finish updating docs for fixes using code-block plus a few other improvements

Examples

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   fix 5 all bond/break 10 2 1.2

   fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829

Examples

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   fix 5 all bond/create 10 1 2 0.8 1

   fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3

For unabridged example scripts and files, see examples/USER/reaction.

.. parsed-literal::

.. code-block:: LAMMPS

   molecule mol1 pre_reacted_topology.txt

   molecule mol2 post_reacted_topology.txt

following command would add an additional thermostat to the group of

all currently-reacting atoms:

.. parsed-literal::

.. code-block:: LAMMPS

   fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1

Examples

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   fix 1 all bond/swap 50 0.5 1.3 598934

Boltzmann criterion.  To do this, the fix creates its own compute of

style *temp*\ , as if this command had been issued:

.. parsed-literal::

.. code-block:: LAMMPS

   compute fix-ID_temp all temp

Examples

""""""""

.. parsed-literal::

.. code-block:: LAMMPS

   fix 1 all box/relax iso 0.0 vmax 0.001

   fix 2 water box/relax aniso 0.0 dilate partial

this, the fix creates its own computes of style "temp" and "pressure",

as if these commands had been issued:

.. parsed-literal::

.. code-block:: LAMMPS

   compute fix-ID_temp group-ID temp

   compute fix-ID_press group-ID pressure fix-ID_temp virial

energy. Instead, the fix energy can be explicitly added to the

potential energy using one of these two variants:

.. parsed-literal::

.. code-block:: LAMMPS

   variable emin equal pe+f_1