Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F85944331
fix_atc.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Oct 3, 05:28
Size
10 KB
Mime Type
text/html
Expires
Sat, Oct 5, 05:28 (2 d)
Engine
blob
Format
Raw Data
Handle
21302847
Attached To
rLAMMPS lammps
fix_atc.html
View Options
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix atc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID groupID atc type paramfile
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>atc = style name of this fix command
<LI>type = <I>thermal</I> or <I>two_temperature</I> or <I>hardy</I>
<PRE> <I>thermal</I> = thermal coupling with field: temperature
<I>two_temperature</I> = electron-phonon coupling with field, temperature and electron_temperature
<I>hardy</I> = Hardy on-the-fly post-processing
</PRE>
<LI>paramfile = file with material parameters (not specified for <I>hardy</I> type)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix AtC atc_atoms atc thermal Ar_thermal.dat
fix AtC atc_atoms atc transfer hardy
</PRE>
<P><B>Description:</B>
</P>
<P>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:
</P>
<CENTER><IMG SRC = "JPG/atc_nanotube.jpg">
</CENTER>
<P>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.
</P>
<P>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.
</P>
<P>Coupling and post-processing can be combined in the same simulations
using separate fix atc commands.
</P>
<P>Note that mesh computations and storage run in serial (not
parallelized) so performance will degrade when large element counts
are used.
</P>
<P>For detailed exposition of the theory and algorithms implemented in
this fix, please see the papers <A HREF = "#Wagner">here</A> and <A HREF = "#Zimmerman">here</A>.
Please refer to the standard finite element (FE) texts, such as <A HREF = "#Hughes">this
book</A>, for the basics of FE simulation.
</P>
<HR>
<P><I>Thermal</I> and <I>two_temperature</I> (coupling) types use a Verlet
time-integration algorithm. The <I>hardy</I> type does not contain its own
time-integrator and must be used with a separate fix that does contain
one, e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, etc.
</P>
<P>A set of example input files with the attendant material files are
included in the examples/USER/atc directory of the LAMMPS
distribution.
</P>
<P>An extensive set of additional documentation pages for the options
turned on via the <A HREF = "fix_modify.html">fix_modify</A> 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.
</P>
<P>The following commands are typical of a coupling problem:
</P>
<PRE> # ... commands to create and initialize the MD system
</PRE>
<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>
<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>
<PRE> # specify the control method for the type of coupling
# physics control_type
fix_modify AtC transfer thermal control flux
</PRE>
<PRE> # specify the initial values for the empirical field "temperature"
# field node_group value
fix_modify AtC transfer initial temperature all 30.0
</PRE>
<PRE> # create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output atc_fe_output 100
</PRE>
<PRE> run 1000
</PRE>
<P>The following commands are typical of a post-processing (Hardy) problem:
</P>
<PRE> # ... commands to create and initialize the MD system
</PRE>
<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>
<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>
<PRE> # change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100
</PRE>
<PRE> # start with no field defined
fix_modify AtC transfer fields none
</PRE>
<PRE> # add mass density, potential energy density, stress and temperature
fix_modify AtC transfer fields add density energy stress temperature
</PRE>
<PRE> # create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output nvtFE 100 text
</PRE>
<PRE> run 1000
</PRE>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. The <A HREF = "fix_modify.html">fix_modify</A> 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
<A HREF = "Section_howto.html#4_15">output commands</A>. No parameter of this fix
can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>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 <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P>After specifying this fix in your input script, several other
<A HREF = "fix_modify.html">fix_modify</A> commands are used to setup the problem,
e.g. define the finite element mesh and prescribe initial and boundary
conditions.
