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Renamed born method born_matrix in all classes. Changed compute_born to compute_born_matrix. Changed the compute coding to suit the LAMMPS style rules better.

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Germain Clavier
2022-01-21 18:39:16 +01:00
parent 8531622966
commit 3ff1902b57
15 changed files with 202 additions and 234 deletions
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23
doc/src/compute_born.rst → doc/src/compute_born_matrix.rst
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@ -1,24 +1,24 @@
.. index:: compute born
.. index:: compute born/matrix
compute born command
====================
compute born/matrix command
===========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID born
compute ID group-ID born/matrix
* ID, group-ID are documented in :doc:`compute <compute>` command
* born = style name of this compute command
* born/matrix = style name of this compute command
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all born
compute 1 all born/matrix
Description
"""""""""""
@ -49,7 +49,7 @@ as a 6x6 symmetric matrix:
In the above expression, :math:`\sigma` stands for the virial stress
tensor, :math:`\delta` is the Kronecker delta and the usual notation apply for
the number of particle, the temperature and volume respectively :math:`N`,
:math:`T` and :math:`V`. :math `k_{B}` is the Boltzmann constant.
:math:`T` and :math:`V`. :math:`k_{B}` is the Boltzmann constant.
The Born term is a symmetric 6x6 matrix by construction and as such can be
expressed as 21 independent terms. The terms are ordered corresponding to the
@ -75,7 +75,7 @@ The output can be accessed using usual Lammps routines:
.. code-block:: LAMMPS
compute 1 all born
compute 1 all born/matrix
compute 2 all pressure NULL virial
variable S1 equal -c_2[1]
variable S2 equal -c_2[2]
@ -112,9 +112,10 @@ Restrictions
The Born term can be decomposed as a product of two terms. The first one
is a general term which depends on the configuration. The second one is
specific to every interaction composing your forcefield (non-bonded,
bonds, angle...). Currently not all interaction implement the born
method giving first and second order derivatives and an error will
be raised if you try to use this compute with such interactions.
bonds, angle...). Currently not all interaction implement the *born_matrix*
method giving first and second order derivatives and a warning will
be raised if you try to use this compute with such interactions. The returned
values of this forcefield component is currently zero.
Default
"""""""