Update Errors_messages.rst
This commit is contained in:
Jacob Gissinger
@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Bonds defined but no bond types*
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*Bonds defined but no bond types*
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The data file header lists bonds but no bond types.
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The data file header lists bonds but no bond types.
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*Bond/react: Cannot use fix bond/react with non-molecular systems*
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Only systems with bonds that can be changed can be used. Atom_style
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template does not qualify.
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*Bond/react: Invalid template atom ID in map file*
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Atom IDs in molecule templates range from 1 to the number of atoms in the template.
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*Bond/react: Rmax cutoff is longer than pairwise cutoff*
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This is not allowed because bond creation is done using the pairwise
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neighbor list.
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*Bond/react: Molecule template ID for fix bond/react does not exist*
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A valid molecule template must have been created with the molecule
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command.
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*Bond/react: Reaction templates must contain the same number of atoms*
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There should be a one-to-one correspondence between atoms in the
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pre-reacted and post-reacted templates, as specified by the map file.
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*Bond/react: Unknown section in map file*
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Please ensure reaction map files are properly formatted.
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*Bond/react: Atom/Bond type affected by reaction too close to template edge*
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This means an atom which changes type or connectivity during the
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reaction is too close to an 'edge' atom defined in the map
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file. This could cause incorrect assignment of bonds, angle, etc.
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Generally, this means you must include more atoms in your templates,
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such that there are at least two atoms between each atom involved in
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the reaction and an edge atom.
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*Bond/react: Fix bond/react needs ghost atoms from farther away*
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This is because a processor needs to map the entire unreacted
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molecule template onto simulation atoms it knows about. The
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comm_modify cutoff command can be used to extend the communication
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range.
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*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
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Self-explanatory.
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*Bond/react: First neighbors of chiral atoms must be of mutually different types*
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Self-explanatory.
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*Bond/react: Chiral atoms must have exactly four first neighbors*
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Self-explanatory.
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*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
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The coordinates of atoms in the pre-reacted template are used to determine
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chirality.
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*Bond/react special bond generation overflow*
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The number of special bonds per-atom created by a reaction exceeds the
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system setting. See the read_data or create_box command for how to
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specify this value.
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*Bond/react topology/atom exceed system topology/atom*
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The number of bonds, angles etc per-atom created by a reaction exceeds
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the system setting. See the read_data or create_box command for how to
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specify this value.
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*Both restart files must use % or neither*
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*Both restart files must use % or neither*
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Self-explanatory.
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Self-explanatory.
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@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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acquire needed info, The comm_modify cutoff command can be used to
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acquire needed info, The comm_modify cutoff command can be used to
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extend the communication range.
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extend the communication range.
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*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
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Only systems with bonds that can be changed can be used. Atom_style
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template does not qualify.
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*Fix bond/react: Invalid template atom ID in map file*
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Atom IDs in molecule templates range from 1 to the number of atoms in the template.
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*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
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This is not allowed because bond creation is done using the pairwise
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neighbor list.
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*Fix bond/react: Molecule template ID for fix bond/react does not exist*
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A valid molecule template must have been created with the molecule
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command.
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*Fix bond/react: Reaction templates must contain the same number of atoms*
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There should be a one-to-one correspondence between atoms in the
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pre-reacted and post-reacted templates, as specified by the map file.
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*Fix bond/react: Unknown section in map file*
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Please ensure reaction map files are properly formatted.
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*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
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This means an atom which changes type or connectivity during the
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reaction is too close to an 'edge' atom defined in the map
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file. This could cause incorrect assignment of bonds, angle, etc.
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Generally, this means you must include more atoms in your templates,
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such that there are at least two atoms between each atom involved in
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the reaction and an edge atom.
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*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
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This is because a processor needs to map the entire unreacted
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molecule template onto simulation atoms it knows about. The
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comm_modify cutoff command can be used to extend the communication
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range.
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*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
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Self-explanatory.
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*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
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Self-explanatory.
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*Fix bond/react: Chiral atoms must have exactly four first neighbors*
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Self-explanatory.
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*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
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The coordinates of atoms in the pre-reacted template are used to determine
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chirality.
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*Fix bond/react special bond generation overflow*
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The number of special bonds per-atom created by a reaction exceeds the
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system setting. See the read_data or create_box command for how to
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specify this value.
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*Fix bond/react topology/atom exceed system topology/atom*
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The number of bonds, angles etc per-atom created by a reaction exceeds
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the system setting. See the read_data or create_box command for how to
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specify this value.
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*Fix bond/swap cannot use dihedral or improper styles*
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*Fix bond/swap cannot use dihedral or improper styles*
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These styles cannot be defined when using this fix.
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These styles cannot be defined when using this fix.
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