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Try to improve the pair style hybrid docs

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This specifically tries to avoid the ambiguous use of "mixing" and
clarify that similar is still different when pair styles are concerned.
See discussion here: https://matsci.org/t/confusion-about-mixing-and-pair-coeff-section/38317/3
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Axel Kohlmeyer
2021-09-15 13:48:47 -04:00
parent 1b91bfbfa1
commit c1fa663dd8
1 changed files with 28 additions and 20 deletions
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doc/src/pair_hybrid.rst
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@ -198,8 +198,8 @@ same:
Coefficients must be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as described above, or in the
data file read by the :doc:`read_data <read_data>` commands, or by
mixing as described below.
PairCoeffs or PairIJCoeffs section of the data file read by the
:doc:`read_data <read_data>` command, or by mixing as described below.
For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles,
every atom type pair I,J (where I <= J) must be assigned to at least one
@ -208,14 +208,21 @@ examples above, or in the data file read by the :doc:`read_data
<read_data>`, or by mixing as described below. Also all sub-styles
must be used at least once in a :doc:`pair_coeff <pair_coeff>` command.
.. note::
LAMMPS never performs mixing of parameters from different sub-styles,
**even** if they use the same type of coefficients, e.g. contain
a Lennard-Jones potential variant. Those parameters must be provided
explicitly.
If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
atom types, you have 3 choices. You can assign the pair of atom types
to some sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ
potential). Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled*
simulations, you can use this form of the pair_coeff command in your
input script:
input script or the "PairIJ Coeffs" section of your data file:
.. code-block:: LAMMPS
@ -238,19 +245,20 @@ styles with different requirements.
----------
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
:doc:`special_bonds <special_bonds>` command. Different weights can be
assigned to different pair hybrid sub-styles via the :doc:`pair_modify
special <pair_modify>` command. This allows multiple force fields to be
used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
Different force fields (e.g. CHARMM vs. AMBER) may have different rules
for applying exclusions or wheights that change the strength of pairwise
non-bonded interactions between pairs of atoms that are also 1-2, 1-3,
and 1-4 neighbors in the molecular bond topology. This is normally a
global setting defined the :doc:`special_bonds <special_bonds>` command.
However, different weights can be assigned to different hybrid
sub-styles via the :doc:`pair_modify special <pair_modify>` command.
This allows multiple force fields to be used in a model of a hybrid
system, however, there is no consistent approach to determine parameters
automatically for the interactions **between** atoms of the two force
fields, thus this approach this is only recommended when particles
described by the different force fields do not mix.
Here is an example for mixing CHARMM and AMBER: The global *amber*
Here is an example for combining CHARMM and AMBER: The global *amber*
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
@ -260,7 +268,7 @@ then overrides them with 0.0 only for CHARMM:
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
The this input achieves the same effect:
This input achieves the same effect:
.. code-block:: LAMMPS
@ -270,9 +278,9 @@ The this input achieves the same effect:
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
Here is an example for combining Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where - for the
Tersoff part of the system - the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: