[gpaw-users] Problems with calculating all electron wave functions in parallel mode
Varadharajan Srinivasan
varadharajan.srinivasan at gmail.com
Fri Sep 15 09:05:43 CEST 2017
Thanks, Mikael. I saw this paper just this morning and was wondering if I
could find the implementation and adapt to FD as well.
Best,
Vardha.
On Fri, Sep 15, 2017 at 12:27 PM, Kuisma, Mikael <mikael.j.kuisma at jyu.fi>
wrote:
> Hi!
>
> >I am actually interested in computing projections of time-propagated
> Kohn-Sham states with the initial KS states. Does a tool for this already
> exist?
>
> Yes! In case of LCAO-TDDFT, it does! Check out our recent development just
> accepted JCTC. In practice, we project the time dependent density matrix to
> initial KS states and analyse the content of excitations within linear
> response calculations in real time. However, the method itself is not
> restricted to linear response calculations.
>
> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00589
>
> It is not yet added to git, but soon will be.
>
> BR,
> Mikael Kuisma
>
> Academy of Finland Post Doc
>
> Nanoscience Center
> Department of Chemistry
> University of Jyväskylä
> P.O. Box 35
> FIN-40014 University of Jyväskylä
> Finland
>
> E-mail: mikael.j.kuisma (at) jyu.fi
> Phone: +358 40 077 4114
>
> https://scholar.google.se/citations?user=w0eP9esAAAAJ
>
> Visiting address: NSC, 3rd floor, YN320
> ------------------------------
> *Lähettäjä:* gpaw-users-bounces at listserv.fysik.dtu.dk [
> gpaw-users-bounces at listserv.fysik.dtu.dk] käyttäjän Varadharajan
> Srinivasan via gpaw-users [gpaw-users at listserv.fysik.dtu.dk] puolesta
> *Lähetetty:* 15. syyskuuta 2017 9:33
> *Vastaanottaja:* Jens Jørgen Mortensen
> *Kopio:* gpaw-users
> *Aihe:* Re: [gpaw-users] Problems with calculating all electron wave
> functions in parallel mode
>
> Not yet. But hopefully eventually.
>
> Vardha,
>
> On Fri, Sep 15, 2017 at 11:01 AM, Jens Jørgen Mortensen <jjmo at dtu.dk>
> wrote:
>
>> On 09/14/2017 09:08 PM, Varadharajan Srinivasan wrote:
>>
>>> Dear Jens,
>>>
>>> I am actually interested in computing projections of time-propagated
>>> Kohn-Sham states with the initial KS states. Does a tool for this already
>>> exist? I wasn't aware so I wanted to code one. However, I was not sure if
>>> pseudo wave functions in PAW would be useful for this. So I am trying to
>>> get all-electron wave functions along my time-propagated simulation. Since
>>> that is parallel I also wanted the PS2AE to work in the same framework.
>>>
>>> This might be a very round about way of getting the projections and
>>> would be unnecessary if such a tool is already in existence. If not, I
>>> guess my trials might eventually contribute to making one. I would really
>>> appreciate any help in this regard.
>>>
>>
>> Do your atoms move?
>>
>> Jens Jørgen
>>
>>
>>> Vardha.
>>>
>>> On Thu, Sep 14, 2017 at 1:46 PM, Jens Jørgen Mortensen <jjmo at dtu.dk
>>> <mailto:jjmo at dtu.dk>> wrote:
>>>
>>> On 09/13/2017 08:16 PM, Varadharajan Srinivasan wrote:
>>>
>>> Hi Jens,
>>>
>>> I installed and tried out the development version and am
>>> getting it to work in parallel mode as well.
>>>
>>>
>>> Thanks for checking. Note that the current implementation will
>>> not run any faster in parallel!
>>>
>>> Jens Jørgen
>>>
>>>
>>> Thanks,
>>> Vardha.
>>>
>>> On Tue, Sep 12, 2017 at 7:32 PM, Varadharajan Srinivasan
>>> <varadharajan.srinivasan at gmail.com
>>> <mailto:varadharajan.srinivasan at gmail.com>
>>> <mailto:varadharajan.srinivasan at gmail.com
>>> <mailto:varadharajan.srinivasan at gmail.com>>> wrote:
>>>
>>> Ok I will try and report.
