diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 2c86525cc7..f4858614ea 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -429,7 +429,7 @@ void CreateAtoms::add_single() coord = lamda; } else coord = xone; - // if atom is in my subbox, create it + // if atom/molecule is in my subbox, create it if (coord[0] >= sublo[0] && coord[0] < subhi[0] && coord[1] >= sublo[1] && coord[1] < subhi[1] && @@ -481,7 +481,7 @@ void CreateAtoms::add_random() zhi = MIN(zhi,domain->regions[nregion]->extent_zhi); } - // generate random positions for each new atom within bounding box + // generate random positions for each new atom/molecule within bounding box // iterate until atom is within region and triclinic simulation box // if final atom position is in my subbox, create it @@ -615,7 +615,7 @@ void CreateAtoms::add_lattice() if (style == REGION) if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue; - // test if atom is in my subbox + // test if atom/molecule position is in my subbox if (triclinic) { domain->x2lamda(x,lamda); diff --git a/src/force.cpp b/src/force.cpp index d9d299e968..23699fdb2a 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -568,6 +568,12 @@ void Force::set_special(int narg, char **arg) { if (narg == 0) error->all(FLERR,"Illegal special_bonds command"); + // defaults + + special_lj[1] = special_lj[2] = special_lj[3] = 0.0; + special_coul[1] = special_coul[2] = special_coul[3] = 0.0; + special_angle = special_dihedral = special_extra = 0; + int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg],"amber") == 0) {