diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 4e216828d3..4f4cda32e5 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages ` *Bonds defined but no bond types* The data file header lists bonds but no bond types. -*Bond/react: Cannot use fix bond/react with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom_style - template does not qualify. - -*Bond/react: Invalid template atom ID in map file* - Atom IDs in molecule templates range from 1 to the number of atoms in the template. - -*Bond/react: Rmax cutoff is longer than pairwise cutoff* - This is not allowed because bond creation is done using the pairwise - neighbor list. - -*Bond/react: Molecule template ID for fix bond/react does not exist* - A valid molecule template must have been created with the molecule - command. - -*Bond/react: Reaction templates must contain the same number of atoms* - There should be a one-to-one correspondence between atoms in the - pre-reacted and post-reacted templates, as specified by the map file. - -*Bond/react: Unknown section in map file* - Please ensure reaction map files are properly formatted. - -*Bond/react: Atom/Bond type 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 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 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. - -*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* - Self-explanatory. - -*Bond/react: First neighbors of chiral atoms must be of mutually different types* - Self-explanatory. - -*Bond/react: Chiral atoms must have exactly four first neighbors* - Self-explanatory. - -*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword* - The coordinates of atoms in the pre-reacted template are used to determine - chirality. - -*Bond/react special bond generation overflow* - The number of special bonds per-atom created by a reaction exceeds the - system setting. See the read_data or create_box command for how to - specify this value. - -*Bond/react topology/atom exceed system topology/atom* - The number of bonds, angles etc per-atom created by a reaction exceeds - the system setting. See the read_data or create_box command for how to - specify this value. - *Both restart files must use % or neither* Self-explanatory. @@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages ` acquire needed info, The comm_modify cutoff command can be used to extend the communication range. +*Fix bond/react: Cannot use fix bond/react with non-molecular systems* + Only systems with bonds that can be changed can be used. Atom_style + template does not qualify. + +*Fix bond/react: Invalid template atom ID in map file* + Atom IDs in molecule templates range from 1 to the number of atoms in the template. + +*Fix bond/react: Rmax cutoff is longer than pairwise cutoff* + This is not allowed because bond creation is done using the pairwise + neighbor list. + +*Fix bond/react: Molecule template ID for fix bond/react does not exist* + A valid molecule template must have been created with the molecule + command. + +*Fix bond/react: Reaction templates must contain the same number of atoms* + There should be a one-to-one correspondence between atoms in the + pre-reacted and post-reacted templates, as specified by the map file. + +*Fix bond/react: Unknown section in map file* + Please ensure reaction map files are properly formatted. + +*Fix bond/react: Atom/Bond type 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 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. + +*Fix bond/react: Fix bond/react needs ghost atoms from farther away* + 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. + +*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* + Self-explanatory. + +*Fix bond/react: First neighbors of chiral atoms must be of mutually different types* + Self-explanatory. + +*Fix bond/react: Chiral atoms must have exactly four first neighbors* + Self-explanatory. + +*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword* + The coordinates of atoms in the pre-reacted template are used to determine + chirality. + +*Fix bond/react special bond generation overflow* + The number of special bonds per-atom created by a reaction exceeds the + system setting. See the read_data or create_box command for how to + specify this value. + +*Fix bond/react topology/atom exceed system topology/atom* + The number of bonds, angles etc per-atom created by a reaction exceeds + the system setting. See the read_data or create_box command for how to + specify this value. + *Fix bond/swap cannot use dihedral or improper styles* These styles cannot be defined when using this fix.