Re: [Wien] TELNES calculation procedure
If I remember correctly: x lapw2 -qtl gives only the diagonal qtls and thus telnes WITHOUT orientation dependency. x qtl -telnes gives also cross-terms for orientation dependent ELNES. PS: Yes, x qtl -tenes overwrites a previous case.qtl file from x lapw2 -qtl I'm not sure, but maybe you need the weight files and the actual EF, which are produced in the lapw2 step (and you don't have them in your directory from a previous lapw2 step ? Am 11.11.2020 um 20:38 schrieb Gavin Abo: From looking at the post at https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20597.html it looks like the steps are: run_lapw x qtl -telnes (or x lapw2 -qtl) x telnes3 According to section "8.24.3 Practical considerations" in the WIEN2k 19.1/19.2 usersguide on page 201 [ http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ], qtl creates a case.qtl file: /create the case.qtl file using x qtl -telnes/ The "x lapw2 -qtl" could also be used instead to create a case.qtl according to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19805.html One of the differences between the two qtl commands is that "x qtl" has case.inq: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03631.html The "x lapw2 -qtl" is probably unnecessary as case.qtl would be overwritten by "x qtl -telnes" in your steps: x lapw2 -qtl x qtl -telnes You may want to read the following post about the state of WIEN2k 14.2 that are using: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20514.html Program command: run_lapw -> Package: SRC_lapw0, SRC_lapw1, SRC_lapw2 Program command: x qtl -telnes -> Package: SRC_qtl Program command: x telnes3 -> Package: SRC_telnes3 Using the above cross referencing between WIEN2k commands and packages, you might also want to check the WIEN2k update page: http://susi.theochem.tuwien.ac.at/reg_user/updates/ If you see any of these packages updated in the list in a later version (16.1 ... 19.2 ), it can indicate a bug existed in previous version (e.g. 14.2). Not sure, but maybe what you are describing is related to this post: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15953.html Hopefully the above can help. In addition, if of interest, I have posted my patch file qtlpara_lapw.patch that only works for WIEN2k 19.2 at https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2 It has Prof. Blaha's fix that he provide at https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20660.html The patch also has a fix for resolving the "single: label not found" error. A test case showing that the "single: label not found" was resolved is given below: diamond.struct at: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20645.html username@computername:~/wiendata/diamond$ ls diamond.struct username@computername:~/wiendata/diamond$ init_lapw -b ... username@computername:~/wiendata/diamond$ cat .machines cat: .machines: No such file or directory username@computername:~/wiendata/diamond$ run_lapw ... in cycle 11 ETEST: .000145755000 CTEST: .0033029 hup: Command not found. STOP LAPW0 END STOP LAPW1 END STOP LAPW2 END STOP CORE END STOP MIXER END ec cc and fc_conv 1 1 1 > stop username@computername:~/wiendata/diamond$ cp $WIENROOT/SRC_templates/case.innes diamond.innes username@computername:~/wiendata/diamond$ x qtl -p -telnes single: label not found. 0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/username/WIEN2k/qtlpara qtl.def failed username@computername:~/wiendata/diamond$ cd $WIENROOT username@computername:~/WIEN2k$ wget https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/19.2/qtlpara_lapw.patch ... 2020-11-11 11:25:44 (2.52 MB/s) - ‘qtlpara_lapw.patch’ saved [129/129] username@computername:~/WIEN2k$ patch -b qtlpara_lapw qtlpara_lapw.patch patching file qtlpara_lapw username@computername:~/WIEN2k$ cd ~/wiendata/diamond/ username@computername:~/wiendata/diamond$ x qtl -p -telnes running qtl in single mode STOP QTL END 6.6u 0.0s 0:06.85 98.5% 0+0k 952+8056io 4pf+0w On 11/8/2020 5:34 PM, yunxx133 University of Minnesota wrote: Dear Wien2k users, I have a question regarding the procedure to calculate EELS core-loss edges (TELNES3). In the Wien2k manual, the procedure described is: run_lapw x lapw1 x qtl -telnes x telnes3 However, I've found that some users add 'x lapw2 -qtl' like the procedure for XSPEC. run_lapw x lapw1 x lapw2 -qtl x qtl -telnes x telnes3 I observed that without the 'lapw2 -qtl', in the simulation, the onset of an edge is always at 0 eV not taking into account a proper/real onset of a spectrum. For example, let's say an edge presumably starting at 535 eV is simulated. If I enter the onset energy of 530 eV in .innes, the resulting .elnes file should have a spectrum starting from 5 eV (onset at 5 eV = 535 eV). However, the result shows the onset at 0 eV regardless of the onset energy set in .innew.
