forked from lijiext/lammps
Updating fix_atc files for current version of user-atc
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10857 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
jzimmer
parent
71928fcd96
commit
f8425be4e7
467
doc/fix_atc.html
467
doc/fix_atc.html
|
|
@ -1,239 +1,238 @@
|
|||
<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><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#howto_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#start_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>
|
||||
<h3>fix atc command </h3>
|
||||
<h2><a class="anchor" id="syntax">
|
||||
Syntax</a></h2>
|
||||
<p>fix <fixID> <group> atc <type> <parameter_file></p>
|
||||
<ul>
|
||||
<li>fixID = name of fix</li>
|
||||
<li>group = name of group fix is to be applied</li>
|
||||
<li>type<br/>
|
||||
= thermal : thermal coupling with fields: temperature <br/>
|
||||
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br/>
|
||||
= hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) <br/>
|
||||
= field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) <br/>
|
||||
</li>
|
||||
<li>parameter_file = name of the file with material parameters. <br/>
|
||||
note: Neither hardy nor field requires a parameter file </li>
|
||||
</ul>
|
||||
<h2><a class="anchor" id="examples">
|
||||
Examples</a></h2>
|
||||
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
|
||||
<code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
|
||||
<code> fix AtC internal atc hardy </code> <br/>
|
||||
<code> fix AtC internal atc field </code> <br/>
|
||||
</p>
|
||||
<h2><a class="anchor" id="description">
|
||||
Description</a></h2>
|
||||
<p>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.</p>
|
||||
<CENTER><IMG SRC = "JPG/atc_nanotube.jpg"> </CENTER>
|
||||
<p>The following coupling example is typical, but non-exhaustive:<br/>
|
||||
</p>
|
||||
<p><code> # ... commands to create and initialize the MD system <br/>
|
||||
</code></p>
|
||||
<p><code> # initial fix to designate coupling type and group to apply it to <br/>
|
||||
# tag group physics material_file <br/>
|
||||
fix AtC internal atc thermal Ar_thermal.mat<br/>
|
||||
<br/>
|
||||
# create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/>
|
||||
# nx ny nz region periodicity <br/>
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/>
|
||||
<br/>
|
||||
# specify the control method for the type of coupling <br/>
|
||||
# physics control_type <br/>
|
||||
fix_modify AtC thermal control flux <br/>
|
||||
<br/>
|
||||
# specify the initial values for the empirical field "temperature" <br/>
|
||||
# field node_group value <br/>
|
||||
fix_modify AtC initial temperature all 30.<br/>
|
||||
<br/>
|
||||
# create an output stream for nodal fields <br/>
|
||||
# filename output_frequency <br/>
|
||||
fix_modify AtC output atc_fe_output 100<br/>
|
||||
<br/>
|
||||
</code></p>
|
||||
<p><code> run 1000 <br/>
|
||||
</code></p>
|
||||
<p>likewise for this post-processing example: <br/>
|
||||
</p>
|
||||
<p><code> # ... commands to create and initialize the MD system <br/>
|
||||
</code></p>
|
||||
<p><code> # initial fix to designate post-processing and the group to apply it to <br/>
|
||||
# no material file is allowed nor required <br/>
|
||||
fix AtC internal atc hardy <br/>
|
||||
<br/>
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/>
|
||||
fix AtC kernel quartic_sphere 10.0 <br/>
|
||||
<br/>
|
||||
# create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/>
|
||||
# with periodicity this effectively creats a system average <br/>
|
||||
fix_modify AtC mesh create 1 1 1 box p p p <br/>
|
||||
<br/>
|
||||
# change from default lagrangian map to eulerian <br/>
|
||||
# refreshed every 100 steps <br/>
|
||||
fix_modify AtC atom_element_map eulerian 100 <br/>
|
||||
<br/>
|
||||
# start with no field defined <br/>
|
||||
# add mass density, potential energy density, stress and temperature <br/>
|
||||
fix_modify AtC fields add density energy stress temperature <br/>
|
||||
<br/>
|
||||
# create an output stream for nodal fields <br/>
|
||||
# filename output_frequency <br/>
|
||||
fix_modify AtC output nvtFE 100 text <br/>
|
||||
</code></p>
|
||||
<p><code> run 1000 <br/>
|
||||
</code></p>
|
||||
<p>the mesh's linear interpolation functions can be used as the localization function <br/>
|
||||
by using the field option: <br/>
|
||||
</p>
|
||||
<p><code> fix AtC internal atc field <br/>
|
||||
<br/>
|
||||
fix_modify AtC mesh create 1 1 1 box p p p <br/>
|
||||
<br/>
|
||||
... <br/>
|
||||
<br/>
|
||||
</code></p>
|
||||
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/>
|
||||
For detailed exposition of the theory and algorithms please see:<br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
|
||||
</li>
|
||||
<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
|
||||
</li>
|
||||
<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
|
||||
</li>
|
||||
<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
|
||||
</li>
|
||||
<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
|
||||
</li>
|
||||
<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
|
||||
</li>
|
||||
<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
|
||||
<h2><a class="anchor" id="restrictions">
|
||||
restrictions</a></h2>
|
||||
