[Pw_forum] Ph.x code help
Samin, Adib J.
samin.2 at buckeyemail.osu.edu
Wed Aug 27 15:44:05 CEST 2014
Actually, I was running it with two processors on one node but after trying it with one processor it worked. So thanks again for all your help.
In any case, I was just doing this example to get familiar with the procedure and I am planning to use it for my own research. In that case the simulation will be more complicated involving many atoms. How would I know how many processors to use?
Is there a general rule of thumb that I can use to help guide me for the future?
Thanks,
Adib Samin
________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
Sent: Wednesday, August 27, 2014 3:53 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Ph.x code help
did you try to run both the scf and the ph.x job with 1 node and 1 proc?
On Tue, Aug 26, 2014 at 6:32 PM, Samin, Adib J. <samin.2 at buckeyemail.osu.edu<mailto:samin.2 at buckeyemail.osu.edu>> wrote:
Yes it is.
Thanks,
Adib Samin
________________________________________
From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org>> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com<mailto:vincenzo.verdolino at gmail.com>>
Sent: Tuesday, August 26, 2014 12:12 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Ph.x code help
Quick question
Is the Pseudo Potential the one suggested in the test input file? I see you are usin a pz one...i don't know but could you double check that??
Sent from my iPhone
> On 26/ago/2014, at 17:53, "Samin, Adib J." <samin.2 at buckeyemail.osu.edu<mailto:samin.2 at buckeyemail.osu.edu>> wrote:
>
> Dear Quantum Espresso Users,
>
> Thanks again for all your help. I was finally able to run the ph.x code but I am still not generating the dynamical matrix but rather a blank file.
> I have attached the output of the ph.x code for the input files below. Any help on this matter would be appraciated.
>
> Atomic displacements:
> There are 2 irreducible representations
>
> Representation 1 3 modes -T_2g G_25' G_5+ To be done
>
> Representation 2 3 modes -T_1u G_15 G_4- Not done in this run
>
> Compute atoms: 1, 2,
>
>
>
> Alpha used in Ewald sum = 0.7000
> PHONON : 0.56s CPU 0.61s WALL
>
>
>
> Representation # 1 modes # 1 2 3
>
> Self-consistent Calculation
>
> iter # 1 total cpu time : 0.9 secs av.it<http://av.it>.: 5.0
> thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.189E-06
>
> iter # 2 total cpu time : 1.3 secs av.it<http://av.it>.: 9.5
> thresh= 0.434E-04 alpha_mix = 0.700 |ddv_scf|^2 = 0.320E-08
>
> iter # 3 total cpu time : 1.7 secs av.it<http://av.it>.: 9.5
> thresh= 0.566E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.278E-10
>
> iter # 4 total cpu time : 2.1 secs av.it<http://av.it>.: 8.8
> thresh= 0.528E-06 alpha_mix = 0.700 |ddv_scf|^2 = 0.296E-13
>
> iter # 5 total cpu time : 2.5 secs av.it<http://av.it>.: 9.4
> thresh= 0.172E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.287E-15
>
> End of self-consistent calculation
>
> Convergence has been achieved
>
> Stopping because representation 2 is not done
>
>
> Thanks,
>
> Adib Samin
>
>
> Adib Samin
> Postdoc
> The Department of Aerospace and Mechanical Engineering
> The Ohio State University
>
>
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org>> on behalf of Samin, Adib J. <samin.2 at buckeyemail.osu.edu<mailto:samin.2 at buckeyemail.osu.edu>>
> Sent: Tuesday, August 26, 2014 11:08 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Ph.x code help
>
> Thank you so much for all your help. I was finally able to run the code by reducing the number of processors being used.
> I still have one question however. The si.dynG file I am creating seems to be a blank file. Is that correct?
> I am currently attempting to run dynmat.x to diagonalize the matrix but I am concerned because I don't see the matrix.
>
> Thanks,
>
> Adib Samin
>
>
>
>
>
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org>> on behalf of Vincenzo Verdolino <vincenzo.verdolino at gmail.com<mailto:vincenzo.verdolino at gmail.com>>
> Sent: Tuesday, August 26, 2014 10:53 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Ph.x code help
>
> 12 pros is fine for the scf but try to change it for ph.x
>
> Sent from my iPhone
>
>> On 26/ago/2014, at 16:19, "Samin, Adib J." <samin.2 at buckeyemail.osu.edu<mailto:samin.2 at buckeyemail.osu.edu>> wrote:
>>
>> Thank you for your response. I am still getting errors running the code. I am indeed running it in parallel using 12 processors. How do I check for the consistencies mentioned below?
>> Any clarification would be greatly appreciated.
