final batch of converted AtC doc files

doc/src/atc_add_molecule.rst

@@ -0,0 +1,48 @@
+.. index:: fix_modify AtC add_molecule
+
+fix_modify AtC add_molecule command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* add_molecule = name of the AtC sub-command
+* *small* or *large* = can be *small* if molecule size < cutoff radius, must be *large* otherwise
+* tag = tag for tracking a molecule
+* *group-ID* = LAMMPS defined group-ID
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   group WATERGROUP type 1 2
+   fix_modify AtC add_molecule small water WATERGROUP
+
+Description
+"""""""""""
+
+Associates a tag with all molecules corresponding to a specified group.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC add_species <atc_add_species>`
+- :doc:`fix_modify AtC remove_species <atc_remove_species>`
+- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
+
+Default
+"""""""
+
+None.

doc/src/atc_add_species.rst

@@ -0,0 +1,49 @@
+.. index:: fix_modify AtC add_species
+
+fix_modify AtC add_species command
+==================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> add_species <tag> <group|type> <ID>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* add_species = name of the AtC sub-command
+* tag = tag for tracking a species
+* *group* or *type* = LAMMPS defined group or type of atoms
+* ID = name of group or type number
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC add_species gold type 1
+   group GOLDGROUP type 1
+   fix_modify AtC add_species gold group GOLDGROUP
+
+Description
+"""""""""""
+
+Associates a tag with all atoms of a specified type or within a specified group.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
+- :doc:`fix_modify AtC remove_species <atc_remove_species>`
+- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
+
+Default
+"""""""
+
+None.

doc/src/atc_atomic_charge.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC atomic_charge
+
+fix_modify AtC atomic_charge command
+====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> <include|omit> atomic_charge
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* *include* or *omit* = switch to activate/deactivate inclusion of intrinsic atomic charge in ATC
+* atomic_charge = name of the AtC sub-command
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC include atomic_charge
+
+Description
+"""""""""""
+
+Determines whether AtC tracks the total charge as a finite element
+field.
+
+Restrictions
+""""""""""""
+
+Required for: *electrostatics*
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+If the atom charge is defined, default is on, otherwise default is off.

doc/src/atc_boundary_dynamics.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC boundary_dynamics
+
+fix_modify AtC boundary_dynamics command
+========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* boundary_dynamics = name of the AtC sub-command
+* *on* or *damped_harmonic* *prescribed* *coupled* *none*
+
+
+Description
+"""""""""""
+
+Sets different schemes for controlling boundary atoms.  *on* will integrate
+the boundary atoms using the velocity-verlet algorithm.  *damped_harmonic*
+uses a mass/spring/dashpot for the boundary atoms with added arguments
+of the damping and spring constants followed by the ratio of the
+boundary type mass to the desired mass.  *prescribed* forces the boundary
+atoms to follow the finite element displacement.  *coupled* does the same.
+
+Restrictions
+""""""""""""
+
+Boundary atoms must be specified.  When using swaps between internal and
+boundary atoms, the initial configuration must have already correctly
+partitioned the two.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*prescribed on*

doc/src/atc_consistent_fe_initialization.rst

@@ -12,7 +12,7 @@ Syntax
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * consistent_fe_initialization = name of the AtC sub-command
-* *on* or *off* = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
+* *on* or *off* = switch to activate/deactivate the initial setting of the FE intrinsic field to match the projected MD field
 
 Examples
 """"""""

doc/src/atc_mass_matrix.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC mass_matrix
+
+fix_modify AtC mass_matrix command
+==================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> mass_matrix <fe|md_fe>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* mass_matrix = name of the AtC sub-command
+* *fe* or *md_fe* = activate/deactivate using the FE mass matrix in the MD region
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC mass_matrix fe
+
+Description
+"""""""""""
+
+Determines whether AtC uses the FE mass matrix based on Gaussian
+quadrature or based on atomic quadrature in the MD region. This is
+useful for fully overlapping simulations to improve efficiency.
+
+Restrictions
+""""""""""""
+
+Should not be used unless the FE region is contained within the MD
+region, otherwise the method will be unstable and inaccurate.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*md_fe*

doc/src/atc_material.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC material
+
+fix_modify AtC material command
+===============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> material <elementset_name> <material_id>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* material = name of the AtC sub-command
+* elementset_name = name of the elementset
+* material_id = ID of the material
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC material gap_region 1
+
+Description
+"""""""""""
+
+Sets the material model in *elementset_name* to be of type *material_id*\ .
+
+Restrictions
+""""""""""""
+
+The element set must already be created and the material must be
+specified in the material file given the the atc fix on construction
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+All elements default to the first material in the material file.

