Re: [Wien] problem with w2w
You might want to try my patch (w2w_main.patch), which you can get at https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2 (click WIEN2k-Patches and Download ZIP)? I think this will improve the error message in w2w.error from what you got to: 'w2w' - can't open definition file w2w.def You mentioned that you ran the command: w2w. Did you launch w2w with the x command: x w2w? The x is important, because it is a link to the x_lapw script that should create the w2w.def file. Check for the w2w.def file, does it exist, is it non-empty, and does it have read permissions? On 7/21/2015 3:15 AM, Patrik Wealth wrote: Hi Prof Blaha and Wien2k users, I have a question regarding wien2wannier interface. The command w2w returns 'w2w - Error' and when I check the error file it's written 'w2w' - can't open definition file. I have installed Wien2k_14.2 without any error. I was able to run all previous steps for bulk GaAs (namely, creating the bulk bandstructure with wien2k, preparing a separate directory, running init_w2w and running lapw1 again) without any problem. Does anyone know where the problem is or at least point me in the right direction? By the way, lapw1.def file has been created, if this is the mentioned definition file. I appreciate any help. Thanks in advance Patrik ___ 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] Error in write_inwf when running init_w2w
Colleagues, In my first attempt to run wannier, I've encountered the following error message triggered by write_inwf when running init_w2w (without quotes): *** write_inwf File /work/jspirko/WIEN2k-14.2-20141018/write_inwf, line 145 except KeyError as e: ^ SyntaxError: invalid syntax *** The test case was fully converged ZnO. Afterwards, prepare_w2wdir TARGET generated the expected files in TARGET, cd to TARGET was followed by init_w2w:, x kgen -fbz and x findbands was done, chose range Emin = -0.1 eV and Emax = 0.0 eV at VBM, and then write_inwf gave the above error. Note 1: wannier90 is installed Note 2: I have checked the mailing list for a similar error but found none. Any instruction for a fix would be highly appreciated. Why does the caret appear in the error message? Regards, Kamil Klier ___ 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] Error in write_inwf when running init_w2w
It looks like the caret is pointing to the python as keyword. What version of python are you using? You can probably check with the following terminal command (of note, V should be uppercase): python -V It seems that python version 2.6 or newer is needed in order to recognize the as keyword occurring to the python documentation [ https://docs.python.org/2.7/whatsnew/2.6.html#pep-3110-exception-handling-changes ]. However, in the WIEN2k 14.2 usersguide [ http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ], it seems to mention in section 8.2 BerryPI (Modern theory of polarization) on page 137 that version 2.7 of python is required. On 7/21/2015 8:50 PM, Kamil Klier ( Faculty/Staff - Professor Emeritus ) wrote: Colleagues, In my first attempt to run wannier, I've encountered the following error message triggered by write_inwf when running init_w2w (without quotes): *** write_inwf File /work/jspirko/WIEN2k-14.2-20141018/write_inwf, line 145 except KeyError as e: ^ SyntaxError: invalid syntax *** The test case was fully converged ZnO. Afterwards, prepare_w2wdir TARGET generated the expected files in TARGET, cd to TARGET was followed by init_w2w:, x kgen -fbz and x findbands was done, chose range Emin = -0.1 eV and Emax = 0.0 eV at VBM, and then write_inwf gave the above error. Note 1: wannier90 is installed Note 2: I have checked the mailing list for a similar error but found none. Any instruction for a fix would be highly appreciated. Why does the caret appear in the error message? Regards, Kamil Klier ___ 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] problem with w2w
