labelmap command — LAMMPS documentation

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# labelmap command

## Syntax

    labelmap option args

- option = atom or bond or angle or dihedral or improper or clear or write

      clear = no args
      write arg = filename
      atom or bond or angle or dihedral or improper
        args = list of one or more numeric-type/type-label pairs

## Examples

    labelmap atom 1 c1 2 hc 3 cp 4 nt
    labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
    labelmap atom $(label2type(atom,carbon)) C  # change type label from 'carbon' to 'C'
    labelmap clear
    labelmap write mymap.include
    labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """

## Description

Added in version 15Sep2022.

Define alphanumeric type labels to associate with one or more numeric atom, bond, angle, dihedral or improper types. A collection of type labels for all atom types, bond types, etc. is stored as a label map.

The label map can also be defined by the read_data command when it reads these sections in a data file: Atom Type Labels, Bond Type Labels, etc. See the Howto type labels doc page for a general discussion of how type labels can be used. See (Gissinger) for a discussion of the type label implementation in LAMMPS and its uses.

Valid type labels can contain any alphanumeric character, but must not start with a number, a ‘#’, or a ‘*’ character. They can contain other standard ASCII characters such as angular or square brackets ‘<’ and ‘>’ or ‘[’ and ‘]’, parenthesis ‘(’ and ‘)’, dash ‘-’, underscore ‘_’, plus ‘+’ and equals ‘=’ signs and more. They must not contain blanks or any other whitespace. Note that type labels must be put in single or double quotation marks if they contain the ‘#’ character or if they contain a double (”) or single quotation mark (‘). If the label contains both a single and a double quotation mark, then triple quotation (“””) must be used. When enclosing a type label with quotation marks, the LAMMPS input parser may require adding leading or trailing blanks around the type label so it can identify the enclosing quotation marks. Those blanks will be removed when defining the label.

A labelmap command can only modify the label map for one type-kind (atom types, bond types, etc). Any number of numeric-type/type-label pairs may follow. If a type label already exists for the same numeric type, it will be overwritten. Type labels must be unique; assigning the same type label to multiple numeric types within the same type-kind is not allowed. When reading and writing data files, it is required that there is a label defined for every numeric type within a given type-kind in order to write out the type label section for that type-kind.

The clear option resets the label map and thus discards all previous settings.

The write option takes a filename as argument and writes the current label mappings to a file as a sequence of labelmap commands, so the file can be copied into a new LAMMPS input file or read in using the include command.

## Restrictions

This command must come after the simulation box is defined by a read_data, read_restart, or create_box command.

Label maps are currently not supported when using the KOKKOS package.

## Related commands

read_data, write_data, molecule, fix bond/react

## Default

none

(Gissinger) J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).