a couple more inputs and some formatting tuning/tweaking

doc/src/atc_atom_element_map.rst

@@ -0,0 +1,41 @@
+.. index:: fix_modify AtC atom_element_map
+
+fix_modify AtC atom_element_map command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> atom_element_map <eulerian|lagrangian> [<frequency>]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* atom_element_map = name of the AtC sub-command
+* *eulerian* or *lagrangian* = frame of reference
+* frequency = frequency of updating atom-to-continuum maps based on the current configuration - (only for eulerian)
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify atc atom_element_map eulerian 100
+
+Description
+"""""""""""
+
+Changes frame of reference from *eulerian* to *lagrangian* or vice versa
+and sets the frequency for which the map from atoms to elements is
+reformed and all the attendant data is recalculated.
+
+Restrictions
+""""""""""""
+
+Cannot change map type after initialization.
+
+Default
+"""""""
+
+*lagrangian*

doc/src/atc_boundary_type.rst

@@ -1,7 +1,7 @@
 .. index:: fix_modify AtC boundary type
 
 fix_modify AtC boundary type command
-=============================================
+====================================
 
 Syntax
 """"""

doc/src/atc_electron_integration.rst

@@ -12,8 +12,8 @@ Syntax
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * extrinsic electron_integration = name of the AtC sub-command
-* integration\_type = *explicit* or *implicit* or *steadydescriptor*
-* num\_subcycle\_steps = number of subcycle steps for the electron time integration (optional)
+* integration_type = *explicit* or *implicit* or *steadydescriptor*
+* num_subcycle_steps = number of subcycle steps for the electron time integration (optional)
 
 
 Examples
@@ -35,10 +35,10 @@ dynamics.
 Restrictions
 """"""""""""
 
-For use only with the two\_temperature type of the AtC fix (see
+For use only with the two_temperature type of the AtC fix (see
 :doc:`fix atc <fix_atc>` command)
 
 Default
 """""""
 
-*implicit* and *subcycle\_steps* = 1
+*implicit* and *subcycle_steps* = 1

doc/src/atc_internal_element_set.rst

@@ -0,0 +1,51 @@
+.. index:: fix_modify AtC internal_element_set
+
+fix_modify AtC internal_element_set command
+===========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> internal_element_set <element_set_name>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* internal_element_set = name of the AtC sub-command
+* element_set_name = name of element set defining internal region, or *off*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC internal_element_set myElementSet
+   fix_modify AtC internal_element_set off
+
+Description
+"""""""""""
+
+Enables AtC to base the region for internal atoms to be an element
+set. If no ghost atoms are used, all the AtC atoms must be constrained
+to remain in this element set by the user, e.g., with walls. If boundary
+atoms are used in conjunction with Eulerian atom maps AtC will partition
+all atoms of a boundary or internal type to be of type internal if they
+are in the internal region or to be of type boundary otherwise.
+
+Restrictions
+""""""""""""
+
+If boundary atoms are used in conjunction with Eulerian atom maps, the
+Eulerian reset frequency must be an integer multiple of the Lammps
+reneighbor frequency.
+
+Related AtC Sub-commands
+""""""""""""""""""""""""
+
+- :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
+- :doc:`fix_modify AtC boundary type <atc_boundary_type>`
+
+Default
+"""""""
+
+*off*

doc/src/atc_mesh_add_to_nodeset.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_nodeset = name of the AtC sub-command
+* mesh create_nodeset = name of the AtC sub-command
 * id = id to assign to the collection of FE nodes
 * <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added
 

doc/src/atc_mesh_create_elementset.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_elementset = name of the AtC sub-command
+* mesh create_elementset = name of the AtC sub-command
 * id = id to assign to the collection of FE nodes
 * <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements
 

doc/src/atc_mesh_create_faceset_box.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_faceset = name of the AtC sub-command
+* mesh create_faceset = name of the AtC sub-command
 * id = id to assign to the collection of FE faces
 * box = use bounding box to define FE faces
 * <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces

doc/src/atc_mesh_create_faceset_plane.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_faceset = name of the AtC sub-command
+* mesh create_faceset = name of the AtC sub-command
 * id = id to assign to the collection of FE faces
 * plane = use plane to define faceset
 * <val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]

doc/src/atc_mesh_create_nodeset.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_nodeset = name of the AtC sub-command
+* mesh create_nodeset = name of the AtC sub-command
 * id = id to assign to the collection of FE nodes
 * <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes
 

doc/src/atc_mesh_delete_elements.rst

@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> mesh delete_elements <id>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh create\_elementset = name of the AtC sub-command
+* mesh create_elementset = name of the AtC sub-command
 * id = id of the element set
 
 Examples

doc/src/atc_mesh_nodeset_to_elementset.rst

@@ -11,9 +11,9 @@ Syntax
    fix_modify <AtC fixID> mesh nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* mesh nodeset\_to\_elementset = name of the AtC sub-command
-* nodeset\_id = id of desired nodeset from which to create the elementset 
-* elementset\_id = id to assign to the collection of FE elements
+* mesh nodeset_to_elementset = name of the AtC sub-command
+* nodeset_id = id of desired nodeset from which to create the elementset
+* elementset_id = id to assign to the collection of FE elements
 * <max/min> = flag to choose either the maximal or minimal elementset
 
 Examples

doc/src/atc_time_integration.rst

@@ -1,7 +1,7 @@
 .. index:: fix_modify AtC time_integration
 
 fix_modify AtC time_integration command
-=============================================
+=======================================
 
 Syntax
 """"""
@@ -11,7 +11,7 @@ Syntax
    fix_modify <AtC fixID> time_integration <descriptor>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
-* time\_integration = name of the AtC sub-command
+* time_integration = name of the AtC sub-command
 * descriptor =  *gear* or *fractional_step* or *verlet*
 
 
@@ -36,7 +36,7 @@ Options for thermal time integration:
   atomic velocity update with 2nd order Verlet, nodal temperature update
   with 3rd or 4th order Gear, thermostats based on controlling power
 
-*fractional\_step*
+*fractional_step*
   atomic velocity update with 2nd order Verlet, mixed nodal temperature
   update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
   thermostats based on controlling discrete energy changes
@@ -49,7 +49,7 @@ Options for momentum time integration:
   atomic velocity update with 2nd order Verlet, nodal temperature update
   with 2nd order Verlet, kinetostats based on controlling force
 
-*fractional\_step*
+*fractional_step*
   atomic velocity update with 2nd order Verlet, mixed nodal momentum
   update, 2nd order Verlet for continuum and exact 2nd order Verlet for
   atomic contributions, kinetostats based on controlling discrete

doc/src/fix_atc.rst

@@ -12,7 +12,7 @@ Syntax
 
 * fixID = name of fix
 * group = name of group fix is to be applied
-* type = *thermal* or *two\_temperature* or *hardy* or *field*
+* type = *thermal* or *two_temperature* or *hardy* or *field*
 
 .. parsed-literal::
 
@@ -21,7 +21,7 @@ Syntax
     *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)
 
-* parameter\_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
+* parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
 
 Examples
 """"""""
@@ -39,7 +39,7 @@ Description
 This fix is the beginning to creating a coupled FE/MD simulation and/or
 an on-the-fly estimation of continuum fields. The coupled versions of
 this fix do Verlet integration and the post-processing does not. After
-instantiating this fix, several other fix\_modify commands will be
+instantiating this fix, several other fix_modify commands will be
 needed to set up the problem, e.g. define the finite element mesh and
 prescribe initial and boundary conditions.
 
@@ -118,7 +118,7 @@ Note coupling and post-processing can be combined in the same simulations using
 
 ----------
 
-**Restart, fix\_modify, output, run start/stop, minimize info:**
+**Restart, fix_modify, output, run start/stop, minimize info:**
 
 No information about this fix is written to :doc:`binary restart files
 <restart>`.  The :doc:`fix_modify <fix_modify>` options relevant to this
@@ -131,7 +131,7 @@ invoked during :doc:`energy minimization <minimize>`.
 Restrictions
 """"""""""""
 
-Thermal and two\_temperature (coupling) types use a Verlet
+Thermal and two_temperature (coupling) types use a Verlet
 time-integration algorithm. The hardy type does not contain its own
 time-integrator and must be used with a separate fix that does contain
 one, e.g. nve, nvt, etc. In addition, currently:
@@ -147,7 +147,7 @@ After specifying this fix in your input script, several other
 e.g. define the finite element mesh and prescribe initial and boundary
 conditions.
 
-*fix\_modify* commands for setup:
+*fix_modify* commands for setup:
 
 * :doc:`fix_modify AtC mesh create <atc_mesh_create>`
 * :doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
@@ -164,10 +164,10 @@ conditions.
 * :doc:`fix_modify AtC internal_quadrature <atc_internal_quadrature>`
 * :doc:`fix_modify AtC time_integration <atc_time_integration>`
 * :doc:`fix_modify AtC extrinsic electron_integration <atc_electron_integration>`
-* `fix_modify AtC internal_element_set <USER/atc/man_internal_element_set.html>`_
+* :doc:`fix_modify AtC internal_element_set <atc_internal_element_set>`
 * `fix_modify AtC decomposition <USER/atc/man_decomposition.html>`_
 
-*fix\_modify* commands for boundary and initial conditions:
+*fix_modify* commands for boundary and initial conditions:
 
 * `fix_modify AtC initial <USER/atc/man_initial.html>`_
 * `fix_modify AtC fix <USER/atc/man_fix_nodes.html>`_
@@ -177,7 +177,7 @@ conditions.
 * `fix_modify AtC source <USER/atc/man_source.html>`_
 * `fix_modify AtC remove_source <USER/atc/man_remove_source.html>`_
 
-*fix\_modify* commands for control and filtering:
+*fix_modify* commands for control and filtering:
 
 * `fix_modify AtC control <USER/atc/man_control.html>`_
 * `fix_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
@@ -193,7 +193,7 @@ conditions.
 * `fix_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
 * `fix_modify AtC poisson_solver <USER/atc/man_poisson_solver.html>`_
 
-*fix\_modify* commands for output:
+*fix_modify* commands for output:
 
 * `fix_modify AtC output <USER/atc/man_output.html>`_
 * `fix_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
@@ -204,7 +204,7 @@ conditions.
 * `fix_modify AtC write_restart <USER/atc/man_write_restart.html>`_
 * `fix_modify AtC read_restart <USER/atc/man_read_restart.html>`_
 
-*fix\_modify* commands for post-processing:
+*fix_modify* commands for post-processing:
 
 * `fix_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
 * `fix_modify AtC fields <USER/atc/man_hardy_fields.html>`_
@@ -216,9 +216,9 @@ conditions.
 * `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
 * `fix_modify AtC set <USER/atc/man_set.html>`_
 
-miscellaneous *fix\_modify* commands:
+miscellaneous *fix_modify* commands:
 
-* `fix_modify AtC atom_element_map <USER/atc/man_atom_element_map.html>`_
+* :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
 * `fix_modify AtC atom_weight <USER/atc/man_atom_weight.html>`_
 * `fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights.html>`_
 * `fix_modify AtC reset_time <USER/atc/man_reset_time.html>`_