From aakimov at z.rochester.edu Wed Aug 1 00:51:51 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Tue, 31 Jul 2012 18:51:51 -0400 (EDT) Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: <506381840.196445.1343774362000.JavaMail.root@asems02.its.rochester.edu> Message-ID: <48885545.196582.1343775111266.JavaMail.root@asems02.its.rochester.edu> Dear all, I tried to perform md simulations in Quantum Espresso in 2 different ways: 1) simply run a single continuous trajectory (e.g. 10 steps) 2) run first step of MD as a new calculation (restart_mode = from_scratch, default) and run all other (remaining 9) steps as restarts (restart_mode = restart), doing this for every step As a result after a few steps the total energies, atomic forces and position started to deviate between two approaches. I suspect that some information from the previous step may be dropped during the restart (e.g. by using the first-order Euler scheme instead of the Verlet algorithm), eventually leading to such divergence. So my question is: what is restart algorithm for MD in quantum espresso and is there any possibility to use method 2 (see above) without accumulation of the integration errors? Also can someone clarify why if i specify nstep = 1 in my input file (request to perform a single MD step), the program actually makes 2 MD steps? Thank you, Alexey -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From yuewen.fang at gmail.com Wed Aug 1 04:21:58 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Wed, 1 Aug 2012 10:21:58 +0800 Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? Message-ID: Dear all, I want to create a new pesudo potential with virtual.x, but error occurs. It shows *different nqf are not implemented*, but i don't know to handle this problem and I am also puzzled by the words such as nqf and nqls in the file virtual.f90 which locate at ~/espresso/upftools. If it is convenient for you, pls give me some advice to curb the problem. Thank you. Regards Y.-W. Fang The details are showed below: console ~/Examples/pwscf/Ding0731/test1/virtual 09:56:41 >virtual.x Generate the UPF pseudopotential for a virtual atom combining two pseudopootentials in UPF format Input PP file # 1 in UPF format > F.pbe-n-van.UPF IOS= 0 1 4 Reading pseudopotential file in UPF format... ikk2 525 525 525 525 525 525 0 0 0 0 0 0 0 0 0 0 ...done Input PP file # 2 in UPF format > O.pbe-van_ak.UPF IOS= 0 2 4 Reading pseudopotential file in UPF format... ikk2 525 525 525 525 525 525 0 0 507 507 507 507 0 0 0 0 ...done New Pseudo = x F.pbe-n-van.UPF + (1-x) O.pbe-van_ak.UPF mixing parameter x [0 i am calculating Tc for YC( ytrium carbide) but it gives error NaN I have all positive frequency in the phonon spectrum why the error comes ? i have given my input file 1. pw.x input &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , la2F = .true., / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 16 16 16 0 0 0 2 pw.x input&CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 8 8 8 0 0 0 ph.x input &INPUTPH outdir = '/home/bds/yc2test/' , prefix = 'yc1' , fildyn = 'yc1.dyn' , fildvscf = 'yc1dv' , ldisp = .true., nq1 = 4 , nq2 = 4 , nq3 = 4 , epsil = .false., elph = .true., fpol = .false. , recover = .false. , tr2_ph=1.0d-12, trans=.true., amass(1) = 88.9058, amass(2) = 12.017, / output error shows alha2F.dat # E(THz) 0.005 0.010 0.015 0.020 0.025 0.030 0.035 0.040 0.045 0.050 0.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.0754 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.1508 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.2261 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3015 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3769 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.4523 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.5276 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6030 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6784 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.7538 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.8291 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9045 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9799 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.0553 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.1307 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2060 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2814 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.3568 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.4322 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5075 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5829 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.6583 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.7337 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8090 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8844 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.9598 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.0352 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1106 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1859 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.2613 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.3367 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4121 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4874 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.5628 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.6382 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7136 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7889 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.8643 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.9397 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0151 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0905 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.1658 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.2412 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3166 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3920 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.4673 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.5427 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6181 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6935 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.7688 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.8442 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9196 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9950 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.0704 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.1457 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2211 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2965 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.3719 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.4472 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5226 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5980 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.6734 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.7487 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8241 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8995 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.9749 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.0503 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.1256 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2010 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2764 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.3518 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.4271 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5025 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5779 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.6533 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.7286 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8040 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8794 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.9548 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.0302 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1055 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1809 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.2563 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.3317 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4070 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4824 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.5578 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.6332 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7085 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7839 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.8593 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.9347 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0101 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0854 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.1608 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.2362 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3116 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3869 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.4623 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.5377 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6131 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6884 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.7638 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.8392 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9146 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9899 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.0653 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.1407 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2161 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2915 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.3668 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.4422 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5176 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5930 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.6683 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.7437 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8191 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8945 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.9698 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.0452 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1206 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1960 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.2714 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.3467 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4221 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4975 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.5729 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.6482 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7236 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7990 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.8744 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.9497 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.0251 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1005 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1759 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.2513 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.3266 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4020 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4774 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.5528 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.6281 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7035 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7789 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.8543 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.9296 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0050 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0804 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.1558 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.2312 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3065 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3819 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.4573 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.5327 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6080 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6834 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.7588 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.8342 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9095 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9849 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.0603 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.1357 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2111 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2864 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.3618 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.4372 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5126 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5879 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.6633 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.7387 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8141 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8894 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.9648 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.0402 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1156 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1910 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.2663 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.3417 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4171 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4925 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.5678 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.6432 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7186 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7940 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.8693 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.9447 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0201 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0955 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.1709 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.2462 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3216 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3970 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.4724 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.5477 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6231 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6985 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.7739 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.8492 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.9246 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 15.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN B sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/9b82e2d8/attachment-0001.htm From 1009ukumar at gmail.com Wed Aug 1 08:19:48 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Wed, 1 Aug 2012 11:49:48 +0530 Subject: [Pw_forum] Hirshfeld Charges In-Reply-To: References: Message-ID: > > Hi All, > Hi Gulcin, > > I want to calculate Hirshfeld on each carbon and lithium for > graphene-lithium system to be able to analyze the charge transfer from > lithium to graphene. > > you can find the lowdin charges associated with each atom using processing code, projwfc.x after scf and nscf calculations in QE package.. hope it helps. good luck. ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/dd2eb08c/attachment.htm From akohlmey at gmail.com Wed Aug 1 08:34:19 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 1 Aug 2012 08:34:19 +0200 Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? In-Reply-To: References: Message-ID: On Wed, Aug 1, 2012 at 4:21 AM, Yue-Wen Fang wrote: > Dear all, > > I want to create a new pesudo potential with virtual.x, but error occurs. > It shows different nqf are not implemented, but i don't know to handle > this problem and I am also puzzled by the words such as nqf and nqls in the > file virtual.f90 which locate at ~/espresso/upftools. nqf obviously refers to the number of Q-functions. please check out the derivation of ultra-soft pseudopotentials for details. > If it is convenient for you, pls give me some advice to curb the problem. for creating useful "mixed" pseudopotentials with virtual.x, the two original potential files have to be (technically) as similar as possible. in many cases it unfortunately means, that you have to (re-)create the two potentials yourself based on the provided data (with a few tweaks here and there) to make certain, they are compatible. axel. > Thank you. > > Regards > Y.-W. Fang > > The details are showed below: > console ~/Examples/pwscf/Ding0731/test1/virtual 09:56:41 >virtual.x > > Generate the UPF pseudopotential for a virtual atom > combining two pseudopootentials in UPF format > > Input PP file # 1 in UPF format > F.pbe-n-van.UPF > IOS= 0 1 4 > Reading pseudopotential file in UPF format... > ikk2 525 525 525 525 525 > 525 > 0 0 0 0 0 0 > 0 0 0 0 > ...done > > Input PP file # 2 in UPF format > O.pbe-van_ak.UPF > IOS= 0 2 4 > Reading pseudopotential file in UPF format... > ikk2 525 525 525 525 525 > 525 > 0 0 507 507 507 507 > 0 0 0 0 > ...done > > New Pseudo = x F.pbe-n-van.UPF + (1-x) O.pbe-van_ak.UPF > mixing parameter x [0 pseudopotentials have different mesh > 799 737 > 0.000000000000000E+000 0.000000000000000E+000 > 206.066269763000 81.0552407574000 > pseudopotentials have different mesh > INTERPOLATE = T > interpolate rho_atc > done > interpolate vloc0 > interpolate betar > interpolate betar > interpolate betar > interpolate betar > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from Virtual : error # 1 > different nqf are not implemented (yet) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%% > > stopping ... > Fatal error; unknown error handler > May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is > 197 > Fatal error; unknown error handler > May be MPI call before MPI_INIT. Error message is MPI_ABORT and code is 197 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > virtual.x 000000000053C9DD Unknown Unknown Unknown > virtual.x 000000000040FC51 errore_ 94 > error_handler.f90 > virtual.x 000000000040BF61 compute_virtual_ 312 > virtual.f90 > virtual.x 00000000004050F4 MAIN__ 107 > virtual.f90 > virtual.x 0000000000404C6A Unknown Unknown Unknown > libc.so.6 0000003606A1C4BB Unknown Unknown Unknown > virtual.x 0000000000404BAA Unknown Unknown Unkn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From akohlmey at gmail.com Wed Aug 1 08:38:20 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 1 Aug 2012 08:38:20 +0200 Subject: [Pw_forum] Hirshfeld Charges In-Reply-To: References: Message-ID: On Tue, Jul 31, 2012 at 9:37 PM, Gulcin Kucukdalyan wrote: > Hi All, > > I want to calculate Hirshfeld on each carbon and lithium for > graphene-lithium system to be able to analyze the charge transfer from > lithium to graphene. wouldn't it be better to postprocess the electron density directly? e.g. to compute density differences? all methods to collect charge density on atomic sites suffer from making some assumptions about how to partition the density, which indeed goes against on of the very principles of quantum mechanics (that you cannot "label" electrons). cheers, axel. > > Can someone please explain to me how can i do it by using quantum-espresso? > > Thanks, > > Gulcin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From degironc at sissa.it Wed Aug 1 10:41:51 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 01 Aug 2012 10:41:51 +0200 Subject: [Pw_forum] Hirshfeld Charges In-Reply-To: References: Message-ID: <5018EBCF.4040300@sissa.it> Dear Gulcin, as already commented on by Axel the decomposition of the charge density in atomic contributions is a quite qualitative operation and no particular emphasis to any such decomposition should be given. In QE this can be done looking to atomic-wfc projected density of states (integrated up to the Fermi energy), see projwfc.x code and/or by Bader decomposition. One can extract the total charge density with the pp.x code and then there is a separate code computing Bader charge (look at http://theory.cm.utexas.edu/bader/) To my knowledge in QE Hirshfeld decomposition is not implemented. It is certainly possible to write a post processing code to extract this information but ... that would be just another, arbitrary, way of making this decomposition and no one had a strong motivation to do that. If you are interested in implementing it yourself and contribute this post-processing tool to the community it would be welcome. I would then look at 1) the pp.x code to see from where and how the scf charge density is extracted 2) the potinit.f90 and atomic_rho.f90 routines in PW/src where the superposition of atomic charges for the initial guess of the potential is built. Combining these info it should be possible to compute Hirshfeld charges. If you are interested in charge transfer the following recent paper could be of interest Title: Rigorous Definition of Oxidation States of Ions in Solids Author(s): Jiang Lai; Levchenko Sergey V.; Rappe Andrew M. Source: PHYSICAL REVIEW LETTERS Volume: 108 Issue: 16 Article Number: 166403 DOI: 10.1103/PhysRevLett.108.166403 Published: APR 19 2012 best, stefano On 07/31/2012 09:37 PM, Gulcin Kucukdalyan wrote: > Hi All, > > I want to calculate Hirshfeld on each carbon and lithium for > graphene-lithium system to be able to analyze the charge transfer from > lithium to graphene. > > Can someone please explain to me how can i do it by using quantum-espresso? > > Thanks, > > Gulcin > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/bbd005dd/attachment.htm From Adriano.Mosca.Conte at roma2.infn.it Wed Aug 1 11:35:09 2012 From: Adriano.Mosca.Conte at roma2.infn.it (Adriano Mosca Conte) Date: Wed, 1 Aug 2012 11:35:09 +0200 Subject: [Pw_forum] hibrid functionals In-Reply-To: <5018EBCF.4040300@sissa.it> References: <5018EBCF.4040300@sissa.it> Message-ID: <7986df2d174870b3a45258704d300df0.squirrel@webmail.roma2.infn.it> Hallo everybody, in the last version of espresso I read that, among functionals, there are also hybrid ones, like B3LYP. I did not find further information about it on the manual. Did somebody already use them? How do they work? Is it sufficient to generate a pseudo with a b3lyp functional, and use it in espresso, or are there other things to set up? Is the b3lyp implemented also in "atomic" for pseudos generation? Thank you, Adriano From bfazi90 at gmail.com Wed Aug 1 13:33:17 2012 From: bfazi90 at gmail.com (bf azi) Date: Wed, 1 Aug 2012 16:03:17 +0430 Subject: [Pw_forum] vdW_kernel_table Message-ID: Dear all How to generate vdW_kernel_table and Where vdW_kernel_table with ASCII format input in "pwscf.in"? Thanks a lot Bani Adam Faculty of Science Egypt From degironc at sissa.it Wed Aug 1 14:11:07 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 01 Aug 2012 14:11:07 +0200 Subject: [Pw_forum] vdW_kernel_table In-Reply-To: References: Message-ID: <50191CDB.4010309@sissa.it> it is explained (and done) in vdwDF_example in PW stefano On 08/01/2012 01:33 PM, bf azi wrote: > Dear all > > How to generate vdW_kernel_table and Where vdW_kernel_table with ASCII > format input in "pwscf.in"? > > Thanks a lot > > Bani Adam > Faculty of Science > Egypt > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From lorenzo.paulatto at impmc.upmc.fr Wed Aug 1 14:15:05 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 1 Aug 2012 14:15:05 +0200 Subject: [Pw_forum] vdW_kernel_table In-Reply-To: References: Message-ID: On 1 August 2012 13:33, bf azi wrote: > How to generate vdW_kernel_table and Where vdW_kernel_table with ASCII > format input in "pwscf.in"? > > I keep a pre-generated table in my dropbox, you can download it from here: < https://www.dropbox.com/s/oi2h3u3jhlx0sne/vdW_kernel_table.gz> (do not forget to decompress it with gunzip) Anyway, it only takes 10 minutes to generate it with the generate_vdW_kernel_table.x code, as explained in the example. -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/9bf2b2ad/attachment.htm From zafartariq2003 at yahoo.com Wed Aug 1 14:36:50 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Wed, 1 Aug 2012 05:36:50 -0700 (PDT) Subject: [Pw_forum] error while compiling quantum espresso Message-ID: <1343824610.84925.YahooMailClassic@web121403.mail.ne1.yahoo.com> Dear lorenzo We try a lot of versions of espresso. Some "Latest versions" gives syntex error. But older that 4.2 gvies Error : checking dummy main to link with fortran libraries .... Unknown Linking to fortran libraries from c fails and make.sys file is attached. best regards Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/cc2ace70/attachment.htm From zafartariq2003 at yahoo.com Wed Aug 1 14:40:22 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Wed, 1 Aug 2012 05:40:22 -0700 (PDT) Subject: [Pw_forum] error while compiling quantum espresso Message-ID: <1343824822.25890.YahooMailClassic@web121405.mail.ne1.yahoo.com> Dear lorenzo I am soryy I cant attach make.sys file in previous mail. Now I attach it and before it i mail you at your email address but it bounce back. We try a lot of versions of espresso. Some "Latest versions" gives syntex error. But older that 4.2 gvies Error : checking dummy main to link with fortran libraries .... Unknown Linking to fortran libraries from c fails and make.sys file is attached. best regards Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120801/7a9a585e/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys.tar.gz Type: application/x-gzip Size: 2084 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120801/7a9a585e/attachment-0001.bin From yuewen.fang at gmail.com Thu Aug 2 05:02:00 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Thu, 2 Aug 2012 11:02:00 +0800 Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? In-Reply-To: References: Message-ID: Dear Axel, Based on your reply, I chose two similar Pseudo Potentials namely N.pbe-van-bm.UPF and O.pbe-van-bm.UPF and have succeeded in generating a new mixed PP. But, how to confirm the pp's quality? What tests about PP I should make? Thank you very much! Y. -W. Fang 2012/8/1 Axel Kohlmeyer > On Wed, Aug 1, 2012 at 4:21 AM, Yue-Wen Fang > wrote: > > Dear all, > > > > I want to create a new pesudo potential with virtual.x, but error > occurs. > > It shows different nqf are not implemented, but i don't know to handle > > this problem and I am also puzzled by the words such as nqf and nqls in > the > > file virtual.f90 which locate at ~/espresso/upftools. > > nqf obviously refers to the number of Q-functions. please check > out the derivation of ultra-soft pseudopotentials for details. > > > If it is convenient for you, pls give me some advice to curb the > problem. > > for creating useful "mixed" pseudopotentials with virtual.x, > the two original potential files have to be (technically) as > similar as possible. in many cases it unfortunately means, > that you have to (re-)create the two potentials yourself > based on the provided data (with a few tweaks here and > there) to make certain, they are compatible. > > axel. > > > Thank you. > > > > Regards > > Y.