[MMTK] Update Re: NetCDF convention

Konrad Hinsen hinsen at cnrs-orleans.fr
Fri Sep 5 14:31:09 UTC 2008

On Sep 4, 2008, at 21:57, Jay Billings wrote:

> There's a bit of a problem with the output though. I tried opening  
> "rotation.nc" in nMoldyn and received an error that "This  
> trajectory does not include time information" and "This is most  
> probably not a trajectory file".

That trajectory does indeed have no time information. Since it is not  
the result of any dynamics, this is quite appropriate. nMOLDYN  
calculates dynamical correlation functions and thus requires time- 
dependent input data. However, it should better produce only the  
first error message, not the second one. It is perfectly fine to have  
trajectories without time stamps of course.

> universe.time = 0
> ....
> for i in range(20):
>      ....
>      universe.time = i

Try this:

for i in range(20):
	snapshot(data = {'time': 10.*i})

An example you can look at for inspiration is the DCD-to-netCDF  
converter that comes with nMOLDYN. It writes trajectories with time  

> On a happier note, I can report that MMTK-2.5.23 and nMoldyn-2.2.5  
> work on x86_64 Fedora 9 with numpy. I couldn't get ScientificPython  
> to work with Numeric and I had to copy the numpy include files to / 
> usr/include/numpy, but other than that, everything works fine and  
> all tests were successful. :)

Numeric is known to have problems on 64-bit machines, so your choice  
of NumPy is the right one. If ScientificPython did not find the NumPy  
header files, there is probably something wrong with the Python or  
NumPy installation in that machine. ScientificPython looks for the  
header files in the directory defined by

os.path.join(sys.prefix, "lib/python%s.%s/site-packages/numpy/core/ 
include" % sys.version_info [:2])

This is the recommended strategy for NumPy-dependend modules. It is  
possible that your NumPy is somewhere else if Fedora modified the  
directory setup for Python, as some Linux distributions unfortunately  
do. In that case, there isn't much that I can do about it.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
Web: http://dirac.cnrs-orleans.fr/~hinsen/

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