Boxmaker creates boxes of specific density filled with molecules

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Usage:
    boxmaker.py <basename> [option1 value1...]
    
    boxmaker.py <basename> [+boolean_option -other_boolean_option]
    same as
    boxmaker.py <basename> [boolean_option on other_boolean_option off]
    
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If existing boxmaker reads boxmaker.<basename> as configuration file. The
syntax used is:

# comment line
option1 = value1
option2 = value2
...

Note that shortcuts rather than actual option names can be used at all times,
however this is not recommended in the configuration file for clarities sake.

Options with units will be converted to the system specified by the
<basename>.tremolo file if autodim=on. If the value is preceeded by ! the unit
convertion can be switched off for this specific value.
 
o List of name-value options:

tremofiledir
    (Optional if autodim=off)
    Shortcut: tf
    Default: ./
    
    <basename>.tremolo is needed to dertermine the targed system of units. tf
    specifies where to find the file.
    
potentialsfiledir
    Shortcut: pf
    Default: ./
    
    <basename>.potentials is needed internally for MoleCuilders element
    mapping. Also, if automass=on, it's needed to automatically determine the
    input molecules molar mass.
    pf specifies where to find the file.
    
outfilename
    Shortcut: o
    Default: out
    
    The name stem of the output files. By default its out.xyz and out.data

source
    Shortcut: i
    Default: None
    
    The full path to the molecule file used to fill the box. Supports any format
    MoleCuilder does.
    
molarmass
    (Optional if automass=on)
    Shortcut: m
    Default: None
    
    Specify the molar mass of the input molecule. Value with unit.
    
    E.g.: molarmass = 23.45e-3 kg/mol
    E.g.: molarmass = !66.3333
    
density
    Shortcut: rho
    Default: None
    
    Specify the desired density of the box. Value with unit.
    
temp
    (Optional)
    Shortcut: t
    Default: None
    
    If specified and postprocessing is on, the resulting data-file is given an
    additional
    
    # INPUTCONV temp <converted value>
    
    header-line. Value with unit.

number
    Shortcut: n
    Default: 1000

    How many molecules is the box supposed to contain? Might be internally
    changed if cubicdomain=on.
    
    If number is a vector the box is filled by x*y*z molecules, ignoring
    the option cubicdomain.
    
    E.g.: number = 4 3 9
    
o List of boolean options:

cubicdomain
    Shortcut: cd
    Default: on
    
    If on the box is filled with n*n*n molecules where n is the nearest power
    of 3 to fit number. Ignored if number is a vector. 
    
cubiccell
    Shortcut: cc
    Default: off
    
    Normally the cuboid of an elementary cell is the input molecules bounding
    box, scaled to fit the desired molecular volume. If on the elementary cells
    strictly cubic. Its the only way to archive a cubic simulation area (given
    cubicdomain is on), but its very likely that molecules will overlap unless
    its near cubic.
    
autorotate
    Shortcut: ar
    Default: off
    
    Uses MoleCuilder to rotate the input molecule in a way such that the
    bouding box' volume is minimized, leading to a higher possible density
    without overlap.
    
autodim
    Shortcut: ad
    Default: on
    
    If on units will be converted to the system specified in the tremolo-file.
    
postprocess
    Shortcut: pp
    Default: on
    
    Adds "# INPUTCONV shift center" to the resulting data file. If a
    temperature is given its added as well.
    
automass
    Shortcut: am
    Default: on
    
    If specified boxmaker tries to determine the molar mass using the
    <basename>.potentials file.