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CaGe V0.3

Fullgen

Fullgen is a generation program which generates fullerenes. Fullerenes are spherically shaped molecules built of carbon atoms where every carbon atom has bonds to exactly three other carbon atoms so that each carbon ring consists of either five atoms (pentagon) or six atoms (hexagon). Unlike other fullerene generators, fullgen generates complete lists and it is currently the fastest fullerene generator. The generation of all fullerenes with 60 atoms takes less than one minute. The number of vertices (atoms) can be selected by two sliders named "Minimal number of vertices" and "Maximal number of vertices". If the "Min=Max"--checkbutton is not switched on, then these two sliders can have different values. The following description of the output options holds for all graph generation programs:
  • 3D representation:

    Exactly if this checkbutton is switched on, then three--dimensional embeddings will be generated (using spring). Where these embeddings are sent to depends on which of the radiobuttons named "RasMol", "GeomView" or "File" is switched on. If you switch on the checkbutton, "RasMol" will be taken per default. But you can as well choose the output direction by directly selecting a radiobutton. The checkbutton will then be switched on automatically. The only possibility to prevent 3D embeddings is to switch off the checkbutton.
  • RasMol: The 3D representation will be sent to RasMol (if provided on your computer).
  • GeomView: The 3D representation will be sent to GeomView: (if provided on your computer).
  • File: The 3D representation will be sent to a file. The file will contain data in writegraph3d code (see section Codes for description). The name of the file can be entered in the "Filename"--entry below. However, if the "automatic"--checkbutton is switched on, then the filename will be determined automatically. It is a good choice to let CaGe determine the filename, for two reasons: The first is that CaGe considers all options used while building the filename. So by having a look at the name of a file you know how its contents were generated. The second reason is that CaGe chooses the same filename that fullgen would if you generated the fullerenes without using CaGe (the only difference is that CaGe adds the suffix ".3d"). So the filenames are consistent. Now, because it is such a good idea to let CaGe determine the filename, CaGe automatically invokes the "automatic"--checkbutton if you switch on the "File"--radiobutton. If you want to choose the filename by yourself, then you should just enter the filename entry. In this case CaGe assumes that you want to store 3D embeddings in a file, so it switches on the "File"--radiobutton automatically. Furthermore, the "automatic"--checkbutton is switched off.
  • 2D representation:

    Exactly if this checkbutton is switched on, then two--dimensional embeddings will be generated (using schlegel). Where these embeddings are sent to depends on whether the "Display" or the "File"--radiobutton is switched on. The behaviour of the checkbutton and the radiobuttons is the same as for 3D representation. The same holds for the filename (here the suffix ".2d" instead of ".3d" is added). It is possible to generate 2D and 3D embeddings simultaneously. However, it is not possible to direct one of these representations into a file and the other one onto the display. So if these two directions collide, then CaGe will switch off one representation checkbutton. If the 2D embeddings are sent to a file, then this file will contain data in writegraph2d code.
  • Adjacency information:

    Exactly if this checkbutton it switched on, then pure adjacency information will be generated. Where this information is sent to depends on whether the "File" or the "Pipe"--checkbutton is switched on (both can be switched on simultaneously). If the information is sent to a file, then for the name of the file the same holds as for the 3D representation (no suffix will be added). If the information is sent to a pipe, then the "Program call"--entry must contain a program call, i.e. a program name and --- if needed --- some options. An example of a program call is "cat". This program takes the adjacency information as input and writes it to the standard output channel. There are two different codes in which the adjacency information can be represented: writegraph2d and planar_code. See section Codes for a description. Which code is chosen depends on which of the related radiobuttons is switched on. Default is writegraph2d since it is an ASCII code.


    • Widget interactions: You have seen that there are several widget interactions. There are various reasons for them:
  • Inferences: If you select a widget which provides a special option, then CaGe automatically sets all general options on which the special option depends. For example, if you enter the "Filename" entry for 3D representation, then CaGe assumes that you want to generate 3D embeddings and send them to a file. So it automatically switches on the "File"--radiobutton and the "3D representation"--checkbutton.
  • Group dependencies: This is the opposite to inferences. If a general option is not invoked, then all related special options must not be invoked. For example, if you switch off the "3D representation"--checkbutton, then no 3D embeddings will be generated. So all radiobuttons and the "automatic"--checkbutton are switched off (the "Filename"--entry could be cleared as well, but this is not done).
  • Conflicts: Most of the widgets are not independent of each other. Not all combinations of options are allowed. So if a combination is not allowed, then the related widgets are changed. An easy example is that you cannot choose a filename by yourself and by CaGe simultaneously. So if you invoke a "Filename"--entry, the related "automatic"--checkbutton must be switched off. Another example is described above (see item "2D representation"). Sometimes conflicts are prevented automatically by providing an appropriate widget type. For example, since it is not possible to direct 3D representations to RasMol and to GeomView and to a file simultaneously, radiobuttons instead of checkbuttons are provided to direct the 3D output.
  • Defaults: This is a special case of group dependencies where the special options to be chosen are not unique. In this case CaGe chooses default options. For example, if you switch on the "3D representation"--checkbutton, then by default the output will be directed to RasMol. Another example: If you switch on a "File"--radiobutton, then by default the related "automatic"--button will be switched on.
    • These interactions basically concern the output options. However, conflicts may also occur using extra options or basic options, so there the related technique is used as well.

    Extra options:

    The following options are options which are rarely used. Some of them are so specific that you must know about the details of the generation program fullgen. Such options are not explained in detail. Instead the related option which you would have to use for a direct call of fullgen is provided. It is enclosed in brackets "{" and "}". For a further description of such an option see the original manual of fullgen.
  • IPR: If you switch on the "IPR"--checkbutton, only fullerenes with isolated pentagons are generated. An isolated pentagon is a pentagon which is surrounded only by hexagons.
  • Dual output: If this checkbutton is switched on, then every generated fullerene is dualized before it is read by CaGe, i.e. every vertex becomes a face and every face becomes a vertex. The result of such a dualization is a triangulation.
  • Spiral statistics: {spistat}If you switch on this checkbutton, then a statistics about the number of spirals in the generated fullerenes will be written to the logfile. In this case the minimum and the maximum number of vertices must be the same.
  • Symmetry statistics: {symstat} If you switch on this checkbutton, then a statistics about the symmetries in the generated fullerenes will be written to the logfile. There are 28 different symmetry groups which can occur in a fullerene, named e.g. S i, Ci, Cih ...
  • Symmetry filter:
    If you click this button, another window appears where you can filter fullerenes which have a certain symmetry. There are 28 different symmetry groups. For every generated fullerene its symmetry group is determined. If the related checkbutton is switched on (i.e. the symmetry is valid), the fullerene will be sent to CaGe by fullgen, otherwise it will be dropped. By default, all symmetries are valid. If you change the default, the "Symmetry filter"--button will be highlighted. Note that the restriction to some symmetries will not speed up the generation process. Only a simple filter is invoked. Except the checkbuttons, there are three more buttons inside the "Symmetry filter for fullerenes"--window: By clicking "Clear all" you switch off all checkbuttons (after that, you should switch on at least one checkbutton), by clicking "Set all" you switch on all checkbuttons, by clicking "Done" you close the window. If you close the window, its contents remains valid. Closing the window is just good for decreasing the confusion arising by too many windows on the display.
  • Select cases:
    {case}The generation of fullerenes can be split into three disjoint parts (cases). By default, all cases are considered. If you restrict the generation to one case, the "Select cases"--button will be highlighted. By clicking "Done" you close the window. The selected case remains valid.