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Merge pull request #3 from lammps/master 

rebase
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Jacob Gissinger 2018-02-24 23:49:27 -07:00 committed by GitHub
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2
doc/Makefile
View File

@ -21,7 +21,7 @@ HAS_VIRTUALENV = YES
endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
SOURCES=$(wildcard src/*.txt)
SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check

10
doc/src/Manual.txt
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@ -1,9 +1,9 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Jan 2018 version">
<META NAME="docnumber" CONTENT="22 Feb 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
17 Jan 2018 version :c,h4
22 Feb 2018 version :c,h4
Version info: :h4
@ -176,11 +176,11 @@ END_RST -->
5.1 "Measuring performance"_acc_1 :ulb,b
5.2 "Algorithms and code options to boost performace"_acc_2 :b
5.3 "Accelerator packages with optimized styles"_acc_3 :b
5.3.1 "GPU package"_accelerate_gpu.html :ulb,b
5.3.1 "GPU package"_accelerate_gpu.html :b
5.3.2 "USER-INTEL package"_accelerate_intel.html :b
5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
5.3.4 "USER-OMP package"_accelerate_omp.html :b
5.3.5 "OPT package"_accelerate_opt.html :ule,b
5.3.5 "OPT package"_accelerate_opt.html :b
5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b

3
doc/src/Section_commands.txt
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@ -979,6 +979,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"lj/cut/coul/long (gikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/coul/wolf (o)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
@ -1012,7 +1013,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"reax"_pair_reax.html,
"rebo (oi)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"snap"_pair_snap.html,
"snap (k)"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (giko)"_pair_sw.html,
"table (gko)"_pair_table.html,

17
doc/src/Section_intro.txt
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@ -507,11 +507,15 @@ we'll be pleased to add them to the
"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
site.
The core group of LAMMPS developers is at Sandia National Labs:
The primary LAMMPS developers are at Sandia National Labs and Temple University:
Steve Plimpton, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Paul Crozier, pscrozi at sandia.gov :ul
Stan Moore, stamoor at sandia.gov
Axel Kohlmeyer, akohlmey at gmail.com :ul
Past primary developers include Paul Crozier and Mark Stevens,
both at Sandia, and Ray Shan, now at Materials Design.
The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
@ -519,19 +523,20 @@ the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU package
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
As discussed in "Section 13"_Section_history.html, LAMMPS
originated as a cooperative project between DOE labs and industrial

2
doc/src/Section_tools.txt
View File

@ -184,7 +184,7 @@ doxygen tool :h4,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
the "Doxygen"_http://doxygen.org software.
the "Doxygen software"_http://doxygen.org.
See the included README file for details.

46
doc/src/USER/atc/man_add_molecule.html
View File

@ -7,24 +7,22 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
<div class="navigation" id="top">
<div class="tabs">
<ul>
<li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
<li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li><a href="dirs.html"><span>Directories</span></a></li>
</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
</p>
<ul>
@ -35,21 +33,21 @@ syntax</a></h2>
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> group WATERGROUP type 1 2 </code> <br/>
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Associates a tag with all molecules corresponding to a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No defaults for this command. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_add_species.html
View File

@ -7,24 +7,22 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
<div class="navigation" id="top">
<div class="tabs">
<ul>
<li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
<li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li><a href="dirs.html"><span>Directories</span></a></li>
</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
</p>
<ul>
@ -35,21 +33,21 @@ syntax</a></h2>
<li>&lt;ID&gt; = name of group or type number <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No defaults for this command. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_atom_element_map.html
View File

@ -7,42 +7,40 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
<div class="navigation" id="top">
<div class="tabs">
<ul>
<li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
<li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li><a href="dirs.html"><span>Directories</span></a></li>
</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Cannot change map type after initialization. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>lagrangian </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_atom_weight.html
View File

@ -7,24 +7,22 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
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<div class="tabs">
<ul>
<li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
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<li><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li><a href="dirs.html"><span>Directories</span></a></li>
</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
<ul>
<li>&lt;method&gt; = <br/>
@ -36,22 +34,22 @@ syntax</a></h2>
read_in: list of values for atoms are read-in from specified file <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>lattice </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_atomic_charge.html
View File

@ -7,41 +7,39 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
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<div class="tabs">
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</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
<ul>
<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc compute include atomic_charge </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Determines whether AtC tracks the total charge as a finite element field </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Required for: electrostatics </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>if the atom charge is defined, default is on, otherwise default is off </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

