-
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 : 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.
- For detailed exposition of the theory and algorithms please see:
-
-
-
- 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.
-
- - 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.
-
- - Zimmerman, JA; Jones, RE; Templeton, JA, A material frame approach for evaluating continuum variables in atomistic simulations. Journal of Computational Physics (2010), 229:2364.
-
- - 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, 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.
-
- - 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, 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.
--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
-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 -
- fix_modify AtC filter -
- fix_modify AtC filter scale -
- fix_modify AtC filter type -
- fix_modify AtC equilibrium_start -
- fix_modify AtC extrinsic exchange -
- man_charge_control -
- 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 gradients -
- 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
- -Generated on 21 Aug 2013 for ATC by - -
1.6.1
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