[gpaw-users] Problems with calculating all electron wave functions in parallel mode
Kuisma, Mikael
mikael.j.kuisma at jyu.fi
Fri Sep 15 08:57:38 CEST 2017
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<mailto: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> <mailto: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>>
<mailto: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>> <mailto: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>>> <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<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/utilities/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/aseinterface.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/aseinterface.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/wavefunctions/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_descriptor.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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