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