[ase-users] Import Jacapo Calculator

[Marcin Dulak]

Hi,

On 09/16/12 18:37, Hesam wrote:
> Thanks Marcin for the help.
>
> I installed the python scientific on Ubuntu and now I can import the 
> jacapo successfully but I can't use the jacapo calculator and get an 
> error. i.e. when I want to run
>
> *for x in np.linspace (0.95 , 1.05 , 5):
>   silicon.set_cell (cell * x, scale_atoms =True)
>   calc = Jacapo (pw =250 ,xc='PBE', nbands =30 , ft =0.1 , kpts =(4 ,4 
> ,4))*
>
> I get the following error:
>
> *hesam at hesam-VirtualBox:~$ python Test_Jacapo.py
> Traceback (most recent call last):
>   File "Test_Jacapo.py", line 15, in <module>
>     silicon.get_potential_energy ()
>   File "/usr/lib/python2.7/dist-packages/ase/atoms.py", line 548, in 
> get_potential_energy
>     return self._calc.get_potential_energy(self)
>   File 
> "/usr/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py", 
> line 2307, in get_potential_energy
>     self.calculate()
>   File 
> "/usr/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py", 
> line 2818, in calculate
>     f = open(txt, 'r')
> IOError: [Errno 2] No such file or directory: 'out.txt'
> *
on Ubuntu you need to set additional variables DACAPOPATH, 
DACAPOEXE_SERIAL and DACAPOEXE_PARALLEL
https://wiki.fysik.dtu.dk/dacapo/Installation#installation-of-prebuilt-binaries
and in order to run dacapo in parallel you need to create a hostfile file.
The following should run dacapo on two cores on ubuntu 12.04 (after 
configuring dtufys repository):
sudo apt-get install dacapo
export DACAPOEXE_SERIAL=/usr/bin/dacapo_serial.run
export DACAPOEXE_PARALLEL=/usr/bin/dacapo_mpi.run
export DACAPOPATH=/usr/share/dacapo-psp
echo $'localhost\nlocalhost' > hostfile
PBS_NODEFILE=hostfile python 
/usr/lib/python2.7/dist-packages/ase/test/jacapo/jacapo.py

Please consider using GPAW instead (sudo apt-get install gpaw).
Dacapo is no longer maintained.

Marcin

> *
> Thanks
> Hesam
> *
> On Sun, Sep 16, 2012 at 11:37 AM, Marcin Dulak 
> <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>
>     Hi,
>
>
>     On 09/16/12 17:22, Hesam wrote:
>>     Many Thanks Marcin,
>>
>>     I have installed scientific python on windows. However when I try
>>     to import ase.calculators.jacapo I get the following error:
>>
>>     >>> import ase.calculators.jacapo
>>     Traceback (most recent call last):
>>       File "<stdin>", line 1, in <module>
>>       File
>>     "C:\Python27\lib\site-packages\ase\calculators\jacapo\__init__.py",
>>     line 16, in <module>
>>         from jacapo import *
>>       File
>>     "C:\Python27\lib\site-packages\ase\calculators\jacapo\jacapo.py",
>>     line 20, in <module>
>>         from Scientific.IO.NetCDF import NetCDFFile as netCDF
>>       File "C:\Python27\lib\site-packages\Scientific\IO\NetCDF.py",
>>     line 169, in <module>
>>         from Scientific_netcdf import *
>>     ImportError: DLL load failed: %1 is not a valid Win32 application.
>     i doubt you will be able to compile dacapo on windows, so the
>     effort of making
>     ScientificPython to work on windows is probably not worth it.
>     Moreover, even the ASE itself is not fully functional on windows.
>
>     Marcin
>
>
>>
>>     Is there any package with all libraries in it? Since I installed
>>     pythonxy and I thought it contains all the libraries.
>>
>>     Thanks
>>     Hesam
>>
>>     On Sun, Sep 16, 2012 at 5:33 AM, Marcin Dulak
>>     <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>>
>>         On 09/16/12 03:58, Hesam wrote:
>>>         Hi,
>>>
>>         yes, you need ScientificPython version at least 2.8 with
>>         netcdf support.
>>         On ubuntu:
>>         sudo apt-get install python-scientific
>>
>>         Marcin
>>
>>>         When I want to import from jacapo calculator I got the error
>>>         that it couldn't find Scientific module.
>>>         Where is that module? Do I need to install some other package?
>>>
>>>         >>> from ase.calculators.jacapo import *
>>>
>>>         Traceback (most recent call last):
>>>           File "<pyshell#8>", line 1, in <module>
>>>             from ase.calculators.jacapo import *
>>>           File
>>>         "C:\Python27\lib\site-packages\ase\calculators\jacapo\__init__.py",
>>>         line 1, in <module>
>>>             import Scientific
>>>         ImportError: No module named Scientific
>>>
>>>         I can successfully import ase itself but when I try to
>>>         import from jacapo I get the error.
>>>         Thanks
>>
>>
>>         -- 
>>         ***********************************
>>           
>>         Marcin Dulak
>>         Technical University of Denmark
>>         Department of Physics
>>         Building 307, Room 229
>>         DK-2800 Kongens Lyngby
>>         Denmark
>>         Tel.:(+45) 4525 3157  <tel:%28%2B45%29%204525%203157>
>>         Fax.:(+45) 4593 2399  <tel:%28%2B45%29%204593%202399>
>>         email:Marcin.Dulak at fysik.dtu.dk  <mailto:Marcin.Dulak at fysik.dtu.dk>
>>
>>         ***********************************
>>
>>
>
>
>     -- 
>     ***********************************
>       
>     Marcin Dulak
>     Technical University of Denmark
>     Department of Physics
>     Building 307, Room 229
>     DK-2800 Kongens Lyngby
>     Denmark
>     Tel.:(+45) 4525 3157  <tel:%28%2B45%29%204525%203157>
>     Fax.:(+45) 4593 2399  <tel:%28%2B45%29%204593%202399>
>     email:Marcin.Dulak at fysik.dtu.dk  <mailto:Marcin.Dulak at fysik.dtu.dk>
>
>     ***********************************
>
>


-- 
***********************************
  
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

***********************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20120916/d8052897/attachment.html>