</P>
<P>fix_modify commands for setup:
</P>
<UL><LI><A HREF = "USER/atc/man_fem_mesh.html">fix_modify AtC fem create mesh</A>
<LI><A HREF = "USER/atc/man_mesh_nodeset.html">fix_modify AtC mesh create_nodeset</A>
<LI><A HREF = "USER/atc/man_mesh_faceset.html">fix_modify AtC mesh create_faceset</A>
<LI><A HREF = "USER/atc/man_mesh_elemset.html">fix_modify AtC mesh create_elementset</A>
<LI><A HREF = "USER/atc/man_transfer_internal.html">fix_modify AtC transfer internal</A>
<LI><A HREF = "USER/atc/man_transfer_boundary.html">fix_modify AtC transfer boundary</A>
<LI><A HREF = "USER/atc/man_internal_quadrature.html">fix_modify AtC transfer internal_quadrature</A>
<LI><A HREF = "USER/atc/man_time_integration.html">fix_modify AtC transfer pmfc</A>
<LI><A HREF = "USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</A>
</UL>
<P>fix_modify commands for boundary and initial conditions:
</P>
<UL><LI><A HREF = "USER/atc/man_initial.html">fix_modify AtC transfer initial</A>
<LI><A HREF = "USER/atc/man_fix_nodes.html">fix_modify AtC transfer fix</A>
<LI><A HREF = "USER/atc/man_unfix_nodes.html">fix_modify AtC transfer unfix</A>
<LI><A HREF = "USER/atc/man_fix_flux.html">fix_modify AtC transfer fix_flux</A>
<LI><A HREF = "USER/atc/man_unfix_flux.html">fix_modify AtC transferunfix_flux</A>
<LI><A HREF = "USER/atc/man_source.html">fix_modify AtC transfer source</A>
<LI><A HREF = "USER/atc/man_remove_source.html">fix_modify AtC transfer remove_source</A>
</UL>
<P>fix_modify commands for control and filtering:
</P>
<UL><LI><A HREF = "USER/atc/man_thermal_control.html">fix_modify AtC transfer thermal control</A>
<LI><A HREF = "USER/atc/man_time_filter.html">fix_modify AtC transfer filter</A>
<LI><A HREF = "USER/atc/man_filter_scale.html">fix_modify AtC transfer filter scale</A>
<LI><A HREF = "USER/atc/man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</A>
<LI><A HREF = "USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</A>
</UL>
<P>fix_modify commands for output:
</P>
<UL><LI><A HREF = "USER/atc/man_transfer_output.html">fix_modify AtC transfer output</A>
<LI><A HREF = "USER/atc/man_transfer_atomic_output.html">fix_modify AtC transfer atomic_output</A>
<LI><A HREF = "USER/atc/man_mesh_output.html">fix_modify AtC mesh output</A>
<LI><A HREF = "USER/atc/man_write_restart.html">fix_modify AtC transfer write_restart</A>
<LI><A HREF = "USER/atc/man_read_restart.html">fix_modify AtC transfer read_restart</A>
</UL>
<P>fix_modify commands for post-processing:
</P>
<UL><LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC transfer fields</A>
<LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC transfer gradients</A>
<LI><A HREF = "USER/atc/man_hardy_rates.htm">fix_modify AtC transfer rates</A>
<LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC transfer computes</A>
<LI><A HREF = "USER/atc/man_hardy_set.html">fix_modify AtC set</A>
<LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</A>
<LI><A HREF = "USER/atc/man_boundary_integral.html">fix_modify AtC boundary_integral</A>
<LI><A HREF = "USER/atc/man_contour_integral.html">fix_modify AtC contour_integral</A>
</UL>
<P>miscellaneous fix_modify commands:
</P>
<UL><LI><A HREF = "USER/atc/man_atom_element_map.htm">fix_modify AtC transfer atom_element_map</A>
<LI><A HREF = "USER/atc/man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</A>
</UL>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Wagner"></A>
<P><B>(Wagner)</B> Wagner, Jones, Templeton, Parks, Special Issue of
Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
</P>
<A NAME = "Zimmerman"></A>
<P><B>(Zimmerman)</B> Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
Issue of Modelling and Simulation in Materials Science and
Engineering, 12, S319 (2004).
</P>
<A NAME = "Hughes"></A>
<P><B>(Hughes)</B> T.J.R Hughes, "The Finite Element Method," Dover (2003).
</P>
</HTML>
Event Timeline
Log In to Comment