jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15442 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-08-05 15:38:38 +00:00
parent 42cc69b843
commit ce7581b869
11 changed files with 538 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
doc/html/_sources/create_atoms.txt
View File

@ -211,9 +211,11 @@ should evaluate to a zero or non-zero value based on one or two or
three variables which will store the x, y, or z coordinates of an atom
(one variable per coordinate). If used, these other variables must be
:doc:`internal-style variables <variable>` defined in the input script;
their initial numeric value can be anything. The *set* keyword is
used to identify the names of these other variables, one variable for
the x-coordinate of a created atom, one for y, and one for z.
their initial numeric value can be anything. They must be
internal-style variables, because this command updates their values
directly. The *set* keyword is used to identify the names of these
other variables, one variable for the x-coordinate of a created atom,
one for y, and one for z.
When an atom is created, its x,y,z coordinates become the values for
any *set* variable that is defined. The *var* variable is then

53
doc/html/_sources/variable.txt
View File

@ -11,7 +11,7 @@ Syntax
variable name style args ...
* name = name of variable to define
* style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *equal* or *internal* or *vector* or *atom*
* style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *internal* or *equal* or *vector* or *atom*
.. parsed-literal::
*delete* = no args
@ -41,6 +41,7 @@ Syntax
*file* arg = filename
*atomfile* arg = filename
*python* arg = function
*internal* arg = numeric value
*equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI, version, on, off, true, false, yes, no
@ -87,6 +88,7 @@ Examples
variable b equal c_myTemp
variable b atom x*y/vol
variable foo string myfile
variable foo internal 3.5
variable myPy python increase
variable f file values.txt
variable temp world 300.0 310.0 320.0 ${Tfinal}
@ -121,7 +123,8 @@ input script that atom-style variables are used; they get their
per-atom values from a file rather than from a formula. Variables of
style *python* can be hooked to Python functions using code you
provide, so that the variable gets its value from the evaluation of
the Python code.
the Python code. Variables of style *internal* are used by a few
commands in LAMMPS which set their value directly.
.. note::
@ -161,13 +164,22 @@ simulation.
Variables of style *equal* and *vector* and *atom* can be used
as inputs to various other LAMMPS commands which evaluate their
formulas as needed, e.g. at different timesteps during a
:doc:`run <run>`. Variables of style *python* can be used in place of
an equal-style variable so long as the associated Python function, as
defined by the :doc:`python <python>` command, returns a numeric value.
Thus any command that states it can use an equal-style variable as an
argument, can also use such a python-style variable. This means that
when the LAMMPS command evaluates the variable, the Python function
will be executed.
:doc:`run <run>`.
Variables of style *internal* can be used in place of an equal-style
variable, except by commands that set the value in the internal-style
variable. Thus any command that states it can use an equal-style
variable as an argument, can also use an internal-style variable.
This means that when the LAMMPS command evaluates the variable, it
will use the value set (internally) by another LAMMPS command.
Variables of style *python* can be used in place of an equal-style
variable so long as the associated Python function, as defined by the
:doc:`python <python>` command, returns a numeric value. Thus any
command that states it can use an equal-style variable as an argument,
can also use such a python-style variable. This means that when the
LAMMPS command evaluates the variable, the Python function will be
executed.
.. note::
@ -182,12 +194,12 @@ simulation.
script.
There are two exceptions to this rule. First, variables of style
*string*\ , *getenv*\ , *equal*\ , *vector*\ , *atom*\ , and *python* ARE
redefined each time the command is encountered. This allows these
style of variables to be redefined multiple times in an input script.
In a loop, this means the formula associated with an *equal* or *atom*
style variable can change if it contains a substitution for another
variable, e.g. $x or v_x.
*string*\ , *getenv*\ , *equal*\ , *vector*\ , *atom*\ , *internal*\ , and
*python* ARE redefined each time the command is encountered. This
allows these style of variables to be redefined multiple times in an
input script. In a loop, this means the formula associated with an
*equal* or *atom* style variable can change if it contains a
substitution for another variable, e.g. $x or v_x.
Second, as described below, if a variable is iterated on to the end of
its list of strings via the :doc:`next <next>` command, it is removed
@ -378,7 +390,7 @@ will be assigned to that atom. IDs can be listed in any order.
For the *python* style a Python function name is provided. This needs
to match a function name specified in a :doc:`python <python>` command
which returns a value to this variable as defined by its *return*
keyword. For exampe these two commands would be self-consistent:
keyword. For example these two commands would be self-consistent:
.. parsed-literal::
@ -402,6 +414,15 @@ python-style variable can be used in place of an equal-style variable
anywhere in an input script, e.g. as an argument to another command
that allows for equal-style variables.
For the *internal* style a numeric value is provided. This value will
be assigned to the variable until a LAMMPS command sets it to a new
value. There are currently only two LAMMPS commands that require
*internal* variables as inputs, because they reset them:
:doc:`create_atoms <create_atoms>` and :doc:`fix controller <fix_controller>`. As mentioned above, an
internal-style variable can be used in place of an equal-style
variable anywhere else in an input script, e.g. as an argument to
another command that allows for equal-style variables.
----------

