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lammps/doc/src/fix_atc.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix atc command :h3
[Syntax:]
fix <fixID> <group> atc <type> <parameter_file> :pre
fixID = name of fix :l
group = name of group fix is to be applied :l
type = {thermal} or {two_temperature} or {hardy} or {field} :l
{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) :pre
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule
[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 :pre
[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.
:c,image(JPG/atc_nanotube.jpg)
The following coupling example is typical, but non-exhaustive:
# ... commands to create and initialize the MD system :pre
# 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 :pre
# 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 :pre
# specify the control method for the type of coupling
# physics control_type
fix_modify AtC thermal control flux :pre
# specify the initial values for the empirical field "temperature"
# field node_group value
fix_modify AtC initial temperature all 30 :pre
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output atc_fe_output 100 :pre
run 1000 :pre
likewise for this post-processing example:
# ... commands to create and initialize the MD system :pre
# 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 :pre
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
fix AtC kernel quartic_sphere 10.0 :pre
# 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 :pre
# change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100 :pre
# start with no field defined
# add mass density, potential energy density, stress and temperature
fix_modify AtC fields add density energy stress temperature :pre
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC output nvtFE 100 text :pre
run 1000 :pre
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.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html 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"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html.
[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. :ul
[Related commands:]
After specifying this fix in your input script, several other "fix_modify"_fix_modify.html 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"_USER/atc/man_mesh_create.html
"fix_modify AtC mesh quadrature"_USER/atc/man_mesh_quadrature.html
"fix_modify AtC mesh read"_USER/atc/man_mesh_read.html
"fix_modify AtC mesh write"_USER/atc/man_mesh_write.html
"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_create_nodeset.html
"fix_modify AtC mesh add_to_nodeset"_USER/atc/man_mesh_add_to_nodeset.html
"fix_modify AtC mesh create_faceset box"_USER/atc/man_mesh_create_faceset_box.html
"fix_modify AtC mesh create_faceset plane"_USER/atc/man_mesh_create_faceset_plane.html
"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_create_elementset.html
"fix_modify AtC mesh delete_elements"_USER/atc/man_mesh_delete_elements.html
"fix_modify AtC mesh nodeset_to_elementset"_USER/atc/man_mesh_nodeset_to_elementset.html
"fix_modify AtC boundary"_USER/atc/man_boundary.html
"fix_modify AtC internal_quadrature"_USER/atc/man_internal_quadrature.html
"fix_modify AtC time_integration (thermal)"_USER/atc/man_thermal_time_integration.html
"fix_modify AtC time_integration (momentum)"_USER/atc/man_momentum_time_integration.html
"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html
"fix_modify AtC internal_element_set"_USER/atc/man_internal_element_set.html
"fix_modify AtC decomposition"_USER/atc/man_decomposition.html :ul
fix_modify commands for boundary and initial conditions:
"fix_modify AtC initial"_USER/atc/man_initial.html
"fix_modify AtC fix"_USER/atc/man_fix_nodes.html
"fix_modify AtC unfix"_USER/atc/man_unfix_nodes.html
"fix_modify AtC fix_flux"_USER/atc/man_fix_flux.html
"fix_modify AtC unfix_flux"_USER/atc/man_unfix_flux.html
"fix_modify AtC source"_USER/atc/man_source.html
"fix_modify AtC remove_source"_USER/atc/man_remove_source.html :ul
fix_modify commands for control and filtering:
