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.. 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 (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
Examples
""""""""
.. parsed-literal::
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
.. parsed-literal::
The following coupling example is typical, but non-exhaustive:
# ... commands to create and initialize the MD system
.. parsed-literal::
# 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
.. parsed-literal::
# 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
.. parsed-literal::
# specify the control method for the type of coupling
# physics control_type
fix_modify AtC thermal control flux
.. parsed-literal::
# specify the initial values for the empirical field "temperature"
# field node_group value
fix_modify AtC initial temperature all 30
.. parsed-literal::
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output atc_fe_output 100
.. parsed-literal::
run 1000
likewise for this post-processing example:
.. parsed-literal::
# ... commands to create and initialize the MD system
.. parsed-literal::
# 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
.. parsed-literal::
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
fix AtC kernel quartic_sphere 10.0
.. parsed-literal::
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
# with periodicity this effectively creats a system average
fix_modify AtC mesh create 1 1 1 box p p p
.. parsed-literal::
# change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100
.. parsed-literal::
# start with no field defined
# add mass density, potential energy density, stress and temperature
fix_modify AtC fields add density energy stress temperature
.. parsed-literal::
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output nvtFE 100 text
.. parsed-literal::
run 1000
the mesh's linear interpolation functions can be used as the localization function
by using the field option:
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 :ref:`output commands <howto_15>`. 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.
* Currently,
* - the coupling is restricted to thermal physics
* - the FE computations are done in serial on each processor.
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 <USER/atc/man_mesh_create>`
* :doc:`fix_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature>`
* :doc:`fix_modify AtC mesh read <USER/atc/man_mesh_read>`
* :doc:`fix_modify AtC mesh write <USER/atc/man_mesh_write>`
* :doc:`fix_modify AtC mesh create_nodeset <USER/atc/man_mesh_create_nodeset>`
* :doc:`fix_modify AtC mesh add_to_nodeset <USER/atc/man_mesh_add_to_nodeset>`
* :doc:`fix_modify AtC mesh create_faceset box <USER/atc/man_mesh_create_faceset_box>`
* :doc:`fix_modify AtC mesh create_faceset plane <USER/atc/man_mesh_create_faceset_plane>`
* :doc:`fix_modify AtC mesh create_elementset <USER/atc/man_mesh_create_elementset>`
* :doc:`fix_modify AtC mesh delete_elements <USER/atc/man_mesh_delete_elements>`
* :doc:`fix_modify AtC mesh nodeset_to_elementset <USER/atc/man_mesh_nodeset_to_elementset>`
* :doc:`fix_modify AtC boundary <USER/atc/man_boundary>`
* :doc:`fix_modify AtC internal_quadrature <USER/atc/man_internal_quadrature>`
* :doc:`fix_modify AtC time_integration (thermal) <USER/atc/man_thermal_time_integration>`
* :doc:`fix_modify AtC time_integration (momentum) <USER/atc/man_momentum_time_integration>`
* :doc:`fix_modify AtC extrinsic electron_integration <USER/atc/man_electron_integration>`
* :doc:`fix_modify AtC internal_element_set <USER/atc/man_internal_element_set>`
* :doc:`fix_modify AtC decomposition <USER/atc/man_decomposition>`
fix_modify commands for boundary and initial conditions:
* :doc:`fix_modify AtC initial <USER/atc/man_initial>`
* :doc:`fix_modify AtC fix <USER/atc/man_fix_nodes>`
* :doc:`fix_modify AtC unfix <USER/atc/man_unfix_nodes>`
* :doc:`fix_modify AtC fix_flux <USER/atc/man_fix_flux>`
* :doc:`fix_modify AtC unfix_flux <USER/atc/man_unfix_flux>`
