Re: [Wien] EFG dependence on magnetic field
Many thanks for your guidance. Actually my system has magnetic (2) and non-magnetic (3) species. As B_ext. means we are apply magnetic field on the whole system then why do we need to select natorb = 2 ? Bext is applied to the iatoms (i.e., in atomic spheres) that you specify in case.inorb. The program searches for file case.vorbup, if it finds it, Bext energy is add to Vxc in atomic spheres and in interstitial region [ http://www.wien2k.at/reg_user/textbooks/orbital_potentials.pdf (section "4.1 LAPW0 package" on page 6)]. Secondly could you please clarify to me about "adjusting the "direction of Bext in terms of lattice vectors" line in case.inorb.". Any example please or guidance that how to make it. For example, y = x*tan(theta) = 1*tan(32 degrees) = 0.62487 [ https://en.wikipedia.org/wiki/Trigonometry ] Consider a cubic lattice with the "direction of Bext in terms of lattice vectors" set to: 1 0.62487 0 Calculation of the angle between vector (1,0,0) and vector (1,0.62487,0) with octave: username@computername:~/wiendata/case$ octave octave:1> a=[1 0 0] a = 1 0 0 octave:2> b=[1 0.62487 0] b = 1.0 0.62487 0.0 octave:3> angle_rad=acos(dot(a,b)/(norm(a)*norm(b))) angle_rad = 0.55851 octave:4> angle_deg=angle_rad*180/pi angle_deg = 32.000 This gives an angle of 32 degrees with respect to the (100) axis. Reference: http://www.mathworks.com/matlabcentral/newsreader/view_thread/151925 ___ 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] berryPI code
The error suggests that "x w2w -so -up" did not go through. Please try to run this command manually in the same directory, just to confirm the error. Also there is a trace back information in your segfault report. I would go into specified lines of the sources code and look for hints. I assume that SCF cycle with SOC + orbital potential is completed error free prior to running BerryPI. Also the k-mesh of 10:10:10 is an overkill for the first run. Starting with 4:4:4 and checking convergence while increasing the mesh is more practical. Oleg > On Sep 6, 2015, at 04:12, nilofar hadaeghi wrote: > > Dear all > I am working on the berryPI code and I have faced the following error. > Can anyine help me please? > Best regards, > [hadaeghi@cm6 YbB6]$ berrypi -o -j -k10:10:10 > [ BerryPI ] +++Version 1.2 (Mar 12, 2014) > > [ BerryPI ] Python version: 2.7.3 > [ BerryPI ] Numpy version: 1.6.2 > [ BerryPI ] Calculation with an additional orbital potential is activated > [ BerryPI ] Spin polarization is activated automatically with adding > orbital potential > [ BerryPI ] Calculation with spin-orbit coupling is activated > [ BerryPI ] Proceed with the k-mesh [10, 10, 10] > Please make sure that W2W is installed before trying to run BerryPI > [ BerryPI ] Starting BerryPI Automation for YbB6 > [ BerryPI ] New working directory: > /home/hadaeghi/berry-for-thesis/YbB6/GGA/6/SE=-6/YbB6/YbB6 > [ BerryPI ] w2kpath = /usr/local/codes/wien2k/v14.2 > [ BerryPI ] pypath = /usr/bin/python2.7 > [ BerryPI ] bppath = /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI > [ BerryPI ] Calling command: rm -f YbB6.broyd* > [ BerryPI ] Copied YbB6.struct to YbB6.ksym > [ BerryPI ] Calling command: echo "0 10 10 10 0" | x kgen -fbz > 1 symmetry operations without inversion > NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G) > length of reciprocal lattice vectors: 0.802 0.802 0.802 0.000 > 0.000 0.000 > Specify 3 mesh-divisions (n1,n2,n3): > Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift) >1000 k-points generated, ndiv= 10 10 10 > KGEN ENDS > 0.021u 0.001s 0:00.04 50.0%0+0k 8+1320io 0pf+0w > [ BerryPI ] Calling command: cp YbB6.klist YbB6.klist_w90 > [ BerryPI ] Calling command: x lapw1 -up -orb > LAPW1 END > 508.786u 14.630s 9:19.76 93.5%0+0k 1400+1637312io 0pf+0w > [ BerryPI ] Calling command: x lapw1 -dn -orb > LAPW1 END > 501.829u 62.532s 10:30.68 89.4%0+0k 1376+1794624io 0pf+0w > [ BerryPI ] Calling command: x lapwso -up -orb > LAPWSO END > 302.212u 3.411s 6:10.04 82.5%0+0k 29552+3724216io 7pf+0w > [ BerryPI ] Determine number of bloch bands in spin-polarized mode > based on *.scf2(up/dn) > [ BerryPI ] spin = up > [ BerryPI ] Number of bloch bands is [1, 42] > [ BerryPI ] spin = dn > [ BerryPI ] Number of bloch bands is [1, 42] > [ BerryPI ] Calling command: /usr/bin/python2.7 > /usr/local/codes/wien2k/v14.2/write_inwf -mode MMN -bands 1 42 > [ BerryPI ] Calling command: write_win > [ BerryPI ] Calling command: /usr/bin/python2.7 > /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/win2nnkp.py YbB6 > [ BerryPI ] file YbB6.scf2up found; will extract the Fermi energy > :FER : F E R M I - ENERGY(TETRAH.M.)