[gpaw-users] calc.get_pseudo_wave_function error in tutorial "Creating wave function cube files"

Pu ZHANG puzhang0702 at gmail.com
Fri Aug 1 15:32:58 CEST 2014 

I see. The cubeWF.py reads the file CO.gpw, which is generated by:

from ase import Atoms
from gpaw import GPAW
d = 1.1 # bondlength of hydrogen molecule
a = 5.0 # sidelength of unit cell
c = a / 2
atoms = Atoms('CO', positions=[(c - d / 2, c, c), (c + d / 2, c, c)],
cell=(a, a, a))
calc = GPAW(nbands=5, h=0.2, txt=None)
atoms.set_calculator(calc)
# Start a calculation:
energy = atoms.get_potential_energy()
# Save wave functions:
calc.write('CO.gpw', mode='all')

Best regards, Pu Zhang
--
Postdoc
The group of Structured Electromagnetic Materials
Department of Photonics Engineering
Technical University of Denmark
Ørsteds Plads, Building 345v, 166
2800, Kgs. Lyngby
E-mail: puzha at fotonik.dtu.dk
Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
Phone: 45 25 36 43
Fax: 45 93 65 81


On Fri, Aug 1, 2014 at 3:26 PM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk>
wrote:

>
> On 08/01/2014 03:10 PM, Pu ZHANG wrote:
>
> I'm sorry I'm not sure which script you are referring to. Do you mean the
> script used for compilation?
>
>
> No, the cubeWF.py script will read a gpw-file and write cube files (I'm
> guessing).  To debug this, I would need your gpw-file or a script that can
> calculate it.
>
> Jens Jørgen
>
>
>  Then I'm using the gpaw compiled previously by our cluster
> administrator. I don't know the details.
>
>  Thanks!
>
>   Best regards, Pu Zhang
>  --
> Postdoc
> The group of Structured Electromagnetic Materials
>  Department of Photonics Engineering
> Technical University of Denmark
> Ørsteds Plads, Building 345v, 166
>  2800, Kgs. Lyngby
> E-mail: puzha at fotonik.dtu.dk
> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
> Phone: 45 25 36 43
> Fax: 45 93 65 81
>
>
> On Fri, Aug 1, 2014 at 3:03 PM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk>
> wrote:
>
>>
>> On 08/01/2014 02:56 PM, Pu ZHANG wrote:
>>
>> Hi, Jens!
>>
>>  Thanks a lot for the reply!
>>
>>  Yes, I was running in parallel. And it does work if I use only one
>> processor. The script is as follows:
>>
>>
>>  To fix this when it runs in parallel, we would need to see the script
>> that generated the gpw-file.
>>
>> Jens Jørgen
>>
>>
>>
>>  job script
>> -------------
>>  #!/bin/bash
>> #PBS -N cubeWF
>>  #PBS -e $PBS_JOBNAME.$PBS_JOBID.err
>> #PBS -o $PBS_JOBNAME.$PBS_JOBID.log
>> #PBS -q fotonano
>>  #PBS -A fotonano
>> #PBS -l nodes=1:ppn=2
>> #PBS -l walltime=02:00:00
>>
>>  source $PBS_O_HOME/.bashrc
>> module purge
>> module load npa-cluster-setup
>>
>>  ulimit -s unlimited
>> cd $PBS_O_WORKDIR
>>
>>  module load python2.7.numpy.scipy.scientific.ase.gpaw.inelastica
>> module load gpaw-setups/0.9.9672
>> xc=`which xc-info`
>>  xc_h=$(dirname $(dirname $xc))
>> export LD_LIBRARY_PATH=$xc_h/lib:$LD_LIBRARY_PATH
>>
>>  m=`which mpirun`
>> m_h=$(dirname $(dirname $m))
>> export LD_LIBRARY_PATH=$m_h/lib:$LD_LIBRARY_PATH
>>
>>  export GPAW_FFTWSO="libmkl_intel_lp64.so"
>>
>>  mpirun -np $PBS_NP gpaw-python "cubeWF.py" > RUN.out
>>  -------------
>>
>>   Best regards, Pu Zhang
>>  --
>> Postdoc
>> The group of Structured Electromagnetic Materials
>>  Department of Photonics Engineering
>> Technical University of Denmark
>> Ørsteds Plads, Building 345v, 166
>>  2800, Kgs. Lyngby
>> E-mail: puzha at fotonik.dtu.dk
>> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>> Phone: 45 25 36 43