42
doc/src/USER/atc/man_boundary.html
View File

@ -7,38 +7,36 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
</center>
<hr>
<!-- Generated by Doxygen 1.6.1 -->
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<ul>
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</div>
<div class="contents">
<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
<ul>
<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

42
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<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>prescribed on </p>
</div>
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doc/src/USER/atc/man_boundary_faceset.html
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<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p>fix_modify AtC boundary_faceset is obndy </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>This is only valid when fe_md_boundary is set to faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
<a href="http://www.doxygen.org/index.html">

48
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<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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doc/src/USER/atc/man_consistent_fe_initialization.html
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<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Default is off </p>
</div>
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48
doc/src/USER/atc/man_contour_integral.html
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<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset</li>
<li>axis (string) : x or y or z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_control">fix_modify AtC control </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
<p><br/>
</p>
@ -46,22 +44,22 @@ syntax</a></h2>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p>
</div>

46
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<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control momentum none <br/>
</p>
<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
@ -44,21 +42,21 @@ syntax</a></h2>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_control_thermal.html
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<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br/>
@ -46,25 +44,25 @@ syntax</a></h2>
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none<br/>
rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p>

46
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<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for use with thermal physics using the fractional step method. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>correction_max_iterations is 20 </p>
</div>
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46
doc/src/USER/atc/man_decomposition.html
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<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC decomposition &lt;type&gt;</p>
<ul>
<li>&lt;type&gt; = <br/>
@ -32,20 +30,20 @@ syntax</a></h2>
distributed_memory: only owned nodal information on processor <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>replicated_memory </p>
</div>
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44
doc/src/USER/atc/man_electron_integration.html
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<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
</p>
<ul>
@ -32,20 +30,20 @@ syntax</a></h2>
</li>
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
</p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>implicit<br/>
subcycle_steps = 1 </p>
</div>

46
doc/src/USER/atc/man_equilibrium_start.html
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<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc equilibrium_start on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only needed before filtering is begun</p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>on </p>
</div>
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48
doc/src/USER/atc/man_extrinsic_exchange.html
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<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Switches energy exchange between the MD system and electron system on and off</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only valid for use with two_temperature type of AtC fix.</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>on </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_fe_md_boundary.html
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<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see for how to specify the faceset name. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Interpolate. </p>
</div>
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syntax</a></h2>
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<h3><a class="anchor" id="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
description</a></h2>
Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <br/>
</p>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Creates a uniform mesh in a rectangular region</p>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>creates only uniform rectangular grids in a rectangular region</p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
none
<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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doc/src/USER/atc/man_filter_scale.html
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<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC filter scale &lt;scale&gt; <br/>
</p>
<ul>
<li>scale (real) = characteristic time scale of the filter <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC filter scale 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>0. </p>
</div>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC filter type exponential </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Specifies the type of time filter used. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No default. </p>
</div>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_fix_atc">fix atc command </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p>
<ul>
<li>fixID = name of fix</li>
@ -38,15 +36,15 @@ syntax</a></h2>
<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>
<h4><a class="anchor" id="examples">
examples</a></h4>
<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>
<h4><a class="anchor" id="description">
description</a></h4>
<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>
<p>The following coupling example is typical, but non-exhaustive:<br/>
</p>
@ -134,16 +132,16 @@ description</a></h2>
</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>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<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>
<h4><a class="anchor" id="related">
related</a></h4>
<p>fix_modify commands for setup: <br/>
</p>
<ul>
@ -243,8 +241,8 @@ related</a></h2>
<li><a class="el" href="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>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only normal fluxes (Neumann data) can be prescribed. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
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46
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
<code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Creates a constraint on the values of the specified field at specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/>
</p>
<ul>
@ -35,8 +33,8 @@ syntax</a></h2>
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> compute virial all stress/atom </code> <br/>
<code> fix_modify AtC computes add virial volume </code> <br/>
<code> fix_modify AtC computes delete virial </code> <br/>
@ -44,20 +42,20 @@ examples</a></h2>
<code> compute centrosymmetry all centro/atom </code> <br/>
<code> fix_modify AtC computes add centrosymmetry number </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
Per-atom compute must be specified before corresponding continuum field can be requested <br/>
</p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>See manual page for compute </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No defaults exist for this command </p>
</div>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC fields &lt;all | none&gt; <br/>
fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
@ -56,24 +54,24 @@ syntax</a></h2>
type_concentration: volume fraction of a specific atom type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC fields add velocity temperature </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
<code> fix_modify AtC fields none </code> <br/>
followed by <br/>
<code> fix_modify AtC fields add velocity temperature </code> <br/>
will only output the velocity and temperature fields. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
<h4><a class="anchor" id="related">
related</a></h4>
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>By default, no fields are output </p>
</div>
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<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
@ -33,21 +31,21 @@ syntax</a></h2>
<li>fields (keyword) = <br/>
gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
<code> fix_modify AtC gradients delete velocity </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No gradients are calculated by default </p>
</div>
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<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@ -40,22 +38,22 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
<code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No default </p>
</div>
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doc/src/USER/atc/man_hardy_on_the_fly.html
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<h1><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
</p>
@ -32,24 +30,24 @@ syntax</a></h2>
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC on_the_fly bond on </code> <br/>
<code> fix_modify AtC on_the_fly kernel </code> <br/>
<code> fix_modify AtC on_the_fly kernel off </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
</p>
</div>

