fix atc command — LAMMPS 15 May 2015 version documentation

# 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.