[gpaw-users] a write problem

[Marcin Dulak]

Hi,

i would suggest to uninstall the ubuntu package:
sudo apt-get remove gpaw
Then clean all the traces of gpaw and install the ubuntu package again.
As a general rule: never install packages manually (from tarballs) using 
root account,
and when installing on a users account use meaningful directory name 
prefixes (for example
gpaw could be installed under ${HOME}/ gpaw-0.7.2.6974 
<https://wiki.fysik.dtu.dk/gpaw-files/gpaw-0.7.2.6974.tar.gz>-1, then a 
link made: ln -s ${HOME}/ gpaw-0.7.2.6974 
<https://wiki.fysik.dtu.dk/gpaw-files/gpaw-0.7.2.6974.tar.gz>-1 ~/gpaw)

Best regards,

Marcin

Yuelin Li wrote:
> Thanks.
> I finally got around to take a closer look. As I have tried to install 
> gpaw several time, it is confusing for me that I do not know what is 
> the exactly the installation that is working. What not helping is that 
> when I do search, I have many gpaw directories,  which is the one to 
> do the developer's installation?
>
> I believe the installation that is working for me is the ubunto 
> package, which one is it? Or should I delete all these and reinstall 
> the package to figure out?
>
> ----------------------------------------------------------------
> ylli at ubuntu:~$ sudo find / -name gpaw
> /home/ylli/gpaw
> /home/ylli/gpaw/build/lib.linux-i686-2.6/gpaw
> /usr/share/pyshared/gpaw
> /usr/share/pyshared-data/gpaw
> /usr/share/doc/gpaw
> /usr/bin/gpaw
> /usr/local/bin/gpaw
> /usr/local/lib/python2.6/dist-packages/gpaw
> /usr/lib/python2.6/dist-packages/gpaw
>
>
>
>
> On 12/15/2010 9:01, Christian Glinsvad wrote:
>>
>> You'll need to perform a developer installation of the latest version:
>> https://wiki.fysik.dtu.dk/gpaw/devel/developer_installation.html#developer-installation 
>>
>>
>> Regards
>> Christian Glinsvad
>>
>> Yuelin Li wrote:
>>> Chris,
>>>
>>> thanks for the help. I do need help. I am using the ubunto 
>>> installation, how do i fix that?
>>>
>>> After I generate the ftd file, I will know if I need help to extract 
>>> the fourier transform data.
>>>
>>> Best,
>>>
>>> Yuelin
>>>
>>>
>>> On 12/15/2010 5:34 AM, Christian Glinsvad wrote:
>>>> Hi Yuelin
>>>>
>>>> I've fixed this in the latest GPAW (r7445). Thanks for letting us 
>>>> know.
>>>>
>>>> On a side note, let me know if you need help extracting the fourier
>>>> transforms from the file 'bda_fourier.ftd' e.g. for plotting.
>>>>
>>>> Regards
>>>> Christian Glinsvad
>>>>
>>>> Yuelin Li wrote:
>>>>> I have this problem:
>>>>>
>>>>> _______________________________________
>>>>> Traceback (most recent call last):
>>>>> File "testTDDFT.py", line 26, in <module>
>>>>> obs.write('bda_fourier.ftd')
>>>>> File "/soft/gpaw/gpaw-0.7.2/gpaw/tddft/fourier.py", line 224, in 
>>>>> write
>>>>> tar = Writer(filename)
>>>>> TypeError: __init__() takes exactly 3 arguments (2 given)
>>>>> _________________________________________
>>>>>
>>>>>
>>>>> when runing this script
>>>>>
>>>>> _____________________________________________
>>>>>
>>>>> from gpaw.tddft import TDDFT
>>>>> from gpaw.tddft.fourier import DensityFourierTransform
>>>>>
>>>>> time_step = 4.0 # 1 attoseconds = 0.041341 autime
>>>>> iterations = 5000 # 5000 x 4 as => 20 fs
>>>>> kick_strength = [0.0,5e-3,0.0] # Kick to y-direction
>>>>> frequencies = [4.26,6.27,13.0, \
>>>>> 16.9,18.1,19.9] # Pre-determined peak frequencies in eV
>>>>> sigma = 0.05 # Width of Gaussian envelope in eV
>>>>>
>>>>> td_calc = TDDFT('bda_gs.gpw')
>>>>>
>>>>> td_calc.absorption_kick(kick_strength=kick_strength)
>>>>>
>>>>> obs = DensityFourierTransform(timestep, frequencies, sigma)
>>>>> obs.initialize(td_calc)
>>>>>
>>>>> td_calc.propagate(time_step, iterations, 'bda_dm.dat', 'bda_td.gpw')
>>>>>
>>>>> obs.write('bda_fourier.ftd')
>>>>>
>>>>> _______________________________________________
>>>>> gpaw-users mailing list
>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>
>>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

-- 
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Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

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