= 0.5478304981 > [ BerryPI ] Ef = 0.5478304981 Ry > [ BerryPI ] YbB6.fermiup is present and will be removed > ... done > [ BerryPI ] Fermi energy is written to YbB6.fermiup > [ BerryPI ] Calling command: x w2w -so -up > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PCRoutineLine > Source > w2wc 0042D9ED almgen_70 almgen.F > w2wc 00423E21 l2mmn_ 72 l2mmn.f > w2wc 004223C6 MAIN__226 main.f > w2wc 004038CC Unknown Unknown Unknown > libc.so.6 003B06621735 Unknown Unknown Unknown > w2wc 004037A9 Unknown Unknown Unknown > 2.519u 1.093s 0:04.25 84.7%0+0k 2696+7392io 10pf+0w > error: command /usr/local/codes/wien2k/v14.2/w2wc upw2w.def failed > [ BerryPI ] ERROR: in automation of YbB6 > [ BerryPI ] ERROR --> x w2w -so -up > Command 'x w2w -so -up' returned non-zero exit status 9 > Traceback (most recent call last): > File "/usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/berrypi", > line 917, in >[bAutomationErrorChk,phasesRaw] = rawBerryPhase(configFile) > TypeError: 'bool' object is not iterable > [hadaeghi@cm6 YbB6]$ > ___ > 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:
[Wien] QUESTION regarding p-n junction DOS
Dear Prof. Blaha and WIEN2K users, I have a question regarding physics. We tried to do a calculation for an organic(p-type)-inorganic(n-type) interface for p-n junction photodiode. First we did a calculation for organic part, then the inorganic part and finally both together. All three of them were performed for the same unitcell size. But while plotting DOSfor the interface, the organic donor [p-type](as reported in literature) DOS shifts to lower energy, making it n-type. I do not know where is the problem. Some literature suggests that part of the DOS (organic part) need to be shifted with respect to the vacuum level. How to do that? I will be highly obliged if you can kindly give me your suggestions regarding this. Thank you very much, with kind regards, Prasenjit Roy Electronic Structures of Materials Radboud University Nijmegen +31 (0) 24 36 52805 ___ 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] berryPI code
Dear all I am working on the berryPI code and I have faced the following error. Can anyine help me please? Best regards, [hadaeghi@cm6 YbB6]$ berrypi -o -j -k10:10:10 [ BerryPI ] +++Version 1.2 (Mar 12, 2014) [ BerryPI ] Python version: 2.7.3 [ BerryPI ] Numpy version: 1.6.2 [ BerryPI ] Calculation with an additional orbital potential is activated [ BerryPI ] Spin polarization is activated automatically with adding orbital potential [ BerryPI ] Calculation with spin-orbit coupling is activated [ BerryPI ] Proceed with the k-mesh [10, 10, 10] Please make sure that W2W is installed before trying to run BerryPI [ BerryPI ] Starting BerryPI Automation for YbB6 [ BerryPI ] New working directory: /home/hadaeghi/berry-for-thesis/YbB6/GGA/6/SE=-6/YbB6/YbB6 [ BerryPI ] w2kpath = /usr/local/codes/wien2k/v14.2 [ BerryPI ] pypath = /usr/bin/python2.7 [ BerryPI ] bppath = /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI [ BerryPI ] Calling command: rm -f YbB6.broyd* [ BerryPI ] Copied YbB6.struct to YbB6.ksym [ BerryPI ] Calling command: echo "0 10 10 10 0" | x kgen -fbz 1 symmetry operations without inversion NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G) length of reciprocal lattice vectors: 0.802 0.802 0.802 0.000 0.000 0.000 Specify 3 mesh-divisions (n1,n2,n3): Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift) 1000 k-points generated, ndiv= 10 10 10 KGEN ENDS 0.021u 0.001s 0:00.04 