-
fix atc command -
-Syntax: -
-fix ID groupID atc type paramfile --
- ID, group-ID are documented in fix command - -
- atc = style name of this fix command - -
- type = thermal or two_temperature or hardy
-
-
thermal = thermal coupling with field: temperature - two_temperature = electron-phonon coupling with field, temperature and electron_temperature - hardy = Hardy on-the-fly post-processing -
- - paramfile = file with material parameters (not specified for hardy type) -
Examples: -
-fix AtC atc_atoms atc thermal Ar_thermal.dat -fix AtC atc_atoms atc transfer hardy --
Description: -
-This fix creates a coupled finite element (FE) and molecular dynamics -(MD) simulation and/or an on-the-fly estimation of continuum fields, -where a FE mesh is specified and overlaps the particles, something -like this: -
-
-Interscale operators are defined that construct continuum fields from -atomic data. Coupled simulations use FE projection approximated on a -discrete field. Currently, coupling is restricted to thermal physics. -The Hardy module can use either FE projection or integration Kernels -evaluated at mesh points. -
-Coupling methods enable appropriate corrections to the atomic data to -be made based on the FE field. For example, a Gaussian isokinetic -thermostat can apply heat sources to the atoms that varies in space on -the same scale as the FE element size. Meshes are not created -automatically and must be specified on LAMMPS regions with prescribed -element sizes. -
-Coupling and post-processing can be combined in the same simulations -using separate fix atc commands. -
-Note that mesh computations and storage run in serial (not -parallelized) so performance will degrade when large element counts -are used. -
-For detailed exposition of the theory and algorithms implemented in -this fix, please see the papers here and here. -Please refer to the standard finite element (FE) texts, such as this -book, for the basics of FE simulation. -
-- -
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. fix nve, fix nvt, etc. -
-A set of example input files with the attendant material files are -included in the examples/USER/atc directory of the LAMMPS -distribution. -
-An extensive set of additional documentation pages for the options -turned on via the fix_modify command for this fix -are inlcluded in the doc/USER/atc directory of the LAMMPS -distribution. Individual doc pages are listed and linked to below. -
-The following commands are typical of a coupling problem: -
-# ... 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 fem create mesh 12 2 2 mdRegion f p p --
# specify the control method for the type of coupling - # physics control_type - fix_modify AtC transfer thermal control flux --
# specify the initial values for the empirical field "temperature" - # field node_group value - fix_modify AtC transfer initial temperature all 30.0 --
# create an output stream for nodal fields - # filename output_frequency - fix_modify AtC transfer output atc_fe_output 100 --
run 1000 --
The following commands are typical of a post-processing (Hardy) problem: -
-# ... 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 --
# 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 fem create mesh 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 - fix_modify AtC transfer fields none --
# add mass density, potential energy density, stress and temperature - fix_modify AtC transfer fields add density energy stress temperature --
# create an output stream for nodal fields - # filename output_frequency - fix_modify AtC transfer output nvtFE 100 text --
run 1000 --
- -
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: -
-This fix is part of the USER-ATC package. It is only enabled if -LAMMPS was built with that package, which also requires the ATC -library be built and linked with LAMMPS. See the Making -LAMMPS section for more info. -
-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 fem create mesh -
- fix_modify AtC mesh create_nodeset -
- fix_modify AtC mesh create_faceset -
- fix_modify AtC mesh create_elementset -
- fix_modify AtC transfer internal -
- fix_modify AtC transfer boundary -
- fix_modify AtC transfer internal_quadrature -
- fix_modify AtC transfer pmfc -
- fix_modify AtC extrinsic electron_integration -
fix_modify commands for boundary and initial conditions: -
-- fix_modify AtC transfer initial -
- fix_modify AtC transfer fix -
- fix_modify AtC transfer unfix -
- fix_modify AtC transfer fix_flux -
- fix_modify AtC transferunfix_flux -
- fix_modify AtC transfer source -
- fix_modify AtC transfer remove_source -
fix_modify commands for control and filtering: -
-- fix_modify AtC transfer thermal control -
- fix_modify AtC transfer filter -
- fix_modify AtC transfer filter scale -
- fix_modify AtC transfer equilibrium_start -
- fix_modify AtC extrinsic exchange -
fix_modify commands for output: -
-- fix_modify AtC transfer output -
- fix_modify AtC transfer atomic_output -
- fix_modify AtC mesh output -
- fix_modify AtC transfer write_restart -
- fix_modify AtC transfer read_restart -
fix_modify commands for post-processing: -
-- fix_modify AtC transfer fields -
- fix_modify AtC transfer gradients -
- fix_modify AtC transfer rates -
- fix_modify AtC transfer computes -
- fix_modify AtC set -
- fix_modify AtC transfer on_the_fly -
- fix_modify AtC boundary_integral -
- fix_modify AtC contour_integral -
miscellaneous fix_modify commands: -
- -Default: none -
-- - - -
(Wagner) Wagner, Jones, Templeton, Parks, Special Issue of -Computer Methods and Applied Mechanics, 197, 3351-3365 (2008). -
- - -(Zimmerman) Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special -Issue of Modelling and Simulation in Materials Science and -Engineering, 12, S319 (2004). -
- - -(Hughes) T.J.R Hughes, "The Finite Element Method," Dover (2003). -
- +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
+