22
doc/html/create_atoms.html
View File

@ -310,16 +310,18 @@ keyword is the name of an <a class="reference internal" href="variable.html"><sp
should evaluate to a zero or non-zero value based on one or two or
three variables which will store the x, y, or z coordinates of an atom
(one variable per coordinate). If used, these other variables must be
<a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> defined in the input script, but
their formula can by anything. The <em>set</em> keyword is used to identify
the names of these other variables, one variable for the x-coordinate
of a created atom, one for y, and one for z.</p>
<p>When an atom is created, its x, y, or z coordinates override the
formula for any <em>set</em> variable that is defined. The <em>var</em> variable is
then evaluated. If the returned value is 0.0, the atom is not
created. If it is non-zero, the atom is created. After all atoms are
created, the formulas defined for all of the <em>set</em> variables are
restored to their original strings.</p>
<a class="reference internal" href="variable.html"><span class="doc">internal-style variables</span></a> defined in the input script;
their initial numeric value can be anything. They must be
internal-style variables, because this command updates their values
directly. The <em>set</em> keyword is used to identify the names of these
other variables, one variable for the x-coordinate of a created atom,
one for y, and one for z.</p>
<p>When an atom is created, its x,y,z coordinates become the values for
any <em>set</em> variable that is defined. The <em>var</em> variable is then
evaluated. If the returned value is 0.0, the atom is not created. If
it is non-zero, the atom is created. After all atoms are created, the
formulas defined for all of the <em>set</em> variables are restored to their
original strings.</p>
<p>As an example, these commands can be used in a 2d simulation, to
create a sinusoidal surface. Note that the surface is &#8220;rough&#8221; due to
individual lattice points being &#8220;above&#8221; or &#8220;below&#8221; the mathematical

3
doc/html/dump.html
View File

@ -310,6 +310,9 @@ parallel via the MPI-IO library. For the remainder of this doc page,
you should thus consider the <em>atom</em> and <em>atom/mpiio</em> styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.</p>
<p>The precision of values output to text-based dump files can be
controlled by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify format</span></a> command and
its options.</p>
<hr class="docutils" />
<p>The <em>style</em> keyword determines what atom quantities are written to the
file and in what format. Settings made via the