Re: [Wien] TELNES calculation procedure
From looking at the post at https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20597.html it looks like the steps are: run_lapw x qtl -telnes (or x lapw2 -qtl) x telnes3 According to section "8.24.3 Practical considerations" in the WIEN2k 19.1/19.2 usersguide on page 201 [ http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ], qtl creates a case.qtl file: /create the case.qtl file using x qtl -telnes/ The "x lapw2 -qtl" could also be used instead to create a case.qtl according to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19805.html One of the differences between the two qtl commands is that "x qtl" has case.inq: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03631.html The "x lapw2 -qtl" is probably unnecessary as case.qtl would be overwritten by "x qtl -telnes" in your steps: x lapw2 -qtl x qtl -telnes You may want to read the following post about the state of WIEN2k 14.2 that are using: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20514.html Program command: run_lapw -> Package: SRC_lapw0, SRC_lapw1, SRC_lapw2 Program command: x qtl -telnes -> Package: SRC_qtl Program command: x telnes3 -> Package: SRC_telnes3 Using the above cross referencing between WIEN2k commands and packages, you might also want to check the WIEN2k update page: http://susi.theochem.tuwien.ac.at/reg_user/updates/ If you see any of these packages updated in the list in a later version (16.1 ... 19.2 ), it can indicate a bug existed in previous version (e.g. 14.2). Not sure, but maybe what you are describing is related to this post: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15953.html Hopefully the above can help. In addition, if of interest, I have posted my patch file qtlpara_lapw.patch that only works for WIEN2k 19.2 at https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2 It has Prof. Blaha's fix that he provide at https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20660.html The patch also has a fix for resolving the "single: label not found" error. A test case showing that the "single: label not found" was resolved is given below: diamond.struct at: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20645.html username@computername:~/wiendata/diamond$ ls diamond.struct username@computername:~/wiendata/diamond$ init_lapw -b ... username@computername:~/wiendata/diamond$ cat .machines cat: .machines: No such file or directory username@computername:~/wiendata/diamond$ run_lapw ... in cycle 11 ETEST: .000145755000 CTEST: .0033029 hup: Command not found. STOP LAPW0 END STOP LAPW1 END STOP LAPW2 END STOP CORE END STOP MIXER END ec cc and fc_conv 1 1 1 > stop username@computername:~/wiendata/diamond$ cp $WIENROOT/SRC_templates/case.innes diamond.innes username@computername:~/wiendata/diamond$ x qtl -p -telnes single: label not found. 0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/username/WIEN2k/qtlpara qtl.def failed username@computername:~/wiendata/diamond$ cd $WIENROOT username@computername:~/WIEN2k$ wget https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/19.2/qtlpara_lapw.patch ... 2020-11-11 11:25:44 (2.52 MB/s) - ‘qtlpara_lapw.patch’ saved [129/129] username@computername:~/WIEN2k$ patch -b qtlpara_lapw qtlpara_lapw.patch patching file qtlpara_lapw username@computername:~/WIEN2k$ cd ~/wiendata/diamond/ username@computername:~/wiendata/diamond$ x qtl -p -telnes running qtl in single mode STOP QTL END 6.6u 0.0s 0:06.85 98.5% 0+0k 952+8056io 4pf+0w On 11/8/2020 5:34 PM, yunxx133 University of Minnesota wrote: Dear Wien2k users, I have a question regarding the procedure to calculate EELS core-loss edges (TELNES3). In the Wien2k manual, the procedure described is: run_lapw x lapw1 x qtl -telnes x telnes3 However, I've found that some users add 'x lapw2 -qtl' like the procedure for XSPEC. run_lapw x lapw1 x lapw2 -qtl x qtl -telnes x telnes3 I observed that without the 'lapw2 -qtl', in the simulation, the onset of an edge is always at 0 eV not taking into account a proper/real onset of a spectrum. For example, let's say an edge presumably starting at 535 eV is simulated. If I enter the onset energy of 530 eV in .innes, the resulting .elnes file should have a spectrum starting from 5 eV (onset at 5 eV = 535 eV). However, the result shows the onset at 0 eV regardless of the onset energy set in .innew. On the other hand, if I include lapw2 -qtl, the onset energy in the resulting data shifts as expected, i.e. starting at 5 eV. Thus, I came to the conclusion that the simulation including 'x lapw2 -qtl' can correctly simulate the edges as opposed to the manual. Could anyone confirm whether this sounds right? or could anyone point out what I am missing here? For your information, the version that I used for this was wien2k 14.2. Thank you for reading and I will wait to hear any insight from e
Re: [Wien] TELNES calculation
Thank you Pavel. I will do accordingly. Best regards Ali From: Wien on behalf of Pavel Ondračka Sent: 24 March 2020 10:38:44 To: A Mailing list for WIEN2k users Subject: Re: [Wien] TELNES calculation Dear Ali, please do core holes only for atoms with multiplicity 1 (otherwise you add multiple core hole at once, and you will get interaction between them, which is what you want to avoid with the supercell in the first place)! Just name (number) one oxygen atom for every non-equivalent oxygen position, so that the symmetry is reduced as needed. Than of course you do the core hole and TELNES calculations just for the named atoms and sum the spectra with weights according to the correct multiplicities. Best regards Pavel On Tue, 2020-03-24 at 07:37 +, Ali Baghizhadeh wrote: > Dear Prof. Blaha > Thank you very much. I did create supercell (2x2x1) and I am using > LDA+U. Again some oxygen have multiplicity of 3, which may result in > increase in the intensity of that specific oxygen. Currently I do > non-spin polarized calculations, but I wish to introduce AFM state in > the cell, on Fe ions. As oxygen is non-magnetic, I do not know how > much the spin state of Fe ions will affect the TELNES spectra? > > Best regards > Ali > From: Wien on behalf of > Peter Blaha > Sent: 24 March 2020 07:05:43 > To: wien@zeus.theochem.tuwien.ac.at > Subject: Re: [Wien] TELNES calculation > > ad 1) no case.inm has no effect on telnes. It is used only during > run_lapw. > ad 2) Yes, you should do the calculations for all non-equivalent O > atoms > and sum the results including their multiplicity. (at least when you > see > some differences in their corresponding DOS). > > What you did not mention: You should create a supercell and create > the > core holes in the supercells. Please read the corresponding > literature > (or the XAS/TELNES sections in the UG and in our workshop lectures). > > And: LuFeO3 is certainly a correlated material. Use GGA+U or mBJ for > these calculations. > > Am 23.03.2020 um 22:42 schrieb Ali Baghizhadeh: > > Dear WIEN2k users > > > > I am trying to calculate the K-edge of oxygen in h-LuFeO3 using > TELNES > > program. I have two questions regarding a structure having few > oxygen > > ions of different Wyckoff positions and multiplicity. For K-edge > oxygen > > calculation, I assume we change the occupancy of specific oxygen > in > > case.inc and add an electron to background in case.inm to run SCF. > > > > 1- After SCF convergence and before TELNES, should we modify > > again case.inm and remove the additional background electron or > not? > > > > 2- Should we repeat SCF calculation for all non-equivalent oxygens > in > > the structure and sum spectra of all oxygens, to represent the > > experimental spectrum? > > > > Thank you in advance. > > > > > > Ali Baghi zadeh > > > > > > ___ > > Wien mailing list > > Wien@zeus.theochem.tuwien.ac.at > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] TELNES calculation
Dear Ali, please do core holes only for atoms with multiplicity 1 (otherwise you add multiple core hole at once, and you will get interaction between them, which is what you want to avoid with the supercell in the first place)! Just name (number) one oxygen atom for every non-equivalent oxygen position, so that the symmetry is reduced as needed. Than of course you do the core hole and TELNES calculations just for the named atoms and sum the spectra with weights according to the correct multiplicities. Best regards Pavel On Tue, 2020-03-24 at 07:37 +, Ali Baghizhadeh wrote: > Dear Prof. Blaha > Thank you very much. I did create supercell (2x2x1) and I am using > LDA+U. Again some oxygen have multiplicity of 3, which may result in > increase in the intensity of that specific oxygen. Currently I do > non-spin polarized calculations, but I wish to introduce AFM state in > the cell, on Fe ions. As oxygen is non-magnetic, I do not know how > much the spin state of Fe ions will affect the TELNES spectra? > > Best regards > Ali > From: Wien on behalf of > Peter Blaha > Sent: 24 March 2020 07:05:43 > To: wien@zeus.theochem.tuwien.ac.at > Subject: Re: [Wien] TELNES calculation > > ad 1) no case.inm has no effect on telnes. It is used only during > run_lapw. > ad 2) Yes, you should do the calculations for all non-equivalent O > atoms > and sum the results including their multiplicity. (at least when you > see > some differences in their corresponding