-W. Fang > > > > The details are showed below: > > console ~/Examples/pwscf/Ding0731/test1/virtual 09:56:41 >virtual.x > > > > Generate the UPF pseudopotential for a virtual atom > > combining two pseudopootentials in UPF format > > > > Input PP file # 1 in UPF format > F.pbe-n-van.UPF > > IOS= 0 1 4 > > Reading pseudopotential file in UPF format... > > ikk2 525 525 525 525 525 > > 525 > > 0 0 0 0 0 0 > > 0 0 0 0 > > ...done > > > > Input PP file # 2 in UPF format > O.pbe-van_ak.UPF > > IOS= 0 2 4 > > Reading pseudopotential file in UPF format... > > ikk2 525 525 525 525 525 > > 525 > > 0 0 507 507 507 507 > > 0 0 0 0 > > ...done > > > > New Pseudo = x F.pbe-n-van.UPF + (1-x) O.pbe-van_ak.UPF > > mixing parameter x [0 > pseudopotentials have different mesh > > 799 737 > > 0.000000000000000E+000 0.000000000000000E+000 > > 206.066269763000 81.0552407574000 > > pseudopotentials have different mesh > > INTERPOLATE = T > > interpolate rho_atc > > done > > interpolate vloc0 > > interpolate betar > > interpolate betar > > interpolate betar > > interpolate betar > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from Virtual : error # 1 > > different nqf are not implemented (yet) > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%% > > > > stopping ... > > Fatal error; unknown error handler > > May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and > code is > > 197 > > Fatal error; unknown error handler > > May be MPI call before MPI_INIT. Error message is MPI_ABORT and code is > 197 > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > Image PC Routine Line > Source > > virtual.x 000000000053C9DD Unknown Unknown > Unknown > > virtual.x 000000000040FC51 errore_ 94 > > error_handler.f90 > > virtual.x 000000000040BF61 compute_virtual_ 312 > > virtual.f90 > > virtual.x 00000000004050F4 MAIN__ 107 > > virtual.f90 > > virtual.x 0000000000404C6A Unknown Unknown > Unknown > > libc.so.6 0000003606A1C4BB Unknown Unknown > Unknown > > virtual.x 0000000000404BAA Unknown Unknown Unkn > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/89d294c7/attachment.htm From physics.skgupta at gmail.com Thu Aug 2 08:40:41 2012 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Thu, 2 Aug 2012 12:10:41 +0530 Subject: [Pw_forum] from frc_blk : error # Message-ID: Dear PWSCF user Greetings *For Phonon calculation:* After successfully running q2r.in. But matdyn.in running &input amass(1)=65.409, amass(2)=15.9994, asr='crystal', flfrc='zno.fc', flfrq='zno.freq' / ............... ............. I am getting this error like this %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from frc_blk : error # 1 wrong total_weight %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Please suggest me. Best Regards Sanjeev -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/528d5806/attachment.htm From degironc at sissa.it Thu Aug 2 09:06:02 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 02 Aug 2012 09:06:02 +0200 Subject: [Pw_forum] from frc_blk : error # In-Reply-To: References: Message-ID: <501A26DA.3080202@sissa.it> dear Sanjeev, matdyn computes the weight of the contribution of a pair of atoms to the dynamical matrix on the basis of their separation. the weight is 1 if the separation is inside an expanded Wigner-Seitz cell, 0 if it is outside and an appropriate fraction if it is ON one or more planes at the border [wsweight=1/(number_of_planes +1]. This check is done with a threshold (10-6 in PW/src/wsweight.f90) and for numerical reasons the result may not be correct if the atomic coordinated are defined at the same level of accuracy. you can try to 1) play with this threshold (for instance, reduce it to 10^-5) and see if this solves the problem and results make sense. 2) increase the accuracy used in atomic coordinates of your system. best stefano On 08/02/2012 08:40 AM, Sanjeev Gupta wrote: > Dear PWSCF user > Greetings > > > > *For Phonon calculation:* > After successfully running q2r.in. But matdyn.in running > &input > amass(1)=65.409, > amass(2)=15.9994, > asr='crystal', > flfrc='zno.fc', > flfrq='zno.freq' > / > ............... > ............. > > I am getting this error like this > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from frc_blk : error # 1 > wrong total_weight > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Please suggest me. > Best Regards > Sanjeev > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/c40da109/attachment.htm From masoudnahali at gmail.com Thu Aug 2 16:43:22 2012 From: masoudnahali at gmail.com (Masoud) Date: Thu, 2 Aug 2012 16:43:22 +0200 Subject: [Pw_forum] plotrho.x refuses plotting charge ! Message-ID: Hi plotrho.x in some cases refuses plotting electron density contour map and just plots the black circles showing atom's cores. It is weird since with the same input file on another computer system I can get the right map. I 'd like to know that there is some dependencies between plotrho.x and writing postscript(ps) files in a computer system or something else can cause the issue ?! the input files: &inputpp prefix = 'Arm-55-O2-2eb' outdir = '../tmp/' filplot = 'A2-p-charge' plot_num= 0, / &plot nfile=1, iflag = 2, output_format = 2, weight(1)=1.0, fileout = 'A2.p.rho.dat', e1(1)=8.0, e1(2)=0.0, e1(3)=0.0, e2(1)=0.0, e2(2)=8.5, e2(3)=0.0, x0(1)=-1.0, x0(2)=0.0, x0(3)=0.0, nx=200, ny=200 / A2.p.rho.dat A2.p.rho.ps n 0.0 0.5 12 Best Wishes, m ---------------------------------------- Masoud Nahali International School for Advanced Studies (SISSA) Babol University of Technology (NIT) masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/b858e629/attachment.htm From rainbee1988 at gmail.com Thu Aug 2 21:13:47 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 2 Aug 2012 15:13:47 -0400 Subject: [Pw_forum] some variables in QE Message-ID: Dear all users, When I tried to run the h2o, n and nh4+ examples of qe-4.3.2, it said that do_ee, nelec, nelup and neldw could not match the namelists. And there are no the four variables in the pw.x namelists, of course. How to solve it? Thanks, Ruibin -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/03659a61/attachment.htm From rainbee1988 at gmail.com Thu Aug 2 21:50:33 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 2 Aug 2012 15:50:33 -0400 Subject: [Pw_forum] Illegal instruction Message-ID: Dear all, What does the 'Illegal instruction' error mean? I tried to run pw.x for a nanoparticle, it seemed that everything was ok until this message came out after about 1 min. Thanks, Ruibin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/1f88f7d3/attachment.htm From rainbee1988 at gmail.com Thu Aug 2 21:51:38 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 2 Aug 2012 15:51:38 -0400 Subject: [Pw_forum] not existed variables Message-ID: Dear all users, When I tried to run the h2o, n and nh4+ examples of qe-4.3.2, it said that do_ee, nelec, nelup and neldw could not match the namelists. And there are no the four variables in the pw.x namelists, of course. How to solve it? Thanks, Ruibin -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/cec03a3a/attachment.htm From rainbee1988 at gmail.com Thu Aug 2 21:52:13 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 2 Aug 2012 15:52:13 -0400 Subject: [Pw_forum] not existed variables Message-ID: Dear all users, When I tried to run the h2o, n and nh4+ examples of qe-4.3.2, it said that do_ee, nelec, nelup and neldw could not match the namelists. And there are no the four variables in the pw.x namelists, of course. How to solve it? Thanks, Ruibin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120802/60e05a51/attachment.htm From akohlmey at gmail.com Thu Aug 2 21:54:38 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 2 Aug 2012 19:54:38 +0000 Subject: [Pw_forum] Illegal instruction In-Reply-To: References: Message-ID: <1100901006-1343937281-cardhu_decombobulator_blackberry.rim.net-323566954-@b27.c7.bise7.blackberry> Illegal instruction means that you have an executable that was compiled for a different CPU family or generation. Axel -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: Ruibin Liu Sender: pw_forum-bounces at pwscf.org Date: Thu, 2 Aug 2012 15:50:33 To: Reply-To: PWSCF Forum Subject: [Pw_forum] Illegal instruction _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From flux_ray12 at 163.com Sat Aug 4 13:39:15 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 4 Aug 2012 19:39:15 +0800 (CST) Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? In-Reply-To: References: Message-ID: <7cb82d84.1f846.138f16ea29e.Coremail.flux_ray12@163.com> Dear Yuewen: I'd like to quote a paragraph from L. Vitos' book "Computational quantum mechanics for materials engineers - the EMTO method and applications" at the beginning of page 9: "This simple model (VCA method) suffers from numerous weaknesses, e.g., it is unable to describe correctly the bond proportion and volume effects, and its application has been limited to alloys with nearly identical chemical species." So, it is difficult to "exam" whether your mixed potential works well. You may just do some works and compare your results with other persons. If you wanna use VCA to calculate the energies of alloys, I think Prof. S. de Gironcoli's PRL papers and his Ph.D dissertation are the best. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-02 11:02:00,"Yue-Wen Fang" wrote: Dear Axel, Based on your reply, I chose two similar Pseudo Potentials namely N.pbe-van-bm.UPF and O.pbe-van-bm.UPF and have succeeded in generating a new mixed PP. But, how to confirm the pp's quality? What tests about PP I should make? Thank you very much! Y. -W. Fang 2012/8/1 Axel Kohlmeyer On Wed, Aug 1, 2012 at 4:21 AM, Yue-Wen Fang wrote: > Dear all, > > I want to create a new pesudo potential with virtual.x, but error occurs. > It shows different nqf are not implemented, but i don't know to handle > this problem and I am also puzzled by the words such as nqf and nqls in the > file virtual.f90 which locate at ~/espresso/upftools. nqf obviously refers to the number of Q-functions. please check out the derivation of ultra-soft pseudopotentials for details. > If it is convenient for you, pls give me some advice to curb the problem. for creating useful "mixed" pseudopotentials with virtual.x, the two original potential files have to be (technically) as similar as possible. in many cases it unfortunately means, that you have to (re-)create the two potentials yourself based on the provided data (with a few tweaks here and there) to make certain, they are compatible. axel. > Thank you. > > Regards > Y.-W. Fang > > The details are showed below: > console ~/Examples/pwscf/Ding0731/test1/virtual 09:56:41 >virtual.x > > Generate the UPF pseudopotential for a virtual atom > combining two pseudopootentials in UPF format > > Input PP file # 1 in UPF format > F.pbe-n-van.UPF > IOS= 0 1 4 > Reading pseudopotential file in UPF format... > ikk2 525 525 525 525 525 > 525 > 0 0 0 0 0 0 > 0 0 0 0 > ...done > > Input PP file # 2 in UPF format > O.pbe-van_ak.UPF > IOS= 0 2 4 > Reading pseudopotential file in UPF format... > ikk2 525 525 525 525 525 > 525 > 0 0 507 507 507 507 > 0 0 0 0 > ...done > > New Pseudo = x F.pbe-n-van.UPF + (1-x) O.pbe-van_ak.UPF > mixing parameter x [0 pseudopotentials have different mesh > 799 737 > 0.000000000000000E+000 0.000000000000000E+000 > 206.066269763000 81.0552407574000 > pseudopotentials have different mesh > INTERPOLATE = T > interpolate rho_atc > done > interpolate vloc0 > interpolate betar > interpolate betar > interpolate betar > interpolate betar > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from Virtual : error # 1 > different nqf are not implemented (yet) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%% > > stopping ... > Fatal error; unknown error handler > May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is > 197 > Fatal error; unknown error handler > May be MPI call before MPI_INIT. Error message is MPI_ABORT and code is 197 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > virtual.x 000000000053C9DD Unknown Unknown Unknown > virtual.x 000000000040FC51 errore_ 94 > error_handler.f90 > virtual.x 000000000040BF61 compute_virtual_ 312 > virtual.f90 > virtual.x 00000000004050F4 MAIN__ 107 > virtual.f90 > virtual.x 0000000000404C6A Unknown Unknown Unknown > libc.so.6 0000003606A1C4BB Unknown Unknown Unknown > virtual.x 0000000000404BAA Unknown Unknown Unkn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120804/96c46362/attachment.htm From nicola.marzari at epfl.ch Sat Aug 4 14:19:55 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Sat, 04 Aug 2012 14:19:55 +0200 Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? In-Reply-To: <7cb82d84.1f846.138f16ea29e.Coremail.flux_ray12@163.com> References: <7cb82d84.1f846.138f16ea29e.Coremail.flux_ray12@163.com> Message-ID: <501D136B.5040702@epfl.ch> On 04/08/2012 13:39, GAO Zhe wrote: > If you wanna use VCA to calculate the energies of alloys, I think Prof. > S. de Gironcoli's PRL papers and his Ph.D dissertation are the best. Agreed! Just in case, the PhD is here: http://library.epfl.ch/en/theses/?nr=1087 nicola ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From pandey.bramha at gmail.com Sun Aug 5 11:43:43 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sun, 5 Aug 2012 15:13:43 +0530 Subject: [Pw_forum] output format of d3.x Message-ID: Dear* *All PW users and developers,* *Once i had requested for the calculation of thermodynamical properties of materials which i have done using QHA. Sir now i wanted to study the anharmonic behaviour of that materials at high temperature using d3.x in qe. Sir the output format of d3.x was discussed in* http://www.democritos.it/pipermail/pw_forum/2012-February/023255.html*. But here i am unable to understand the output file format of d3.x due to less knowledge in programming part. Sir please help me in this regard. I shall be highly obliged to you. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/8fa991c3/attachment.htm From sohailphysics at yahoo.co.in Sun Aug 5 13:38:46 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Sun, 5 Aug 2012 19:38:46 +0800 (SGT) Subject: [Pw_forum] optical properties Message-ID: <1344166726.90269.YahooMailClassic@web190901.mail.sg3.yahoo.com> Dear All I am using QE 4.2.1 I would like to know that can we use QE to calculate optical properties.....dielectric function,energy loss function,absorption and reflectance spectra Sohail KKU Saudi Arabia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/33b10f9b/attachment.htm From flux_ray12 at 163.com Sun Aug 5 13:43:22 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 5 Aug 2012 19:43:22 +0800 (CST) Subject: [Pw_forum] optical properties In-Reply-To: <1344166726.90269.YahooMailClassic@web190901.mail.sg3.yahoo.com> References: <1344166726.90269.YahooMailClassic@web190901.mail.sg3.yahoo.com> Message-ID: <6069e667.6ee8.138f698c0a2.Coremail.flux_ray12@163.com> For your purpose, I think QE + Yambo will help you a lot~ -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-05 19:38:46,"Sohail Ahmad" wrote: | Dear All I am using QE 4.2.1 I would like to know that can we use QE to calculate optical properties.....dielectric function,energy loss function,absorption and reflectance spectra Sohail KKU Saudi Arabia | -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/480448b2/attachment.htm From yuewen.fang at gmail.com Sun Aug 5 15:53:35 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Sun, 5 Aug 2012 21:53:35 +0800 Subject: [Pw_forum] How to create a new pseudo potential with virtual.x? In-Reply-To: <501D136B.5040702@epfl.ch> References: <7cb82d84.1f846.138f16ea29e.Coremail.flux_ray12@163.com> <501D136B.5040702@epfl.ch> Message-ID: Dear GAO and nicola , Your advice is very useful. I have download the phd thesis by following your instructions. It's very kind of you! Thank you! Regards! Yuewen 2012/8/4 Nicola Marzari > On 04/08/2012 13:39, GAO Zhe wrote: > > If you wanna use VCA to calculate the energies of alloys, I think Prof. > > S. de Gironcoli's PRL papers and his Ph.D dissertation are the best. > > Agreed! Just in case, the PhD is here: > http://library.epfl.ch/en/theses/?nr=1087 > > nicola > > ---------------------------------------------------------------------- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/31f96293/attachment.htm From bdslipun at gmail.com Sun Aug 5 15:57:17 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 5 Aug 2012 19:27:17 +0530 Subject: [Pw_forum] Fwd: problem of Tc calculation in electron phonon coefficents In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: 2012/8/1 Subject: problem of Tc calculation in electron phonon coefficents To: PWSCF Forum i am calculating Tc for YC( ytrium carbide) but it gives error NaN I have all positive frequency in the phonon spectrum why the error comes ? i have given my input file 1. pw.x input &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , la2F = .true., / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 16 16 16 0 0 0 2 pw.x input&CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 8 8 8 0 0 0 ph.x input &INPUTPH outdir = '/home/bds/yc2test/' , prefix = 'yc1' , fildyn = 'yc1.dyn' , fildvscf = 'yc1dv' , ldisp = .true., nq1 = 4 , nq2 = 4 , nq3 = 4 , epsil = .false., elph = .true., fpol = .false. , recover = .false. , tr2_ph=1.0d-12, trans=.true., amass(1) = 88.9058, amass(2) = 12.017, / output error shows alha2F.dat # E(THz) 0.005 0.010 0.015 0.020 0.025 0.030 0.035 0.040 0.045 0.050 0.