>>>
>>> Vardha.
>>>
>>> On Tue, Sep 12, 2017 at 3:02 PM, Jens Jørgen Mortensen
>>> <jjmo at dtu.dk <mailto:jjmo at dtu.dk> <mailto:jjmo at dtu.dk
>>> <mailto:jjmo at dtu.dk>>> wrote:
>>>
>>> On 09/11/2017 07:44 PM, Varadharajan Srinivasan wrote:
>>>
>>> Yes it does. I am sorry I had forgotten to add
>>> that. It
>>> only fails when run in parallel.
>>>
>>>
>>> It should work Ok in parallel also. Can you try the
>>> latest
>>> development version of ASE+GPAW?
>>>
>>> Jens Jørgen
>>>
>>>
>>> Vardha.
>>>
>>>
>>> On Mon, Sep 11, 2017 at 3:02 PM, Jens Jørgen
>>> Mortensen
>>> <jjmo at dtu.dk <mailto:jjmo at dtu.dk>
>>> <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>> <mailto:jjmo at dtu.dk
>>> <mailto:jjmo at dtu.dk>
>>>
>>>
>>> <mailto:jjmo at dtu.dk <mailto:jjmo at dtu.dk>>>> wrote:
>>>
>>> On 09/10/2017 02:26 PM, Varadharajan
>>> Srinivasan via
>>> gpaw-users wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to obtain all electron wave
>>> functions
>>> from a
>>> ground-state calculation on guanine. Having
>>> performed the GS
>>> calculation in domain parallel mode, I wrote
>>> a
>>> script to get
>>> the all electron wave function using the
>>> ps2ae
>>> utility. The
>>> code used is attached below. However, I
>>> get the
>>> following
>>> error. I have seen some similar posts in
>>> the forum
>>> but there
>>> was no response. I would greatly
>>> appreciate some
>>> advice on
>>> this issue.
>>>
>>>
>>> Does the script work OK when you run it in
>>> serial?
>>>
>>> Jens Jørgen
>>>
>>>
>>> Vardha.
>>> IISER Bhopal
>>> India
>>>
>>> Number of Atomic Orbitals: 49
>>>
>>> Number of Bands in Calculation: 50
>>>
>>> Bands to Converge: 40 Lowest Bands
>>>
>>> Number of Valence Electrons: 56
>>>
>>> rank=0 L00: Traceback (most recent call
>>> last):
>>>
>>> rank=0 L01: File "trial.py", line 19, in
>>> <module>
>>>
>>> rank=0 L02: wf =
>>> twf_gs.get_wave_function(band, ae=False)
>>>
>>> rank=0 L03: File
>>> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/utilit
>>> ies/ps2ae.py",
>>> line 97, in get_wave_function
>>>
>>> rank=0 L04: pad=True, periodic=True)
>>>
>>> rank=0 L05: File
>>> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/aseint
>>> erface.py",
>>> line 458, in get_pseudo_wave_function
>>>
>>> rank=0 L06: periodic=periodic)
>>>
>>> rank=0 L07: File
>>> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/aseint
>>> erface.py",
>>> line 465, in get_pseudo_wave_function
>>>
>>> rank=0 L08: periodic=periodic)
>>>
>>> rank=0 L09: File
>>> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/wavefu
>>> nctions/base.py",
>>> line 404, in get_wave_function_array
>>>
>>> rank=0 L10: psit_G =
>>> self.gd.collect(psit_G)
>>>
>>> rank=0 L11: File
>>> "/opt/gpaw-intelmpi/lib/python2.7/site-packages/gpaw/grid_d
>>> escriptor.py",
>>> line 502, in collect
>>>
>>> rank=0 L12: A_xg[..., b0:e0, b1:e1,
>>> b2:e2] = a_xg
>>>
>>> rank=0 L13: ValueError: could not
>>> broadcast input
>>> array from
>>> shape (115,107,83) into shape (23,53,83)
>>>
>>> GPAW CLEANUP (node 0): <type
>>> 'exceptions.ValueError'>
>>> occurred. Calling MPI_Abort!
>>>
>>> application called
>>> MPI_Abort(MPI_COMM_WORLD, 42) -
>>> process 0
>>>
>>>
>>>
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