Loading doc/src/Errors_messages.rst +2 −2 Original line number Diff line number Diff line Loading @@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` *Bond/react: Atom affected by reaction too close to template edge* This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. *Bond/react: Fix bond/react needs ghost atoms from farther away* This is because a processor needs to superimpose the entire unreacted This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm\_modify cutoff command can be used to extend the communication range. Loading src/USER-REACTION/fix_bond_react.h +8 −9 Original line number Diff line number Diff line Loading @@ -239,18 +239,17 @@ Atom IDs in molecule templates range from 1 to the number of atoms in the templa E or W: Bond/react: Atom affected by reaction %s too close to template edge This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. E: Bond/react: Fix bond/react needs ghost atoms from farther away This is because a processor needs to superimpose the entire unreacted molecule template onto simulation atoms it knows about. The comm_modify cutoff command can be used to extend the communication range. This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm_modify cutoff command can be used to extend the communication range. E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted Loading Loading
doc/src/Errors_messages.rst +2 −2 Original line number Diff line number Diff line Loading @@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` *Bond/react: Atom affected by reaction too close to template edge* This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. *Bond/react: Fix bond/react needs ghost atoms from farther away* This is because a processor needs to superimpose the entire unreacted This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm\_modify cutoff command can be used to extend the communication range. Loading
src/USER-REACTION/fix_bond_react.h +8 −9 Original line number Diff line number Diff line Loading @@ -239,18 +239,17 @@ Atom IDs in molecule templates range from 1 to the number of atoms in the templa E or W: Bond/react: Atom affected by reaction %s too close to template edge This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. E: Bond/react: Fix bond/react needs ghost atoms from farther away This is because a processor needs to superimpose the entire unreacted molecule template onto simulation atoms it knows about. The comm_modify cutoff command can be used to extend the communication range. This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm_modify cutoff command can be used to extend the communication range. E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted Loading