397
doc/html/fix_controller.html Normal file
View File

@ -0,0 +1,397 @@
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>fix controller command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>fix controller command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="fix-controller-command">
<span id="index-0"></span><h1>fix controller command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">controller</span> <span class="n">Nevery</span> <span class="n">alpha</span> <span class="n">Kp</span> <span class="n">Ki</span> <span class="n">Kd</span> <span class="n">pvar</span> <span class="n">setpoint</span> <span class="n">cvar</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>controller = style name of this fix command</li>
<li>Nevery = invoke controller every this many timesteps</li>
<li>alpha = coupling constant for PID equation (see units discussion below)</li>
<li>Kp = proportional gain in PID equation (unitless)</li>
<li>Ki = integral gain in PID equation (unitless)</li>
<li>Kd = derivative gain in PID equation (unitless)</li>
<li>pvar = process variable of form c_ID, c_ID[N], f_ID, f_ID[N], or v_name</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>setpoint = desired value of process variable (same units as process variable)</li>
<li>cvar = name of control variable</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">100</span> <span class="mf">1.0</span> <span class="mf">0.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">c_thermo_temp</span> <span class="mf">1.5</span> <span class="n">tcontrol</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">100</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mf">100.0</span> <span class="n">v_pxxwall</span> <span class="mf">1.01325</span> <span class="n">xwall</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">10000</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mi">2000</span> <span class="n">v_avpe</span> <span class="o">-</span><span class="mf">3.785</span> <span class="n">tcontrol</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This fix enables control of a LAMMPS simulation using a control loop
feedback mechanism known as a proportional-integral-derivative (PID)
controller. The basic idea is to define a &#8220;process variable&#8221; which is
a quantity that can be monitor during a running simulation. A desired
target value is chosen for the process variable. A &#8220;control variable&#8221;
is also defined which is an adjustable attribute of the simulation
which the process variable will respond to. The PID controller
continuously adjusts the control variable based on the difference
between the process variable and the target.</p>
<p>Here are examples of ways in which this fix can be used. The
examples/pid directory contains a script that implements the simple
thermostat.</p>
<table border="1" class="docutils">
<colgroup>
<col width="49%" />
<col width="25%" />
<col width="25%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Goal</td>
<td>process variable</td>
<td>control variable</td>
</tr>
<tr class="row-even"><td>Simple thermostat</td>
<td>instantaneous T</td>
<td>thermostat target T</td>
</tr>
<tr class="row-odd"><td>Find melting temperature</td>
<td>average PE per atom</td>
<td>thermostat target T</td>
</tr>
<tr class="row-even"><td>Control pressure in non-periodic system</td>
<td>force on wall</td>
<td>position of wall</td>
</tr>
<tr class="row-odd"><td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For this fix to work, the control variable must actually induce
a change in a running LAMMPS simulation. Typically this will only
occur if there is some other command (e.g. a thermostat fix) which
uses the control variable as an input parameter. This could be done
directly or indirectly, e.g. the other command uses a variable as
input whose formula uses the control variable. The other command
should alter its behavior dynamically as the variable changes.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If there is a command you think could be used in this fashion,
but does not currently allow a variable as an input parameter, please
notify the LAMMPS developers. It is often not difficult to enable a
command to use a variable as an input parameter.</p>
</div>
<p>The group specified with this command is ignored. However, note that
the process variable may be defined by calculations performed by
computes and fixes which store their own &#8220;group&#8221; definitions.</p>
<p>The PID controller is invoked once each <em>Nevery</em> timesteps.</p>
<p>The PID controller is implemented as a discretized version of
the following dynamic equation:</p>
<img alt="_images/fix_controller1.jpg" class="align-center" src="_images/fix_controller1.jpg" />
<p>where <em>c</em> is the continuous time analog of the control variable,
<em>e</em>=<em>pvar</em>-<em>setpoint</em> is the error in the process variable, and
<em>alpha</em>, <em>Kp</em>, <em>Ki</em>, and <em>Kd</em> are constants set by the corresponding
keywords described above. The discretized version of this equation is:</p>
<img alt="_images/fix_controller2.jpg" class="align-center" src="_images/fix_controller2.jpg" />
<p>where <em>tau</em> = <em>Nevery</em><em>timestep is the time interval between updates,
