Re: [QE-users] Third party packages to plot Band structure and density of states

[B S Bhushan]

Thanks Suresh ji...


On Tue, Jun 12, 2018 at 11:24 AM, Suresh A 
wrote:

> Dear Busan,
>   Gnuplot is enough to plot good quality pictures and also one can
> plot dos and band structure side by side. Only thing needed is to go
> through command lines of gnuplot. Other than gnuplot, one may try qtiplot
> and grace software.
>
>  Yours Sincerely,
>
> A.Suresh,
> Research Scholar,
> School of Physics,
> Madurai Kamaraj University,
> Madurai.
>
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Re: [QE-users] Third party packages to plot Band structure and density of states

[B S Bhushan]

Thank you.


On Mon, Jun 11, 2018 at 5:50 PM, Saibabu Madas 
wrote:

> Hi,
>
>
> I use xmgrace (in ubuntu) for plotting band structure and DOS side by
> side. For installation, please follow the instructions given in this link :
> https://ubuntuforums.org/showthread.php?t=442322
>
>
> Best regards,
>
> *Madas Saibabu*
>
> Early Stage Researcher
>
>
> *ELI-HU Non-Profit Ltd.*
>
> Computational and Applied Materials Science Group
> ----------
> *From:* users  on behalf of B S
> Bhushan 
> *Sent:* Monday, June 11, 2018 14:10
> *To:* Quantum Espresso users Forum
> *Subject:* Re: [QE-users] Third party packages to plot Band structure and
> density of states
>
> Is there any package either open source or commercial that allows to plot
> both band structure and DOS in single image side by side, please ???
>
> On Mon, Jun 11, 2018 at 5:35 PM, Paolo Giannozzi 
> wrote:
>
>> Gnuplot can produce publication-quality pictures, if you know how (I
>> don't). Grace (http://plasma-gate.weizmann.ac.il/Grace/) reads the same
>> data as gnuplot, has a graphical interface and is somewhat easier to use.
>> There are some nice graphical interfaces for QE, but they are commercial
>> products.
>>
>> Paolo
>>
>> On Mon, Jun 11, 2018 at 10:33 AM, B S Bhushan 
>> wrote:
>>
>>> Dear Experts,
>>>
>>> Can you please name some codes or softwares to plot band structure and
>>> density of states obtained from quantum espresso. I found that the quality
>>> of figures produced from GNUPLOT is low. Please suggest some alternatives.
>>>
>>> Especially which code allows to plot both band structure and DOS side by
>>> side over same energy range.
>>>
>>> Please suggest.
>>>
>>>
>>> With Sincere Regards,
>>> B S Bhushan,
>>> Ph.D Scholar,
>>> Indian Institute of Information Technology and Management, Gwalior,
>>> India.
>>>
>>>
>>>
>>> ___
>>> users mailing list
>>> users@lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>
>>
>>
>> --
>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
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>>
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Re: [QE-users] Third party packages to plot Band structure and density of states

[B S Bhushan]

Is there any package either open source or commercial that allows to plot
both band structure and DOS in single image side by side, please ???

On Mon, Jun 11, 2018 at 5:35 PM, Paolo Giannozzi 
wrote:

> Gnuplot can produce publication-quality pictures, if you know how (I
> don't). Grace (http://plasma-gate.weizmann.ac.il/Grace/) reads the same
> data as gnuplot, has a graphical interface and is somewhat easier to use.
> There are some nice graphical interfaces for QE, but they are commercial
> products.
>
> Paolo
>
> On Mon, Jun 11, 2018 at 10:33 AM, B S Bhushan 
> wrote:
>
>> Dear Experts,
>>
>> Can you please name some codes or softwares to plot band structure and
>> density of states obtained from quantum espresso. I found that the quality
>> of figures produced from GNUPLOT is low. Please suggest some alternatives.
>>
>> Especially which code allows to plot both band structure and DOS side by
>> side over same energy range.
>>
>> Please suggest.
>>
>>
>> With Sincere Regards,
>> B S Bhushan,
>> Ph.D Scholar,
>> Indian Institute of Information Technology and Management, Gwalior, India.
>>
>>
>>
>> ___
>> users mailing list
>> users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
> ___
> users mailing list
> users@lists.quantum-espresso.org
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>
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[QE-users] Third party packages to plot Band structure and density of states

[B S Bhushan]

Dear Experts,

Can you please name some codes or softwares to plot band structure and
density of states obtained from quantum espresso. I found that the quality
of figures produced from GNUPLOT is low. Please suggest some alternatives.

Especially which code allows to plot both band structure and DOS side by
side over same energy range.

Please suggest.


With Sincere Regards,
B S Bhushan,
Ph.D Scholar,
Indian Institute of Information Technology and Management, Gwalior, India.
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Re: [QE-users] Band Structure and DOS contradiction in doped graphene

[B S Bhushan]

Dear Dr. Apsi,

Thank you for the explanation.

I considered the Fermi energy value from Non-self consistent calculation
(NSCF).
As you say broadening is responsible for these few states on the fermi
energy, will it be helpful if I change the smearing type???
(Pardon me if the question is pointless, I am not yet very good with the
core physics stuff)

I have used m-v smearing for the calculations, what if I use the tetrahedra
or other smearing method...  will it be helpful to avoid this issue ??
Requesting your insight, please.


Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com


On Tue, May 22, 2018 at 2:42 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
wrote:

>
> Dear B S Bhushan,
>
>   To me it looks like
>
>  1) QE/PWscf sets the Fermi level in the band gap, at some arbitrary
> energy just so that the number of electrons is conserved: It could be
> higher (but hardly lower). This is normal, as the energy position is not
> specifically defined so long as the number of electrons is correct (or, the
> Fermi level can be anywhere in the band gap just as it is far enough from
> the valence and conduction band edges)
>
>  2) the program to calculate DOS does not realign the Fermi energy, so
> with the broadening there appears some intensity at the Fermi energy
>
>   After you check that this is the correct assumption (for example that
> the occupation of all bands is either 0 or 1), you can manually shift the
> Fermi energy to mid-gap in the plots; or, some people do not show the Fermi
> energy at all in systems with gap but align the energy scale so that the
> top of the valence band ("valence band maximum", "VBM") is at zero.
>
>   Which value of Fermi energy do you use actually, the one from the
> self-consistent or non-self-consistent calculation?
>
> Greetings from Sunny Paris,
>
>apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
> -=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>
>
>
> On Mon, 21 May 2018, B S Bhushan wrote:
>
> Dear Experts,
>> I am analyzing doped graphene using pbe functional.
>> Where, I end up having contradictory DOS and Band structure.
>>
>> The Band structure shows a small band gap at the fermi level, however,
>> the DOS shows few states on the fermi level.
>>
>> What should I call the system in such cases, metallic or semi-metall
>> ic or semi-conducting ???
>>
>> or have I done something wrong ???
>>
>> The link below contains the figures and input scripts used by me.
>> https://drive.google.com/open?id=11Q7xfMGCHJDUlPK0amTnWO-y4R70ZQWj
>>
>> Please suggest.
>>
>>
>> Sincerely,
>> B S Bhushan,
>> Ph.D Scholar,
>> ABV- Indian Institute of Information Technology and Management, Gwalior.
>> www.bsbhushan.com
>>
>>
>>
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[QE-users] Band Structure and DOS contradiction in doped graphene

[B S Bhushan]

 Dear Experts,

I am analyzing doped graphene using pbe functional.
Where, I end up having contradictory DOS and Band structure.

The Band structure shows a small band gap at the fermi level, however, the
DOS shows few states on the fermi level.

What should I call the system in such cases, *metallic *or* semi-metallic *
or* semi-conducting *???

or have I done something wrong ???

The link below contains the figures and input scripts used by me.
https://drive.google.com/open?id=11Q7xfMGCHJDUlPK0amTnWO-y4R70ZQWj

Please suggest.


Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com
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[QE-users] Band Structure and DOS contradiction

[B S Bhushan]

Dear Dr. Giovanni,
Thank you very much for your response. Apologies... if the mail is received
multiple times.
I think my earlier mail has not reached to the forum due to exceeded
attachment size limit.

Here, I am sending the mail again with the images of graphene system,
Bandstructure and DOS, as well as the input scripts attached as a google
drive link.
The system is a 5*5 graphene cell with single Sulfur dopant.

https://drive.google.com/open?id=11Q7xfMGCHJDUlPK0amTnWO-y4R70ZQWj

Thanks.

Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com


On Wed, May 16, 2018 at 6:06 PM, Giovanni Cantele <
giovanni.cant...@spin.cnr.it> wrote:

> Maybe you could send input files and a plot of DOS and band structure to
> help people to figure out
> what is happening.
>
> If DOS and band structure do not agree with each other, I would not trust
> to either!!!
>
> What do you mean that you repeat the calculation with **different theory**
> 
>
> Giovanni
>
>
>
> On 16 May 2018, at 13:17, B S Bhushan <ecebhus...@gmail.com> wrote:
>
> Dear Experts,
>
> I am analyzing defected graphene with different dopants.
> In very few cases... I end up having contradictory DOS and Band structure.
>
> The Band structure shows a small band gap at the fermi level, however, the
> DOS shows states on the fermi level.
> Same result appears even if the calculation is repeated with different
> theory.
> In such cases, Should I depend on the Band structure or the DOS.
> What should I call the system, *metallic *or* semi-metallic *or
> * semi-conducting *???
>
> Please suggest.
>
>
> Sincerely,
> B S Bhushan,
> Ph.D Scholar,
> ABV- Indian Institute of Information Technology and Management, Gwalior.
> www.bsbhushan.com
>
>
> ___
> users mailing list
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>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cant...@spin.cnr.it <giovanni.cant...@spin.cnr.it>
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.fisica.unina.it/~cantele
>
>
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Re: [QE-users] Band Structure and DOS contradiction

[B S Bhushan]

 Dear Dr. Giovanni,
Thank you very much for your response.

Google drive link below contains the images of structure, Bandstructure and
DOS, as well as the input scripts.
The system is a 5*5 graphene cell with single Sulfur dopant.

https://drive.google.com/open?id=11Q7xfMGCHJDUlPK0amTnWO-y4R70ZQWj

Thanks..

