forked from lijiext/lammps
240 lines
10 KiB
HTML
240 lines
10 KiB
HTML
<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.html">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.html">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>
|