Data files

  VIEWMOL uses a data file named viewmolrc for getting informations about atoms and a number of user preferred settings. There may be three of these files. VIEWMOL looks at first in the current directory for this file, then in the users HOME directory for a file .viewmolrc and finally in the directory where the environment variable VIEWMOLPATH points to. In one of these three locations such a file must be found. The file should contain the following data:

• Lines of the format:
  <symbol> <rad> <rd> <gd> <bd> <rl> <gl> <bl> <surface>
  <symbol> is an atomic symbol, <rad> is the Van der Waals radius of this atom in Ångstrøms, <rd>, <gd> and <bd> are the red, green and blue colour for the darkest part of this atom and <rl>, <gl> and <bl> are the red, green and blue colour for the lightest part of the atom. There are four reserved strings for <symbol>. If <symbol> is bd the following description describes a bond (stick). Currently only the <rad> field is interpreted as the radius of the sticks. All other fields are ignored and the stick is drawn with the surface description of the atom it belongs to. uc specifies a unit cell corner. Radius and colour given here affect the appearance of the unit cell. ps and ms specify the surface properties for the postive and negative isosurface, respectively, used to draw wave function related topics. In these cases the radius is not used. <surface> is an optional specification for the surface used when stick, ball, or cup drawing with surfaces is activated. <surface> is a list of one or more of the following options
  • emission <r> <g> <b>
    The emission colour of the surface. Using this option causes the surface to emit light. <r>, <g>, and <b> are the red, green and blue components for the light colour.
  • ambient <r> <g> <b>
    The ambient light which is reflected by the surface. <r>, <g>, and <b> are the red, green and blue components for the light colour.
  • specular <r> <g> <b>
    The specular light which is reflected by the surface. <r>, <g>, and <b> are the red, green and blue components for the light colour.
  • shininess <n>
    A parameter whichs determines the kind of reflection. <n> can be in the range 0 ... 128.
  • alpha <n>
    This parameter determines the transparency of the surface.
  All colour specifications can be between 0.0 and 1.0. The total length of a line specifying an atom is restricted to 132 characters. The keywords for the surface specifications can be abbreviated with the first two letters.
• plotwidth=<x>
  This line can be used to change the width of the spectrum plotted in LaTeX. <x> is the new width in 0.1 mm. The height of the plot is half the width. Normally the plot has a width of 160 mm (<x>=1600).
• wavenumber=<from>:<to>
  This restricts the range of wave numbers plotted in the spectrum to <from> cm to <to> cm.
• MO-energy=<from>:<to>
  This restricts the range of energies plotted in the MO energy level/density of states diagram to <from> Hartrees to <to> Hartrees.
• rayshade=<file_name>
  <file_name> is the full path to the RAYSHADE programme in your installation. Any options may also be included at the end of the file name. VIEWMOL checks the existence of the executable file before it enables the Start raytracing menu button. Therefore <file_name> must include the full path name. Environment variables in the path name will be interpreted.
• display_rle=<file_name>
  <file_name> is the full path to the display programme for RLE files in your installation. If this is specified the resulting RLE file is displayed by means of this display programme after the RAYSHADE programme has finished. Any option may also be included at the end of the file name. VIEWMOL checks the existence of the executable file before calling it. Therefore <file_name> must include the full path name. Environment variables in the path name will be interpreted.
• moloch=<file_name>
   <file_name> is the full path to the moloch programme from the TURBOMOLE package in your installation. If this file name is not specified drawing of molecular orbitals and of electron densities from TURBOMOLE outputs is only possible if the molecule possesses C symmetry. Environment variables in the path name will be interpreted.
• www=<command>
  <command> is the command (including all options) to start a World Wide Web browser in your installation. If this command is not specified you will not be able to read the online manual. <command> must contain '%s' at the place where the file name goes and must contain the full path name to your browser (e. g. if your browser can be started by typing '/usr/local/bin/xmosaic viewmol.html' then 'www=/usr/local/bin/xmosaic %s' is the required line in the
  viewmolrc file). Environment variables in the path name will be interpreted.
• paper_size=<x>,<y>
  This is the paper size for the plotter which is accessible by the plotter pens. <x> and <y> are in millimetres. These values are used for setting the SC (scale) command in the plotter files correctly. The default values are suitable for an HP LaserJet III. Most plotter documentations contain these values.
• geometry=<width>x<height>+<xoff>+<yoff>