On Thu, May 17, 2018 at 12:27 PM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Dear Dr. Giovanni,
> Thank you very much for your response.
>
> Attached are the Bandstructure and DOS plots, and the input scripts.
> The system is a 5*5 graphene cell with single Sulfur dopant.
>
> Thanks.
>
>
> On Thu, May 17, 2018 at 12:18 PM, B S Bhushan <ecebhus...@gmail.com>
> wrote:
>
>> Dear Dr. Giovanni,
>> Thank you very much for your response.
>>
>> Attached are the Bandstructure and DOS plots, and the input scripts.
>> The system is a 5*5 graphene cell with single Sulfur dopant.
>>
>>
>>
>>
>> On Wed, May 16, 2018 at 6:06 PM, Giovanni Cantele <
>> giovanni.cant...@spin.cnr.it> wrote:
>>
>>> Maybe you could send input files and a plot of DOS and band structure to
>>> help people to figure out
>>> what is happening.
>>>
>>> If DOS and band structure do not agree with each other, I would not
>>> trust to either!!!
>>>
>>> What do you mean that you repeat the calculation with **different
>>> theory** 
>>>
>>> Giovanni
>>>
>>>
>>>
>>> On 16 May 2018, at 13:17, B S Bhushan <ecebhus...@gmail.com> wrote:
>>>
>>> Dear Experts,
>>>
>>> I am analyzing defected graphene with different dopants.
>>> In very few cases... I end up having contradictory DOS and Band
>>> structure.
>>>
>>> The Band structure shows a small band gap at the fermi level, however,
>>> the DOS shows states on the fermi level.
>>> Same result appears even if the calculation is repeated with different
>>> theory.
>>> In such cases, Should I depend on the Band structure or the DOS.
>>> What should I call the system, *metallic *or* semi-metallic *or*
>>> semi-conducting *???
>>>
>>> Please suggest.
>>>
>>>
>>> Sincerely,
>>> B S Bhushan,
>>> Ph.D Scholar,
>>> ABV- Indian Institute of Information Technology and Management, Gwalior.
>>> www.bsbhushan.com
>>>
>>>
>>> ___
>>> users mailing list
>>> users@lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>>
>>> --
>>>
>>> Giovanni Cantele, PhD
>>> CNR-SPIN
>>> c/o Dipartimento di Fisica
>>> Universita' di Napoli "Federico II"
>>> Complesso Universitario M. S. Angelo - Ed. 6
>>> Via Cintia, I-80126, Napoli, Italy
>>> e-mail: giovanni.cant...@spin.cnr.it <giovanni.cant...@spin.cnr.it>
>>> Phone: +39 081 676910
>>> Skype contact: giocan74
>>>
>>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>>> Web page: http://people.fisica.unina.it/~cantele
>>>
>>>
>>> ___
>>> users mailing list
>>> users@lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>
>>
>
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[QE-users] Band Structure and DOS contradiction

[B S Bhushan]

 Dear Experts,

I am analyzing defected graphene with different dopants.
In very few cases... I end up having contradictory DOS and Band structure.

The Band structure shows a small band gap at the fermi level, however, the
DOS shows states on the fermi level.
Same result appears even if the calculation is repeated with different
theory.
In such cases, Should I depend on the Band structure or the DOS.
What should I call the system, *metallic *or* semi-metallic *or*
semi-conducting *???

Please suggest.


Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com
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[Pw_forum] pdos of MoS2

[B S Bhushan]

Dear Experts,

I have calculated the pdos of MoS2 sheet... Where, I have observed two s
orbitals and two p orbital pdos files for Mo. The no. of pdos files for d
orbital is only one, though.
The electron configuration of Mo is [Kr] 5s1 4d5. Then, How am I getting
two s and two p pdos files ???

The input scripts and the screen shot have been attached with  the mail.

Awaiting your suggestions,

Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV - Indian Institute of Information Technology and Management, Gwalior,
India.


mos2_nscf.in
Description: Binary data


mos2.in
Description: Binary data


pdos_mos2.in
Description: Binary data


dos_mos2.in
Description: Binary data
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Re: [Pw_forum] problem calculating pdos (projwfc.x)

[B S Bhushan]

I have enough memory on the disk... and used same pool of processors as
used for pw.x.
Yet, I am not getting why the error is appearing ??


On Tue, Jan 9, 2018 at 4:01 PM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Dear experts,
>
> I am trying to calculate the DOS and PDOS of transition metal adsorbed
> graphene supercell.
>
> DOS has been computed successfully, however I am getting problem with PDOS
> (projwfc.x). The error is shown below,
>
> 
> ---
>  Calling pprojwave 
>
>   Problem Sizes
>   natomwfc =  188
>   nbnd =  120
>   nkstot   =  365
>   npwx =  774
>   nkb  =  400
>
>
>  %%%
> %%%
>  Error in routine davcio (10):
>  error while reading from file "/home/external/iiitm/santhib/
> g_fe_pd_11/./g_fe_pd_11.wfc46"
>  %%%
> %%%
> 
> 
>
> Attached are the input script of vc-relax and nscf,  and the output error
> file.
>
>
>
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[Pw_forum] problem calculating pdos (projwfc.x)

[B S Bhushan]

Dear experts,

I am trying to calculate the DOS and PDOS of transition metal adsorbed
graphene supercell.

DOS has been computed successfully, however I am getting problem with PDOS
(projwfc.x). The error is shown below,


---
 Calling pprojwave 

  Problem Sizes
  natomwfc =  188
  nbnd =  120
  nkstot   =  365
  npwx =  774
  nkb  =  400


 %%%
%%%
 Error in routine davcio (10):
 error while reading from file "/home/external/iiitm/santhib/
g_fe_pd_11/./g_fe_pd_11.wfc46"
 %%%
%%%



Attached are the input script of vc-relax and nscf,  and the output error
file.


pdos.out
Description: Binary data


vc_relax.in
Description: Binary data


nscf.in
Description: Binary data
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Re: [Pw_forum] error- dE0s is positive which should never happen

[B S Bhushan]

Ok...

I have rerun the calculation... surprisingly, it completed without any
error.
Any way... Thank you Dr. Ullah for your kind reply.



On Wed, Dec 20, 2017 at 4:32 PM, Saif Ullah <kiterunn...@gmail.com> wrote:

> Dear Bhushan,
>
> It means that you have already achieved (nearly achieved) the convergence
> as can be concluded from the following sentence by prof. Paolo
> (This kind of errors invariably happens when you are very close
>
> to the minimum and you have some numerical noise on forces. It
> is useless in my opinion to insist: your system is sufficiently
> relaxed
>
>
> Paolo)
>
> I'm surely not a QE expert but when I have this kind of problem, I usually
> change (a bit) the positions of few atoms and do a relax calculation
> following by an scf-calc.
>
> Regards
> Saif
>
> Saif Ullah
> Departamento de Física
> Instituto de Ciências Exatas - ICE
> Universidade Federal de Juiz de Fora - UFJF
> Juiz de Fora - MG - Brazil - CEP 36036-330
> sul...@fisica.ufjf.br
> Cell# +55 32 9110-7851
> https://www.researchgate.net/profile/Saif_Ullah41
>
> On Tue, Dec 19, 2017 at 11:43 AM, B S Bhushan <ecebhus...@gmail.com>
> wrote:
>
>> Dear Dr. Saif,
>>
>> I have through this link before posting the error. However, I could not
>> find a solution to my problem there.
>>
>>
>> On Tue, Dec 19, 2017 at 6:07 PM, Saif Ullah <kiterunn...@gmail.com>
>> wrote:
>>
>>> It is a well-known error.
>>>
>>> The following links may be helpful.
>>> http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html
>>> https://www.mail-archive.com/pw_forum@pwscf.org/msg29759.html
>>>
>>> Regards
>>> Saif
>>>
>>>
>>> On Tue, Dec 19, 2017 at 7:38 AM, B S Bhushan <ecebhus...@gmail.com>
>>> wrote:
>>>
>>>> Dear experts...
>>>>
>>>> I have received this following error when I was trying to optimize a
>>>> doped graphene sheet.
>>>>
>>>> %%%%%%%%
>>>> %%
>>>>  Error in routine bfgs (1):
>>>>  dE0s is positive which should never happen
>>>>  %%%
>>>> %%%
>>>>
>>>> Please suggest me how to avoid this error.
>>>>
>>>> Thank you very much for your precious time and knowledge.
>>>>
>>>> Sincerely,
>>>> B S Bhushan,
>>>> Ph.D Scholar,
>>>> ABV-IIITM Gwalior, India.
>>>>
>>>>
>>>>
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>>>>
>>>
>>>
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Re: [Pw_forum] error- dE0s is positive which should never happen

[B S Bhushan]

Dear Dr. Saif,

I have through this link before posting the error. However, I could not
find a solution to my problem there.


On Tue, Dec 19, 2017 at 6:07 PM, Saif Ullah <kiterunn...@gmail.com> wrote:

> It is a well-known error.
>
> The following links may be helpful.
> http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html
> https://www.mail-archive.com/pw_forum@pwscf.org/msg29759.html
>
> Regards
> Saif
>
>
> On Tue, Dec 19, 2017 at 7:38 AM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Dear experts...
>>
>> I have received this following error when I was trying to optimize a
>> doped graphene sheet.
>>
>> 
>> %%
>>  Error in routine bfgs (1):
>>  dE0s is positive which should never happen
>>  %%%
>> %%%
>>
>> Please suggest me how to avoid this error.
>>
>> Thank you very much for your precious time and knowledge.
>>
>> Sincerely,
>> B S Bhushan,
>> Ph.D Scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>>
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[Pw_forum] error- dE0s is positive which should never happen

[B S Bhushan]

Dear experts...

I have received this following error when I was trying to optimize a doped
graphene sheet.


%%
 Error in routine bfgs (1):
 dE0s is positive which should never happen
 %%%
%%%

Please suggest me how to avoid this error.

Thank you very much for your precious time and knowledge.

Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV-IIITM Gwalior, India.
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Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Ok... Then the problem might be with the environment or something.

I will contact my HPC admin.

Thank you so much Dr. Andrea.

