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Updated documentation

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This commit is contained in:
Aidan Thompson
2022-01-30 16:18:34 -07:00
parent 0f85809acf
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doc/src/compute_born_matrix.rst
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@ -12,13 +12,19 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* born/matrix = style name of this compute command
* the keyword *numdiff* may be appended
.. parsed-literal::
*numdiff* values = delta virial-ID
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all born/matrix
compute 1 all born/matrix numdiff 1.0e-4 myvirial
Description
"""""""""""
@ -96,6 +102,20 @@ solid the virial stress can have large variations between timesteps and average
values can be slow to converge. This term is better computed using
instantaneous values.
The *numdiff* keyword uses finite differences of energy to numerically
approximate the derivative. This is useful when using interaction styles
for which the analytical derivatives have not been implemented.
The keyword requirs the additional values *delta* and *virial-ID*
giving the size of the applied strain and the ID of the pressure compute
that provides the virial tensor, requiring that it use the virial
keyword e.g.
.. code-block:: LAMMPS
compute myvirial all pressure NULL virial
compute 1 all born/matrix numdiff 1.0e-4 myvirial
**Output info:**
This compute calculates a global array with the number of rows=21.
@ -110,15 +130,17 @@ Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
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 force field (non-bonded,
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 force field component is currently zero.
bonds, angle...). Currently not all LAMMPS interaction styles
implement the *born_matrix*
method giving first and second order derivatives and LAMMPS will
exit with an error if this compute is used with such interactions,
unless the *numdiff* option is also used.
Default
"""""""