next set of converted AtC documentation

doc/src/atc_control_momentum.rst

@@ -0,0 +1,77 @@
+.. index:: fix_modify AtC control momentum
+
+fix_modify AtC control momentum command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
+   fix_modify AtC control momentum none
+   fix_modify AtC control momentum rescale <frequency>
+   fix_modify AtC control momentum glc_displacement
+   fix_modify AtC control momentum glc_velocity
+   fix_modify AtC control momentum hoover
+   fix_modify AtC control momentum flux [faceset face_set_id, interpolate]
+   
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* control = name of the AtC sub-command
+* physics_type = *thermal* or *momentum*
+* solution_parameter = *max_iterations* or *tolerance*
+* value = solution_parameter value
+* momentum option = *none* or *rescale* or *glc_displacement* or *glc_velocity* *hoover* or *flux*
+* frequency = time step frequency for applying displacement and velocity rescaling
+* faceset_id = id of boundary face set (optional, only for *faceset*)
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC control momentum none
+   fix_modify AtC control momentum flux faceset bndy_faces
+   fix_modify AtC control momentum glc_velocity
+
+Description
+"""""""""""
+
+The general version of *control* sets the numerical parameters for the
+matrix solvers used in the specified control algorithm.  Many solution
+approaches require iterative solvers, and these methods enable users to
+provide the maximum number of iterations and the relative tolerance.
+
+The *control momentum* version sets the momentum exchange mechanism from
+the finite elements to the atoms, managed through a control algorithm.
+*rescale* computes a scale factor for each atom to match the finite
+element temperature.  *hoover* is a Gaussian least-constraint isokinetic
+thermostat enforces that the nodal restricted atomic temperature matches
+the finite element temperature.  *flux* is a similar mode, but rather
+adds energy to the atoms based on conservation of energy.
+
+*correction_max_iterations* sets the maximum number of iterations to
+compute the 2nd order in time correction term for lambda with the
+fractional step method. The method uses the same tolerance as the
+controller's matrix solver.
+
+Restrictions
+""""""""""""
+
+Only for be used with the specific controllers *thermal* or *momentum*.
+They are ignored if a lumped solution is requested.
+
+*control momentum* is only for be used with specific transfers: elastic
+*rescale* not valid with time filtering activated
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC control thermal <atc_control_thermal>`
+
+Default
+"""""""
+
+- *max_iterations* is the number of rows in the matrix.
+- *tolerance* is 1.0e-10.

doc/src/atc_control_thermal.rst

@@ -0,0 +1,87 @@
+.. index:: fix_modify AtC control thermal
+
+fix_modify AtC control thermal command
+======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
+   fix_modify <AtC fixID> control thermal <control_type> <optional_args>
+   fix_modify <AtC fixID> control thermal rescale <frequency>
+   fix_modify <AtC fixID> control thermal flux <boundary_integration_type> <faceset_id>
+   fix_modify <AtC fixID> control thermal correction_max_iterations <max_iterations>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* control = name of the AtC sub-command
+* physics_type = *thermal* or *momentum*
+* solution_parameter = *max_iterations* or *tolerance*
+* value = solution_parameter value
+* thermal control_type = *none* or *rescale* or *hoover* or *flux*
+* frequency = time step frequency for applying velocity rescaling
+* boundary_integration_type = *faceset* or *interpolate* (optional)
+* faceset_id = id of boundary face set (optional, only for *faceset*)
+* correction_max_iterations = maximum number of iterations that will be used by iterative matrix solvers for *thermal* physics type
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC control thermal none
+   fix_modify AtC control thermal rescale 10
+   fix_modify AtC control thermal hoover
+   fix_modify AtC control thermal flux
+   fix_modify AtC control thermal flux faceset bndy_faces
+   fix_modify AtC control thermal correction_max_iterations 10
+
+Description
+"""""""""""
+
+The general version of *control* sets the numerical parameters for the
+matrix solvers used in the specified control algorithm.  Many solution
+approaches require iterative solvers, and these methods enable users to
+provide the maximum number of iterations and the relative tolerance.
+
+The *control thermal* version sets the energy exchange mechanism from
+the finite elements to the atoms, managed through a control algorithm.
+*rescale* computes a scale factor for each atom to match the finite
+element temperature.  *hoover* is a Gaussian least-constraint isokinetic
+thermostat enforces that the nodal restricted atomic temperature matches
+the finite element temperature.  *flux* is a similar mode, but rather
+adds energy to the atoms based on conservation of energy. *hoover* and
+*flux* allow the prescription of sources or fixed temperatures on the
+atoms.
+
+*correction_max_iterations* sets the maximum number of iterations to
+compute the 2nd order in time correction term for lambda with the
+fractional step method. The method uses the same tolerance as the
+controller's matrix solver.
+
+Restrictions
+""""""""""""
+
+Only for be used with the specific controllers *thermal* or *momentum*.
+They are ignored if a lumped solution is requested.
+
+*control thermal* is only for be used with specific transfers: thermal (*rescale*\ , *hoover*\ , *flux*\ ), *two_temperature* (*flux*\ ).
+*rescale* not valid with time filtering activated
+
+*correction_max_iterations* is only for use with *thermal* physics using
+the fractional step method.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC control momentum <atc_control_momentum>`
+
+Default
+"""""""
+
+- *max_iterations* is the number of rows in the matrix.
+- *tolerance* is 1.0e-10.
+- *rescale* frequency is 1
+- *flux* boundary_integration_type is *interpolate*
+- *correction_max_iterations* is 20

doc/src/atc_fix.rst

@@ -1,7 +1,7 @@
 .. index:: fix_modify AtC fix
 
-fix_modify AtC initial command
-==============================
+fix_modify AtC fix command
+==========================
 
