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fix atc command

Syntax: 

fix   atc
  • 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.

    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 commands for boundary and initial conditions:

    fix_modify commands for control and filtering:

    fix_modify commands for output:

    fix_modify commands for post-processing:

    miscellaneous fix_modify commands:

    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.