109 lines
3.8 KiB
ReStructuredText
109 lines
3.8 KiB
ReStructuredText
.. index:: labelmap
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labelmap command
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==================
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Syntax
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""""""
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.. code-block:: LAMMPS
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labelmap option args
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* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
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.. parsed-literal::
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*clear* = no args
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*write* arg = filename
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*atom* or *bond* or *angle* or *dihedral* or *improper*
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args = list of one or more numeric-type/type-label pairs
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Examples
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""""""""
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.. code-block:: LAMMPS
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labelmap atom 1 c1 2 hc 3 cp 4 nt
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labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
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labelmap atom $(label2type(atom,carbon)) C # change type label from 'carbon' to 'C'
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labelmap clear
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labelmap write mymap.include
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labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
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Description
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"""""""""""
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.. versionadded:: 15Sep2022
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Define alphanumeric type labels to associate with one or more numeric
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atom, bond, angle, dihedral or improper types. A collection of type
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labels for all atom types, bond types, etc. is stored as a label map.
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The label map can also be defined by the :doc:`read_data <read_data>`
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command when it reads these sections in a data file: Atom Type Labels,
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Bond Type Labels, etc. See the :doc:`Howto type labels
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<Howto_type_labels>` doc page for a general discussion of how type
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labels can be used. See :ref:`(Gissinger) <Typelabel1>` for a
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discussion of the type label implementation in LAMMPS and its uses.
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Valid type labels can contain any alphanumeric character, but must not
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start with a number, a '#', or a '*' character. They can contain other
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standard ASCII characters such as angular or square brackets '<' and '>'
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or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
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'+' and equals '=' signs and more. They must not contain blanks or any
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other whitespace. Note that type labels must be put in single or double
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quotation marks if they contain the '#' character or if they contain a
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double (") or single quotation mark ('). If the label contains both
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a single and a double quotation mark, then triple quotation (""") must
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be used. When enclosing a type label with quotation marks, the
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LAMMPS input parser may require adding leading or trailing blanks
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around the type label so it can identify the enclosing quotation
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marks. Those blanks will be removed when defining the label.
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A *labelmap* command can only modify the label map for one type-kind
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(atom types, bond types, etc). Any number of numeric-type/type-label
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pairs may follow. If a type label already exists for the same numeric
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type, it will be overwritten. Type labels must be unique; assigning the
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same type label to multiple numeric types within the same type-kind is
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not allowed. When reading and writing data files, it is required that
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there is a label defined for *every* numeric type within a given
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type-kind in order to write out the type label section for that
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type-kind.
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The *clear* option resets the label map and thus discards all previous
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settings.
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The *write* option takes a filename as argument and writes the current
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label mappings to a file as a sequence of *labelmap* commands, so the
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file can be copied into a new LAMMPS input file or read in using the
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:doc:`include <include>` command.
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----------
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Restrictions
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""""""""""""
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This command must come after the simulation box is defined by a
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:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
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:doc:`create_box <create_box>` command.
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Label maps are currently not supported when using the KOKKOS package.
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Related commands
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""""""""""""""""
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:doc:`read_data <read_data>`, :doc:`write_data <write_data>`,
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:doc:`molecule <molecule>`, :doc:`fix bond/react <fix_bond_react>`
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Default
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"""""""
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none
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-----------
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.. _Typelabel1:
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**(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).
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