48
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<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
@ -33,22 +31,22 @@ syntax</a></h2>
<li>fields (keyword) = <br/>
rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
<code> fix_modify AtC rates delete stress </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No rates are calculated by default </p>
</div>
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<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_initial">fix_modify AtC initial </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets the initial values for the specified field at the specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
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<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>on for coupling methods, off for post-processors off </p>
</div>
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<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
<ul>
<li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see atom_element_map_type and boundary </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>off </p>
</div>
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<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc internal_quadrature off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
<h2><a class="anchor" id="optional">
optional</a></h2>
<h4><a class="anchor" id="optional">
optional</a></h4>
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>on </p>
</div>
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<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@ -40,21 +38,21 @@ syntax</a></h2>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No default </p>
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doc/src/USER/atc/man_localized_lambda.html
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<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc control localized_lambda on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Default is off. </p>
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<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to use or not use lumped matrix for lambda solve </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
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<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to mask out certain dimensions from the atomic regulator </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
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default</a></h4>
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<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
<ul>
<li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc mass_matrix fe </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Default is off </p>
</div>
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doc/src/USER/atc/man_material.html
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<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_material">fix_modify AtC material </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC material gap_region 2</code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets the material model in elementset_name to be of type material_id. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>All elements default to the first material in the material file. </p>
</div>
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<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id of FE nodeset to be added to</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to add nodes to an already existing FE nodeset. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p>
</div>
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<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
</p>
<ul>
@ -32,21 +30,21 @@ syntax</a></h2>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
</div>
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<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE element</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p>
</div>
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<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@ -32,19 +30,19 @@ syntax</a></h2>
<li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>The default options are units = lattice and the use of outer faces </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

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doc/src/USER/atc/man_mesh_create_faceset_plane.html
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<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@ -32,19 +30,19 @@ syntax</a></h2>
<li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>The default option is units = lattice. </p>
</div>
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doc/src/USER/atc/man_mesh_create_nodeset.html
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<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE nodes</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Coordinates are assumed to be in lattice units. </p>
</div>
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46
doc/src/USER/atc/man_mesh_delete_elements.html
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<h1><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p>
<ul>
<li>&lt;element_set&gt; = name of an element set </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC delete_elements gap </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Deletes a group of elements from the mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
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<h1><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p>
<ul>
<li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li>
<li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li>
<li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>None. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Unless specified, the maximal element set is created </p>
</div>
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<h1><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh output &lt;file_prefix&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh output meshData </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>none </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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46
doc/src/USER/atc/man_mesh_quadrature.html
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<h1><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh quadrature &lt;quad&gt;</p>
<ul>
<li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh quadrature face </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>(Re-)assigns the quadrature style for the existing mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>filename = name of file containing mesh to be read</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>periodicity flags are false by default </p>
</div>
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<h1><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC mesh write &lt;filename&gt;</p>
<ul>
<li>filename = name of file to write mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Writes a mesh to a text file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
<a href="http://www.doxygen.org/index.html">

48
doc/src/USER/atc/man_momentum_time_integration.html
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@ -7,24 +7,22 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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<body>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p>
<ul>
@ -33,24 +31,24 @@ syntax</a></h2>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc time_integration verlet </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

48
doc/src/USER/atc/man_output.html
View File

@ -7,24 +7,22 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_output">fix_modify AtC output </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
<ul>
<li>filename_prefix (string) = prefix for data files</li>
@ -37,23 +35,23 @@ syntax</a></h2>
tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC output heatFE 100 </code> <br/>
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
<code> fix_modify AtC output index step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>no default format output indexed by time </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

