add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs

2020-03-13 11:06:11 -04:00 · 2020-03-13 11:06:11 -04:00 · 80d413b86c
parent 5a81f69495
commit 80d413b86c
29 changed files with 117 additions and 18 deletions
--- a/doc/src/atc_atom_element_map.rst
+++ b/doc/src/atc_atom_element_map.rst
@ -35,6 +35,11 @@ Restrictions

 Cannot change map type after initialization.

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_boundary_type.rst
+++ b/doc/src/atc_boundary_type.rst
@ -34,6 +34,11 @@ Restrictions

 None.

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_control_localized_lambda.rst
+++ b/doc/src/atc_control_localized_lambda.rst
@ -0,0 +1,46 @@
+.. index:: fix_modify AtC control localized_lambda
+
+fix_modify AtC control localized_lambda command
+===============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> control localized_lambda <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* control localized_lambda = name of the AtC sub-command
+* *on* or *off* = Toggles state of localization algorithm
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC control localized_lambda on
+
+Description
+"""""""""""
+
+Turns the localization algorithms *on* or *off* for control algorithms
+to restrict the influence of FE coupling or boundary conditions to a
+region near the boundary of the MD region.  Control algorithms will not
+affect atoms in elements not possessing faces on the boundary of the
+region.  Flux-based control is localized via row-sum lumping while
+quantity control is done by solving a truncated matrix equation.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+off
--- a/doc/src/atc_control_momentum.rst
+++ b/doc/src/atc_control_momentum.rst
@ -68,7 +68,8 @@ They are ignored if a lumped solution is requested.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC control thermal <atc_control_thermal>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC control thermal <atc_control_thermal>`

 Default
 """""""
--- a/doc/src/atc_control_thermal.rst
+++ b/doc/src/atc_control_thermal.rst
@ -75,7 +75,8 @@ the fractional step method.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC control momentum <atc_control_momentum>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC control momentum <atc_control_momentum>`

 Default
 """""""
--- a/doc/src/atc_decomposition.rst
+++ b/doc/src/atc_decomposition.rst
@ -37,6 +37,11 @@ Restrictions

 None.

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_electron_integration.rst
+++ b/doc/src/atc_electron_integration.rst
@ -38,6 +38,11 @@ Restrictions
 For use only with the two_temperature type of the AtC fix (see
 :doc:`fix atc <fix_atc>` command)

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_fix.rst
+++ b/doc/src/atc_fix.rst
@ -37,7 +37,8 @@ The keyword *all* is reserved and thus not available as nodeset name.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC unfix <atc_unfix>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC unfix <atc_unfix>`

 Default
 """""""
--- a/doc/src/atc_fix_flux.rst
+++ b/doc/src/atc_fix_flux.rst
@ -39,7 +39,8 @@ Only normal fluxes (Neumann data) can be prescribed.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`

 Default
 """""""
--- a/doc/src/atc_initial.rst
+++ b/doc/src/atc_initial.rst
@ -33,6 +33,11 @@ Restrictions

 The keyword *all* is reserved and thus not available as nodeset name.

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_internal_element_set.rst
+++ b/doc/src/atc_internal_element_set.rst
@ -42,6 +42,7 @@ reneighbor frequency.
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
 - :doc:`fix_modify AtC boundary type <atc_boundary_type>`

--- a/doc/src/atc_internal_quadrature.rst
+++ b/doc/src/atc_internal_quadrature.rst
@ -35,6 +35,11 @@ Optional region tag specifies which finite element nodes will be treated
 as being within the MD region. This option is only valid with
 internal_quadrature off.

