edits to doc pages
This commit is contained in:
Steve Plimpton
@ -33,6 +33,7 @@ Settings howto
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:maxdepth: 1
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Howto_2d
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Howto_type_labels
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Howto_triclinic
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Howto_thermostat
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Howto_barostat
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125
doc/src/Howto_type_labels.rst
Normal file
125
doc/src/Howto_type_labels.rst
Normal file
@ -0,0 +1,125 @@
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Type labels
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===========
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Each atom in LAMMPS has an associated atom type. Likewise each bond,
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angle, dihedral, improper enumerated in a data file read by the
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:doc:`read_data <read_data>` command has a bond type, angle type, etc.
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By default, type values are integers from 1 to Ntypes, wherever they
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appear in LAMMPS input or output files. However, LAMMPS also has the
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option to use alphanumeric strings, called type labels, for these
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values in its input and output.
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This can be useful in various scenarios. For example, type labels can
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make inputs more readable and compatible with other inputs (e.g. data
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files, molecule template files read by the :doc:`molecule <molecule>`
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command), particularly if a force field uses alphanumeric atom types.
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See a list of other commands below which can use label types in
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interesting ways.
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A collection of one or more type labels for one category of types
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(atom types, bond types, etc) is stored as a "label map" which is
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simply a list of numeric types and associated type labels. Within a
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map, each type label must be unique. It can be assigned to only one
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numeric type. Not all numeric types need have a type label assigned.
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There can be mutliple label maps defined for a single type category,
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e.g. atom types. There is a default label map which has no mapID.
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Additional label maps each have a mapID, which is a string containing
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only alphanumeric characters and underscores.
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Valid type labels can contain any alphanumeric character, but cannot
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start with a number. They can also contain any of these characters:
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square brackets "[" and "]", dash "-", underscore "_", JAKE what other
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chars are allowed? Note that type labels cannot contain the symbols
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'#' or '*'.
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As explained below, for certain command in LAMMPS, it is useful to
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define type labels so that the atom types that make up a given bond,
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angle, dihedral, or improper can be deduced from the type label. A
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standard way to do that is to define the type label for the bond by
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enclosing the constituent atom types in square brackets. E.g. define
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a C-H bond with a type label "[C][H]".
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There are two ways to define label maps. One is via the
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:doc:`labelmap <labelmap>` command, which has an optional *mapID*
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keyword to allow creation of type labels in either a default map or an
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additional map with a mapID. The other is via the :doc:`read_data
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<read_data>` command. A data file can have sections such as Atom Type
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Labels, Bond Type Lables, etc, which associate type labels with
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numeric types. Only default label maps can be defined in this manner.
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If defined, default label maps can be written out to data files by the
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:doc:`write_data <write_data>` command. They are also written to and
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read from restart files, by the :doc:`write_restart <write_restart>`
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and :doc:`read_restart <read_restart>` commands. Label maps with
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mapIDs cannot be written to either data or restart files by these
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commands.
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----------
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Use of type labels in LAMMPS input or output
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""""""""""""""""""""""""""""""""""""""""""""
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Any LAMMPS input script command which takes a numeric type as an
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argument, can use the associated type label instead, with the optional
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mapID prepended, followed by a double colon "::". If a type label is
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not defined for a particular numeric type, only its numeric type can
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be used.
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The first example uses a default label map for bond types. The second
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uses a label map with mapID = Map2.
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.. code-block:: LAMMPS
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bond_coeff 2 80.0 1.2 # numeric type
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labelmap bond 2 [C][H]
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bond_coeff [C][H] 80.0 1.2 # type label
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or
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.. code-block:: LAMMPS
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bond_coeff 2 80.0 1.2 # numeric type
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labelmap bond 2 [C][H] mapID Map2
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bond_coeff Map2::[C][H] 80.0 1.2 # type label
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Support for type labels is a work-in-progress for LAMMPS as of
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Nov 2021. If an input script command allows substituting for a
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numeric type argument with a type label, it will be mentioned on that
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command's doc page. If not yet supported, any input script command
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that requires a numeric type can instead use a variable with a
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labelmap function that converts a type label to a numeric type, as in
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the last example above. See the :doc:`variable <variable>` command
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for details.
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For example, here is how the bond_coeff command could be used with a
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type label if it did not yet support them, either with an explicit
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variable command or an implicit variable used in the bond_coeff
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command.