48
doc/src/USER/atc/man_output_elementset.html
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@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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<h1><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p>
<ul>
<li>set_name (string) = name of elementset to be integrated over</li>
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC output eset1 mass_density </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

48
doc/src/USER/atc/man_output_nodeset.html
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@ -7,24 +7,22 @@
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<div class="contents">
<h1><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p>
<ul>
<li>nodeset_name (string) = name of nodeset to be operated on</li>
@ -32,20 +30,20 @@ syntax</a></h2>
sum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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doc/src/USER/atc/man_pair_interactions.html
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<h1><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/>
fix_modify AtC bond_interactions &lt;on|off&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC bond_interactions on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>include bonds and/or pairs in the stress and heat flux computations </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>pair interactions: on, bond interactions: off </p>
</div>
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<h1><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = perioidicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC read_restart [file_name] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC read_restart ATC_state </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Reads the current state of the fields from a named text-based restart file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<div class="contents">
<h1><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a molecule type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC remove_molecule water </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Removes tag designated for tracking a specified set of molecules. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC remove_source &lt;field&gt; &lt;element_set&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Remove a domain source. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
<a href="http://www.doxygen.org/index.html">

46
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<h1><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify_AtC delete_species &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC remove_species gold </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Removes tag designated for tracking a specified species. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>No defaults for this command. </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

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<h1><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC reset_atomic_reference_positions </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc reset_atomic_reference_positions </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p><code> </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p><code> Default is off </code></p>
</div>
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<h1><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC reset_time </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc reset_time 0.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Resets the simulation time counter. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h2><a class="anchor" id="syntax">
syntax</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC kernel_bandwidth </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc reset_time 8 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Only is used if kernel functions are being used. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Number of sample locations. </p>
</div>
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<h1><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC sample_frequency [freq]</p>
<ul>
<li>freq (int) : frequency to sample field in number of steps </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC sample_frequency 10 </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
<h4><a class="anchor" id="related">
related</a></h4>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p><code> none </code></p>
</div>
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<h1><a class="anchor" id="man_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_set">fix_modify AtC set </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p>
<ul>
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
</li>
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC set reference_potential_energy </code> <br/>
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Defaults to lammps zero point i.e. isolated atoms </p>
</div>
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<h1><a class="anchor" id="man_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_source">fix_modify AtC source </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC source &lt;field&gt; &lt;element_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_source_integration.html
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@ -7,36 +7,34 @@
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<body>
<center>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<div class="contents">
<h1><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC source_integration &lt; fe | atom&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc source_integration atom </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
<p>Default is fe </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

42
doc/src/USER/atc/man_temperature_definition.html
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@ -7,37 +7,35 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC temperature_definition &lt;kinetic|total&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc temperature_definition kinetic </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>kinetic </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

48
doc/src/USER/atc/man_thermal_time_integration.html
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@ -7,24 +7,22 @@
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</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
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<div class="contents">
<h1><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p>
<ul>
@ -33,23 +31,23 @@ syntax</a></h2>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc time_integration gear </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_time_filter.html
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@ -7,24 +7,22 @@
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</head>
<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<h1><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC filter &lt;on | off | equilibrate&gt; <br/>
</p>
<ul>
@ -32,22 +30,22 @@ syntax</a></h2>
</li>
<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc transfer filter on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a> <br/>
<a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>off </p>
</div>
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doc/src/USER/atc/man_track_displacement.html
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<div class="contents">
<h1><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC track_displacement &lt;on/off&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc track_displacement on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Some constitutive models require the displacement field </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>on </p>
</div>
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doc/src/USER/atc/man_unfix_flux.html
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<h1><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
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<h1><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC unfix &lt;field&gt; &lt;nodeset&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC unfix temperature groupNAME </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Removes constraint on field values for specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

