Re: [Wien] core leakage problem
Dear L. Dobysheva Thank you for your suggestions. I have over come the problem. The forces have reached around 1 mRy/**. Now the issue is the Si 100 layer saturated with H but the system is behaving like a metal. I am unable to find its reason or some wrong approach followed in my calculations. On Tue, Jul 14, 2015 at 12:09 PM, Lyudmila Dobysheva lyuk...@mail.ru wrote: On 14.07.2015 10:29, Muhammad Sajjad wrote: I used second method according to my understanding. After structure generation and init_lapw, applied the switch *MSEC1a in case.inm* and The userguide says that after init lapw you should make run lapw -fc 1 [another runXX script or additional options are of course also possible] then run the calculations using *run_lapw -fc 0.5 -ec 0.0001 -cc 0.001 80* I don't know what is 80 here. But the calculations are not proceeding and what I found from*case.dayfile* is Calculating 2relax in /home/sajjadm/sajjad/flexibleSi/silayer/2relax on kw12165 with PID 9457 using WIEN2k_14.2 (Release 15/10/2014) in /opt/share/WIEN2K/v14.2-ifort-11.1.075.app 2relax.inM and .minrestart have been created by pairhess lapw1 -p -c(21:44:23) starting parallel lapw1 at Mon Jul 13 21:44:23 AST 2015 - starting parallel LAPW1 jobs at Mon Jul 13 21:44:23 AST 2015 running LAPW1 in parallel mode (using .machines) 5 number_of_parallel_jobs [1] 14781 [2] 14797 [3] 14813 [4] 14829 [5] 14845 In terminal, top command is not showing 5 processors running lapw1 but before it was going on. I am afraid nobody is able to find the reason with this info. Maybe this is an occasional system crash or something else. Try and find it. Please clarify that how to use* the shell script min lapw, together with the program mini*?I mean which* command* do I need to run? As far as I understand you, this is a first method, while you used a second one? Userguide: When using the second method we recommend you read carefully $WIEN-ROOT/SRC mixer/README 5.2.pdf. Section 5.3.2 Minimization of internal parameters describes the first method. Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ 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 Doctoral Fellow KAUST, KSA. ___ 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] core leakage problem
Yes. Please think. --- 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 13, 2015 03:50, Muhammad Sajjad sajja...@gmail.com wrote: I used the command run_lapw -p -I -i 60 -fc 1. DO I need to change it ? On Mon, Jul 13, 2015 at 11:33 AM, Laurence Marks l-ma...@northwestern.edu wrote: No. On Jul 13, 2015 4:37 PM, Muhammad Sajjad sajja...@gmail.com wrote: Thank you professor L.Marks I followed your first two points and ran calculation. I did not fix the center of slab but relax the whole structure and the minimized forces are :FOR001: 1.ATOM 60.004776 -0.02 -0.03 60.004776 total forces :FOR002: 2.ATOM 33.431081 -0.03 0.03 33.431081 total forces :FOR003: 3.ATOM 33.431078 0.03 -0.03 33.431078 total forces :FOR004: 4.ATOM 60.004776 0.03 0.03 60.004776 total forces :FOR005: 5.ATOM 33.434049 0.02 0.01 -33.434049 total forces :FOR006: 6.ATOM 60.056705 0.01 -0.01 -60.056705 total forces :FOR007: 7.ATOM 60.056708 -0.01 0.00 -60.056708 total forces :FOR008: 8.ATOM 33.434051 -0.02 -0.01 -33.434051 total forces :FOR009: 9.ATOM 32.291125 0.00 0.00 -32.291125 total forces :FOR010: 10.ATOM 32.291121 0.00 0.00 -32.291121 total forces :FOR011: 11.ATOM 32.312836 0.00 0.00 32.312836 total forces :FOR012: 12.ATOM 32.312836 0.00 0.00 32.312836 total forces Is this calculation reliable? On Sun, Jul 12, 2015 at 4:33 PM, Laurence Marks l-ma...@northwestern.edu wrote: A few points: a) Your Si-H distance is too small, it should be about 1.45 Angstroms and you have 1.0 Angstroms. With a better value most of your problems will probably go away. b) To do a surface calculation you must use the DFT equilibrium lattice parameters, not the bulk ones. If you do not the results will be wrong. c) For a surface calculation you need the distance between the two surfaces across the vacuum gap to be equal to or smaller than the distance between the two surfaces across the crystal. I personally prefer to make the bulk material twice as wide as the vacuum gap, so the atomic relaxations at the center of the crystal are as small as possible. (Some people will fix the center of the slab, but I think that is bad physics.) Your bulk crystal is way too small. On Sun, Jul 12, 2015 at 7:27 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear All I am performing structural relaxation for Si (100) with H at its top and bottom (structure is attached, vacuum is 12 A). I have inspect the mailing list in detail (like http://www.wien2k.