[Pw_forum] XSpectra and US or PAW pseudos?
Matteo Calandra
matteo.calandra at impmc.jussieu.fr
Sun Aug 30 17:56:36 CEST 2015
Dear Adrian,
you seem to have two different problems. The first one concerns
the different version of QE (5.0.2 and 5.2.0). In this case you say that the
xanes.dat is useless. I do not understand what do you mean.
I downloaded the two directories you post and in one (5.2.0) there is a
file labeled
default.dat that hardly differs from the one in (5.0.2) labeled xanes.dat.
I did xmgrace of the two files and I cannot spot any difference.
So I do not understand this point.
Independently of this, you should anyway be aware
(and so must the XSpextra users) that
a bug has been introduced in the 5.1.2 and in the 5.2.0, so in this case
it is better either to usethe 5.0.2 or the SVN where the bug is
corrected. Still I do not think that this bug is relevant for you.
Concerning the segmentation fault that you are getting.
In my opinion (even if I do not have all the informations) this occurs as
you are using pseudopotentials with no gipaw reconstruction data.
As you notice,the sigsev occurs in read_recon, the routine that reads
GIPAW reconstruction
data.
In Quantum Espresso there are three kind of pseudopotentials,
Norm Conserving (NC), Ultrasoft (US) and PAW.
XSpectra is not compatible with PAW. So you cannot use them.
NC and US can be used. However they need to include GIPAW
information (Gauge Invariant Projected Augmented Wave).
If you take any pseudo from the pseudo library you won't get
any GIPAW data in the pseudo. You need to regenerate the pseudopotential
and include GIPAW projectors.
You can find information on how to include GIPAW data in a US or NC
pseudopotential here:
ftp://ftp.impmc.jussieu.fr/pub/users/calandra/Trieste_2012/
the file is Lecture_XAS.pptx
It is a quite old set of lectures (2012) but it should still be fine.
Please remember that all atomic species (and not only the absorbing
atom, i.e. the one with the core hole) need to have GIPAW data.
Also note that at least two GIPAW projectors / angular momentum
channel are needed to have converged spectra in the energy region
[e_f, e_f+40 eV]. More if you need to converge the spectrum to higher
energies.
I hope this solves your problems.
Matteo
Le 29/08/2015 12:00, pw_forum-request at pwscf.org a écrit :
>
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 28 Aug 2015 12:34:19 +0200
> From: Adrian H?hn <adrian.huehn at thch.uni-bonn.de>
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <55E0392B.7080908 at thch.uni-bonn.de>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hello Delphine,
>
> thanks for your quick reply! This seems to be a contradiction to my
> observations. Maybe I did not write this in detail, but I was only able
> to get sensible results when calculating diamond USPP spectra with
> v.5.0.2. The same setup fails with the recent v.5.2.0. To be more
> specific: Both PWscf and the XSspectra calculations run on both
> versions, but the data from "xanes.dat" is useless on the recent 5.2.0.
> I uploaded the setups.
> http://www.file-upload.net/download-10870211/diamondh_uspp_5.0.2.tar.gz.html
> http://www.file-upload.net/download-10870213/diamondh_uspp_5.2.0.tar.gz.html
>
> Concerning my problem with periclase or magnesium pseudopotentials (my
> last trials are with NC): do you think this could also trigger the
> segmentation fault?
> I recompiled QE 5.0.2 without parallelization (./configure
> --disable-parallel) but this does not make any difference.
>
> At I deeper look I can see, that the code fails at the same point,
> perhaps when "paw_recon(xiabs)" is accessed.
> espresso-5.0.2/XSpectra/src/xspectra.f90:461 or
> espresso-5.2.0/XSpectra/src/xspectra.f90:592
> [code]
> 456 !
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> 457 ! Reads reconstruction files
> 458 !
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
> 459
> 460 CALL read_core_abs(filecore,core_wfn)
> 461 IF ( .NOT. paw_recon(xiabs)%gipaw_data_in_upf_file ) &
> ! SEGFAULT !
