diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst new file mode 100644 index 0000000000..0fe8cdde3a --- /dev/null +++ b/doc/src/atc_atom_element_map.rst @@ -0,0 +1,41 @@ +.. index:: fix_modify AtC atom_element_map + +fix_modify AtC atom_element_map command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify atom_element_map [] + +* AtC fixID = ID of :doc:`fix atc ` instance +* atom_element_map = name of the AtC sub-command +* *eulerian* or *lagrangian* = frame of reference +* frequency = frequency of updating atom-to-continuum maps based on the current configuration - (only for eulerian) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify atc atom_element_map eulerian 100 + +Description +""""""""""" + +Changes frame of reference from *eulerian* to *lagrangian* or vice versa +and sets the frequency for which the map from atoms to elements is +reformed and all the attendant data is recalculated. + +Restrictions +"""""""""""" + +Cannot change map type after initialization. + +Default +""""""" + +*lagrangian* diff --git a/doc/src/atc_boundary_type.rst b/doc/src/atc_boundary_type.rst index c18f8cc640..72cd5aeb27 100644 --- a/doc/src/atc_boundary_type.rst +++ b/doc/src/atc_boundary_type.rst @@ -1,7 +1,7 @@ .. index:: fix_modify AtC boundary type fix_modify AtC boundary type command -============================================= +==================================== Syntax """""" diff --git a/doc/src/atc_electron_integration.rst b/doc/src/atc_electron_integration.rst index 83f8efcef3..3bf9a91ba2 100644 --- a/doc/src/atc_electron_integration.rst +++ b/doc/src/atc_electron_integration.rst @@ -12,8 +12,8 @@ Syntax * AtC fixID = ID of :doc:`fix atc ` instance * extrinsic electron_integration = name of the AtC sub-command -* integration\_type = *explicit* or *implicit* or *steadydescriptor* -* num\_subcycle\_steps = number of subcycle steps for the electron time integration (optional) +* integration_type = *explicit* or *implicit* or *steadydescriptor* +* num_subcycle_steps = number of subcycle steps for the electron time integration (optional) Examples @@ -35,10 +35,10 @@ dynamics. Restrictions """""""""""" -For use only with the two\_temperature type of the AtC fix (see +For use only with the two_temperature type of the AtC fix (see :doc:`fix atc ` command) Default """"""" -*implicit* and *subcycle\_steps* = 1 +*implicit* and *subcycle_steps* = 1 diff --git a/doc/src/atc_internal_element_set.rst b/doc/src/atc_internal_element_set.rst new file mode 100644 index 0000000000..8f2c5cd298 --- /dev/null +++ b/doc/src/atc_internal_element_set.rst @@ -0,0 +1,51 @@ +.. index:: fix_modify AtC internal_element_set + +fix_modify AtC internal_element_set command +=========================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify internal_element_set + +* AtC fixID = ID of :doc:`fix atc ` instance +* internal_element_set = name of the AtC sub-command +* element_set_name = name of element set defining internal region, or *off* + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC internal_element_set myElementSet + fix_modify AtC internal_element_set off + +Description +""""""""""" + +Enables AtC to base the region for internal atoms to be an element +set. If no ghost atoms are used, all the AtC atoms must be constrained +to remain in this element set by the user, e.g., with walls. If boundary +atoms are used in conjunction with Eulerian atom maps AtC will partition +all atoms of a boundary or internal type to be of type internal if they +are in the internal region or to be of type boundary otherwise. + +Restrictions +"""""""""""" + +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 +"""""""""""""""""""""""" + +- :doc:`fix_modify AtC atom_element_map ` +- :doc:`fix_modify AtC boundary type ` + +Default +""""""" + +*off* diff --git a/doc/src/atc_mesh_add_to_nodeset.rst b/doc/src/atc_mesh_add_to_nodeset.rst index 579da425da..56fb55b6cb 100644 --- a/doc/src/atc_mesh_add_to_nodeset.rst +++ b/doc/src/atc_mesh_add_to_nodeset.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh add_to_nodeset * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_nodeset = name of the AtC sub-command +* mesh create_nodeset = name of the AtC sub-command * id = id to assign to the collection of FE nodes * = coordinates of the bounding box that contains the desired nodes to be added diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst index d2bc39426a..24408cb830 100644 --- a/doc/src/atc_mesh_create_elementset.rst +++ b/doc/src/atc_mesh_create_elementset.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh create_elementset * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_elementset = name of the AtC sub-command +* mesh create_elementset = name of the AtC sub-command * id = id to assign to the collection of FE nodes * = coordinates of the bounding box that contains only the desired elements diff --git a/doc/src/atc_mesh_create_faceset_box.rst b/doc/src/atc_mesh_create_faceset_box.rst index 6915534025..2a80fae0c1 100644 --- a/doc/src/atc_mesh_create_faceset_box.rst +++ b/doc/src/atc_mesh_create_faceset_box.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh create_faceset box [units] * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_faceset = name of the AtC sub-command +* mesh create_faceset = name of the AtC sub-command * id = id to assign to the collection of FE faces * box = use bounding box to define FE faces * = coordinates of the bounding box that is coincident with the desired FE faces diff --git a/doc/src/atc_mesh_create_faceset_plane.rst b/doc/src/atc_mesh_create_faceset_plane.rst index a6b8e53175..5cf7659ac2 100644 --- a/doc/src/atc_mesh_create_faceset_plane.rst +++ b/doc/src/atc_mesh_create_faceset_plane.