Convert a first set of AtC documentation html files to rst and add infrastructure files and links

doc/src/Manual.rst

@@ -72,6 +72,7 @@ every LAMMPS command.
    angles
    dihedrals
    impropers
+   fix_modify_atc_commands
 
 Indices and tables
 ==================

doc/src/atc_mesh_create.rst

@@ -0,0 +1,46 @@
+.. index:: fix_modify AtC mesh create
+
+fix_modify AtC mesh create command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mesh create = name of the AtC sub-command
+* nx ny nz = number of elements in x-, y-, and z-direction
+* region-ID = ID of region that is to be meshed
+* f or p = periodicity flags for x-, y-, and z-direction
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh create 10 1 1 feRegion p p p
+
+Description
+"""""""""""
+
+Creates a uniform mesh in a rectangular region.
+
+Restrictions
+""""""""""""
+
+Creates only uniform rectangular grids in a rectangular region
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
+
+Default
+"""""""
+
+When created, the mesh defaults to gauss2 (2-point Gaussian)
+quadrature. Use the :doc:`fix_modify AtC mesh quadrature
+<atc_mesh_quadrature>` command to change the quadrature style.

doc/src/atc_mesh_create_nodeset.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC mesh create_nodeset
+
+fix_modify AtC mesh create_nodeset command
+==========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   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
+* 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
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
+
+Description
+"""""""""""
+
+Command to assign an id to a set of FE nodes to be used subsequently in
+defining boundary conditions.
+
+Restrictions
+""""""""""""
+
+None
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create <atc_mesh_create>`
+:doc:`fix_modify AtC mesh read <atc_mesh_read>`
+
+Default
+"""""""
+
+Coordinates are assumed to be in lattice units.

doc/src/atc_mesh_quadrature.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC mesh quadrature
+
+fix_modify AtC mesh quadrature command
+======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mesh quatrature <quad>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mesh quadrature = name of the AtC sub-command
+* quad = *nodal* or *gauss1* or *gauss2* or *gauss3* or *face*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh quadrature face
+
+Description
+"""""""""""
+
+(Re-)assigns the quadrature style for an existing mesh.  When a mesh is
+created its quadrature method defaults to gauss2.  Use this call to
+change it after the fact.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create <atc_mesh_create>`
+
+Default
+"""""""
+
+None.

doc/src/atc_mesh_read.rst

@@ -0,0 +1,46 @@
+.. index:: fix_modify AtC mesh read
+
+fix_modify AtC mesh read command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mesh read <f|p> <f|p> <f|p>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mesh read = name of the AtC sub-command
+* filename = name of the file containing the mesh to be read
+* f or p = periodicity flags for x-, y-, and z-direction (optional)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh read myComponent.mesh p p p
+   fix_modify AtC mesh read myOtherComponent.exo
+
+Description
+"""""""""""
+
+Reads a mesh from a text or exodus file, and assigns periodic boundary
+conditions if needed.
+
+Restrictions
+""""""""""""
+
+None
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create <atc_mesh_create>`
+:doc:`fix_modify AtC mesh write <atc_mesh_write>`
+
+Default
+"""""""
+
+Periodicity flags are set to false (f) by default.

doc/src/atc_mesh_write.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC mesh write
+
+fix_modify AtC mesh write command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mesh write <f|p> <f|p> <f|p>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mesh write = name of the AtC sub-command
+* filename = name of the file containing the mesh to be write
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh write myMesh.mesh
+
+Description
+"""""""""""
+
+Writes a mesh to a text file.
+
+Restrictions
+""""""""""""
+
+None
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create <atc_mesh_create>`
+:doc:`fix_modify AtC mesh read <atc_mesh_read>`
+
+Default
+"""""""
+
+None.

doc/src/fix_atc.rst

@@ -36,7 +36,12 @@ Examples
 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 needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+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
+needed to set up the problem, e.g. define the finite element mesh and
+prescribe initial and boundary conditions.
 
 .. image:: JPG/atc_nanotube.jpg
    :align: center
@@ -115,17 +120,21 @@ Note coupling and post-processing can be combined in the same simulations using
 
 **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 fix are listed below.  No global scalar or vector or
-per-atom quantities are stored by this fix for access by various
-:doc:`output commands <Howto_output>`.  No parameter of this fix can be
-used with the *start/stop* keywords of the :doc:`run <run>` command.
-This fix is not invoked during :doc:`energy minimization <minimize>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  The :doc:`fix_modify <fix_modify>` options relevant to this
+fix are listed below.  No global scalar or vector or per-atom quantities
+are stored by this fix for access by various :doc:`output commands
+<Howto_output>`.  No parameter of this fix can be used with the
+*start/stop* keywords of the :doc:`run <run>` command.  This fix is not
+invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-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:
+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:
 
 * the coupling is restricted to thermal physics
 * the FE computations are done in serial on each processor.
@@ -133,15 +142,18 @@ Thermal and two\_temperature (coupling) types use a Verlet time-integration algo
 Related commands
 """"""""""""""""
 
-After specifying this fix in your input script, several other :doc:`fix_modify <fix_modify>` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
+After specifying this fix in your input script, several other
+:doc:`fix_modify <fix_modify>` commands are used to setup the problem,
+e.g. define the finite element mesh and prescribe initial and boundary
+conditions.
 
 *fix\_modify* commands for setup:
 
-* `fix_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
-* `fix_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
-* `fix_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
-* `fix_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
-* `fix_modify AtC mesh create_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
+* :doc:`fix_modify AtC mesh create <atc_mesh_create>`
+* :doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
+* :doc:`fix_modify AtC mesh read <atc_mesh_read>`
+* :doc:`fix_modify AtC mesh write <atc_mesh_write>`
+* :doc:`fix_modify AtC mesh create_nodeset <atc_mesh_create_nodeset>`
 * `fix_modify AtC mesh add_to_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
 * `fix_modify AtC mesh create_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
 * `fix_modify AtC mesh create_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_

doc/src/fix_modify_atc_commands.rst

@@ -0,0 +1,8 @@
+fix_modify AtC commands
+############################
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   atc_*