On Mon, Nov 13, 2017 at 5:06 PM, Andrea Ferretti <andrea.ferre...@unimore.it
> wrote:

>
> Dear Bhushan,
>
> I've re-run your scf+nscf using both qe-6.0 and 6.2 and both result in the
> same amount of disk usage (about 1GB for scf and 23 GB for nscf), which
> sounds reasonable given the size of the problem you are running (you have
> relatively large cell*nkpt parameters)
>
> take care
> Andrea
>
>
> The input scripts in support of the query raised in earlier reply are
>> attached here.
>>
>> On Thu, Nov 9, 2017 at 10:37 PM, B S Bhushan <ecebhus...@gmail.com>
>> wrote:
>>   Dear Dr. Andea Thank you so much.
>>
>> Dear Dr. Lorenzo, YES I read your mail, and I replied with thanks as well.
>>
>> I am facing a new problem with QE-6.2 on my supercomputer account.
>>
>> I had run a SCF for doped graphene structure with 48 atoms, and then
>> tried to run NSCF calculation (I wanted to
>> calculate DOS ultimately).
>> The NSCF calculation stopped in between because the calculation has
>> already consumed 80 GB and the disk ran out of
>> memory.
>> I am a bit surprised... because I have never seen an NSCF calculation
>> taking too much of memory before.
>> I am not getting why this case has happened.
>>
>> Can any of u plz suggest.
>>
>> I am very thankful for your precious time and knowledge.
>>
>>
>> Sincerely,
>> B S Bhushan
>> ABV-IIITM Gwalior, India.
>>
>>
>>
>> On Tue, Nov 7, 2017 at 4:10 PM, Lorenzo Paulatto <paul...@gmail.com>
>> wrote:
>>   Dear BS,
>> Did you read my email? Was it not clear at some point?
>>
>> Kind regards
>>
>> --
>> Lorenzo Paulatto
>> Written on a virtual keyboard with real fingers
>>
>> On 7 Nov 2017 10:37 a.m., "B S Bhushan" <ecebhus...@gmail.com> wrote:
>>   Seems like the dos.x of QE-6.2 can not find xml data from NSCF
>> produced using QE-6.1.
>> The following error was shown,
>>
>> 
>> -
>> ---
>>  Program DOS v.6.2 (svn rev. 13949:13950) starts on  7Nov2017 at 13:22:50
>>
>>  This program is part of the open-source Quantum ESPRESSO suite
>>  for quantum simulation of materials; please cite
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>>   URL http://www.quantum-espresso.org;,
>>  in publications or presentations arising from this work. More
>> details at
>>  http://www.quantum-espresso.org/quote
>>
>>  Parallel version (MPI), running on 1 processors
>>
>>  MPI processes distributed on 1 nodes
>>
>>  %%%
>> %%%
>>  Error in routine pw_readschemafile (1):
>>  xml data file not found
>>  %%%
>> %%%
>>
>>  stopping ...
>> 
>> --
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> 
>> --
>> 
>> -
>> --
>>
>>
>> should I do the VC-relax and NSCF again using QE-6.2 ??
>>
>> Please Suggest...
>>
>> Thank you very much for your kind support.
>>
>> Sincerely,
>> B S Bhushan
>> Ph.D Scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>> On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <ecebhus...@gmail.com>
>> wrote:
>>   Thank you very very much Dr. Andrea.
>> I have a question sir...
>> If I install the QE-6.2 on my supercomputer and run dos.x directly on the
>> NSCF outputs produced using
>> QE-6.1 will it w

Re: [Pw_forum] Problem with PDOS (format/variable-type mismatch)

[B S Bhushan]

Recompiling the code helped.
Problem solved.

Thank you so much Dr. Paolo and Dr. Lorenzo.

On Sat, Nov 11, 2017 at 1:54 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> On Sat, Nov 11, 2017 at 6:08 AM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
> I have made the below change in the last occurrence of nlmchi at line 2185
>> as you suggested...
>> [...] However, Still I am getting the same error.
>>
>
> you haven't recompiled
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
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Re: [Pw_forum] Problem with PDOS (format/variable-type mismatch)

[B S Bhushan]

Dear Dr. Paolo,

I have made the below change in the last occurrence of nlmchi at line 2185
as you suggested...

WRITE(iunproj,'(2i5,1x,a4,1x,a2,1x,3i5)') &
  nwfc, nlmchi(nwfc)%na, atm(ityp(nlmchi(nwfc)%na)), &
  nlmchi(nwfc)%els, nlmchi(nwfc)%n, nlmchi(nwfc)%l,
*nlmchi(nwfc)%m*

However, Still I am getting the same error.

Can u please suggest.

sincerely,
B S Bhushan

On Fri, Nov 10, 2017 at 7:52 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> It was fixed some time ago. In the WRITE at line 2185 of projwfc.f90,
> replace the last occurrence of "nlmchi" with "nlmchi%m"
>
> Paolo
>
> On Fri, Nov 10, 2017 at 12:54 PM, B S Bhushan <ecebhus...@gmail.com>
> wrote:
>
>> Dear Experts,
>>
>> I was calculating DOS and PDOS of a doped graphene system.
>> There was no problem calculating DOS using dos.x.
>> However, I received an error while calculating PDOS using projwfc.x
>> "format/variable-type mismatch".
>> the error is as below,
>>
>> 
>>  Program PROJWFC v.6.1 (svn rev. 13369) starts on 10Nov2017 at 14:
>> 5:25
>>
>>  This program is part of the open-source Quantum ESPRESSO suite
>>  for quantum simulation of materials; please cite
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>   URL http://www.quantum-espresso.org;,
>>  in publications or presentations arising from this work. More
>> details at
>>  http://www.quantum-espresso.org/quote
>>
>>  Parallel version (MPI), running on48 processors
>>  R & G space division:  proc/nbgrp/npool/nimage =  48
>>
>>  Reading data from directory:
>>  ./graphitic.save
>>
>>Info: using nr1, nr2, nr3 values from input
>>
>>Info: using nr1, nr2, nr3 values from input
>>
>>  IMPORTANT: XC functional enforced from input :
>>  Exchange-correlation  = PBE ( 1  4  3  4 0 0)
>>  Any further DFT definition will be discarded
>>  Please, verify this is what you really want
>>
>>file C.pbe-rrkjus.UPF: wavefunction(s)  2S 2P renormalized
>>file N.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized
>>
>>  Parallelization info
>>  
>>  sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>>  Min 232  93 2516156 4088 585
>>  Max 233  95 2616161 4091 590
>>  Sum   111554483   1237   775611   196271   28211
>>
>>
>>  negative rho (up, down):  9.688E-05 0.000E+00
>>
>>  Gaussian broadening (read from file): ngauss,degauss=  -10.005000
>>
>>
>>  Calling pprojwave 
>>
>>   Problem Sizes
>>   natomwfc =  200
>>   nbnd =  121
>>   nkstot   =  365
>>   npwx =  526
>>   nkb  =  400
>>
>> forrtl: severe (61): format/variable-type mismatch, unit 33, file
>> /home/external/iiitm/santhib/graphitic/PDOS_proj.projwfc_up
>> Image  PCRoutineLine
>> Source
>> projwfc.x  00A875FE  Unknown   Unknown
>> Unknown
>> projwfc.x  00A86096  Unknown   Unknown
>> Unknown
>> projwfc.x  00A3AEB2  Unknown   Unknown
>> Unknown
>> projwfc.x  009D760B  Unknown   Unknown
>> Unknown
>> projwfc.x  009D6B72  Unknown   Unknown
>> Unknown
>> projwfc.x  00A27B81  Unknown   Unknown
>> Unknown
>> projwfc.x  0041BCD7  pprojwave_   2185
>> projwfc.f90
>> projwfc.x  0040695B  MAIN__224
>> projwfc.f90
>> projwfc.x  0040626C  Unknown   Unknown
>> Unknown
>> libc.so.6  003FF541ECDD  Unknown   Unknown
>> Unknown
>> projwfc.x  00406169  Unknown   Unknown
>> Unknown
>> 
>> 
>> --
>>
>> Please suggest, what should I do to avoid this problem.
>>
>> I will be very thankful for your precious time and knowledge.
>>
>> Sinc

[Pw_forum] Problem with PDOS (format/variable-type mismatch)

[B S Bhushan]

Dear Experts,

I was calculating DOS and PDOS of a doped graphene system.
There was no problem calculating DOS using dos.x.
However, I received an error while calculating PDOS using projwfc.x
"format/variable-type mismatch".
the error is as below,


 Program PROJWFC v.6.1 (svn rev. 13369) starts on 10Nov2017 at 14: 5:25

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org;,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Parallel version (MPI), running on48 processors
 R & G space division:  proc/nbgrp/npool/nimage =  48

 Reading data from directory:
 ./graphitic.save

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1, nr2, nr3 values from input

 IMPORTANT: XC functional enforced from input :
 Exchange-correlation  = PBE ( 1  4  3  4 0 0)
 Any further DFT definition will be discarded
 Please, verify this is what you really want

   file C.pbe-rrkjus.UPF: wavefunction(s)  2S 2P renormalized
   file N.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized

 Parallelization info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Min 232  93 2516156 4088 585
 Max 233  95 2616161 4091 590
 Sum   111554483   1237   775611   196271   28211


 negative rho (up, down):  9.688E-05 0.000E+00

 Gaussian broadening (read from file): ngauss,degauss=  -10.005000


 Calling pprojwave 

  Problem Sizes
  natomwfc =  200
  nbnd =  121
  nkstot   =  365
  npwx =  526
  nkb  =  400

forrtl: severe (61): format/variable-type mismatch, unit 33, file
/home/external/iiitm/santhib/graphitic/PDOS_proj.projwfc_up
Image  PCRoutineLine
Source
projwfc.x  00A875FE  Unknown   Unknown  Unknown
projwfc.x  00A86096  Unknown   Unknown  Unknown
projwfc.x  00A3AEB2  Unknown   Unknown  Unknown
projwfc.x  009D760B  Unknown   Unknown  Unknown
projwfc.x  009D6B72  Unknown   Unknown  Unknown
projwfc.x  00A27B81  Unknown   Unknown  Unknown
projwfc.x  0041BCD7  pprojwave_   2185
projwfc.f90
projwfc.x  0040695B  MAIN__224
projwfc.f90
projwfc.x  0040626C  Unknown   Unknown  Unknown
libc.so.6  003FF541ECDD  Unknown   Unknown  Unknown
projwfc.x  00406169  Unknown   Unknown  Unknown
--

Please suggest, what should I do to avoid this problem.

I will be very thankful for your precious time and knowledge.

Sincerely,
B S Bhushan
Ph.D Scholar,
ABV-IIITM Gwalior, India.
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Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

The input scripts in support of the query raised in earlier reply are
attached here.

