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update docs for create_bonds

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Axel Kohlmeyer
2023-06-28 10:06:31 -04:00
parent 5d027fc92c
commit a50993dac1
1 changed files with 27 additions and 18 deletions
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doc/src/create_bonds.rst
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@ -86,19 +86,20 @@ data file for a complex system of molecules.
.. note:: .. note::
If the system has no bonds (angles, dihedrals, impropers) to begin with, If the system has no bonds (angles, dihedrals, impropers) to begin
or if more bonds per atom are being added than currently exist, then you with, or if more bonds per atom are being added than currently exist,
must ensure that the number of bond types and the maximum number of then you must ensure that the number of bond types and the maximum
bonds per atom are set to large enough values, and similarly for number of bonds per atom are set to large enough values, and
angles, dihedrals, and impropers, otherwise an error may occur when too many similarly for angles, dihedrals, impropers, and special neighbors,
bonds (angles, dihedrals, impropers) are added to an atom. If the otherwise an error may occur when too many bonds (angles, dihedrals,
:doc:`read_data <read_data>` command is used to define the system, these impropers) are added to an atom. If the :doc:`read_data <read_data>`
parameters can be set via the "bond types" and "extra bond per atom" command is used to define the system, these parameters can be set via
fields in the header section of the data file. If the its optional *extra/bond/types*, *extra/bond/per/atom*, and similar
:doc:`create_box <create_box>` command is used to define the system, keywords to the command. If the :doc:`create_box <create_box>`
these two parameters can be set via its optional *bond/types* and command is used to define the system, these two parameters can be set
*extra/bond/per/atom* arguments, and similarly for angles, dihedrals, and via its optional *bond/types* and *extra/bond/per/atom* arguments,
impropers. See the doc pages for these two commands for details. and similarly for angles, dihedrals, and impropers. See the
corresponding documentation pages for these two commands for details.
---------- ----------
@ -112,7 +113,7 @@ For a bond to be created, an :math:`I,J` pair of atoms must be a distance
:math:`D` apart such that :math:`r_\text{min} \le D \le r_\text{max}`. :math:`D` apart such that :math:`r_\text{min} \le D \le r_\text{max}`.
The following settings must have been made in an input script before The following settings must have been made in an input script before
this style is used: the *many* style is used:
* special_bonds weight for 1--2 interactions must be 0.0 * special_bonds weight for 1--2 interactions must be 0.0
* a :doc:`pair_style <pair_style>` must be defined * a :doc:`pair_style <pair_style>` must be defined
@ -121,10 +122,13 @@ this style is used:
skin :math:`\ge r_\text{max}` skin :math:`\ge r_\text{max}`
These settings are required so that a neighbor list can be created to These settings are required so that a neighbor list can be created to
search for nearby atoms. Pairs of atoms that are already bonded search for nearby atoms. Pairs of atoms that are already bonded cannot
cannot appear in the neighbor list, to avoid creation of duplicate appear in the neighbor list, to avoid creation of duplicate bonds. The
bonds. The neighbor list for all atom type pairs must also extend to neighbor list for all atom type pairs must also extend to a distance
a distance that encompasses the *rmax* for new bonds to create. that encompasses the *rmax* for new bonds to create. When using
periodic boundary conditions, the box length in each periodic dimension
must be larger than *rmax*, so that no bonds are created between the
system and its own periodic image.
.. note:: .. note::
@ -219,6 +223,11 @@ This command cannot be used with molecular systems defined using
molecule template files via the :doc:`molecule <molecule>` and molecule template files via the :doc:`molecule <molecule>` and
:doc:`atom_style template <atom_style>` commands. :doc:`atom_style template <atom_style>` commands.
For style *many*, no :doc:`kspace style <kspace_style>` must be
defined. Also, the *rmax* value must be smaller than any periodic box
length and the neighbor list cutoff (largest pair cutoff plus neighbor
skin).
Related commands Related commands
"""""""""""""""" """"""""""""""""