Thank you Gavin! If I run w2w with x, it complains '(x) command w2w does not exist - exit'. However, all interface commands (write_inwf, ...) run without x. The w2w.def file does NOT exist. I should mention that when I run init_w2w (without x, it complains with x), it creates case.ksym file, it runs kgen and also find_bands but it skips write_w2win and jumps to the next steps which are write_win and wannier90.x -pp and finishes here without going to write_w2wdef. SO two files (case.w2win and w2w.def) are missing. I checked the compile message in 'SRC_w2w/compile.msg'. It does not have any error, there is only the following warning: make: warning: Clock skew detected. Your build may be incomplete. where does it go wrong? Thanks again Patrik From: Gavin Abo gs...@crimson.ua.edu Date: Tue, Jul 21, 2015 at 5:34 PM Subject: Re: [Wien] problem with w2w To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at You might want to try my patch (w2w_main.patch), which you can get at https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2 (click WIEN2k-Patches and Download ZIP)? I think this will improve the error message in w2w.error from what you got to: 'w2w' - can't open definition file w2w.def You mentioned that you ran the command: w2w. Did you launch w2w with the x command: x w2w? The x is important, because it is a link to the x_lapw script that should create the w2w.def file. Check for the w2w.def file, does it exist, is it non-empty, and does it have read permissions? On 7/21/2015 3:15 AM, Patrik Wealth wrote: Hi Prof Blaha and Wien2k users, I have a question regarding wien2wannier interface. The command w2w returns 'w2w - Error' and when I check the error file it's written 'w2w' - can't open definition file. I have installed Wien2k_14.2 without any error. I was able to run all previous steps for bulk GaAs (namely, creating the bulk bandstructure with wien2k, preparing a separate directory, running init_w2w and running lapw1 again) without any problem. Does anyone know where the problem is or at least point me in the right direction? By the way, lapw1.def file has been created, if this is the mentioned definition file. I appreciate any help. Thanks in advance Patrik ___ 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] problem with w2w
Check which x_lapw file it is running. It seems like it might be running x_lapw from an old WIEN2k version or the WIEN2k 14.2 x_lapw file that you installed could be damaged (i.e., is missing the w2w code), which could cause the '(x) command w2w does not exist - exit' error. On my system, I run the command: x -h w2w It gives in the output: x w2w [-up/-dn -c -so -p] This partially indicates that is running an x_lapw that should contain the w2w code. On 7/21/2015 3:02 PM, Patrik Wealth wrote: Thank you Gavin! If I run w2w with x, it complains '(x) command w2w does not exist - exit'. However, all interface commands (write_inwf, ...) run without x. The w2w.def file does NOT exist. I should mention that when I run init_w2w (without x, it complains with x), it creates case.ksym file, it runs kgen and also find_bands but it skips write_w2win and jumps to the next steps which are write_win and wannier90.x -pp and finishes here without going to write_w2wdef. SO two files (case.w2win and w2w.def) are missing. I checked the compile message in 'SRC_w2w/compile.msg'. It does not have any error, there is only the following warning: make: warning: Clock skew detected. Your build may be incomplete. where does it go wrong? Thanks again Patrik From: *Gavin Abo* gs...@crimson.ua.edu mailto:gs...@crimson.ua.edu Date: Tue, Jul 21, 2015 at 5:34 PM Subject: Re: [Wien] problem with w2w To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at mailto:wien@zeus.theochem.tuwien.ac.at You might want to try my patch (w2w_main.patch), which you can get at https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2 (click WIEN2k-Patches and Download ZIP)? I think this will improve the error message in w2w.error from what you got to: 'w2w' - can't open definition file w2w.def You mentioned that you ran the command: w2w. Did you launch w2w with the x command: x w2w? The x is important, because it is a link to the x_lapw script that should create the w2w.def file. Check for the w2w.def file, does it exist, is it non-empty, and does it have read permissions? On 7/21/2015 3:15 AM, Patrik Wealth wrote: Hi Prof Blaha and Wien2k users, I have a question regarding wien2wannier interface. The command w2w returns 'w2w - Error' and when I check the error file it's written 'w2w' - can't open definition file. I have installed Wien2k_14.2 without any error. I was able to run all previous steps for bulk GaAs (namely, creating the bulk bandstructure with wien2k, preparing a separate directory, running init_w2w and running lapw1 again) without any problem. Does anyone know where the problem is or at least point me in the right direction? By the way, lapw1.def file has been created, if this is the mentioned definition file. I appreciate any help. Thanks in advance Patrik ___ 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] Metallic Behavior of Si 100 layer