46
doc/src/USER/atc/man_write_atom_weights.html
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<h1><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC write_atom_weights &lt;filename&gt; &lt;frequency&gt;</p>
<ul>
<li>&lt;filename&gt; = name of file that atomic weights are written to <br/>
@ -32,19 +30,19 @@ syntax</a></h2>
<li>&lt;frequency&gt; = how often writes will occur <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command for writing the values of atomic weights to a specified file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="related">
related</a></h4>
<h4><a class="anchor" id="default">
default</a></h4>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
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<li><a href="annotated.html"><span>Classes</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li><a href="dirs.html"><span>Directories</span></a></li>
</ul>
</div>
</div>
<div class="contents">
<h1><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<h3><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h3><h4><a class="anchor" id="syntax">
syntax</a></h4>
<p>fix_modify AtC write_restart [file_name] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<h4><a class="anchor" id="examples">
examples</a></h4>
<p><code> fix_modify AtC write_restart restart.mydata </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h4><a class="anchor" id="related">
related</a></h4>
<p>see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<h4><a class="anchor" id="default">
default</a></h4>
<p>none </p>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

2
doc/src/body.txt
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@ -6,7 +6,7 @@
:line
Body particles :h3
Body particles :h1
[Overview:]

13
doc/src/fix_atc.txt
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@ -90,13 +90,11 @@ likewise for this post-processing example:
run 1000 :pre
the mesh's linear interpolation functions can be used as the localization function
by using the field option:
by using the field option:
fix AtC internal atc field
fix_modify AtC mesh create 1 1 1 box p p p
...
... :pre
Note coupling and post-processing can be combined in the same simulations using separate fixes.
@ -108,11 +106,10 @@ No information about this fix is written to "binary restart files"_restart.html.
[Restrictions:]
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.
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. In addition, currently:
Currently,
- the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor. :ul
the coupling is restricted to thermal physics :ulb,l
the FE computations are done in serial on each processor. :l,ule
[Related commands:]

10
doc/src/fix_gcmc.txt
View File

@ -95,8 +95,8 @@ which will result in roughly one MC move per atom or molecule
per MC cycle.
All inserted particles are always added to two groups: the default
group "all" and the fix group specified in the fix command (which can
also be "all"). In addition, particles are also added to any groups
group "all" and the fix group specified in the fix command.
In addition, particles are also added to any groups
specified by the {group} and {grouptype} keywords. If inserted
particles are individual atoms, they are assigned the atom type given
by the type argument. If they are molecules, the type argument has no
@ -104,6 +104,12 @@ effect and must be set to zero. Instead, the type of each atom in the
inserted molecule is specified in the file read by the
"molecule"_molecule.html command.
NOTE: Care should be taken to apply fix gcmc only to
a group that contains only those atoms and molecules
that you wish to manipulate using Monte Carlo.
Hence it is generally not a good idea to specify
the default group "all" in the fix command, although it is allowed.
This fix cannot be used to perform GCMC insertions of gas atoms or
molecules other than the exchanged type, but GCMC deletions,
and MC translations, and rotations can be performed on any atom/molecule in

15
doc/src/group.txt
View File

@ -13,11 +13,13 @@ group command :h3
group ID style args :pre
ID = user-defined name of the group :ulb,l
style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
style = {delete} or {clear} or {empty} or {region} or \
{type} or {id} or {molecule} or {variable} or \
{include} or {subtract} or {union} or {intersect} or \
{dynamic} or {static} :l
{delete} = no args
{clear} = no args
{empty} = no args
{region} args = region-ID
{type} or {id} or {molecule}
args = list of one or more atom types, atom IDs, or molecule IDs
@ -41,6 +43,7 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
keyword = {region} or {var} or {every}
{region} value = region-ID
{var} value = name of variable
{property} value = name of per-atom property
{every} value = N = update group every this many timesteps
{static} = no args :pre
:ule
@ -99,6 +102,10 @@ e.g. using the "run every"_run.html command if a fix or compute or
other operation expects the atoms in the group to remain constant, but
LAMMPS does not check for this.
The {empty} style creates an empty group, which is useful for commands
like "fix gcmc"_fix_gcmc.html or with complex scripts that add atoms
to a group.
The {region} style puts all atoms in the region volume into the group.
Note that this is a static one-time assignment. The atoms remain
assigned (or not assigned) to the group even in they later move out of
@ -215,7 +222,11 @@ conditions are applied. If the {region} keyword is used, atoms not in
the specified region are removed from the dynamic group. If the {var}
keyword is used, the variable name must be an atom-style or
atomfile-style variable. The variable is evaluated and atoms whose
per-atom values are 0.0, are removed from the dynamic group.
per-atom values are 0.0, are removed from the dynamic group. If the {property}
keyword is used, the per-atom property name must be a previously defined
per-atom property. The per-atom property is evaluated and atoms whose
values are 0.0 are removed from the dynamic group, otherwise they
are added to the group.
The assignment of atoms to a dynamic group is done at the beginning of
each run and on every timestep that is a multiple of {N}, which is the

