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Update pair_3b_table.rst

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changed documentation and file name from pair style 3b/table to threebody/table
This commit is contained in:
Christoph Scherer
2022-06-01 16:11:47 +02:00
committed by GitHub
parent a833baac80
commit c1e301ac1a
1 changed files with 15 additions and 15 deletions
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doc/src/pair_3b_table.rst
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@ -1,7 +1,7 @@
.. index:: pair_style 3b/table
.. index:: pair_style threebody/table
pair_style 3b/table command
===========================
pair_style threebody/table command
==================================
Syntax
""""""
@ -10,7 +10,7 @@ Syntax
pair_style style
* style = *3b/table*
* style = *threebody/table*
Examples
@ -18,7 +18,7 @@ Examples
.. code-block:: LAMMPS
pair_style 3b/table
pair_style threebody/table
pair_coeff * * spce.3b type
pair_coeff * * GaN.3b Ga N Ga
@ -26,11 +26,11 @@ Examples
Description
"""""""""""
The *3b/table* style is a pair style for generic tabulated three-body
The *threebody/table* style is a pair style for generic tabulated three-body
interactions. It has been developed for (coarse-grained) simulations
(of water) with Kernel-based machine learning (ML) potentials
(:ref:`Scherer2 <Scherer2>`). As for the pair style :doc:`pair_style sw
<pair_sw>` or :doc:`pair_style sw/3b/table <pair_sw_3b_table>`, the energy of
<pair_sw>` or :doc:`pair_style sw/threebody/table <pair_sw_threebody_table>`, the energy of
a system is computed as a sum over three-body terms:
.. math::
@ -43,14 +43,14 @@ Stillinger-Weber potential, all forces are not calculated analytically,
but read in from a three-body force/energy table which can be generated
with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca.
Only a single pair_coeff command is used with the *3b/table* style
which specifies a three-body potential (".3b") file with parameters for all
Only a single pair_coeff command is used with the *threebody/table* style
which specifies a threebody potential (".3b") file with parameters for all
needed elements. These are then mapped to LAMMPS atom types by specifying
N_el additional arguments after the ".3b" filename in the pair_coeff command,
where N_el is the number of LAMMPS atom types:
* ".3b" filename
* N_el element names = mapping of 3b elements to atom types
* N_el element names = mapping of threebody elements to atom types
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
to specify the path for the potential file.
@ -67,8 +67,8 @@ pair_coeff command:
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the ".3b" file. The final C argument maps LAMMPS atom type 4
to the C element in the 3b file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a *3b/table*
to the C element in the threebody file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a *threebody/table*
potential is used as part of the *hybrid* pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.
@ -193,7 +193,7 @@ This allows for a very efficient force calculation
with the stored force constants and energies. Due to the know table structure, the lookup
can be done efficiently. It has been tested (:ref:`Scherer2 <Scherer2>`) that with a reasonably
small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential
with tabulated three-body interactions (:doc:`pair_style sw/table <pair_sw_3b_table>`) while
with tabulated three-body interactions (:doc:`pair_style sw/angle/table <pair_sw_angle_table>`) while
the table format of this pair style allows for more flexible three-body interactions.
As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the
@ -204,7 +204,7 @@ simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify 3b parameters for all permutations of the two elements
specify threebody parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
@ -254,7 +254,7 @@ in the tutorial folder.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair sw/3b/table <pair_sw_3b_table>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair sw/angle/table <pair_sw_angle_table>`
----------