 Syntax
 """"""

doc/src/atc_fix_flux.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC fix_flux
+
+fix_modify AtC fix_flux command
+===============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> fix_flux <field> <face_set> <value|function>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* fix_flux = name of the AtC sub-command
+* field = field kind name valid for type of physics: *temperature* or *electron_temperature*
+* face_set = name of set of element faces
+* *value* or *function* = value or name of function followed by its parameters
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC fix_flux temperature faceSet 10.0
+
+Description
+"""""""""""
+
+Command for fixing normal fluxes e.g. heat_flux. This command only
+prescribes the normal component of the physical flux, e.g. heat (energy)
+flux. The units are in AtC units, i.e. derived from the LAMMPS length,
+time, and mass scales.
+
+Restrictions
+""""""""""""
+
+Only normal fluxes (Neumann data) can be prescribed.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`
+
+Default
+"""""""
+
+None.

doc/src/atc_internal_element_set.rst

@@ -39,8 +39,8 @@ 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
-""""""""""""""""""""""""
+Related AtC commands
+""""""""""""""""""""
 
 - :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
 - :doc:`fix_modify AtC boundary type <atc_boundary_type>`

doc/src/atc_remove_source.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC remove_source
+
+fix_modify AtC remove_source command
+====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> remove_source <field> <element_set>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* remove_source = name of the AtC sub-command
+* field = field kind name valid for type of physics: *temperature* or *electron_temperature*
+* element_set = name of set of elements
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC remove_source temperature groupNAME
+
+Description
+"""""""""""
+
+Remove a domain source.
+
+Restrictions
+""""""""""""
+
+The keyword *all* is reserved and thus not available as element_set name.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC source <atc_source>`
+
+Default
+"""""""
+
+None.

doc/src/atc_source.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC source
+
+fix_modify AtC source command
+==============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> source <field> <element_set> <value|function>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* source = name of the AtC sub-command
+* field = field kind name valid for type of physics: *temperature* or *electron_temperature*
+* element_set = name of set of elements
+* *value* or *function* = value or name of function followed by its parameters
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC source temperature middle temporal_ramp 10.0 0.0
+
+Description
+"""""""""""
+
+Add domain sources to the mesh. The units are consistent with LAMMPS's
+units for mass, length and time and are defined by the PDE being solved,
+e.g. for thermal transfer the balance equation is for energy and source
+is energy per time.
+
+Restrictions
+""""""""""""
+
+The keyword *all* is reserved and thus not available as element_set name.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC remove_source <atc_remove_source>`
+
+Default
+"""""""
+
+None.

doc/src/atc_unfix.rst

@@ -1,6 +1,6 @@
 .. index:: fix_modify AtC unfix
 
-fix_modify AtC initial command
+fix_modify AtC unfix command
 ==============================
 
 Syntax

doc/src/atc_unfix_flux.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC unfix_flux
+
+fix_modify AtC unfix_flux command
+=================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> unfix_flux <field> <face_set> <value|function>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* unfix_flux = name of the AtC sub-command
+* field = field kind name valid for type of physics: *temperature* or *electron_temperature*
+* face_set = name of set of element faces
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC unfix_flux temperature faceSet
+
+Description
+"""""""""""
+
+Command for removing prescribed normal fluxes e.g. heat_flux, stress.
+
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+:doc:`fix_modify AtC fix_flux <atc_fix_flux>`
+
+Default
+"""""""
+
+None.

doc/src/fix_atc.rst

@@ -172,17 +172,15 @@ conditions.
 * :doc:`fix_modify AtC initial <atc_initial>`
 * :doc:`fix_modify AtC fix <atc_fix>`
 * :doc:`fix_modify AtC unfix <atc_unfix>`
-* `fix_modify AtC fix_flux <USER/atc/man_fix_flux.html>`_
-* `fix_modify AtC unfix_flux <USER/atc/man_unfix_flux.html>`_
-* `fix_modify AtC source <USER/atc/man_source.html>`_
-* `fix_modify AtC remove_source <USER/atc/man_remove_source.html>`_
+* :doc:`fix_modify AtC fix_flux <atc_fix_flux>`
+* :doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`
+* :doc:`fix_modify AtC source <atc_source>`
+* :doc:`fix_modify AtC remove_source <atc_remove_source>`
 
 *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>`_
-* `fix_modify AtC control thermal correction_max_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
-* `fix_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
+* :doc:`fix_modify AtC control thermal <atc_control_thermal>`
+* :doc:`fix_modify AtC control momentum <atc_control_momentum>`
 * `fix_modify AtC control localized_lambda <USER/atc/man_localized_lambda.html>`_
 * `fix_modify AtC control lumped_lambda_solve <USER/atc/man_lumped_lambda_solve.html>`_
 * `fix_modify AtC control mask_direction <USER/atc/man_mask_direction.html>`_ control