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.. code-block:: LAMMPS
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labelmap bond 2 [C][H]
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variable bond2 equal blabel([C][H])
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bond_coeff ${bond2} 80.0 1.2
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.. code-block:: LAMMPS
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labelmap bond 2 [C][H]
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bond_coeff $(blabel([C][H])) 80.0 1.2
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Support for output of type labels in dump files will be added to
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LAMMPS soon (as of Nov 2021).
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----------
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Commands that can use label types in interesting ways
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"""""""""""""""""""""""""""""""""""""""""""""""""""""
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Provide a few details on these to spark user's interest? If not yet
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implemented, just say this is planned, as of Nov 2021.
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fix bond/react
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pair_style kim
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other?
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@ -22,6 +22,9 @@ Examples
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angle_coeff * 5.0
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angle_coeff 2*10 5.0
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JAKE add an example with 2 lines. First = labelmap command, second =
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use the type label.
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Description
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"""""""""""
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@ -31,7 +34,11 @@ Angle coefficients can also be set in the data file read by the
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:doc:`read_data <read_data>` command or in a restart file.
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N can be specified in one of two ways. An explicit numeric value can
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be used, as in the first example above. Or N can be a :doc:`type label <labelmap>`.
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be used, as in the first example above. Or N can be a type label,
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which is an alphanumeric string defined by the :doc:`labelmap
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<labelmap>` command or in a section of a data file read by the
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:doc:`read_data <read_data>` command.
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For numeric values only, a wild-card asterisk can be used to set the
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coefficients for multiple angle types. This takes the form "\*" or
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"\*n" or "n\*" or "m\*n". If N = the number of angle types, then an
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@ -40,9 +47,10 @@ leading asterisk means all types from 1 to n (inclusive). A trailing
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asterisk means all types from n to N (inclusive). A middle asterisk
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means all types from m to n (inclusive).
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Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
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for the same angle type. For example, these commands set the coeffs
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for all angle types, then overwrite the coeffs for just angle type 2:
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Note that using an :doc:`angle_coeff <angle_coeff>` command can
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override a previous setting for the same angle type. For example,
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these commands set the coeffs for all angle types, then overwrite the
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coeffs for just angle type 2:
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.. code-block:: LAMMPS
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@ -50,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
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angle_coeff 2 50.0 107.0
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A line in a data file that specifies angle coefficients uses the exact
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same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
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script, except that wild-card asterisks should not be used since
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coefficients for all N types must be listed in the file. For example,
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under the "Angle Coeffs" section of a data file, the line that
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corresponds to the first example above would be listed as
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same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
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command in an input script, except that wild-card asterisks should not
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be used since coefficients for all N types must be listed in the file.
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For example, under the "Angle Coeffs" section of a data file, the line
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that corresponds to the first example above would be listed as
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.. parsed-literal::
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@ -21,7 +21,10 @@ Examples
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bond_coeff 5 80.0 1.2
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bond_coeff * 30.0 1.5 1.0 1.0
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bond_coeff 1*4 30.0 1.5 1.0 1.0
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bond_coeff 1 harmonic 200.0 1.0
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bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
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JAKE add an example with 2 lines. First = labelmap command, second =
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use the type label.
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Description
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"""""""""""
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@ -31,8 +34,12 @@ The number and meaning of the coefficients depends on the bond style.
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Bond coefficients can also be set in the data file read by the
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:doc:`read_data <read_data>` command or in a restart file.
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N can be specified in one of several ways. An explicit numeric value can
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be used, as in the first example above. Or N can be a :doc:`type label <labelmap>`.
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N can be specified in one of several ways. An explicit numeric value
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can be used, as in the first example above. Or N can be a type label,
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which is an alphanumeric string defined by the :doc:`labelmap
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<labelmap>` command or in a section of a data file read by the
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:doc:`read_data <read_data>` command.
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For numeric values only, a wild-card asterisk can be used to set the
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coefficients for multiple bond types. This takes the form "\*" or
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"\*n" or "n\*" or "m\*n". If N = the number of bond types, then an
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@ -22,6 +22,9 @@ Examples
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dihedral_coeff * 80.0 1 3 0.5
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dihedral_coeff 2* 80.0 1 3 0.5
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JAKE add an example with 2 lines. First = labelmap command, second =
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use the type label.
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Description
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"""""""""""
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@ -31,7 +34,11 @@ Dihedral coefficients can also be set in the data file read by the
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:doc:`read_data <read_data>` command or in a restart file.