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh create_faceset plane [units] * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_faceset = name of the AtC sub-command +* mesh create_faceset = name of the AtC sub-command * id = id to assign to the collection of FE faces * plane = use plane to define faceset * ,, = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2] diff --git a/doc/src/atc_mesh_create_nodeset.rst b/doc/src/atc_mesh_create_nodeset.rst index d2e2dd5a9a..dd7b8630be 100644 --- a/doc/src/atc_mesh_create_nodeset.rst +++ b/doc/src/atc_mesh_create_nodeset.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh create_nodeset * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_nodeset = name of the AtC sub-command +* mesh create_nodeset = name of the AtC sub-command * id = id to assign to the collection of FE nodes * = coordinates of the bounding box that contains only the desired nodes diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst index e9e7eed79b..dfab9677b7 100644 --- a/doc/src/atc_mesh_delete_elements.rst +++ b/doc/src/atc_mesh_delete_elements.rst @@ -11,7 +11,7 @@ Syntax fix_modify mesh delete_elements * AtC fixID = ID of :doc:`fix atc ` instance -* mesh create\_elementset = name of the AtC sub-command +* mesh create_elementset = name of the AtC sub-command * id = id of the element set Examples diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst index da3063b0f1..a1ec879787 100644 --- a/doc/src/atc_mesh_nodeset_to_elementset.rst +++ b/doc/src/atc_mesh_nodeset_to_elementset.rst @@ -11,9 +11,9 @@ Syntax fix_modify mesh nodeset_to_elementset * AtC fixID = ID of :doc:`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 +* 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 * = flag to choose either the maximal or minimal elementset Examples diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst index 438537088a..0780ece4fb 100644 --- a/doc/src/atc_time_integration.rst +++ b/doc/src/atc_time_integration.rst @@ -1,7 +1,7 @@ .. index:: fix_modify AtC time_integration fix_modify AtC time_integration command -============================================= +======================================= Syntax """""" @@ -11,7 +11,7 @@ Syntax fix_modify time_integration * AtC fixID = ID of :doc:`fix atc ` instance -* time\_integration = name of the AtC sub-command +* time_integration = name of the AtC sub-command * descriptor = *gear* or *fractional_step* or *verlet* @@ -36,7 +36,7 @@ Options for thermal time integration: atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power -*fractional\_step* +*fractional_step* atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes @@ -49,7 +49,7 @@ Options for momentum time integration: atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force -*fractional\_step* +*fractional_step* atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 617ce9ca05..6ad61f48b4 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -12,7 +12,7 @@ Syntax * fixID = name of fix * group = name of group fix is to be applied -* type = *thermal* or *two\_temperature* or *hardy* or *field* +* type = *thermal* or *two_temperature* or *hardy* or *field* .. parsed-literal:: @@ -21,7 +21,7 @@ Syntax *hardy* = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) *field* = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) -* parameter\_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file +* parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file Examples """""""" @@ -39,7 +39,7 @@ Description This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After -instantiating this fix, several other fix\_modify commands will be +instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. @@ -118,7 +118,7 @@ Note coupling and post-processing can be combined in the same simulations using ---------- -**Restart, fix\_modify, output, run start/stop, minimize info:** +**Restart, fix_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options relevant to this @@ -131,7 +131,7 @@ invoked during :doc:`energy minimization `. Restrictions """""""""""" -Thermal and two\_temperature (coupling) types use a Verlet +Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently: @@ -147,7 +147,7 @@ After specifying this fix in your input script, several other e.g. define the finite element mesh and prescribe initial and boundary conditions. -*fix\_modify* commands for setup: +*fix_modify* commands for setup: * :doc:`fix_modify AtC mesh create ` * :doc:`fix_modify AtC mesh quadrature ` @@ -164,10 +164,10 @@ conditions. * :doc:`fix_modify AtC internal_quadrature ` * :doc:`fix_modify AtC time_integration ` * :doc:`fix_modify AtC extrinsic electron_integration ` -* `fix_modify AtC internal_element_set `_ +* :doc:`fix_modify AtC internal_element_set ` * `fix_modify AtC decomposition `_ -*fix\_modify* commands for boundary and initial conditions: +*fix_modify* commands for boundary and initial conditions: * `fix_modify AtC initial `_ * `fix_modify AtC fix `_ @@ -177,7 +177,7 @@ conditions. * `fix_modify AtC source `_ * `fix_modify AtC remove_source `_ -*fix\_modify* commands for control and filtering: +*fix_modify* commands for control and filtering: * `fix_modify AtC control `_ * `fix_modify AtC control thermal `_ @@ -193,7 +193,7 @@ conditions. * `fix_modify AtC extrinsic exchange `_ * `fix_modify AtC poisson_solver `_ -*fix\_modify* commands for output: +*fix_modify* commands for output: * `fix_modify AtC output `_ * `fix_modify AtC output nodeset `_ @@ -204,7 +204,7 @@ conditions. * `fix_modify AtC write_restart `_ * `fix_modify AtC read_restart `_ -*fix\_modify* commands for post-processing: +*fix_modify* commands for post-processing: * `fix_modify AtC kernel `_ * `fix_modify AtC fields `_ @@ -216,9 +216,9 @@ conditions. * `fix_modify AtC sample_frequency `_ * `fix_modify AtC set `_ -miscellaneous *fix\_modify* commands: +miscellaneous *fix_modify* commands: -* `fix_modify AtC atom_element_map `_ +* :doc:`fix_modify AtC atom_element_map ` * `fix_modify AtC atom_weight `_ * `fix_modify AtC write_atom_weights `_ * `fix_modify AtC reset_time `_ diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 393fb39e58..81c2bb3789 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -826,6 +826,7 @@ ethernet etol etot etotal +Eulerian eulerimplicit Europhys ev