diff --git a/doc/src/atc_add_molecule.rst b/doc/src/atc_add_molecule.rst new file mode 100644 index 0000000000..dc0f0318ac --- /dev/null +++ b/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 add_molecule + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC remove_species ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_add_species.rst b/doc/src/atc_add_species.rst new file mode 100644 index 0000000000..0b39379e62 --- /dev/null +++ b/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 add_species + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_species ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_atomic_charge.rst b/doc/src/atc_atomic_charge.rst new file mode 100644 index 0000000000..4b3d34b815 --- /dev/null +++ b/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 atomic_charge + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +If the atom charge is defined, default is on, otherwise default is off. diff --git a/doc/src/atc_boundary_dynamics.rst b/doc/src/atc_boundary_dynamics.rst new file mode 100644 index 0000000000..696d091094 --- /dev/null +++ b/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 boundary_dynamics + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*prescribed on* diff --git a/doc/src/atc_consistent_fe_initialization.rst b/doc/src/atc_consistent_fe_initialization.rst index ed755a7239..3241752262 100644 --- a/doc/src/atc_consistent_fe_initialization.rst +++ b/doc/src/atc_consistent_fe_initialization.rst @@ -12,7 +12,7 @@ Syntax * AtC fixID = ID of :doc:`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 """""""" diff --git a/doc/src/atc_mass_matrix.rst b/doc/src/atc_mass_matrix.rst new file mode 100644 index 0000000000..eb586b933b --- /dev/null +++ b/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 mass_matrix + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*md_fe* diff --git a/doc/src/atc_material.rst b/doc/src/atc_material.rst new file mode 100644 index 0000000000..471bffffb2 --- /dev/null +++ b/doc/src/atc_material.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC material + +fix_modify AtC material command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify material + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +All elements default to the first material in the material file. diff --git a/doc/src/atc_remove_molecule.rst b/doc/src/atc_remove_molecule.rst new file mode 100644 index 0000000000..a654cd5c1d --- /dev/null +++ b/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 remove_molecule + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_species ` + +Default +""""""" + +None. diff --git a/doc/src/atc_remove_species.rst b/doc/src/atc_remove_species.rst new file mode 100644 index 0000000000..20e1f6a742 --- /dev/null +++ b/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 remove_species + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_source_integration.rst b/doc/src/atc_source_integration.rst new file mode 100644 index 0000000000..b10e6c7e2a --- /dev/null +++ b/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 source_integration + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +Default is *fe* diff --git a/doc/src/atc_temperature_definition.rst b/doc/src/atc_temperature_definition.rst new file mode 100644 index 0000000000..b5a27467ca --- /dev/null +++ b/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 temperature_definition + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*kinetic* diff --git a/doc/src/atc_track_displacement.rst b/doc/src/atc_track_displacement.rst new file mode 100644 index 0000000000..043f42ea9c --- /dev/null +++ b/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 track_displacement + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*on* diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index d87405632c..81a16b907a 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -227,19 +227,19 @@ miscellaneous *fix_modify* commands: * :doc:`fix_modify AtC fe_md_boundary ` * :doc:`fix_modify AtC boundary_faceset ` * :doc:`fix_modify AtC consistent_fe_initialization ` -* `fix_modify AtC mass_matrix `_ -* `fix_modify AtC material `_ -* `fix_modify AtC atomic_charge `_ -* `fix_modify AtC source_integration `_ -* `fix_modify AtC temperature_definition `_ -* `fix_modify AtC track_displacement `_ -* `fix_modify AtC boundary_dynamics `_ -* `fix_modify AtC add_species `_ -* `fix_modify AtC add_molecule `_ -* `fix_modify AtC remove_species `_ -* `fix_modify AtC remove_molecule `_ +* :doc:`fix_modify AtC mass_matrix ` +* :doc:`fix_modify AtC material ` +* :doc:`fix_modify AtC atomic_charge ` +* :doc:`fix_modify AtC source_integration ` +* :doc:`fix_modify AtC temperature_definition ` +* :doc:`fix_modify AtC track_displacement ` +* :doc:`fix_modify AtC boundary_dynamics ` +* :doc:`fix_modify AtC add_species ` +* :doc:`fix_modify AtC add_molecule ` +* :doc:`fix_modify AtC remove_species ` +* :doc:`fix_modify 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 """"""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 26ec6b924c..e63cf1f65a 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -874,6 +874,7 @@ fdotr fdt Fehlberg Fellinger +fe femtosecond femtoseconds fene