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N can be specified in one of two ways. An explicit numeric value can
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be used, as in the first example above. Or N can be a :doc:`type label <labelmap>`.
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be used, as in the first example above. Or N can be a type label,
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which is an alphanumeric string defined by the :doc:`labelmap
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<labelmap>` command or in a section of a data file read by the
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:doc:`read_data <read_data>` command.
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For numeric values only, a wild-card asterisk can be used to set the
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coefficients for multiple dihedral types. This takes the form "\*" or
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"\*n" or "n\*" or "m\*n". If N = the number of dihedral types, then
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@ -32,7 +32,11 @@ file read by the :doc:`read_data <read_data>` command or in a restart
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file.
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N can be specified in one of two ways. An explicit numeric value can
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be used, as in the first example above. Or N can be a :doc:`type label <labelmap>`.
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be used, as in the first example above. Or N can be a type label,
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which is an alphanumeric string defined by the :doc:`labelmap
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<labelmap>` command or in a section of a data file read by the
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:doc:`read_data <read_data>` command.
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For numeric values only, a wild-card asterisk can be used to set the
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coefficients for multiple improper types. This takes the form "\*" or
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"\*n" or "n\*" or "m\*n". If N = the number of improper types, then
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@ -8,16 +8,17 @@ Syntax
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.. code-block:: LAMMPS
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labelmap interaction numeric-type type-label ... keyword values
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labelmap type-kind numeric-type type-label ... keyword arg
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* interaction = *atom* or *bond* or *angle* or *dihedral* or *improper*
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* one or more numeric-type/type-label pairs may be appended
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* keyword = *map/assign*
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* type-kind = *atom* or *bond* or *angle* or *dihedral* or *improper*
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* one or more numeric-type/type-label pairs may be specified
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* zero or more keyword/arg pairs may be appended
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* keyword = *mapID*
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.. parsed-literal::
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*map/assign* value = mapID
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mapID = name of auxiliary label map
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*mapID* arg = name
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name = ID for the label map
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|
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Examples
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""""""""
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@ -26,78 +27,54 @@ Examples
|
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|
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labelmap atom 3 carbon
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labelmap bond 1 [c1][c2] 2 [c1][hc]
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labelmap bond 1 [c1][c2] 2 [c1][hc] mapID myMap
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JAKE: give an example of a command using variable labelmap func (see below)
|
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|
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Description
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"""""""""""
|
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|
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Define or replace the alphanumeric type label associated with a
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numeric atom, bond, angle, dihedral or improper type. Type labels are
|
||||
strings that can be assigned to each interaction type. Pairing each
|
||||
numeric type used by LAMMPS with a character-based type can be
|
||||
helpful in a variety of situations. For example, type labels can make
|
||||
various inputs more readable and compatible with other inputs (data
|
||||
files, molecule templates, etc.), particularly if your model's force
|
||||
field uses alphanumeric atom types. The default type label map can
|
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also be defined by :doc:`data files <read_data>` using the relevant
|
||||
Type Label sections.
|
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Define alphanumeric type labels to associate with one or more numeric
|
||||
atom, bond, angle, dihedral or improper types. A collection of type
|
||||
labels for a particular type-kind (atom types, bond types, etc) is
|
||||
stored as a label map. As explained below, this command also allows
|
||||
definition of multiple label maps for the same type-kind by use of the
|
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mapID keyword.
|
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|
||||
.. note::
|
||||
Label maps can also be defined by the :doc:`read_data <read_data>`
|
||||
command when it reads these sections in a data file: Atom Type Labels,
|
||||
Bond Type Lables, etc. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
If substituting numeric types with type labels is currently
|
||||
supported by a given command, this feature will be mentioned on
|
||||
that command's doc page. Or, for input script commands, type labels
|
||||
can be processed using :doc:`variable <variable>` syntax using
|
||||
labelmap functions.
|
||||
As explained on the Howto page, valid type labels can contain any
|
||||
alphanumeric character, but cannot start with a number. They can also
|
||||
contain any of these characters: square brackets "[" and "]", dash
|
||||
"-", underscore "_", JAKE what other chars are allowed? Note that
|
||||
type labels cannot contain the symbols '#' or '*'.
