[gpaw-users] Problems with calculating all electron wave functions in parallel mode
Varadharajan Srinivasan
varadharajan.srinivasan at gmail.com
Fri Sep 15 08:33:07 CEST 2017
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_
>> 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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