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md1.html
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<html>
<head>
<title>
MD1 - Molecular Dynamics Simulation
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
MD1 <br> Molecular Dynamics Simulation
</h1>
<hr>
<p>
<b>MD1</b>
is a FORTRAN90 program which
is the first of a series of programs that show
a typical molecular dynamics simulation.
</p>
<h3 align = "center">
Usage:
</h3>
<p>
<dl>
<dt>
<b>md1</b> < <i>input.txt</i> > <i>output.txt</i>
</dt>
<dd>
reads the input file <i>input.txt</i>, and writes the output
to <i>output.txt</i>. Also expects to read a file with a
name like <i>sample0.txt</i> (specified in the input file)
with initial point locations, and will write an output
file with a name like <i>sample1.txt</i> containing the
updated point locations.
</dd>
</dl>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f_src/crystal_coordinates/crystal_coordinates.html">
CRYSTAL_COORDINATES</a>,
a FORTRAN90 program which
generates suitable coordinates for a set of molecules in a rectangular slab.
</p>
<p>
<a href = "../../f_src/md_openmp/md_openmp.html">
MD_OPENMP</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation using OpenMP.
<p>
<p>
<a href = "../../f_src/md2/md2.html">
MD2</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f_src/md3/md3.html">
MD3</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f_src/md3glue/md3glue.html">
MD3GLUE</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f77_src/mdbnch/mdbnch.html">
MDBNCH</a>,
a FORTRAN77 program which
is a benchmark molecular simulation calculation.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
Matthew Allen, Dominic 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.
</li>
<li>
Philipp Janert,<br>
Gnuplot in Action: Understanding Data with Graphs,<br>
Manning, 2008,<br>
ISBN: 1-933988-39-8.
</li>
<li>
Dennis Rapaport,<br>
An Introduction to Interactive Molecular-Dynamics Simulation,<br>
Computers in Physics,<br>
Volume 11, Number 4, July/August 1997, pages 337-347.
</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 = "md1.f90">md1.f90</a>, the source code.
</li>
<li>
<a href = "md1.sh">md1.sh</a>,
commands to compile the source code.
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<b>STEP0</b> is the initial data:
<ul>
<li>
<a href = "md1_sample0.txt">md1_sample0.txt</a>,
a file containing the initial point positions.
</li>
</ul>
</p>
<p>
<b>STEP1</b> reads the initial data from <b>STEP0</b>, runs for 100 steps,
and writes the new data:
<ul>
<li>
<a href = "md1_input1.txt">md1_input1.txt</a>,
a short input file of user parameter values.
</li>
<li>
<a href = "md1_output1.txt">md1_output1.txt</a>,
printed output from a run of the program, which can
be fed directly into GNUPLOT for time evolution plots.
</li>
<li>
<a href = "md1_sample1.txt">md1_sample1.txt</a>,
a file containing the updated point positions, velocities
and accelerations.
</li>
</ul>
</p>
<p>
<b>STEP2</b> reads the data from <b>STEP1</b>, runs for 100 more steps,
and writes the new data:
<ul>
<li>
<a href = "md1_input2.txt">md1_input2.txt</a>,
a short input file of user parameter values.
</li>
<li>
<a href = "md1_output2.txt">md1_output2.txt</a>,
printed output from a run of the program, which can
be fed directly into GNUPLOT for time evolution plots.
</li>
<li>
<a href = "md1_sample2.txt">md1_sample2.txt</a>,
a file containing the updated point positions, velocities
and accelerations.
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>PARTICLES</b> is a module for atom property data.
</li>
<li>
<b>SIMULATION_CONTROL</b> is a module for simulation control data.
</li>
<li>
<b>POTENTIAL</b> is a module with the parameters of the Lennard-Jones potential.
</li>
<li>
<b>STATISTICS</b> is a module with statistical quantities.
</li>
<li>
<b>MAIN</b> is the main program for the MD1 molecular dynamics program.
</li>
<li>
<b>INITIALIZE</b> controls the initialization procedure.
</li>
<li>
<b>READ_SAMPLE</b> reads the initial sample from file unit 1.
</li>
<li>
<b>READ_INPUT</b> reads the parameters controlling the simulation.
</li>
<li>
<b>INITIAL_PRINTOUT</b> prints information on the run parameters.
</li>
<li>
<b>EVOLVE_SAMPLE</b> controls the time evolution of the system.
</li>
<li>
<b>REFOLD_POSITIONS</b> folds exiting particles back into the box.
</li>
<li>
<b>COMPUTE_FORCES</b> computes the forces on atoms.
</li>
<li>
<b>COMPUTE_TEMPERATURE</b> updates the kinetic energy and computes temperature.
</li>
<li>
<b>TERMINATE</b> carries out the termination procedures.
</li>
<li>
<b>PRINT_STATISTICS</b> prints statistics from the calculation.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>WRITE_SAMPLE</b> writes the final sample to file unit 2.
</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 31 October 2005.
</i>
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