2009-09-25 01:42:17 +08:00
|
|
|
"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 ID groupID atc type paramfile :pre
|
|
|
|
|
|
|
|
|
|
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
|
|
|
|
atc = style name of this fix command :l
|
|
|
|
|
type = {thermal} or {two_temperature} or {hardy} :l
|
|
|
|
|
{thermal} = thermal coupling with field: temperature
|
|
|
|
|
{two_temperature} = electron-phonon coupling with field, temperature and electron_temperature
|
2009-09-25 02:06:18 +08:00
|
|
|
{hardy} = Hardy on-the-fly post-processing :pre
|
2009-09-25 01:42:17 +08:00
|
|
|
paramfile = file with material parameters (not specified for {hardy} type) :l,ule
|
|
|
|
|
|
|
|
|
|
[Examples:]
|
|
|
|
|
|
|
|
|
|
fix AtC atc_atoms atc thermal Ar_thermal.dat
|
|
|
|
|
fix AtC atc_atoms atc transfer hardy :pre
|
|
|
|
|
|
|
|
|
|
[Description:]
|
|
|
|
|
|
|
|
|
|
This fix creates a coupled finite element (FE) and molecular dynamics
|
2009-09-29 03:50:12 +08:00
|
|
|
(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:
|
|
|
|
|
|
|
|
|
|
:c,image(JPG/atc_nanotube.jpg)
|
|
|
|
|
|
2009-09-25 01:42:17 +08:00
|
|
|
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
|
2009-09-29 03:50:12 +08:00
|
|
|
element sizes.
|
|
|
|
|
|
|
|
|
|
Coupling and post-processing can be combined in the same simulations
|
|
|
|
|
using separate fix atc commands.
|
2009-09-25 01:42:17 +08:00
|
|
|
|
2009-09-29 03:50:12 +08:00
|
|
|
Note that mesh computations and storage run in serial (not
|
|
|
|
|
parallelized) so performance will degrade when large element counts
|
|
|
|
|
are used.
|
2009-09-25 01:42:17 +08:00
|
|
|
|
|
|
|
|
For detailed exposition of the theory and algorithms implemented in
|
|
|
|
|
this fix, please see the papers "here"_#Wagner and "here"_#Zimmerman.
|
|
|
|
|
Please refer to the standard finite element (FE) texts, such as "this
|
|
|
|
|
book"_#Hughes, for the basics of FE simulation.
|
|
|
|
|
|
|
|
|
|
:line
|
|
|
|
|
|
2009-09-25 01:43:29 +08:00
|
|
|
{Thermal} and {two_temperature} (coupling) types use a Verlet
|
|
|
|
|
time-integration algorithm. The {hardy} type does not contain its own
|
2009-09-25 01:42:17 +08:00
|
|
|
time-integrator and must be used with a separate fix that does contain
|
2010-04-03 00:51:06 +08:00
|
|
|
one, e.g. "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, etc.
|
2009-09-25 01:42:17 +08:00
|
|
|
|
|
|
|
|
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"_fix_modify.html 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 :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 fem create mesh 12 2 2 mdRegion f p p :pre
|
|
|
|
|
|
|
|
|
|
# specify the control method for the type of coupling
|
|
|
|
|
# physics control_type
|
|
|
|
|
fix_modify AtC transfer thermal control flux :pre
|
|
|
|
|
|
|
|
|
|
# specify the initial values for the empirical field "temperature"
|
|
|
|
|
# field node_group value
|
|
|
|
|
fix_modify AtC transfer initial temperature all 30.0 :pre
|
|
|
|
|
|
|
|
|
|
# create an output stream for nodal fields
|
|
|
|
|
# filename output_frequency
|
|
|
|
|
fix_modify AtC transfer output atc_fe_output 100 :pre
|
|
|
|
|
|
|
|
|
|
run 1000 :pre
|
|
|
|
|
|
|
|
|
|
The following commands are typical of a post-processing (Hardy) problem:
|
|
|
|
|
|
|
|
|
|
# ... 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
|
|
|
|
|
|
|
|
|
|
# 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 :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
|
|
|
|
|
fix_modify AtC transfer fields none :pre
|
|
|
|
|
|
|
|
|
|
# add mass density, potential energy density, stress and temperature
|
|
|
|
|
fix_modify AtC transfer fields add density energy stress temperature :pre
|
|
|
|
|
|
|
|
|
|
# create an output stream for nodal fields
|
|
|
|
|
# filename output_frequency
|
|
|
|
|
fix_modify AtC transfer output nvtFE 100 text :pre
|
|
|
|
|
|
|
|
|
|
run 1000 :pre
|
|
|
|
|
|
|
|
|
|
: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
|
2011-08-26 01:01:01 +08:00
|
|
|
"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
|
2009-09-25 01:42:17 +08:00
|
|
|
command. This fix is not invoked during "energy
|
|
|
|
|
minimization"_minimize.html.
