diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index d520f1a88e..53a9a1ca50 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -86,19 +86,20 @@ data file for a complex system of molecules. .. note:: - If the system has no bonds (angles, dihedrals, impropers) to begin with, - or if more bonds per atom are being added than currently exist, then you - must ensure that the number of bond types and the maximum number of - bonds per atom are set to large enough values, and similarly for - angles, dihedrals, and impropers, otherwise an error may occur when too many - bonds (angles, dihedrals, impropers) are added to an atom. If the - :doc:`read_data ` command is used to define the system, these - parameters can be set via the "bond types" and "extra bond per atom" - fields in the header section of the data file. If the - :doc:`create_box ` command is used to define the system, - these two parameters can be set via its optional *bond/types* and - *extra/bond/per/atom* arguments, and similarly for angles, dihedrals, and - impropers. See the doc pages for these two commands for details. + If the system has no bonds (angles, dihedrals, impropers) to begin + with, or if more bonds per atom are being added than currently exist, + then you must ensure that the number of bond types and the maximum + number of bonds per atom are set to large enough values, and + similarly for angles, dihedrals, impropers, and special neighbors, + otherwise an error may occur when too many bonds (angles, dihedrals, + impropers) are added to an atom. If the :doc:`read_data ` + command is used to define the system, these parameters can be set via + its optional *extra/bond/types*, *extra/bond/per/atom*, and similar + keywords to the command. If the :doc:`create_box ` + command is used to define the system, these two parameters can be set + via its optional *bond/types* and *extra/bond/per/atom* arguments, + 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}`. 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 * a :doc:`pair_style ` must be defined @@ -121,10 +122,13 @@ this style is used: skin :math:`\ge r_\text{max}` These settings are required so that a neighbor list can be created to -search for nearby atoms. Pairs of atoms that are already bonded -cannot appear in the neighbor list, to avoid creation of duplicate -bonds. The neighbor list for all atom type pairs must also extend to -a distance that encompasses the *rmax* for new bonds to create. +search for nearby atoms. Pairs of atoms that are already bonded cannot +appear in the neighbor list, to avoid creation of duplicate bonds. The +neighbor list for all atom type pairs must also extend to a distance +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:: @@ -219,6 +223,11 @@ This command cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and :doc:`atom_style template ` commands. +For style *many*, no :doc:`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 """"""""""""""""