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complete update of the hybrid documentation for hybrid/scaled

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Axel Kohlmeyer
2021-04-09 22:50:51 -04:00
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doc/src/pair_hybrid.rst
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@ -59,35 +59,40 @@ 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.
forces, energies and stresses computed by each sub-style. Because of
the additional complexity, the *hybrid/scaled* style will have more
overhead and thus will be a bit slower than *hybrid/overlay*.
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
metal atoms interact with each other via an *eam* potential, the
surface atoms interact with each other via a *lj/cut* potential, and
the metal/surface interaction is also computed via a *lj/cut*
potential. The *hybrid/overlay* style could be used as in the second
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using *lj/cut* and *coul/long* together gives the same result as if
the *lj/cut/coul/long* potential were used by itself. In this case,
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.
be used for a simulation of a metal droplet on a LJ surface. The metal
atoms interact with each other via an *eam* potential, the surface atoms
interact with each other via a *lj/cut* potential, and the metal/surface
interaction is also computed via a *lj/cut* potential. The
*hybrid/overlay* style could be used as in the second example above,
where multiple potentials are superposed in an additive fashion to
compute the interaction between atoms. In this example, using *lj/cut*
and *coul/long* together gives the same result as if the
*lj/cut/coul/long* potential were used by itself. In this case, 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; there may be fractional
contributions from sub-styles or contributions may be subtracted with a
negative scale factor. Furthermore, since the scale factors can be
variables that may change during a simulation, which would allow, for
instance, 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. 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.
*hybrid/scaled* pair style, each sub-style is prefixed with a scale
factor. The scale factor is either a floating point number or an equal
style (or equivalent) variable. Each sub-style's name is followed by its
usual arguments, as illustrated in the examples 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
@ -164,7 +169,7 @@ 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* and *hybrid/scaled* style, each atom type pair
For the *hybrid/overlay* and *hybrid/scaled* styles, 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
@ -187,15 +192,15 @@ 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 or restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands, or by mixing as described
below.
data file read by the :doc:`read_data <read_data>` commands, 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.
<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.
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
@ -208,22 +213,22 @@ input script:
.. code-block:: LAMMPS
pair_coeff 2 3 none
pair_coeff 2 3 none
or this form in the "Pair Coeffs" section of the data file:
.. parsed-literal::
3 none
3 none
If an assignment to *none* is made in a simulation with the
*hybrid/overlay* pair style, it wipes out all previous assignments of
that atom type pair to sub-styles.
*hybrid/overlay* or *hybrid/scaled* pair style, it wipes out all
previous assignments of that pair of atom types to sub-styles.
Note that you may need to use an :doc:`atom_style <atom_style>` hybrid
command in your input script, if atoms in the simulation will need
attributes from several atom styles, due to using multiple pair
potentials.
styles with different requirements.
----------
@ -232,8 +237,9 @@ 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
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
described by the different force fields do not mix.
@ -307,28 +313,27 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
could even add a second interaction for 1-1 to be computed by another
pair style, assuming pair_style hybrid/overlay is used.
But you should not, as a general rule, attempt to exclude the
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
But you should not, as a general rule, attempt to exclude the many-body
interactions for some subset of the type pairs within the set of 1,3,4
interactions, e.g. exclude 1-1 or 1-3 interactions. That is not
conceptually well-defined for many-body interactions, since the
potential will typically calculate energies and foces for small groups
of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
find the additional atoms in the group. It is typically non-physical
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.
find the additional atoms in the group.
However, you can still use the pair_coeff none setting or the
:doc:`neigh_modify exclude <neigh_modify>` command to exclude certain
type pairs from the neighbor list that will be passed to a many-body
sub-style. This will alter the calculations made by a many-body
potential, since it builds its list of 3-body, 4-body, etc
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.
potential beyond the specific pairs, since it builds its list of 3-body,
4-body, etc interactions from the pair lists. You will need to think
**carefully** as to whether excluding such pairs produces a physically
meaningful result for your model.
For example, imagine you have two atom types in your model, type 1 for
atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
surface, but not between the surfaces. Then either of these two command
sequences would implement that model:
.. code-block:: LAMMPS
@ -345,9 +350,9 @@ Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.
Here is another example, using hybrid/overlay, to use 2 many-body
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
Here is another example to use 2 many-body potentials together in an
overlapping manner using hybrid/overlay. Imagine you have CNT (C atoms)
on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:
@ -358,9 +363,9 @@ atoms are type 2. Something like this will work:
pair_coeff * * airebo CH.airebo NULL C
Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.
interactions, you would need to **modify** the SiC.tersoff potential
file to turn off C/C interaction, i.e. by setting the appropriate
coefficients to 0.0.
----------
@ -368,18 +373,19 @@ Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page.
page. Pair style *hybrid/scaled* does (currently) not support the
*gpu*, *omp*, *kk*, or *intel* suffix.
Since the *hybrid* and *hybrid/overlay* styles delegate computation to
the individual sub-styles, the suffix versions of the *hybrid* and
*hybrid/overlay* styles are used to propagate the corresponding suffix
to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate
computation to the individual sub-styles, the suffix versions of the
*hybrid* and *hybrid/overlay* styles are used to propagate the
corresponding suffix to all sub-styles, if those versions
exist. Otherwise the non-accelerated version will be used.
The individual accelerated sub-styles are part of the GPU, USER-OMP
and OPT packages, respectively. They are only enabled if LAMMPS was
built with those packages. See the :doc:`Build package <Build_package>`
doc page for more info.
The individual accelerated sub-styles are part of the GPU, KOKKOS,
USER-INTEL, USER-OMP, and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the :doc:`Build
package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
@ -397,17 +403,17 @@ Any pair potential settings made via the
:doc:`pair_modify <pair_modify>` command are passed along to all
sub-styles of the hybrid potential.
For atom type pairs I,J and I != J, if the sub-style assigned to I,I
and J,J is the same, and if the sub-style allows for mixing, then the
For atom type pairs I,J and I != J, if the sub-style assigned to I,I and
J,J is the same, and if the sub-style allows for mixing, then the
coefficients for I,J can be mixed. This means you do not have to
specify a pair_coeff command for I,J since the I,J type pair will be
assigned automatically to the sub-style defined for both I,I and J,J
and its coefficients generated by the mixing rule used by that
sub-style. For the *hybrid/overlay* style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the "pair_modify" command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.
assigned automatically to the sub-style defined for both I,I and J,J and
its coefficients generated by the mixing rule used by that sub-style.
For the *hybrid/overlay* and *hybrid/scaled* style, there is an
additional requirement that both the I,I and J,J pairs are assigned to a
single sub-style. See the :doc:`pair_modify <pair_modify>` command for
details of mixing rules. See the See the doc page for the sub-style to
see if allows for mixing.
The hybrid pair styles supports the :doc:`pair_modify <pair_modify>`
shift, table, and tail options for an I,J pair interaction, if the
@ -418,7 +424,10 @@ 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.
commands need to be re-specified in the restart input script. For pair
style *hybrid/scaled* also the names of any variables used as scale
factors are restored, but not the variables themselves, so those may
need to be redefined when continuing from a restart.
These pair styles support the use of the *inner*\ , *middle*\ , and
*outer* keywords of the :doc:`run_style respa <run_style>` command, if
@ -435,7 +444,7 @@ 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.
pair styles and pair styles from the OPT package.
Related commands
""""""""""""""""