|
||||
|
||||
.. note::
|
||||
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 a given numeric
|
||||
type, it will be overwritten. Type labels must be unique; assigning
|
||||
the same type label to multiple numeric types is not allowed. Note
|
||||
that there is no requirement that a type label be defined for every
|
||||
numeric type.
|
||||
|
||||
Type labels cannot start with a number.
|
||||
|
||||
The label map of only one type of interaction (atom, bond, etc.) may
|
||||
be modified by a given *labelmap* command. Any number of
|
||||
numeric-type/type-label pairs may follow. If a type label already
|
||||
exists for a given numeric type, it will be overwritten. Types labels
|
||||
must be unique; assigning the same type label to multiple numeric
|
||||
types is not permitted. There does not need to be a type label
|
||||
associated with every numeric type; in this case, those types without
|
||||
a label must be referenced by their numeric type.
|
||||
|
||||
For certain features, it is necessary to be able to extract the
|
||||
atom types that make up a given bond, angle, dihedral or improper. The
|
||||
standard way to write multi-atom interaction types is to enclose the
|
||||
constituent atom types in brackets. For example, a bond type between
|
||||
atom type 'C' and 'H' is written as:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff [C][H] 80.0 1.2
|
||||
|
||||
In some circumstances, it may be helpful to define extra label maps in
|
||||
addition to the default one. An auxiliary label map can be created and
|
||||
populated using the *map/assign* keyword. Type labels of auxiliary
|
||||
label maps can be referenced by prefixing the type label with the
|
||||
mapID followed by "::". For example, a type label "C" assigned to a
|
||||
label map named "Map2" can be created and referenced as follows:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
labelmap bond 1 [C][H] map/assign Map2
|
||||
bond_coeff Map2::[C][H] 80.0 1.2
|
||||
|
||||
Auxiliary label maps are not written to restart or data files. Due to
|
||||
the syntax for auxiliary maps, type labels cannot contain the
|
||||
substring "::". The default label map has no prefix.
|
||||
It may sometimes be useful to define multiple label maps for a single
|
||||
type-kind. This can be done using the *mapID* keyword. The specified
|
||||
*name* is the mapID assigned to the label map. The ID of a label map
|
||||
can only contain alphanumeric characters and underscores. If the
|
||||
*mapID* keyword is not used, the specified type labels are assigned to
|
||||
the default label map for each type-kind, which has no mapID.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Type labels cannot contain the symbols '#' or '*'. This command must
|
||||
come after the simulation box is defined by a :doc:`read_data <read_data>`,
|
||||
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
|
||||
command.
|
||||
This command must come after the simulation box is defined by a
|
||||
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
||||
:doc:`create_box <create_box>` command.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
@ -108,4 +85,5 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option default is no type label map.
|
||||
If the mapID keyword is not used, specified type labels are assigned
|
||||
to the default map for the type-kind.
|
||||
|
||||
@ -70,8 +70,9 @@ and underscores.
|
||||
A single template can contain multiple molecules, listed one per file.
|
||||
Some of the commands listed above currently use only the first
|
||||
molecule in the template, and will issue a warning if the template
|
||||
contains multiple molecules. The :doc:`atom_style template <atom_style>` command allows multiple-molecule templates
|
||||
to define a system with more than one templated molecule.
|
||||
contains multiple molecules. The :doc:`atom_style template
|
||||
<atom_style>` command allows multiple-molecule templates to define a
|
||||
system with more than one templated molecule.
|
||||
|
||||
Each filename can be followed by optional keywords which are applied
|
||||
only to the molecule in the file as used in this template. This is to
|
||||
@ -173,12 +174,15 @@ These are the allowed section keywords for the body of the file.
|
||||
* *Special Bond Counts, Special Bonds* = special neighbor info
|
||||
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
|
||||
|
||||
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
|
||||
atom, bond, etc. type can be listed either as a number (numeric type)
|
||||
or as an alphanumeric :doc:`type label <labelmap>`. Type labels cannot
|
||||
start with a number, and a label map must have previously been defined
|
||||
by a :doc:`labelmap <labelmap>` or :doc:`read_data <read_data>`
|
||||
command.
