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Final batch of index cleanup and code-blocks

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This commit is contained in:
Richard Berger
2020-02-27 11:08:04 -05:00
parent 9ef5949798
commit 25ec8d36a8
63 changed files with 690 additions and 702 deletions
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36
doc/src/pair_python.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style python
.. index:: pair_style python
pair\_style python command
==========================
pair_style python command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python cutoff
@ -17,14 +17,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff \* \* py_pot.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
pair_style hybrid/overlay coul/long 12.0 python 12.0
pair_coeff \* \* coul/long
pair_coeff \* \* python py_pot.LJCutSPCE OW NULL
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
Description
"""""""""""
@ -62,9 +62,9 @@ two are supposed to be using the 'LJ1' parameters and the third the
'LJ2' parameters, then you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* py_pot.LJCutMelt LJ1 LJ1 LJ2
pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2
The first two arguments **must** be \* \* so as to span all LAMMPS atom
types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
@ -83,10 +83,10 @@ placeholders for atom types that will be used with other potentials.
The python potential file has to start with the following code:
.. parsed-literal::
.. code-block:: python
from __future_\_ import print_function
#
from __future__ import print_function
class LAMMPSPairPotential(object):
def __init__(self):
self.pmap=dict()
@ -115,7 +115,7 @@ Here is an example for a single type Lennard-Jones potential class
which the parameters epsilon and sigma are both 1.0:
.. parsed-literal::
.. code-block:: python
class LJCutMelt(LAMMPSPairPotential):
def __init__(self):
@ -140,7 +140,7 @@ value of the internal potential parameter data structure. Following
the *LJCutMelt* example, here are the two functions:
.. parsed-literal::
.. code-block:: python
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
@ -181,10 +181,10 @@ the *LJCutMelt* example, here are the two functions:
for an example LAMMPS input of how to build a table file:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff \* \* py_pot.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
@ -199,7 +199,7 @@ After switching the pair style to *table*\ , the potential tables need
to be assigned to the LAMMPS atom types like this:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table linear 2000
pair_coeff 1 1 melt.table lj