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.0754 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.1508 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.2261 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3015 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3769 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.4523 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.5276 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6030 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6784 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.7538 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.8291 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9045 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9799 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.0553 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.1307 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2060 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2814 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.3568 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.4322 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5075 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5829 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.6583 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.7337 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8090 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8844 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.9598 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.0352 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1106 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1859 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.2613 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.3367 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4121 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4874 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.5628 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.6382 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7136 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7889 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.8643 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.9397 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0151 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0905 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.1658 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.2412 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3166 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3920 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.4673 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.5427 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6181 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6935 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.7688 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.8442 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9196 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9950 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.0704 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.1457 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2211 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2965 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.3719 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.4472 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5226 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5980 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.6734 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.7487 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8241 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8995 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.9749 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.0503 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.1256 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2010 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2764 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.3518 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.4271 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5025 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5779 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.6533 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.7286 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8040 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8794 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.9548 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.0302 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1055 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1809 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.2563 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.3317 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4070 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4824 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.5578 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.6332 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7085 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7839 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.8593 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.9347 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0101 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0854 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.1608 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.2362 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3116 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3869 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.4623 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.5377 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6131 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6884 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.7638 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.8392 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9146 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9899 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.0653 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.1407 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2161 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2915 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.3668 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.4422 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5176 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5930 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.6683 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.7437 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8191 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8945 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.9698 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.0452 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1206 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1960 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.2714 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.3467 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4221 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4975 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.5729 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.6482 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7236 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7990 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.8744 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.9497 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.0251 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1005 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1759 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.2513 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.3266 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4020 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4774 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.5528 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.6281 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7035 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7789 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.8543 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.9296 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0050 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0804 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.1558 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.2312 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3065 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3819 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.4573 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.5327 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6080 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6834 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.7588 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.8342 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9095 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9849 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.0603 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.1357 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2111 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2864 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.3618 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.4372 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5126 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5879 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.6633 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.7387 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8141 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8894 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.9648 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.0402 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1156 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1910 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.2663 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.3417 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4171 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4925 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.5678 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.6432 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7186 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7940 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.8693 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.9447 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0201 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0955 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.1709 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.2462 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3216 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3970 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.4724 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.5477 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6231 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6985 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.7739 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.8492 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.9246 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 15.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN B sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/98bd0af9/attachment-0001.htm From sohailphysics at yahoo.co.in Sun Aug 5 18:11:09 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Mon, 6 Aug 2012 00:11:09 +0800 (SGT) Subject: [Pw_forum] installation Message-ID: <1344183069.35769.YahooMailClassic@web190902.mail.sg3.yahoo.com> I wish to install QE on my laptop (Toshiba/8GB RAM/i7 Processor/750 GB HD) For this I installed fedora 17 and trying to install recent fortran composer but it always gives initilaizing and then arcitecture mismatch Can any body help Sohail KKU Saudi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/d91cfac8/attachment.htm From yuewen.fang at gmail.com Mon Aug 6 04:43:24 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 6 Aug 2012 10:43:24 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? Message-ID: Dear all, I generated a new pp of Ti according to the official instruction named "Notes on pseudopotential generation ~Paolo Giannozzi" with *ld1.x*, but when I wanted to generate a virtual pp of Ti and O with *virual.x*, an error happened, it prompted that the parameters named *"nqf"* and *"nqlc" *couldn't be found in the UPF of Ti, then I checked the UPF and tried to searched the *"nqf"*, but failed. I am confirmed that I strictly followed the official instruction when I was creating the pp of Ti, but why the generated UPF doesn't contain the parameter of nqf and nqlc? I have known the nqf is number of Q-function, but haven't known the meaning of nqlc. Dear friends, have you ever met the similar problem? Regards! Yuewen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/1309a0fe/attachment.htm From tube77 at gmail.com Mon Aug 6 06:48:06 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Sun, 05 Aug 2012 23:48:06 -0500 Subject: [Pw_forum] DCFT3 : 2538-2605 error when performing q2r.x Message-ID: Dear, PW users I'm trying to calculate the phonon dispersion for graphene on IBM AIX v6.1 (serial) with ESSL, I compiled the espresso package using './configure' and there was no problem when compiling. But the run stops when performing 'q2r.x' which gives a runtime error messages, --------------------------------- DCFT3 : 2538-2030 The transform length (ARG NO. 9) is not an allowed value. The next higher allowed value is (2). DCFT3 : 2538-2099 End of input argument error reporting. For more information, refer to Engineering and Scientific Subroutine Library Guide and Reference (SA22-7904). DCFT3 : 2538-2604 Execution terminating due to error count for error number 2099. DCFT3 : 2538-2605 Message summary: 2030 - 1 DCFT3 : 2538-2605 Message summary: 2099 - 1 ---------------------------------- So I copied all the output files from 'pw.x' and 'ph.x' to other Linux machine (ifort with MKL) and run the 'q2r.x' with the same input file. Then it was ok. Calculated phonon dispersion for the graphene looked as I expected. There was no negative frequencies as expected from 'acoustic sum rule'. However, there is another problem when I run the whole calculation (pw.x, ph.x and q2r.x) on the Linux machine. The input files below ran ok. But I get negative frequency for one of the acoustic mode near Gamma. Let me summarize, (1) I get 'DCFT3' error on AIX (XL-fortran with ESSL) when I run 'q2r.x'. (2) No run time errors on Linux (ifort with MKL) but negative frequency. Please share your experiences and give me advices. Thank you. Input files : ================================ cat > $INPUT << EOF &control calculation = 'scf', restart_mode = 'from_scratch', prefix = '$NAME', pseudo_dir = '$PSEUDO_DIR/', outdir = '$OUT_DIR/', wf_collect = .TRUE. tstress = .TRUE. tprnfor = .TRUE. etot_conv_thr = 1.d-5 forc_conv_thr = 1.d-4 / &system ibrav = 0, celldm(1) = 2.687 nat = 2, ntyp = 1, ecutwfc = 45.0, ecutrho = 450.0, occupations = 'smearing', smearing = 'mp', degauss = 0.03, / &electrons diagonalization = 'cg', mixing_mode = 'plain', mixing_beta = 0.7, conv_thr = 1.0d-8, / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF CELL_PARAMETERS 0.86602500 1.50000000 0.00000000 -0.86602500 1.50000000 0.00000000 0.00000000 0.00000000 8.66602500 ATOMIC_POSITIONS (alat) C 0.000000000 1.000000000 0.000000000 C 0.000000000 2.000000000 0.000000000 K_POINTS automatic 16 16 1 0 0 0 EOF ========================= > pw.x cat > $INPUT << EOF Phonons of graphene &inputph tr2_ph = 1.d-14, prefix = '$NAME', outdir = '$OUT_DIR/', fildyn = '$NAME.dyn', ldisp = .true., nq1 = 8, nq2 = 8, nq3 = 1, amass(1) = 12.0107, / EOF ========================= > ph.x cat > $INPUT << EOF &input fildyn = '$NAME.dyn' flfrc = '$NAME.881.fc' zasr = 'simple' / EOF ========================= > q2r.x JISEOK KIM, Ph.D. Postdoctoral Research Associate Department of Materials Science and Engineering University of Texas at Dallas 800 W. Campbell Rd. RL10 Richardson, TX 75080 (413)386-6285 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/e2f532e4/attachment.htm From akohlmey at gmail.com Mon Aug 6 06:49:47 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 06:49:47 +0200 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: On Mon, Aug 6, 2012 at 4:43 AM, Yue-Wen Fang wrote: > Dear all, > > I generated a new pp of Ti according to the official instruction named > "Notes on pseudopotential generation ~Paolo Giannozzi" with ld1.x, but when > I wanted to generate a virtual pp of Ti and O with virual.x, an error > happened, it prompted that the parameters named "nqf" and "nqlc" couldn't be > found in the UPF of Ti, then I checked the UPF and tried to searched the > "nqf", but failed. three comments: 1: it makes *very* little sense to create a virtual Ti-O pseudopotential 2: last time i checked, ld1.x could not create vanderbilt style ultasoft pseudopotentials. both potentials have to be of the same type *and* then use the same valence configurations and pseudization 3: pseudopotential generation is a bit of a black art. it is highly recommended that you spend more time learning and understanding the process before messing with this. there are many ways to mess up a pseudopotential, even if you follow the general instructions. axel. > I am confirmed that I strictly followed the official instruction when I > was creating the pp of Ti, but why the generated UPF doesn't contain the > parameter of nqf and nqlc? I have known the nqf is number of Q-function, but > haven't known the meaning of nqlc. how about just reading through the sources? a quick survey with grep reveals that nqlc is 2*lmax+ with lmax being the maximum l of the beta functions in the pseudopotential. axel. > Dear friends, have you ever met the similar problem? > > Regards! > Yuewen > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From ptao10b at imr.ac.cn Mon Aug 6 09:44:36 2012 From: ptao10b at imr.ac.cn (Peng Tao) Date: Mon, 6 Aug 2012 15:44:36 +0800 (GMT+08:00) Subject: [Pw_forum] negative a2f(w) DOS Message-ID: <115428b.80e3.138fae482b1.Coremail.ptao10b@imr.ac.cn> Dear all, I get the negative a2f(w) in the file "a2F.dos*" when run the example07. Is it a sign of not convergence? Thank you very much! Here is part of the output file a2F.dos1: 0.000031 -0.00000283 -0.00000137 -0.00000141 -0.00000005 0.000093 -0.00007635 -0.00003688 -0.00003813 -0.00000134 0.000155 -0.00035348 -0.00017074 -0.00017654 -0.00000620 0.000217 -0.00096995 -0.00046851 -0.00048442 -0.00001702 0.000279 -0.00206149 -0.00099575 -0.00102958 -0.00003617 0.000341 -0.00376384 -0.00181802 -0.00187979 -0.00006603 0.000403 -0.00621274 -0.00300090 -0.00310285 -0.00010899 0.000465 -0.04893506 -0.02435778 -0.02440985 -0.00016744 0.000527 -0.02731389 -0.01349134 -0.01357881 -0.00024374 0.000589 -0.03395255 -0.01641623 -0.01719604 -0.00034028 0.000651 -0.04039925 -0.01901221 -0.02092760 -0.00045944 0.000713 -0.04639784 -0.02108392 -0.02471030 -0.00060361 Best wishes, Peng Tao -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/a7da4040/attachment.htm From degliesposti at bo.imm.cnr.it Mon Aug 6 12:06:46 2012 From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi) Date: Mon, 06 Aug 2012 12:06:46 +0200 Subject: [Pw_forum] Quantum Espresso (4.3.2) and pure openmp runs Message-ID: <501F9736.9040105@bo.imm.cnr.it> Dear all, I have a (maybe basic) question on the performance of Quantum Espresso with respect to openmp, even if I do not realise if the answer lies in the way QE handles different levels of parallelism or lies at the system level instead. However, I am running QE 4.3.2 on a quad-core machine with 2 CPUs 64bit. SO is Debian stable, and it recognises 16 threads in the CPU table. I have compiled QE with pure openmp support (gcc) without any MPI environment. The question is: even if I do NOT set the OMP_NUM_THREADS variable at runtime, from the table of the "top" command my process now uses 1000 % CPU time, as if it were "parallelised" over 10 threads. Is this real? Is there some kind of default when pw.x is invoked? If so, how is openmp parallelism exploited by QE? Thanks for your time and support. -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 email: degliesposti -AT- bo.imm.cnr.it web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/ From akohlmey at gmail.com Mon Aug 6 12:20:59 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 12:20:59 +0200 Subject: [Pw_forum] Quantum Espresso (4.3.2) and pure openmp runs In-Reply-To: <501F9736.9040105@bo.imm.cnr.it> References: <501F9736.9040105@bo.imm.cnr.it> Message-ID: On Mon, Aug 6, 2012 at 12:06 PM, Cristian Degli Esposti Boschi wrote: > Dear all, > > I have a (maybe basic) question on the performance of Quantum Espresso > with respect to openmp, even if I do not realise if the answer lies in > the way QE handles different levels of parallelism or lies at the system > level instead. > > However, I am running QE 4.3.2 on a quad-core machine with 2 CPUs 64bit. > SO is Debian stable, and it recognises 16 threads in the CPU table. > > I have compiled QE with pure openmp support (gcc) without any MPI > environment. > > The question is: even if I do NOT set the OMP_NUM_THREADS variable > at runtime, from the table of the "top" command my process > now uses 1000 % CPU time, as if it were "parallelised" over 10 threads. > > Is this real? Is there some kind of default when pw.x is invoked? > If so, how is openmp parallelism exploited by QE? this has nothing to do with QE but is a typical implementation default. if OMP_NUM_THREADS is not set, most OpenMP runtime environment automatically default to using all CPU cores for threads. the fact that you see about 1000% and not 1600% is probably due to the limited threading during the course of execution for your specific input. in any case, you are more likely to get better performance with hyperthreading disabled and/or OMP_NUM_THREADS set to 8. BTW: this default behavior of OpenMP is a major nuisance for codes that can do both MPI and OpenMP, so that any reasonable system admin will set up machines, so that OMP_NUM_THREADS is explicitly set to 1 by default in the system environment. axel. > > Thanks for your time and support. > > -- > Cristian Degli Esposti Boschi > CNR-IMM, Sezione di Bologna, > via Gobetti, 101, 40129, Bologna, Italia > tel. ++39 051 6399152, fax ++39 051 6399216 > email: degliesposti -AT- bo.imm.cnr.it > web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From akohlmey at gmail.com Mon Aug 6 12:28:07 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 12:28:07 +0200 Subject: [Pw_forum] Quantum Espresso (4.3.2) and pure openmp runs In-Reply-To: References: <501F9736.9040105@bo.imm.cnr.it> Message-ID: i should probably add, that you are likely to get better performance using MPI, since there are many ways to do rather efficient distributed data parallelization, while OpenMP multi-threading requires a lot of little changes that are not always easy to add (and thus some of which are still missing) and thus generally parallelizes less well. axel. On Mon, Aug 6, 2012 at 12:20 PM, Axel Kohlmeyer wrote: > On Mon, Aug 6, 2012 at 12:06 PM, Cristian Degli Esposti Boschi > wrote: >> Dear all, >> >> I have a (maybe basic) question on the performance of Quantum Espresso >> with respect to openmp, even if I do not realise if the answer lies in >> the way QE handles different levels of parallelism or lies at the system >> level instead. >> >> However, I am running QE 4.3.2 on a quad-core machine with 2 CPUs 64bit. >> SO is Debian stable, and it recognises 16 threads in the CPU table. >> >> I have compiled QE with pure openmp support (gcc) without any MPI >> environment. >> >> The question is: even if I do NOT set the OMP_NUM_THREADS variable >> at runtime, from the table of the "top" command my process >> now uses 1000 % CPU time, as if it were "parallelised" over 10 threads. >> >> Is this real? Is there some kind of default when pw.x is invoked? >> If so, how is openmp parallelism exploited by QE? > > this has nothing to do with QE but is a typical implementation default. > if OMP_NUM_THREADS is not set, most OpenMP runtime environment > automatically default to using all CPU cores for threads. the fact > that you see about 1000% and not 1600% is probably due to the > limited threading during the course of execution for your specific > input. in any case, you are more likely to get better performance > with hyperthreading disabled and/or OMP_NUM_THREADS set to 8. > > BTW: this default behavior of OpenMP is a major nuisance for > codes that can do both MPI and OpenMP, so that any reasonable > system admin will set up machines, so that OMP_NUM_THREADS > is explicitly set to 1 by default in the system environment. > > axel. > > >> >> Thanks for your time and support. >> >> -- >> Cristian Degli Esposti Boschi >> CNR-IMM, Sezione di Bologna, >> via Gobetti, 101, 40129, Bologna, Italia >> tel. ++39 051 6399152, fax ++39 051 6399216 >> email: degliesposti -AT- bo.imm.cnr.it >> web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/ >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From yuewen.fang at gmail.com Mon Aug 6 15:17:15 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 6 Aug 2012 21:17:15 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: > three comments: > 1: it makes *very* little sense to create a virtual Ti-O pseudopotential > Dr. Axel, I want to create a virtual F-O pp in fact, Ti-O was proposed as an example. > 2: last time i checked, ld1.x could not create vanderbilt style ultasoft > pseudopotentials. both potentials have to be of the same type *and* > then use the same valence configurations and pseudization > In my latest work, I need the F-O virtual vanderbilt style pp, but present PPs of F and O downloaded from the quantum espresso website cannot be used by virtual.x to create a new virtual pp because of different nql and nqlc. So I have to use ld1.x to create new pp of F and O. I checked the Input file description of ld1.x in quantum espresso, it tells us some details about "tm" index that * .true. for Troullier-Martins pseudization [PRB 43, 1993 (1991)] * .false. for Rabe-Rappe-Kaxiras-Joannopoulos pseudization [PRB 41, 1227 (1990), erratum PRB 44, 13175 (1991)] Is it means that we only can get tm style and rrkj style pp using ld1.x? If it is, is any other way to get vanderbilt pp of F and O? > 3: pseudopotential generation is a bit of a black art. it is highly > recommended that you spend more time learning and understanding > the process before messing with this. there are many ways to > mess up a pseudopotential, even if you follow the general instructions. > Yeah, the pp generation is actually a challenge thing for me and need much experience. The process is