From cbd8d07dafeb07b8f9a5a3061ddbcaa6f13a5278 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 12 Mar 2020 16:34:42 -0400
Subject: [PATCH] convert elementset AtC commands

---
 doc/src/atc_mesh_create_elementset.rst      | 45 +++++++++++++++++++
 doc/src/atc_mesh_delete_elements.rst        | 43 ++++++++++++++++++
 doc/src/atc_mesh_nodeset_to_elementset.rst  | 49 +++++++++++++++++++++
 doc/src/fix_atc.rst                         |  6 +--
 doc/utils/sphinx-config/false_positives.txt |  1 +
 5 files changed, 141 insertions(+), 3 deletions(-)
 create mode 100644 doc/src/atc_mesh_create_elementset.rst
 create mode 100644 doc/src/atc_mesh_delete_elements.rst
 create mode 100644 doc/src/atc_mesh_nodeset_to_elementset.rst

diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst
new file mode 100644
index 0000000000..f657198751
--- /dev/null
+++ b/doc/src/atc_mesh_create_elementset.rst
@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC mesh create_elementset
+
+fix_modify AtC mesh create_elementset command
+=============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   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
+* 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
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100
+
+Description
+"""""""""""
+
+Command to assign an id to a set of FE elements to be used subsequently
+in defining material and mesh-based operations.
+
+Restrictions
+""""""""""""
+
+Only viable for rectangular grids.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
+:doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`
+
+Default
+"""""""
+
+Coordinates are assumed to be in lattice units.
diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst
new file mode 100644
index 0000000000..c7f86abfd6
--- /dev/null
+++ b/doc/src/atc_mesh_delete_elements.rst
@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC mesh delete_elements
+
+fix_modify AtC mesh delete_elements command
+=============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   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
+* id = id of the element set
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh delete_elements gap
+
+Description
+"""""""""""
+
+Deletes a group of elements from the mesh.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
+:doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`
+
+Default
+"""""""
+
+None.
diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst
new file mode 100644
index 0000000000..0df933aaeb
--- /dev/null
+++ b/doc/src/atc_mesh_nodeset_to_elementset.rst
@@ -0,0 +1,49 @@
+.. index:: fix_modify AtC mesh nodeset_to_elementset
+
+fix_modify AtC mesh nodeset_to_elementset command
+=================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   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
+* <max/min> = flag to choose either the maximal or minimal elementset
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min
+
+
+Description
+"""""""""""
+
+Command to create an elementset from an existing nodeset. Either the
+minimal element set of elements with all nodes in the set, or maximal
+element set with all elements with at least one node in the set, can be
+created.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
+:doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
+
+Default
+"""""""
+
+Unless specified, the maximal element set is created.
diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst
index 165dad223d..0798dbc033 100644
--- a/doc/src/fix_atc.rst
+++ b/doc/src/fix_atc.rst
@@ -157,9 +157,9 @@ conditions.
 * :doc:`fix_modify AtC mesh add_to_nodeset <atc_mesh_add_to_nodeset>`
 * :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
 * :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
-* `fix_modify AtC mesh create_elementset <USER/atc/man_mesh_create_elementset.html>`_
-* `fix_modify AtC mesh delete_elements <USER/atc/man_mesh_delete_elements.html>`_
-* `fix_modify AtC mesh nodeset_to_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
+* :doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
+* :doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
+* :doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`
 * `fix_modify AtC boundary <USER/atc/man_boundary.html>`_
 * `fix_modify AtC internal_quadrature <USER/atc/man_internal_quadrature.html>`_
 * `fix_modify AtC time_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index a28b82212f..61c8b3ab70 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -746,6 +746,7 @@ electronegative
 electronegativity
 Eleftheriou
 ElementN
+elementset
 elif
 Elj
 Ellad