9
doc/src/lammps.book
View File

@ -20,6 +20,7 @@ Section_python.html
Section_errors.html
Section_history.html
lammps_tutorials.html
tutorial_bash_on_windows.html
tutorial_drude.html
tutorial_github.html
@ -28,6 +29,7 @@ tutorial_pylammps.html
body.html
manifolds.html
lammps_commands.html
angle_coeff.html
angle_style.html
atom_modify.html
@ -138,7 +140,6 @@ fix_adapt_fep.html
fix_addforce.html
fix_addtorque.html
fix_append_atoms.html
fix_atc.html
fix_atom_swap.html
fix_ave_atom.html
fix_ave_chunk.html
@ -277,6 +278,7 @@ fix_spring_self.html
fix_srd.html
fix_store_force.html
fix_store_state.html
fix_surface_global.html
fix_temp_berendsen.html
fix_temp_csvr.html
fix_temp_rescale.html
@ -423,11 +425,13 @@ pair_airebo.html
pair_awpmd.html
pair_beck.html
pair_body.html
pair_body_rounded_polygon.html
pair_bop.html
pair_born.html
pair_brownian.html
pair_buck.html
pair_buck_long.html
pair_buck6d_coul_gauss.html
pair_charmm.html
pair_class2.html
pair_colloid.html
@ -539,6 +543,7 @@ bond_zero.html
angle_charmm.html
angle_class2.html
angle_cosine.html
angle_cosine_buck6d.html
angle_cosine_delta.html
angle_cosine_periodic.html
angle_cosine_shift.html
@ -578,11 +583,13 @@ improper_distance.html
improper_fourier.html
improper_harmonic.html
improper_hybrid.html
improper_inversion_harmonic.html
improper_none.html
improper_ring.html
improper_umbrella.html
improper_zero.html
fix_atc.html
USER/atc/man_add_molecule.html
USER/atc/man_add_species.html
USER/atc/man_atom_element_map.html

10
doc/src/lammps_commands.txt Normal file
View File

@ -0,0 +1,10 @@
LAMMPS Commands :h1
The following pages contain the detailed documentation of all
LAMMPS commands included in this version of LAMMPS. Generic
commands are listed first (in alphabetical order) followed by
command categories like compute styles or pair styles and so on.
The documentation for the USER-ATC package fix_modify commands
follow at the very end of this manual.

6
doc/src/lammps_tutorials.txt Normal file
View File

@ -0,0 +1,6 @@
Tutorials :h2
The following pages contain some in-depth tutorials for
selected topics, that did not fit into any other place
in the manual.

2
doc/src/manifolds.txt
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@ -6,7 +6,7 @@
:line
Manifolds (surfaces) :h3
Manifolds (surfaces) :h1
[Overview:]

28
doc/src/pair_lj.txt
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@ -32,6 +32,8 @@ pair_style lj/cut/coul/long/omp command :h3
pair_style lj/cut/coul/msm command :h3
pair_style lj/cut/coul/msm/gpu command :h3
pair_style lj/cut/coul/msm/omp command :h3
pair_style lj/cut/coul/wolf command :h3
pair_style lj/cut/coul/wolf/omp command :h3
pair_style lj/cut/tip4p/cut command :h3
pair_style lj/cut/tip4p/cut/omp command :h3
pair_style lj/cut/tip4p/long command :h3
@ -63,6 +65,10 @@ args = list of arguments for a particular style :ul
{lj/cut/coul/msm} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/wolf} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -115,6 +121,10 @@ pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
pair_style lj/cut/coul/wolf 0.2 5. 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5 :pre
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
@ -179,6 +189,24 @@ that a term is added for the "core/shell
model"_Section_howto.html#howto_25 to allow charges on core and shell
particles to be separated by r = 0.0.
Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf
summation method, described in "Wolf"_#Wolf1, given by:
:c,image(Eqs/pair_coul_wolf.jpg)
where {alpha} is the damping parameter, and erfc() is the
complementary error-function terms. This potential
is essentially a short-range, spherically-truncated,
charge-neutralized, shifted, pairwise {1/r} summation. With a
manipulation of adding and subtracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough {alpha} damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
a long enough cutoff and small enough alpha parameter, the energy and
forces calculated by the Wolf summation method approach those of the
Ewald sum. So it is a means of getting effective long-range
interactions with a short-range potential.
Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P
water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless
site located a short distance away from the oxygen atom along the

