Django does come with a convenient database abstraction layer (DBAL) but unfortunately this DBAL is not very talkative. In case you get an error messages along the lines of ValueError: "<FooClass>" needs to have a value for field "fooclass" before this many-to-many relationship can be used.
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On Ubuntu, you may upgrade your system to the next (development) release by issuing update-manager -d either on a root shell or using sudo. However, using the graphical interface gives you no diagnostic output in case anything fails. For example, you get which is not helpful at all, as upgrading […]
Sometimes jobs need some local disk space for temporary data that should neither be part of the backup nor too slow to write huge amounts of data to. A common way to help users out is to define some scratch directory. Using PBS/torque, you can request access to this local […]
In case you get an error message similar to the following one directly after initialization, it’s pretty sure an issue with your checkfile. Most probably it does not exist – and this is Gaussian’s way of telling you so. In any case, you can use the strace command to see […]
Using different programs for diagrams within one single document can be a never ending story of unmatching graphics. For example, matplotlib used a different interpolation method for colormaps than pgfplots. Disregarding alpha components, the following script produces a matching colormap. Just specify the matplotlib colormap name as command line argument […]
Sometimes chemical structures are not enough to present your data. Instead of adding tables, you can graphically annotate compounds. For example the results of a charge fitting procedure (hence the decimal values for electron charges) can be visualized as follows Here is how to do it: Download the indigo toolkit […]
As usual, a new day in the lab requires new function plots. But now that you have a different data source, you may observe some potential pitfalls with pgfplots.
Update Christopher Mayne wrote: ‘I’ve since not only corrected the portion of the code that throws the error, but added some lines to automatically detect linear elements and make the necessary changes to the Gaussian input file (i.e. “A” -> “L” and removing undefined dihedrals). These fixes are in our […]
Today MATE decided to take NumLock serious. It’s settings manager was unsure what state of NumLock was desired and thus changing it over and over. In that case, typing on a notebook can be rather tedious as you happen to press the keys in order to get a specific character […]
The post_save hook from django.db.models.signals is executed right after the parent object has been stored in the database. As there is no hook for creation of updates of dependent objects, you have several alternatives: Attach to the post_save hook of your dependent model. This may work for all cases, where […]
If you do NPT simulations with namd2, you may get the following message: FATAL ERROR: Periodic cell has become too small for original patch grid! Unfortunately, namd2 does not support automatic restarts in this case. Here is a small wrapper script, that automates this process. Just prepare your namd.conf as […]
Gaussian sometimes gives error messages, that merely transport the information that something went terribly wrong. Of course, there is practically no hint on what Gaussian was trying to do at this point. On this page, I list the complete error messages and the corresponding solutions that worked for me in […]