|
||||
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
|
||||
atom/bond/angle/etc type can be specified either as a number (numeric
|
||||
type) or as an alphanumeric type label. The latter is only allowed if
|
||||
type lables have been defined, either by the :doc:`labelmap
|
||||
<labelmap>` command or in data files read by the :doc:`read_data
|
||||
<read_data>` command which have sections for Atom Type Labels, Bond
|
||||
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
If a Bonds section is specified then the Special Bond Counts and
|
||||
Special Bonds sections can also be used, if desired, to explicitly
|
||||
@ -186,25 +190,26 @@ list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
|
||||
details below). This is optional since if these sections are not
|
||||
included, LAMMPS will auto-generate this information. Note that
|
||||
LAMMPS uses this info to properly exclude or weight bonded pairwise
|
||||
interactions between bonded atoms. See the
|
||||
:doc:`special_bonds <special_bonds>` command for more details. One
|
||||
reason to list the special bond info explicitly is for the
|
||||
:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the
|
||||
bonds between nuclear cores and Drude electrons in a different manner.
|
||||
interactions between bonded atoms. See the :doc:`special_bonds
|
||||
<special_bonds>` command for more details. One reason to list the
|
||||
special bond info explicitly is for the :doc:`thermalized Drude
|
||||
oscillator model <Howto_drude>` which treats the bonds between nuclear
|
||||
cores and Drude electrons in a different manner.
|
||||
|
||||
.. note::
|
||||
|
||||
Whether a section is required depends on how the molecule
|
||||
template is used by other LAMMPS commands. For example, to add a
|
||||
molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords
|
||||
and Types sections are required. To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
|
||||
Whether a section is required depends on how the molecule template
|
||||
is used by other LAMMPS commands. For example, to add a molecule
|
||||
via the :doc:`fix deposit <fix_deposit>` command, the Coords and
|
||||
Types sections are required. To add a rigid body via the :doc:`fix
|
||||
pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
|
||||
required, since the molecule will be treated as a rigid body. Some
|
||||
sections are optional. For example, the :doc:`fix pour <fix_pour>`
|
||||
command can be used to add "molecules" which are clusters of
|
||||
finite-size granular particles. If the Diameters section is not
|
||||
specified, each particle in the molecule will have a default diameter
|
||||
of 1.0. See the doc pages for LAMMPS commands that use molecule
|
||||
templates for more details.
|
||||
specified, each particle in the molecule will have a default
|
||||
diameter of 1.0. See the doc pages for LAMMPS commands that use
|
||||
molecule templates for more details.
|
||||
|
||||
Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
||||
|
||||
@ -36,9 +36,13 @@ by the :doc:`read_data <read_data>` command or in a restart file.
|
||||
|
||||
I and J can be specified in one of several ways. Explicit numeric
|
||||
values can be used for each, as in the first example above. Or, one
|
||||
or both of the types in the I,J pair may be a :doc:`type label <labelmap>`.
|
||||
LAMMPS sets the coefficients for the symmetric J,I interaction to the
|
||||
same values.
|
||||
or both of the types in the I,J pair can be a type label, which is an
|
||||
alphanumeric string defined by the :doc:`labelmap <labelmap>` command
|
||||
or in a section of a data file read by the :doc:`read_data
|
||||
<read_data>` command, and which converts internally to a numeric type.
|
||||
In either case I <= J is required. Interally, LAMMPS will set
|
||||
coefficients for the symmetric J,I interaction to the same values as
|
||||
the I <= J interaction.
|
||||
|
||||
For numeric values only, a wildcard asterisk can be used in place of
|
||||
or in conjunction with the I,J arguments to set the coefficients for
|
||||
@ -47,9 +51,11 @@ multiple pairs of atom types. This takes the form "\*" or "\*n" or
|
||||
with no numeric values means all types from 1 to N. A leading
|
||||
asterisk means all types from 1 to n (inclusive). A trailing asterisk
|
||||
means all types from n to N (inclusive). A middle asterisk means all
|
||||
types from m to n (inclusive). Note that only type pairs with I <= J
|
||||
are considered; if asterisks imply type pairs where J < I, they are
|
||||
ignored.
|
||||
types from m to n (inclusive). For the asterisk syntax, only type
|
||||
pairs with I <= J are considered; if asterisks imply type pairs where
|
||||
J < I, they are ignored (no error as with non-asterisk arguments).
|
||||
Again interally, LAMMPS will set the coefficients for the symmetric
|
||||
J,I interactions to the same values as the I <= J interactions.
