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improve formatting

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Axel Kohlmeyer
2022-04-15 17:12:31 -04:00
parent 69d9c5187e
commit cbb4abc55c
1 changed files with 17 additions and 22 deletions
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doc/src/Howto_bpm.rst
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@ -3,7 +3,6 @@ Bonded particle models
The BPM package implements bonded particle models which can be used to The BPM package implements bonded particle models which can be used to
simulate mesoscale solids. Solids are constructed as a collection of simulate mesoscale solids. Solids are constructed as a collection of
particles which each represent a coarse-grained region of space much particles which each represent a coarse-grained region of space much
larger than the atomistic scale. Particles within a solid region are larger than the atomistic scale. Particles within a solid region are
then connected by a network of bonds to provide solid elasticity. then connected by a network of bonds to provide solid elasticity.
@ -47,31 +46,27 @@ this, LAMMPS requires :doc:`newton <newton>` bond off such that all
processors containing an atom know when a bond breaks. Additionally, processors containing an atom know when a bond breaks. Additionally,
one must do either (A) or (B). one must do either (A) or (B).
(A) A) Use the following special bond settings
Use the following special bond settings .. code-block:: LAMMPS
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1 special_bonds lj 0 1 1 coul 1 1 1
These settings accomplish two goals. First, they turn off 1-3 and 1-4 These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds. in case bonds break between neighbor list builds.
(B) B) Alternatively, one can simply overlay pair interactions such that all
bonded particles also feel pair interactions. This can be
accomplished by using the *overlay/pair* keyword present in all bpm
bond styles and by using the following special bond settings
Alternatively, one can simply overlay pair interactions such that all .. code-block:: LAMMPS
bonded particles also feel pair interactions. This can be accomplished
by using the *overlay/pair* keyword present in all bpm bond styles and
by using the following special bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1 special_bonds lj/coul 1 1 1