2
doc/src/read_data.txt
View File

@ -547,7 +547,7 @@ charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
dpd: atom-ID atom-type theta x y z
edpd: atom-ID atom-type edpd_temp edpd_cv x y z
mdpd: atom-ID atom-type x y z
mdpd: atom-ID atom-type rho x y z
tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type ellipsoidflag density x y z

52
doc/src/tutorial_pylammps.txt
View File

@ -6,14 +6,14 @@
:line
PyLammps Tutorial :h1
PyLammps Tutorial :h3
<!-- RST
.. contents::
END_RST -->
Overview :h2
Overview :h4
PyLammps is a Python wrapper class which can be created on its own or use an
existing lammps Python object. It creates a simpler, Python-like interface to
@ -23,16 +23,16 @@ C++ code implementation. Finally, the IPyLammps wrapper builds on top of
PyLammps and adds some additional features for IPython integration into IPython
notebooks, e.g. for embedded visualization output from dump/image.
Comparison of lammps and PyLammps interfaces :h3
Comparison of lammps and PyLammps interfaces :h5
lammps.lammps :h4
lammps.lammps :h6
uses C-Types
direct memory access to native C++ data
provides functions to send and receive data to LAMMPS
requires knowledge of how LAMMPS internally works (C pointers, etc) :ul
lammps.PyLammps :h4
lammps.PyLammps :h6
higher-level abstraction built on top of original C-Types interface
manipulation of Python objects
@ -41,11 +41,11 @@ shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
Quick Start :h2
Quick Start :h4
System-wide Installation :h3
System-wide Installation :h5
Step 1: Building LAMMPS as a shared library :h4
Step 1: Building LAMMPS as a shared library :h6
To use LAMMPS inside of Python it has to be compiled as shared library. This
library is then loaded by the Python interface. In this example we enable the
@ -60,7 +60,7 @@ make yes-MOLECULE :pre
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre
Step 2: Installing the LAMMPS Python package :h4
Step 2: Installing the LAMMPS Python package :h6
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation.
@ -71,12 +71,12 @@ python install.py :pre
NOTE: Recompiling the shared library requires reinstalling the Python package
Installation inside of a virtualenv :h3
Installation inside of a virtualenv :h5
You can use virtualenv to create a custom Python environment specifically tuned
for your workflow.
Benefits of using a virtualenv :h4
Benefits of using a virtualenv :h6
isolation of your system Python installation from your development installation
installation can happen in your user directory without root access (useful for HPC clusters)
@ -87,7 +87,7 @@ you can even install specific old versions of a package if necessary :ul
apt-get install python-virtualenv :pre
Creating a virtualenv with lammps installed :h4
Creating a virtualenv with lammps installed :h6
# create virtualenv name 'testing' :pre
@ -107,7 +107,7 @@ source testing/bin/activate :pre
(testing) deactivate :pre
Creating a new instance of PyLammps :h2
Creating a new instance of PyLammps :h4
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new {lammps} instance is created.
@ -121,7 +121,7 @@ from lammps import lammps, PyLammps
lmp = lammps()
L = PyLammps(ptr=lmp) :pre
Commands :h2
Commands :h4
Sending a LAMMPS command with the existing library interfaces is done using
the command method of the lammps object instance.
@ -155,7 +155,7 @@ them automatically to a final command string.
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre
System state :h2
System state :h4
In addition to dispatching commands directly through the PyLammps object, it
also provides several properties which allow you to query the system state.
@ -208,7 +208,7 @@ List of groups present in the current system :dd
:dle
Working with LAMMPS variables :h2
Working with LAMMPS variables :h4
LAMMPS variables can be both defined and accessed via the PyLammps interface.
@ -229,7 +229,7 @@ property of this object.
print(a.value)
a.value = 4 :pre
Retrieving the value of an arbitrary LAMMPS expressions :h2
Retrieving the value of an arbitrary LAMMPS expressions :h4
LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
@ -240,7 +240,7 @@ result = L.eval("pe") # potential energy :pre
result = L.eval("v_t/2.0") :pre
Accessing atom data :h2
Accessing atom data :h4
All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
@ -263,7 +263,7 @@ L.atoms\[0\].position = (1.0, 0.0) :pre
# set position in 3D simulation
L.atoms\[0\].position = (1.0, 0.0, 1.) :pre
Evaluating thermo data :h2
Evaluating thermo data :h4
Each simulation run usually produces thermo output based on system state,
computes, fixes or variables. The trajectories of these values can be queried
@ -291,7 +291,7 @@ steps = L.runs\[0\].step
ke = L.runs\[0\].ke
plt.plot(steps, ke) :pre
Error handling with PyLammps :h2
Error handling with PyLammps :h4
Compiling the shared library with C++ exception support provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
@ -304,7 +304,7 @@ current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
Using PyLammps in IPython notebooks and Jupyter :h2
Using PyLammps in IPython notebooks and Jupyter :h4
If the LAMMPS Python package is installed for the same Python interpreter as
IPython, you can use PyLammps directly inside of an IPython notebook inside of
@ -320,7 +320,7 @@ Python environment (this assumes you followed the Quick Start instructions):
jupyter notebook :pre
IPyLammps Examples :h2
IPyLammps Examples :h4
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
@ -328,7 +328,7 @@ directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
Validating a dihedral potential :h3
Validating a dihedral potential :h5
This example showcases how an IPython Notebook can be used to compare a simple
LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
@ -353,7 +353,7 @@ plot inside the IPython notebook.
:c,image(JPG/pylammps_dihedral.jpg)
Running a Monte Carlo relaxation :h3
Running a Monte Carlo relaxation :h5
This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
simulation, computing and plotting energy terms and even embedding video output.
@ -424,7 +424,7 @@ The energies of each iteration are collected in a Python list and finally plotte
The IPython notebook also shows how to use dump commands and embed video files
inside of the IPython notebook.
Using PyLammps and mpi4py (Experimental) :h2
Using PyLammps and mpi4py (Experimental) :h4
PyLammps can be run in parallel using mpi4py. This python package can be installed using
@ -451,7 +451,7 @@ mpirun -np 4 python melt.py :pre
IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
Feedback and Contributing :h2
Feedback and Contributing :h4
If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also

