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first working version, forces only, no restart

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Axel Kohlmeyer
2021-04-08 21:02:28 -04:00
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doc/src/pair_hybrid.rst
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@ -2,6 +2,7 @@
.. index:: pair_style hybrid/kk
.. index:: pair_style hybrid/overlay
.. index:: pair_style hybrid/overlay/kk
.. index:: pair_style hybrid/scaled
pair_style hybrid command
=========================
@ -13,6 +14,8 @@ pair_style hybrid/overlay command
Accelerator Variants: *hybrid/overlay/kk*
pair_style hybrid/scale command
Syntax
""""""
@ -20,8 +23,10 @@ Syntax
pair_style hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ...
pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
* style1,style2 = list of one or more pair styles and their arguments
* factor1,factor2 = scale factors for pair styles, may be a variable
Examples
""""""""
@ -37,15 +42,24 @@ Examples
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long
variable one equal ramp(1.0,0.0)
variable two equal 1.0-v_one
pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
pair_coeff 1 1 lj/cut 1.0 1.0 2.5
pair_coeff 1 1 morse 1.0 1.0 1.0 2.5
Description
"""""""""""
The *hybrid* and *hybrid/overlay* styles enable the use of multiple
pair styles in one simulation. With the *hybrid* style, exactly one
pair style is assigned to each pair of atom types. With the
*hybrid/overlay* style, one or more pair styles can be assigned to
each pair of atom types. The assignment of pair styles to type pairs
is made via the :doc:`pair_coeff <pair_coeff>` command.
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
use of multiple pair styles in one simulation. With the *hybrid* style,
exactly one pair style is assigned to each pair of atom types. With the
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
be assigned to each pair of atom types. The assignment of pair styles
to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command.
The *hybrid/scaled* style differs from the *hybrid/overlay* style by
requiring a factor for each pair style that is used to scale all
forces and energies computed by the pair style.
Here are two examples of hybrid simulations. The *hybrid* style could
be used for a simulation of a metal droplet on a LJ surface. The
@ -61,12 +75,19 @@ it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.
The *hybrid/scaled* style enables more complex combinations of pair
styles than a simple sum as *hybrid/overlay* does. Furthermore, since
the scale factors can be variables, they can change during a simulation
which would allow to smoothly switch between two different pair styles
or two different parameter sets.
All pair styles that will be used are listed as "sub-styles" following
the *hybrid* or *hybrid/overlay* keyword, in any order. Each
sub-style's name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.
the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the
*hybrid/scaled* pair style each sub-style is prefixed with its scale
factor. The scale factor may be an equal style (or equivalent)
variable. Each sub-style's name is followed by its usual arguments, as
illustrated in the example above. See the doc pages of individual pair
styles for a listing and explanation of the appropriate arguments.
Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
@ -143,16 +164,16 @@ one sub-style. Just as with a simulation using a single pair style,
if you specify the same atom type pair in a second pair_coeff command,
the previous assignment will be overwritten.
For the *hybrid/overlay* style, each atom type pair I,J can be
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then the
second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:
For the *hybrid/overlay* and *hybrid/scaled* style, each atom type pair
I,J can be assigned to one or more sub-styles. If you specify the same
atom type pair in a second pair_coeff command with a new sub-style, then
the second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify the
same atom type pair in a second pair_coeff command with a sub-style that
has already been defined for that pair of atoms, then the new pair
coefficients simply override the previous ones, as in the normal usage
of the pair_coeff command. E.g. these two sets of commands are the
same:
.. code-block:: LAMMPS
@ -170,19 +191,20 @@ data file or restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands, or by mixing as described
below.
For both the *hybrid* and *hybrid/overlay* styles, every atom type
pair I,J (where I <= J) must be assigned to at least one sub-style via
the :doc:`pair_coeff <pair_coeff>` command as in the examples above, or
in the data file read by the :doc:`read_data <read_data>`, 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
sub-style via the :doc:`pair_coeff <pair_coeff>` command as in the
examples above, or in the data file read by the :doc:`read_data
<read_data>`, or by mixing as described below.
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>`
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* and *hybrid/overlay* simulations, you
can use this form of the pair_coeff command in your input script:
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:
.. code-block:: LAMMPS
@ -260,7 +282,10 @@ the specific syntax, requirements and restrictions.
----------
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the :doc:`compute pair <compute_pair>` command.
individual sub-style can be accessed and output via the :doc:`compute
pair <compute_pair>` command. Note that in the case of pair style
*hybrid/scaled* this is the **unscaled** potential energy of the
selected sub-style.
----------
@ -388,12 +413,12 @@ The hybrid pair styles supports the :doc:`pair_modify <pair_modify>`
shift, table, and tail options for an I,J pair interaction, if the
associated sub-style supports it.
For the hybrid pair styles, the list of sub-styles and their
respective settings are written to :doc:`binary restart files <restart>`, so a :doc:`pair_style <pair_style>` command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.
For the hybrid pair styles, the list of sub-styles and their respective
settings are written to :doc:`binary restart files <restart>`, so a
:doc:`pair_style <pair_style>` command does not need to specified in an
input script that reads a restart file. However, the coefficient
information is not stored in the restart file. Thus, pair_coeff
commands need to be re-specified in the restart input script.
These pair styles support the use of the *inner*\ , *middle*\ , and
*outer* keywords of the :doc:`run_style respa <run_style>` command, if
@ -409,6 +434,9 @@ e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.
Pair style *hybrid/scaled* currently only works for non-accelerated
pair styles.
Related commands
""""""""""""""""