forked from johannesgerer/jburkardt-f
-
Notifications
You must be signed in to change notification settings - Fork 1
/
md2.html
253 lines (222 loc) · 6.41 KB
/
md2.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
<html>
<head>
<title>
MD2 - Molecular Dynamics Simulation
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
MD2 <br> Molecular Dynamics Simulation
</h1>
<hr>
<p>
<b>MD2</b>
is a FORTRAN90 program which
is the second of a series of programs that show
a typical molecular dynamics simulation.
</p>
<p>
<b>MD2</b> is a somewhat more sophisticated version of <b>MD1</b>.
In particular, the potential is stored in numerical tables
during the initialization phase. In the force loop, simple
table lookup is performed. For the Lennard-Jones potential,
the speed improvement is not very great, but for other potentials,
this method may be preferred.
</p>
<h3 align = "center">
Usage:
</h3>
<p>
<dl>
<dt>
<b>md2</b> < <i>md2.inp</i> > <i>md2.out</i>
</dt>
<dd>
reads the input file <i>md2.inp</i>, and writes the output
to <i>md2.out</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 Programs:
</h3>
<p>
<a href = "../../f_src/crystal_coordinates/crystal_coordinates.html">
CRYSTAL_COORDINATES</a>,
a FORTRAN90 program which
can be used to generate suitable coordinates for a set
of molecules in a rectangular slab. This data can be used
as the initial data by MD2.
</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/md1/md1.html">
MD1</a>,
a FORTRAN90 program which
is a simpler version of MD2.
</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
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>
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 = "md2.f90">md2.f90</a>, the source code.
</li>
<li>
<a href = "md2.sh">md2.sh</a>,
commands to compile the source code.
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "md2_input.txt">md2_input.txt</a>,
a short input file of user parameter values.
</li>
<li>
<a href = "md2_output.txt">md2_output.txt</a>,
printed output from a run of the program.
</li>
<li>
<a href = "md2_sample0.txt">md2_sample0.txt</a>,
a file containing the initial point positions.
</li>
<li>
<a href = "md2_sample1.txt">md2_sample1.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 28 October 2005.
</i>
<!-- John Burkardt -->
</body>
<!-- Initial HTML skeleton created by HTMLINDEX. -->
</html>