+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
 Default
 """""""

--- a/doc/src/atc_mesh_add_to_nodeset.rst
+++ b/doc/src/atc_mesh_add_to_nodeset.rst
@ -35,7 +35,8 @@ None
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh create_nodeset <atc_mesh_create_nodeset>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh create_nodeset <atc_mesh_create_nodeset>`


 Default
--- a/doc/src/atc_mesh_create.rst
+++ b/doc/src/atc_mesh_create.rst
@ -36,7 +36,8 @@ Creates only uniform rectangular grids in a rectangular region
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`

 Default
 """""""
--- a/doc/src/atc_mesh_create_elementset.rst
+++ b/doc/src/atc_mesh_create_elementset.rst
@ -36,6 +36,7 @@ Only viable for rectangular grids.
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
 - :doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`

--- a/doc/src/atc_mesh_create_faceset_box.rst
+++ b/doc/src/atc_mesh_create_faceset_box.rst
@ -40,7 +40,8 @@ Only viable for rectangular grids.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`

 Default
 """""""
--- a/doc/src/atc_mesh_create_faceset_plane.rst
+++ b/doc/src/atc_mesh_create_faceset_plane.rst
@ -39,7 +39,8 @@ Only viable for rectangular grids.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`

 Default
 """""""
--- a/doc/src/atc_mesh_create_nodeset.rst
+++ b/doc/src/atc_mesh_create_nodeset.rst
@ -36,7 +36,8 @@ None
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh add_to_nodeset <atc_mesh_add_to_nodeset>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh add_to_nodeset <atc_mesh_add_to_nodeset>`

 Default
 """""""
--- a/doc/src/atc_mesh_delete_elements.rst
+++ b/doc/src/atc_mesh_delete_elements.rst
@ -34,6 +34,7 @@ None.
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
 - :doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`

--- a/doc/src/atc_mesh_nodeset_to_elementset.rst
+++ b/doc/src/atc_mesh_nodeset_to_elementset.rst
@ -40,6 +40,7 @@ None.
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
 - :doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`

--- a/doc/src/atc_mesh_quadrature.rst
+++ b/doc/src/atc_mesh_quadrature.rst
@ -36,7 +36,8 @@ None.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC mesh create <atc_mesh_create>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh create <atc_mesh_create>`

 Default
 """""""
--- a/doc/src/atc_mesh_read.rst
+++ b/doc/src/atc_mesh_read.rst
@ -37,6 +37,7 @@ None
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC mesh create <atc_mesh_create>`
 - :doc:`fix_modify AtC mesh write <atc_mesh_write>`

--- a/doc/src/atc_mesh_write.rst
+++ b/doc/src/atc_mesh_write.rst
@ -34,6 +34,7 @@ None
 Related AtC commands
 """"""""""""""""""""

+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
 - :doc:`fix_modify AtC mesh create <atc_mesh_create>`
 - :doc:`fix_modify AtC mesh read <atc_mesh_read>`

--- a/doc/src/atc_remove_source.rst
+++ b/doc/src/atc_remove_source.rst
@ -35,7 +35,8 @@ The keyword *all* is reserved and thus not available as element_set name.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC source <atc_source>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC source <atc_source>`

 Default
 """""""
--- a/doc/src/atc_source.rst
+++ b/doc/src/atc_source.rst
@ -39,7 +39,8 @@ 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>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC remove_source <atc_remove_source>`

 Default
 """""""
--- a/doc/src/atc_time_integration.rst
+++ b/doc/src/atc_time_integration.rst
@ -66,10 +66,11 @@ Restrictions

 None.

-Related commands
-""""""""""""""""

-:doc:`fix atc <fix_atc>`
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`

 Default
 """""""
--- a/doc/src/atc_unfix.rst
+++ b/doc/src/atc_unfix.rst
@ -35,7 +35,8 @@ The keyword *all* is reserved and thus not available as nodeset name.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC fix <atc_fix>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC fix <atc_fix>`

 Default
 """""""
--- a/doc/src/atc_unfix_flux.rst
+++ b/doc/src/atc_unfix_flux.rst
@ -36,7 +36,8 @@ None.
 Related AtC commands
 """"""""""""""""""""

-:doc:`fix_modify AtC fix_flux <atc_fix_flux>`
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC fix_flux <atc_fix_flux>`

 Default
 """""""
--- a/doc/src/fix_atc.rst
+++ b/doc/src/fix_atc.rst
@ -139,6 +139,8 @@ 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.

+.. _atc_fix_modify:
+
 Related commands
 """"""""""""""""

@ -181,7 +183,7 @@ conditions.

 * :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>`_
+* :doc:`fix_modify AtC control localized_lambda <atc_control_localized_lambda>`
 * `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
 * `fix_modify AtC filter <USER/atc/man_time_filter.html>`_