50.0% 0+0k 8+1320io 0pf+0w [ BerryPI ] Calling command: cp YbB6.klist YbB6.klist_w90 [ BerryPI ] Calling command: x lapw1 -up -orb LAPW1 END 508.786u 14.630s 9:19.76 93.5% 0+0k 1400+1637312io 0pf+0w [ BerryPI ] Calling command: x lapw1 -dn -orb LAPW1 END 501.829u 62.532s 10:30.68 89.4% 0+0k 1376+1794624io 0pf+0w [ BerryPI ] Calling command: x lapwso -up -orb LAPWSO END 302.212u 3.411s 6:10.04 82.5% 0+0k 29552+3724216io 7pf+0w [ BerryPI ] Determine number of bloch bands in spin-polarized mode based on *.scf2(up/dn) [ BerryPI ] spin = up [ BerryPI ] Number of bloch bands is [1, 42] [ BerryPI ] spin = dn [ BerryPI ] Number of bloch bands is [1, 42] [ BerryPI ] Calling command: /usr/bin/python2.7 /usr/local/codes/wien2k/v14.2/write_inwf -mode MMN -bands 1 42 [ BerryPI ] Calling command: write_win [ BerryPI ] Calling command: /usr/bin/python2.7 /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/win2nnkp.py YbB6 [ BerryPI ] file YbB6.scf2up found; will extract the Fermi energy :FER : F E R M I - ENERGY(TETRAH.M.)= 0.5478304981 [ BerryPI ] Ef = 0.5478304981 Ry [ BerryPI ] YbB6.fermiup is present and will be removed ... done [ BerryPI ] Fermi energy is written to YbB6.fermiup [ BerryPI ] Calling command: x w2w -so -up forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLine Source w2wc 0042D9ED almgen_70 almgen.F w2wc 00423E21 l2mmn_ 72 l2mmn.f w2wc 004223C6 MAIN__226 main.f w2wc 004038CC Unknown Unknown Unknown libc.so.6 003B06621735 Unknown Unknown Unknown w2wc 004037A9 Unknown Unknown Unknown 2.519u 1.093s 0:04.25 84.7% 0+0k 2696+7392io 10pf+0w error: command /usr/local/codes/wien2k/v14.2/w2wc upw2w.def failed [ BerryPI ] ERROR: in automation of YbB6 [ BerryPI ] ERROR --> x w2w -so -up Command 'x w2w -so -up' returned non-zero exit status 9 Traceback (most recent call last): File "/usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/berrypi", line 917, in [bAutomationErrorChk,phasesRaw] = rawBerryPhase(configFile) TypeError: 'bool' object is not iterable [hadaeghi@cm6 YbB6]$ ___ 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] EFG dependence on magnetic field
Dear Gavin Many thanks for your guidance. Actually my system has magnetic (2) and non-magnetic (3) species. As B_ext. means we are apply magnetic field on the whole system then why do we need to select natorb = 2 ? Secondly could you please clarify to me about "adjusting the "direction of Bext in terms of lattice vectors" line in case.inorb. ". Any example please or guidance that how to make it. On Sat, Sep 5, 2015 at 5:18 PM, Gavin Abo wrote: > See comments below: > > Thank you very much for your prompt response. What I understood is > 1. run init_lapw > 2. add case inorb and case.indm files with format as (I have two > magnetic ions Co) > > == case.inorb = > 3 1 0 nmod, natorb, ipr > PRATT 1.0BROYD/PRATT, mixing > 1 1 2 iatom nlorb, lorb > > 2 1 2 iatom nlorb, lorb > > 8. Bext 0. 0. 1. direction == > == case.indm = -9. Emin cutoff energy > 1 number of atoms for which density matrix is calculated 1 1 2 index of > 1st atom, number of L's, L1 > > 2 1 2 index of 1st atom, number of L's, L1 > > 0 0 r-index, (l,s)index == > > 3. use the command runsp_lapw -p -orb -cc 0.0001 -ec 0.0001 > > Am I right? > > > I think your steps look fine, but your inorb and indm files look > problematic. You have two iatom lines (natorb of 2) in case.inorb, but you > only have natorb set for one iatom. This is likely why you are getting the > error "forrtl: severe (59): list-directed I/O syntax error, unit 5, file > /scratch/sajjadm/work/EFG/mfieldBaCoGeO/001B/001B.inorb". In case.indm, > you have two "index of x atom" lines, but you have the "number of atoms" > line set to 1 instead of 2. > > It is also noted that the effect of 8 T might be very small [ > http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11093.html > ]. > > > Can we apply B_ext at some angle say 32 degree with [100]? > > > You should be able to by adjusting the "direction of Bext in terms of > lattice vectors" line in case.inorb. > > ___ > 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