doc/src/atc_remove_molecule.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC remove_molecule
+
+fix_modify AtC remove_molecule command
+======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> remove_molecule <tag>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* remove_molecule = name of the AtC sub-command
+* tag = tag for tracking a molecule
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC remove_molecule water
+
+Description
+"""""""""""
+
+Removes tag designated for tracking a specified set of molecules.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC add_species <atc_add_species>`
+- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
+- :doc:`fix_modify AtC remove_species <atc_remove_species>`
+
+Default
+"""""""
+
+None.

doc/src/atc_remove_species.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC remove_species
+
+fix_modify AtC remove_species command
+=====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> remove_species <tag>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* remove_species = name of the AtC sub-command
+* tag = tag for tracking a species
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC remove_species gold
+
+Description
+"""""""""""
+
+Removes tag designated for tracking a specified species.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC add_species <atc_add_species>`
+- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
+- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
+  
+Default
+"""""""
+
+None.

doc/src/atc_source_integration.rst

@@ -0,0 +1,42 @@
+.. index:: fix_modify AtC source_integration
+
+fix_modify AtC source_integration command
+=========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> source_integration <fe|atom>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* source_integration = name of the AtC sub-command
+* *fe* or *atom* = (undocumented)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC source_integration atom
+
+Description
+"""""""""""
+
+(undocumented)
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+Default is *fe*

doc/src/atc_temperature_definition.rst

@@ -0,0 +1,48 @@
+.. index:: fix_modify AtC temperature_definition
+
+fix_modify AtC temperature_definition command
+=============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> temperature_definition <kinetic|total>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* temperature_definition = name of the AtC sub-command
+* *kinetic* or *total* = (undocumented)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC temperature_definition kinetic
+
+Description
+"""""""""""
+
+Change the definition for the atomic temperature used to create the
+finite element temperature.  The kinetic option is based only on the
+kinetic energy of the atoms while the total option uses the total energy
+(kinetic + potential) of an atom.
+
+Restrictions
+""""""""""""
+
+This command is only valid when using thermal coupling.  Also, while not
+a formal restriction, the user should ensure that associating a
+potential energy with each atom makes physical sense for the total
+option to be meaningful.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*kinetic*

doc/src/atc_track_displacement.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC track_displacement
+
+fix_modify AtC track_displacement command
+=========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> track_displacement <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* track_displacement = name of the AtC sub-command
+* *on* or *off* = (undocumented)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC track_displacement on
+
+Description
+"""""""""""
+
+Determines whether displacement is tracked or not. For solids problems
+this is a useful quantity, but for fluids it is not relevant.
+
+Restrictions
+""""""""""""
+
+Some constitutive models require the displacement field.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*on*

doc/src/fix_atc.rst

@@ -227,19 +227,19 @@ miscellaneous *fix_modify* commands:
 * :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
 * :doc:`fix_modify AtC boundary_faceset <atc_boundary_faceset>`
 * :doc:`fix_modify AtC consistent_fe_initialization <atc_consistent_fe_initialization>`
-* `fix_modify AtC mass_matrix <USER/atc/man_mass_matrix.html>`_
-* `fix_modify AtC material <USER/atc/man_material.html>`_
-* `fix_modify AtC atomic_charge <USER/atc/man_atomic_charge.html>`_
-* `fix_modify AtC source_integration <USER/atc/man_source_integration.html>`_
-* `fix_modify AtC temperature_definition <USER/atc/man_temperature_definition.html>`_
-* `fix_modify AtC track_displacement <USER/atc/man_track_displacement.html>`_
-* `fix_modify AtC boundary_dynamics <USER/atc/man_boundary_dynamics.html>`_
-* `fix_modify AtC add_species <USER/atc/man_add_species.html>`_
-* `fix_modify AtC add_molecule <USER/atc/man_add_molecule.html>`_
-* `fix_modify AtC remove_species <USER/atc/man_remove_species.html>`_
-* `fix_modify AtC remove_molecule <USER/atc/man_remove_molecule.html>`_
+* :doc:`fix_modify AtC mass_matrix <atc_mass_matrix>`
+* :doc:`fix_modify AtC material <atc_material>`
+* :doc:`fix_modify AtC atomic_charge <atc_atomic_charge>`
+* :doc:`fix_modify AtC source_integration <atc_source_integration>`
+* :doc:`fix_modify AtC temperature_definition <atc_temperature_definition>`
+* :doc:`fix_modify AtC track_displacement <atc_track_displacement>`
+* :doc:`fix_modify AtC boundary_dynamics <atc_boundary_dynamics>`
+* :doc:`fix_modify AtC add_species <atc_add_species>`
+* :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
+* :doc:`fix_modify AtC remove_species <atc_remove_species>`
+* :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
 
-Note: a set of example input files with the attendant material files are included with this package
+Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders.
 
 Default
 """""""

doc/utils/sphinx-config/false_positives.txt

@@ -874,6 +874,7 @@ fdotr
 fdt
 Fehlberg
 Fellinger
+fe
 femtosecond
 femtoseconds
 fene