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rearrange and rewformulate content of the tip4p pair style docs to make it more obvious

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Axel Kohlmeyer
2023-11-30 14:53:24 -05:00
parent 2825aeff48
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1 changed files with 34 additions and 28 deletions
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doc/src/pair_lj_cut_tip4p.rst
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@ -58,6 +58,40 @@ Examples
Description
"""""""""""
The *lj/cut/tip4p* styles implement the TIP4P water model of
:ref:`(Jorgensen) <Jorgensen2>` and similar models, which introduce a
massless site M located a short distance away from the oxygen atom along
the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as pair_style
arguments and are used to identify the TIP4P-like molecules and
determine the position of the M site from the positions of the hydrogen
and oxygen atoms of the water molecules. The M site location is used
for all Coulomb interactions instead of the oxygen atom location, also
with all other atom types, while the location of the oxygen atom is used
for the Lennard-Jones interactions. Style *lj/cut/tip4p/cut* uses a
cutoff for Coulomb interactions; style *lj/cut/tip4p/long* is for use
with a long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
given by
@ -91,34 +125,6 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
The *lj/cut/tip4p* styles implement the TIP4P
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
Coefficients
""""""""""""