Loading doc/src/fix_bond_react.txt +1 −1 Original line number Diff line number Diff line Loading @@ -318,7 +318,7 @@ unwanted by-products. Therefore, bond/react provides the option to delete a user-specified set of atoms. These pre-reaction atoms are identified in the map file. A deleted atom must still be included in the post-reaction molecule template, in which it cannot be bonded to an undeleted atom. In addition to deleting unwanted reaction an atom that is not deleted. In addition to deleting unwanted reaction by-products, this feature can be used to remove specific topologies, such as small rings, that may be otherwise indistinguishable. Loading doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -507,6 +507,7 @@ deepskyblue defgrad deformable del deleteIDs Dellago delocalization delocalized Loading src/USER-MISC/fix_bond_react.cpp +2 −2 Original line number Diff line number Diff line Loading @@ -1653,13 +1653,13 @@ void FixBondReact::find_landlocked_atoms(int myrxn) } } // additionally, if a deleted atom is bonded to a undeleted atom, bad // additionally, if a deleted atom is bonded to an atom that is not deleted, bad for (int i = 0; i < onemol->natoms; i++) { if (delete_atoms[i][myrxn] == 1) { int ii = reverse_equiv[i][1][myrxn] - 1; for (int j = 0; j < twomol_nxspecial[ii][0]; j++) { if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) { error->one(FLERR,"A deleted atom cannot be bonded to an undeleted atom"); error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted"); } } } Loading Loading
doc/src/fix_bond_react.txt +1 −1 Original line number Diff line number Diff line Loading @@ -318,7 +318,7 @@ unwanted by-products. Therefore, bond/react provides the option to delete a user-specified set of atoms. These pre-reaction atoms are identified in the map file. A deleted atom must still be included in the post-reaction molecule template, in which it cannot be bonded to an undeleted atom. In addition to deleting unwanted reaction an atom that is not deleted. In addition to deleting unwanted reaction by-products, this feature can be used to remove specific topologies, such as small rings, that may be otherwise indistinguishable. Loading
doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -507,6 +507,7 @@ deepskyblue defgrad deformable del deleteIDs Dellago delocalization delocalized Loading
src/USER-MISC/fix_bond_react.cpp +2 −2 Original line number Diff line number Diff line Loading @@ -1653,13 +1653,13 @@ void FixBondReact::find_landlocked_atoms(int myrxn) } } // additionally, if a deleted atom is bonded to a undeleted atom, bad // additionally, if a deleted atom is bonded to an atom that is not deleted, bad for (int i = 0; i < onemol->natoms; i++) { if (delete_atoms[i][myrxn] == 1) { int ii = reverse_equiv[i][1][myrxn] - 1; for (int j = 0; j < twomol_nxspecial[ii][0]; j++) { if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) { error->one(FLERR,"A deleted atom cannot be bonded to an undeleted atom"); error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted"); } } } Loading