> 462 CALL read_recon ( filerecon(xiabs), xiabs, paw_recon(xiabs)
> ) !*apsi
> [\code]
>
>
>
> Am 28.08.2015 um 00:56 schrieb Delphine Cabaret:
>> Dear Adrian,
>>
>> Concerning your first question, v.5.0.2 contains a bug related to the
>> parallelization
>> that could be at the origin of the regression you observed.
>> This bug has been corrected in the version available on the SVN.
>> I suggest you to go on with the v.5.0.2 for the moment.
>>
>> Regards
>>
>> D. Cabaret
>>
>>
>> Le 27/08/2015 21:58, Adrian H?hn a ?crit :
>>> Dear Developers and Users,
>>>
>>> when using XSpectra everything goes fine when go through the following
>>> tutorial:
>>> http://www.ictp.it/~rgebauer/Matteo_XAS.tar.gz
>>> going further I could nicely reproduce the experimental carbon K-edge
>>> X-ray absorption spectrum using PBE.
>>> I could also generate spectra using this US pseudopotential:
>>> http://theossrv1.epfl.ch/uploads/Main/NoBackup/pbe.0.3.1.tgz
>>> (of course it was also modified to generate the core-hole). Here seems
>>> to be a regression when using the latest version 5.2.0. At least I only
>>> got consistent results, when using v.5.0.2.
>>>
>>> Next I wanted to calculate the magnesium K-edge in Periclase. I tested
>>> the Mg pseudopotentials from the pslibraries, thereunder the NC and the
>>> USPP variants. BOTH lead to a segfault. I already messed with th
>>> generation parameters of the Mg pseudopotential and changed the
>>> r_paw(1)-parameter in the XSpectra input but no avail.
>>> I built QE with GCC 5.2 under Arch Linux on my local machine, but the
>>> problem applies at our cluster (using the Intel compiler) as well.
>>> Did I miss anything? The Inputs and results are added to the archives.
>>>
>>> I firstly planned to calculate Mg K-edge spectra of MgO2 species on a
>>> Au(111)-surface using PAW pseudopotentials, but I am willing to use USPP
>>> or NCPP if they work better with XSpectra.
>>>
>>> Regards
>>> Adrian Huehn
>>>
>>>
>>> Mulliken Institute for Theoretical Chemistry
>>> University of Bonn
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 28 Aug 2015 11:09:47 +0000 (UTC)
> From: Yevgen Melikhov <melikhovyy at yahoo.com>
> Subject: [Pw_forum] XSpectra and US or PAW pseudos?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <835045780.2539875.1440760187563.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Adrian,
> Sorry, I did not get from your email whether you used PAW pseudopotential?Did you try the one available on http://www.quantum-espresso.org/pseudopotentials/ , i.e. the one Mg.pbe-nsp-bpaw.UPF
> Also, you are able to perform SCF calculations, are not you? With hole and without?
> What is the output of upf2plotcore.sh looks reasonable?
> Good luck,Yevgen.
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> ------------------------------
>
> Message: 3
> Date: Fri, 28 Aug 2015 14:02:52 +0200
> From: Adrian H?hn <adrian.huehn at thch.uni-bonn.de>
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
> To: Yevgen Melikhov <melikhovyy at yahoo.com>, PWSCF Forum
> <pw_forum at pwscf.org>
> Message-ID: <55E04DEC.7000905 at thch.uni-bonn.de>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Yevgen
>
> I did many convergency tests (using PWscf) on MgO and MgO2 using various
> PAW pseudopotentials (all without core-hole). All successfully. As I was
> not able to do any PAW XSpectra calculations on the diamond-testbed my
> last trials are based on NC and US pseudopotentials. This
> Mg.pbe-nsp-bpaw.UPF
> <http://www.quantum-espresso.org/wp-content/uploads/upf_files/Mg.pbe-nsp-bpaw.UPF>
> was the file I used for my first calculations. I have no idea how I
> modify it using ATOMPAW because until now I used ld1 for PP generation,
> so I excluded it until now.