On Thu, Nov 9, 2017 at 10:37 PM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Dear Dr. Andea Thank you so much.
>
> Dear Dr. Lorenzo, YES I read your mail, and I replied with thanks as well.
>
> I am facing a new problem with *QE-6.2* on my supercomputer account.
>
> I had run a SCF for doped graphene structure with 48 atoms, and then tried
> to run NSCF calculation (I wanted to calculate DOS ultimately).
> The NSCF calculation stopped in between because the calculation has already*
> consumed 80 GB* and the disk ran out of memory.
> I am a bit surprised... because I have never seen an NSCF calculation
> taking too much of memory before.
> I am not getting why this case has happened.
>
> Can any of u plz suggest.
>
> I am very thankful for your precious time and knowledge.
>
>
> Sincerely,
> B S Bhushan
> ABV-IIITM Gwalior, India.
>
>
>
> On Tue, Nov 7, 2017 at 4:10 PM, Lorenzo Paulatto <paul...@gmail.com>
> wrote:
>
>> Dear BS,
>> Did you read my email? Was it not clear at some point?
>>
>> Kind regards
>>
>> --
>> Lorenzo Paulatto
>> Written on a virtual keyboard with real fingers
>>
>> On 7 Nov 2017 10:37 a.m., "B S Bhushan" <ecebhus...@gmail.com> wrote:
>>
>> Seems like the dos.x of QE-6.2 can not find xml data from NSCF produced
>> using QE-6.1.
>> The following error was shown,
>>
>> 
>> 
>> 
>>  Program DOS v.6.2 (svn rev. 13949:13950) starts on  7Nov2017 at 13:22:50
>>
>>  This program is part of the open-source Quantum ESPRESSO suite
>>  for quantum simulation of materials; please cite
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>>
>>   URL http://www.quantum-espresso.org;,
>>  in publications or presentations arising from this work. More
>> details at
>>  http://www.quantum-espresso.org/quote
>>
>>  Parallel version (MPI), running on 1 processors
>>
>>  MPI processes distributed on 1 nodes
>>
>>  %%%
>> %%%
>>  Error in routine pw_readschemafile (1):
>>  xml data file not found
>>  %%%
>> %%%
>>
>>  stopping ...
>> 
>> --
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> ------------
>> --
>> --------
>> 
>> ---
>>
>>
>> *should I do the VC-relax and NSCF again using QE-6.2 ??*
>>
>> Please Suggest...
>>
>> Thank you very much for your kind support.
>>
>> Sincerely,
>> B S Bhushan
>> Ph.D Scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>> On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <ecebhus...@gmail.com>
>> wrote:
>>
>>> Thank you very very much Dr. Andrea.
>>>
>>> I have a question sir...
>>> If I install the QE-6.2 on my supercomputer and run dos.x directly on
>>> the NSCF outputs produced using QE-6.1 will it work properly.
>>> Or I have to do VC-relax and NSCF again using QE-6.2.
>>>
>>> Please suggest... Your answer will save a lot of time for time.
>>>
>>> Thank you so so much for your precious time and knowledge.
>>>
>>> Sincerely,
>>> B S Bhushan
>>>
>>> On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261...@dal.ca> wrote:
>>>
>>>> I think the input to dos.x (I call it dos.in) looks like this:
>>>>
>>>>  
>>>>outdir='./'
>>>>prefix=‘graphene'
>>>>fildos=‘graphene.dos',
>>>>Emin=-10.0, Emax=16, De

Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Dear Dr. Andea Thank you so much.

Dear Dr. Lorenzo, YES I read your mail, and I replied with thanks as well.

I am facing a new problem with *QE-6.2* on my supercomputer account.

I had run a SCF for doped graphene structure with 48 atoms, and then tried
to run NSCF calculation (I wanted to calculate DOS ultimately).
The NSCF calculation stopped in between because the calculation has already*
consumed 80 GB* and the disk ran out of memory.
I am a bit surprised... because I have never seen an NSCF calculation
taking too much of memory before.
I am not getting why this case has happened.

Can any of u plz suggest.

I am very thankful for your precious time and knowledge.


Sincerely,
B S Bhushan
ABV-IIITM Gwalior, India.



On Tue, Nov 7, 2017 at 4:10 PM, Lorenzo Paulatto <paul...@gmail.com> wrote:

> Dear BS,
> Did you read my email? Was it not clear at some point?
>
> Kind regards
>
> --
> Lorenzo Paulatto
> Written on a virtual keyboard with real fingers
>
> On 7 Nov 2017 10:37 a.m., "B S Bhushan" <ecebhus...@gmail.com> wrote:
>
> Seems like the dos.x of QE-6.2 can not find xml data from NSCF produced
> using QE-6.1.
> The following error was shown,
>
> 
> 
> 
>  Program DOS v.6.2 (svn rev. 13949:13950) starts on  7Nov2017 at 13:22:50
>
>  This program is part of the open-source Quantum ESPRESSO suite
>  for quantum simulation of materials; please cite
>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>  "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>
>   URL http://www.quantum-espresso.org;,
>  in publications or presentations arising from this work. More details
> at
>  http://www.quantum-espresso.org/quote
>
>  Parallel version (MPI), running on 1 processors
>
>  MPI processes distributed on 1 nodes
>
>  %%%
> %%%
>  Error in routine pw_readschemafile (1):
>  xml data file not found
>  %%%
> %%%
>
>  stopping ...
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --
> 
> 
> -----------
>
>
> *should I do the VC-relax and NSCF again using QE-6.2 ??????*
>
> Please Suggest...
>
> Thank you very much for your kind support.
>
> Sincerely,
> B S Bhushan
> Ph.D Scholar,
> ABV-IIITM Gwalior, India.
>
>
> On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Thank you very very much Dr. Andrea.
>>
>> I have a question sir...
>> If I install the QE-6.2 on my supercomputer and run dos.x directly on the
>> NSCF outputs produced using QE-6.1 will it work properly.
>> Or I have to do VC-relax and NSCF again using QE-6.2.
>>
>> Please suggest... Your answer will save a lot of time for time.
>>
>> Thank you so so much for your precious time and knowledge.
>>
>> Sincerely,
>> B S Bhushan
>>
>> On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261...@dal.ca> wrote:
>>
>>> I think the input to dos.x (I call it dos.in) looks like this:
>>>
>>>  
>>>outdir='./'
>>>prefix=‘graphene'
>>>fildos=‘graphene.dos',
>>>Emin=-10.0, Emax=16, DeltaE=0.002
>>> /
>>>
>>> You run dos.x after the nscf run. I think the nscf.in should contain
>>> the relaxed structure.
>>>
>>> For the definition of Emin, Emax and DeltaE, see the online dos.x manual.
>>>
>>>
>>> Cheers,
>>>
>>> Vahid
>>>
>>> Vahid Askarpour
>>> Department of Physics and Atmospheric Science
>>> Dalhousie University,
>>> Halifax, NS, Canada
>>>
>>> On Nov 6, 2017, at 4:19 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>>>
>>> Dear Experts,
>>>
>>> I am trying t

Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Ok...

Thank you very much Dr. Lorenzo.

On Tue, Nov 7, 2017 at 1:38 PM, Lorenzo Paulatto <paul...@gmail.com> wrote:

> no need to do vc-relax: you do scf with the final crystal geometry, than
> nscf
>
> On 07/11/17 07:11, B S Bhushan wrote:
> > Thank you very very much Dr. Andrea.
> >
> > I have a question sir...
> > If I install the QE-6.2 on my supercomputer and run dos.x directly on
> > the NSCF outputs produced using QE-6.1 will it work properly.
> > Or I have to do VC-relax and NSCF again using QE-6.2.
> >
> > Please suggest... Your answer will save a lot of time for time.
> >
> > Thank you so so much for your precious time and knowledge.
> > Sincerely,
> > B S Bhushan
> >
> > On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261...@dal.ca
> > <mailto:vh261...@dal.ca>> wrote:
> >
> > I think the input to dos.x (I call it dos.in <http://dos.in>) looks
> > like this:
> >
> >   
> > outdir='./'
> > prefix=‘graphene'
> > fildos=‘graphene.dos',
> > Emin=-10.0, Emax=16, DeltaE=0.002
> > /
> >
> > You run dos.x after the nscf run. I think the nscf.in
> > <http://nscf.in> should contain the relaxed structure.
> >
> > For the definition of Emin, Emax and DeltaE, see the online dos.x
> > manual.
> >
> >
> > Cheers,
> >
> > Vahid
> >
> > Vahid Askarpour
> > Department of Physics and Atmospheric Science
> > Dalhousie University,
> > Halifax, NS, Canada
> >
> >> On Nov 6, 2017, at 4:19 PM, B S Bhushan <ecebhus...@gmail.com
> >> <mailto:ecebhus...@gmail.com>> wrote:
> >>
> >> Dear Experts,
> >>
> >> I am trying to extract the DOS profiles for some graphene systems
> >> using Supercomputing facility.
> >>
> >> First, I performed VC-relax and then NSCF (I have not manually
> >> updated the relaxed coordinates in the nscf input file, since nscf
> >> automatically reads them from previous scf run). Then I tried to
> >> execute dos.x, however I am getting segmentation fault error as
> >> shown below.
> >>
> >> %%
> >>  Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at
> >> 23:32:32
> >>
> >>  This program is part of the open-source Quantum ESPRESSO suite
> >>  for quantum simulation of materials; please cite
> >>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502
> >> (2009);
> >>   URL http://www.quantum-espresso.org
> >> <http://www.quantum-espresso.org/>",
> >>  in publications or presentations arising from this work. More
> >> details at
> >> http://www.quantum-espresso.org/quote
> >> <http://www.quantum-espresso.org/quote>
> >>
> >>  Parallel version (MPI), running on16 processors
> >>  R & G space division:  proc/nbgrp/npool/nimage =  16
> >>
> >>Info: using nr1, nr2, nr3 values from input
> >>
> >>Info: using nr1, nr2, nr3 values from input
> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> Image  PCRoutineLine
> >>   Source
> >> dos.x  0073A4B1  qexml_module_mp_q
> >> 3753  qexml.f90
> >> dos.x  0055AD27  pw_restart_mp_rea
> >> 2101  pw_restart.f90
> >> dos.x  005579E4  pw_restart_mp_pw_
> >> 1057  pw_restart.f90
> >> dos.x  0040A828  read_xml_file_
> >> 240  read_file.f90
> >> dos.x  00406331  MAIN__
> >>  95  dos.f90
> >> dos.x  0040621C  Unknown
> >>  Unknown  Unknown
> >> libc.so.6  003FF541ECDD  Unknown
> >>  Unknown  Unknown
> >> dos.x  00406119  Unknown
> >>  Unknown  Unknown
> >> %%
> >>
> >>
> >> I am not getting any error, if I run dos.x directly after
> >> vc-relax. However, If I run dos.x after NSCF the error appears.
> >>
> >> The input script for vc-relax, nscf are attached with the mail her

Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Seems like the dos.x of QE-6.2 can not find xml data from NSCF produced
using QE-6.1.
The following error was shown,


 Program DOS v.6.2 (svn rev. 13949:13950) starts on  7Nov2017 at 13:22:50

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
 "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
  URL http://www.quantum-espresso.org;,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Parallel version (MPI), running on 1 processors

 MPI processes distributed on 1 nodes

 %%
 Error in routine pw_readschemafile (1):
 xml data file not found
 %%

 stopping ...
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
---


*should I do the VC-relax and NSCF again using QE-6.2 ??*

Please Suggest...