>> Fax: 45 93 65 81
>>
>>
>> On Fri, Aug 1, 2014 at 2:38 PM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk
>> > wrote:
>>
>>>  On 07/28/2014 05:13 PM, Pu ZHANG wrote:
>>>
>>> From the error information it seems something's wrong with the argument
>>> when calling the function get_pseudo_wave_function. But I searched around
>>> and couldn't figure out the problem. Have anyone ever had such a problem?
>>>
>>>
>>>  Are you running this in parallel?  If yes - then try running it in
>>> serial. Could you show us your input script?
>>>
>>> Jens Jørgen
>>>
>>>
>>>  Thanks!
>>>
>>>   Best regards, Pu Zhang
>>>  --
>>> Postdoc
>>> The group of Structured Electromagnetic Materials
>>>  Department of Photonics Engineering
>>> Technical University of Denmark
>>> Ørsteds Plads, Building 345v, 166
>>>  2800, Kgs. Lyngby
>>> E-mail: puzha at fotonik.dtu.dk
>>> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>>> Phone: 45 25 36 43
>>> Fax: 45 93 65 81
>>>
>>>
>>> On Fri, Jul 25, 2014 at 3:06 PM, Pu ZHANG <puzhang0702 at gmail.com> wrote:
>>>
>>>>  Dear all,
>>>>
>>>>  Execution of the tutorial example "Creating wave function cube files"
>>>> leads to error related to calc.get_pseudo_wave_function.
>>>>
>>>>  The script is
>>>> https://wiki.fysik.dtu.dk/gpaw/tutorials/plotting/plot_wave_functions.html,
>>>> and the error message looks like:
>>>>
>>>>  Traceback (most recent call last):
>>>>   File "cubeWF.py", line 14, in <module>
>>>>     wf = calc.get_pseudo_wave_function(band=band)
>>>>   File
>>>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/aseinterface.py",
>>>> line 407, in get_pseudo_wave_function
>>>>     pad=False)
>>>>   File
>>>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/aseinterface.py",
>>>> line 412, in get_pseudo_wave_function
>>>>     psit_G = self.wfs.get_wave_function_array(band, kpt, spin)
>>>>   File
>>>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/wavefunctions/base.py",
>>>> line 401, in get_wave_function_array
>>>>     psit_G = self.gd.collect(psit_G)
>>>>   File
>>>> "/zdata/groups/common/nicpa/2014-may/XeonX5550/python/2.7.6/packages/gpaw/0.10.0.11364/intel-14.0.1/lib/python2.7/site-packages/gpaw/grid_descriptor.py",
>>>> line 459, in collect
>>>>     A_xg[..., b0:e0, b1:e1, b2:e2] = a_xg
>>>> ValueError: could not broadcast input array from shape (23,23,23) into
>>>> shape (11,23,23)
>>>> GPAW CLEANUP (node 0): <type 'exceptions.ValueError'> occurred.
>>>>  Calling MPI_Abort!
>>>> [n-62-13-7:00605] 1 more process has sent help message
>>>> help-mpi-runtime.txt / mpi_init:warn-fork
>>>> [n-62-13-7:00605] Set MCA parameter "orte_base_help_aggregate" to 0 to
>>>> see all help / error messages
>>>>
>>>>  Any idea? Is there extra information shall I provide to help diagnose
>>>> the problem?
>>>>
>>>>  Thanks!
>>>>   Best regards, Pu Zhang
>>>>  --
>>>> Postdoc
>>>> The group of Structured Electromagnetic Materials
>>>>  Department of Photonics Engineering
>>>> Technical University of Denmark
>>>> Ørsteds Plads, Building 345v, 166
>>>>  2800, Kgs. Lyngby
>>>> E-mail: puzha at fotonik.dtu.dk
>>>> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>>>> Phone: 45 25 36 43
>>>> Fax: 45 93 65 81
>>>>
>>>
>>>
>>>
>>>  _______________________________________________
>>> gpaw-users mailing listgpaw-users at listserv.fysik.dtu.dkhttps://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>>>
>>
>>
>
>
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