and the subsripted variables indicated the values of *c</em> and <em>e</em> at
successive updates.</p>
<p>From the first equation, it is clear that if the three gain values
<em>Kp</em>, <em>Ki</em>, <em>Kd</em> are dimensionless constants, then <em>alpha</em> must have
units of [unit <em>cvar</em>]/[unit <em>pvar</em>]/[unit time] e.g. [ eV/K/ps
]. The advantage of this unit scheme is that the value of the
constants should be invariant under a change of either the MD timestep
size or the value of <em>Nevery</em>. Similarly, if the LAMMPS <a class="reference internal" href="units.html"><span class="doc">unit style</span></a> is changed, it should only be necessary to change
the value of <em>alpha</em> to reflect this, while leaving <em>Kp</em>, <em>Ki</em>, and
<em>Kd</em> unaltered.</p>
<p>When choosing the values of the four constants, it is best to first
pick a value and sign for <em>alpha</em> that is consistent with the
magnitudes and signs of <em>pvar</em> and <em>cvar</em>. The magnitude of <em>Kp</em>
should then be tested over a large positive range keeping <em>Ki</em>=<em>Kd</em>=0.
A good value for <em>Kp</em> will produce a fast reponse in <em>pvar</em>, without
overshooting the <em>setpoint</em>. For many applications, proportional
feedback is sufficient, and so <em>Ki</em>=<em>Kd</em>=0 can be used. In cases where
there is a substantial lag time in the response of <em>pvar</em> to a change
in <em>cvar</em>, this can be counteracted by increasing <em>Kd</em>. In situations
where <em>pvar</em> plateaus without reaching <em>setpoint</em>, this can be
counteracted by increasing <em>Ki</em>. In the language of Charles Dickens
(or Donald Trump), <em>Kp</em> represents the error of the present, <em>Ki</em> the
error of the past, and <em>Kd</em> the error yet to come.</p>
<p>Because this fix updates <em>cvar</em>, but does not initialize its value,
the initial value is that assigned by the user in the internal-style
variable command. This value is used (by the other LAMMPS command that
used the variable) until this fix performs its first update of <em>cvar</em>
after <em>Nevery</em> timesteps. On the first update, the value of the
derivative term is set to zero, because the value of <em>e_n-1</em> is not
yet defined.</p>
<hr class="docutils" />
<p>The process variable <em>pvar</em> can be specified as the output of a
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or the evaluation of a
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity.</p>
<p>If <em>pvar</em> begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page
for details. If no bracketed integer is appended, the scalar
calculated by the compute is used. If a bracketed integer is
appended, the Ith value of the vector calculated by the compute is
used. Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If <em>pvar</em> begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
details. Note that some fixes only produce their values on certain
timesteps, which must be compatible with when fix controller
references the values, or else an error results. If no bracketed integer
is appended, the scalar calculated by the fix is used. If a bracketed
integer is appended, the Ith value of the vector calculated by the fix
is used. Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If <em>pvar</em> begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has been
previously defined in the input script. Only equal-style variables
can be referenced. See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command for
details. Note that variables of style <em>equal</em> define a formula which
can reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of specifying the process
variable.</p>
<p>The target value <em>setpoint</em> for the process variable must be a numeric
value, in whatever units <em>pvar</em> is defined for.</p>
<p>The control variable <em>cvar</em> must be the name of an <a class="reference internal" href="variable.html"><span class="doc">internal-style variable</span></a> previously defined in the input script. Note
that it is not specified with a &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221; prefix, just the name of the
variable. It must be an internal-style variable, because this fix
updates its value directly. Note that other commands can use an
equal-style versus internal-style variable interchangeably.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currenlty, no information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global vector with 3 values which can be accessed
by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The values
can be accessed on any timestep, though they are only updated on
timesteps that are a multiple of <em>Nevery</em>.</p>
<p>The three values are the most recent updates made to the control
variable by each of the 3 terms in the PID equation above. The first
value is the proportional term, the second is the integral term, the
third is the derivative term.</p>
<p>The units of the vector values will be whatever units the control
variable is in. The vector values calculated by this fix are
&#8220;extensive&#8221;.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>