|
|
|
|
|
|
2009-09-25 01:49:17 +08:00
|
|
|
[Restrictions:]
|
|
|
|
|
|
2011-08-27 02:53:00 +08:00
|
|
|
This fix is part of the USER-ATC package. It is only enabled if
|
2009-09-25 01:49:17 +08:00
|
|
|
LAMMPS was built with that package, which also requires the ATC
|
|
|
|
|
library be built and linked with LAMMPS. See the "Making
|
2011-08-26 00:46:23 +08:00
|
|
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
2009-09-25 01:42:17 +08:00
|
|
|
|
|
|
|
|
[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 fem create mesh"_USER/atc/man_fem_mesh.html
|
|
|
|
|
"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_nodeset.html
|
|
|
|
|
"fix_modify AtC mesh create_faceset"_USER/atc/man_mesh_faceset.html
|
|
|
|
|
"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_elemset.html
|
|
|
|
|
"fix_modify AtC transfer internal"_USER/atc/man_transfer_internal.html
|
|
|
|
|
"fix_modify AtC transfer boundary"_USER/atc/man_transfer_boundary.html
|
|
|
|
|
"fix_modify AtC transfer internal_quadrature"_USER/atc/man_internal_quadrature.html
|
|
|
|
|
"fix_modify AtC transfer pmfc"_USER/atc/man_time_integration.html
|
|
|
|
|
"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html :ul
|
|
|
|
|
|
|
|
|
|
fix_modify commands for boundary and initial conditions:
|
|
|
|
|
|
|
|
|
|
"fix_modify AtC transfer initial"_USER/atc/man_initial.html
|
|
|
|
|
"fix_modify AtC transfer fix"_USER/atc/man_fix_nodes.html
|
|
|
|
|
"fix_modify AtC transfer unfix"_USER/atc/man_unfix_nodes.html
|
|
|
|
|
"fix_modify AtC transfer fix_flux"_USER/atc/man_fix_flux.html
|
|
|
|
|
"fix_modify AtC transferunfix_flux"_USER/atc/man_unfix_flux.html
|
|
|
|
|
"fix_modify AtC transfer source"_USER/atc/man_source.html
|
|
|
|
|
"fix_modify AtC transfer remove_source"_USER/atc/man_remove_source.html :ul
|
|
|
|
|
|
|
|
|
|
fix_modify commands for control and filtering:
|
|
|
|
|
|
|
|
|
|
"fix_modify AtC transfer thermal control"_USER/atc/man_thermal_control.html
|
|
|
|
|
"fix_modify AtC transfer filter"_USER/atc/man_time_filter.html
|
|
|
|
|
"fix_modify AtC transfer filter scale"_USER/atc/man_filter_scale.html
|
|
|
|
|
"fix_modify AtC transfer equilibrium_start"_USER/atc/man_equilibrium_start.html
|
|
|
|
|
"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html :ul
|
|
|
|
|
|
|
|
|
|
fix_modify commands for output:
|
|
|
|
|
|
|
|
|
|
"fix_modify AtC transfer output"_USER/atc/man_transfer_output.html
|
|
|
|
|
"fix_modify AtC transfer atomic_output"_USER/atc/man_transfer_atomic_output.html
|
|
|
|
|
"fix_modify AtC mesh output"_USER/atc/man_mesh_output.html
|
|
|
|
|
"fix_modify AtC transfer write_restart"_USER/atc/man_write_restart.html
|
|
|
|
|
"fix_modify AtC transfer read_restart"_USER/atc/man_read_restart.html :ul
|
|
|
|
|
|
|
|
|
|
fix_modify commands for post-processing:
|
|
|
|
|
|
|
|
|
|
"fix_modify AtC transfer fields"_USER/atc/man_hardy_fields.html
|
|
|
|
|
"fix_modify AtC transfer gradients"_USER/atc/man_hardy_gradients.html
|
2010-05-07 23:11:21 +08:00
|
|
|
"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.html
|
2009-09-25 01:42:17 +08:00
|
|
|
"fix_modify AtC transfer computes"_USER/atc/man_hardy_computes.html
|
|
|
|
|
"fix_modify AtC set"_USER/atc/man_hardy_set.html
|
|
|
|
|
"fix_modify AtC transfer on_the_fly"_USER/atc/man_hardy_on_the_fly.html
|
|
|
|
|
"fix_modify AtC boundary_integral"_USER/atc/man_boundary_integral.html
|
|
|
|
|
"fix_modify AtC contour_integral"_USER/atc/man_contour_integral.html :ul
|
|
|
|
|
|
|
|
|
|
miscellaneous fix_modify commands:
|
|
|
|
|
|
2010-05-07 23:11:21 +08:00
|
|
|
"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.html
|
2009-09-25 01:42:17 +08:00
|
|
|
"fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul
|
|
|
|
|
|
|
|
|
|
[Default:] none
|
|
|
|
|
|
|
|
|
|
:line
|
|
|
|
|
|
|
|
|
|
:link(Wagner)
|
|
|
|
|
[(Wagner)] Wagner, Jones, Templeton, Parks, Special Issue of
|
|
|
|
|
Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
|
|
|
|
|
|
|
|
|
|
:link(Zimmerman)
|
|
|
|
|
[(Zimmerman)] Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
|
|
|
|
|
Issue of Modelling and Simulation in Materials Science and
|
|
|
|
|
Engineering, 12, S319 (2004).
|
|
|
|
|
|
|
|
|
|
:link(Hughes)
|
|
|
|
|
[(Hughes)] T.J.R Hughes, "The Finite Element Method," Dover (2003).
|
