source: utils/HOWTO-boxmaker@ b136f6

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Last change on this file since b136f6 was b82ede, checked in by Frederik Heber <heber@…>, 13 years ago

Very basic documentation on how to use boxmaker
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[b82ede]1Boxmaker creates boxes of specific density filled with molecules
2
3==========================================================
4
5Usage:
6 boxmaker.py <basename> [option1 value1...]
7
8 boxmaker.py <basename> [+boolean_option -other_boolean_option]
9 same as
10 boxmaker.py <basename> [boolean_option on other_boolean_option off]
11
12==========================================================
13
14If existing boxmaker reads boxmaker.<basename> as configuration file. The
15syntax used is:
16
17# comment line
18option1 = value1
19option2 = value2
20...
21
22Note that shortcuts rather than actual option names can be used at all times,
23however this is not recommended in the configuration file for clarities sake.
24
25Options with units will be converted to the system specified by the
26<basename>.tremolo file if autodim=on. If the value is preceeded by ! the unit
27convertion can be switched off for this specific value.
28
29o List of name-value options:
30
31tremofiledir
32 (Optional if autodim=off)
33 Shortcut: tf
34 Default: ./
35
36 <basename>.tremolo is needed to dertermine the targed system of units. tf
37 specifies where to find the file.
38
39potentialsfiledir
40 Shortcut: pf
41 Default: ./
42
43 <basename>.potentials is needed internally for MoleCuilders element
44 mapping. Also, if automass=on, it's needed to automatically determine the
45 input molecules molar mass.
46 pf specifies where to find the file.
47
48outfilename
49 Shortcut: o
50 Default: out
51
52 The name stem of the output files. By default its out.xyz and out.data
53
54source
55 Shortcut: i
56 Default: None
57
58 The full path to the molecule file used to fill the box. Supports any format
59 MoleCuilder does.
60
61molarmass
62 (Optional if automass=on)
63 Shortcut: m
64 Default: None
65
66 Specify the molar mass of the input molecule. Value with unit.
67
68 E.g.: molarmass = 23.45e-3 kg/mol
69 E.g.: molarmass = !66.3333
70
71density
72 Shortcut: rho
73 Default: None
74
75 Specify the desired density of the box. Value with unit.
76
77temp
78 (Optional)
79 Shortcut: t
80 Default: None
81
82 If specified and postprocessing is on, the resulting data-file is given an
83 additional
84
85 # INPUTCONV temp <converted value>
86
87 header-line. Value with unit.
88
89number
90 Shortcut: n
91 Default: 1000
92
93 How many molecules is the box supposed to contain? Might be internally
94 changed if cubicdomain=on.
95
96 If number is a vector the box is filled by x*y*z molecules, ignoring
97 the option cubicdomain.
98
99 E.g.: number = 4 3 9
100
101o List of boolean options:
102
103cubicdomain
104 Shortcut: cd
105 Default: on
106
107 If on the box is filled with n*n*n molecules where n is the nearest power
108 of 3 to fit number. Ignored if number is a vector.
109
110cubiccell
111 Shortcut: cc
112 Default: off
113
114 Normally the cuboid of an elementary cell is the input molecules bounding
115 box, scaled to fit the desired molecular volume. If on the elementary cells
116 strictly cubic. Its the only way to archive a cubic simulation area (given
117 cubicdomain is on), but its very likely that molecules will overlap unless
118 its near cubic.
119
120autorotate
121 Shortcut: ar
122 Default: off
123
124 Uses MoleCuilder to rotate the input molecule in a way such that the
125 bouding box' volume is minimized, leading to a higher possible density
126 without overlap.
127
128autodim
129 Shortcut: ad
130 Default: on
131
132 If on units will be converted to the system specified in the tremolo-file.
133
134postprocess
135 Shortcut: pp
136 Default: on
137
138 Adds "# INPUTCONV shift center" to the resulting data file. If a
139 temperature is given its added as well.
140
141automass
142 Shortcut: am
143 Default: on
144
145 If specified boxmaker tries to determine the molar mass using the
146 <basename>.potentials file.
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