4
doc/html/genindex.html
View File

@ -1034,6 +1034,10 @@
</dt>
<dt><a href="fix_controller.html#index-0">fix controller</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>

2
doc/html/searchindex.js
View File

File diff suppressed because one or more lines are too long

4
doc/html/thermo_modify.html
View File

@ -230,8 +230,8 @@ is more than one field. The <em>int</em> and <em>float</em> keywords take a sin
format argument and are applied to all integer or floating-point
quantities output. The setting for <em>M string</em> also takes a single
format argument which is used for the Mth value output in each line,
e.g. the 5th column of output is output in high precision for &#8220;format
5 %20.15g&#8221;.</p>
e.g. the 5th column is output in high precision for &#8220;format 5
%20.15g&#8221;.</p>
<p>The <em>format</em> keyword can be used multiple times. The precedence is
that for each value in a line of output, the <em>M</em> format (if specified)
is used, else the <em>int</em> or <em>float</em> setting (if specified) is used,

50
doc/html/variable.html
View File

@ -133,7 +133,7 @@
</div>
<ul class="simple">
<li>name = name of variable to define</li>
<li>style = <em>delete</em> or <em>index</em> or <em>loop</em> or <em>world</em> or <em>universe</em> or <em>uloop</em> or <em>string</em> or <em>format</em> or <em>getenv</em> or <em>file</em> or <em>atomfile</em> or <em>python</em> or <em>equal</em> or <em>vector</em> or <em>atom</em></li>
<li>style = <em>delete</em> or <em>index</em> or <em>loop</em> or <em>world</em> or <em>universe</em> or <em>uloop</em> or <em>string</em> or <em>format</em> or <em>getenv</em> or <em>file</em> or <em>atomfile</em> or <em>python</em> or <em>internal</em> or <em>equal</em> or <em>vector</em> or <em>atom</em></li>
</ul>
<pre class="literal-block">
<em>delete</em> = no args
@ -163,6 +163,7 @@
<em>file</em> arg = filename
<em>atomfile</em> arg = filename
<em>python</em> arg = function
<em>internal</em> arg = numeric value
<em>equal</em> or <em>vector</em> or <em>atom</em> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI, version, on, off, true, false, yes, no
@ -205,6 +206,7 @@ variable b equal xcm(mol1,x)/2.0
variable b equal c_myTemp
variable b atom x*y/vol
variable foo string myfile
variable foo internal 3.5
variable myPy python increase
variable f file values.txt
variable temp world 300.0 310.0 320.0 ${Tfinal}
@ -239,7 +241,8 @@ input script that atom-style variables are used; they get their
per-atom values from a file rather than from a formula. Variables of
style <em>python</em> can be hooked to Python functions using code you
provide, so that the variable gets its value from the evaluation of
the Python code.</p>
the Python code. Variables of style <em>internal</em> are used by a few
commands in LAMMPS which set their value directly.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">As discussed in <a class="reference internal" href="Section_commands.html#cmd-2"><span class="std std-ref">Section 3.2</span></a> of the
@ -277,14 +280,21 @@ when it is invoked.</p>
<p class="last">Variables of style <em>equal</em> and <em>vector</em> and <em>atom</em> can be used
as inputs to various other LAMMPS commands which evaluate their
formulas as needed, e.g. at different timesteps during a
<a class="reference internal" href="run.html"><span class="doc">run</span></a>. Variables of style <em>python</em> can be used in place of
an equal-style variable so long as the associated Python function, as
defined by the <a class="reference internal" href="python.html"><span class="doc">python</span></a> command, returns a numeric value.
Thus any command that states it can use an equal-style variable as an
argument, can also use such a python-style variable. This means that
when the LAMMPS command evaluates the variable, the Python function
will be executed.</p>
<a class="reference internal" href="run.html"><span class="doc">run</span></a>.</p>
</div>
<p>Variables of style <em>internal</em> can be used in place of an equal-style
variable, except by commands that set the value in the internal-style