>
> The upf2plotcore.sh script does not work with recent UPF versions so my
> tries are based on the wave function of the ld1.x calculation.
>
> Thanks for your kind help
> Adrian
>
> Am 28.08.2015 um 13:09 schrieb Yevgen Melikhov:
>> Dear Adrian,
>>
>> Sorry, I did not get from your email whether you used PAW pseudopotential?
>> Did you try the one available on
>> http://www.quantum-espresso.org/pseudopotentials/ , i.e. the one
>> Mg.pbe-nsp-bpaw.UPF
>> <http://www.quantum-espresso.org/wp-content/uploads/upf_files/Mg.pbe-nsp-bpaw.UPF>
>>
>> Also, you are able to perform SCF calculations, are not you? With hole
>> and without?
>>
>> What is the output of upf2plotcore.sh looks reasonable?
>>
>> Good luck,
>> Yevgen.
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
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> ------------------------------
>
> Message: 4
> Date: Fri, 28 Aug 2015 17:37:40 +0430
> From: Elham <e.chemistry83 at gmail.com>
> Subject: Re: [Pw_forum] Choice of Pseudopotential
> To: pw_forum at pwscf.org
> Message-ID:
> <CAMCFADShTEWMpYeCUog0SV-4V6MmzYO3H7dyykMb-wqeKQMOMA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Dr. Youssef
>
> Thanks so much.
>
> Elham Ashori
>
> Ph.D. student of Physical Chemistry
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> ------------------------------
>
> Message: 5
> Date: Fri, 28 Aug 2015 13:36:07 +0000 (UTC)
> From: Yevgen Melikhov <melikhovyy at yahoo.com>
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
> To: Adrian H?hn <adrian.huehn at thch.uni-bonn.de>, PWSCF Forum
> <pw_forum at pwscf.org>
> Message-ID:
> <492818802.2649245.1440768967270.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Adrian,
>
> Sorry, I was confused whether the problem you referred was during <pw.x> calculations (using Mg pseudopotential) or during <xspectra.x> calculations. Now it is clearer. Sorry that I cannot help you in this!
>
> Good luck,Yevgen.
>
> Institute of Physics PASWarsaw, Poland
>
> From: Adrian H?hn <adrian.huehn at thch.uni-bonn.de>
> To: Yevgen Melikhov <melikhovyy at yahoo.com>; PWSCF Forum <pw_forum at pwscf.org>
> Sent: Friday, 28 August 2015, 14:02
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
>
> Dear Yevgen
>
> I did many convergency tests (using PWscf) on MgO and MgO2 using various PAW pseudopotentials (all without core-hole). All successfully. As I was not able to do any PAW XSpectra calculations on the diamond-testbed my last trials are based on NC and US pseudopotentials. This Mg.pbe-nsp-bpaw.UPF was the file I used for my first calculations. I have no idea how I modify it using ATOMPAW because until now I used ld1 for PP generation, so I excluded it until now.
>
> The upf2plotcore.sh script does not work with recent UPF versions so my tries are based on the wave function of the ld1.x calculation.
>
> Thanks for your kind help
> Adrian
>
> Am 28.08.2015 um 13:09 schrieb Yevgen Melikhov:
>
>
>
> Dear Adrian,
> Sorry, I did not get from your email whether you used PAW pseudopotential? Did you try the one available on http://www.quantum-espresso.org/pseudopotentials/ , i.e. the one Mg.pbe-nsp-bpaw.UPF
> Also, you are able to perform SCF calculations, are not you? With hole and without?
> What is the output of upf2plotcore.sh looks reasonable?
> Good luck, Yevgen.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
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> ------------------------------
>
> Message: 6
> Date: Fri, 28 Aug 2015 21:00:55 +0430
> From: Mojtaba Mirseraji <quantum.pwscf at gmail.com>
> Subject: Re: [Pw_forum] sh: 1: Error in running of ElaStic code
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPw9g84eNYoZJxA49GJW4QJvxcac6OGZ-UqmQihZfdz9FCLgAQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Bahadir Salmankurt
>
> Yes, I have read it and sgroup is carried out correctly but when I run
> the "Elastic_Setup_Espresso", that error was occurred, unfortunately
> !!!!!