<p>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.</p>
|
||||
<p>Currently,</p>
|
||||
<ul>
|
||||
<li>the coupling is restricted to thermal physics</li>
|
||||
<li>the FE computations are done in serial on each processor.</li>
|
||||
</ul>
|
||||
<h2><a class="anchor" id="related">
|
||||
related</a></h2>
|
||||
<p>fix_modify commands for setup: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_mesh_create.html">fix_modify AtC mesh create</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_read.html">fix_modify AtC mesh read</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_write.html">fix_modify AtC mesh write</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_boundary.html">fix_modify AtC boundary</a></li>
|
||||
<li><a class="el" href="USER/atc/man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
|
||||
<li><a class="el" href="USER/atc/man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
|
||||
<li><a class="el" href="USER/atc/man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
|
||||
<li><a class="el" href="USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
|
||||
<li><a class="el" href="USER/atc/man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
|
||||
<li><a class="el" href="USER/atc/man_decomposition.html">fix_modify AtC decomposition</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for boundary and initial conditions:<br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_initial.html">fix_modify AtC initial</a></li>
|
||||
<li><a class="el" href="USER/atc/man_fix_nodes.html">fix_modify AtC fix</a></li>
|
||||
<li><a class="el" href="USER/atc/man_unfix_nodes.html">fix_modify AtC unfix</a></li>
|
||||
<li><a class="el" href="USER/atc/man_fix_flux.html">fix_modify AtC fix_flux</a></li>
|
||||
<li><a class="el" href="USER/atc/man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
|
||||
<li><a class="el" href="USER/atc/man_source.html">fix_modify AtC source</a></li>
|
||||
<li><a class="el" href="USER/atc/man_remove_source.html">fix_modify AtC remove_source</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for control and filtering: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_control.html">fix_modify AtC control</a></li>
|
||||
<li><a class="el" href="USER/atc/man_control_thermal.html">fix_modify AtC control thermal</a></li>
|
||||
<li><a class="el" href="USER/atc/man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
|
||||
<li><a class="el" href="USER/atc/man_control_momentum.html">fix_modify AtC control momentum</a></li>
|
||||
<li><a class="el" href="USER/atc/man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
|
||||
<li><a class="el" href="USER/atc/man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mask_direction.html">fix_modify AtC control mask_direction</a></li>
|
||||
<li><a class="el" href="USER/atc/man_time_filter.html">fix_modify AtC filter</a></li>
|
||||
<li><a class="el" href="USER/atc/man_filter_scale.html">fix_modify AtC filter scale</a></li>
|
||||
<li><a class="el" href="USER/atc/man_filter_type.html">fix_modify AtC filter type</a></li>
|
||||
<li><a class="el" href="USER/atc/man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
|
||||
<li><a class="el" href="USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
|
||||
<li>man_charge_control</li>
|
||||
<li><a class="el" href="USER/atc/man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for output: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_output.html">fix_modify AtC output</a></li>
|
||||
<li><a class="el" href="USER/atc/man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_output_elementset.html">fix_modify AtC output elementset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
|
||||
<li><a class="el" href="USER/atc/man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mesh_output.html">fix_modify AtC mesh output</a></li>
|
||||
<li><a class="el" href="USER/atc/man_write_restart.html">fix_modify AtC write_restart</a></li>
|
||||
<li><a class="el" href="USER/atc/man_read_restart.html">fix_modify AtC read_restart</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for post-processing: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_hardy_kernel.html">fix_modify AtC kernel</a></li>
|
||||
<li><a class="el" href="USER/atc/man_hardy_fields.html">fix_modify AtC fields</a></li>
|
||||
<li><a class="el" href="USER/atc/man_hardy_gradients.html">fix_modify AtC gradients</a></li>
|
||||
<li><a class="el" href="USER/atc/man_hardy_rates.html">fix_modify AtC rates</a></li>
|
||||
<li><a class="el" href="USER/atc/man_hardy_computes.html">fix_modify AtC computes</a></li>
|
||||
<li><a class="el" href="USER/atc/man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
|
||||
<li><a class="el" href="USER/atc/man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
|
||||
<li><a class="el" href="USER/atc/man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
|
||||
<li><a class="el" href="USER/atc/man_set.html">fix_modify AtC set</a></li>
|
||||
</ul>
|
||||
<p>miscellaneous fix_modify commands: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="USER/atc/man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
|
||||
<li><a class="el" href="USER/atc/man_atom_weight.html">fix_modify AtC atom_weight</a></li>
|
||||
<li><a class="el" href="USER/atc/man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
