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crystal_coordinates.html
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<html>
<head>
<title>
CRYSTAL_COORDINATES - Coordinates of a 3D "Slab" of points.
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
CRYSTAL_COORDINATES <br> Coordinates of a 3D "Slab" of points
</h1>
<hr>
<p>
<b>CRYSTAL_COORDINATES</b>
is a FORTRAN90 program which
generates the coordinates of a set of 4 * NX * NY * NZ
points in a rectangular block of NX * NY * NZ cells, with
face-centered cubic symmetry.
</p>
<p>
The user is allowed to specify the width of a cell, and the
maximum magnitude of a random displacement of each point.
</p>
<p>
The coordinate data is written to a file that can be used
for visualization, or more likely as the initial condition for
the coordinates of molecules in a molecular dynamics simulation.
</p>
<p>
If the initial line of the output file is removed, the remainder becomes
an "XYZ" file which can be plotted by several programs.
</p>
<h3 align = "center">
Usage:
</h3>
<p>
<dl>
<dt>
<b>crystal_coordinates</b>
</dt>
<dd>
begins the program.
</dd>
</dl>
</p>
<p>
Inputs:
<dl>
<dt>
<b>a</b>
</dt>
<dd>
the lattice spacing, or cell width, in Angstroms.
</dd>
<dt>
<b>nx</b>
</dt>
<dd>
the number of cells in the X direction.
</dd>
<dt>
<b>ny</b>
</dt>
<dd>
the number of cells in the Y direction.
</dd>
<dt>
<b>nz</b>
</dt>
<dd>
the number of cells in the Z direction.
</dd>
<dt>
<b>displac</b>
</dt>
<dd>
the maximum magnitude of a random displacement applied to
every node coordinate.
</dd>
<dt>
<b>file_name</b>
</dt>
<dd>
the name of the file into which the coordinate data is to be stored.
</dd>
</dl>
</p>
<p>
The output file has a single initial line of the form
<pre>
% F <i>n</i> <i>x-width</i> <i>y-width</i> <i>z-width</i>
</pre>
where
<dl>
<dt>
<b>n</b>
</dt>
<dd>
is the number of points.
</dd>
<dt>
<b>x-width, y-width, z-width</b>
</dt>
<dd>
are the total widths of the slab in the X, Y and Z directions.
</dd>
</dl>
followed by <i>n</i> lines, each containing the (X,Y,Z) coordinates
of a point.
</p>
<h3 align = "center">
Related Programs:
</h3>
<p>
<a href = "../../f_src/md1/md1.html">
MD1</a>,
a FORTRAN90 program which
is a molecular dynamics simulation program.
</p>
<p>
<a href = "../../f_src/md2/md2.html">
MD2</a>,
a FORTRAN90 program which
is a molecular dynamics simulation program.
</p>
<p>
<a href = "../../f_src/md3/md3.html">
MD3</a>,
a FORTRAN90 program which
is a molecular dynamics simulation program.
</p>
<p>
<a href = "../../f_src/md3glue/md3glue.html">
MD3GLUE</a>,
a FORTRAN90 program which
is a molecular dynamics simulation program.
</p>
<p>
<a href = "../../f77_src/mdbnch/mdbnch.html">
MDBNCH</a>,
a FORTRAN77 program which
carries out a molecular dynamics benchmark.
</p>
<p>
<a href = "../../m_src/xyz_display/xyz_display.html">
XYZ_DISPLAY</a>,
a MATLAB program which
reads XYZ information defining points in 3D, and displays
an image in the MATLAB graphics window.
</p>
<p>
<a href = "../../cpp_src/xyz_display_opengl/xyz_display_opengl.html">
XYZ_DISPLAY_OPENGL</a>,
a C++ program which
reads XYZ information defining points in 3D, and displays
an image using OpenGL.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
Matthew Allen, DJ Tildesley,<br>
Computer Simulation of Liquids,<br>
Oxford University Press, 1987,<br>
ISBN: 0198556454,<br>
LC: QC145.2.
</li>
<li>
Furio Ercolessi,<br>
A Molecular Dynamics Primer,<br>
<a href = "../../pdf/ercolessi.pdf">ercolessi.pdf</a>
</li>
<li>
Dennis Rapaport,<br>
The Art of Molecular Dynamics Simulation,<br>
Cambridge University Press, 2004,<br>
ISBN: 0521825687.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "crystal_coordinates.f90">crystal_coordinates.f90</a>,
the source code.
</li>
<li>
<a href = "crystal_coordinates.sh">crystal_coordinates.sh</a>,
commands to compile the source code.
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "crystal_10_10_10_input.txt">crystal_10_10_10_input.txt</a>,
input for a 10 x 10 x 10 slab.
</li>
<li>
<a href = "crystal_10_10_10.txt">crystal_10_10_10.txt</a>,
the coordinate file.
</li>
<li>
<a href = "crystal_10_10_10_output.txt">crystal_10_10_10_output.txt</a>,
the output from a run of the program.
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>MAIN</b> is the main program for CRYSTAL_COORDINATES.
</li>
<li>
<b>GENERATE_CRYSTAL</b> generates the atomic coordinates.
</li>
<li>
<b>GET_UNIT</b> returns a free FORTRAN unit number.
</li>
<li>
<b>READ_PARAMETERS</b> obtains the parameters from the user.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 17 October 2005.
</i>
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