>>
>> Thanks,
>>
>> Adib Samin
>>
>>
>>
>>
>>
>>
>> ________________________________________
>> From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org>> on behalf of Ari P Seitsonen <Ari.P.Seitsonen at iki.fi<mailto:Ari.P.Seitsonen at iki.fi>>
>> Sent: Tuesday, August 26, 2014 9:59 AM
>> To: PWSCF Forum
>> Subject: Re: [Pw_forum] Ph.x code help
>>
>> Dear Adib Samin,
>>
>> How did you try to run the example, parallellising over the
>> representations/q vectors? If yes, how many MPI tasks did you ask for, how
>> many partitions for the representations/q vectors? Please check whether
>> these are consistent.
>>
>> Greetings from Sunny Montrouge,
>>
>> apsi
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi<mailto:Ari.P.Seitsonen at iki.fi> / http://www.iki.fi/~apsi/
>> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>> Mobile (F) : +33 789 37 24 25<tel:%2B33%20789%2037%2024%2025> (CH) : +41 79 71 90 935<tel:%2B41%2079%2071%2090%20935>
>>
>>
>>> On Tue, 26 Aug 2014, Samin, Adib J. wrote:
>>>
>>>
>>> Thank you for your help.
>>>
>>> I have attached below the scf.in<http://scf.in> file. I hope that helps in diagnosing the
>>> problem.
>>>
>>> &control
>>> calculation='scf'
>>> restart_mode='from_scratch',
>>> pseudo_dir='./'
>>> outdir='/nfs/11/osu7834/'
>>> prefix='SIPH',
>>> /
>>> &system
>>> ibrav=2, celldm(1)=10.20, nat=2, ntyp=1,
>>> ecutwfc =16.0
>>> /
>>> &electrons
>>> conv_thr = 1.0d-9
>>> mixing_beta = 0.7
>>> /
>>> ATOMIC_SPECIES
>>> Si 28.0855 Si.pz-vbc.UPF
>>> ATOMIC_POSITIONS
>>> Si 0.00 0.00 0.00
>>> Si 0.25 0.25 0.25
>>> K_POINTS
>>> 10
>>> 0.1250000 0.1250000 0.1250000 1.00
>>> 0.1250000 0.1250000 0.3750000 3.00
>>> 0.1250000 0.1250000 0.6250000 3.00
>>> 0.1250000 0.1250000 0.8750000 3.00
>>> 0.1250000 0.3750000 0.3750000 3.00
>>> 0.1250000 0.3750000 0.6250000 6.00
>>> 0.1250000 0.3750000 0.8750000 6.00
>>> 0.1250000 0.6250000 0.6250000 3.00
>>> 0.3750000 0.3750000 0.3750000 1.00
>>> 0.3750000 0.3750000 0.6250000 3.00
>>>
>>>
>>> Thanks,
>>>
>>> Adib Samin
>>>
>>>
>>> Adib Samin
>>>
>>> Postdoc
>>>
>>> The Department of Aerospace and Mechanical Engineering
>>>
>>> The Ohio State University
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ____________________________________________________________________________
>>> From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org>> on behalf of
>>> Vincenzo Verdolino <vincenzo.verdolino at gmail.com<mailto:vincenzo.verdolino at gmail.com>>
>>> Sent: Tuesday, August 26, 2014 5:38 AM
>>> To: PWSCF Forum
>>> Subject: Re: [Pw_forum] Ph.x code help
>>> Dear,
>>>
>>> just make sure you
>>>
>>> cp -r -f SIPH.save /nfs/11/osu7834/
>>>
>>> sometimes it happens that your outir in the scf calculation is not the same
>>> specified in your ph.x calculation
>>>
>>> could you also paste the scf.in<http://scf.in> job file?
>>>
>>> thanks
>>>
>>> vincenzo
>>>
>>>
>>> On Mon, Aug 25, 2014 at 10:07 PM, Samin, Adib J.
>>> <samin.2 at buckeyemail.osu.edu<mailto:samin.2 at buckeyemail.osu.edu>> wrote:
>>>
>>> Dear Quantum Espresso users,
>>>
>>>
>>> I am trying to run the ph.x executable using a simple silicon
>>> example which I found online. I first perform the scf
>>> calculation and save the results and then use the same
>>> outdirectory and prefix when running the ph.x code. However, I
>>> keep getting the same error which says:
>>>
>>> 'Error in routine image_q_irr (1):
>>>
>>> some images have no rapp'
>>>
>>> I have attached the ph input file.
>>>
>>> I would really appreciate it if someone can help explain to me
>>> why this is happening.
>>>
>>>
>>> Phonons of Si at Gamma
>>> &inputph
>>> tr2_ph=1.0d-14,
>>> amass(1)=28.0855,
>>> prefix='SIPH',
>>> outdir='/nfs/11/osu7834/'
>>> fildyn='si.dynG',
>>> /
>>> 0.0 0.0 0.0
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Adib Samin
>>>
>>>
>>>
>>>
>>> Adib Samin
>>>
>>> Postdoc
>>>
>>> The Department of Aerospace and Mechanical Engineering
>>>
>>> The Ohio State University
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
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