Syntax:
fix ID groupID atc type paramfile
thermal = thermal coupling with field: temperature two_temperature = electron-phonon coupling with field, temperature and electron_temperature hardy = Hardy on-the-fly post-processing
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 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:
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).