2009-09-25 01:42:17 +08:00
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<HTML>
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<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>
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<HR>
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<H3>fix atc command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID groupID atc type paramfile
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>atc = style name of this fix command
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<LI>type = <I>thermal</I> or <I>two_temperature</I> or <I>hardy</I>
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2009-09-25 02:06:18 +08:00
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<PRE> <I>thermal</I> = thermal coupling with field: temperature
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2009-09-25 01:42:17 +08:00
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<I>two_temperature</I> = electron-phonon coupling with field, temperature and electron_temperature
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2009-09-25 02:06:18 +08:00
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<I>hardy</I> = Hardy on-the-fly post-processing
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</PRE>
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<LI>paramfile = file with material parameters (not specified for <I>hardy</I> type)
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2009-09-25 01:42:17 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix AtC atc_atoms atc thermal Ar_thermal.dat
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fix AtC atc_atoms atc transfer hardy
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix creates a coupled finite element (FE) and molecular dynamics
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2009-09-29 03:50:12 +08:00
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(MD) simulation and/or an on-the-fly estimation of continuum fields,
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where a FE mesh is specified and overlaps the particles, something
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like this:
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</P>
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<CENTER><IMG SRC = "JPG/atc_nanotube.jpg">
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</CENTER>
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<P>Interscale operators are defined that construct continuum fields from
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2009-09-25 01:42:17 +08:00
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atomic data. Coupled simulations use FE projection approximated on a
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discrete field. Currently, coupling is restricted to thermal physics.
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The Hardy module can use either FE projection or integration Kernels
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evaluated at mesh points.
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</P>
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<P>Coupling methods enable appropriate corrections to the atomic data to
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be made based on the FE field. For example, a Gaussian isokinetic
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thermostat can apply heat sources to the atoms that varies in space on
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the same scale as the FE element size. Meshes are not created
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automatically and must be specified on LAMMPS regions with prescribed
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2009-09-29 03:50:12 +08:00
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element sizes.
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</P>
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<P>Coupling and post-processing can be combined in the same simulations
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using separate fix atc commands.
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2009-09-25 01:42:17 +08:00
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</P>
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2009-09-29 03:50:12 +08:00
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<P>Note that mesh computations and storage run in serial (not
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parallelized) so performance will degrade when large element counts
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are used.
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2009-09-25 01:42:17 +08:00
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</P>
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<P>For detailed exposition of the theory and algorithms implemented in
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this fix, please see the papers <A HREF = "#Wagner">here</A> and <A HREF = "#Zimmerman">here</A>.
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Please refer to the standard finite element (FE) texts, such as <A HREF = "#Hughes">this
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book</A>, for the basics of FE simulation.
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</P>
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<HR>
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2009-09-25 01:43:29 +08:00
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<P><I>Thermal</I> and <I>two_temperature</I> (coupling) types use a Verlet
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time-integration algorithm. The <I>hardy</I> type does not contain its own
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2009-09-25 01:42:17 +08:00
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time-integrator and must be used with a separate fix that does contain
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2009-09-25 01:43:29 +08:00
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one, e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, etc.
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2009-09-25 01:42:17 +08:00
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</P>
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<P>A set of example input files with the attendant material files are
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included in the examples/USER/atc directory of the LAMMPS
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distribution.
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</P>
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<P>An extensive set of additional documentation pages for the options
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turned on via the <A HREF = "fix_modify.html">fix_modify</A> command for this fix
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are inlcluded in the doc/USER/atc directory of the LAMMPS
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distribution. Individual doc pages are listed and linked to below.
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</P>
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<P>The following commands are typical of a coupling problem:
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</P>
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<PRE> # ... commands to create and initialize the MD system
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</PRE>
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<PRE> # initial fix to designate coupling type and group to apply it to
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# tag group physics material_file
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fix AtC internal atc thermal Ar_thermal.mat
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</PRE>
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<PRE> # create a uniform 12 x 2 x 2 mesh that covers region contain the group
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# nx ny nz region periodicity
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fix_modify AtC fem create mesh 12 2 2 mdRegion f p p
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</PRE>
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<PRE> # specify the control method for the type of coupling
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# physics control_type
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fix_modify AtC transfer thermal control flux
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</PRE>
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<PRE> # specify the initial values for the empirical field "temperature"
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# field node_group value
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fix_modify AtC transfer initial temperature all 30.0
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</PRE>
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<PRE> # create an output stream for nodal fields
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# filename output_frequency
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fix_modify AtC transfer output atc_fe_output 100
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</PRE>
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<PRE> run 1000
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</PRE>
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<P>The following commands are typical of a post-processing (Hardy) problem:
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</P>
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<PRE> # ... commands to create and initialize the MD system
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</PRE>
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<PRE> # initial fix to designate post-processing and the group to apply it to
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# no material file is allowed nor required
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fix AtC internal atc hardy
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</PRE>
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<PRE> # create a uniform 1 x 1 x 1 mesh that covers region contain the group
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# with periodicity this effectively creats a system average
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fix_modify AtC fem create mesh 1 1 1 box p p p
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</PRE>
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<PRE> # change from default lagrangian map to eulerian
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# refreshed every 100 steps
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fix_modify AtC atom_element_map eulerian 100
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</PRE>
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<PRE> # start with no field defined
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fix_modify AtC transfer fields none
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</PRE>
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<PRE> # add mass density, potential energy density, stress and temperature
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fix_modify AtC transfer fields add density energy stress temperature
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</PRE>
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<PRE> # create an output stream for nodal fields
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# filename output_frequency
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fix_modify AtC transfer output nvtFE 100 text
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</PRE>
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<PRE> run 1000
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</PRE>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. The <A HREF = "fix_modify.html">fix_modify</A> options
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relevant to this fix are listed below. No global scalar or vector or
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per-atom quantities are stored by this fix for access by various
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<A HREF = "Section_howto.html#4_15">output commands</A>. No parameter of this fix
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can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
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command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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2009-09-25 01:49:17 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>This fix is part of the "user-atc" package. It is only enabled if
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LAMMPS was built with that package, which also requires the ATC
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library be built and linked with LAMMPS. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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2009-09-25 01:42:17 +08:00
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</P>
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<P><B>Related commands:</B>
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</P>
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<P>After specifying this fix in your input script, several other
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<A HREF = "fix_modify.html">fix_modify</A> commands are used to setup the problem,
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e.g. define the finite element mesh and prescribe initial and boundary
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conditions.