involved too many parameters. Thank you very much Yuewen > axel. > > > how about just reading through the sources? > a quick survey with grep reveals that nqlc is > 2*lmax+ with lmax being the maximum l of > the beta functions in the pseudopotential. > Sorry, Dr Axel, I know it is far more than enough by just reading the sources because I am a newcomer. I haven't been skilled in using grep index, thank you for your instruction and i will take more efforts to make it. > axel. > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/a1d25479/attachment.htm From abmus007 at gmail.com Mon Aug 6 16:24:47 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Mon, 6 Aug 2012 15:24:47 +0100 Subject: [Pw_forum] equilibrium lattice constant of magnetite Message-ID: Dear QE users Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is a spinel ferrimagnetic material. The expt lattice constant was 15.87 and I have been trying to find the equilibrium lattice constant (celldm(1)) between 15.80 - 16.00 and all i get is a straight line graph instead of the usual exponential curve graph. I have tried all l could most esp with starting_magnetization but the results are the same. My input is pasted below pls help me to get the appropriate graph. The kind of the graph I got is attached. Thanks &control calculation = 'scf', restart_mode ='from_scratch', prefix = 'Fe3O4', pseudo_dir = '/home/abolore/Programs/Pseudos/', outdir = './tmp/' / &system ibrav = 2, celldm(1)= $15.80-16.00, nat = 3, ntyp = 3, ecutwfc = 40, ecutrho = 400, starting_magnetization(1) = 0.7, starting_magnetization(2) = -0.5, starting_magnetization(3) = 0.0, nspin = 2, occupations='smearing', smearing='gaussian', degauss = 0.05, / &electrons diagonalization = 'david', mixing_mode = 'plain', mixing_beta = 0.7 / ATOMIC_SPECIES Fe1 55.845 Fe.pz-nd-rrkjus.UPF Fe2 55.845 Fe.pz-nd-rrkjus.UPF O 16.000 O.pz-rrkjus.UPF ATOMIC_POSITIONS Fe1 0.125 0.125 0.125 Fe2 0.500 0.500 0.500 O 0.2548 0.2548 0.2548 K_POINTS (automatic) 8 8 8 1 1 1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/aa3117c4/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: lat.ps Type: application/postscript Size: 19714 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120806/aa3117c4/attachment-0001.ps From yuewen.fang at gmail.com Mon Aug 6 16:33:42 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 6 Aug 2012 22:33:42 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: Dear Dr. Axel, You said ld1.x cannot generate van-style* ultrasoft* pseudopotential, but can ld1.x generate van-style *norm-conserving* pseudopotential? I think ld1.x can't make it. Regards! Yuewen 2012/8/6 Yue-Wen Fang > > three comments: >> 1: it makes *very* little sense to create a virtual Ti-O pseudopotential >> > Dr. Axel, I want to create a virtual F-O pp in fact, Ti-O was proposed as > an example. > >> 2: last time i checked, ld1.x could not create vanderbilt style ultasoft >> pseudopotentials. both potentials have to be of the same type *and* >> then use the same valence configurations and pseudization >> > In my latest work, I need the F-O virtual vanderbilt style pp, but present > PPs of F and O downloaded from the quantum espresso website cannot be used > by virtual.x to create a new virtual pp because of different nql and nqlc. > So I have to use ld1.x to create new pp of F and O. > I checked the Input file description of ld1.x in quantum espresso, it > tells us some details about "tm" index that > > * .true. for Troullier-Martins pseudization [PRB 43, 1993 (1991)] > > * .false. for Rabe-Rappe-Kaxiras-Joannopoulos pseudization > [PRB 41, 1227 (1990), erratum PRB 44, 13175 (1991)] > > Is it means that we only can get tm style and rrkj style pp using ld1.x? > If it is, is any other way to get vanderbilt pp of F and O? > >> 3: pseudopotential generation is a bit of a black art. it is highly >> recommended that you spend more time learning and understanding >> the process before messing with this. there are many ways to >> mess up a pseudopotential, even if you follow the general >> instructions. >> > Yeah, the pp generation is actually a challenge thing for me and need much > experience. The process is involved too many parameters. > Thank you very much > Yuewen > > >> axel. >> >> >> how about just reading through the sources? >> a quick survey with grep reveals that nqlc is >> 2*lmax+ with lmax being the maximum l of >> the beta functions in the pseudopotential. >> > Sorry, Dr Axel, I know it is far more than enough by just reading the > sources because I am a newcomer. I haven't been skilled in using grep > index, thank you for your instruction and i will take more efforts to make > it. > > > >> axel. >> >> >> >> >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >> International Centre for Theoretical Physics, Trieste. Italy. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/ad80aa12/attachment.htm From jiachen at princeton.edu Mon Aug 6 16:34:32 2012 From: jiachen at princeton.edu (jia chen) Date: Mon, 6 Aug 2012 10:34:32 -0400 Subject: [Pw_forum] equilibrium lattice constant of magnetite In-Reply-To: References: Message-ID: Dear Abolore Musari, I guess the number of atoms should be 14, instead of 3. Regards Jia On Mon, Aug 6, 2012 at 10:24 AM, Abolore Musari wrote: > Dear QE users > Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is a > spinel ferrimagnetic material. The expt lattice constant was 15.87 and I > have been trying to find the equilibrium lattice constant (celldm(1)) > between 15.80 - 16.00 and all i get is a straight line graph instead of the > usual exponential curve graph. I have tried all l could most esp with > starting_magnetization but the results are the same. My input is pasted > below pls help me to get the appropriate graph. > The kind of the graph I got is attached. > Thanks > > &control > calculation = 'scf', > restart_mode ='from_scratch', > prefix = 'Fe3O4', > pseudo_dir = '/home/abolore/Programs/Pseudos/', > outdir = './tmp/' > / > &system > ibrav = 2, > celldm(1)= $15.80-16.00, > nat = 3, > ntyp = 3, > ecutwfc = 40, > ecutrho = 400, > starting_magnetization(1) = 0.7, > starting_magnetization(2) = -0.5, > starting_magnetization(3) = 0.0, > nspin = 2, > occupations='smearing', > smearing='gaussian', > degauss = 0.05, > / > &electrons > diagonalization = 'david', > mixing_mode = 'plain', > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Fe1 55.845 Fe.pz-nd-rrkjus.UPF > Fe2 55.845 Fe.pz-nd-rrkjus.UPF > O 16.000 O.pz-rrkjus.UPF > > ATOMIC_POSITIONS > Fe1 0.125 0.125 0.125 > Fe2 0.500 0.500 0.500 > O 0.2548 0.2548 0.2548 > > K_POINTS (automatic) > 8 8 8 1 1 1 > > > > > > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/a31926f6/attachment.htm From abmus007 at gmail.com Mon Aug 6 16:38:50 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Mon, 6 Aug 2012 15:38:50 +0100 Subject: [Pw_forum] installation In-Reply-To: <1344183069.35769.YahooMailClassic@web190902.mail.sg3.yahoo.com> References: <1344183069.35769.YahooMailClassic@web190902.mail.sg3.yahoo.com> Message-ID: Dear Sohail, I think the shortest way to solve this problem is to get a Mandriva linux and you can be sure of no error. thanks Musari A.A On Sun, Aug 5, 2012 at 5:11 PM, Sohail Ahmad wrote: > I wish to install QE on my laptop > (Toshiba/8GB RAM/i7 Processor/750 GB HD) > > For this > I installed fedora 17 and trying to install recent fortran composer but it > always gives > > initilaizing and then arcitecture mismatch > > Can any body help > > Sohail > KKU > Saudi > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/087d39f6/attachment.htm From abmus007 at gmail.com Mon Aug 6 16:42:17 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Mon, 6 Aug 2012 15:42:17 +0100 Subject: [Pw_forum] equilibrium lattice constant of magnetite In-Reply-To: References: Message-ID: Thanks so much Jia But Sir the atomic positions in the input is for 3 atoms, should l leave the atomic position and change the number of atom or my atomic position is wrong?? thanks Musari A. A UNAAB Nigeria On Mon, Aug 6, 2012 at 3:34 PM, jia chen wrote: > Dear Abolore Musari, > > I guess the number of atoms should be 14, instead of 3. > > Regards > Jia > > On Mon, Aug 6, 2012 at 10:24 AM, Abolore Musari wrote: > >> Dear QE users >> Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is >> a spinel ferrimagnetic material. The expt lattice constant was 15.87 and I >> have been trying to find the equilibrium lattice constant (celldm(1)) >> between 15.80 - 16.00 and all i get is a straight line graph instead of the >> usual exponential curve graph. I have tried all l could most esp with >> starting_magnetization but the results are the same. My input is pasted >> below pls help me to get the appropriate graph. >> The kind of the graph I got is attached. >> Thanks >> >> &control >> calculation = 'scf', >> restart_mode ='from_scratch', >> prefix = 'Fe3O4', >> pseudo_dir = '/home/abolore/Programs/Pseudos/', >> outdir = './tmp/' >> / >> &system >> ibrav = 2, >> celldm(1)= $15.80-16.00, >> nat = 3, >> ntyp = 3, >> ecutwfc = 40, >> ecutrho = 400, >> starting_magnetization(1) = 0.7, >> starting_magnetization(2) = -0.5, >> starting_magnetization(3) = 0.0, >> nspin = 2, >> occupations='smearing', >> smearing='gaussian', >> degauss = 0.05, >> / >> &electrons >> diagonalization = 'david', >> mixing_mode = 'plain', >> mixing_beta = 0.7 >> / >> ATOMIC_SPECIES >> Fe1 55.845 Fe.pz-nd-rrkjus.UPF >> Fe2 55.845 Fe.pz-nd-rrkjus.UPF >> O 16.000 O.pz-rrkjus.UPF >> >> ATOMIC_POSITIONS >> Fe1 0.125 0.125 0.125 >> Fe2 0.500 0.500 0.500 >> O 0.2548 0.2548 0.2548 >> >> K_POINTS (automatic) >> 8 8 8 1 1 1 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Jia Chen > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/8608ce1f/attachment.htm From jiachenchem at gmail.com Mon Aug 6 16:48:15 2012 From: jiachenchem at gmail.com (Jia Chen) Date: Mon, 6 Aug 2012 10:48:15 -0400 Subject: [Pw_forum] equilibrium lattice constant of magnetite In-Reply-To: References: Message-ID: Hi, You need to figure out numbers of each atomic specie and positions of each atom, ibrav = 2 only gives you three fcc lattice vectors. I don't think it implies fd3m space group. Bests Jia On Mon, Aug 6, 2012 at 10:42 AM, Abolore Musari wrote: > Thanks so much Jia > But Sir the atomic positions in the input is for 3 atoms, should l leave > the atomic position and change the number of atom or my atomic position is > wrong?? > thanks > Musari A. A > UNAAB Nigeria > > > On Mon, Aug 6, 2012 at 3:34 PM, jia chen wrote: > >> Dear Abolore Musari, >> >> I guess the number of atoms should be 14, instead of 3. >> >> Regards >> Jia >> >> On Mon, Aug 6, 2012 at 10:24 AM, Abolore Musari wrote: >> >>> Dear QE users >>> Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is >>> a spinel ferrimagnetic material. The expt lattice constant was 15.87 and I >>> have been trying to find the equilibrium lattice constant (celldm(1)) >>> between 15.80 - 16.00 and all i get is a straight line graph instead of the >>> usual exponential curve graph. I have tried all l could most esp with >>> starting_magnetization but the results are the same. My input is pasted >>> below pls help me to get the appropriate graph. >>> The kind of the graph I got is attached. >>> Thanks >>> >>> &control >>> calculation = 'scf', >>> restart_mode ='from_scratch', >>> prefix = 'Fe3O4', >>> pseudo_dir = '/home/abolore/Programs/Pseudos/', >>> outdir = './tmp/' >>> / >>> &system >>> ibrav = 2, >>> celldm(1)= $15.80-16.00, >>> nat = 3, >>> ntyp = 3, >>> ecutwfc = 40, >>> ecutrho = 400, >>> starting_magnetization(1) = 0.7, >>> starting_magnetization(2) = -0.5, >>> starting_magnetization(3) = 0.0, >>> nspin = 2, >>> occupations='smearing', >>> smearing='gaussian', >>> degauss = 0.05, >>> / >>> &electrons >>> diagonalization = 'david', >>> mixing_mode = 'plain', >>> mixing_beta = 0.7 >>> / >>> ATOMIC_SPECIES >>> Fe1 55.845 Fe.pz-nd-rrkjus.UPF >>> Fe2 55.845 Fe.pz-nd-rrkjus.UPF >>> O 16.000 O.pz-rrkjus.UPF >>> >>> ATOMIC_POSITIONS >>> Fe1 0.125 0.125 0.125 >>> Fe2 0.500 0.500 0.500 >>> O 0.2548 0.2548 0.2548 >>> >>> K_POINTS (automatic) >>> 8 8 8 1 1 1 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> Jia Chen >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/e02bd38b/attachment-0001.htm From bamideleibrahim at yahoo.com Mon Aug 6 16:58:30 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Mon, 6 Aug 2012 07:58:30 -0700 (PDT) Subject: [Pw_forum] equilibrium lattice constant of magnetite In-Reply-To: References: Message-ID: <1344265110.84369.YahooMailNeo@web39402.mail.mud.yahoo.com> Dear Abolore, Read this article it contains all the atomic positions for the compound. You need to know that for this compound Z=8. http://www.springerlink.com/content/p27870432mt31374/fulltext.pdf ? Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. ________________________________ From: Abolore Musari To: PWSCF Forum Sent: Monday, August 6, 2012 4:42 PM Subject: Re: [Pw_forum] equilibrium lattice constant of magnetite Thanks so much Jia But Sir the atomic positions in the input is for 3 atoms, should l leave the atomic position and change the number of atom or my atomic position is wrong?? thanks Musari A. A UNAAB Nigeria On Mon, Aug 6, 2012 at 3:34 PM, jia chen wrote: Dear Abolore Musari, > > >I guess the number of atoms should be 14, instead of 3. > > >Regards >Jia > > >On Mon, Aug 6, 2012 at 10:24 AM, Abolore Musari wrote: > >Dear QE users >>Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is a spinel ferrimagnetic material. The expt lattice constant was 15.87 and I have been trying to find the equilibrium lattice constant (celldm(1)) between 15.80 - 16.00 and all i get is a straight line graph instead of the usual exponential curve graph. I have tried all l could most esp with starting_magnetization but the results are the same. My input is pasted below pls help me to get the appropriate graph. >>The kind of the graph I got is attached. >>Thanks >> >>&control >>??? calculation = 'scf', >>??? restart_mode ='from_scratch', >>??? prefix = 'Fe3O4', >>??? pseudo_dir = '/home/abolore/Programs/Pseudos/', >>??? outdir = './tmp/' >>?/ >>?&system >>??? ibrav = 2, >>??? celldm(1)= $15.80-16.00, >>??? nat = 3, >>??? ntyp = 3, >>??? ecutwfc = 40, >>??? ecutrho = 400, >>??? starting_magnetization(1) = 0.7, >>??? starting_magnetization(2) = -0.5, >>??? starting_magnetization(3) = 0.0, >>??? nspin = 2, >>??? occupations='smearing', >>??? smearing='gaussian', >>??? degauss = 0.05, >>?/ >>?&electrons >>?? diagonalization = 'david', >>?? mixing_mode = 'plain', >>?? mixing_beta = 0.7 >>?/ >>ATOMIC_SPECIES >>??? Fe1???? 55.845?? Fe.pz-nd-rrkjus.UPF >>??? Fe2??? ?55.845??? ? Fe.pz-nd-rrkjus.UPF >>???? O????? 16.000??? ? O.pz-rrkjus.UPF >> >>ATOMIC_POSITIONS >>Fe1 0.125? 0.125? 0.125? >>Fe2 0.500? 0.500? 0.500 >>O??? 0.2548 0.2548 0.2548 >>? >>K_POINTS (automatic) >>? 8 8 8 1 1 1 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > >-- >Jia Chen > > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/3e3c6170/attachment.htm From akohlmey at gmail.com Mon Aug 6 16:59:54 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 16:59:54 +0200 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: On Mon, Aug 6, 2012 at 4:33 PM, Yue-Wen Fang wrote: > > Dear Dr. Axel, > > You said ld1.x cannot generate van-style ultrasoft pseudopotential, but > can ld1.x generate van-style norm-conserving pseudopotential? I think ld1.x > can't make it. i don't understand what you are asking here. there is a difference between multi-projector norm-conserving pseudopotentials and vanderbilt style ultra-soft potentials. that being said, there is nothing inherently bad about rrkj ultrasofts. axel. > > Regards! > Yuewen > > > 2012/8/6 Yue-Wen Fang >> >> >>> three comments: >>> 1: it makes *very* little sense to create a virtual Ti-O pseudopotential >> >> Dr. Axel, I want to create a virtual F-O pp in fact, Ti-O was proposed as >> an example. >>> >>> 2: last time i checked, ld1.x could not create vanderbilt style ultasoft >>> pseudopotentials. both potentials have to be of the same type *and* >>> then use the same valence configurations and pseudization >> >> In my latest work, I need the F-O virtual vanderbilt style pp, but >> present PPs of F and O downloaded from the quantum espresso website cannot >> be used by virtual.x to create a new virtual pp because of different nql and >> nqlc. So I have to use ld1.x to create new pp of F and O. >> I checked the Input file description of ld1.x in quantum espresso, it >> tells us some details about "tm" index that >> >> * .true. for Troullier-Martins pseudization [PRB 43, 1993 (1991)] >> >> * .false. for Rabe-Rappe-Kaxiras-Joannopoulos pseudization >> [PRB 41, 1227 (1990), erratum PRB 44, 13175 (1991)] >> >> Is it means that we only can get tm style and rrkj style pp using ld1.x? >> If it is, is any other way to get vanderbilt pp of F and O? >>> >>> 3: pseudopotential generation is a bit of a black art. it is highly >>> recommended that you spend more time learning and understanding >>> the process before messing with this. there are many ways to >>> mess up a pseudopotential, even if you follow the general >>> instructions. >> >> Yeah, the pp generation is actually a challenge thing for me and need >> much experience. The process is involved too many parameters. >> Thank you very much >> Yuewen >> >>> >>> axel. >>> >>> >>> how about just reading through the sources? >>> a quick survey with grep reveals that nqlc is >>> 2*lmax+ with lmax being the maximum l of >>> the beta functions in the pseudopotential. >> >> Sorry, Dr Axel, I know it is far more than enough by just reading the >> sources because I am a newcomer. I haven't been skilled in using grep index, >> thank you for your instruction and i will take more efforts to make it. >> >> >>> >>> axel. >>> >>> >>> >>> >>> > _______________________________________________ >>> > Pw_forum mailing list >>> > Pw_forum at pwscf.org >>> > http://www.democritos.it/mailman/listinfo/pw_forum >>> > >>> >>> >>> >>> -- >>> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >>> International Centre for Theoretical Physics, Trieste. Italy. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From akohlmey at gmail.com Mon Aug 6 17:05:50 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 17:05:50 +0200 Subject: [Pw_forum] installation In-Reply-To: References: <1344183069.35769.YahooMailClassic@web190902.mail.sg3.yahoo.com> Message-ID: On Mon, Aug 6, 2012 at 4:38 PM, Abolore Musari wrote: > > Dear Sohail, > I think the shortest way to solve this problem is to get a Mandriva linux > and you can be sure of no error. congratulations for providing advice that is not only incorrect, but also will cause a *lot* of work for no good reason. the errors of the original poster result from using compilation or linking flags for the intel compilers that are not compatible with the hardware. *no* change of linux distribution will fix that. a better approach would be to not use the intel compilers at all and rather the "native" gfortran compiler that ships with the distribution. there also are fftw3/fftw2, blas/lapack/atlas/scalapack OpenMPI/MPICH and everything compiled to be consistent with the bundled gfortran compiler. when running on a laptop, it is sheer folly to try and optimize for the last 5% of performance. at best one would run only test calculations anyway. a serious calculation should be run on a serious machine. full stop. ;) axel. > > thanks > Musari A.A > > On Sun, Aug 5, 2012 at 5:11 PM, Sohail Ahmad > wrote: >> >> I wish to install QE on my laptop >> (Toshiba/8GB RAM/i7 Processor/750 GB HD) >> >> For this >> I installed fedora 17 and trying to install recent fortran composer but >> it always gives >> >> initilaizing and then arcitecture mismatch >> >> Can any body help >> >> Sohail >> KKU >> Saudi >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From yuewen.fang at gmail.com Mon Aug 6 17:06:16 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 6 Aug 2012 23:06:16 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: Dear Sir, I mean that can we create norm-conserving pp using ld1.x? > > Dear Dr. Axel, > > > > You said ld1.x cannot generate van-style ultrasoft pseudopotential, > but > > can ld1.x generate van-style norm-conserving pseudopotential? I think > ld1.x > > can't make it. > > i don't understand what you are asking here. > > there is a difference between multi-projector > norm-conserving pseudopotentials and > vanderbilt style ultra-soft potentials. that > being said, there is nothing inherently > bad about rrkj ultrasofts. > > axel. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/9771e214/attachment.htm From akohlmey at gmail.com Mon Aug 6 17:11:16 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 17:11:16 +0200 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: On Mon, Aug 6, 2012 at 5:06 PM, Yue-Wen Fang wrote: > Dear Sir, I mean that can we create norm-conserving pp using ld1.x? sure you can. particularly the regular kind (one projector per l). that is the foundation for almost any pseudopotential. axel. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From yuewen.fang at gmail.com Mon Aug 6 17:19:38 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 6 Aug 2012 23:19:38 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: Thank you, sir, but it seems that you ignore some questions shown below in our emails. Have you seen these paragraphs before? Regards! three comments: > 1: it makes *very* little sense to create a virtual Ti-O pseudopotential > Dr. Axel, I want to create a virtual F-O pp in fact, Ti-O was proposed as an example. > 2: last time i checked, ld1.x could not create vanderbilt style ultasoft > pseudopotentials. both potentials have to be of the same type *and* > then use the same valence configurations and pseudization > In my latest work, I need the F-O virtual vanderbilt style pp, but present PPs of F and O downloaded from the quantum espresso website cannot be used by virtual.x to create a new virtual pp because of different nql and nqlc. So I have to use ld1.x to create new pp of F and O. I checked the Input file description of ld1.x in quantum espresso, it tells us some details about "tm" index that * .true. for Troullier-Martins pseudization [PRB 43, 1993 (1991)] * .false. for Rabe-Rappe-Kaxiras-Joannopoulos pseudization [PRB 41, 1227 (1990), erratum PRB 44, 13175 (1991)] Is it means that we only can get tm style and rrkj style pp using ld1.x? If it is, is any other way to get vanderbilt pp of F and O? > 3: pseudopotential generation is a bit of a black art. it is highly > recommended that you spend more time learning and understanding > the process before messing with this. there are many ways to > mess up a pseudopotential, even if you follow the general instructions. > Yeah, the pp generation is actually a challenge thing for me and need much experience. The process is involved too many parameters. Thank you very much Yuewen > axel. > > > how about just reading through the sources? > a quick survey with grep reveals that nqlc is > 2*lmax+ with lmax being the maximum l of > the beta functions in the pseudopotential. > Sorry, Dr Axel, I know it is far more than enough by just reading the sources because I am a newcomer. I haven't been skilled in using grep index, thank you for your instruction and i will take more efforts to make it. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/93aa0ff0/attachment-0001.htm From akohlmey at gmail.com Mon Aug 6 17:32:15 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Aug 2012 17:32:15 +0200 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: On Mon, Aug 6, 2012 at 5:19 PM, Yue-Wen Fang wrote: > > Thank you, sir, but it seems that you ignore some questions shown below in > our emails. Have you seen these paragraphs before? rather than having me to go through all your e-mails and remember what i answered and what i didn't, why don't you just reformulate the question? that will make it easier for everybody. thanks, axel. > Regards! -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From degliesposti at bo.imm.cnr.it Mon Aug 6 17:34:30 2012 From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi) Date: Mon, 06 Aug 2012 17:34:30 +0200 Subject: [Pw_forum] Quantum Espresso (4.3.2) and pure openmp runs (Axel Kohlmeyer) In-Reply-To: References: Message-ID: <1e4fedd0cf2e561730e7ff032283026c@www.bo.imm.cnr.it> Thanks for the reply regarding pure OpenMP runs, it clarifies a lot. -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 email: degliesposti -AT- bo.imm.cnr.it web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/ From abmus007 at gmail.com Mon Aug 6 18:05:10 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Mon, 6 Aug 2012 17:05:10 +0100 Subject: [Pw_forum] equilibrium lattice constant of magnetite In-Reply-To: <1344265110.84369.YahooMailNeo@web39402.mail.mud.yahoo.com> References: <1344265110.84369.YahooMailNeo@web39402.mail.mud.yahoo.com> Message-ID: Thanks bamidele. It will be appreciated if u can assist with the said material. thanks for the infomation and thanking you in anticipation of favourable assiatance Musari A.A On Mon, Aug 6, 2012 at 3:58 PM, bamidele ibrahim wrote: > Dear Abolore, > Read this article it contains all the atomic positions for the compound. > You need to know that for this compound Z=8. > http://www.springerlink.com/content/p27870432mt31374/fulltext.pdf > > Adetunji Bamidele Ibrahim(PhD Student) > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > > ------------------------------ > *From:* Abolore Musari > *To:* PWSCF Forum > *Sent:* Monday, August 6, 2012 4:42 PM > *Subject:* Re: [Pw_forum] equilibrium lattice constant of magnetite > > Thanks so much Jia > But Sir the atomic positions in the input is for 3 atoms, should l leave > the atomic position and change the number of atom or my atomic position is > wrong?? > thanks > Musari A. A > UNAAB Nigeria > > On Mon, Aug 6, 2012 at 3:34 PM, jia chen wrote: > > Dear Abolore Musari, > > I guess the number of atoms should be 14, instead of 3. > > Regards > Jia > > On Mon, Aug 6, 2012 at 10:24 AM, Abolore Musari wrote: > > Dear QE users > Sir, I am try to find the lattice constant of magnetite (Fe3O4) which is a > spinel ferrimagnetic material. The expt lattice constant was 15.87 and I > have been trying to find the equilibrium lattice constant (celldm(1)) > between 15.80 - 16.00 and all i get is a straight line graph instead of the > usual exponential curve graph. I have tried all l could most esp with > starting_magnetization but the results are the same. My input is pasted > below pls help me to get the appropriate graph. > The kind of the graph I got is attached. > Thanks > > &control > calculation = 'scf', > restart_mode ='from_scratch', > prefix = 'Fe3O4', > pseudo_dir = '/home/abolore/Programs/Pseudos/', > outdir = './tmp/' > / > &system > ibrav = 2, > celldm(1)= $15.80-16.00, > nat = 3, > ntyp = 3, > ecutwfc = 40, > ecutrho = 400, > starting_magnetization(1) = 0.7, > starting_magnetization(2) = -0.5, > starting_magnetization(3) = 0.0, > nspin = 2, > occupations='smearing', > smearing='gaussian', > degauss = 0.05, > / > &electrons > diagonalization = 'david', > mixing_mode = 'plain', > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Fe1 55.845 Fe.pz-nd-rrkjus.UPF > Fe2 55.845 Fe.pz-nd-rrkjus.UPF > O 16.000 O.pz-rrkjus.UPF > > ATOMIC_POSITIONS > Fe1 0.125 0.125 0.125 > Fe2 0.500 0.500 0.500 > O 0.2548 0.2548 0.2548 > > K_POINTS (automatic) > 8 8 8 1 1 1 > > > > > > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Jia Chen > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/dc173567/attachment.htm From ustc.scgyer at gmail.com Mon Aug 6 18:11:35 2012 From: ustc.scgyer at gmail.com (xiaochuan Ge) Date: Mon, 6 Aug 2012 18:11:35 +0200 Subject: [Pw_forum] cp.x output: .pos Message-ID: The trajectory of the coordinates of atoms is printed out in ${prefix}.pos file. Before the structrue of this file is:\ step number and time of the snapshot 1 coordinates of all the atoms step number and time of the snapshot 2 coordinates of all the atoms ...... That is, different snapshots are separated by an extra line which indicates the step number and the time of this snapshot. But with the newest version that I compiled on cineca-plx, this extra line disappears. Now all the snapshots are mixed together, which is quite inconvenient for me to check some information. I checked the src of the printout_base.f90, it seems that nothing has been changed for this file. Is there anyone knows what happened, and how could I make a easy change to the code in order to recover the previous function? Thanks in advance. =================== Ge Xiaochuan(Giovanni) 3rd year PHD Student Condensed Matter SISSA,Italy =================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/602e77a9/attachment.htm From mgtmentink at lbl.gov Mon Aug 6 22:18:36 2012 From: mgtmentink at lbl.gov (Matthijs Mentink) Date: Mon, 6 Aug 2012 13:18:36 -0700 Subject: [Pw_forum] Difference in implementation in matdyn.x between versions 4.2.1 and 5.0.0? Message-ID: Dear all, I am trying to calculate the phonon DOS of Nb3Sn, using matdyn.x. For this I do a self-consistent calculation with 666 automatic k-points and then a phonon calculation with 666 automatic q-points. After doing q2r (see below), I calculate the phonon dos with matdyn.x (also see below). -- q2r.in &input fildyn='Nb3Sn.dyn', flfrc='Nb3Sn.fc', / -- matdyn.x &input asr='simple', amass(1)=92.90638, amass(2)=118.710, flfrc='Nb3Sn.fc', dos=.true., fldos='Nb3Sn_300K_pz_free.phdos', flfrq='Nb3Sn_300K_pz_free.freq' nk1=24, nk2=24, nk3=24 / Basically, I extrapolate from 666 automatic q-points to 24-24-24 automatic q-points and then calculate the phonon dos. This seems to work just fine in espresso-4.2.1, with a phonon dos very close to what I expect, but the result is dramatically different in espresso 5.0.0. Furthermore, when I use espresso 5.0.0 to calculate everything and then use matdyn.x from version 4.2.1, I get a very spiky unfiltered version with a result close to what I expect (and want), whereas in version 5.0.0 of matdyn.x I get a phonon dos with very broad peaks, with considerable softening at low frequencies, which is something that I do not expect to see. It should also be noted that I am using 1.90e-3 Ry of broadening. Basically, it seems that the implementation of matdyn.x has changed from version 4.2.1 (which incidentally gave the same result as 4.3.2) to version 5.0.0. Anybody have any idea what I am doing wrong here? thanks in advance, Matthijs -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120806/be051c98/attachment.htm From baroni at sissa.it Tue Aug 7 01:21:35 2012 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 7 Aug 2012 01:21:35 +0200 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: no matter what ld1.x or any other code can (or cannot) do for you, as Axel said, it makes very little sense, I am afraid, to study a Ti->O (or O-Ti, for that matter) substitution using the vca. SB On Aug 6, 2012, at 5:32 PM, Axel Kohlmeyer wrote: > On Mon, Aug 6, 2012 at 5:19 PM, Yue-Wen Fang wrote: >> >> Thank you, sir, but it seems that you ignore some questions shown below in >> our emails. Have you seen these paragraphs before? > > rather than having me to go through all your e-mails > and remember what i answered and what i didn't, > why don't you just reformulate the question? > > that will make it easier for everybody. > > thanks, > axel. > >> Regards! > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/57e11372/attachment-0001.htm From yuewen.fang at gmail.com Tue Aug 7 02:58:26 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 7 Aug 2012 08:58:26 +0800 Subject: [Pw_forum] Why my generated pp doesn't contain the information of number of Q-function(nqf)? In-Reply-To: References: Message-ID: Dear Axel, I've got your meaning. Thank you~ Regards! Yuewen 2012/8/7 Stefano Baroni > no matter what ld1.x or any other code can (or cannot) do for you, as Axel > said, it makes very little sense, I am afraid, to study a Ti->O (or O-Ti, > for that matter) substitution using the vca. SB > > On Aug 6, 2012, at 5:32 PM, Axel Kohlmeyer wrote: > > On Mon, Aug 6, 2012 at 5:19 PM, Yue-Wen Fang > wrote: > > > Thank you, sir, but it seems that you ignore some questions shown below in > > our emails. Have you seen these paragraphs before? > > > rather than having me to go through all your e-mails > and remember what i answered and what i didn't, > why don't you just reformulate the question? > > that will make it easier for everybody. > > thanks, > axel. > > Regards! > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/49035b1c/attachment.htm From mahdi_msg2010 at yahoo.co.uk Tue Aug 7 09:40:52 2012 From: mahdi_msg2010 at yahoo.co.uk (mahdi Davari) Date: Tue, 7 Aug 2012 08:40:52 +0100 (BST) Subject: [Pw_forum] Gamma point algorithm Message-ID: <1344325252.91456.YahooMailNeo@web171401.mail.ir2.yahoo.com> Dear All When I am determining optical spectra of some metals it needs?degauss?for electron charges in ` scf ` calculations. The problem is that when I want to run turbo_lanczos it says that there is a problem in gamma point?algorithm Help plz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/e7d17a64/attachment.htm From subacalvince at gmail.com Tue Aug 7 14:59:36 2012 From: subacalvince at gmail.com (Nyaruanda Calvince) Date: Tue, 7 Aug 2012 15:59:36 +0300 Subject: [Pw_forum] find out Message-ID: hi friendds! am doing band calculation and my input is &inputpp prefix='Si_exc1', filband='bands.dat' lsym=.true. output is. what is the problem here! thanks in advance Program BANDS v.4.3.2 starts on 7Aug2012 at 14:44:57 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 1 processors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from do_bands : error # 1 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/a0156ae3/attachment.htm From fratesi at mater.unimib.it Tue Aug 7 15:10:57 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Tue, 07 Aug 2012 15:10:57 +0200 Subject: [Pw_forum] find out In-Reply-To: References: Message-ID: <502113E1.7060500@mater.unimib.it> Hi! Your input namelist is not closed by a "/". Also notice that in espresso-5 the namelist would be called "&bands" HTH Guido On 08/07/2012 02:59 PM, Nyaruanda Calvince wrote: > hi friendds! > am doing band calculation and my input is > > &inputpp > prefix='Si_exc1', > filband='bands.dat' > lsym=.true. > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From subacalvince at gmail.com Tue Aug 7 15:16:39 2012 From: subacalvince at gmail.com (Nyaruanda Calvince) Date: Tue, 7 Aug 2012 16:16:39 +0300 Subject: [Pw_forum] thanks Message-ID: av solved problem thru mike supoort. cheers wonderful people -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/f60b8179/attachment.htm From rainbee1988 at gmail.com Tue Aug 7 21:02:20 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Tue, 7 Aug 2012 15:02:20 -0400 Subject: [Pw_forum] non-existed variables Message-ID: Dear all, There are three examples, H2O, NH4+ and N2 in the dipole example of qe-4.3.2, and their input files include several variables like do_ee, nelec, nelup and neldw in the SYSTEM nalists. What do those variables mean? I can not find them in INPUT_PW.txt file. How to fix it? Thanks! Ruibin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120807/d5b9b6a1/attachment.htm From dmitry at korotin.name Wed Aug 8 13:20:43 2012 From: dmitry at korotin.name (Dmitry Korotin) Date: Wed, 8 Aug 2012 17:20:43 +0600 Subject: [Pw_forum] QE plugins system Message-ID: Dear QE Developers, is there some guide or instruction or specification of new QE plugins system? The idea of plugins is brilliant! I want to transform my code into plugin but need some info about how it is organized. (Of course I can check existing plugins and do a similar thing but it is inconvenient way). Thank you in advance. -- Best regards, Dr. Dmitry Korotin Institute of Metal Physics S. Kovalevskaya, 18 620990 Yekaterinburg Russia From lmartinsamos at gmail.com Wed Aug 8 13:49:26 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 8 Aug 2012 13:49:26 +0200 Subject: [Pw_forum] QE plugins system In-Reply-To: References: Message-ID: Dear Dimitry, the "QE plugin system" is at the moment more something like an "automatic download, untar and compile" procedure, a part for the case of PLUMED and the future release of QMMM. We call "plugin" anything which is not related to "core routines" and is installed by some automatic procedure. There are different kinds of "plugins" inside QE at the moment: 1) like W90, WANT and YAMBO --> postprocessing-like codes, that are completely PW/PH routine independent. They just read some output. For making such kind of plugin, we just need an URL with the .tar.gz release and we will add the necessary lines to the Makefiles in order to have an automatic installation. If you have write access to QE repository, you can follow what has been already done in install/plugins_list and install/plugins_makefile. 2) Like NEB, TDDFPT ...--> codes that call some PW/PH routines as they are (without the need of patching lines ...). Same as in the 1) case. 3) Like PLUMED --> some routines of PW/PH need to be patched. In this case, we construct "empty routines" (like plugin_forces.f90 or plugin_initialization.f90). If you are in this case, we can have a skype meeting to understand the best way for including your work. 4) something else ---> as in 3) we can have a skype meeting. let me know best regards Layla 2012/8/8 Dmitry Korotin > Dear QE Developers, > is there some guide or instruction or specification of new QE plugins > system? > The idea of plugins is brilliant! I want to transform my code into > plugin but need some info about how it is organized. > > (Of course I can check existing plugins and do a similar thing but it > is inconvenient way). > > Thank you in advance. > -- > > Best regards, > Dr. Dmitry Korotin > > Institute of Metal Physics > S. Kovalevskaya, 18 > 620990 Yekaterinburg > Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/03d019b8/attachment.htm From elie.moujaes at hotmail.co.uk Wed Aug 8 16:18:46 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 8 Aug 2012 15:18:46 +0100 Subject: [Pw_forum] reading_namelist error #19 Message-ID: Hello all, I am trying to relax a structure with 8 atoms (5 carbons and three hydrogens) but a few seconds after execution, the code stops with the error: reading_namelist error # 19namelist system which means there is an error in the SYSTEM part. However I checked it several times and could not spot any errors. Any help please? &control prefix='structure', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true., verbosity='high', pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/Graphyne/GRAPHYNEDIR', / &system ibrav= 0, celldm(1)= 9.008277, nat=8, ntyp= 2, ecutwfc =32, ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 / &electrons conv_thr=1.D-7, mixing_beta=0.3D0, mixing_mode='local-TF', diago_david_ndim=2, N.B: I have realised that when celldm(1) (9.008277 Bohrs) option is removed, I do not get this particular error again. Thank you Elie Mouyt University of NottinghamNG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/49bedae0/attachment.htm From nicola.marzari at epfl.ch Wed Aug 8 16:27:42 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Wed, 08 Aug 2012 16:27:42 +0200 Subject: [Pw_forum] reading_namelist error #19 In-Reply-To: References: Message-ID: <5022775E.7010609@epfl.ch> On 08/08/2012 16:18, Elie M wrote: > Hello all, > > &system > ibrav= 0, celldm(1)= 9.008277, nat=8, ntyp= 2, ecutwfc =32, > ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 your unit cell is not well defined - ibrav 0 requires cell_parameters http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#id1486403 ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From elie.moujaes at hotmail.co.uk Wed Aug 8 16:30:32 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 8 Aug 2012 15:30:32 +0100 Subject: [Pw_forum] reading_namelist error #19 In-Reply-To: <5022775E.7010609@epfl.ch> References: , <5022775E.7010609@epfl.ch> Message-ID: Professor Marzari, Sorry my mistake, I have not pasted the CELL_PARAMETERS section. The error is still there with the presence of CELL_PARAMETERS. Thanks &control prefix='Graphyne', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true., verbosity='high', pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/Graphyne/GRAPHYNEDIR', / &system ibrav= 0, nat=8, ntyp= 2, ecutwfc =32, ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 / &electrons conv_thr=1.D-7, mixing_beta=0.3D0, mixing_mode='local-TF', diago_david_ndim=2, / &ions ion_dynamics='bfgs' / &cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) {hexagonal} 0.500000000 0.866025404 0.000000000 0.500000000 -0.866025404 0.000000000 0.000000000 0.000000000 6.293266205 ............. > Date: Wed, 8 Aug 2012 16:27:42 +0200 > From: nicola.marzari at epfl.ch > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] reading_namelist error #19 > > On 08/08/2012 16:18, Elie M wrote: > > Hello all, > > > > &system > > ibrav= 0, celldm(1)= 9.008277, nat=8, ntyp= 2, ecutwfc =32, > > ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 > > > your unit cell is not well defined - ibrav 0 requires cell_parameters > > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#id1486403 > > > > ---------------------------------------------------------------------- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/b5bd15e9/attachment.htm From pchen at ion.chem.utk.edu Wed Aug 8 20:00:56 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Wed, 8 Aug 2012 14:00:56 -0400 Subject: [Pw_forum] LSDA+U calculation on band gap Message-ID: Dear All, According to the experiments, the material's ground state is afm and the band gap is ~2.30 eV in 4K. In the magnetic field, the spin moments are aligned in the field direction (we call it "fm state") and the band gap is ~2.34 eV. But from the calculation results, when U>=5 eV, the fm spin up gap is less than that of afm state which is different from experimental results. (I guess we should choose spin up gap to represent fm state gap since spin down gap is larger). From the calculated gap value, U=8 eV is close to experimental results, but the gap in fm state is less. Please let me know what I can do to improve the results? U afm gap fm spin up fm spin down 4 1.49 1.723 1.731 5 1.81 1.77 2.01 6 1.922 1.912 2.273 8 2.265 2.076 2.634 -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/bda7185b/attachment-0001.htm From masoudnahali at gmail.com Wed Aug 8 20:44:23 2012 From: masoudnahali at gmail.com (Masoud) Date: Wed, 8 Aug 2012 20:44:23 +0200 Subject: [Pw_forum] reading_namelist error #19 Message-ID: Hi *Elie* As I know in the new version of Quantum Espresso the CELL_PARAMETERS card is different with the version 4. it is something like: cell_parameters {alat|Bohr|Angstrom} Also you 'd better get noticed that the XCrysDen is going to be compatible with such parameters especially when you use ibrav=0, so you should use it carefully. For example you may read position of atoms wrong with the current version of XCrysDen. Please change the parameters appropriately and check your job again. Also you can contact me in private and send me your input file to be checked. Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali Professor Marzari, Sorry my mistake, I have not pasted the CELL_PARAMETERS section. The error is still there with the presence of CELL_PARAMETERS. Thanks &control prefix='Graphyne', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true., verbosity='high', pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo', outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/Graphyne/GRAPHYNEDIR', / &system ibrav= 0, nat=8, ntyp= 2, ecutwfc =32, ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 / &electrons conv_thr=1.D-7, mixing_beta=0.3D0, mixing_mode='local-TF', diago_david_ndim=2, / &ions ion_dynamics='bfgs' / &cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) {hexagonal} 0.500000000 0.866025404 0.000000000 0.500000000 -0.866025404 0.000000000 0.000000000 0.000000000 6.293266205 ............. >* Date: Wed, 8 Aug 2012 16:27:42 +0200 *>* From: nicola.marzari at epfl.ch *>* To: pw_forum at pwscf.org *>* Subject: Re: [Pw_forum] reading_namelist error #19 *> * *>* On 08/08/2012 16:18, Elie M wrote: *>* > Hello all, *>* > *>* > &system *>* > ibrav= 0, celldm(1)= 9.008277, nat=8, ntyp= 2, ecutwfc =32, *>* > ecutrho=288,occupations='smearing', smearing='mv',degauss=0.02 *> * *> * *>* your unit cell is not well defined - ibrav 0 requires cell_parameters *> * *>* http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#id1486403 *> * *> * *> * *>* ---------------------------------------------------------------------- *>* Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/6350b2da/attachment.htm From himm0013 at umn.edu Wed Aug 8 20:49:33 2012 From: himm0013 at umn.edu (Burak Himmetoglu) Date: Wed, 8 Aug 2012 13:49:33 -0500 Subject: [Pw_forum] LSDA+U calculation on band gap In-Reply-To: References: Message-ID: Hello Peng, One can compute U for the AFM and FM states separately using linear response. Then, using the calculated U values for each state, you can recompute the gaps. This approach might resolve the issue. Best regards, Burak On Wed, Aug 8, 2012 at 1:00 PM, Peng Chen wrote: > Dear All, > > According to the experiments, the material's ground state is afm and the > band gap is ~2.30 eV in 4K. > In the magnetic field, the spin moments are aligned in the field direction > (we call it "fm state") and the > band gap is ~2.34 eV. But from the calculation results, when U>=5 eV, the > fm spin up gap is less > than that of afm state which is different from experimental results. (I > guess we should choose spin > up gap to represent fm state gap since spin down gap is larger). From the > calculated gap value, > U=8 eV is close to experimental results, but the gap in fm state is less. > Please let me know what > I can do to improve the results? > > > U afm gap fm spin up fm spin down > 4 1.49 1.723 1.731 > 5 1.81 1.77 2.01 > 6 1.922 1.912 2.273 > 8 2.265 2.076 2.634 > > > -- > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/ec1c8bae/attachment.htm From bfazi90 at gmail.com Wed Aug 8 21:18:21 2012 From: bfazi90 at gmail.com (bf azi) Date: Wed, 8 Aug 2012 23:48:21 +0430 Subject: [Pw_forum] VDW-DF2 Message-ID: Hi Dear all In my system Van der waals interaction play important role and I use PBE-Ultrasoft pseudopotential in my system and dft_input="vdm-df2" , But my Result not good and Diagram of Energy via Distance have not good Minimum. Can help me please? Bani Adam Faculty of Science Egypt From degironc at sissa.it Wed Aug 8 21:33:08 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 08 Aug 2012 21:33:08 +0200 Subject: [Pw_forum] VDW-DF2 In-Reply-To: References: Message-ID: <5022BEF4.5050000@sissa.it> probably is just a typo in your massage but the god keyword is not vdm-df2 but vdW-DF2 check you are using the latest version of the code... there was a problem at a given point with the way the LDA part was added at a given point (basically it was added twice...) stefano On 08/08/2012 09:18 PM, bf azi wrote: > Hi Dear all > > In my system Van der waals interaction play important role and I use > PBE-Ultrasoft pseudopotential in my system and dft_input="vdm-df2" , > But my Result not good and Diagram of Energy via Distance have not > good Minimum. > > Can help me please? > > > Bani Adam > Faculty of Science > Egypt > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From pchen at ion.chem.utk.edu Wed Aug 8 21:59:35 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Wed, 8 Aug 2012 15:59:35 -0400 Subject: [Pw_forum] LSDA+U calculation on band gap In-Reply-To: References: Message-ID: Dear Dr. Burak, U is different for AFM and FM states? The problem now is I can not make the U calculation correct. Dr. Matteo is helping me with great patient, but still no luck now. On Wed, Aug 8, 2012 at 2:49 PM, Burak Himmetoglu wrote: > Hello Peng, > > One can compute U for the AFM