/
md1.html
278 lines (246 loc) · 7.1 KB
/
md1.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
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
<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>
<!-- John Burkardt -->
</body>
<!-- Initial HTML skeleton created by HTMLINDEX. -->
</html>