  This option specifies the size and the position of the main window. The syntax is the same as for X windows applications. <width> and <height> are the width and the height of the window. Only square windows are possible. Specifying two different values will result in a warning and a window which has the same height than width. <xoff> and <yoff> are the x and y offset, respectively, of the windows lower left corner with respect to the lower left corner of the screen.
• background <where> <colour>
• background <where> =<n>
  This option can be used to specify own background colours. <where> is one of the strings: main, spectrum, optimization, or mo for the main window (where the molecule is drawn), the spectrum window, the optimization history window, or the MO energy diagram window. <colour> is one of the strings: white, black, red, skyblue, green, yellow, magenta, cyan, or blue. Using this kind of option is equivalent to selecting a new background using the colour editor when the window was opened. =<n> can be used to define an arbitrary colour. <n> is an integer defining the colour in the lowest 24 bits. The bits 0 ... 7 contain the red component of the colour, the bits 8 ... 15 the green component and the bits 16 ... 23 the blue component. If <n> is preceded by 0x it is interpreted as a hexadecimal value else as decimal one.
• foreground <where> <colour>
• foreground <where> =<n>
  This option can be used to specify own foreground colours. <where> is one of the strings: spectrum, energy, grad, or mo for the spectrum, the energy curve, the gradient norm curve or the MO energy levels. <colour> and =<n> have the same meaning as in the background option above.
• <model> <type> <resolution>
  This option selects <model> drawing as the default. <model> may be one of the strings: sticks, balls, or cups. <type> may set to one of the strings: dots, lines, or surface. if <type> is not specified surface is the default. <resolution> is an optional integer in the range 1 ... 30 which specifies the resolution of the spheres. A large value causes a smooth surface, but also increased drawing time. The default is 10. If this option is not set wire model is the default.
• isosurface=<from>:<to>,<actual>
  This option can be used to set the slider range for the isosurface to <from> to <to>. <actual> is optional. If it is not specified it is set to a reasonable default.
• resolution for density of states=<from>:<to>,<actual>
   This option is the equivalence to the isosurface option for the resolution for density of states.
• bond length [<unit>] = <format>
  This option can be used to set the unit and format of the bond lengths displayed by clicking on atoms. <unit> is optional and may be one of the strings pm, bohr, or au. The default is to use Ångstrøms. <format> can be any valid Fortran format string which must contain the specification for printing a floating point number.
• bond angle=<format>
  This option can be used to set the format of the bond angles displayed by clicking on atoms. <format> can be any valid Fortran format string which must contain the specification for printing a floating point number.
• torsion=<format>
  This option can be used to set the format of the torsion angles displayed by clicking on atoms. <format> can be any valid Fortran format string which must contain the specification for printing a floating point number.
• arrow=<n>
  This option specifies the resolution of the arrowhead. <n> may be any integer.
• buffermode=<mode>
  This option specifies the configuration of the graphics buffer. <mode> can be set either to colour map or to RGB. In the first case the graphics buffer is configured in double buffered colour map mode, which does not provide the possibility to do lighting calculations. Therefore the Surface option in the drawing modes menu is not available in this mode. RGB configures the graphics buffer in single buffered RGB mode, which provides the possibility to do lighting calculation, but moving the molecule will cause flickering of the picture. The default graphics buffer mode is double buffered RGB mode and this mode is always used if the hardware permits it. The buffermode option is only thought for running VIEWMOL on 8-bit graphics adapters, which do not support the double buffered RGB mode (IBM).
• no z-buffer
  This option switches off the use of the z-buffer. If a z-buffer is available it should be used, since otherwise the drawings may look very strange. This option is only thought for running VIEWMOL on graphics adapters, which do not have a z-buffer. If the option is set in these cases, VIEWMOL will not complain about the non-existing z-buffer.
• interpolation=<method>
   This option sets the default interpolation method for wave function related topics. <method> may be one of the strings: none, linear, or logarithmic. Default is linear.
• grid=<from>:<to>,<actual>
   This option can be used to set minimum, maximum, and default values for the grid granularity slider in the wave function dialogue box. <actual> is optional.

Any line starting with '#' is treated as a comment. VIEWMOL also accepts standard X Windows resources in .Xdefaults for changing colours and/or fonts in the dialogue boxes, e. g.:

Viewmol*fontList:   -*-ergonomic-*-*-*-*-20-*-*-*-*-*-*-*
Viewmol*background: salmon