>
> Thanks
>
> Mojtaba
>
> On 8/27/15, Bahad?r salmankurt <bsalmankurt at gmail.com> wrote:
>> Dear Mojtaba Mirseraji
>>
>> Did you read 'READ ME'? There is the explanation about sgroup in README.
>>
>>
>> Regards
>>
>>
>> 2015-08-27 21:23 GMT+03:00 Mojtaba Mirseraji <quantum.pwscf at gmail.com>:
>>
>>> Dear Bahadir
>>>
>>> I could solve the problem but a new problem has occured:
>>>
>>> ".... Oops sh: 1: sgroup: not found."
>>>
>>> How to solve it?
>>>
>>> Thanks
>>>
>>> Mojtaba Mirseraji
>>> Ph.D. Candidate
>>> Department of Physics
>>> Arak Univ.
>>> IRAN
>>>
>>>
>>> On 8/25/15, Bahad?r salmankurt <bsalmankurt at gmail.com> wrote:
>>>> Dear Mojtaba Mirseraji
>>>>
>>>> please add these line to .bashrc
>>>>
>>>> export PATH=$PATH:$Elas-tic:.
>>>>
>>>> export BERRYPI_PATH=$Elas-tic/SRC_BerryPI/BerryPI
>>>>
>>>> export BERRYPI_PYTHON=/usr/bin/python3.2 ===> change version according
>>> to
>>>> yours.
>>>>
>>>> alias berrypi="${BERRYPI_PYTHON} ${BERRYPI_PATH}/berrypi"
>>>>
>>>>
>>>> if you overcome this problem then another problem occur -if happen -,
>>> type
>>>> this to command line
>>>>
>>>>
>>>> *sudo apt-get install python-numpy python-scipy python-matplotlib
>>>> ipython
>>>> ipython-notebook python-pandas python-sympy python-nose*
>>>>
>>>>
>>>> Bests
>>>>
>>>> Bahadir
>>>>
>>>> Sakarya University, TURKEY
>>>>
>>>> 2015-08-25 19:27 GMT+03:00 Mojtaba Mirseraji <quantum.pwscf at gmail.com>:
>>>>
>>>>> Dear All
>>>>>
>>>>> I run ./sgroup successfully but when I want to use:
>>>>> ./Elastic_Setup
>>>>>
>>>>> I face to this error:
>>>>>
>>>>> ".... Oops sh: 1: Elastic_Setup_Espresso: not found."
>>>>>
>>>>> but I see the code of Elastic_Setup_Espresso !!!!
>>>>>
>>>>> I do not know why this problem happens!!!
>>>>> Please help me
>>>>> you can find this code:
>>>>> http://exciting-code.org/elastic
>>>>>
>>>>>
>>>>> Regards
>>>>>
>>>>> Mojtaba Mirseraji
>>>>> Ph.D. Candidate
>>>>> Department of Physics
>>>>> Arak Univ.
>>>>> IRAN
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 28 Aug 2015 18:31:03 +0200
> From: Delphine Cabaret <delphine.cabaret at impmc.upmc.fr>
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <55E08CC7.5010904 at impmc.upmc.fr>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hello Adrian
>
> You are right about the contradiction because I wrote v5.0.2 twice in
> my email and I apologize for it (it was late). To be clear, it is the
> version v.5.2.0. that contains a bug. Thus it is better to use the v5.0.2.
>
> Regards
>
> Delphine
>
> Le 28/08/2015 12:34, Adrian H?hn a ?crit :
>> Hello Delphine,
>>
>> thanks for your quick reply! This seems to be a contradiction to my
>> observations. Maybe I did not write this in detail, but I was only able
>> to get sensible results when calculating diamond USPP spectra with
>> v.5.0.2. The same setup fails with the recent v.5.2.0. To be more
>> specific: Both PWscf and the XSspectra calculations run on both
>> versions, but the data from "xanes.dat" is useless on the recent 5.2.0.