variable. Thus any command that states it can use an equal-style
variable as an argument, can also use an internal-style variable.
This means that when the LAMMPS command evaluates the variable, it
will use the value set (internally) by another LAMMPS command.</p>
<p>Variables of style <em>python</em> can be used in place of an equal-style
variable so long as the associated Python function, as defined by the
<a class="reference internal" href="python.html"><span class="doc">python</span></a> command, returns a numeric value. Thus any
command that states it can use an equal-style variable as an argument,
can also use such a python-style variable. This means that when the
LAMMPS command evaluates the variable, the Python function will be
executed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When a variable command is encountered in the input script and
@ -298,12 +308,12 @@ will override a corresponding index variable setting in the input
script.</p>
</div>
<p>There are two exceptions to this rule. First, variables of style
<em>string</em>, <em>getenv</em>, <em>equal</em>, <em>vector</em>, <em>atom</em>, and <em>python</em> ARE
redefined each time the command is encountered. This allows these
style of variables to be redefined multiple times in an input script.
In a loop, this means the formula associated with an <em>equal</em> or <em>atom</em>
style variable can change if it contains a substitution for another
variable, e.g. $x or v_x.</p>
<em>string</em>, <em>getenv</em>, <em>equal</em>, <em>vector</em>, <em>atom</em>, <em>internal</em>, and
<em>python</em> ARE redefined each time the command is encountered. This
allows these style of variables to be redefined multiple times in an
input script. In a loop, this means the formula associated with an
<em>equal</em> or <em>atom</em> style variable can change if it contains a
substitution for another variable, e.g. $x or v_x.</p>
<p>Second, as described below, if a variable is iterated on to the end of
its list of strings via the <a class="reference internal" href="next.html"><span class="doc">next</span></a> command, it is removed
from the list of active variables, and is thus available to be
@ -463,7 +473,7 @@ appear in the set, will remain 0.0.</p>
<p>For the <em>python</em> style a Python function name is provided. This needs
to match a function name specified in a <a class="reference internal" href="python.html"><span class="doc">python</span></a> command
which returns a value to this variable as defined by its <em>return</em>
keyword. For exampe these two commands would be self-consistent:</p>
keyword. For example these two commands would be self-consistent:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">foo</span> <span class="n">python</span> <span class="n">myMultiply</span>
<span class="n">python</span> <span class="n">myMultiply</span> <span class="k">return</span> <span class="n">v_foo</span> <span class="nb">format</span> <span class="n">f</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
</pre></div>
@ -482,6 +492,14 @@ it is a numeric value (integer or floating point), then the
python-style variable can be used in place of an equal-style variable
anywhere in an input script, e.g. as an argument to another command
that allows for equal-style variables.</p>
<p>For the <em>internal</em> style a numeric value is provided. This value will
be assigned to the variable until a LAMMPS command sets it to a new
value. There are currently only two LAMMPS commands that require
<em>internal</em> variables as inputs, because they reset them:
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> and <a class="reference internal" href="fix_controller.html"><span class="doc">fix controller</span></a>. As mentioned above, an
internal-style variable can be used in place of an equal-style
variable anywhere else in an input script, e.g. as an argument to
another command that allows for equal-style variables.</p>
<hr class="docutils" />
<p>For the <em>equal</em> and <em>vector</em> and <em>atom</em> styles, a single string is
specified which represents a formula that will be evaluated afresh