"fix_modify AtC control"_USER/atc/man_control.html
"fix_modify AtC control thermal"_USER/atc/man_control_thermal.html
"fix_modify AtC control thermal correction_max_iterations"_USER/atc/man_control_thermal_correction_max_iterations.html
"fix_modify AtC control momentum"_USER/atc/man_control_momentum.html
"fix_modify AtC control localized_lambda"_USER/atc/man_localized_lambda.html
"fix_modify AtC control lumped_lambda_solve"_USER/atc/man_lumped_lambda_solve.html
"fix_modify AtC control mask_direction"_USER/atc/man_mask_direction.html control
"fix_modify AtC filter"_USER/atc/man_time_filter.html
"fix_modify AtC filter scale"_USER/atc/man_filter_scale.html
"fix_modify AtC filter type"_USER/atc/man_filter_type.html
"fix_modify AtC equilibrium_start"_USER/atc/man_equilibrium_start.html
"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html
"fix_modify AtC poisson_solver"_USER/atc/man_poisson_solver.html :ul
fix_modify commands for output:
"fix_modify AtC output"_USER/atc/man_output.html
"fix_modify AtC output nodeset"_USER/atc/man_output_nodeset.html
"fix_modify AtC output elementset"_USER/atc/man_output_elementset.html
"fix_modify AtC output boundary_integral"_USER/atc/man_boundary_integral.html
"fix_modify AtC output contour_integral"_USER/atc/man_contour_integral.html
"fix_modify AtC mesh output"_USER/atc/man_mesh_output.html
"fix_modify AtC write_restart"_USER/atc/man_write_restart.html
"fix_modify AtC read_restart"_USER/atc/man_read_restart.html :ul
fix_modify commands for post-processing:
"fix_modify AtC kernel"_USER/atc/man_hardy_kernel.html
"fix_modify AtC fields"_USER/atc/man_hardy_fields.html
"fix_modify AtC grdients"_USER/atc/man_hardy_gradients.html
"fix_modify AtC rates"_USER/atc/man_hardy_rates.html
"fix_modify AtC computes"_USER/atc/man_hardy_computes.html
"fix_modify AtC on_the_fly"_USER/atc/man_hardy_on_the_fly.html
"fix_modify AtC pair_interactions/bond_interactions"_USER/atc/man_pair_interactions.html
"fix_modify AtC sample_frequency"_USER/atc/man_sample_frequency.html
"fix_modify AtC set"_USER/atc/man_set.html :ul
miscellaneous fix_modify commands:
"fix_modify AtC atom_element_map"_USER/atc/man_atom_element_map.html
"fix_modify AtC atom_weight"_USER/atc/man_atom_weight.html
"fix_modify AtC write_atom_weights"_USER/atc/man_write_atom_weights.html
"fix_modify AtC reset_time"_USER/atc/man_reset_time.html
"fix_modify AtC reset_atomic_reference_positions"_USER/atc/man_reset_atomic_reference_positions.html
"fix_modify AtC fe_md_boundary"_USER/atc/man_fe_md_boundary.html
"fix_modify AtC boundary_faceset"_USER/atc/man_boundary_faceset.html
"fix_modify AtC consistent_fe_initialization"_USER/atc/man_consistent_fe_initialization.html
"fix_modify AtC mass_matrix"_USER/atc/man_mass_matrix.html
"fix_modify AtC material"_USER/atc/man_material.html
"fix_modify AtC atomic_charge"_USER/atc/man_atomic_charge.html
"fix_modify AtC source_integration"_USER/atc/man_source_integration.html
"fix_modify AtC temperature_definition"_USER/atc/man_temperature_definition.html
"fix_modify AtC track_displacement"_USER/atc/man_track_displacement.html
"fix_modify AtC boundary_dynamics"_USER/atc/man_boundary_dynamics.html
"fix_modify AtC add_species"_USER/atc/man_add_species.html
"fix_modify AtC add_molecule"_USER/atc/man_add_molecule.html
"fix_modify AtC remove_species"_USER/atc/man_remove_species.html
"fix_modify AtC remove_molecule"_USER/atc/man_remove_molecule.html :ul
Note: a set of example input files with the attendant material files are included with this package
[Default:]
None
:line
For detailed exposition of the theory and algorithms please see:
:link(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.
:link(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.
:link(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.
:link(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.
:link(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.
:link(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.
:link(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.
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