From 80d413b86c684d8d02120400dfbeee72a683dc45 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 13 Mar 2020 11:06:11 -0400 Subject: [PATCH] add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs --- doc/src/atc_atom_element_map.rst | 5 +++ doc/src/atc_boundary_type.rst | 5 +++ doc/src/atc_control_localized_lambda.rst | 46 ++++++++++++++++++++++ doc/src/atc_control_momentum.rst | 3 +- doc/src/atc_control_thermal.rst | 3 +- doc/src/atc_decomposition.rst | 5 +++ doc/src/atc_electron_integration.rst | 5 +++ doc/src/atc_fix.rst | 3 +- doc/src/atc_fix_flux.rst | 3 +- doc/src/atc_initial.rst | 5 +++ doc/src/atc_internal_element_set.rst | 1 + doc/src/atc_internal_quadrature.rst | 5 +++ doc/src/atc_mesh_add_to_nodeset.rst | 3 +- doc/src/atc_mesh_create.rst | 3 +- doc/src/atc_mesh_create_elementset.rst | 1 + doc/src/atc_mesh_create_faceset_box.rst | 3 +- doc/src/atc_mesh_create_faceset_plane.rst | 3 +- doc/src/atc_mesh_create_nodeset.rst | 3 +- doc/src/atc_mesh_delete_elements.rst | 1 + doc/src/atc_mesh_nodeset_to_elementset.rst | 1 + doc/src/atc_mesh_quadrature.rst | 3 +- doc/src/atc_mesh_read.rst | 1 + doc/src/atc_mesh_write.rst | 1 + doc/src/atc_remove_source.rst | 3 +- doc/src/atc_source.rst | 3 +- doc/src/atc_time_integration.rst | 7 ++-- doc/src/atc_unfix.rst | 3 +- doc/src/atc_unfix_flux.rst | 3 +- doc/src/fix_atc.rst | 4 +- 29 files changed, 117 insertions(+), 18 deletions(-) create mode 100644 doc/src/atc_control_localized_lambda.rst diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst index 0fe8cdde3a..11f58d0841 100644 --- 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 ` + Default """"""" diff --git a/doc/src/atc_boundary_type.rst b/doc/src/atc_boundary_type.rst index 72cd5aeb27..26b40e5a12 100644 --- 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 ` + Default """"""" diff --git a/doc/src/atc_control_localized_lambda.rst b/doc/src/atc_control_localized_lambda.rst new file mode 100644 index 0000000000..eb286756b7 --- /dev/null +++ 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 control localized_lambda + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +off diff --git a/doc/src/atc_control_momentum.rst b/doc/src/atc_control_momentum.rst index 69790a79ab..7a9e88c721 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC control thermal ` Default """"""" diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst index 0cd4904e2d..dc3f28f8eb 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC control momentum ` Default """"""" diff --git a/doc/src/atc_decomposition.rst b/doc/src/atc_decomposition.rst index 2a056bab78..50d11bf52f 100644 --- 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 ` + Default """"""" diff --git a/doc/src/atc_electron_integration.rst b/doc/src/atc_electron_integration.rst index 3bf9a91ba2..e3928a69fb 100644 --- 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 ` command) +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + Default """"""" diff --git a/doc/src/atc_fix.rst b/doc/src/atc_fix.rst index 4e955ea4e4..d3ba972508 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC unfix ` Default """"""" diff --git a/doc/src/atc_fix_flux.rst b/doc/src/atc_fix_flux.rst index 461d615162..12699e9163 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC unfix_flux ` Default """"""" diff --git a/doc/src/atc_initial.rst b/doc/src/atc_initial.rst index ab0f922a6c..fd45da0679 100644 --- 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 ` + Default """"""" diff --git a/doc/src/atc_internal_element_set.rst b/doc/src/atc_internal_element_set.rst index 8dfa55eadb..4a376f55a3 100644 --- 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 ` - :doc:`fix_modify AtC atom_element_map ` - :doc:`fix_modify AtC boundary type ` diff --git a/doc/src/atc_internal_quadrature.rst b/doc/src/atc_internal_quadrature.rst index 7b503bca8e..b171914021 100644 --- 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 ` + Default """"""" diff --git a/doc/src/atc_mesh_add_to_nodeset.rst b/doc/src/atc_mesh_add_to_nodeset.rst index 56fb55b6cb..f9f6f575fe 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_nodeset ` Default diff --git a/doc/src/atc_mesh_create.rst b/doc/src/atc_mesh_create.rst index 404102ccd9..b17bb8ac0d 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh quadrature ` Default """"""" diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst index 24408cb830..3cb406e7bc 100644 --- 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 ` - :doc:`fix_modify AtC mesh delete_elements ` - :doc:`fix_modify AtC mesh nodeset_to_elementset ` diff --git a/doc/src/atc_mesh_create_faceset_box.rst b/doc/src/atc_mesh_create_faceset_box.rst index 2a80fae0c1..09b099d179 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_faceset plane ` Default """"""" diff --git a/doc/src/atc_mesh_create_faceset_plane.rst b/doc/src/atc_mesh_create_faceset_plane.rst index 5cf7659ac2..035e584044 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_faceset box ` Default """"""" diff --git a/doc/src/atc_mesh_create_nodeset.rst b/doc/src/atc_mesh_create_nodeset.rst index dd7b8630be..a2f9d74d07 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh add_to_nodeset ` Default """"""" diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst index dfab9677b7..9785f0adf6 100644 --- 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 ` - :doc:`fix_modify AtC mesh create_elementset ` - :doc:`fix_modify AtC mesh nodeset_to_elementset ` diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst index a1ec879787..d8721cc295 100644 --- 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 ` - :doc:`fix_modify AtC mesh create_elementset ` - :doc:`fix_modify AtC mesh delete_elements ` diff --git a/doc/src/atc_mesh_quadrature.rst b/doc/src/atc_mesh_quadrature.rst index 4efee0433a..0c9bd4b30f 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create ` Default """"""" diff --git a/doc/src/atc_mesh_read.rst b/doc/src/atc_mesh_read.rst index 7ba4431f84..9848e12b07 100644 --- 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 ` - :doc:`fix_modify AtC mesh create ` - :doc:`fix_modify AtC mesh write ` diff --git a/doc/src/atc_mesh_write.rst b/doc/src/atc_mesh_write.rst index c09ba2b87e..dbb8f9c219 100644 --- 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 ` - :doc:`fix_modify AtC mesh create ` - :doc:`fix_modify AtC mesh read ` diff --git a/doc/src/atc_remove_source.rst b/doc/src/atc_remove_source.rst index 587d04731b..d98b7933da 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC source ` Default """"""" diff --git a/doc/src/atc_source.rst b/doc/src/atc_source.rst index 9c3849070f..6df4b67d1c 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC remove_source ` Default """"""" diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst index 0780ece4fb..382f11d459 100644 --- 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 ` +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` Default """"""" diff --git a/doc/src/atc_unfix.rst b/doc/src/atc_unfix.rst index 1241d51bae..12ee37bbde 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fix ` Default """"""" diff --git a/doc/src/atc_unfix_flux.rst b/doc/src/atc_unfix_flux.rst index a756f63a75..da9d1b4aba 100644 --- 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 ` +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fix_flux ` Default """"""" diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index b22d3359d1..b2d1da9317 100644 --- 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 ` * :doc:`fix_modify AtC control momentum ` -* `fix_modify AtC control localized_lambda `_ +* :doc:`fix_modify AtC control localized_lambda ` * `fix_modify AtC control lumped_lambda_solve `_ * `fix_modify AtC control mask_direction `_ control * `fix_modify AtC filter `_