DOS). > > What you did not mention: You should create a supercell and create > the > core holes in the supercells. Please read the corresponding > literature > (or the XAS/TELNES sections in the UG and in our workshop lectures). > > And: LuFeO3 is certainly a correlated material. Use GGA+U or mBJ for > these calculations. > > Am 23.03.2020 um 22:42 schrieb Ali Baghizhadeh: > > Dear WIEN2k users > > > > I am trying to calculate the K-edge of oxygen in h-LuFeO3 using > TELNES > > program. I have two questions regarding a structure having few > oxygen > > ions of different Wyckoff positions and multiplicity. For K-edge > oxygen > > calculation, I assume we change the occupancy of specific oxygen > in > > case.inc and add an electron to background in case.inm to run SCF. > > > > 1- After SCF convergence and before TELNES, should we modify > > again case.inm and remove the additional background electron or > not? > > > > 2- Should we repeat SCF calculation for all non-equivalent oxygens > in > > the structure and sum spectra of all oxygens, to represent the > > experimental spectrum? > > > > Thank you in advance. > > > > > > Ali Baghi zadeh > > > > > > ___ > > Wien mailing list > > Wien@zeus.theochem.tuwien.ac.at > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] TELNES calculation
Dear Prof. Blaha Thank you very much. I did create supercell (2x2x1) and I am using LDA+U. Again some oxygen have multiplicity of 3, which may result in increase in the intensity of that specific oxygen. Currently I do non-spin polarized calculations, but I wish to introduce AFM state in the cell, on Fe ions. As oxygen is non-magnetic, I do not know how much the spin state of Fe ions will affect the TELNES spectra? Best regards Ali From: Wien on behalf of Peter Blaha Sent: 24 March 2020 07:05:43 To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] TELNES calculation ad 1) no case.inm has no effect on telnes. It is used only during run_lapw. ad 2) Yes, you should do the calculations for all non-equivalent O atoms and sum the results including their multiplicity. (at least when you see some differences in their corresponding DOS). What you did not mention: You should create a supercell and create the core holes in the supercells. Please read the corresponding literature (or the XAS/TELNES sections in the UG and in our workshop lectures). And: LuFeO3 is certainly a correlated material. Use GGA+U or mBJ for these calculations. Am 23.03.2020 um 22:42 schrieb Ali Baghizhadeh: > Dear WIEN2k users > > I am trying to calculate the K-edge of oxygen in h-LuFeO3 using TELNES > program. I have two questions regarding a structure having few oxygen > ions of different Wyckoff positions and multiplicity. For K-edge oxygen > calculation, I assume we change the occupancy of specific oxygen in > case.inc and add an electron to background in case.inm to run SCF. > > 1- After SCF convergence and before TELNES, should we modify > again case.inm and remove the additional background electron or not? > > 2- Should we repeat SCF calculation for all non-equivalent oxygens in > the structure and sum spectra of all oxygens, to represent the > experimental spectrum? > > Thank you in advance. > > > Ali Baghi zadeh > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] TELNES calculation
ad 1) no case.inm has no effect on telnes. It is used only during run_lapw. ad 2) Yes, you should do the calculations for all non-equivalent O atoms and sum the results including their multiplicity. (at least when you see some differences in their corresponding DOS). What you did not mention: You should create a supercell and create the core holes in the supercells. Please read the corresponding literature (or the XAS/TELNES sections in the UG and in our workshop lectures). And: LuFeO3 is certainly a correlated material. Use GGA+U or mBJ for these calculations. Am 23.03.2020 um 22:42 schrieb Ali Baghizhadeh: Dear WIEN2k users I am trying to calculate the K-edge of oxygen in h-LuFeO3 using TELNES program. I have two questions regarding a structure having few oxygen ions of different Wyckoff positions and multiplicity. For K-edge oxygen calculation, I assume we change the occupancy of specific oxygen in case.inc and add an electron to background in case.inm to run SCF. 1- After SCF convergence and before TELNES, should we modify again case.inm and remove the additional background electron or not? 2- Should we repeat SCF calculation for all non-equivalent oxygens in the structure and sum spectra of all oxygens, to represent the experimental spectrum? Thank you in advance. Ali Baghi zadeh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
