fix <fixID> <group> atc <type> <parameter_file>
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
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:
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.
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,
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:
Note: a set of example input files with the attendant material files are included with this package
none
1.6.1