forked from TUM-I5/MolSim
-
Notifications
You must be signed in to change notification settings - Fork 1
/
.molsim.1
181 lines (165 loc) · 4.34 KB
/
.molsim.1
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
.\" Manpage for MolSim
.TH man 1 "14 May 2024" "1.0" "MolSim man page"
.SH NAME
MolSim \- Particle dynamics simulation
.SH SYNOPSIS
MolSim [OPTIONS] FILE
.SH DESCRIPTION
MolSim is a particle simulation program created for the PSE Molecular Dynamics course at TUM. It reads particle information from FILE, simulates particle dynamics, and outputs results in VTK format.
.SH OPTIONS
.TP
\fB-d, --delta_t=VALUE\fR
Set the time step (default: 0.014).
.TP
\fB-e, --end_time=VALUE\fR
Set the end time for simulation (default: 0.28).
.TP
\fB--epsilon=VALUE\fR
Set the depth of LJ potential well (default: 5).
.TP
\fB--sigma=VALUE\fR
Set the Zero crossing of LJ potential (default: 1).
.TP
\fB-l, --log_level=LEVEL\fR
Set the logging level (default: 3).
.br
The loglevel are set as following:
.br
.br
1=trace,
2=debug,
3=info,
4=warn,
5=err,
6=critical,
7=off
.br
.TP
\fB-c\fR
Specify that the given input file describes clusters.
.br
For the format of the input file, refer to the \fBCluster Format\fR section.
.br
.TP
\fB-a\fR
Specify that the given input file describes ASCII art particles.
.br
For the format of the input file, refer to the \fBASCII Art Format\fR section.
.br
.TP
\fB-x\fR
Specify that the given input file is an XML file.
.br
For the format of the input file, refer to the \fBXML Format\fR section.
.br
.TP
\fB-s, --simtype=VALUE\fR
Specify simulation type (default: 0).
.br
0 = PlanetSimulation
.br
.br
1 = LennardJonesSimulation
.br
.br
2 = LennardJonesSimulation with Linked Cells
.br
.br
3 = LennardJonesSimulation with Linked Cells + Boundary Conditions
.br
.br
4 = Lennard Jones simulation with Linked Cells + Boundary Conditions + Different Particle types + Gravity
.br
.TP
\fB-w, --writetype=VALUE\fR
Specify writer type (default: 0).
.br
0 = VTKWriter
.br
.br
1 = XYZWriter
.br
.br
2 = XMLWriter
.br
.br
3 = Empty i.e. no output
.br
.TP
\fB-p\fR
Run performance measurements (incompatible with -l, -w).
.TP
\fB-P, --parallel\fR
Specify parallel strategy (static, task)
.TP
\fB-h, --help\fR
Display help message.
.SH INPUT FILE
MolSim supports different types of input file formats:
\fBParticle Input Format\fR:
.br
This format is used for providing particle data directly.
The file starts with optional comment lines denoted by '#' at the beginning of each line.
The first non-comment line must be an integer indicating the number of particle data sets.
Then, every following line specifies a particle.
Each line of particle consists of these parameters in order, seperated by spaces.
.br
- XYZ coordinates (3 double values)
.br
- Velocities (2 or 3 double values)
.br
- Mass (1 double value)
\fBCluster Format\fR:
.br
This format is used for specifying clusters (Example: see input/clusters.txt).
The file can contain comment lines starting with '#' and empty lines which are going to be ignored.
Each other line specifies a cluster with the first character indicating the cluster type followed by parameters separated by spaces.
These parameters depend on the cluster type.
.br
.br
.br
Cuboid Cluster:
.br
- 'C' for cuboid
.br
- Position in x, y, z directions (3 double values)
.br
- Width, height, depth of the cluster (3 double values)
.br
- Spacing between particles (1 double value)
.br
- Mass of the particles (1 double value)
.br
- Brownian mean velocity (1 double value)
.br
- Velocity in x, y, z directions (3 double values)
.br
- Dimensionality (1 integer value)
\fBASCII Art Format\fR:
.br
This format is used for specifying the Particles using ASCII arts (Example: see input/tum.txt).
It can contain multiple ASCII arts, where every particle in an ASCII art has the same properties.
Each ASCII art specification should be seperated by a single empty line.
.br
An Ascii art specification has the following format:
.br
- One line with three doubles specifying the origin of the art (top left corner)
.br
- One line specifying additional 6 double parameters (vx, vy, vz, mass, spacing, meanVel)
.br
- One line of characters seperated with spaces which represent partciles in the art
.br
- Arbritrary many lines of Ascii art, ending with EOF or empty line if there is another art.
\fBXML Format\fR:
.br
This format takes XML files as an input to parse every kind of model parameters.
To see the required format of the XML-files, have a look at the Doxygen documentation
or in src/io/xsd/simulation.xsd.
.SH BUGS
No known bugs.
.SH AUTHORS
Jimin Kim
.br
Noah Schlenker
.br
Christian Nix