diff --git a/doc/src/atc_mesh_output.rst b/doc/src/atc_mesh_output.rst new file mode 100644 index 0000000000..63756df98e --- /dev/null +++ b/doc/src/atc_mesh_output.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC mesh output + +fix_modify AtC mesh output command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh output + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh output = name of the AtC sub-command +* file_prefix = prefix of various generated output files + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh output meshData + + +Description +""""""""""" + +Command to output mesh and associated data: nodesets, facesets, and +elementsets. This data is only output once upon initialization since +currently the mesh is static. Creates binary (EnSight, "gold" format) +output of mesh data. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output.rst b/doc/src/atc_output.rst index 699449b981..3fb1491be1 100644 --- a/doc/src/atc_output.rst +++ b/doc/src/atc_output.rst @@ -16,11 +16,13 @@ Syntax * filename_prefix = prefix for data files (for *output*) * frequency = frequency of output in time-steps (for *output*) * optional keywords for *output*: + - text = creates text output of index, step and nodal variable values for unique nodes - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes - binary = creates binary EnSight output - vector_components = outputs vectors as scalar components - tensor_components = outputs tensor as scalar components (for use with ParaView) + * *step* or *time* = index output by step or by time (for *output index*) diff --git a/doc/src/atc_output_boundary_integral.rst b/doc/src/atc_output_boundary_integral.rst new file mode 100644 index 0000000000..71a3e03ac2 --- /dev/null +++ b/doc/src/atc_output_boundary_integral.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC output boundary_integral + +fix_modify AtC output boundary_integral command +=============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output boundary_integral faceset [name] + +* AtC fixID = ID of :doc:`fix atc ` instance +* output boundary_integral = name of the AtC sub-command +* fieldname = name of hardy field +* faceset = required keyword +* name= name of faceset + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output boundary_integral stress faceset loop1 + + +Description +""""""""""" + +Calculates a surface integral of the given field dotted with the outward +normal of the faces and puts output in the "GLOBALS" file. + +Restrictions +"""""""""""" + +Must be used with the hardy/field type of :doc:`fix atc ` + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_contour_integral.rst b/doc/src/atc_output_contour_integral.rst new file mode 100644 index 0000000000..24678ef6cc --- /dev/null +++ b/doc/src/atc_output_contour_integral.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC output contour_integral + +fix_modify AtC output contour_integral command +============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output contour_integral faceset [axis [x|y|z]] + +* AtC fixID = ID of :doc:`fix atc ` instance +* output contour_integral = name of the AtC sub-command +* fieldname = name of hardy field +* faceset = required keyword +* name = name of faceset +* *axis x* or *axis y* or *axis z* = (optional) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output contour_integral stress faceset loop1 + + +Description +""""""""""" + +Calculates a surface integral of the given field dotted with the outward +normal of the faces and puts output in the "GLOBALS" file. + +Restrictions +"""""""""""" + +Must be used with the hardy/field type of :doc:`fix atc ` + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_nodeset.rst b/doc/src/atc_output_nodeset.rst new file mode 100644 index 0000000000..eb12a2344e --- /dev/null +++ b/doc/src/atc_output_nodeset.rst @@ -0,0 +1,49 @@ +.. index:: fix_modify AtC output nodeset + +fix_modify AtC output nodeset command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output nodeset + +* AtC fixID = ID of :doc:`fix atc ` instance +* output nodeset = name of the AtC sub-command +* nodeset_name= name of nodeset to be operated on +* operation = *sum* + + * *sum* = creates nodal sum over nodes in specified nodeset + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output nodeset nset1 sum + + +Description +""""""""""" + +Performs operation over the nodes belonging to specified nodeset and +outputs resulting variable values to GLOBALS file. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix atc command ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_volume_integral.rst b/doc/src/atc_output_volume_integral.rst new file mode 100644 index 0000000000..464d43cbce --- /dev/null +++ b/doc/src/atc_output_volume_integral.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC output volume_integral + +fix_modify AtC output volume_integral command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output volume_integral + +* AtC fixID = ID of :doc:`fix atc ` instance +* output volume_integral = name of the AtC sub-command +* elementset_name= name of elementset to be integrated over +* fieldname = name of field to integrate + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output volume_integral eset1 mass_density + + +Description +""""""""""" + +Performs volume integration of specified field over elementset and +outputs resulting variable values to GLOBALS file. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix atc command ` + +Default +""""""" + +None. diff --git a/doc/src/atc_read_restart.rst b/doc/src/atc_read_restart.rst new file mode 100644 index 0000000000..11ba4519a4 --- /dev/null +++ b/doc/src/atc_read_restart.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC read_restart + +fix_modify AtC read_restart command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify read_restart + +* AtC fixID = ID of :doc:`fix atc ` instance +* read_restart = name of the AtC sub-command +* file_name = name of AtC restart file + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC read_restart restart.mydata.AtC + + +Description +""""""""""" + +Reads the current state of the AtC fields from a named text-based restart file. + +Restrictions +"""""""""""" + +The restart file only contains fields and their time derivatives. The +reference positions of the atoms and the commands that initialize the +fix are not saved e.g. an identical mesh containing the same atoms will +have to be recreated. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC write_restart ` + +Default +""""""" + +None. diff --git a/doc/src/atc_write_restart.rst b/doc/src/atc_write_restart.rst new file mode 100644 index 0000000000..e4f19dea10 --- /dev/null +++ b/doc/src/atc_write_restart.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC write_restart + +fix_modify AtC write_restart command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify write_restart + +* AtC fixID = ID of :doc:`fix atc ` instance +* write_restart = name of the AtC sub-command +* file_name = name of AtC restart file + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC write_restart restart.mydata.AtC + + +Description +""""""""""" + +Dumps the current state of the fields to a named text-based restart +file. This done when the command is invoked and not repeated, unlike +the otherwise similar LAMMPS command. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC read_restart ` + +Default +""""""" + +None. diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 479adba548..cffbab3fc1 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -18,8 +18,8 @@ Syntax *thermal* = thermal coupling with fields: temperature *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature - *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) + *hardy* = on-the-fly post-processing using kernel localization functions + *field* = on-the-fly post-processing using mesh-based localization functions * parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file @@ -196,13 +196,13 @@ conditions. *fix_modify* commands for output: * :doc:`fix_modify AtC output ` -* `fix_modify AtC output nodeset `_ -* `fix_modify AtC output elementset `_ -* `fix_modify AtC output boundary_integral `_ -* `fix_modify AtC output contour_integral `_ -* `fix_modify AtC mesh output `_ -* `fix_modify AtC write_restart `_ -* `fix_modify AtC read_restart `_ +* :doc:`fix_modify AtC output nodeset ` +* :doc:`fix_modify AtC output volume_integral ` +* :doc:`fix_modify AtC output boundary_integral ` +* :doc:`fix_modify AtC output contour_integral ` +* :doc:`fix_modify AtC mesh output ` +* :doc:`fix_modify AtC write_restart ` +* :doc:`fix_modify AtC read_restart ` *fix_modify* commands for post-processing: