Re: [XMakemol-discuss] Manual adjustment of bounding box

[Matt Hodges]

>>>>> Wolfram Quester writes:

 > I finished my work on the bounding box. Well, there is still quite
 > a lot to clean up. It is a mixture between your suggestions and my
 > wishes. For every frame a bbox_xyz can be given in the .xyz-file.
 > This is usefull if the density of the system changes over time. I f
 > for one frame no bbox_xyz is given, the bbox of the previous frame
 > is used. I had to move the definition of the bounding_box to
 > globals.h and use typedef. I had no success to get it to compile
 > otherways.

Thanks, Wolfram. I've applied your changes without any problems. I'm
not sure I like the idea of using the previous frame data if none is
specified; I would prefer falling back to calculating the bounding
box automatically.

 > In the attached File a short simulation run is shown. To get the
 > wished result switch to track->center. The simulation shows a
 > system of 108 particles interacting via a Lennard-Jones-potential.
 > It starts in a crystalline phase and then the temperature increases
 > an the system melts. This is just an example. It is not scientific
 > at all. The system is to small, simulation time to short...

I haven't looked at the code yet, but I've tried to understand the
new features as a user. Several points:

(1) In the Edit->Bounding Box dialog, I found "by hand" to be
    confusing. To me this suggests that it only refers to editing the
    widgets in the dialog, but this also means use the values from the
    input file?

(2) If values are specified in the input file, I think they should be
    used by default.

(3) I couldn't understand why the bounding box moves around slightly
    after changing the orientation, even though the bbox_xyz
    coordinates in the XYZ file are all the same.

I'll have a look at the code soon.

Best regards,

Matt