next batch of converted files. one more section to go.

doc/src/atc_hardy_on_the_fly.rst

@@ -8,7 +8,7 @@ Syntax
 
 .. parsed-literal::
 
-   fix_modify <AtC fixID> on_the_fly on_the_fly <bond|kernel> <on|off>
+   fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * on_the_fly = name of the AtC sub-command

doc/src/atc_pair_interactions.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC pair_interactions
+
+fix_modify AtC pair_interactions command
+========================================
+
+fix_modify AtC bond_interactions command
+========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> pair_interactions <on|off>
+   fix_modify <AtC fixID> bond_interactions <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* *pair_interactions* or *bond_interactions* = name of the AtC sub-command
+* *on* or *off* = activate or deactivate
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC pair_interactions off
+   fix_modify AtC bond_interactions on
+
+Description
+"""""""""""
+
+Include bonds and/or pairs in stress and heat flux computations.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*pair_interactions*\ : on, *bond_interactions*\ : off

doc/src/atc_sample_frequency.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC sample_frequency
+
+fix_modify AtC sample_frequency command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> sample_frequency <freq>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* sample_frequency = name of the AtC sub-command
+* freq = frequency to sample fields in number of steps
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC sample_frequency 10
+
+Description
+"""""""""""
+
+Specifies a frequency at which fields are computed for the case where
+time filters are being applied.
+
+Restrictions
+""""""""""""
+
+Must be used with :doc:`fix atc hardy <fix_atc>` and is only relevant when time filters are being used.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.
+

doc/src/atc_set_reference_pe.rst

@@ -0,0 +1,50 @@
+.. index:: fix_modify AtC set reference_potential_energy
+
+fix_modify AtC set reference_potential_energy command
+=====================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* set reference_potential_energy = name of the AtC sub-command
+* value = optional user specified zero point for PE in native LAMMPS energy units
+* filename = optional user specified string for file of nodal PE values to be read-in
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC set reference_potential_energy
+   fix_modify AtC set reference_potential_energy -0.05
+   fix_modify AtC set reference_potential_energy myPEvalues 
+
+Description
+"""""""""""
+
+Used to set various quantities for the post-processing algorithms. It
+sets the zero point for the potential energy density using the value
+provided for all nodes, or from the current configuration of the lattice
+if no value is provided, or values provided within the specified
+filename.
+
+Restrictions
+""""""""""""
+
+Must be used with :doc:`fix atc hardy <fix_atc>` or :doc:`fix atc field <fix_atc>`.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+Defaults to the LAMMPS zero point i.e. isolated atoms.
+

doc/src/fix_atc.rst

@@ -212,9 +212,9 @@ conditions.
 * :doc:`fix_modify AtC rates <atc_hardy_rates>`
 * :doc:`fix_modify AtC computes <atc_hardy_computes>`
 * :doc:`fix_modify AtC on_the_fly <atc_hardy_on_the_fly>`
-* `fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions.html>`_
-* `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
-* `fix_modify AtC set <USER/atc/man_set.html>`_
+* :doc:`fix_modify AtC pair/bond_interactions <atc_pair_interactions>`
+* :doc:`fix_modify AtC sample_frequency <atc_sample_frequency>`
+* :doc:`fix_modify AtC set <atc_set_reference_pe>`
 
 miscellaneous *fix_modify* commands: