Dear Matteo,Thank you for this elaborate reply. This weekend I figured out the most severe problems, I had. Yes, this segfault was produced by not including gipaw information. Dump error of mine.
Concerning my upload, I apologize that both directories are not exactly consistent but anyway, the only dat-file contained in diamondh_uspp_5.2.0.tar.gz is the xanes.dat (see attachement for comparison). But as this issue is resolved with an appropriate version and because the calculations contain some lousy mistake (see below) it is not relevant anymore.
I already know the tutorial by heart, but this did not save me from another error: The full wave function is contained in the <prefix>.wfc (ld1.wfc) file while only the radial part of the 1s state is needed. As fledgling I did not get this aspect. So I always replaced the wfc-file from the tutorial with the wfc from ld1-output. In the tutorial this error is catched by using the (legacy) upf2plotcore.sh script. I found this error only by comparison of the script's output with the wfc file. I also needed a compatible UPF-file I could not produce myself with a recent version of the atomic package. So it if known it is easy to create the necessary wfc-file manually. For me it is also not trivial to apply the information in the hands-on to USPPs. So I think although it is a neat and detailed tutorial, it is not up to date.
PAW are not compatible??? With a now hopefully fine setup I produced some quiet promising XAS spectra of MgO. I cannot say it for sure but in this tests some relevant peaks are repoduced using a 2x2x2 and a 3x3x3 supercells. I cannot ensure that they are not faulty, but the features are visible.
Here is my setup with the work directories scrubbed: http://www.file-upload.net/download-10876487/messing_with_PAW.tar.gz.html Experimental reference: 2013 J. Phys.: Conf. Ser. 417 012065So although the PAW results are wrong. Did I correctly generate the pseudopotential concerning a reference state?
During generation I also did not ionize the reference state because I did not want to touch more parameters than needed. The results still looked acceptable. Does this necessarily lead to spurious errors?
How do I correctly include a reference state to a pseudopotential from the PSlibrary?
Thanks again for your kind reply. Regards Adrian Mulliken Center for Theoretical Chemistry, University of Bonn Am 30.08.2015 um 17:56 schrieb Matteo Calandra:
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-requ...@pwscf.org a écrit :---------------------------------------------------------------------- Message: 1 Date: Fri, 28 Aug 2015 12:34:19 +0200 From: Adrian H?hn<adrian.hu...@thch.uni-bonn.de> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos? To: PWSCF Forum<pw_forum@pwscf.org> Message-ID:<55e0392b.7080...@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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum------------------------------ Message: 2 Date: Fri, 28 Aug 2015 11:09:47 +0000 (UTC) From: Yevgen Melikhov<melikho...@yahoo.com> Subject: [Pw_forum] XSpectra and US or PAW pseudos? To: PWSCF Forum<pw_forum@pwscf.org> Message-ID: <835045780.2539875.1440760187563.javamail.ya...@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 onhttp://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. -------------- next part -------------- An HTML attachment was scrubbed... URL:http://pwscf.org/pipermail/pw_forum/attachments/20150828/71e094d9/attachment-0001.html ------------------------------ Message: 3 Date: Fri, 28 Aug 2015 14:02:52 +0200 From: Adrian H?hn<adrian.hu...@thch.uni-bonn.de> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos? To: Yevgen Melikhov<melikho...@yahoo.com>, PWSCF Forum <pw_forum@pwscf.org> Message-ID:<55e04dec.7000...@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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum-------------- next part -------------- An HTML attachment was scrubbed... URL:http://pwscf.org/pipermail/pw_forum/attachments/20150828/a02d7e14/attachment-0001.html ------------------------------ Message: 4 Date: Fri, 28 Aug 2015 17:37:40 +0430 From: Elham<e.chemistr...@gmail.com> Subject: Re: [Pw_forum] Choice of Pseudopotential To:pw_forum@pwscf.org Message-ID: <camcfadshtewmpyecuog0sv-4v6mmzyo3h7dyykmb-wqekqm...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Dr. Youssef Thanks so much. Elham Ashori Ph.D. student of Physical Chemistry -------------- next part -------------- An HTML attachment was scrubbed... URL:http://pwscf.org/pipermail/pw_forum/attachments/20150828/118ff336/attachment-0001.html ------------------------------ Message: 5 Date: Fri, 28 Aug 2015 13:36:07 +0000 (UTC) From: Yevgen Melikhov<melikho...@yahoo.com> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos? To: Adrian H?hn<adrian.hu...@thch.uni-bonn.de>, PWSCF Forum <pw_forum@pwscf.org> Message-ID: <492818802.2649245.1440768967270.javamail.ya...@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.hu...@thch.uni-bonn.de> To: Yevgen Melikhov<melikho...@yahoo.com>; PWSCF Forum<pw_forum@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 helpAdrianAm 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 onhttp://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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum-------------- next part --------------An HTML attachment was scrubbed... URL:http://pwscf.org/pipermail/pw_forum/attachments/20150828/dccc8706/attachment-0001.html ------------------------------ Message: 6 Date: Fri, 28 Aug 2015 21:00:55 +0430 From: Mojtaba Mirseraji<quantum.pw...@gmail.com> Subject: Re: [Pw_forum] sh: 1: Error in running of ElaStic code To: PWSCF Forum<pw_forum@pwscf.org> Message-ID: <capw9g84enyozjxa49gjw4qjvxcac6ogz-uqmqihzfdz9fcl...@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<bsalmank...@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.pw...@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<bsalmank...@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 accordingtoyours. alias berrypi="${BERRYPI_PYTHON} ${BERRYPI_PATH}/berrypi" if you overcome this problem then another problem occur -if happen -,typethis 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.pw...@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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum_______________________________________________ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum------------------------------ Message: 7 Date: Fri, 28 Aug 2015 18:31:03 +0200 From: Delphine Cabaret<delphine.caba...@impmc.upmc.fr> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos? To: PWSCF Forum<pw_forum@pwscf.org> Message-ID:<55e08cc7.5010...@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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum_______________________________________________ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/
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