2
doc/src/variable.txt
View File

@ -689,7 +689,7 @@ increase in increments of z, starting at x, until a is reached. At
that point the timestep increases in increments of c, from a to b,
then after b, increments by z are resumed until y is reached. For any
current timestep, the next timestep in the sequence is returned. Thus
if stride(1000,2000,100,1350,1360,1) is used in a variable by the
if stride2(1000,2000,100,1350,1360,1) is used in a variable by the
"dump_modify every"_dump_modify.html command, it will generate the
sequence of output timesteps:

108
examples/USER/meso/edpd/in.edpd
View File

@ -1,54 +1,54 @@
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500

104
examples/USER/meso/mdpd/in.mdpd
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@ -1,52 +1,52 @@
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
lattice fcc 6
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
#dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
lattice fcc 6
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
#dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000

108
examples/USER/meso/tdpd/in.tdpd
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@ -1,54 +1,54 @@
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * cc 1 1.0
set atom * cc 2 1.0
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * cc 1 1.0
set atom * cc 2 1.0
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100

78
examples/USER/mgpt/log.lammps
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@ -1,78 +0,0 @@
LAMMPS (23 Oct 2015)
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
# input for relaxed vacancy formation energy at constant pressure
echo screen
Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
1 by 1 by 1 MPI processor grid
Created 250 atoms
Deleted 1 atoms, new total = 249
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.1712
ghost atom cutoff = 13.1712
binsize = 6.58562 -> bins = 5 5 5
Memory usage per processor = 4.66978 Mbytes
Step Volume Temp PotEng TotEng Press
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms
92.4% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-73.9945109564 -74.0063705487 -74.0063705557
Force two-norm initial, final = 0.0366227 8.09081e-05
Force max component initial, final = 0.00730948 8.05242e-06
Final line search alpha, max atom move = 1 8.05242e-06
Iterations, force evaluations = 139 139
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43
Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44
Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04
Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00297 | | | 0.07
Nlocal: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1479 ave 1479 max 1479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7936 ave 7936 max 7936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15872 ave 15872 max 15872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15872
Ave neighs/atom = 63.743
Neighbor list builds = 4
Dangerous builds = 0
number of atoms = 249
atomic volume (a.u.) = 121.863
total energy (ry/atom) = -0.594428679162064
pressure (gpa) = -1.15783109519801
249 121.863 -148.012741111354 -1.15783109519801
121.863 -0.594428679162064 -1.15783109519801
Total wall time: 0:00:04

8
examples/gcmc/in.gcmc.co2
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@ -58,21 +58,21 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
group oxygen dynamic all var oxygen
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)

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