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anticipate the upcoming 23 oct 2015 patch

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This commit is contained in:
Axel Kohlmeyer
2015-10-22 19:52:03 -04:00
parent d75b4730d9
commit 09187ebabd
78 changed files with 584 additions and 1534 deletions
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30
src/atom.cpp
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@ -950,7 +950,8 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2;
@ -966,6 +967,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset)
atom1 += id_offset;
atom2 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
@ -1001,7 +1003,8 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset)
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3;
@ -1018,6 +1021,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset)
atom2 += id_offset;
atom3 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
@ -1068,7 +1072,8 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset)
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1087,6 +1092,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset)
atom3 += id_offset;
atom4 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
@ -1153,7 +1159,8 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset)
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1172,6 +1179,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset)
atom3 += id_offset;
atom4 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
@ -1496,17 +1504,17 @@ void Atom::add_molecule(int narg, char **arg)
if (find_molecule(arg[0]) >= 0)
error->all(FLERR,"Reuse of molecule template ID");
// may over-allocate if not all args are mol files, but OK for srealloc
molecules = (Molecule **)
memory->srealloc(molecules,(nmolecule+narg-1)*sizeof(Molecule *),
"atom::molecules");
// 1st molecule in set stores nset = # of mols, others store nset = 0
// ifile = count of molecules in set
// index = argument index where next molecule starts, updated by constructor
int ifile = 1;
int index = 1;
while (1) {
molecules[nmolecule] = new Molecule(lmp,narg,arg,ifile);
molecules = (Molecule **)
memory->srealloc(molecules,(nmolecule+1)*sizeof(Molecule *),
"atom::molecules");
molecules[nmolecule] = new Molecule(lmp,narg,arg,index);
molecules[nmolecule]->nset = 0;
molecules[nmolecule-ifile+1]->nset++;
nmolecule++;