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Clarified rules about SNAP elements and LAMMPS types

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This commit is contained in:
Aidan Thompson
2021-03-09 19:19:36 -07:00
parent 9329ab6ab8
commit 2162d2fb3f
1 changed files with 15 additions and 8 deletions
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doc/src/pair_snap.rst
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@ -88,9 +88,12 @@ that will be used with other potentials.
The name of the SNAP coefficient file usually ends in the
".snapcoeff" extension. It may contain coefficients
for many SNAP elements. The only requirement is that it
contain at least those element names appearing in the
LAMMPS mapping list.
for many SNAP elements. The only requirement is that
each of the unique element names appearing in the
LAMMPS pair_coeff command appear exactly once in
the SNAP coefficient file. It is okay if the SNAP coefficient file
contains additional elements not in the pair_coeff command,
except when using *chemflag* (see below).
The name of the SNAP parameter file usually ends in the ".snapparam"
extension. It contains a small number
of parameters that define the overall form of the SNAP potential.
@ -129,7 +132,7 @@ line must contain two integers:
This is followed by one block for each of the *nelem* elements.
The first line of each block contains three entries:
* Element symbol (text string)
* Element name (text string)
* R = Element radius (distance units)
* w = Element weight (dimensionless)
@ -166,8 +169,8 @@ where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components,
:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients
for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}`
is the symmetric *K* by *K* matrix of quadratic coefficients.
The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
for each element, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
The SNAP coefficient file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
in each element block, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum
components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP
@ -181,8 +184,12 @@ at the expense of a significant increase in computational cost :ref:`(Cusentino)
where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components
for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and
:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector
of linear coefficients for element :math:`\mu_i`. The SNAP element file should contain
a total of :math:`K N_{elem}^3` coefficients for each of the :math:`N_{elem}` elements.
of linear coefficients for element :math:`\mu_i`. The SNAP coefficient file should contain
a total of :math:`K N_{elem}^3` coefficients in each element block,
where :math:`N_{elem}` is the number of elements in the SNAP coefficient file,
which must equal the number of unique elements appearing in the
LAMMPS pair_coeff command, to avoid ambiguity in the
number of coefficients.
The keyword *chunksize* is only applicable when using the
pair style *snap* with the KOKKOS package and is ignored otherwise.