|
||||
|
||||
Note that a pair_coeff command can override a previous setting for the
|
||||
same I,J pair. For example, these commands set the coeffs for all I,J
|
||||
@ -68,8 +74,8 @@ specified, which sets the coefficients for type I interacting with
|
||||
type I. This is because the section has exactly N lines, where N =
|
||||
the number of atom types. For this reason, the wild-card asterisk
|
||||
should also not be used as part of the I argument. Thus in a data
|
||||
file, the line corresponding to the first example above would be listed
|
||||
as
|
||||
file, the line corresponding to the first example above would be
|
||||
listed as
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
@ -477,7 +477,7 @@ These are the section keywords for the body of the file.
|
||||
|
||||
* *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections
|
||||
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
|
||||
* *Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels* = type label map
|
||||
* *Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels* = type label maps
|
||||
* *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs* = force field sections
|
||||
* *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections
|
||||
|
||||
@ -547,11 +547,13 @@ input script.
|
||||
ID = angle type (1-N)
|
||||
label = alphanumeric type label
|
||||
|
||||
See the *Atom Type Labels* section for more details about how angle
|
||||
types are interpreted when reading one or more data files that contain
|
||||
angle type label sections. See the :doc:`labelmap <labelmap>` command
|
||||
for a discussion about how to format angle type labels and use type
|
||||
label maps.
|
||||
Define alphanumeric type labels for each numeric angle type. These
|
||||
can be used in the Angles section in place of a numeric type, but only
|
||||
if the this section appears before the Angles section.
|
||||
|
||||
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
|
||||
allowed syntax of type labels and a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -599,8 +601,15 @@ example:
|
||||
The 3 atoms are ordered linearly within the angle. Thus the central
|
||||
atom (around which the angle is computed) is the atom2 in the list.
|
||||
E.g. H,O,H for a water molecule. The *Angles* section must appear
|
||||
after the *Atoms* section. All values in this section must be
|
||||
integers (1, not 1.0).
|
||||
after the *Atoms* section.
|
||||
|
||||
All values in this section must be integers (1, not 1.0). However,
|
||||
the type can be a numeric value or an alphanumeric label. The latter
|
||||
is only allowed if the type label has been defined by the
|
||||
:doc:`labelmap <labelmap>` command or an Angle Type Labels section
|
||||
earlier in the data file. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -626,29 +635,13 @@ integers (1, not 1.0).
|
||||
ID = numeric atom type (1-N)
|
||||
label = alphanumeric type label
|
||||
|
||||
Type labels can be used to make data files more general, by defining
|
||||
atom, bond, etc. types in terms of user-provided strings instead of
|
||||
numbers. If a type label section exists for a given interaction
|
||||
(atom, bond, angle, dihedral or improper), then all types must be
|
||||
assigned a type label for that interaction. Type label sections must
|
||||
come before any section that utilizes that type. Type labels can be
|
||||
directly substituted for numeric types listed in the *Atoms*, *Bonds*,
|
||||
etc. sections of data files. If numeric types are used, each
|
||||
interaction type is first converted into its corresponding type label
|
||||
before being read into LAMMPS. Data files assign all types to the
|
||||
default label map; if the type label does not already exist, the type
|
||||
label is created as a new type and assigned to the default label map.
|
||||
The corresponding interaction coefficients listed in the data file are
|
||||
associated to this type. There must be enough space in the per-type
|
||||
data arrays to create new types; see the *extra/atom/types* keyword
|
||||
for how to reserve extra space for new types, e.g., when reading
|
||||
multiple data files. Note that, in this case, the numeric-to-label
|
||||
mapping within a data file does not necessary correspond to that of
|
||||
the simulation; once the default label map is fully defined, the
|
||||
:doc:`write_data <write_data>` command can be used to print out the
|
||||
default label map at a given point in a simulation. See the
|
||||
:doc:`labelmap <labelmap>` command for more discussion on how to use
|
||||
type label maps.
|
||||
Define alphanumeric type labels for each numeric atom type. These
|
||||
can be used in the Atoms section in place of a numeric type, but only
|
||||
if the Atom Type Labels section appears before the Atoms section.
|
||||
|
||||
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
|
||||
allowed syntax of type labels and a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -773,6 +766,13 @@ not used (e.g. an atomic system with no bonds), and you don't care if
|
||||
unique atom IDs appear in dump files, then the atom-IDs can all be set
|
||||
to 0.