8
doc/src/create_atoms.txt
View File

@ -196,9 +196,11 @@ should evaluate to a zero or non-zero value based on one or two or
three variables which will store the x, y, or z coordinates of an atom
(one variable per coordinate). If used, these other variables must be
"internal-style variables"_variable.html defined in the input script;
their initial numeric value can be anything. The {set} keyword is
used to identify the names of these other variables, one variable for
the x-coordinate of a created atom, one for y, and one for z.
their initial numeric value can be anything. They must be
internal-style variables, because this command updates their values
directly. The {set} keyword is used to identify the names of these
other variables, one variable for the x-coordinate of a created atom,
one for y, and one for z.
When an atom is created, its x,y,z coordinates become the values for
any {set} variable that is defined. The {var} variable is then

54
doc/src/variable.txt
View File

@ -13,7 +13,7 @@ variable command :h3
variable name style args ... :pre
name = name of variable to define :ulb,l
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {format} or {getenv} or {file} or {atomfile} or {python} or {equal} or {internal} or {vector} or {atom} :l
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {format} or {getenv} or {file} or {atomfile} or {python} or {internal} or {equal} or {vector} or {atom} :l
{delete} = no args
{index} args = one or more strings
{loop} args = N
@ -41,6 +41,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
{file} arg = filename
{atomfile} arg = filename
{python} arg = function
{internal} arg = numeric value
{equal} or {vector} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI, version, on, off, true, false, yes, no
@ -83,6 +84,7 @@ variable b equal xcm(mol1,x)/2.0
variable b equal c_myTemp
variable b atom x*y/vol
variable foo string myfile
variable foo internal 3.5
variable myPy python increase
variable f file values.txt
variable temp world 300.0 310.0 320.0 $\{Tfinal\}
@ -119,7 +121,8 @@ input script that atom-style variables are used; they get their
per-atom values from a file rather than from a formula. Variables of
style {python} can be hooked to Python functions using code you
provide, so that the variable gets its value from the evaluation of
the Python code.
the Python code. Variables of style {internal} are used by a few
commands in LAMMPS which set their value directly.
NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the
manual, an input script can use "immediate" variables, specified as
@ -153,13 +156,22 @@ when it is invoked.
NOTE: Variables of style {equal} and {vector} and {atom} can be used
as inputs to various other LAMMPS commands which evaluate their
formulas as needed, e.g. at different timesteps during a
"run"_run.html. Variables of style {python} can be used in place of
an equal-style variable so long as the associated Python function, as
defined by the "python"_python.html command, returns a numeric value.
Thus any command that states it can use an equal-style variable as an
argument, can also use such a python-style variable. This means that
when the LAMMPS command evaluates the variable, the Python function
will be executed.
"run"_run.html.
Variables of style {internal} can be used in place of an equal-style
variable, except by commands that set the value in the internal-style
variable. Thus any command that states it can use an equal-style
variable as an argument, can also use an internal-style variable.
This means that when the LAMMPS command evaluates the variable, it
will use the value set (internally) by another LAMMPS command.
Variables of style {python} can be used in place of an equal-style
variable so long as the associated Python function, as defined by the
"python"_python.html command, returns a numeric value. Thus any
command that states it can use an equal-style variable as an argument,
can also use such a python-style variable. This means that when the
LAMMPS command evaluates the variable, the Python function will be
executed.
NOTE: When a variable command is encountered in the input script and
the variable name has already been specified, the command is ignored.
@ -172,12 +184,12 @@ will override a corresponding index variable setting in the input
script.
There are two exceptions to this rule. First, variables of style
{string}, {getenv}, {equal}, {vector}, {atom}, and {python} ARE
redefined each time the command is encountered. This allows these
style of variables to be redefined multiple times in an input script.
In a loop, this means the formula associated with an {equal} or {atom}
style variable can change if it contains a substitution for another
variable, e.g. $x or v_x.
{string}, {getenv}, {equal}, {vector}, {atom}, {internal}, and
{python} ARE redefined each time the command is encountered. This
allows these style of variables to be redefined multiple times in an
input script. In a loop, this means the formula associated with an
{equal} or {atom} style variable can change if it contains a
substitution for another variable, e.g. $x or v_x.
Second, as described below, if a variable is iterated on to the end of
its list of strings via the "next"_next.html command, it is removed
@ -360,7 +372,7 @@ appear in the set, will remain 0.0.
For the {python} style a Python function name is provided. This needs
to match a function name specified in a "python"_python.html command
which returns a value to this variable as defined by its {return}
keyword. For exampe these two commands would be self-consistent:
keyword. For example these two commands would be self-consistent:
variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py :pre
@ -382,6 +394,16 @@ python-style variable can be used in place of an equal-style variable
anywhere in an input script, e.g. as an argument to another command
that allows for equal-style variables.
For the {internal} style a numeric value is provided. This value will
be assigned to the variable until a LAMMPS command sets it to a new
value. There are currently only two LAMMPS commands that require
{internal} variables as inputs, because they reset them:
"create_atoms"_create_atoms.html and "fix
controller"_fix_controller.html. As mentioned above, an
internal-style variable can be used in place of an equal-style
variable anywhere else in an input script, e.g. as an argument to
another command that allows for equal-style variables.
:line
For the {equal} and {vector} and {atom} styles, a single string is