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### fix atc command

Syntax:

    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

       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:

      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.

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

       # ... 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 creats 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:

  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 binary restart files. The 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 output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

  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 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:

  - fix_modify AtC mesh create
  - fix_modify AtC mesh quadrature
  - fix_modify AtC mesh read
  - fix_modify AtC mesh write
  - fix_modify AtC mesh create_nodeset
  - fix_modify AtC mesh add_to_nodeset
  - fix_modify AtC mesh create_faceset box
  - fix_modify AtC mesh create_faceset plane
  - fix_modify AtC mesh create_elementset
  - fix_modify AtC mesh delete_elements
  - fix_modify AtC mesh nodeset_to_elementset
  - fix_modify AtC boundary
  - fix_modify AtC internal_quadrature
  - fix_modify AtC time_integration (thermal)
  - fix_modify AtC time_integration (momentum)
  - fix_modify AtC extrinsic electron_integration
  - fix_modify AtC internal_element_set
  - fix_modify AtC decomposition

  fix_modify commands for boundary and initial conditions:

  - fix_modify AtC initial
  - fix_modify AtC fix
  - fix_modify AtC unfix
  - fix_modify AtC fix_flux
  - fix_modify AtC unfix_flux
  - fix_modify AtC source
  - fix_modify AtC remove_source

  fix_modify commands for control and filtering:

  - fix_modify AtC control
  - fix_modify AtC control thermal
  - fix_modify AtC control thermal correction_max_iterations
  - fix_modify AtC control momentum
  - fix_modify AtC control localized_lambda
  - fix_modify AtC control lumped_lambda_solve
  - fix_modify AtC control mask_direction control
  - fix_modify AtC filter
  - fix_modify AtC filter scale
  - fix_modify AtC filter type
  - fix_modify AtC equilibrium_start
  - fix_modify AtC extrinsic exchange
  - fix_modify AtC poisson_solver

  fix_modify commands for output:

  - 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

  fix_modify commands for post-processing:

  - fix_modify AtC kernel
  - fix_modify AtC fields
  - fix_modify AtC grdients
  - fix_modify AtC rates
  - fix_modify AtC computes
  - fix_modify AtC on_the_fly
  - fix_modify AtC pair_interactions/bond_interactions
  - fix_modify AtC sample_frequency
  - fix_modify AtC set

  miscellaneous fix_modify commands:

  - fix_modify AtC atom_element_map
  - fix_modify AtC atom_weight
  - fix_modify AtC write_atom_weights
  - fix_modify AtC reset_time
  - fix_modify AtC reset_atomic_reference_positions
  - fix_modify AtC fe_md_boundary
  - fix_modify AtC boundary_faceset
  - 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

  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, 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.

  (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) 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) 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, 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) 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, 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.