and FM states separately using linear > response. Then, using the calculated U values for each state, you can > recompute the gaps. This approach might resolve the issue. > > Best regards, > > Burak > > On Wed, Aug 8, 2012 at 1:00 PM, Peng Chen wrote: > >> Dear All, >> >> According to the experiments, the material's ground state is afm and the >> band gap is ~2.30 eV in 4K. >> In the magnetic field, the spin moments are aligned in the field >> direction (we call it "fm state") and the >> band gap is ~2.34 eV. But from the calculation results, when U>=5 eV, the >> fm spin up gap is less >> than that of afm state which is different from experimental results. (I >> guess we should choose spin >> up gap to represent fm state gap since spin down gap is larger). From the >> calculated gap value, >> U=8 eV is close to experimental results, but the gap in fm state is less. >> Please let me know what >> I can do to improve the results? >> >> >> U afm gap fm spin up fm spin down >> 4 1.49 1.723 1.731 >> 5 1.81 1.77 2.01 >> 6 1.922 1.912 2.273 >> 8 2.265 2.076 2.634 >> >> >> -- >> Best Regards. >> Peng >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/5ea0d29b/attachment.htm From himm0013 at umn.edu Wed Aug 8 22:18:32 2012 From: himm0013 at umn.edu (Burak Himmetoglu) Date: Wed, 8 Aug 2012 15:18:32 -0500 Subject: [Pw_forum] LSDA+U calculation on band gap In-Reply-To: References: Message-ID: Hello Peng, Yes, in principle U is different for different states. The difference might be small, but it can be very critical in your case, since the AFM and FM gaps are very close. Best regards, Burak On Wed, Aug 8, 2012 at 2:59 PM, Peng Chen wrote: > Dear Dr. Burak, > > U is different for AFM and FM states? The problem now is I can not make > the U calculation correct. Dr. Matteo is helping me with great patient, > but still no luck now. > > > On Wed, Aug 8, 2012 at 2:49 PM, Burak Himmetoglu wrote: > >> Hello Peng, >> >> One can compute U for the AFM and FM states separately using linear >> response. Then, using the calculated U values for each state, you can >> recompute the gaps. This approach might resolve the issue. >> >> Best regards, >> >> Burak >> >> On Wed, Aug 8, 2012 at 1:00 PM, Peng Chen wrote: >> >>> Dear All, >>> >>> According to the experiments, the material's ground state is afm and the >>> band gap is ~2.30 eV in 4K. >>> In the magnetic field, the spin moments are aligned in the field >>> direction (we call it "fm state") and the >>> band gap is ~2.34 eV. But from the calculation results, when U>=5 eV, >>> the fm spin up gap is less >>> than that of afm state which is different from experimental results. (I >>> guess we should choose spin >>> up gap to represent fm state gap since spin down gap is larger). From >>> the calculated gap value, >>> U=8 eV is close to experimental results, but the gap in fm state is >>> less. Please let me know what >>> I can do to improve the results? >>> >>> >>> U afm gap fm spin up fm spin down >>> 4 1.49 1.723 1.731 >>> 5 1.81 1.77 2.01 >>> 6 1.922 1.912 2.273 >>> 8 2.265 2.076 2.634 >>> >>> >>> -- >>> Best Regards. >>> Peng >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120808/f41ad241/attachment-0001.htm From mtorabi at uwo.ca Fri Aug 10 18:22:55 2012 From: mtorabi at uwo.ca (Amin Torabi) Date: Fri, 10 Aug 2012 12:22:55 -0400 Subject: [Pw_forum] zns/zno surface Message-ID: Dear PWSCF experts, I am willing to find out how doping of oxygen in a surface of ZnS (wurtzite) changes its band structure. I have a slab model composed of 8 layers of ZnS, in which 2 sulfur atoms are replace with oxygen, and a 15 Angstrom vacuum on top of the surface. I am relaxing only the first two layers. Now, my question is the sulfur or oxygen atoms on the top level resembles the surface that I am interested in; however, the sulfur (or zinc) atoms at the bottom are artifact of the model. How should I saturate them? Can you please take a look on my input file and let me know if you have any suggestion? Thanks &CONTROL calculation = 'relax' prefix = 'orig' pseudo_dir = '/home/p/' outdir = './tmp' tstress = .true tprnfor = .true / &SYSTEM ibrav = 12 A = 11.3772 B = 11.3772 C = 40.0 cosAB = -0.5 nat = 153 ntyp = 3 ecutwfc = 30 ecutrho = 300 occupations = 'smearing' degauss = 0.01 smearing = 'gauss' / &ELECTRONS mixing_mode = 'local-TF' mixing_beta = 0.3 / &IONS / ATOMIC_SPECIES Zn 65.409 Zn.pbe-van.UPF S 32.066 S.pbe-van_bm.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS angstrom Zn 1.896209796 1.094779514 3.1132225450 0 0 0 S 0.000002678 2.189555203 2.3306235650 0 0 0 S 1.896209090 1.094779922 5.4413927710 0 0 0 Zn 0.000001973 2.189555611 6.2239919760 0 0 0 Zn 1.896209796 1.094779514 9.3347611820 0 0 0 S 0.000002678 2.189555203 8.5521622020 0 0 0 S 1.896209090 1.094779922 11.662931408 0 0 0 Zn 0.000001973 2.189555611 12.445530613 0 0 0 Zn 1.896209796 1.094779514 15.556299819 0 0 0 S 0.000002678 2.189555203 14.773700839 0 0 0 S 1.896209090 1.094779922 17.884470045 0 0 0 Zn 0.000001973 2.189555611 18.667069250 0 0 0 Zn 1.896209796 1.094779514 21.777838456 S 0.000002678 2.189555203 20.995239476 S 1.896209090 1.094779922 24.106008682 Zn 0.000001973 2.189555611 24.888607887 S 0.000002678 2.189555203 27.216778113 Zn 0.000005649 4.379109319 3.1132225450 0 0 0 S -1.896201469 5.473885008 2.3306235650 0 0 0 S 0.000004943 4.379109727 5.4413927710 0 0 0 Zn -1.896202174 5.473885416 6.2239919760 0 0 0 Zn 0.000005649 4.379109319 9.3347611820 0 0 0 S -1.896201469 5.473885008 8.5521622020 0 0 0 S 0.000004943 4.379109727 11.662931408 0 0 0 Zn -1.896202174 5.473885416 12.445530613 0 0 0 Zn 0.000005649 4.379109319 15.556299819 0 0 0 S -1.896201469 5.473885008 14.773700839 0 0 0 S 0.000004943 4.379109727 17.884470045 0 0 0 Zn -1.896202174 5.473885416 18.667069250 0 0 0 Zn 0.000005649 4.379109319 21.777838456 S -1.896201469 5.473885008 20.995239476 S 0.000004943 4.379109727 24.106008682 Zn -1.896202174 5.473885416 24.888607887 S -1.896201469 5.473885008 27.216778113 Zn -1.896198498 7.663439124 3.1132225450 0 0 0 S -3.792405616 8.758214813 2.3306235650 0 0 0 S -1.896199204 7.663439532 5.4413927710 0 0 0 Zn -3.792406321 8.758215221 6.2239919760 0 0 0 Zn -1.896198498 7.663439124 9.3347611820 0 0 0 S -3.792405616 8.758214813 8.5521622020 0 0 0 S -1.896199204 7.663439532 11.662931408 0 0 0 Zn -3.792406321 8.758215221 12.445530613 0 0 0 Zn -1.896198498 7.663439124 15.556299819 0 0 0 S -3.792405616 8.758214813 14.773700839 0 0 0 S -1.896199204 7.663439532 17.884470045 0 0 0 Zn -3.792406321 8.758215221 18.667069250 0 0 0 Zn -1.896198498 7.663439124 21.777838456 S -3.792405616 8.758214813 20.995239476 S -1.896199204 7.663439532 24.106008682 Zn -3.792406321 8.758215221 24.888607887 S -3.792405616 8.758214813 27.216778113 Zn 5.688625711 1.094783325 3.1132225450 0 0 0 S 3.792418593 2.189559014 2.3306235650 0 0 0 S 5.688625005 1.094783733 5.4413927710 0 0 0 Zn 3.792417888 2.189559422 6.2239919760 0 0 0 Zn 5.688625711 1.094783325 9.3347611820 0 0 0 S 3.792418593 2.189559014 8.5521622020 0 0 0 S 5.688625005 1.094783733 11.662931408 0 0 0 Zn 3.792417888 2.189559422 12.445530613 0 0 0 Zn 5.688625711 1.094783325 15.556299819 0 0 0 S 3.792418593 2.189559014 14.773700839 0 0 0 S 5.688625005 1.094783733 17.884470045 0 0 0 Zn 3.792417888 2.189559422 18.667069250 0 0 0 Zn 5.688625711 1.094783325 21.777838456 S 3.792418593 2.189559014 20.995239476 S 5.688625005 1.094783733 24.106008682 Zn 3.792417888 2.189559422 24.888607887 S 3.792418593 2.189559014 27.216778113 Zn 3.792421564 4.379113130 3.1132225450 0 0 0 S 1.896214446 5.473888819 2.3306235650 0 0 0 S 3.792420858 4.379113538 5.4413927710 0 0 0 Zn 1.896213741 5.473889227 6.2239919760 0 0 0 Zn 3.792421564 4.379113130 9.3347611820 0 0 0 S 1.896214446 5.473888819 8.5521622020 0 0 0 S 3.792420858 4.379113538 11.662931408 0 0 0 Zn 1.896213741 5.473889227 12.445530613 0 0 0 Zn 3.792421564 4.379113130 15.556299819 0 0 0 S 1.896214446 5.473888819 14.773700839 0 0 0 S 3.792420858 4.379113538 17.884470045 0 0 0 Zn 1.896213741 5.473889227 18.667069250 0 0 0 Zn 3.792421564 4.379113130 21.777838456 S 1.896214446 5.473888819 20.995239476 O 3.792420858 4.379113538 23.706008682 Zn 1.896213741 5.473889227 24.888607887 O 1.896214446 5.473888819 26.816778113 Zn 1.896217417 7.663442935 3.1132225450 0 0 0 S 0.000010299 8.758218624 2.3306235650 0 0 0 S 1.896216711 7.663443343 5.4413927710 0 0 0 Zn 0.000009594 8.758219032 6.2239919760 0 0 0 Zn 1.896217417 7.663442935 9.3347611820 0 0 0 S 0.000010299 8.758218624 8.5521622020 0 0 0 S 1.896216711 7.663443343 11.662931408 0 0 0 Zn 0.000009594 8.758219032 12.445530613 0 0 0 Zn 1.896217417 7.663442935 15.556299819 0 0 0 S 0.000010299 8.758218624 14.773700839 0 0 0 S 1.896216711 7.663443343 17.884470045 0 0 0 Zn 0.000009594 8.758219032 18.667069250 0 0 0 Zn 1.896217417 7.663442935 21.777838456 S 0.000010299 8.758218624 20.995239476 S 1.896216711 7.663443343 24.106008682 Zn 0.000009594 8.758219032 24.888607887 S 0.000010299 8.758218624 27.216778113 Zn 9.481041626 1.094787136 3.1132225450 0 0 0 S 7.584834508 2.189562825 2.3306235650 0 0 0 S 9.481040920 1.094787544 5.4413927710 0 0 0 Zn 7.584833803 2.189563233 6.2239919760 0 0 0 Zn 9.481041626 1.094787136 9.3347611820 0 0 0 S 7.584834508 2.189562825 8.5521622020 0 0 0 S 9.481040920 1.094787544 11.662931408 0 0 0 Zn 7.584833803 2.189563233 12.445530613 0 0 0 Zn 9.481041626 1.094787136 15.556299819 0 0 0 S 7.584834508 2.189562825 14.773700839 0 0 0 S 9.481040920 1.094787544 17.884470045 0 0 0 Zn 7.584833803 2.189563233 18.667069250 0 0 0 Zn 9.481041626 1.094787136 21.777838456 S 7.584834508 2.189562825 20.995239476 S 9.481040920 1.094787544 24.106008682 Zn 7.584833803 2.189563233 24.888607887 S 7.584834508 2.189562825 27.216778113 Zn 7.584837479 4.379116941 3.1132225450 0 0 0 S 5.688630361 5.473892630 2.3306235650 0 0 0 S 7.584836773 4.379117349 5.4413927710 0 0 0 Zn 5.688629656 5.473893038 6.2239919760 0 0 0 Zn 7.584837479 4.379116941 9.3347611820 0 0 0 S 5.688630361 5.473892630 8.5521622020 0 0 0 S 7.584836773 4.379117349 11.662931408 0 0 0 Zn 5.688629656 5.473893038 12.445530613 0 0 0 Zn 7.584837479 4.379116941 15.556299819 0 0 0 S 5.688630361 5.473892630 14.773700839 0 0 0 S 7.584836773 4.379117349 17.884470045 0 0 0 Zn 5.688629656 5.473893038 18.667069250 0 0 0 Zn 7.584837479 4.379116941 21.777838456 S 5.688630361 5.473892630 20.995239476 S 7.584836773 4.379117349 24.106008682 Zn 5.688629656 5.473893038 24.888607887 S 5.688630361 5.473892630 27.216778113 Zn 5.688633332 7.663446746 3.1132225450 0 0 0 S 3.792426214 8.758222435 2.3306235650 0 0 0 S 5.688632626 7.663447154 5.4413927710 0 0 0 Zn 3.792425509 8.758222843 6.2239919760 0 0 0 Zn 5.688633332 7.663446746 9.3347611820 0 0 0 S 3.792426214 8.758222435 8.5521622020 0 0 0 S 5.688632626 7.663447154 11.662931408 0 0 0 Zn 3.792425509 8.758222843 12.445530613 0 0 0 Zn 5.688633332 7.663446746 15.556299819 0 0 0 S 3.792426214 8.758222435 14.773700839 0 0 0 S 5.688632626 7.663447154 17.884470045 0 0 0 Zn 3.792425509 8.758222843 18.667069250 0 0 0 Zn 5.688633332 7.663446746 21.777838456 S 3.792426214 8.758222435 20.995239476 S 5.688632626 7.663447154 24.106008682 Zn 3.792425509 8.758222843 24.888607887 S 3.792426214 8.758222435 27.216778113 K_POINTS automatic 3 3 1 0 0 0 -- *************************************** Amin Torabi Ph.D. Student Chemistry Dept. Western University London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120810/a8d2de8e/attachment-0001.htm From bdslipun at gmail.com Fri Aug 10 21:22:13 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Sat, 11 Aug 2012 00:52:13 +0530 Subject: [Pw_forum] Fwd: problem of Tc calculation in electron phonon coefficents In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: 2012/8/5 Subject: Fwd: problem of Tc calculation in electron phonon coefficents To: PWSCF Forum ---------- Forwarded message ---------- From: bhabya sahoo Date: 2012/8/1 Subject: problem of Tc calculation in electron phonon coefficents To: PWSCF Forum i am calculating Tc for YC( ytrium carbide) but it gives error NaN I have all positive frequency in the phonon spectrum why the error comes ? i have given my input file 1. pw.x input &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , la2F = .true., / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 16 16 16 0 0 0 2 pw.x input&CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/bds/yc2test/' , wfcdir = '/home/bds/yc2test/' , pseudo_dir = '/home/bds/bhabya/espresso-4.3.2/pseudo/' , prefix = 'yc1' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.6, nat = 2, ntyp = 2, ecutwfc = 60 , ecutrho = 600 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , / &ELECTRONS / ATOMIC_SPECIES y 88.90580 Y.pw91-nsp-van.UPF c 12.01700 C.pw91-van_ak.UPF ATOMIC_POSITIONS crystal y 0.000000000 0.000000000 0.000000000 c 0.500000000 0.500000000 0.500000000 K_POINTS automatic 8 8 8 0 0 0 ph.x input &INPUTPH outdir = '/home/bds/yc2test/' , prefix = 'yc1' , fildyn = 'yc1.dyn' , fildvscf = 'yc1dv' , ldisp = .true., nq1 = 4 , nq2 = 4 , nq3 = 4 , epsil = .false., elph = .true., fpol = .false. , recover = .false. , tr2_ph=1.0d-12, trans=.true., amass(1) = 88.9058, amass(2) = 12.017, / output error shows alha2F.dat # E(THz) 0.005 0.010 0.015 0.020 0.025 0.030 0.035 0.040 0.045 0.050 0.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.0754 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.1508 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.2261 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3015 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.3769 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.4523 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.5276 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6030 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.6784 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.7538 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.8291 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9045 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 0.9799 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.0553 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.1307 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2060 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.2814 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.3568 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.4322 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5075 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.5829 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.6583 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.7337 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8090 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.8844 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 1.9598 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.0352 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1106 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.1859 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.2613 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.3367 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4121 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.4874 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.5628 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.6382 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7136 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.7889 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.8643 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 2.9397 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0151 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.0905 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.1658 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.2412 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3166 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.3920 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.4673 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.5427 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6181 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.6935 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.7688 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.8442 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9196 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.9950 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.0704 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.1457 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2211 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.2965 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.3719 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.4472 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5226 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.5980 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.6734 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.7487 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8241 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.8995 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 4.9749 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.0503 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.1256 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2010 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.2764 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.3518 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.4271 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5025 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.5779 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.6533 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.7286 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8040 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.8794 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 5.9548 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.0302 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1055 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.1809 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.2563 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.3317 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4070 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.4824 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.5578 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.6332 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7085 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.7839 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.8593 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 6.9347 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0101 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.0854 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.1608 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.2362 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3116 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.3869 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.4623 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.5377 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6131 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.6884 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.7638 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.8392 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9146 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 7.9899 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.0653 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.1407 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2161 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.2915 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.3668 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.4422 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5176 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.5930 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.6683 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.7437 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8191 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.8945 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 8.9698 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.0452 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1206 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.1960 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.2714 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.3467 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4221 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.4975 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.5729 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.6482 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7236 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.7990 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.8744 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 9.9497 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.0251 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1005 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.1759 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.2513 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.3266 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4020 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.4774 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.5528 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.6281 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7035 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.7789 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.8543 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 10.9296 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0050 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.0804 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.1558 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.2312 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3065 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.3819 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.4573 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.5327 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6080 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.6834 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.7588 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.8342 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9095 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 11.9849 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.0603 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.1357 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2111 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.2864 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.3618 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.4372 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5126 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.5879 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.6633 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.7387 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8141 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.8894 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 12.9648 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.0402 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1156 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.1910 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.2663 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.3417 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4171 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.4925 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.5678 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.6432 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7186 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.7940 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.8693 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 13.9447 