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf AND http://www.mail-archive.com/search?q=core+leakagel=wien%40zeus.theochem.tuwien.ac.at) and have resolved the issue by selecting SE -12, but the calculation hang out after LAPW0. Inspection of lapw1_1.error message is Error in LAPW1. Please suggest me the possible solution. One more thing I found in the list If you have core leakage, inspect in case.outputst whether you can take some high-lying core states as valence states instead Is it possible to make it manually with same SE ? or simple done by lowering down SE as I did? Many thanks -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: 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 ___ 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 Doctoral Fellow KAUST, KSA. ___ 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 Doctoral Fellow KAUST, KSA. ___ 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] core leakage problem
I used the command run_lapw -p -I -i 60 -fc 1. DO I need to change it ? On Mon, Jul 13, 2015 at 11:33 AM, Laurence Marks l-ma...@northwestern.edu wrote: No. On Jul 13, 2015 4:37 PM, Muhammad Sajjad sajja...@gmail.com wrote: Thank you professor L.Marks I followed your first two points and ran calculation. I did not fix the center of slab but relax the whole structure and the minimized forces are :FOR001: 1.ATOM 60.004776 -0.02 -0.03 60.004776 total forces :FOR002: 2.ATOM 33.431081 -0.03 0.03 33.431081 total forces :FOR003: 3.ATOM 33.431078 0.03 -0.03 33.431078 total forces :FOR004: 4.ATOM 60.004776 0.03 0.03 60.004776 total forces :FOR005: 5.ATOM 33.434049 0.02 0.01 -33.434049 total forces :FOR006: 6.ATOM 60.056705 0.01 -0.01 -60.056705 total forces :FOR007: 7.ATOM 60.056708 -0.01 0.00 -60.056708 total forces :FOR008: 8.ATOM 33.434051 -0.02 -0.01 -33.434051 total forces :FOR009: 9.ATOM 32.291125 0.00 0.00 -32.291125 total forces :FOR010: 10.ATOM 32.291121 0.00 0.00 -32.291121 total forces :FOR011: 11.ATOM 32.312836 0.00 0.00 32.312836 total forces :FOR012: 12.ATOM 32.312836 0.00 0.00 32.312836 total forces Is this calculation reliable? On Sun, Jul 12, 2015 at 4:33 PM, Laurence Marks l-ma...@northwestern.edu wrote: A few points: a) Your Si-H distance is too small, it should be about 1.45 Angstroms and you have 1.0 Angstroms. With a better value most of your problems will probably go away. b) To do a surface calculation you must use the DFT equilibrium lattice parameters, not the bulk ones. If you do not the results will be wrong. c) For a surface calculation you need the distance between the two surfaces across the vacuum gap to be equal to or smaller than the distance between the two surfaces across the crystal. I personally prefer to make the bulk material twice as wide as the vacuum gap, so the atomic relaxations at the center of the crystal are as small as possible. (Some people will fix the center of the slab, but I think that is bad physics.) Your bulk crystal is way too small. On Sun, Jul 12, 2015 at 7:27 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear All I am performing structural relaxation for Si (100) with H at its top and bottom (structure is attached, vacuum is 12 A). I have inspect the mailing list in detail (like http://www.wien2k.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf AND http://www.mail-archive.com/search?q=core+leakagel=wien%40zeus.theochem.tuwien.ac.at) and have resolved the issue by selecting SE -12, but the calculation hang out after LAPW0. Inspection of lapw1_1.error message is Error in LAPW1. Please suggest me the possible solution. One more thing I found in the list If you have core leakage, inspect in case.outputst whether you can take some high-lying core states as valence states instead Is it possible to make it manually with same SE ? or simple done by lowering down SE as I did? Many thanks -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: 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 ___ 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 Doctoral Fellow KAUST, KSA. ___ 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 Doctoral Fellow KAUST, KSA. ___ 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] core leakage problem
On 13.07.2015 14:51, Muhammad Sajjad wrote: I used the command run_lapw -p -I -i 60 -fc 1. DO I need to With this command you found a self-consistent solution of a density functional problem with a certain accuracy - forces accuracy is equal 1. As you can see the forces in your system are large: :FOR001: 1.ATOM 60.004776 -0.02 -0.03 60.004776 total forces :FOR002: 2.ATOM 33.431081 -0.03 0.03 33.431081 total forces And you should make relaxation of atoms. So, read in userguide about two ways to do this. 5.3.2 Minimization of internal parameters Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ 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] core leakage problem
Thank you Prof. L. Marks As I am not expert in using Wine2k, please suggest me the change, For me I can just change convergence criteria like 0.5 instead of 1. On Mon, Jul 13, 2015 at 1:10 PM, Laurence Marks l-ma...@northwestern.edu wrote: Yes. Please think. --- 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 13, 2015 03:50, Muhammad Sajjad sajja...@gmail.com wrote: I used the command run_lapw -p -I -i 60 -fc 1. DO I need to change it ? On Mon, Jul 13, 2015 at 11:33 AM, Laurence Marks l-ma...@northwestern.edu wrote: No. On Jul 13, 2015 4:37 PM, Muhammad Sajjad sajja...@gmail.com wrote: Thank you professor L.Marks I followed your first two points and ran calculation. I did not fix the center of slab but relax the whole structure and the minimized forces are :FOR001: 1.ATOM 60.004776 -0.02 -0.03 60.004776 total forces :FOR002: 2.ATOM 33.431081 -0.03 0.03 33.431081 total forces :FOR003: 3.ATOM 33.431078 0.03 -0.03 33.431078 total forces :FOR004: 4.ATOM 60.004776 0.03 0.03 60.004776 total forces :FOR005: 5.ATOM 33.434049 0.02 0.01 -33.434049 total forces :FOR006: 6.ATOM 60.056705 0.01 -0.01 -60.056705 total forces :FOR007: 7.ATOM 60.056708 -0.01 0.00 -60.056708 total forces :FOR008: 8.ATOM 33.434051 -0.02 -0.01 -33.434051 total forces :FOR009: 9.ATOM 32.291125 0.00 0.00 -32.291125 total forces :FOR010: 10.ATOM 32.291121 0.00 0.00 -32.291121 total forces :FOR011: 11.ATOM 32.312836 0.00 0.00 32.312836 total forces :FOR012: 12.ATOM 32.312836 0.00 0.00 32.312836 total forces Is this calculation reliable? On Sun, Jul 12, 2015 at 4:33 PM, Laurence Marks l-ma...@northwestern.edu wrote: A few points: a) Your Si-H distance is too small, it should be about 1.45 Angstroms and you have 1.0 Angstroms. With a better value most of your problems will probably go away. b) To do a surface calculation you must use the DFT equilibrium lattice parameters, not the bulk ones. If you do not the results will be wrong. c) For a surface calculation you need the distance between the two surfaces across the vacuum gap to be equal to or smaller than the distance between the two surfaces across the crystal. I personally prefer to make the bulk material twice as wide as the vacuum gap, so the atomic relaxations at the center of the crystal are as small as possible. (Some people will fix the center of the slab, but I think that is bad physics.) Your bulk crystal is way too small. On Sun, Jul 12, 2015 at 7:27 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear All I am performing structural relaxation for Si (100) with H at its top and bottom (structure is attached, vacuum is 12 A). I have inspect the mailing list in detail (like http://www.wien2k.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf AND http://www.mail-archive.com/search?q=core+leakagel=wien%40zeus.theochem.tuwien.ac.at) and have resolved the issue by selecting SE -12, but the calculation hang out after LAPW0. Inspection of lapw1_1.error message is Error in LAPW1. Please suggest me the possible solution. One more thing I found in the list If you have core leakage, inspect in case.outputst whether you can take some high-lying core states as valence states instead Is it possible to make it manually with same SE ? or simple done by lowering down SE as I did? Many thanks -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: 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 ___ 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 Doctoral Fellow KAUST, KSA. ___ 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 Doctoral Fellow KAUST, KSA.