Thank you very much for your kind support.

Sincerely,
B S Bhushan
Ph.D Scholar,
ABV-IIITM Gwalior, India.


On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Thank you very very much Dr. Andrea.
>
> I have a question sir...
> If I install the QE-6.2 on my supercomputer and run dos.x directly on the
> NSCF outputs produced using QE-6.1 will it work properly.
> Or I have to do VC-relax and NSCF again using QE-6.2.
>
> Please suggest... Your answer will save a lot of time for time.
>
> Thank you so so much for your precious time and knowledge.
>
> Sincerely,
> B S Bhushan
>
> On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261...@dal.ca> wrote:
>
>> I think the input to dos.x (I call it dos.in) looks like this:
>>
>>  
>>outdir='./'
>>prefix=‘graphene'
>>fildos=‘graphene.dos',
>>Emin=-10.0, Emax=16, DeltaE=0.002
>> /
>>
>> You run dos.x after the nscf run. I think the nscf.in should contain the
>> relaxed structure.
>>
>> For the definition of Emin, Emax and DeltaE, see the online dos.x manual.
>>
>>
>> Cheers,
>>
>> Vahid
>>
>> Vahid Askarpour
>> Department of Physics and Atmospheric Science
>> Dalhousie University,
>> Halifax, NS, Canada
>>
>> On Nov 6, 2017, at 4:19 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>>
>> Dear Experts,
>>
>> I am trying to extract the DOS profiles for some graphene systems using
>> Supercomputing facility.
>>
>> First, I performed VC-relax and then NSCF (I have not manually updated
>> the relaxed coordinates in the nscf input file, since nscf automatically
>> reads them from previous scf run). Then I tried to execute dos.x, however I
>> am getting segmentation fault error as shown below.
>>
>> %%
>>  Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at 23:32:32
>>
>>  This program is part of the open-source Quantum ESPRESSO suite
>>  for quantum simulation of materials; please cite
>>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>   URL http://www.quantum-espresso.org;,
>>  in publications or presentations arising from this work. More
>> details at
>>  http://www.quantum-espresso.org/quote
>>
>>  Parallel version (MPI), running on16 processors
>>  R & G space division:  proc/nbgrp/npool/nimage =  16
>>
>>Info: using nr1, nr2, nr3 values from input
>>
>>Info: using nr1, nr2, nr3 values from input
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image  PCRoutineLineSource
>> dos.x  0073A4B1  qexml_module_mp_q3753
>> qexml.f90
>> dos.x  0055AD27 

Re: [Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Thank you very very much Dr. Andrea.

I have a question sir...
If I install the QE-6.2 on my supercomputer and run dos.x directly on the
NSCF outputs produced using QE-6.1 will it work properly.
Or I have to do VC-relax and NSCF again using QE-6.2.

Please suggest... Your answer will save a lot of time for time.

Thank you so so much for your precious time and knowledge.

Sincerely,
B S Bhushan

On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261...@dal.ca> wrote:

> I think the input to dos.x (I call it dos.in) looks like this:
>
>  
>outdir='./'
>prefix=‘graphene'
>fildos=‘graphene.dos',
>Emin=-10.0, Emax=16, DeltaE=0.002
> /
>
> You run dos.x after the nscf run. I think the nscf.in should contain the
> relaxed structure.
>
> For the definition of Emin, Emax and DeltaE, see the online dos.x manual.
>
>
> Cheers,
>
> Vahid
>
> Vahid Askarpour
> Department of Physics and Atmospheric Science
> Dalhousie University,
> Halifax, NS, Canada
>
> On Nov 6, 2017, at 4:19 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
> Dear Experts,
>
> I am trying to extract the DOS profiles for some graphene systems using
> Supercomputing facility.
>
> First, I performed VC-relax and then NSCF (I have not manually updated the
> relaxed coordinates in the nscf input file, since nscf automatically reads
> them from previous scf run). Then I tried to execute dos.x, however I am
> getting segmentation fault error as shown below.
>
> %%
>  Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at 23:32:32
>
>  This program is part of the open-source Quantum ESPRESSO suite
>  for quantum simulation of materials; please cite
>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>   URL http://www.quantum-espresso.org;,
>  in publications or presentations arising from this work. More details
> at
>  http://www.quantum-espresso.org/quote
>
>  Parallel version (MPI), running on16 processors
>  R & G space division:  proc/nbgrp/npool/nimage =  16
>
>Info: using nr1, nr2, nr3 values from input
>
>Info: using nr1, nr2, nr3 values from input
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image  PCRoutineLineSource
> dos.x  0073A4B1  qexml_module_mp_q3753
> qexml.f90
> dos.x  0055AD27  pw_restart_mp_rea2101
> pw_restart.f90
> dos.x  005579E4  pw_restart_mp_pw_1057
> pw_restart.f90
> dos.x  0040A828  read_xml_file_240
> read_file.f90
> dos.x  00406331  MAIN__ 95  dos.f90
> dos.x  0040621C  Unknown   Unknown  Unknown
> libc.so.6  003FF541ECDD  Unknown   Unknown  Unknown
> dos.x  00406119  Unknown   Unknown  Unknown
> %%
>
>
> I am not getting any error, if I run dos.x directly after vc-relax.
> However, If I run dos.x after NSCF the error appears.
>
> The input script for vc-relax, nscf are attached with the mail here.
>
> I thank you very much for your precious time and knowledge.
>
>
> Sincerely,
> B S Bhushan
> Ph.D Scholar,
> ABV-IIITM Gwalior, India.
>
>
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[Pw_forum] dos.x : segmentation fault occurred

[B S Bhushan]

Dear Experts,

I am trying to extract the DOS profiles for some graphene systems using
Supercomputing facility.

First, I performed VC-relax and then NSCF (I have not manually updated the
relaxed coordinates in the nscf input file, since nscf automatically reads
them from previous scf run). Then I tried to execute dos.x, however I am
getting segmentation fault error as shown below.

%%
 Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at 23:32:32

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org;,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Parallel version (MPI), running on16 processors
 R & G space division:  proc/nbgrp/npool/nimage =  16

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1, nr2, nr3 values from input
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLineSource
dos.x  0073A4B1  qexml_module_mp_q3753
qexml.f90
dos.x  0055AD27  pw_restart_mp_rea2101
pw_restart.f90
dos.x  005579E4  pw_restart_mp_pw_1057
pw_restart.f90
dos.x  0040A828  read_xml_file_240
read_file.f90
dos.x  00406331  MAIN__ 95  dos.f90
dos.x  0040621C  Unknown   Unknown  Unknown
libc.so.6  003FF541ECDD  Unknown   Unknown  Unknown
dos.x  00406119  Unknown   Unknown  Unknown
%%


I am not getting any error, if I run dos.x directly after vc-relax.
However, If I run dos.x after NSCF the error appears.

The input script for vc-relax, nscf are attached with the mail here.

I thank you very much for your precious time and knowledge.


Sincerely,
B S Bhushan
Ph.D Scholar,
ABV-IIITM Gwalior, India.


graphene.in
Description: Binary data


graphene_nscf.in
Description: Binary data
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Re: [Pw_forum] question regarding nbnd option

[B S Bhushan]

Thank you so much Dr. chen.

On Wed, Nov 1, 2017 at 9:34 PM, Jia Chen <jiachenc...@gmail.com> wrote:

> Dear Bhushan,
>
> It refers to valance electrons here.
>
> Cheers
>
> On Wed, Nov 1, 2017 at 10:54 AM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Dear experts,
>>
>> In the manual it was given as,
>> *Default:* for an insulator, nbnd
>> <http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nbnd> =
>> number of valence bands (nbnd
>> <http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nbnd>
>>  =* # of electrons* /2);
>> for a metal, 20% more (minimum 4 more)
>>
>> My doubt here is, doest the *# of electrons* refer to valance electrons
>> or the total number of electrons (core+valance) in the structure ??
>>
>>
>> Thank you very much.
>>
>>
>> Sincerely,
>>
>> B. S. Bhushan
>> Ph.D scholar,
>> ABV-IIITM, Gwalior, India.
>>
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Re: [Pw_forum] nbnd

[B S Bhushan]

thank you so much experts.

On Wed, Nov 1, 2017 at 9:27 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> On Wed, Nov 1, 2017 at 12:08 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
> does the *# of electrons* refer to valance electrons or the total number
>> of electrons (core+valance) in the structure ?
>>
>
> valence electrons only
>
> Paolo
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
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[Pw_forum] question regarding nbnd option

[B S Bhushan]

Dear experts,

In the manual it was given as,
*Default:* for an insulator, nbnd
<http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nbnd> =
number of valence bands (nbnd
<http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nbnd>
 =* # of electrons* /2);
for a metal, 20% more (minimum 4 more)

My doubt here is, doest the *# of electrons* refer to valance electrons or
the total number of electrons (core+valance) in the structure ??


Thank you very much.


Sincerely,

B. S. Bhushan
Ph.D scholar,
ABV-IIITM, Gwalior, India.
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Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

First, I optimized the structure using LCAO code (ATK) on my local machine.
Then I submitted the same for optimization on HPC.

It worked fine. HPC shown No error.



On Tue, Oct 24, 2017 at 4:09 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> It might also be a problem of tiny numerical differences, due to different
> parallelization/compiler/libraries/phases of the moon, leading the code
> to different execution patterns. It has always been hard to pinpoint the
> origin of those errors.
>
> Paolo
>
> On Tue, Oct 24, 2017 at 10:45 AM, Giuseppe Mattioli <
> giuseppe.matti...@ism.cnr.it> wrote:
>
>>
>> Dear Bhushan
>>
>> > The calculation has successfully completed on my local server without
>> any
>> > error.
>>
>> On mine too.
>>
>> It is likely an issue arising from a compiler or a library error, and
>> it is of course *very difficult* to correct, because we have no access
>> to your hpc facility and such kind of debug is a really time-consuming
>> task. I can only suggest you to ask the hpc system administrator, to
>> tell him that an application is running fine on your local cluster
>> when compiled with a given compiler and linked against a given set of
>> libraries, and it is not on the hpc cluster.
>>
>> HTH
>> Giuseppe
>>
>> Quoting B S Bhushan <ecebhus...@gmail.com>:
>>
>> > Dear Dr.Giuseppe and Dr. Lorenzo,
>> >
>> > The calculation has successfully completed on my local server without
>> any
>> > error.
>> > However, I am not yet sure why I am getting the error on Supercomputer,
>> and
>> > how to get rid of it.
>> >
>> > Thank you.
>> >
>> >
>> > On Mon, Oct 23, 2017 at 9:54 PM, B S Bhushan <ecebhus...@gmail.com>
>> wrote:
>> >
>> >> Dear Dr. Giuseppe,
>> >>
>> >> I have already submitted the same job on a different machine (my local
>> >> server) and awaiting the result. So far I have not seen any error, yet
>> I am
>> >> awaiting the final result.
>> >>
>> >> The error I posted was actually received when I tried to perform it
>> using
>> >> a High Performance computing facility.
>> >>
>> >> I will let you know of the result from my local server.
>> >>
>> >>
>> >> On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhus...@gmail.com>
>> wrote:
>> >>
>> >>> Thank you very much for your support Dr. Lorenzo.
>> >>>
>> >>> I will try these and let you know the result.
>> >>>
>> >>> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
>> >>> ericpaula...@gmail.com> wrote:
>> >>>
>> >>>> Dear B S,
>> >>>>
>> >>>> I've had a look at your input, I see that the C-N distance is already
>> >>>> quite small at the beginning, and become even smaller after a couple
>> of
>> >>>> iteration; definitely smaller that the core radius of the two
>> >>>> pseudopotentials used, which is a typical cause of
>> >>>> diagonalisation problems.
>> >>>>
>> >>>> You should try using some harder pseudopotentials, I've attached two
>> >>>> hard pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not
>> forget
>> >>>> to cite), which should do the trick. Take care of converging the
>> cutoff.
>> >>>> UPDATE: I'm not attaching the pseudos because they don't pass in the
>> list,
>> >>>> I'm sending them privately in a minute
>> >>>>
>> >>>> Please let us know if this solves your problem!
>> >>>>
>> >>>> kind regards
>> >>>>
>> >>>> On 23/10/17 15:08, B S Bhushan wrote:
>> >>>>
>> >>>> Dear Dr. Lorenzo,
>> >>>>
>> >>>> I think the error is occurring in the 4th optimization step.
>> >>>> I have attached the output file for your reference.
>> >>>>
>> >>>>
>> >>>> Awaiting your kind response.
>> >>>> B S Bhushan
>> >>>> Ph.D Scholar,
>> >>>> ABV-IIITM Gwalior, India.
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paul...@gmail.com
>> >

Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

yes... I will.

Thank you very much for your support Dr. Giuseppe.

On Tue, Oct 24, 2017 at 2:15 PM, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear Bhushan
>
> > The calculation has successfully completed on my local server without any
> > error.
>
> On mine too.
>
> It is likely an issue arising from a compiler or a library error, and
> it is of course *very difficult* to correct, because we have no access
> to your hpc facility and such kind of debug is a really time-consuming
> task. I can only suggest you to ask the hpc system administrator, to
> tell him that an application is running fine on your local cluster
> when compiled with a given compiler and linked against a given set of
> libraries, and it is not on the hpc cluster.
>
> HTH
> Giuseppe
>
> Quoting B S Bhushan <ecebhus...@gmail.com>:
>
> > Dear Dr.Giuseppe and Dr. Lorenzo,
> >
> > The calculation has successfully completed on my local server without any
> > error.
> > However, I am not yet sure why I am getting the error on Supercomputer,
> and
> > how to get rid of it.
> >
> > Thank you.
> >
> >
> > On Mon, Oct 23, 2017 at 9:54 PM, B S Bhushan <ecebhus...@gmail.com>
> wrote:
> >
> >> Dear Dr. Giuseppe,
> >>
> >> I have already submitted the same job on a different machine (my local
> >> server) and awaiting the result. So far I have not seen any error, yet
> I am
> >> awaiting the final result.
> >>
> >> The error I posted was actually received when I tried to perform it
> using
> >> a High Performance computing facility.
> >>
> >> I will let you know of the result from my local server.
> >>
> >>
> >> On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhus...@gmail.com>
> wrote:
> >>
> >>> Thank you very much for your support Dr. Lorenzo.
> >>>
> >>> I will try these and let you know the result.
> >>>
> >>> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
> >>> ericpaula...@gmail.com> wrote:
> >>>
> >>>> Dear B S,
> >>>>
> >>>> I've had a look at your input, I see that the C-N distance is already
> >>>> quite small at the beginning, and become even smaller after a couple
> of
> >>>> iteration; definitely smaller that the core radius of the two
> >>>> pseudopotentials used, which is a typical cause of
> >>>> diagonalisation problems.
> >>>>
> >>>> You should try using some harder pseudopotentials, I've attached two
> >>>> hard pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not
> forget
> >>>> to cite), which should do the trick. Take care of converging the
> cutoff.
> >>>> UPDATE: I'm not attaching the pseudos because they don't pass in the
> list,
> >>>> I'm sending them privately in a minute
> >>>>
> >>>> Please let us know if this solves your problem!
> >>>>
> >>>> kind regards
> >>>>
> >>>> On 23/10/17 15:08, B S Bhushan wrote:
> >>>>
> >>>> Dear Dr. Lorenzo,
> >>>>
> >>>> I think the error is occurring in the 4th optimization step.
> >>>> I have attached the output file for your reference.
> >>>>
> >>>>
> >>>> Awaiting your kind response.
> >>>> B S Bhushan
> >>>> Ph.D Scholar,
> >>>> ABV-IIITM Gwalior, India.
> >>>>
> >>>>
> >>>>
> >>>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paul...@gmail.com>
> >>>> wrote:
> >>>>
> >>>>> is it at the first structural relaxation step or later? I'm afraid
> that
> >>>>> doing a vc-relax of a small supercell with a defect could cause an
> >>>>> unphysical crunch
> >>>>>
> >>>>> On 21/10/17 18:52, B S Bhushan wrote:
> >>>>>
> >>>>> Dear Expert,
> >>>>>
> >>>>> I was getting the below error while trying to vc-relax a doped
> graphene.
> >>>>> can you please suggest why is it occurring??
> >>>>>
> >>>>>
> >>>>>  iteration #  9 ecut=30.00 Ry beta=0.70
> >>>>>  Davidson diagonalization with overlap
> >>>>>
> >>

Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Dear Dr.Giuseppe and Dr. Lorenzo,

The calculation has successfully completed on my local server without any
error.
However, I am not yet sure why I am getting the error on Supercomputer, and
how to get rid of it.

Thank you.


On Mon, Oct 23, 2017 at 9:54 PM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Dear Dr. Giuseppe,
>
> I have already submitted the same job on a different machine (my local
> server) and awaiting the result. So far I have not seen any error, yet I am
> awaiting the final result.
>
> The error I posted was actually received when I tried to perform it using
> a High Performance computing facility.
>
> I will let you know of the result from my local server.
>
>
> On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Thank you very much for your support Dr. Lorenzo.
>>
>> I will try these and let you know the result.
>>
>> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
>> ericpaula...@gmail.com> wrote:
>>
>>> Dear B S,
>>>
>>> I've had a look at your input, I see that the C-N distance is already
>>> quite small at the beginning, and become even smaller after a couple of
>>> iteration; definitely smaller that the core radius of the two
>>> pseudopotentials used, which is a typical cause of diagonalisation problems.
>>>
>>> You should try using some harder pseudopotentials, I've attached two
>>> hard pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not forget
>>> to cite), which should do the trick. Take care of converging the cutoff.
>>> UPDATE: I'm not attaching the pseudos because they don't pass in the list,
>>> I'm sending them privately in a minute
>>>
>>> Please let us know if this solves your problem!
>>>
>>> kind regards
>>>
>>> On 23/10/17 15:08, B S Bhushan wrote:
>>>
>>> Dear Dr. Lorenzo,
>>>
>>> I think the error is occurring in the 4th optimization step.
>>> I have attached the output file for your reference.
>>>
>>>
>>> Awaiting your kind response.
>>> B S Bhushan
>>> Ph.D Scholar,
>>> ABV-IIITM Gwalior, India.
>>>
>>>
>>>
>>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paul...@gmail.com>
>>> wrote:
>>>
>>>> is it at the first structural relaxation step or later? I'm afraid that
>>>> doing a vc-relax of a small supercell with a defect could cause an
>>>> unphysical crunch
>>>>
>>>> On 21/10/17 18:52, B S Bhushan wrote:
>>>>
>>>> Dear Expert,
>>>>
>>>> I was getting the below error while trying to vc-relax a doped graphene.
>>>> can you please suggest why is it occurring??
>>>>
>>>>
>>>>  iteration #  9 ecut=30.00 Ry beta=0.70
>>>>  Davidson diagonalization with overlap
>>>>
>>>>  %%%
>>>> %%%
>>>>  Error in routine  cdiaghg (261):
>>>>   problems computing cholesky
>>>>  %%%
>>>> %%%
>>>>
>>>>  stopping ...
>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>>>
>>>>
>>>>
>>>>
>>>> Sincerely,
>>>>
>>>> B S Bhushan,
>>>> Ph.D scholar,
>>>> ABV-IIITM Gwalior, India.
>>>>
>>>>
>>>> ___
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>>>>
>>>> --
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>>>>
>>>>
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>>>
>>>
>>>
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Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Dear Dr. Giuseppe,

I have already submitted the same job on a different machine (my local
server) and awaiting the result. So far I have not seen any error, yet I am
awaiting the final result.

The error I posted was actually received when I tried to perform it using a
High Performance computing facility.

I will let you know of the result from my local server.


