.. index:: fix atc

fix atc command
===============

Syntax
""""""

.. parsed-literal::

   fix <fixID> <group> atc <type> <parameter_file>

* fixID = name of fix
* group = name of group fix is to be applied
* type = *thermal* or *two_temperature* or *hardy* or *field*

.. parsed-literal::

    *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
    *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

Examples
""""""""

.. code-block:: LAMMPS

   fix AtC internal atc thermal Ar_thermal.dat
   fix AtC internal atc two_temperature Ar_ttm.mat
   fix AtC internal atc hardy
   fix AtC internal atc field

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
needed to set up the problem, e.g. define the finite element mesh and
prescribe initial and boundary conditions.

.. image:: JPG/atc_nanotube.jpg
   :align: center

The following coupling example is typical, but non-exhaustive:

.. code-block:: LAMMPS

    # ... commands to create and initialize the MD system

    # initial fix to designate coupling type and group to apply it to
    # tag group physics material_file
    fix AtC internal atc thermal Ar_thermal.mat

    # create a uniform 12 x 2 x 2 mesh that covers region contain the group
    # nx ny nz region periodicity
    fix_modify AtC mesh create 12 2 2 mdRegion f p p

    # specify the control method for the type of coupling
    # physics control_type
    fix_modify AtC thermal control flux

    # specify the initial values for the empirical field "temperature"
    # field node_group value
    fix_modify AtC initial temperature all 30

    # create an output stream for nodal fields
    # filename output_frequency
    fix_modify AtC output atc_fe_output 100

    run 1000

likewise for this post-processing example:

.. code-block:: LAMMPS

    # ... commands to create and initialize the MD system

    # initial fix to designate post-processing and the group to apply it to
    # no material file is allowed nor required
    fix AtC internal atc hardy

    # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
    fix AtC kernel quartic_sphere 10.0

    # create a uniform 1 x 1 x 1 mesh that covers region contain the group
    # with periodicity this effectively creates a system average
    fix_modify AtC mesh create 1 1 1 box p p p

    # change from default lagrangian map to eulerian
    # refreshed every 100 steps
    fix_modify AtC atom_element_map eulerian 100

    # start with no field defined
    # add mass density, potential energy density, stress and temperature
    fix_modify AtC fields add density energy stress temperature

    # create an output stream for nodal fields
    # filename output_frequency
    fix_modify AtC output nvtFE 100 text

    run 1000

the mesh's linear interpolation functions can be used as the localization function
by using the field option:

.. code-block:: LAMMPS

    fix AtC internal atc field
    fix_modify AtC mesh create 1 1 1 box p p p
    ...

Note coupling and post-processing can be combined in the same simulations using separate fixes.

----------

Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

No information about this fix is written to :doc:`binary restart files
<restart>`.  The :doc:`fix_modify <fix_modify>` options relevant to this
fix are listed below.  No global scalar or vector or per-atom quantities
are stored by this fix for access by various :doc:`output commands
<Howto_output>`.  No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command.  This fix is not
invoked during :doc:`energy minimization <minimize>`.

Restrictions
""""""""""""

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:

* the coupling is restricted to thermal physics
* the FE computations are done in serial on each processor.

.. _atc_fix_modify:

Related commands
""""""""""""""""

After specifying this fix in your input script, several other
:doc:`fix_modify <fix_modify>` commands are used to setup the problem,
e.g. define the finite element mesh and prescribe initial and boundary
conditions.

*fix_modify* commands for setup:

* :doc:`fix_modify AtC mesh create <atc_mesh_create>`
* :doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
* :doc:`fix_modify AtC mesh read <atc_mesh_read>`
* :doc:`fix_modify AtC mesh write <atc_mesh_write>`
* :doc:`fix_modify AtC mesh create_nodeset <atc_mesh_create_nodeset>`
* :doc:`fix_modify AtC mesh add_to_nodeset <atc_mesh_add_to_nodeset>`
* :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
* :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
* :doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
* :doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
* :doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`
* :doc:`fix_modify AtC boundary type <atc_boundary_type>`
* :doc:`fix_modify AtC internal_quadrature <atc_internal_quadrature>`
* :doc:`fix_modify AtC time_integration <atc_time_integration>`
* :doc:`fix_modify AtC extrinsic electron_integration <atc_electron_integration>`
* :doc:`fix_modify AtC internal_element_set <atc_internal_element_set>`
* :doc:`fix_modify AtC decomposition <atc_decomposition>`

*fix_modify* commands for boundary and initial conditions:

