some more converted atc fix_modify docs

doc/src/atc_mesh_output.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC mesh output
+
+fix_modify AtC mesh output command
+==================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mesh output <file_prefix>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mesh output = name of the AtC sub-command
+* file_prefix = prefix of various generated output files
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh output meshData
+
+
+Description
+"""""""""""
+
+Command to output mesh and associated data: nodesets, facesets, and
+elementsets. This data is only output once upon initialization since
+currently the mesh is static. Creates binary (EnSight, "gold" format)
+output of mesh data.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.

doc/src/atc_output.rst

@@ -16,11 +16,13 @@ Syntax
 * filename_prefix = prefix for data files (for *output*)
 * frequency = frequency of output in time-steps (for *output*)
 * optional keywords for *output*:
+
   - text = creates text output of index, step and nodal variable values for unique nodes
   - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes
   - binary = creates binary EnSight output
   - vector_components = outputs vectors as scalar components
   - tensor_components = outputs tensor as scalar components (for use with ParaView)
+
 * *step* or *time* = index output by step or by time (for *output index*)
 
 

doc/src/atc_output_boundary_integral.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC output boundary_integral
+
+fix_modify AtC output boundary_integral command
+===============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> output boundary_integral <fieldname> faceset [name]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* output boundary_integral = name of the AtC sub-command
+* fieldname = name of hardy field
+* faceset = required keyword
+* name= name of faceset
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC output boundary_integral stress faceset loop1
+
+
+Description
+"""""""""""
+
+Calculates a surface integral of the given field dotted with the outward
+normal of the faces and puts output in the "GLOBALS" file.
+
+Restrictions
+""""""""""""
+
+Must be used with the hardy/field type of :doc:`fix atc <fix_atc>`
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.

doc/src/atc_output_contour_integral.rst

@@ -0,0 +1,48 @@
+.. index:: fix_modify AtC output contour_integral
+
+fix_modify AtC output contour_integral command
+==============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> output contour_integral <fieldname> faceset <name> [axis [x|y|z]]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* output contour_integral = name of the AtC sub-command
+* fieldname = name of hardy field
+* faceset = required keyword
+* name = name of faceset
+* *axis x* or *axis y* or *axis z* = (optional)
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC output contour_integral stress faceset loop1
+
+
+Description
+"""""""""""
+
+Calculates a surface integral of the given field dotted with the outward
+normal of the faces and puts output in the "GLOBALS" file.
+
+Restrictions
+""""""""""""
+
+Must be used with the hardy/field type of :doc:`fix atc <fix_atc>`
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.

doc/src/atc_output_nodeset.rst

@@ -0,0 +1,49 @@
+.. index:: fix_modify AtC output nodeset
+
+fix_modify AtC output nodeset command
+=====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> output nodeset <nodeset_name> <operation>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* output nodeset = name of the AtC sub-command
+* nodeset_name= name of nodeset to be operated on
+* operation = *sum*
+
+  * *sum* = creates nodal sum over nodes in specified nodeset
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC output nodeset nset1 sum
+
+
+Description
+"""""""""""
+
+Performs operation over the nodes belonging to specified nodeset and
+outputs resulting variable values to GLOBALS file.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix atc command <fix_atc>`
+
+Default
+"""""""
+
+None.

doc/src/atc_output_volume_integral.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC output volume_integral
+
+fix_modify AtC output volume_integral command
+=============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> output volume_integral <elementset_name> <field>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* output volume_integral = name of the AtC sub-command
+* elementset_name= name of elementset to be integrated over
+* fieldname = name of field to integrate
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC output volume_integral eset1 mass_density
+
+
+Description
+"""""""""""
+
+Performs volume integration of specified field over elementset and
+outputs resulting variable values to GLOBALS file.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix atc command <fix_atc>`
+
+Default
+"""""""
+
+None.

doc/src/atc_read_restart.rst

@@ -0,0 +1,48 @@
+.. index:: fix_modify AtC read_restart
+
+fix_modify AtC read_restart command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> read_restart <file_name>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* read_restart = name of the AtC sub-command
+* file_name = name of AtC restart file
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC read_restart restart.mydata.AtC
+
+
+Description
+"""""""""""
+
+Reads the current state of the AtC fields from a named text-based restart file.
+
+Restrictions
+""""""""""""
+
+The restart file only contains fields and their time derivatives.  The
+reference positions of the atoms and the commands that initialize the
+fix are not saved e.g. an identical mesh containing the same atoms will
+have to be recreated.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC write_restart <atc_write_restart>`
+
+Default
+"""""""
+
+None.

doc/src/atc_write_restart.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC write_restart
+
+fix_modify AtC write_restart command
+====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> write_restart <file_name>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* write_restart = name of the AtC sub-command
+* file_name = name of AtC restart file
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC write_restart restart.mydata.AtC
+
+
+Description
+"""""""""""
+
+Dumps the current state of the fields to a named text-based restart
+file.  This done when the command is invoked and not repeated, unlike
+the otherwise similar LAMMPS command.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC read_restart <atc_read_restart>`
+
+Default
+"""""""
+
+None.

doc/src/fix_atc.rst

@@ -18,8 +18,8 @@ Syntax
 
     *thermal* = thermal coupling with fields: temperature
     *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature
-    *hardy* = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
-    *field* = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
+    *hardy* = on-the-fly post-processing using kernel localization functions
+    *field* = on-the-fly post-processing using mesh-based localization functions
 
 * parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
 
@@ -196,13 +196,13 @@ conditions.
 *fix_modify* commands for output:
 
 * :doc:`fix_modify AtC output <atc_output>`
-* `fix_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
-* `fix_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
-* `fix_modify AtC output boundary_integral <USER/atc/man_boundary_integral.html>`_
-* `fix_modify AtC output contour_integral <USER/atc/man_contour_integral.html>`_
-* `fix_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
-* `fix_modify AtC write_restart <USER/atc/man_write_restart.html>`_
-* `fix_modify AtC read_restart <USER/atc/man_read_restart.html>`_
+* :doc:`fix_modify AtC output nodeset <atc_output_nodeset>`
+* :doc:`fix_modify AtC output volume_integral <atc_output_volume_integral>`
+* :doc:`fix_modify AtC output boundary_integral <atc_output_boundary_integral>`
+* :doc:`fix_modify AtC output contour_integral <atc_output_contour_integral>`
+* :doc:`fix_modify AtC mesh output <atc_mesh_output>`
+* :doc:`fix_modify AtC write_restart <atc_write_restart>`
+* :doc:`fix_modify AtC read_restart <atc_read_restart>`
 
 *fix_modify* commands for post-processing: