->improper_atom3);
memory->destroy(atom->improper_atom4);
atom->improper_type = NULL;
atom->improper_atom1 = atom->improper_atom2 =
atom->improper_atom3 = atom->improper_atom4 = NULL;
}
/* ----------------------------------------------------------------------
unpack n lines from Atom section of data file
call style-specific routine to parse line