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</P>
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<P>fix_modify commands for setup:
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</P>
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<UL><LI><A HREF = "USER/atc/man_fem_mesh.html">fix_modify AtC fem create mesh</A>
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<LI><A HREF = "USER/atc/man_mesh_nodeset.html">fix_modify AtC mesh create_nodeset</A>
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<LI><A HREF = "USER/atc/man_mesh_faceset.html">fix_modify AtC mesh create_faceset</A>
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<LI><A HREF = "USER/atc/man_mesh_elemset.html">fix_modify AtC mesh create_elementset</A>
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<LI><A HREF = "USER/atc/man_transfer_internal.html">fix_modify AtC transfer internal</A>
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<LI><A HREF = "USER/atc/man_transfer_boundary.html">fix_modify AtC transfer boundary</A>
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<LI><A HREF = "USER/atc/man_internal_quadrature.html">fix_modify AtC transfer internal_quadrature</A>
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<LI><A HREF = "USER/atc/man_time_integration.html">fix_modify AtC transfer pmfc</A>
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<LI><A HREF = "USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</A>
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</UL>
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<P>fix_modify commands for boundary and initial conditions:
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</P>
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<UL><LI><A HREF = "USER/atc/man_initial.html">fix_modify AtC transfer initial</A>
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<LI><A HREF = "USER/atc/man_fix_nodes.html">fix_modify AtC transfer fix</A>
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<LI><A HREF = "USER/atc/man_unfix_nodes.html">fix_modify AtC transfer unfix</A>
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<LI><A HREF = "USER/atc/man_fix_flux.html">fix_modify AtC transfer fix_flux</A>
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<LI><A HREF = "USER/atc/man_unfix_flux.html">fix_modify AtC transferunfix_flux</A>
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<LI><A HREF = "USER/atc/man_source.html">fix_modify AtC transfer source</A>
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<LI><A HREF = "USER/atc/man_remove_source.html">fix_modify AtC transfer remove_source</A>
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</UL>
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<P>fix_modify commands for control and filtering:
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</P>
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<UL><LI><A HREF = "USER/atc/man_thermal_control.html">fix_modify AtC transfer thermal control</A>
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<LI><A HREF = "USER/atc/man_time_filter.html">fix_modify AtC transfer filter</A>
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<LI><A HREF = "USER/atc/man_filter_scale.html">fix_modify AtC transfer filter scale</A>
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<LI><A HREF = "USER/atc/man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</A>
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<LI><A HREF = "USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</A>
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</UL>
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<P>fix_modify commands for output:
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</P>
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<UL><LI><A HREF = "USER/atc/man_transfer_output.html">fix_modify AtC transfer output</A>
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<LI><A HREF = "USER/atc/man_transfer_atomic_output.html">fix_modify AtC transfer atomic_output</A>
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<LI><A HREF = "USER/atc/man_mesh_output.html">fix_modify AtC mesh output</A>
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<LI><A HREF = "USER/atc/man_write_restart.html">fix_modify AtC transfer write_restart</A>
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<LI><A HREF = "USER/atc/man_read_restart.html">fix_modify AtC transfer read_restart</A>
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</UL>
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<P>fix_modify commands for post-processing:
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</P>
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<UL><LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC transfer fields</A>
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<LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC transfer gradients</A>
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<LI><A HREF = "USER/atc/man_hardy_rates.htm">fix_modify AtC transfer rates</A>
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<LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC transfer computes</A>
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<LI><A HREF = "USER/atc/man_hardy_set.html">fix_modify AtC set</A>
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<LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</A>
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<LI><A HREF = "USER/atc/man_boundary_integral.html">fix_modify AtC boundary_integral</A>
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<LI><A HREF = "USER/atc/man_contour_integral.html">fix_modify AtC contour_integral</A>
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</UL>
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<P>miscellaneous fix_modify commands:
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</P>
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<UL><LI><A HREF = "USER/atc/man_atom_element_map.htm">fix_modify AtC transfer atom_element_map</A>
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<LI><A HREF = "USER/atc/man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</A>
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</UL>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Wagner"></A>
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<P><B>(Wagner)</B> Wagner, Jones, Templeton, Parks, Special Issue of
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Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
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</P>
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<A NAME = "Zimmerman"></A>
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<P><B>(Zimmerman)</B> Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
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Issue of Modelling and Simulation in Materials Science and
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Engineering, 12, S319 (2004).
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</P>
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<A NAME = "Hughes"></A>
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<P><B>(Hughes)</B> T.J.R Hughes, "The Finite Element Method," Dover (2003).
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</P>
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</HTML>
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