On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhus...@gmail.com> wrote:

> Thank you very much for your support Dr. Lorenzo.
>
> I will try these and let you know the result.
>
> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
> ericpaula...@gmail.com> wrote:
>
>> Dear B S,
>>
>> I've had a look at your input, I see that the C-N distance is already
>> quite small at the beginning, and become even smaller after a couple of
>> iteration; definitely smaller that the core radius of the two
>> pseudopotentials used, which is a typical cause of diagonalisation problems.
>>
>> You should try using some harder pseudopotentials, I've attached two hard
>> pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not forget to
>> cite), which should do the trick. Take care of converging the cutoff.
>> UPDATE: I'm not attaching the pseudos because they don't pass in the list,
>> I'm sending them privately in a minute
>>
>> Please let us know if this solves your problem!
>>
>> kind regards
>>
>> On 23/10/17 15:08, B S Bhushan wrote:
>>
>> Dear Dr. Lorenzo,
>>
>> I think the error is occurring in the 4th optimization step.
>> I have attached the output file for your reference.
>>
>>
>> Awaiting your kind response.
>> B S Bhushan
>> Ph.D Scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>>
>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paul...@gmail.com>
>> wrote:
>>
>>> is it at the first structural relaxation step or later? I'm afraid that
>>> doing a vc-relax of a small supercell with a defect could cause an
>>> unphysical crunch
>>>
>>> On 21/10/17 18:52, B S Bhushan wrote:
>>>
>>> Dear Expert,
>>>
>>> I was getting the below error while trying to vc-relax a doped graphene.
>>> can you please suggest why is it occurring??
>>>
>>>
>>>  iteration #  9 ecut=30.00 Ry beta=0.70
>>>  Davidson diagonalization with overlap
>>>
>>>  %%%
>>> %%%
>>>  Error in routine  cdiaghg (261):
>>>   problems computing cholesky
>>>  %%%
>>> %%%
>>>
>>>  stopping ...
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>>
>>>
>>>
>>>
>>> Sincerely,
>>>
>>> B S Bhushan,
>>> Ph.D scholar,
>>> ABV-IIITM Gwalior, India.
>>>
>>>
>>> ___
>>> Pw_forum mailing 
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>>>
>>>
>>> --
>>> Lorenzo Paulatto - Paris
>>>
>>>
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>>
>>
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Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Thank you very much for your support Dr. Lorenzo.

I will try these and let you know the result.

On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
ericpaula...@gmail.com> wrote:

> Dear B S,
>
> I've had a look at your input, I see that the C-N distance is already
> quite small at the beginning, and become even smaller after a couple of
> iteration; definitely smaller that the core radius of the two
> pseudopotentials used, which is a typical cause of diagonalisation problems.
>
> You should try using some harder pseudopotentials, I've attached two hard
> pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not forget to
> cite), which should do the trick. Take care of converging the cutoff.
> UPDATE: I'm not attaching the pseudos because they don't pass in the list,
> I'm sending them privately in a minute
>
> Please let us know if this solves your problem!
>
> kind regards
>
> On 23/10/17 15:08, B S Bhushan wrote:
>
> Dear Dr. Lorenzo,
>
> I think the error is occurring in the 4th optimization step.
> I have attached the output file for your reference.
>
>
> Awaiting your kind response.
> B S Bhushan
> Ph.D Scholar,
> ABV-IIITM Gwalior, India.
>
>
>
> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paul...@gmail.com>
> wrote:
>
>> is it at the first structural relaxation step or later? I'm afraid that
>> doing a vc-relax of a small supercell with a defect could cause an
>> unphysical crunch
>>
>> On 21/10/17 18:52, B S Bhushan wrote:
>>
>> Dear Expert,
>>
>> I was getting the below error while trying to vc-relax a doped graphene.
>> can you please suggest why is it occurring??
>>
>>
>>  iteration #  9 ecut=30.00 Ry beta=0.70
>>  Davidson diagonalization with overlap
>>
>>  %%%
>> %%%
>>  Error in routine  cdiaghg (261):
>>   problems computing cholesky
>>  %%%
>> %%%
>>
>>  stopping ...
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>
>>
>>
>>
>> Sincerely,
>>
>> B S Bhushan,
>> Ph.D scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>> ___
>> Pw_forum mailing 
>> listPw_forum@pwscf.orghttp://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> --
>> Lorenzo Paulatto - Paris
>>
>>
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>
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Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Dear Dr. Giuseppe,

Here I attached the input file for your kind reference.
Please have a look and suggest the modifications I should do in the script
for successful completion of calculation.

Awaiting your reply,

B. S. Bhushan,
Ph.D scholar,
ABV-IIITM Gwalior, India.


On Mon, Oct 23, 2017 at 12:40 AM, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Then you are more entitled than me in providing useful and detailed
> instructions to new and inexperienced users that may help solving
> their problems, rather than generic and not very useful statements.
> Sincerely
> Giuseppe
>
> Jalil Mahdizadeh <saja.mahdiza...@gmail.com> ha scritto:
>
> > The most strangest thing is that you believe there are just 1 reason for
> > broblem in diagolalization. I can write a whole book chapter about the
> > possible causes.
> >
> > --
> > S. J. Mahdizadeh
> >
> > On Oct 22, 2017 4:33 PM, "Giuseppe Mattioli" <
> giuseppe.matti...@ism.cnr.it>
> > wrote:
> >
> >>
> >> Dear Bhushan
> >> Please forget about strange suggestions received in previous messages.
> >> Difficulties in diagonalization such as that reported in your message
> >> depend almost always on 1) badly wrong structures and/or 2) poor
> >> convergence of basis set. It is impossible to say more if you don't
> >> attach any input file, and this should definitely be the best practice
> >> when reporting errors and/or asking for help in this forum.
> >> HTH
> >> Giuseppe
> >>
> >> B S Bhushan <ecebhus...@gmail.com> ha scritto:
> >>
> >> > Dear Expert,
> >> >
> >> > I was getting the below error while trying to vc-relax a doped
> graphene.
> >> > can you please suggest why is it occurring??
> >> >
> >> >
> >> >  iteration #  9 ecut=30.00 Ry beta=0.70
> >> >  Davidson diagonalization with overlap
> >> >
> >> >
> >> > 
> >> %%
> >> >  Error in routine  cdiaghg (261):
> >> >   problems computing cholesky
> >> >
> >> > %%%%%%%%%%%%
> >> %%
> >> >
> >> >  stopping ...
> >> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
> >> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
> >> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
> >> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> >> >
> >> >
> >> >
> >> >
> >> > Sincerely,
> >> >
> >> > B S Bhushan,
> >> > Ph.D scholar,
> >> > ABV-IIITM Gwalior, India.
> >>
> >>
> >>
> >> GIUSEPPE MATTIOLI
> >> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >> Via Salaria Km 29,300 - C.P. 10
> >> I-00015 - Monterotondo Scalo (RM)
> >> Mob (*preferred*) +39 373 7305625
> >> Tel + 39 06 90672342 - Fax +39 06 90672316
> >> E-mail: <giuseppe.matti...@ism.cnr.it>
> >>
> >> ___
> >> Pw_forum mailing list
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> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.matti...@ism.cnr.it>
>
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PnP_new.in
Description: Binary data
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Re: [Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Ok sir.

thank you.

On Sun, Oct 22, 2017 at 6:10 PM, Dr. K. C. Bhamu 
wrote:

>
> Dear Bushan,
>
> Please check your wall time.
>
> Regards
> Bhamu
>
>
> Dr. K. C. Bhamu
> National Postdoctoral Fellow,
> Physical and Materials Chemistry Division
> Mob. No.  +91-9975238952
>
>
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[Pw_forum] Error optmizing doped graphene

[B S Bhushan]

Dear Expert,

I was getting the below error while trying to vc-relax a doped graphene.
can you please suggest why is it occurring??


 iteration #  9 ecut=30.00 Ry beta=0.70
 Davidson diagonalization with overlap

 %%
 Error in routine  cdiaghg (261):
  problems computing cholesky
 %%

 stopping ...
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2




Sincerely,

B S Bhushan,
Ph.D scholar,
ABV-IIITM Gwalior, India.
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Re: [Pw_forum] starting magnetization in nitrogen doped graphene

[B S Bhushan]

Thank you so much Dr. Jiabiao Li

On Thu, Oct 5, 2017 at 5:30 PM, Jibiao Li <jibia...@foxmail.com> wrote:

> Dear B. SanthiBhushan,
>
> As far as your doped configuration is concerned, I guess the use of 0.5 or
> 0.1 as the initial magmom. would not change the final results. To get a
> magnetic ground state, you need to try with paramagnetic and
> antiparamagnetic couplings in the doped structure. I guess the magnetism is
> quite weak.
>
> Best
>
> Jibiao Li
>
>
> ---------- Original --
> *From: * "B S Bhushan";<ecebhus...@gmail.com>;
> *Date: * Thu, Oct 5, 2017 08:25 PM
> *To: * "PWSCF Forum"<pw_forum@pwscf.org>;
> *Subject: * Re: [Pw_forum] starting magnetization in nitrogen doped
> graphene
>
> Dear Dr. Jibiao Li,
>
>
> Can u please briefly explain how the value of starting_magnetization
> affects the calculation.
> What happens if the starting magnetization set to 0.5 instead of 0.1 ?.
> Does it show any impact on the accuracy or computational time?
>
>
> I thank you very much for your precious time and knowledge.
>
>
> Sincerely,
> B. SanthiBhushan,
> Ph.D research scholar,
> ABV-IIITM, Gwalior, India.
>
>
> On Thu, Oct 5, 2017 at 5:18 PM, Jibiao Li <jibia...@foxmail.com> wrote:
>
>> Dear B. SanthiBhushan,
>>
>> Yes, Simply set initial magnetic moments by starting_magnetization(1) and
>> starting_magnetizaiton(2) for carbon and nitrogen. I guess 0.1 is
>> sufficient for any doping configurations in your case.
>>
>> Best
>>
>> Jibiao Li
>>
>>
>> -- Original --
>> *From: * "B S Bhushan";<ecebhus...@gmail.com>;
>> *Date: * Thu, Oct 5, 2017 08:03 PM
>> *To: * "PWSCF Forum"<pw_forum@pwscf.org>;
>> *Subject: * [Pw_forum] starting magnetization in nitrogen doped graphene
>>
>> Dear Experts,
>>
>> I am completely new to spin polarized calculations using QE.
>>
>> I am trying to simulate nitrogen doped graphene (image attached below)
>> considering spin polarization. I have got the below two questions.
>>
>> I have set nspin=2.
>>
>> Q1)  Now, should I have to set starting magnetization for both carbon and
>> nitrogen atomic types (like starting_magnetization(1)=0.5,
>> starting_magnetizaiton(2)=0.5) ?
>>
>> Or mentioning starting magnetization for atomic type carbon is enough
>> (like starting_magnetizaiton(1)=0.5) ?
>>
>> Q2) How to decide the value of starting magnetization ? is it random ?
>> 0.5 considered in my case is enough or not ?
>>
>> I thank you very much for your precious time and knowledge.
>>
>>
>> Sincerely,
>> B. SanthiBhushan,
>> Ph.D research scholar,
>> ABV-IIITM, Gwalior, India.
>>
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Re: [Pw_forum] starting magnetization in nitrogen doped graphene

[B S Bhushan]

Dear Dr. Jibiao Li,


Can u please briefly explain how the value of starting_magnetization
affects the calculation.
What happens if the starting magnetization set to 0.5 instead of 0.1 ?.
Does it show any impact on the accuracy or computational time?


I thank you very much for your precious time and knowledge.


Sincerely,
B. SanthiBhushan,
Ph.D research scholar,
ABV-IIITM, Gwalior, India.