Many thanks Delamora for sending the structure. @ Prof. L. Marks My intention is to study electronic band structure of Si (100), say thickness is 0.384 nm, by varying the strain. I am adding H on the top and bottom to saturate the bonds otherwise free electrons will make Si (100) metallic. I guess the received structures will work fine with my problem. Am I right? True Regards On Mon, Jul 20, 2015 at 5:14 PM, Laurence Marks l-ma...@northwestern.edu wrote: This discussion appears to be useful, and hopefully the structures people are sending will help. That said, there is one deeper issue with this thread. If the intent is to calculate a thin hydrogen terminated silicon layer for which there is experimental data then the model(s) are reasonable. It is also relevant if the idea is to learn about surface calculations. However, if the intent is to model a hydrogen terminated Si (001) surface it is extremely unlikely that any of the models are relevant. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Jul 20, 2015 08:54, delamora delam...@unam.mx wrote: Here I send a possible structure, but it needs optimization. Pablo de la Mora -- *De:* wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de Muhammad Sajjad sajja...@gmail.com *Enviado:* lunes, 20 de julio de 2015 04:22 a. m. *Para:* A Mailing list for WIEN2k users *Asunto:* Re: [Wien] Metallic Behavior of Si 100 layer Dear Delamore and Oleg Thank you very much for your kind suggestions. @Delamore: The attached structure is in fine symmetry and I am trying this for further calculations and will update once done with the calculations. @Oleg: I understood your point. Dangling bonds and less than required Si-Si distance are prominent reason of sending the Si 100 in metallic category. Could you please guide me how to add second H atom at the surface with Si? If possible please add the structure your made. True Regards M. Sajjad KAUST, KSA. On Mon, Jul 20, 2015 at 12:08 AM, Oleg Rubel oru...@lakeheadu.ca wrote: In addition to that: The surface is truncated in a way that each Si has *two* dangling bonds. Thus two H-atoms per one Si at the surface are needed to passivate dangling bonds. I enclosed a sketch (I hope it will come through) where the proposed changes are shown for one Si atom. Note that the H-atoms are oriented to keep tetrahedral coordination of Si. I hope it will help Oleg On Jul 19, 2015, at 3:00 PM, delamora delam...@unam.mx wrote: Sorry, I wanted to say symmetrize De: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de delamora delam...@unam.mx Enviado: domingo, 19 de julio de 2015 02:56 p. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Metallic Behavior of Si 100 layer If you systematize your system you will have a much simpler problem; Here in the SiH100.struct I moved the central plane to 0 0 1/2, then I averaged the positions of the atoms above the plane and the equivalent atom below this plane. After this sgroup changed the structure to a simpler and more symmetric one. Now, here you have 4 Si layers, maybe you can grow the thickness of your system. Pablo De: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de Muhammad Sajjad sajja...@gmail.com Enviado: domingo, 19 de julio de 2015 06:16 a. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Metallic Behavior of Si 100 layer Thank you Oleg, the structure file is attached herewith. On Sun, Jul 19, 2015 at 3:05 PM, Oleg Rubel oru...@lakeheadu.ca wrote: Including the structure file would be helpful. Oleg On Jul 19, 2015 12:24 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear User After relaxation, the Si 100 layer saturated with H is behaving like a metal. I am unable to find its reason or some wrong approach followed in my calculations. Could you please guide me? Many thanks Muhammad Sajjad ___ 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 -- Kind Regards Muhammad Sajjad Post
[Wien] problem with w2w
Hi Prof Blaha and Wien2k users, I have a question regarding wien2wannier interface. The command w2w returns 'w2w - Error' and when I check the error file it's written 'w2w' - can't open definition file. I have installed Wien2k_14.2 without any error. I was able to run all previous steps for bulk GaAs (namely, creating the bulk bandstructure with wien2k, preparing a separate directory, running init_w2w and running lapw1 again) without any problem. Does anyone know where the problem is or at least point me in the right direction? By the way, lapw1.def file has been created, if this is the mentioned definition file. I appreciate any help. Thanks in advance Patrik ___ 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