|
||||
<li><a class="el" href="USER/atc/man_reset_time.html">fix_modify AtC reset_time</a></li>
|
||||
<li><a class="el" href="USER/atc/man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
|
||||
<li><a class="el" href="USER/atc/man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
|
||||
<li><a class="el" href="USER/atc/man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
|
||||
<li><a class="el" href="USER/atc/man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
|
||||
<li><a class="el" href="USER/atc/man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
|
||||
<li><a class="el" href="USER/atc/man_material.html">fix_modify AtC material</a></li>
|
||||
<li><a class="el" href="USER/atc/man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
|
||||
<li><a class="el" href="USER/atc/man_source_integration.html">fix_modify AtC source_integration</a></li>
|
||||
<li><a class="el" href="USER/atc/man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
|
||||
<li><a class="el" href="USER/atc/man_track_displacement.html">fix_modify AtC track_displacement</a></li>
|
||||
<li><a class="el" href="USER/atc/man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
|
||||
<li><a class="el" href="USER/atc/man_add_species.html">fix_modify AtC add_species</a></li>
|
||||
<li><a class="el" href="USER/atc/man_add_molecule.html">fix_modify AtC add_molecule</a></li>
|
||||
<li><a class="el" href="USER/atc/man_remove_species.html">fix_modify AtC remove_species</a></li>
|
||||
<li><a class="el" href="USER/atc/man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
|
||||
</ul>
|
||||
<p>Note: a set of example input files with the attendant material files are included with this package </p>
|
||||
<h2><a class="anchor" id="default">
|
||||
default</a></h2>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
|
|||
338
doc/fix_atc.txt
338
doc/fix_atc.txt
|
|
@ -10,218 +10,234 @@ fix atc command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
fix ID groupID atc type paramfile :pre
|
||||
fix <fixID> <group> atc <type> <parameter_file> :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
|
||||
{hardy} = Hardy on-the-fly post-processing :pre
|
||||
paramfile = file with material parameters (not specified for {hardy} type) :l,ule
|
||||
fixID = name of fix :l
|
||||
group = name of group fix is to be applied :l
|
||||
type = {thermal} or {two_temperature} or {hardy} or {field} :l
|
||||
{thermal} = thermal coupling with fields: temperature
|
||||
{two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
|
||||
{hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||
{field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
|
||||
parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix AtC atc_atoms atc thermal Ar_thermal.dat
|
||||
fix AtC atc_atoms atc transfer hardy :pre
|
||||
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 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
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:
|
||||
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.
|
||||
|
||||
:c,image(JPG/atc_nanotube.jpg)
|
||||
|
||||
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
|
||||
element sizes.
|
||||
|
||||
Coupling and post-processing can be combined in the same simulations
|
||||
using separate fix atc commands.
|
||||
|
||||
Note that mesh computations and storage run in serial (not
|
||||
parallelized) so performance will degrade when large element counts
|
||||
are used.
|
||||
|
||||
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
|
||||
|
||||
{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. "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, etc.
|
||||
|
||||
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:
|
||||
|
||||
The following coupling example is typical, but non-exhaustive:
|
||||
# ... 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
|
||||
# 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:
|
||||
|
||||
# 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 :pre
|
||||
|
||||
# specify the control method for the type of coupling
|
||||
# physics control_type
|
||||
fix_modify AtC thermal control flux :pre
|
||||
|
||||
# specify the initial values for the empirical field "temperature"
|
||||
# field node_group value
|
||||
fix_modify AtC initial temperature all 30 :pre
|
||||
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output atc_fe_output 100 :pre
|
||||
|
||||
run 1000 :pre
|
||||
|
||||
likewise for this post-processing example:
|
||||
|
||||
# ... 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
|
||||
# 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
|
||||
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
||||
fix AtC kernel quartic_sphere 10.0 :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 mesh create 1 1 1 box p p p :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
|
||||
# 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
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
fix_modify AtC fields add density energy stress temperature :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
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output nvtFE 100 text :pre
|
||||
|
||||
run 1000 :pre
|
||||
|
||||
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.
|
||||
|
||||
: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
|
||||
"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
|
||||
command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
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 "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 command. This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
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 "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
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,
|
||||
- the coupling is restricted to thermal physics
|
||||
- the FE computations are done in serial on each processor. :ul
|
||||
|
||||
[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.
|
||||
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 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 AtC mesh create"_USER/atc/man_mesh_create.html
|
||||
"fix_modify AtC mesh quadrature"_USER/atc/man_mesh_quadrature.html
|
||||
"fix_modify AtC mesh read"_USER/atc/man_mesh_read.html
|
||||
"fix_modify AtC mesh write"_USER/atc/man_mesh_write.html
|
||||
"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_create_nodeset.html
|
||||
"fix_modify AtC mesh add_to_nodeset"_USER/atc/man_mesh_add_to_nodeset.html
|
||||
"fix_modify AtC mesh create_faceset box"_USER/atc/man_mesh_create_faceset_box.html
|
||||
"fix_modify AtC mesh create_faceset plane"_USER/atc/man_mesh_create_faceset_plane.html
|
||||
"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_create_elementset.html
|
||||
"fix_modify AtC mesh delete_elements"_USER/atc/man_mesh_delete_elements.html
|
||||
"fix_modify AtC mesh nodeset_to_elementset"_USER/atc/man_mesh_nodeset_to_elementset.html
|
||||
"fix_modify AtC boundary"_USER/atc/man_boundary.html
|
||||
"fix_modify AtC internal_quadrature"_USER/atc/man_internal_quadrature.html
|
||||
"fix_modify AtC time_integration (thermal)"_USER/atc/man_thermal_time_integration.html
|
||||
"fix_modify AtC time_integration (momentum)"_USER/atc/man_momentum_time_integration.html
|
||||
"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html
|
||||
"fix_modify AtC internal_element_set"_USER/atc/man_internal_element_set.html
|
||||
"fix_modify AtC decomposition"_USER/atc/man_decomposition.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 AtC initial"_USER/atc/man_initial.html
|
||||
"fix_modify AtC fix"_USER/atc/man_fix_nodes.html
|
||||
"fix_modify AtC unfix"_USER/atc/man_unfix_nodes.html
|
||||
"fix_modify AtC fix_flux"_USER/atc/man_fix_flux.html
|
||||
"fix_modify AtC unfix_flux"_USER/atc/man_unfix_flux.html
|
||||
"fix_modify AtC source"_USER/atc/man_source.html
|
||||
"fix_modify AtC remove_source"_USER/atc/man_remove_source.html :ul
|
||||
|
||||
fix_modify commands for control and filtering:
|
||||
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 AtC control"_USER/atc/man_control.html
|
||||
"fix_modify AtC control thermal"_USER/atc/man_control_thermal.html
|
||||
"fix_modify AtC control thermal correction_max_iterations"_USER/atc/man_control_thermal_correction_max_iterations.html
|
||||
"fix_modify AtC control momentum"_USER/atc/man_control_momentum.html
|
||||
"fix_modify AtC control localized_lambda"_USER/atc/man_localized_lambda.html
|
||||
"fix_modify AtC control lumped_lambda_solve"_USER/atc/man_lumped_lambda_solve.html
|
||||
"fix_modify AtC control mask_direction"_USER/atc/man_mask_direction.html control
|
||||
"fix_modify AtC filter"_USER/atc/man_time_filter.html
|
||||
"fix_modify AtC filter scale"_USER/atc/man_filter_scale.html
|
||||
"fix_modify AtC filter type"_USER/atc/man_filter_type.html
|
||||
"fix_modify AtC equilibrium_start"_USER/atc/man_equilibrium_start.html
|
||||
"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html
|
||||
"fix_modify AtC poisson_solver"_USER/atc/man_poisson_solver.html :ul
|
||||
|
||||
fix_modify commands for output:
|
||||
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 output"_USER/atc/man_output.html
|
||||
"fix_modify AtC output nodeset"_USER/atc/man_output_nodeset.html
|
||||
"fix_modify AtC output elementset"_USER/atc/man_output_elementset.html
|
||||
"fix_modify AtC output boundary_integral"_USER/atc/man_boundary_integral.html
|
||||