>> I uploaded the setups.
>> http://www.file-upload.net/download-10870211/diamondh_uspp_5.0.2.tar.gz.html
>> http://www.file-upload.net/download-10870213/diamondh_uspp_5.2.0.tar.gz.html
>>
>> Concerning my problem with periclase or magnesium pseudopotentials (my
>> last trials are with NC): do you think this could also trigger the
>> segmentation fault?
>> I recompiled QE 5.0.2 without parallelization (./configure
>> --disable-parallel) but this does not make any difference.
>>
>> At I deeper look I can see, that the code fails at the same point,
>> perhaps when "paw_recon(xiabs)" is accessed.
>> espresso-5.0.2/XSpectra/src/xspectra.f90:461 or
>> espresso-5.2.0/XSpectra/src/xspectra.f90:592
>> [code]
>> 456 !
>> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>> 457 ! Reads reconstruction files
>> 458 !
>> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>>
>> 459
>> 460 CALL read_core_abs(filecore,core_wfn)
>> 461 IF ( .NOT. paw_recon(xiabs)%gipaw_data_in_upf_file ) &
>> ! SEGFAULT !
>> 462 CALL read_recon ( filerecon(xiabs), xiabs, paw_recon(xiabs)
>> ) !*apsi
>> [\code]
>>
>>
>>
>> Am 28.08.2015 um 00:56 schrieb Delphine Cabaret:
>>> Dear Adrian,
>>>
>>> Concerning your first question, v.5.0.2 contains a bug related to the
>>> parallelization
>>> that could be at the origin of the regression you observed.
>>> This bug has been corrected in the version available on the SVN.
>>> I suggest you to go on with the v.5.0.2 for the moment.
>>>
>>> Regards
>>>
>>> D. Cabaret
>>>
>>>
>>> Le 27/08/2015 21:58, Adrian H?hn a ?crit :
>>>> Dear Developers and Users,
>>>>
>>>> when using XSpectra everything goes fine when go through the following
>>>> tutorial:
>>>> http://www.ictp.it/~rgebauer/Matteo_XAS.tar.gz
>>>> going further I could nicely reproduce the experimental carbon K-edge
>>>> X-ray absorption spectrum using PBE.
>>>> I could also generate spectra using this US pseudopotential:
>>>> http://theossrv1.epfl.ch/uploads/Main/NoBackup/pbe.0.3.1.tgz
>>>> (of course it was also modified to generate the core-hole). Here seems
>>>> to be a regression when using the latest version 5.2.0. At least I only
>>>> got consistent results, when using v.5.0.2.
>>>>
>>>> Next I wanted to calculate the magnesium K-edge in Periclase. I tested
>>>> the Mg pseudopotentials from the pslibraries, thereunder the NC and the
>>>> USPP variants. BOTH lead to a segfault. I already messed with th
>>>> generation parameters of the Mg pseudopotential and changed the
>>>> r_paw(1)-parameter in the XSpectra input but no avail.
>>>> I built QE with GCC 5.2 under Arch Linux on my local machine, but the
>>>> problem applies at our cluster (using the Intel compiler) as well.
>>>> Did I miss anything? The Inputs and results are added to the archives.
>>>>
>>>> I firstly planned to calculate Mg K-edge spectra of MgO2 species on a
>>>> Au(111)-surface using PAW pseudopotentials, but I am willing to use USPP
>>>> or NCPP if they work better with XSpectra.
>>>>
>>>> Regards
>>>> Adrian Huehn
>>>>
>>>>
>>>> Mulliken Institute for Theoretical Chemistry
>>>> University of Bonn
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/
--
* * * *
Matteo Calandra, Directeur de Recherche (DR2)
Institut de Minéralogie et de Physique des Milieux Condensés de Paris
Université Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra
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