Re: [Wien] core leakage problem
No. On Jul 13, 2015 4:37 PM, Muhammad Sajjad sajja...@gmail.com wrote: Thank you professor L.Marks I followed your first two points and ran calculation. I did not fix the center of slab but relax the whole structure and the minimized forces are :FOR001: 1.ATOM 60.004776 -0.02 -0.03 60.004776 total forces :FOR002: 2.ATOM 33.431081 -0.03 0.03 33.431081 total forces :FOR003: 3.ATOM 33.431078 0.03 -0.03 33.431078 total forces :FOR004: 4.ATOM 60.004776 0.03 0.03 60.004776 total forces :FOR005: 5.ATOM 33.434049 0.02 0.01 -33.434049 total forces :FOR006: 6.ATOM 60.056705 0.01 -0.01 -60.056705 total forces :FOR007: 7.ATOM 60.056708 -0.01 0.00 -60.056708 total forces :FOR008: 8.ATOM 33.434051 -0.02 -0.01 -33.434051 total forces :FOR009: 9.ATOM 32.291125 0.00 0.00 -32.291125 total forces :FOR010: 10.ATOM 32.291121 0.00 0.00 -32.291121 total forces :FOR011: 11.ATOM 32.312836 0.00 0.00 32.312836 total forces :FOR012: 12.ATOM 32.312836 0.00 0.00 32.312836 total forces Is this calculation reliable? On Sun, Jul 12, 2015 at 4:33 PM, Laurence Marks l-ma...@northwestern.edu wrote: A few points: a) Your Si-H distance is too small, it should be about 1.45 Angstroms and you have 1.0 Angstroms. With a better value most of your problems will probably go away. b) To do a surface calculation you must use the DFT equilibrium lattice parameters, not the bulk ones. If you do not the results will be wrong. c) For a surface calculation you need the distance between the two surfaces across the vacuum gap to be equal to or smaller than the distance between the two surfaces across the crystal. I personally prefer to make the bulk material twice as wide as the vacuum gap, so the atomic relaxations at the center of the crystal are as small as possible. (Some people will fix the center of the slab, but I think that is bad physics.) Your bulk crystal is way too small. On Sun, Jul 12, 2015 at 7:27 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear All I am performing structural relaxation for Si (100) with H at its top and bottom (structure is attached, vacuum is 12 A). I have inspect the mailing list in detail (like http://www.wien2k.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf AND http://www.mail-archive.com/search?q=core+leakagel=wien%40zeus.theochem.tuwien.ac.at) and have resolved the issue by selecting SE -12, but the calculation hang out after LAPW0. Inspection of lapw1_1.error message is Error in LAPW1. Please suggest me the possible solution. One more thing I found in the list If you have core leakage, inspect in case.outputst whether you can take some high-lying core states as valence states instead Is it possible to make it manually with same SE ? or simple done by lowering down SE as I did? Many thanks -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: 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 ___ 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 Doctoral Fellow KAUST, KSA. ___ 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] core leakage problem
A few points: a) Your Si-H distance is too small, it should be about 1.45 Angstroms and you have 1.0 Angstroms. With a better value most of your problems will probably go away. b) To do a surface calculation you must use the DFT equilibrium lattice parameters, not the bulk ones. If you do not the results will be wrong. c) For a surface calculation you need the distance between the two surfaces across the vacuum gap to be equal to or smaller than the distance between the two surfaces across the crystal. I personally prefer to make the bulk material twice as wide as the vacuum gap, so the atomic relaxations at the center of the crystal are as small as possible. (Some people will fix the center of the slab, but I think that is bad physics.) Your bulk crystal is way too small. On Sun, Jul 12, 2015 at 7:27 AM, Muhammad Sajjad sajja...@gmail.com wrote: Dear All I am performing structural relaxation for Si (100) with H at its top and bottom (structure is attached, vacuum is 12 A). I have inspect the mailing list in detail (like http://www.wien2k.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf AND http://www.mail-archive.com/search?q=core+leakagel=wien%40zeus.theochem.tuwien.ac.at) and have resolved the issue by selecting SE -12, but the calculation hang out after LAPW0. Inspection of lapw1_1.error message is Error in LAPW1. Please suggest me the possible solution. One more thing I found in the list If you have core leakage, inspect in case.outputst whether you can take some high-lying core states as valence states instead Is it possible to make it manually with same SE ? or simple done by lowering down SE as I did? Many thanks -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: 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 ___ 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
