Re: XYZ file support. -- June 09, 2011 - 13:38

Hi,

This will require a bit of debugging.  Would you be able to attach the
XYZ file to the task (https://gna.org/task/?7404), say where I should
add it to relax, and include the output of:

$ svn diff > patch

This patch will allow me to see your changes, and I should be able to
help debug.

Cheers,

Edward


On 9 June 2011 13:24, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:
> Hi Eddy,
>
> I am following your instruction below. I failed in the point with $ relax -s
> Structure.test_[han]. I generated a function called
> test_read_xyz_internal1() and I have just modified the file name and the
> directory path. But then if I run the command $ relax -s
> Structure.test_test_read_xyz_internal1, it shows the error message 'the
> script file does not exist'.
>
> Han
>
> On Jun 6, 2011, at 10:21 AM, Edward d'Auvergne wrote:
>
> > Hi Han,
> >
> > I have now created a task for adding the XYZ structure file reading
> > support to relax (https://gna.org/task/index.php?7404).  To start to
> > implement this, I would suggest the following small steps:
> >
> > - First you already have a Gna! account (https://gna.org/users/han87),
> > so creating this can be skipped.
> >
> > - Check out a fresh copy of the xyz branch of relax "svn co
> > http://svn.gna.org/svn/relax/branches/xyz";, or update an already
> > checked out copy "svn up".
> >
> > - Find an XYZ file of a small organic molecule and attach it to the
> > task.  This is for the system test, to check that the data is
> > correctly read.  It should be relatively small so that the system test
> > is quick, but complex enough to be a good test.  Also tell me which
> > directory it should be located in, and if I need to create directories
> > in 'test_suite/shared_data' for it.
> >
> > - Create the system test by duplicating the code of
> > 'test_read_pdb_internal1()' in the file
> > 'test_suite/system_tests/structure.py'.  Remember to keep the methods
> > alphabetically ordered.  Modify the code for the organic molecule.
> >
> > - Then run the test with:
> > $ relax -s Structure.test_[han]
> > replacing [han] with the name of the test.
> >
> > - Once the test is running (but it should be failing), then type:
> > $ svn diff > diff
> > and attach the diff file to the task.
> >
> > This would be a good start, and is how one should code.  Once the
> > system test passes, we will know that the XYZ reading is complete.  If
> > you have any questions, please don't hesitate to ask.
> >
> > Cheers,
> >
> > Edward