"fix_modify AtC output contour_integral"_USER/atc/man_contour_integral.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 AtC write_restart"_USER/atc/man_write_restart.html
|
||||
"fix_modify AtC read_restart"_USER/atc/man_read_restart.html :ul
|
||||
|
||||
fix_modify commands for post-processing:
|
||||
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
|
||||
"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.html
|
||||
"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
|
||||
"fix_modify AtC kernel"_USER/atc/man_hardy_kernel.html
|
||||
"fix_modify AtC fields"_USER/atc/man_hardy_fields.html
|
||||
"fix_modify AtC grdients"_USER/atc/man_hardy_gradients.html
|
||||
"fix_modify AtC rates"_USER/atc/man_hardy_rates.html
|
||||
"fix_modify AtC computes"_USER/atc/man_hardy_computes.html
|
||||
"fix_modify AtC on_the_fly"_USER/atc/man_hardy_on_the_fly.html
|
||||
"fix_modify AtC pair_interactions/bond_interactions"_USER/atc/man_pair_interactions.html
|
||||
"fix_modify AtC sample_frequency"_USER/atc/man_sample_frequency.html
|
||||
"fix_modify AtC set"_USER/atc/man_set.html :ul
|
||||
|
||||
miscellaneous fix_modify commands:
|
||||
miscellaneous fix_modify commands:
|
||||
|
||||
"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.html
|
||||
"fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul
|
||||
"fix_modify AtC atom_element_map"_USER/atc/man_atom_element_map.html
|
||||
"fix_modify AtC atom_weight"_USER/atc/man_atom_weight.html
|
||||
"fix_modify AtC write_atom_weights"_USER/atc/man_write_atom_weights.html
|
||||
"fix_modify AtC reset_time"_USER/atc/man_reset_time.html
|
||||
"fix_modify AtC reset_atomic_reference_positions"_USER/atc/man_reset_atomic_reference_positions.html
|
||||
"fix_modify AtC fe_md_boundary"_USER/atc/man_fe_md_boundary.html
|
||||
"fix_modify AtC boundary_faceset"_USER/atc/man_boundary_faceset.html
|
||||
"fix_modify AtC consistent_fe_initialization"_USER/atc/man_consistent_fe_initialization.html
|
||||
"fix_modify AtC mass_matrix"_USER/atc/man_mass_matrix.html
|
||||
"fix_modify AtC material"_USER/atc/man_material.html
|
||||
"fix_modify AtC atomic_charge"_USER/atc/man_atomic_charge.html
|
||||
"fix_modify AtC source_integration"_USER/atc/man_source_integration.html
|
||||
"fix_modify AtC temperature_definition"_USER/atc/man_temperature_definition.html
|
||||
"fix_modify AtC track_displacement"_USER/atc/man_track_displacement.html
|
||||
"fix_modify AtC boundary_dynamics"_USER/atc/man_boundary_dynamics.html
|
||||
"fix_modify AtC add_species"_USER/atc/man_add_species.html
|
||||
"fix_modify AtC add_molecule"_USER/atc/man_add_molecule.html
|
||||
"fix_modify AtC remove_species"_USER/atc/man_remove_species.html
|
||||
"fix_modify AtC remove_molecule"_USER/atc/man_remove_molecule.html :ul
|
||||
|
||||
[Default:] none
|
||||
Note: a set of example input files with the attendant material files are included with this package
|
||||
|
||||
[Default:]
|
||||
None
|
||||
|
||||
:line
|
||||
|
||||
For detailed exposition of the theory and algorithms please see:
|
||||
|
||||
:link(Wagner)
|
||||
[(Wagner)] Wagner, Jones, Templeton, Parks, Special Issue of
|
||||
Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
|
||||
[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
|
||||
|
||||
:link(Zimmerman)
|
||||
[(Zimmerman)] Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
|
||||
Issue of Modelling and Simulation in Materials Science and
|
||||
Engineering, 12, S319 (2004).
|
||||
:link(Zimmeman2004)
|
||||
[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
|
||||
|
||||
:link(Zimmerman2010)
|
||||
[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
|
||||
|
||||
:link(Templeton2010)
|
||||
[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
|
||||
|
||||
:link(Jones)
|
||||
[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
|
||||
|
||||
:link(Templeton2011)
|
||||
[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
|
||||
|
||||
:link(Mandadapu)
|
||||
[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
|
||||
|
||||
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.
|
||||
|
||||
:link(Hughes)
|
||||
[(Hughes)] T.J.R Hughes, "The Finite Element Method," Dover (2003).
|
||||
|
|
|
|||
Loading…
Reference in New Issue