On Thu, Oct 5, 2017 at 5:18 PM, Jibiao Li <jibia...@foxmail.com> wrote:

> Dear B. SanthiBhushan,
>
> Yes, Simply set initial magnetic moments by starting_magnetization(1) and
> starting_magnetizaiton(2) for carbon and nitrogen. I guess 0.1 is
> sufficient for any doping configurations in your case.
>
> Best
>
> Jibiao Li
>
>
> -- Original --
> *From: * "B S Bhushan";<ecebhus...@gmail.com>;
> *Date: * Thu, Oct 5, 2017 08:03 PM
> *To: * "PWSCF Forum"<pw_forum@pwscf.org>;
> *Subject: * [Pw_forum] starting magnetization in nitrogen doped graphene
>
> Dear Experts,
>
> I am completely new to spin polarized calculations using QE.
>
> I am trying to simulate nitrogen doped graphene (image attached below)
> considering spin polarization. I have got the below two questions.
>
> I have set nspin=2.
>
> Q1)  Now, should I have to set starting magnetization for both carbon and
> nitrogen atomic types (like starting_magnetization(1)=0.5,
> starting_magnetizaiton(2)=0.5) ?
>
> Or mentioning starting magnetization for atomic type carbon is enough
> (like starting_magnetizaiton(1)=0.5) ?
>
> Q2) How to decide the value of starting magnetization ? is it random ? 0.5
> considered in my case is enough or not ?
>
> I thank you very much for your precious time and knowledge.
>
>
> Sincerely,
> B. SanthiBhushan,
> Ph.D research scholar,
> ABV-IIITM, Gwalior, India.
>
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[Pw_forum] starting magnetization in nitrogen doped graphene

[B S Bhushan]

Dear Experts,

I am completely new to spin polarized calculations using QE.

I am trying to simulate nitrogen doped graphene (image attached below)
considering spin polarization. I have got the below two questions.

I have set nspin=2.

Q1)  Now, should I have to set starting magnetization for both carbon and
nitrogen atomic types (like starting_magnetization(1)=0.5,
starting_magnetizaiton(2)=0.5) ?

Or mentioning starting magnetization for atomic type carbon is enough (like
starting_magnetizaiton(1)=0.5) ?

Q2) How to decide the value of starting magnetization ? is it random ? 0.5
considered in my case is enough or not ?

I thank you very much for your precious time and knowledge.


Sincerely,
B. SanthiBhushan,
Ph.D research scholar,
ABV-IIITM, Gwalior, India.
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Re: [Pw_forum] wave function cutoff range for pseudopotentials

[B S Bhushan]

Thank you Dr. Tan.

On Thu, Aug 24, 2017 at 5:36 PM, Tan Hengxin <tanh...@gmail.com> wrote:

> Dear Bhushan,
>
> The best cutoff energy should be the well tested one, which satisfies your
> requests. Generally, I would use the largest cutoff energy for the
> wavefunction in the pseudopotential files as the start point.
>
> I don't think there is a very clear boundary line between uspp and ncpp,
> and, the energy range of ncpp can also be very large. Generally, ncpp would
> be more expensive than uspp.
> What kind of pseudopotential you use should depend on your request again.
> Nobody requires that you must us this or that kind of pseudopotential. The
> one that gives the real physics is the best one.
>
> Best,
> Tan
> THU
>
> On Thu, Aug 24, 2017 at 7:33 PM, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Dear Experts,
>>
>> I'm new to Quantum Espresso. As a starter, I have got few questions while
>> performing simulations.
>>
>> (1) In what range the wavefunction cutoff range for Ultrasoft,
>> normconserving and PAW pseudopotentials lies?
>> I read on google that, for ultrasoft pseudopotentials the wavefunction
>> cutoff ranges from 20-50 Ry, while for norm-conserving pseudopotentials it
>> is from 60-100 Ry. Is it correct ?. or the norm-conserving pseudopotentials
>> can also have range starting from 20-100 Ry ?.
>>
>> (2) I am simulating defects in graphene. Which pseudopotential should I
>> prefer for graphene, Ultrasoft or Norm-conserving or PAW ?
>>
>>
>> I am really thankful for your valuable time and knowledge.
>>
>> Thank you.
>>
>>
>> Sincerely,
>> B. S. Bhushan,
>> CNT Laboratory,
>> ABV - Indian Institute of Information Technology and Management,
>> Gwalior, India.
>>
>>
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>
>
>
> --
>
> Tan Hengxin
> Department of physics, THU.
> Beijing 100084, China
> Office: B403,New Science Building
> E-mail:t <e-mail%3ath...@mails.tsinghua.edu.cn>anh...@gmail.com
>
>
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[Pw_forum] wave function cutoff range for pseudopotentials

[B S Bhushan]

Dear Experts,

I'm new to Quantum Espresso. As a starter, I have got few questions while
performing simulations.

(1) In what range the wavefunction cutoff range for Ultrasoft,
normconserving and PAW pseudopotentials lies?
I read on google that, for ultrasoft pseudopotentials the wavefunction
cutoff ranges from 20-50 Ry, while for norm-conserving pseudopotentials it
is from 60-100 Ry. Is it correct ?. or the norm-conserving pseudopotentials
can also have range starting from 20-100 Ry ?.

(2) I am simulating defects in graphene. Which pseudopotential should I
prefer for graphene, Ultrasoft or Norm-conserving or PAW ?


I am really thankful for your valuable time and knowledge.

Thank you.


Sincerely,
B. S. Bhushan,
CNT Laboratory,
ABV - Indian Institute of Information Technology and Management,
Gwalior, India.
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Re: [Pw_forum] nbnd option

[B S Bhushan]

Thank you Dr. Mattioli,

I missed it some how.

On Wed, Jun 21, 2017 at 7:11 PM, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear B S Bhushan
> Manuals often contain answers!
>
>Variable:   nbnd
>
>Type:   INTEGER
>*Default*:for an insulator, nbnd = number of valence bands
>(nbnd = # of electrons /2);
>for a metal, 20% more (minimum 4 more)
>Description:number of electronic states (bands) to be calculated.
>Note that in spin-polarized calculations the number of
>k-point, not the number of bands per k-point, is doubled
>
> HTH
> Giuseppe
>
> P.S. Please sign all the posts to the forum with name and affiliation.
>
> On Wednesday, June 21, 2017 07:02:59 PM B S Bhushan wrote:
> > Dear experts,
> >
> > What happens if the nbnd option is not mentioned in the script ?.
> > Do the code considers all possible valence bands in such situation ?.
> >
> > Thank you very much for your time.
> >
> > with sincere regards,
> > B S Bhushan
>
> 
> - Article premier - Les hommes naissent et demeurent
> libres et égaux en droits. Les distinctions sociales
> ne peuvent être fondées que sur l'utilité commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la liberté,
> la propriété, la sûreté et la résistance à l'oppression.
> 
>
>Giuseppe Mattioli
>CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>v. Salaria Km 29,300 - C.P. 10
>I 00015 - Monterotondo Stazione (RM), Italy
>Tel + 39 06 90672342 - Fax +39 06 90672316
>E-mail: <giuseppe.matti...@ism.cnr.it>
>http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
>ResearcherID: F-6308-2012
>
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[Pw_forum] nbnd option

[B S Bhushan]

Dear experts,

What happens if the nbnd option is not mentioned in the script ?.
Do the code considers all possible valence bands in such situation ?.

Thank you very much for your time.

with sincere regards,
B S Bhushan
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Re: [Pw_forum] Tetrahedra occupations not provided for NSCF and DOS

[B S Bhushan]

Dear Dr. Lorenzo,

Thank you very much for such a clear explanation. You saved my 20 days of
work.

Regarding the second passage of your reply, I have also extracted the
electronic DOS of graphene with tetrahedra occupations and the resultant
DOS is fine.

Thank you very much Dr for your precious time.



On Wed, May 24, 2017 at 12:22 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> Dear Bushan,
> it is perfectly fine. Actually, smearing is in general more reliable and
> better tested than tetrahedra. The latter can be more efficient, it may
> give nicer picture for the density of states (DOS), and avoids introducing
> an arbitrary smearing value.
>
> In particular, in the case of graphene, using tetrahedra can be plain
> wrong; if I remember correctly it does not work properly for 2D systems.
> This is quite obvious when doing the phonon DOS, that does not go to zero
> at zero frequency, as it should. I don't know if it is a problem also for
> the electronic DOS.
>
>
> On 24 May 2017 at 08:41, B S Bhushan <ecebhus...@gmail.com> wrote:
>
>> Dear QE experts,
>>
>> I have extracted DOS of a 50 atom graphene system.
>> While performing SCF I have considered occupations=smearing, smearing=mv,
>> degauss=0.005.
>> However, while performing "NSCF", I forgot to change the occupations to
>> Tetrahedra and left the occupations option same as in SCF
>> (occupations=smearing, smearing=mv, degauss=0.005).
>>
>> My doubt is, Is it OK to have non-tetrahedra occupations for NSCF ?.
>> Can I proceed to further calculations on the basis of obtained DOS for
>> this system?
>>
>> Thank you very much giving your precious time.
>>
>> your's sincerely,
>> B S Bhushan
>>
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>
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 442 79822 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/421 Boîte courrier 115, 4 place Jussieu 75252 Paris CX 05
>
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[Pw_forum] Tetrahedra occupations not provided for NSCF and DOS

[B S Bhushan]

Dear QE experts,

I have extracted DOS of a 50 atom graphene system.
While performing SCF I have considered occupations=smearing, smearing=mv,
degauss=0.005.
However, while performing "NSCF", I forgot to change the occupations to
Tetrahedra and left the occupations option same as in SCF
(occupations=smearing, smearing=mv, degauss=0.005).

My doubt is, Is it OK to have non-tetrahedra occupations for NSCF ?.
Can I proceed to further calculations on the basis of obtained DOS for this
system?

Thank you very much giving your precious time.

your's sincerely,
B S Bhushan
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[Pw_forum] Tetrahedra occupations not provided for DOS.

[B S Bhushan]

Dear QE experts,

I have extracted DOS of a 50 atom graphene system.
While performing SCF I have considered occupations=smearing, smearing=mv,
degauss=0.005.
However, while performing "NSCF", I forgot to change the occupations to
Tetrahedra and left the occupations option same as in SCF
(occupations=smearing, smearing=mv, degauss=0.005).

My doubt is, Is it OK to have non-tetrahedra occupations for NSCF ?.
Can I proceed to further calculations on the basis of obtained DOS for this
system?

Thank you very much giving your precious time.

your's sincerely,
B S Bhushan
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