* :doc:`fix_modify AtC initial <atc_initial>`
* :doc:`fix_modify AtC fix <atc_fix>`
* :doc:`fix_modify AtC unfix <atc_unfix>`
* :doc:`fix_modify AtC fix_flux <atc_fix_flux>`
* :doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`
* :doc:`fix_modify AtC source <atc_source>`
* :doc:`fix_modify AtC remove_source <atc_remove_source>`

*fix_modify* commands for control and filtering:

* :doc:`fix_modify AtC control thermal <atc_control_thermal>`
* :doc:`fix_modify AtC control momentum <atc_control_momentum>`
* :doc:`fix_modify AtC control localized_lambda <atc_control_localized_lambda>`
* :doc:`fix_modify AtC control lumped_lambda_solve <atc_lumped_lambda_solve>`
* :doc:`fix_modify AtC control mask_direction <atc_mask_direction>`
* :doc:`fix_modify AtC filter <atc_time_filter>`
* :doc:`fix_modify AtC filter scale <atc_filter_scale>`
* :doc:`fix_modify AtC filter type <atc_filter_type>`
* :doc:`fix_modify AtC equilibrium_start <atc_equilibrium_start>`
* :doc:`fix_modify AtC extrinsic exchange <atc_extrinsic_exchange>`
* :doc:`fix_modify AtC poisson_solver <atc_poisson_solver>`

*fix_modify* commands for output:

* :doc:`fix_modify AtC output <atc_output>`
* :doc:`fix_modify AtC output nodeset <atc_output_nodeset>`
* :doc:`fix_modify AtC output volume_integral <atc_output_volume_integral>`
* :doc:`fix_modify AtC output boundary_integral <atc_output_boundary_integral>`
* :doc:`fix_modify AtC output contour_integral <atc_output_contour_integral>`
* :doc:`fix_modify AtC mesh output <atc_mesh_output>`
* :doc:`fix_modify AtC write_restart <atc_write_restart>`
* :doc:`fix_modify AtC read_restart <atc_read_restart>`

*fix_modify* commands for post-processing:

* :doc:`fix_modify AtC kernel <atc_hardy_kernel>`
* :doc:`fix_modify AtC fields <atc_hardy_fields>`
* :doc:`fix_modify AtC gradients <atc_hardy_gradients>`
* :doc:`fix_modify AtC rates <atc_hardy_rates>`
* :doc:`fix_modify AtC computes <atc_hardy_computes>`
* :doc:`fix_modify AtC on_the_fly <atc_hardy_on_the_fly>`
* :doc:`fix_modify AtC pair/bond_interactions <atc_pair_interactions>`
* :doc:`fix_modify AtC sample_frequency <atc_sample_frequency>`
* :doc:`fix_modify AtC set <atc_set_reference_pe>`

miscellaneous *fix_modify* commands:

* :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
* :doc:`fix_modify AtC atom_weight <atc_atom_weight>`
* :doc:`fix_modify AtC write_atom_weights <atc_write_atom_weights>`
* :doc:`fix_modify AtC kernel_bandwidth <atc_kernel_bandwidth>`
* :doc:`fix_modify AtC reset_time <atc_reset_time>`
* :doc:`fix_modify AtC reset_atomic_reference_positions <atc_reset_atomic_reference>`
* :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
* :doc:`fix_modify AtC boundary_faceset <atc_boundary_faceset>`
* :doc:`fix_modify AtC consistent_fe_initialization <atc_consistent_fe_initialization>`
* :doc:`fix_modify AtC mass_matrix <atc_mass_matrix>`
* :doc:`fix_modify AtC material <atc_material>`
* :doc:`fix_modify AtC atomic_charge <atc_atomic_charge>`
* :doc:`fix_modify AtC source_integration <atc_source_integration>`
* :doc:`fix_modify AtC temperature_definition <atc_temperature_definition>`
* :doc:`fix_modify AtC track_displacement <atc_track_displacement>`
* :doc:`fix_modify AtC boundary_dynamics <atc_boundary_dynamics>`
* :doc:`fix_modify AtC add_species <atc_add_species>`
* :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
* :doc:`fix_modify AtC remove_species <atc_remove_species>`
* :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`

Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders.

Default
"""""""
None

----------

For detailed exposition of the theory and algorithms please see:

.. _Wagner:

**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.

.. _Zimmeman2004:

**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.

.. _Zimmerman2010:

**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.

.. _Templeton2010:

**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.

.. _Jones:

**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.

.. _Templeton2011:

**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.

.. _Mandadapu:

**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.

Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