|
||||
|
||||
The atom-type can be a numeric value or an alphanumeric label. The
|
||||
latter is only allowed if the type label has been defined by the
|
||||
:doc:`labelmap <labelmap>` command or an Atom Type Labels section
|
||||
earlier in the data file. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
The molecule ID is a second identifier attached to an atom. Normally, it
|
||||
is a number from 1 to N, identifying which molecule the atom belongs
|
||||
to. It can be 0 if it is a non-bonded atom or if you don't care to
|
||||
@ -993,11 +993,13 @@ script.
|
||||
ID = bond type (1-N)
|
||||
label = alphanumeric type label
|
||||
|
||||
See the *Atom Type Labels* section for more details about how bond
|
||||
types are interpreted when reading one or more data files that contain
|
||||
bond type label sections. See the :doc:`labelmap <labelmap>` command
|
||||
for a discussion about how to format bond type labels and use type
|
||||
label maps.
|
||||
Define alphanumeric type labels for each numeric bond type. These can
|
||||
be used in the Bonds section in place of a numeric type, but only if
|
||||
the this section appears before the Angles section.
|
||||
|
||||
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
|
||||
allowed syntax of type labels and a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -1054,8 +1056,15 @@ label maps.
|
||||
|
||||
12 3 17 29
|
||||
|
||||
The *Bonds* section must appear after the *Atoms* section. All values
|
||||
in this section must be integers (1, not 1.0).
|
||||
The *Bonds* section must appear after the *Atoms* section.
|
||||
|
||||
All values in this section must be integers (1, not 1.0). However,
|
||||
the type can be a numeric value or an alphanumeric label. The latter
|
||||
is only allowed if the type label has been defined by the
|
||||
:doc:`labelmap <labelmap>` command or a Bond Type Labels section
|
||||
earlier in the data file. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -1093,11 +1102,13 @@ Coefficients can also be set via the
|
||||
ID = dihedral type (1-N)
|
||||
label = alphanumeric type label
|
||||
|
||||
See the *Atom Type Labels* section for more details about how dihedral
|
||||
types are interpreted when reading one or more data files that contain
|
||||
dihedral type label sections. See the :doc:`labelmap <labelmap>`
|
||||
command for a discussion about how to format dihedral type labels and
|
||||
use type label maps.
|
||||
Define alphanumeric type labels for each numeric dihedral type. These
|
||||
can be used in the Dihedrals section in place of a numeric type, but
|
||||
only if the this section appears before the Dihedrals section.
|
||||
|
||||
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
|
||||
allowed syntax of type labels and a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -1119,8 +1130,15 @@ use type label maps.
|
||||
12 4 17 29 30 21
|
||||
|
||||
The 4 atoms are ordered linearly within the dihedral. The *Dihedrals*
|
||||
section must appear after the *Atoms* section. All values in this
|
||||
section must be integers (1, not 1.0).
|
||||
section must appear after the *Atoms* section.
|
||||
|
||||
All values in this section must be integers (1, not 1.0). However,
|
||||
the type can be a numeric value or an alphanumeric label. The latter
|
||||
is only allowed if the type label has been defined by the
|
||||
:doc:`labelmap <labelmap>` command or a Dihedral Type Labels section
|
||||
earlier in the data file. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -1212,11 +1230,13 @@ Coefficients can also be set via the
|
||||
ID = improper type (1-N)
|
||||
label = alphanumeric type label
|
||||
|
||||
See the *Atom Type Labels* section for more details about how improper
|
||||
types are interpreted when reading one or more data files that contain
|
||||
improper type label sections. See the :doc:`labelmap <labelmap>`
|
||||
command for a discussion about how to format improper type labels and
|
||||
use type label maps.
|
||||
Define alphanumeric type labels for each numeric improper type. These
|
||||
can be used in the Impropers section in place of a numeric type, but
|
||||
only if the this section appears before the Impropers section.
|
||||
|
||||
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
|
||||
allowed syntax of type labels and a general discussion of how type
|
||||
labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
@ -1238,11 +1258,19 @@ use type label maps.
|
||||
12 3 17 29 13 100
|
||||
|
||||
The ordering of the 4 atoms determines the definition of the improper
|
||||
angle used in the formula for each :doc:`improper style <improper_style>`. See the doc pages for individual styles
|
||||
for details.
|
||||
angle used in the formula for each :doc:`improper style
|
||||
<improper_style>`. See the doc pages for individual styles for
|
||||
details.
|
||||
|
||||
The *Impropers* section must appear after the *Atoms* section. All
|
||||
values in this section must be integers (1, not 1.0).
|
||||
The *Impropers* section must appear after the *Atoms* section.
|
||||
|
||||
All values in this section must be integers (1, not 1.0). However,
|
||||
the type can be a numeric value or an alphanumeric label. The latter
|
||||
is only allowed if the type label has been defined by the
|
||||
:doc:`labelmap <labelmap>` command or a Improper Type Labels section
|
||||
earlier in the data file. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -19,7 +19,7 @@ Syntax
|
||||
*nocoeff* = do not write out force field info
|
||||
*nofix* = do not write out extra sections read by fixes
|
||||
*nolabelmap* = do not write out the default label map
|
||||
*types_style* value = *numeric* or *labels*
|
||||
*types* value = *numeric* or *labels*
|
||||
*pair* value = *ii* or *ij*
|
||||
*ii* = write one line of pair coefficient info per atom type
|
||||
*ij* = write one line of pair coefficient info per IJ atom type pair
|
||||
@ -96,30 +96,36 @@ data file is read.
|
||||
|
||||
----------
|
||||
|
||||
The *nocoeff* keyword requests that no force field parameters should
|
||||
be written to the data file. This can be very helpful, if one wants
|
||||
to make significant changes to the force field or if the parameters
|
||||
are read in separately anyway, e.g. from an include file.
|
||||
Use of the *nocoeff* keyword means no force field parameters are
|
||||
written to the data file. This can be helpful, for example, if you
|
||||
want to make significant changes to the force field or if the force
|
||||
field parameters are read in separately, e.g. from an include file.
|
||||
|
||||
The *nofix* keyword requests that no extra sections read by fixes
|
||||
should be written to the data file (see the *fix* option of the
|
||||
:doc:`read_data <read_data>` command for details). For example, this
|
||||
option excludes sections for user-created per-atom properties
|
||||
from :doc:`fix property/atom <fix_property_atom>`.
|
||||
Use of the *nofix* keyword means no extra sections read by fixes are
|
||||
written to the data file (see the *fix* option of the :doc:`read_data
|
||||
<read_data>` command for details). For example, this option excludes
|
||||
sections for user-created per-atom properties from :doc:`fix
|
||||
property/atom <fix_property_atom>`.
|
||||
|
||||
The *nolabelmap* keyword requests that the default label map should
|
||||
not be written to the data file (see the Type Label sections of
|
||||
:doc:`read_data <read_data>` command for details). By default, if the
|
||||
default label map is fully defined for a given interaction, i.e. every
|
||||
atom, bond, angle, dihedral or improper type has an associated type
|
||||
label, then a type label section for that interaction is written to
|
||||
the data file. The *types_style* keyword indicates how atom, bond,
|
||||
etc. types are written in the Atoms, Bonds, etc. sections. If the
|
||||
value is specified as *numeric*, then numeric types are used. If the
|
||||
value is specified as *labels*, then interaction types are written as
|
||||
type labels using the default label map. When using type labels, the
|
||||
default label map (i.e., Type Label sections) must be written to the
|
||||
data file.
|
||||
The *nolabelmap* and *types* keywords refer to label maps that may be
|
||||
defined for number atom types, bond types, angle types, etc. Label
|
||||
maps can be defined in two ways, either by the :doc:`labelmap
|
||||
<labelmap>` command or in data files read by the :doc:`read_data
|
||||
<read_data>` command which have sections for Atom Type Labels, Bond
|
||||
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
|
||||
<Howto_type_labels>` doc page for the allowed syntax of type labels
|
||||
and a general discussion of how type labels can be used.
|
||||
|
||||
Use of the *nolabelmap* keyword means that even if default type label
|
||||
maps exist for Atoms, Bonds, Angles, etc, they are not written to the
|
||||
data file. By default, they are written if they exist.
|
||||
|
||||
The *types* keyword determins how atom types, bond types, angle types,
|
||||
etc are written into these data file sections: Atoms, Bonds, Angles,
|
||||
etc. The default is the *numeric* setting, even if type label maps
|
||||
exist. If the *labels" setting is used, type labels will be written
|
||||
to the data file, if the corresponding label map exists. Note that
|
||||
when using *types labels*, the *nolabelmap* keyword cannot be used.
|
||||
|
||||
The *pair* keyword lets you specify in what format the pair
|
||||
coefficient information is written into the data file. If the value
|
||||
|
||||
Reference in New Issue
Block a user