* :doc:`fix_modify AtC source <USER/atc/man_source>`
* :doc:`fix_modify AtC remove_source <USER/atc/man_remove_source>`
fix_modify commands for control and filtering:
* :doc:`fix_modify AtC control <USER/atc/man_control>`
* :doc:`fix_modify AtC control thermal <USER/atc/man_control_thermal>`
* :doc:`fix_modify AtC control thermal correction_max_iterations <USER/atc/man_control_thermal_correction_max_iterations>`
* :doc:`fix_modify AtC control momentum <USER/atc/man_control_momentum>`
* :doc:`fix_modify AtC control localized_lambda <USER/atc/man_localized_lambda>`
* :doc:`fix_modify AtC control lumped_lambda_solve <USER/atc/man_lumped_lambda_solve>`
* :doc:`fix_modify AtC control mask_direction <USER/atc/man_mask_direction>` control
* :doc:`fix_modify AtC filter <USER/atc/man_time_filter>`
* :doc:`fix_modify AtC filter scale <USER/atc/man_filter_scale>`
* :doc:`fix_modify AtC filter type <USER/atc/man_filter_type>`
* :doc:`fix_modify AtC equilibrium_start <USER/atc/man_equilibrium_start>`
* :doc:`fix_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange>`
* :doc:`fix_modify AtC poisson_solver <USER/atc/man_poisson_solver>`
fix_modify commands for output:
* :doc:`fix_modify AtC output <USER/atc/man_output>`
* :doc:`fix_modify AtC output nodeset <USER/atc/man_output_nodeset>`
* :doc:`fix_modify AtC output elementset <USER/atc/man_output_elementset>`
* :doc:`fix_modify AtC output boundary_integral <USER/atc/man_boundary_integral>`
* :doc:`fix_modify AtC output contour_integral <USER/atc/man_contour_integral>`
* :doc:`fix_modify AtC mesh output <USER/atc/man_mesh_output>`
* :doc:`fix_modify AtC write_restart <USER/atc/man_write_restart>`
* :doc:`fix_modify AtC read_restart <USER/atc/man_read_restart>`
fix_modify commands for post-processing:
* :doc:`fix_modify AtC kernel <USER/atc/man_hardy_kernel>`
* :doc:`fix_modify AtC fields <USER/atc/man_hardy_fields>`
* :doc:`fix_modify AtC grdients <USER/atc/man_hardy_gradients>`
* :doc:`fix_modify AtC rates <USER/atc/man_hardy_rates>`
* :doc:`fix_modify AtC computes <USER/atc/man_hardy_computes>`
* :doc:`fix_modify AtC on_the_fly <USER/atc/man_hardy_on_the_fly>`
* :doc:`fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions>`
* :doc:`fix_modify AtC sample_frequency <USER/atc/man_sample_frequency>`
* :doc:`fix_modify AtC set <USER/atc/man_set>`
miscellaneous fix_modify commands:
* :doc:`fix_modify AtC atom_element_map <USER/atc/man_atom_element_map>`
* :doc:`fix_modify AtC atom_weight <USER/atc/man_atom_weight>`
* :doc:`fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights>`
* :doc:`fix_modify AtC reset_time <USER/atc/man_reset_time>`
* :doc:`fix_modify AtC reset_atomic_reference_positions <USER/atc/man_reset_atomic_reference_positions>`
* :doc:`fix_modify AtC fe_md_boundary <USER/atc/man_fe_md_boundary>`
* :doc:`fix_modify AtC boundary_faceset <USER/atc/man_boundary_faceset>`
* :doc:`fix_modify AtC consistent_fe_initialization <USER/atc/man_consistent_fe_initialization>`
* :doc:`fix_modify AtC mass_matrix <USER/atc/man_mass_matrix>`
* :doc:`fix_modify AtC material <USER/atc/man_material>`
* :doc:`fix_modify AtC atomic_charge <USER/atc/man_atomic_charge>`
* :doc:`fix_modify AtC source_integration <USER/atc/man_source_integration>`
* :doc:`fix_modify AtC temperature_definition <USER/atc/man_temperature_definition>`
* :doc:`fix_modify AtC track_displacement <USER/atc/man_track_displacement>`
* :doc:`fix_modify AtC boundary_dynamics <USER/atc/man_boundary_dynamics>`
* :doc:`fix_modify AtC add_species <USER/atc/man_add_species>`
* :doc:`fix_modify AtC add_molecule <USER/atc/man_add_molecule>`
* :doc:`fix_modify AtC remove_species <USER/atc/man_remove_species>`
* :doc:`fix_modify AtC remove_molecule <USER/atc/man_remove_molecule>`
Note: a set of example input files with the attendant material files are included with this package
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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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