diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 5d6349a426070f5fb2b03ae53a4beb4bf4e937a7..8f71cd14ec7c4a405cd6f752db30ba7b37100e14 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -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. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index de602063043994fd581fd38fc9b10eca9520f759..aab1dc12f8d9cb60ac39deda779de518bd7fdfed 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -507,6 +507,7 @@ deepskyblue defgrad deformable del +deleteIDs Dellago delocalization delocalized diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index 50efca8d097df34ba7c3016ea823eee7f2e540ed..600bb6a5405c8749a219429bff80ee90fd4ca4f0 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -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"); } } }