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0201 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.0955 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.1709 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.2462 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3216 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.3970 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.4724 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.5477 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6231 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.6985 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.7739 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.8492 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 14.9246 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 15.0000 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN B sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120811/6c9a5759/attachment-0001.htm From iyad.ne at gmail.com Fri Aug 10 21:29:19 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Fri, 10 Aug 2012 15:29:19 -0400 Subject: [Pw_forum] phonon calculations do not converge Message-ID: Dear PW_Forum, I am running phonon calculations for FeSi (a narrow band gap semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 q-points ran successfully and got good phonon values. However when I reach the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. Below are my input files: &control calculation='scf', restart_mode='from_scratch', title='FeSi', outdir='./', prefix='FeSi', pseudo_dir='./', / &system ibrav=1, celldm(1)=8.4165, nat=8, ntyp=2, ecutwfc=60.0, ecutrho= 720.0, / &electrons conv_thr=1.0d-9, mixing_mode='plain', mixing_beta=0.7, diagonalization='david', / ATOMIC_SPECIES Fe 55.847 Fe.pw91-sp-van_ak.UPF Si 28.086 Si.pw91-n_van.UPF ATOMIC_POSITIONS Fe 0.134855265 0.134855265 0.134855265 Fe 0.634855265 0.365144735 0.865144735 Fe 0.865144735 0.634855265 0.365144735 Fe 0.365144735 0.865144735 0.634855265 Si 0.839976366 0.839976366 0.839976366 Si 0.339976366 0.660023634 0.160023634 Si 0.160023634 0.339976366 0.660023634 Si 0.660023634 0.160023634 0.339976366 K_POINTS {automatic} 10 10 10 0 0 0 *********************************** phonons of FeSi &inputph tr2_ph=1.0d-14, prefix='FeSi', amass(1)=55.847, amass(2)=28.086, outdir='./' fildyn='FeSi.dyn', trans=.true., ldisp=.true., nq1=6, nq2=6, nq3=6 recover=.true., alpha_mix(1)=0.30 Any comments and suggestions are welcomed. Thanks IYAD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120810/8520fc09/attachment.htm From wparker at anl.gov Fri Aug 10 23:16:06 2012 From: wparker at anl.gov (William Parker) Date: Fri, 10 Aug 2012 14:16:06 -0700 Subject: [Pw_forum] phonon calculations do not converge In-Reply-To: References: Message-ID: Hi Iyad, How strong is the failure to converge at (0, 1/6, 1/6)? Perhaps a less tight tr2_ph value of, say, 1.0d-10 would get you where you need to be. --William On Aug 10, 2012, at 12:29 PM, Iyad AL-QASIR wrote: > Dear PW_Forum, > > I am running phonon calculations for FeSi (a narrow band gap semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 q-points ran successfully and got good phonon values. However when I reach the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. > > Below are my input files: > > &control > calculation='scf', > restart_mode='from_scratch', > title='FeSi', > outdir='./', > prefix='FeSi', > pseudo_dir='./', > / > &system > ibrav=1, > celldm(1)=8.4165, > nat=8, ntyp=2, > ecutwfc=60.0, > ecutrho= 720.0, > / > &electrons > conv_thr=1.0d-9, > mixing_mode='plain', > mixing_beta=0.7, > diagonalization='david', > / > ATOMIC_SPECIES > Fe 55.847 Fe.pw91-sp-van_ak.UPF > Si 28.086 Si.pw91-n_van.UPF > ATOMIC_POSITIONS > Fe 0.134855265 0.134855265 0.134855265 > Fe 0.634855265 0.365144735 0.865144735 > Fe 0.865144735 0.634855265 0.365144735 > Fe 0.365144735 0.865144735 0.634855265 > Si 0.839976366 0.839976366 0.839976366 > Si 0.339976366 0.660023634 0.160023634 > Si 0.160023634 0.339976366 0.660023634 > Si 0.660023634 0.160023634 0.339976366 > K_POINTS {automatic} > 10 10 10 0 0 0 > *********************************** > phonons of FeSi > &inputph > tr2_ph=1.0d-14, > prefix='FeSi', > amass(1)=55.847, > amass(2)=28.086, > outdir='./' > fildyn='FeSi.dyn', > trans=.true., > ldisp=.true., > nq1=6, nq2=6, nq3=6 > recover=.true., > alpha_mix(1)=0.30 > > Any comments and suggestions are welcomed. > > Thanks > IYAD > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ********************************************************* William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From mariani.alex at rocketmail.com Sat Aug 11 07:47:20 2012 From: mariani.alex at rocketmail.com (Alex Mariani) Date: Fri, 10 Aug 2012 22:47:20 -0700 (PDT) Subject: [Pw_forum] piezoelectric constant In-Reply-To: <1343899805.32911.YahooMailNeo@web141102.mail.bf1.yahoo.com> References: <1343899805.32911.YahooMailNeo@web141102.mail.bf1.yahoo.com> Message-ID: <1344664040.75666.YahooMailNeo@web141106.mail.bf1.yahoo.com> Dear all I want to calculate the piezoelectric constant for PbTio3. How do using the QE code? What is the procedure? Please help me? best regards Alex Mariani Magadh University Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120810/4a18a385/attachment.htm From flux_ray12 at 163.com Sat Aug 11 08:00:24 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 11 Aug 2012 14:00:24 +0800 (CST) Subject: [Pw_forum] piezoelectric constant In-Reply-To: <1344664040.75666.YahooMailNeo@web141106.mail.bf1.yahoo.com> References: <1343899805.32911.YahooMailNeo@web141102.mail.bf1.yahoo.com> <1344664040.75666.YahooMailNeo@web141106.mail.bf1.yahoo.com> Message-ID: <3569a14.4d94.1391444e93e.Coremail.flux_ray12@163.com> Dear Alex: I think you can try Berry Phase implemented in the program pw.x. Reference: David Vanderbilt, Berry-phase theory of proper piezoelectric response, J. Phys. Chem. Solids, 61 (2000), 147 -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-11 13:47:20,"Alex Mariani" wrote: Dear all Iwantto calculatethepiezoelectric constant for PbTio3. Howdo using the QE code? What istheprocedure? Pleasehelpme? best regards Alex Mariani Magadh University Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120811/eec99524/attachment.htm From aakimov at z.rochester.edu Sat Aug 11 19:12:32 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sat, 11 Aug 2012 13:12:32 -0400 (EDT) Subject: [Pw_forum] zns/zno surface In-Reply-To: Message-ID: <587846793.57764.1344705152545.JavaMail.root@asems02.its.rochester.edu> Dear Amin, If you want to saturate bottom (and maybe even top) sulfur/oxygen atoms I would try to put hydrogens on them. This way you can localize electron density on the sulfur/oxigen atoms and avoid dangling bonds. In reality you of course will not see unsaturated O/S atoms on the surface - they will be protonated anyway or carry some other groups on them. However it may be fine to do calculations even without such saturation (especially for the bottom layer). ----- Original Message ----- From: "Amin Torabi" To: "PWSCF Forum" Sent: Friday, August 10, 2012 9:22:55 AM Subject: [Pw_forum] zns/zno surface Dear PWSCF experts, I am willing to find out how doping of oxygen in a surface of ZnS (wurtzite) changes its band structure. I have a slab model composed of 8 layers of ZnS, in which 2 sulfur atoms are replace with oxygen, and a 15 Angstrom vacuum on top of the surface. I am relaxing only the first two layers. Now, my question is the sulfur or oxygen atoms on the top level resembles the surface that I am interested in; however, the sulfur (or zinc) atoms at the bottom are artifact of the model. How should I saturate them? Can you please take a look on my input file and let me know if you have any suggestion? Thanks &CONTROL calculation = 'relax' prefix = 'orig' pseudo_dir = '/home/p/' outdir = './tmp' tstress = .true tprnfor = .true / &SYSTEM ibrav = 12 A = 11.3772 B = 11.3772 C = 40.0 cosAB = -0.5 nat = 153 ntyp = 3 ecutwfc = 30 ecutrho = 300 occupations = 'smearing' degauss = 0.01 smearing = 'gauss' / &ELECTRONS mixing_mode = 'local-TF' mixing_beta = 0.3 / &IONS / ATOMIC_SPECIES Zn 65.409 Zn.pbe-van.UPF S 32.066 S.pbe-van_bm.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS angstrom Zn 1.896209796 1.094779514 3.1132225450 0 0 0 S 0.000002678 2.189555203 2.3306235650 0 0 0 S 1.896209090 1.094779922 5.4413927710 0 0 0 Zn 0.000001973 2.189555611 6.2239919760 0 0 0 Zn 1.896209796 1.094779514 9.3347611820 0 0 0 S 0.000002678 2.189555203 8.5521622020 0 0 0 S 1.896209090 1.094779922 11.662931408 0 0 0 Zn 0.000001973 2.189555611 12.445530613 0 0 0 Zn 1.896209796 1.094779514 15.556299819 0 0 0 S 0.000002678 2.189555203 14.773700839 0 0 0 S 1.896209090 1.094779922 17.884470045 0 0 0 Zn 0.000001973 2.189555611 18.667069250 0 0 0 Zn 1.896209796 1.094779514 21.777838456 S 0.000002678 2.189555203 20.995239476 S 1.896209090 1.094779922 24.106008682 Zn 0.000001973 2.189555611 24.888607887 S 0.000002678 2.189555203 27.216778113 Zn 0.000005649 4.379109319 3.1132225450 0 0 0 S -1.896201469 5.473885008 2.3306235650 0 0 0 S 0.000004943 4.379109727 5.4413927710 0 0 0 Zn -1.896202174 5.473885416 6.2239919760 0 0 0 Zn 0.000005649 4.379109319 9.3347611820 0 0 0 S -1.896201469 5.473885008 8.5521622020 0 0 0 S 0.000004943 4.379109727 11.662931408 0 0 0 Zn -1.896202174 5.473885416 12.445530613 0 0 0 Zn 0.000005649 4.379109319 15.556299819 0 0 0 S -1.896201469 5.473885008 14.773700839 0 0 0 S 0.000004943 4.379109727 17.884470045 0 0 0 Zn -1.896202174 5.473885416 18.667069250 0 0 0 Zn 0.000005649 4.379109319 21.777838456 S -1.896201469 5.473885008 20.995239476 S 0.000004943 4.379109727 24.106008682 Zn -1.896202174 5.473885416 24.888607887 S -1.896201469 5.473885008 27.216778113 Zn -1.896198498 7.663439124 3.1132225450 0 0 0 S -3.792405616 8.758214813 2.3306235650 0 0 0 S -1.896199204 7.663439532 5.4413927710 0 0 0 Zn -3.792406321 8.758215221 6.2239919760 0 0 0 Zn -1.896198498 7.663439124 9.3347611820 0 0 0 S -3.792405616 8.758214813 8.5521622020 0 0 0 S -1.896199204 7.663439532 11.662931408 0 0 0 Zn -3.792406321 8.758215221 12.445530613 0 0 0 Zn -1.896198498 7.663439124 15.556299819 0 0 0 S -3.792405616 8.758214813 14.773700839 0 0 0 S -1.896199204 7.663439532 17.884470045 0 0 0 Zn -3.792406321 8.758215221 18.667069250 0 0 0 Zn -1.896198498 7.663439124 21.777838456 S -3.792405616 8.758214813 20.995239476 S -1.896199204 7.663439532 24.106008682 Zn -3.792406321 8.758215221 24.888607887 S -3.792405616 8.758214813 27.216778113 Zn 5.688625711 1.094783325 3.1132225450 0 0 0 S 3.792418593 2.189559014 2.3306235650 0 0 0 S 5.688625005 1.094783733 5.4413927710 0 0 0 Zn 3.792417888 2.189559422 6.2239919760 0 0 0 Zn 5.688625711 1.094783325 9.3347611820 0 0 0 S 3.792418593 2.189559014 8.5521622020 0 0 0 S 5.688625005 1.094783733 11.662931408 0 0 0 Zn 3.792417888 2.189559422 12.445530613 0 0 0 Zn 5.688625711 1.094783325 15.556299819 0 0 0 S 3.792418593 2.189559014 14.773700839 0 0 0 S 5.688625005 1.094783733 17.884470045 0 0 0 Zn 3.792417888 2.189559422 18.667069250 0 0 0 Zn 5.688625711 1.094783325 21.777838456 S 3.792418593 2.189559014 20.995239476 S 5.688625005 1.094783733 24.106008682 Zn 3.792417888 2.189559422 24.888607887 S 3.792418593 2.189559014 27.216778113 Zn 3.792421564 4.379113130 3.1132225450 0 0 0 S 1.896214446 5.473888819 2.3306235650 0 0 0 S 3.792420858 4.379113538 5.4413927710 0 0 0 Zn 1.896213741 5.473889227 6.2239919760 0 0 0 Zn 3.792421564 4.379113130 9.3347611820 0 0 0 S 1.896214446 5.473888819 8.5521622020 0 0 0 S 3.792420858 4.379113538 11.662931408 0 0 0 Zn 1.896213741 5.473889227 12.445530613 0 0 0 Zn 3.792421564 4.379113130 15.556299819 0 0 0 S 1.896214446 5.473888819 14.773700839 0 0 0 S 3.792420858 4.379113538 17.884470045 0 0 0 Zn 1.896213741 5.473889227 18.667069250 0 0 0 Zn 3.792421564 4.379113130 21.777838456 S 1.896214446 5.473888819 20.995239476 O 3.792420858 4.379113538 23.706008682 Zn 1.896213741 5.473889227 24.888607887 O 1.896214446 5.473888819 26.816778113 Zn 1.896217417 7.663442935 3.1132225450 0 0 0 S 0.000010299 8.758218624 2.3306235650 0 0 0 S 1.896216711 7.663443343 5.4413927710 0 0 0 Zn 0.000009594 8.758219032 6.2239919760 0 0 0 Zn 1.896217417 7.663442935 9.3347611820 0 0 0 S 0.000010299 8.758218624 8.5521622020 0 0 0 S 1.896216711 7.663443343 11.662931408 0 0 0 Zn 0.000009594 8.758219032 12.445530613 0 0 0 Zn 1.896217417 7.663442935 15.556299819 0 0 0 S 0.000010299 8.758218624 14.773700839 0 0 0 S 1.896216711 7.663443343 17.884470045 0 0 0 Zn 0.000009594 8.758219032 18.667069250 0 0 0 Zn 1.896217417 7.663442935 21.777838456 S 0.000010299 8.758218624 20.995239476 S 1.896216711 7.663443343 24.106008682 Zn 0.000009594 8.758219032 24.888607887 S 0.000010299 8.758218624 27.216778113 Zn 9.481041626 1.094787136 3.1132225450 0 0 0 S 7.584834508 2.189562825 2.3306235650 0 0 0 S 9.481040920 1.094787544 5.4413927710 0 0 0 Zn 7.584833803 2.189563233 6.2239919760 0 0 0 Zn 9.481041626 1.094787136 9.3347611820 0 0 0 S 7.584834508 2.189562825 8.5521622020 0 0 0 S 9.481040920 1.094787544 11.662931408 0 0 0 Zn 7.584833803 2.189563233 12.445530613 0 0 0 Zn 9.481041626 1.094787136 15.556299819 0 0 0 S 7.584834508 2.189562825 14.773700839 0 0 0 S 9.481040920 1.094787544 17.884470045 0 0 0 Zn 7.584833803 2.189563233 18.667069250 0 0 0 Zn 9.481041626 1.094787136 21.777838456 S 7.584834508 2.189562825 20.995239476 S 9.481040920 1.094787544 24.106008682 Zn 7.584833803 2.189563233 24.888607887 S 7.584834508 2.189562825 27.216778113 Zn 7.584837479 4.379116941 3.1132225450 0 0 0 S 5.688630361 5.473892630 2.3306235650 0 0 0 S 7.584836773 4.379117349 5.4413927710 0 0 0 Zn 5.688629656 5.473893038 6.2239919760 0 0 0 Zn 7.584837479 4.379116941 9.3347611820 0 0 0 S 5.688630361 5.473892630 8.5521622020 0 0 0 S 7.584836773 4.379117349 11.662931408 0 0 0 Zn 5.688629656 5.473893038 12.445530613 0 0 0 Zn 7.584837479 4.379116941 15.556299819 0 0 0 S 5.688630361 5.473892630 14.773700839 0 0 0 S 7.584836773 4.379117349 17.884470045 0 0 0 Zn 5.688629656 5.473893038 18.667069250 0 0 0 Zn 7.584837479 4.379116941 21.777838456 S 5.688630361 5.473892630 20.995239476 S 7.584836773 4.379117349 24.106008682 Zn 5.688629656 5.473893038 24.888607887 S 5.688630361 5.473892630 27.216778113 Zn 5.688633332 7.663446746 3.1132225450 0 0 0 S 3.792426214 8.758222435 2.3306235650 0 0 0 S 5.688632626 7.663447154 5.4413927710 0 0 0 Zn 3.792425509 8.758222843 6.2239919760 0 0 0 Zn 5.688633332 7.663446746 9.3347611820 0 0 0 S 3.792426214 8.758222435 8.5521622020 0 0 0 S 5.688632626 7.663447154 11.662931408 0 0 0 Zn 3.792425509 8.758222843 12.445530613 0 0 0 Zn 5.688633332 7.663446746 15.556299819 0 0 0 S 3.792426214 8.758222435 14.773700839 0 0 0 S 5.688632626 7.663447154 17.884470045 0 0 0 Zn 3.792425509 8.758222843 18.667069250 0 0 0 Zn 5.688633332 7.663446746 21.777838456 S 3.792426214 8.758222435 20.995239476 S 5.688632626 7.663447154 24.106008682 Zn 3.792425509 8.758222843 24.888607887 S 3.792426214 8.758222435 27.216778113 K_POINTS automatic 3 3 1 0 0 0 -- *************************************** Amin Torabi Ph.D. Student Chemistry Dept. Western University London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From abmus007 at gmail.com Sun Aug 12 06:47:12 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 12 Aug 2012 05:47:12 +0100 Subject: [Pw_forum] phonon calculation Message-ID: Dear sir. Sir l just want to ask how do l know the proper nq1 nq2 nq3 to use in my phonon calculation after my scf calculation. Am sorry l ask this type of question l will be so happy if u can kindly explain thanks Musari. A.A UNAAB Nigeria From manojnarayan86 at gmail.com Sun Aug 12 07:22:29 2012 From: manojnarayan86 at gmail.com (manoj narayanan) Date: Sun, 12 Aug 2012 10:52:29 +0530 Subject: [Pw_forum] Van der Walls interaction Message-ID: Dear users In my calculation with carbon chain between 9 to 12 carbon atoms I have to include Van der walls interaction and I am not clear about it's inclusion in DFT. What all are the key words and parameters for that and how effective is the implementation? Can anyone shed some light in to this. Thanking all in advance Manoj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/91b1104f/attachment.htm From baroni at sissa.it Sun Aug 12 11:01:34 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 12 Aug 2012 11:01:34 +0200 Subject: [Pw_forum] piezoelectric constant In-Reply-To: <1344664040.75666.YahooMailNeo@web141106.mail.bf1.yahoo.com> References: <1343899805.32911.YahooMailNeo@web141102.mail.bf1.yahoo.com> <1344664040.75666.YahooMailNeo@web141106.mail.bf1.yahoo.com> Message-ID: On Aug 11, 2012, at 7:47 AM, Alex Mariani wrote: > > > > Dear all > I want to calculate the piezoelectric constant for PbTio3. > How do using the QE code? > What is the procedure? Simple solution: Perform a set of finite-field calculations and plot the stress as a function of the applied electric field. The slope at zero field gives you the piezoelectric coefficient(s). A more elegant solution (which requires some coding, though) is described in: S. de Gironcoli et al. PRL 62, 2853 (1989), http://link.aps.org/doi/10.1103/PhysRevLett.62.2853 SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/42219648/attachment.htm From baroni at sissa.it Sun Aug 12 11:03:45 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 12 Aug 2012 11:03:45 +0200 Subject: [Pw_forum] phonon calculation In-Reply-To: References: Message-ID: Just try a set of values of your choice, and then vary them until the accuracy of the results (which can be estimated by comparing results obtained from different values of nq1,nq2,nq3) pleases you. SB On Aug 12, 2012, at 6:47 AM, Abolore Musari wrote: > Dear sir. > Sir l just want to ask how do l know the proper nq1 nq2 nq3 to use in > my phonon calculation after my scf calculation. > Am sorry l ask this type of question l will be so happy if u can kindly explain > thanks > Musari. A.A > UNAAB Nigeria > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/95c1ca5c/attachment.htm From flux_ray12 at 163.com Sun Aug 12 11:04:39 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 12 Aug 2012 17:04:39 +0800 (CST) Subject: [Pw_forum] phonon calculation In-Reply-To: References: Message-ID: <70a295cd.e5b9.1391a13f632.Coremail.flux_ray12@163.com> Dear Abolore Musari: In my opinion, lots of paper ran DFPT at 4x4x4 q-mesh. Sometimes (not often), 3x3x3 q-mesh may also provide reasonable results. The easiest way may be similar as k-mesh test, you can gradually increase the q-mesh from 2x2x2 to NxNxN until the frequencies converged (the threshold can be defined by yourself). -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-12 12:47:12,"Abolore Musari" wrote: >Dear sir. >Sir l just want to ask how do l know the proper nq1 nq2 nq3 to use in >my phonon calculation after my scf calculation. >Am sorry l ask this type of question l will be so happy if u can kindly explain >thanks >Musari. A.A >UNAAB Nigeria >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/47d22f3d/attachment.htm From masoudnahali at gmail.com Sun Aug 12 12:41:27 2012 From: masoudnahali at gmail.com (Masoud) Date: Sun, 12 Aug 2012 12:41:27 +0200 Subject: [Pw_forum] Van der Walls interaction Message-ID: Dear Manjo QE can calculate semi-empirical dispersion term, setting "london=.true." you can include such interaction which is weakly calculated by pure DFT in your calculations. I hope it helps. For details please see S. Grimme, J. Comp. Chem. 27, 1787 (2006), and V. Barone et al., J. Comp. Chem. 30, 934 (2009) Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Sun, Aug 12, 2012 at 9:37 AM, Manoj wrote: > > > Dear users > In my calculation with carbon chain between 9 > to 12 carbon atoms I have to include Van der walls interaction and I am not > clear about it's inclusion in DFT. What all are the key words > and parameters for that and how effective is the implementation? Can > anyone shed some light in to this. > > Thanking all in advance > Manoj > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120812/91b1104f/attachment.html > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/fe416cdb/attachment.htm From manojnarayan86 at gmail.com Sun Aug 12 18:06:03 2012 From: manojnarayan86 at gmail.com (manoj narayanan) Date: Sun, 12 Aug 2012 21:36:03 +0530 Subject: [Pw_forum] Van der Walls interaction In-Reply-To: References: Message-ID: Dear Masoud Thank you for your reply, but what my doubt is that QE only includes london dispersion. What about other effects like Keesom and Debye forces ? Yours Sincerely Manoj On Sun, Aug 12, 2012 at 4:11 PM, Masoud wrote: > > Dear Manjo > > QE can calculate semi-empirical dispersion term, setting "london=.true." > you can include such interaction which is weakly calculated by pure DFT in > your calculations. I hope it helps. > For details please see > > S. Grimme, J. Comp. Chem. 27, 1787 (2006), and > V. Barone et al., J. Comp. Chem. 30, 934 (2009) > > > > > Best Wishes, m > > > > > > ---------------------------------------- > Masoud Nahali > SUT > masoud.nahali at gmail.com > alum.sharif.edu/~m_nahali > > > > > > On Sun, Aug 12, 2012 at 9:37 AM, Manoj wrote: > >> >> >> Dear users >> In my calculation with carbon chain between >> 9 >> to 12 carbon atoms I have to include Van der walls interaction and I am >> not >> clear about it's inclusion in DFT. What all are the key words >> and parameters for that and how effective is the implementation? Can >> anyone shed some light in to this. >> >> Thanking all in advance >> Manoj >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20120812/91b1104f/attachment.html >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/711e303b/attachment-0001.htm From masoudnahali at gmail.com Sun Aug 12 19:19:03 2012 From: masoudnahali at gmail.com (Masoud) Date: Sun, 12 Aug 2012 19:19:03 +0200 Subject: [Pw_forum] Van der Walls interaction Message-ID: Dear Manjo The forces between two permanent dipoles and a permanent dipole and a corresponding induced dipole are usually larger than two instantaneously induced dipoles. So I expect that DFT and especially DFT-D can see the two first mentioned forces better than the latter. You can make a clever set of molecules that their Inter-molecular forces change and calculate the energy once with DFT-D and another time with pure DFT. Then you can understand that which of the approaches can predict the trend well. You 'd better not care about absolute values and just check the trend. I hope it helps. Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Sun, Aug 12, 2012 at 6:06 PM, Manoj wrote: > > > Dear Masoud > Thank you for your reply, but what my doubt is > that QE only includes london dispersion. What about other effects like > Keesom and Debye forces ? > > Yours Sincerely > Manoj > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/ae7fbf7d/attachment.htm From iyad.ne at gmail.com Sun Aug 12 20:08:57 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Sun, 12 Aug 2012 14:08:57 -0400 Subject: [Pw_forum] phonon calculations do not converge In-Reply-To: References: Message-ID: Hi William, I will try this and let you know. Thank you very much. Iyad On Fri, Aug 10, 2012 at 5:16 PM, William Parker wrote: > Hi Iyad, > > How strong is the failure to converge at (0, 1/6, 1/6)? Perhaps a less > tight tr2_ph value of, say, 1.0d-10 would get you where you need to be. > > --William > > On Aug 10, 2012, at 12:29 PM, Iyad AL-QASIR wrote: > > > Dear PW_Forum, > > > > I am running phonon calculations for FeSi (a narrow band gap > semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 > q-points ran successfully and got good phonon values. However when I reach > the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. > I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. > > > > Below are my input files: > > > > &control > > calculation='scf', > > restart_mode='from_scratch', > > title='FeSi', > > outdir='./', > > prefix='FeSi', > > pseudo_dir='./', > > / > > &system > > ibrav=1, > > celldm(1)=8.4165, > > nat=8, ntyp=2, > > ecutwfc=60.0, > > ecutrho= 720.0, > > / > > &electrons > > conv_thr=1.0d-9, > > mixing_mode='plain', > > mixing_beta=0.7, > > diagonalization='david', > > / > > ATOMIC_SPECIES > > Fe 55.847 Fe.pw91-sp-van_ak.UPF > > Si 28.086 Si.pw91-n_van.UPF > > ATOMIC_POSITIONS > > Fe 0.134855265 0.134855265 0.134855265 > > Fe 0.634855265 0.365144735 0.865144735 > > Fe 0.865144735 0.634855265 0.365144735 > > Fe 0.365144735 0.865144735 0.634855265 > > Si 0.839976366 0.839976366 0.839976366 > > Si 0.339976366 0.660023634 0.160023634 > > Si 0.160023634 0.339976366 0.660023634 > > Si 0.660023634 0.160023634 0.339976366 > > K_POINTS {automatic} > > 10 10 10 0 0 0 > > *********************************** > > phonons of FeSi > > &inputph > > tr2_ph=1.0d-14, > > prefix='FeSi', > > amass(1)=55.847, > > amass(2)=28.086, > > outdir='./' > > fildyn='FeSi.dyn', > > trans=.true., > > ldisp=.true., > > nq1=6, nq2=6, nq3=6 > > recover=.true., > > alpha_mix(1)=0.30 > > > > Any comments and suggestions are welcomed. > > > > Thanks > > IYAD > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > ********************************************************* > William D. Parker phone: (630) 252-4834 > Computational Postdoctoral Fellow fax: (630) 252-4798 > MSD-212, Rm. C-215 > Argonne National Laboratory > 9700 S. Cass Ave. > Argonne, IL 60439 > ********************************************************* > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- _______________________________ IYAD I. AL-QASIR, PhD Research Associate Department of Nuclear Engineering North Carolina State University Campus Box 7909 2500 Stinson Dr. Raleigh, NC 27695-7909 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/1e25b76d/attachment.htm From dmitry at korotin.name Mon Aug 13 10:08:37 2012 From: dmitry at korotin.name (Dmitry Korotin) Date: Mon, 13 Aug 2012 14:08:37 +0600 Subject: [Pw_forum] QE plugins system In-Reply-To: References: Message-ID: Dear Layla, thank you for the answer. I looks like I have the third or fourth situation and I will skype you to consult. Now my code (LDA+U in Wannier functions basis) is based on QE 4.3 branch and I am looking for an ideal way to transfer it to 5.0 codebase. 2012/8/8 Layla Martin-Samos : > Dear Dimitry, the "QE plugin system" is at the moment more something like an > "automatic download, untar and compile" procedure, a part for the case of > PLUMED and the future release of QMMM. We call "plugin" anything which is > not related to "core routines" and is installed by some automatic procedure. > There are different kinds of "plugins" inside QE at the moment: > > 1) like W90, WANT and YAMBO --> postprocessing-like codes, that are > completely PW/PH routine independent. They just read some output. For making > such kind of plugin, we just need an URL with the .tar.gz release and we > will add the necessary lines to the Makefiles in order to have an automatic > installation. If you have write access to QE repository, you can follow what > has been already done in install/plugins_list and install/plugins_makefile. > > 2) Like NEB, TDDFPT ...--> codes that call some PW/PH routines as they are > (without the need of patching lines ...). Same as in the 1) case. > > 3) Like PLUMED --> some routines of PW/PH need to be patched. In this case, > we construct "empty routines" (like plugin_forces.f90 or > plugin_initialization.f90). If you are in this case, we can have a skype > meeting to understand the best way for including your work. > > 4) something else ---> as in 3) we can have a skype meeting. > > let me know > > best regards > > Layla > > 2012/8/8 Dmitry Korotin >> >> Dear QE Developers, >> is there some guide or instruction or specification of new QE plugins >> system? >> The idea of plugins is brilliant! I want to transform my code into >> plugin but need some info about how it is organized. >> >> (Of course I can check existing plugins and do a similar thing but it >> is inconvenient way). >> >> Thank you in advance. >> -- >> >> Best regards, >> Dr. Dmitry Korotin >> >> Institute of Metal Physics >> S. Kovalevskaya, 18 >> 620990 Yekaterinburg >> Russia >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best regards, Dr. Dmitry Korotin Institute of Metal Physics S. Kovalevskaya, 18 620990 Yekaterinburg Russia From lmartinsamos at gmail.com Mon Aug 13 10:18:43 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 13 Aug 2012 10:18:43 +0200 Subject: [Pw_forum] QE plugins system In-Reply-To: References: Message-ID: Dear Dimitry, maybe you will find more confortable for the porting if we create a dedicated branch? let me know best regards Layla 2012/8/13 Dmitry Korotin > Dear Layla, > thank you for the answer. > I looks like I have the third or fourth situation and I will skype you > to consult. > Now my code (LDA+U in Wannier functions basis) is based on QE 4.3 > branch and I am looking for an ideal way to transfer it to 5.0 > codebase. > > 2012/8/8 Layla Martin-Samos : > > Dear Dimitry, the "QE plugin system" is at the moment more something > like an > > "automatic download, untar and compile" procedure, a part for the case of > > PLUMED and the future release of QMMM. We call "plugin" anything which is > > not related to "core routines" and is installed by some automatic > procedure. > > There are different kinds of "plugins" inside QE at the moment: > > > > 1) like W90, WANT and YAMBO --> postprocessing-like codes, that are > > completely PW/PH routine independent. They just read some output. For > making > > such kind of plugin, we just need an URL with the .tar.gz release and we > > will add the necessary lines to the Makefiles in order to have an > automatic > > installation. If you have write access to QE repository, you can follow > what > > has been already done in install/plugins_list and > install/plugins_makefile. > > > > 2) Like NEB, TDDFPT ...--> codes that call some PW/PH routines as they > are > > (without the need of patching lines ...). Same as in the 1) case. > > > > 3) Like PLUMED --> some routines of PW/PH need to be patched. In this > case, > > we construct "empty routines" (like plugin_forces.f90 or > > plugin_initialization.f90). If you are in this case, we can have a skype > > meeting to understand the best way for including your work. > > > > 4) something else ---> as in 3) we can have a skype meeting. > > > > let me know > > > > best regards > > > > Layla > > > > 2012/8/8 Dmitry Korotin > >> > >> Dear QE Developers, > >> is there some guide or instruction or specification of new QE plugins > >> system? > >> The idea of plugins is brilliant! I want to transform my code into > >> plugin but need some info about how it is organized. > >> > >> (Of course I can check existing plugins and do a similar thing but it > >> is inconvenient way). > >> > >> Thank you in advance. > >> -- > >> > >> Best regards, > >> Dr. Dmitry Korotin > >> > >> Institute of Metal Physics > >> S. Kovalevskaya, 18 > >> 620990 Yekaterinburg > >> Russia > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Best regards, > Dr. Dmitry Korotin > > Institute of Metal Physics > S. Kovalevskaya, 18 > 620990 Yekaterinburg > Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120813/e7de9b31/attachment.htm From dmitry at korotin.name Mon Aug 13 10:28:41 2012 From: dmitry at korotin.name (Dmitry Korotin) Date: Mon, 13 Aug 2012 14:28:41 +0600 Subject: [Pw_forum] QE plugins system In-Reply-To: References: Message-ID: Dear Layla, it would be perfect, but please don't do it right now. I'll contact you when I'll be ready to start commiting. 2012/8/13 Layla Martin-Samos : > Dear Dimitry, maybe you will find more confortable for the porting if we > create a dedicated branch? > > > let me know > > best regards > > Layla > > 2012/8/13 Dmitry Korotin >> >> Dear Layla, >> thank you for the answer. >> I looks like I have the third or fourth situation and I will skype you >> to consult. >> Now my code (LDA+U in Wannier functions basis) is based on QE 4.3 >> branch and I am looking for an ideal way to transfer it to 5.0 >> codebase. >> >> 2012/8/8 Layla Martin-Samos : >> > Dear Dimitry, the "QE plugin system" is at the moment more something >> > like an >> > "automatic download, untar and compile" procedure, a part for the case >> > of >> > PLUMED and the future release of QMMM. We call "plugin" anything which >> > is >> > not related to "core routines" and is installed by some automatic >> > procedure. >> > There are different kinds of "plugins" inside QE at the moment: >> > >> > 1) like W90, WANT and YAMBO --> postprocessing-like codes, that are >> > completely PW/PH routine independent. They just read some output. For >> > making >> > such kind of plugin, we just need an URL with the .tar.gz release and we >> > will add the necessary lines to the Makefiles in order to have an >> > automatic >> > installation. If you have write access to QE repository, you can follow >> > what >> > has been already done in install/plugins_list and >> > install/plugins_makefile. >> > >> > 2) Like NEB, TDDFPT ...--> codes that call some PW/PH routines as they >> > are >> > (without the need of patching lines ...). Same as in the 1) case. >> > >> > 3) Like PLUMED --> some routines of PW/PH need to be patched. In this >> > case, >> > we construct "empty routines" (like plugin_forces.f90 or >> > plugin_initialization.f90). If you are in this case, we can have a skype >> > meeting to understand the best way for including your work. >> > >> > 4) something else ---> as in 3) we can have a skype meeting. >> > >> > let me know >> > >> > best regards >> > >> > Layla >> > >> > 2012/8/8 Dmitry Korotin >> >> >> >> Dear QE Developers, >> >> is there some guide or instruction or specification of new QE plugins >> >> system? >> >> The idea of plugins is brilliant! I want to transform my code into >> >> plugin but need some info about how it is organized. >> >> >> >> (Of course I can check existing plugins and do a similar thing but it >> >> is inconvenient way). >> >> >> >> Thank you in advance. >> >> -- >> >> >> >> Best regards, >> >> Dr. Dmitry Korotin >> >> >> >> Institute of Metal Physics >> >> S. Kovalevskaya, 18 >> >> 620990 Yekaterinburg >> >> Russia >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Best regards, >> Dr. Dmitry Korotin >> >> Institute of Metal Physics >> S. Kovalevskaya, 18 >> 620990 Yekaterinburg >> Russia >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ? ?????????, ??????? ??????? Best regards, Dr. Dmitry Korotin Institute of Metal Physics S. Kovalevskaya, 18 620990 Yekaterinburg Russia From lmartinsamos at gmail.com Mon Aug 13 11:18:27 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 13 Aug 2012 11:18:27 +0200 Subject: [Pw_forum] QE plugins system In-Reply-To: References: Message-ID: OK! cheers Layla 2012/8/13 Dmitry Korotin > Dear Layla, it would be perfect, but please don't do it right now. > I'll contact you when I'll be ready to start commiting. > > 2012/8/13 Layla Martin-Samos : > > Dear Dimitry, maybe you will find more confortable for the porting if we > > create a dedicated branch? > > > > > > let me know > > > > best regards > > > > Layla > > > > 2012/8/13 Dmitry Korotin > >> > >> Dear Layla, > >> thank you for the answer. > >> I looks like I have the third or fourth situation and I will skype you > >> to consult. > >> Now my code (LDA+U in Wannier functions basis) is based on QE 4.3 > >> branch and I am looking for an ideal way to transfer it to 5.0 > >> codebase. > >> > >> 2012/8/8 Layla Martin-Samos : > >> > Dear Dimitry, the "QE plugin system" is at the moment more something > >> > like an > >> > "automatic download, untar and compile" procedure, a part for the case > >> > of > >> > PLUMED and the future release of QMMM. We call "plugin" anything which > >> > is > >> > not related to "core routines" and is installed by some automatic > >> > procedure. > >> > There are different kinds of "plugins" inside QE at the moment: > >> > > >> > 1) like W90, WANT and YAMBO --> postprocessing-like codes, that are > >> > completely PW/PH routine independent. They just read some output. For > >> > making > >> > such kind of plugin, we just need an URL with the .tar.gz release and > we > >> > will add the necessary lines to the Makefiles in order to have an > >> > automatic > >> > installation. If you have write access to QE repository, you can > follow > >> > what > >> > has been already done in install/plugins_list and > >> > install/plugins_makefile. > >> > > >> > 2) Like NEB, TDDFPT ...--> codes that call some PW/PH routines as they > >> > are > >> > (without the need of patching lines ...). Same as in the 1) case. > >> > > >> > 3) Like PLUMED --> some routines of PW/PH need to be patched. In this > >> > case, > >> > we construct "empty routines" (like plugin_forces.f90 or > >> > plugin_initialization.f90). If you are in this case, we can have a > skype > >> > meeting to understand the best way for including your work. > >> > > >> > 4) something else ---> as in 3) we can have a skype meeting. > >> > > >> > let me know > >> > > >> > best regards > >> > > >> > Layla > >> > > >> > 2012/8/8 Dmitry Korotin > >> >> > >> >> Dear QE Developers, > >> >> is there some guide or instruction or specification of new QE plugins > >> >> system? > >> >> The idea of plugins is brilliant! I want to transform my code into > >> >> plugin but need some info about how it is organized. > >> >> > >> >> (Of course I can check existing plugins and do a similar thing but it > >> >> is inconvenient way). > >> >> > >> >> Thank you in advance. > >> >> -- > >> >> > >> >> Best regards, > >> >> Dr. Dmitry Korotin > >> >> > >> >> Institute of Metal Physics > >> >> S. Kovalevskaya, 18 > >> >> 620990 Yekaterinburg > >> >> Russia > >> >> _______________________________________________ > >> >> Pw_forum mailing list > >> >> Pw_forum at pwscf.org > >> >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > > >> > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > >> > >> > >> -- > >> Best regards, > >> Dr. Dmitry Korotin > >> > >> Institute of Metal Physics > >> S. Kovalevskaya, 18 > >> 620990 Yekaterinburg > >> Russia > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > ? ?????????, > ??????? ??????? > > Best regards, > Dr. Dmitry Korotin > > Institute of Metal Physics > S. Kovalevskaya, 18 > 620990 Yekaterinburg > Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120813/fc894b9a/attachment-0001.htm From degironc at sissa.it Mon Aug 13 15:03:10 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 13 Aug 2012 15:03:10 +0200 Subject: [Pw_forum] Van der Walls interaction In-Reply-To: References: Message-ID: <20120813150310.Horde.C4koNR8V4mxQKPsOVYTEFMA@webmail.sissa.it> dispersion interactions, aka vdW, are not included in LAD/GGA/Hybrid functionals this is why DFT-D (switched on by the "london=.true." keyword) introduces an empirical damp-dispersion term interaction between permanent dipoles and the one between permanent charges/dipoles and statically induced dipoles is just electrostatic and is therefore correctly included in the Hartree term. Notice that there are new generation of fully non local XC functionals vdW-DF, vdW-DF2 and soon VV10 (or actually a refinement of it) that are implemented in QE. Check the beginning of Modules/funct.f90 for a list of options and some relevant references. As these functionals are not implemented in the ld1.x code one needs to force their use by the input_dft keyword.. and chose some reasonable, not too different, xc functional for the pseudopotentials. hope this helps stefano Quoting manoj narayanan : > Dear Masoud > Thank you for your reply, but what my doubt is > that QE only includes london dispersion. What about other effects like > Keesom and Debye forces ? > > Yours Sincerely > Manoj > > On Sun, Aug 12, 2012 at 4:11 PM, Masoud wrote: > >> >> Dear Manjo >> >> QE can calculate semi-empirical dispersion term, setting "london=.true." >> you can include such interaction which is weakly calculated by pure DFT in >> your calculations. I hope it helps. >> For details please see >> >> S. Grimme, J. Comp. Chem. 27, 1787 (2006), and >> V. Barone et al., J. Comp. Chem. 30, 934 (2009) >> >> >> >> >> Best Wishes, m >> >> >> >> >> >> ---------------------------------------- >> Masoud Nahali >> SUT >> masoud.nahali at gmail.com >> alum.sharif.edu/~m_nahali >> >> >> >> >> >> On Sun, Aug 12, 2012 at 9:37 AM, Manoj wrote: >> >>> >>> >>> Dear users >>> In my calculation with carbon chain between >>> 9 >>> to 12 carbon atoms I have to include Van der walls interaction and I am >>> not >>> clear about it's inclusion in DFT. What all are the key words >>> and parameters for that and how effective is the implementation? Can >>> anyone shed some light in to this. >>> >>> Thanking all in advance >>> Manoj >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://www.democritos.it/pipermail/pw_forum/attachments/20120812/91b1104f/attachment.html >>> >>> >>> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> From mtorabi at uwo.ca Mon Aug 13 16:27:35 2012 From: mtorabi at uwo.ca (Amin Torabi) Date: Mon, 13 Aug 2012 10:27:35 -0400 Subject: [Pw_forum] zns/zno surface In-Reply-To: <587846793.57764.1344705152545.JavaMail.root@asems02.its.rochester.edu> References: <587846793.57764.1344705152545.JavaMail.root@asems02.its.rochester.edu> Message-ID: Dear Alexey, How could a calculation without saturation be fine? My understanding is that an unsaturated bottom layer will produce a spurious dipole moment which can be large, and can interact with the corresponding dipole moment in other unit cells. On Sat, Aug 11, 2012 at 1:12 PM, Alexey Akimov wrote: > Dear Amin, > > If you want to saturate bottom (and maybe even top) sulfur/oxygen atoms I > would try to put hydrogens on them. This way you can localize electron > density on the sulfur/oxigen atoms and avoid dangling bonds. In reality you > of course will not see unsaturated O/S atoms on the surface - they will be > protonated anyway or carry some other groups on them. However it may be > fine to do calculations even without such saturation (especially for the > bottom layer). > > > > ----- Original Message ----- > From: "Amin Torabi" > To: "PWSCF Forum" > Sent: Friday, August 10, 2012 9:22:55 AM > Subject: [Pw_forum] zns/zno surface > > > > > Dear PWSCF experts, > > > I am willing to find out how doping of oxygen in a surface of ZnS > (wurtzite) changes its band structure. I have a slab model composed of 8 > layers of ZnS, in which 2 sulfur atoms are replace with oxygen, and a 15 > Angstrom vacuum on top of the surface. I am relaxing only the first two > layers. > Now, my question is the sulfur or oxygen atoms on the top level resembles > the surface that I am interested in; however, the sulfur (or zinc) atoms at > the bottom are artifact of the model. How should I saturate them? > > > Can you please take a look on my input file and let me know if you have > any suggestion? Thanks > > > > &CONTROL > calculation = 'relax' > prefix = 'orig' > pseudo_dir = '/home/p/' > outdir = './tmp' > tstress = .true > tprnfor = .true > / > &SYSTEM > ibrav = 12 > A = 11.3772 > B = 11.3772 > C = 40.0 > cosAB = -0.5 > nat = 153 > ntyp = 3 > ecutwfc = 30 > ecutrho = 300 > occupations = 'smearing' > degauss = 0.01 > smearing = 'gauss' > / > &ELECTRONS > mixing_mode = 'local-TF' > mixing_beta = 0.3 > / > &IONS > / > ATOMIC_SPECIES > Zn 65.409 Zn.pbe-van.UPF > S 32.066 S.pbe-van_bm.UPF > O 15.9994 O.pbe-van_ak.UPF > ATOMIC_POSITIONS angstrom > Zn 1.896209796 1.094779514 3.1132225450 0 0 0 > S 0.000002678 2.189555203 2.3306235650 0 0 0 > S 1.896209090 1.094779922 5.4413927710 0 0 0 > Zn 0.000001973 2.189555611 6.2239919760 0 0 0 > Zn 1.896209796 1.094779514 9.3347611820 0 0 0 > S 0.000002678 2.189555203 8.5521622020 0 0 0 > S 1.896209090 1.094779922 11.662931408 0 0 0 > Zn 0.000001973 2.189555611 12.445530613 0 0 0 > Zn 1.896209796 1.094779514 15.556299819 0 0 0 > S 0.000002678 2.189555203 14.773700839 0 0 0 > S 1.896209090 1.094779922 17.884470045 0 0 0 > Zn 0.000001973 2.189555611 18.667069250 0 0 0 > Zn 1.896209796 1.094779514 21.777838456 > S 0.000002678 2.189555203 20.995239476 > S 1.896209090 1.094779922 24.106008682 > Zn 0.000001973 2.189555611 24.888607887 > S 0.000002678 2.189555203 27.216778113 > Zn 0.000005649 4.379109319 3.1132225450 0 0 0 > S -1.896201469 5.473885008 2.3306235650 0 0 0 > S 0.000004943 4.379109727 5.4413927710 0 0 0 > Zn -1.896202174 5.473885416 6.2239919760 0 0 0 > Zn 0.000005649 4.379109319 9.3347611820 0 0 0 > S -1.896201469 5.473885008 8.5521622020 0 0 0 > S 0.000004943 4.379109727 11.662931408 0 0 0 > Zn -1.896202174 5.473885416 12.445530613 0 0 0 > Zn 0.000005649 4.379109319 15.556299819 0 0 0 > S -1.896201469 5.473885008 14.773700839 0 0 0 > S 0.000004943 4.379109727 17.884470045 0 0 0 > Zn -1.896202174 5.473885416 18.667069250 0 0 0 > Zn 0.000005649 4.379109319 21.777838456 > S -1.896201469 5.473885008 20.995239476 > S 0.000004943 4.379109727 24.106008682 > Zn -1.896202174 5.473885416 24.888607887 > S -1.896201469 5.473885008 27.216778113 > Zn -1.896198498 7.663439124 3.1132225450 0 0 0 > S -3.792405616 8.758214813 2.3306235650 0 0 0 > S -1.896199204 7.663439532 5.4413927710 0 0 0 > Zn -3.792406321 8.758215221 6.2239919760 0 0 0 > Zn -1.896198498 7.663439124 9.3347611820 0 0 0 > S -3.792405616 8.758214813 8.5521622020 0 0 0 > S -1.896199204 7.663439532 11.662931408 0 0 0 > Zn -3.792406321 8.758215221 12.445530613 0 0 0 > Zn -1.896198498 7.663439124 15.556299819 0 0 0 > S -3.792405616 8.758214813 14.773700839 0 0 0 > S -1.896199204 7.663439532 17.884470045 0 0 0 > Zn -3.792406321 8.758215221 18.667069250 0 0 0 > Zn -1.896198498 7.663439124 21.777838456 > S -3.792405616 8.758214813 20.995239476 > S -1.896199204 7.663439532 24.106008682 > Zn -3.792406321 8.758215221 24.888607887 > S -3.792405616 8.758214813 27.216778113 > Zn 5.688625711 1.094783325 3.1132225450 0 0 0 > S 3.792418593 2.189559014 2.3306235650 0 0 0 > S 5.688625005 1.094783733 5.4413927710 0 0 0 > Zn 3.792417888 2.189559422 6.2239919760 0 0 0 > Zn 5.688625711 1.094783325 9.3347611820 0 0 0 > S 3.792418593 2.189559014 8.5521622020 0 0 0 > S 5.688625005 1.094783733 11.662931408 0 0 0 > Zn 3.792417888 2.189559422 12.445530613 0 0 0 > Zn 5.688625711 1.094783325 15.556299819 0 0 0 > S 3.792418593 2.189559014 14.773700839 0 0 0 > S 5.688625005 1.094783733 17.884470045 0 0 0 > Zn 3.792417888 2.189559422 18.667069250 0 0 0 > Zn 5.688625711 1.094783325 21.777838456 > S 3.792418593 2.189559014 20.995239476 > S 5.688625005 1.094783733 24.106008682 > Zn 3.792417888 2.189559422 24.888607887 > S 3.792418593 2.189559014 27.216778113 > Zn 3.792421564 4.379113130 3.1132225450 0 0 0 > S 1.896214446 5.473888819 2.3306235650 0 0 0 > S 3.792420858 4.379113538 5.4413927710 0 0 0 > Zn 1.896213741 5.473889227 6.2239919760 0 0 0 > Zn 3.792421564 4.379113130 9.3347611820 0 0 0 > S 1.896214446 5.473888819 8.5521622020 0 0 0 > S 3.792420858 4.379113538 11.662931408 0 0 0 > Zn 1.896213741 5.473889227 12.445530613 0 0 0 > Zn 3.792421564 4.379113130 15.556299819 0 0 0 > S 1.896214446 5.473888819 14.773700839 0 0 0 > S 3.792420858 4.379113538 17.884470045 0 0 0 > Zn 1.896213741 5.473889227 18.667069250 0 0 0 > Zn 3.792421564 4.379113130 21.777838456 > S 1.896214446 5.473888819 20.995239476 > O 3.792420858 4.379113538 23.706008682 > Zn 1.896213741 5.473889227 24.888607887 > O 1.896214446 5.473888819 26.816778113 > Zn 1.896217417 7.663442935 3.1132225450 0 0 0 > S 0.000010299 8.758218624 2.3306235650 0 0 0 > S 1.896216711 7.663443343 5.4413927710 0 0 0 > Zn 0.000009594 8.758219032 6.2239919760 0 0 0 > Zn 1.896217417 7.663442935 9.3347611820 0 0 0 > S 0.000010299 8.758218624 8.5521622020 0 0 0 > S 1.896216711 7.663443343 11.662931408 0 0 0 > Zn 0.000009594 8.758219032 12.445530613 0 0 0 > Zn 1.896217417 7.663442935 15.556299819 0 0 0 > S 0.000010299 8.758218624 14.773700839 0 0 0 > S 1.896216711 7.663443343 17.884470045 0 0 0 > Zn 0.000009594 8.758219032 18.667069250 0 0 0 > Zn 1.896217417 7.663442935 21.777838456 > S 0.000010299 8.758218624 20.995239476 > S 1.896216711 7.663443343 24.106008682 > Zn 0.000009594 8.758219032 24.888607887 > S 0.000010299 8.758218624 27.216778113 > Zn 9.481041626 1.094787136 3.1132225450 0 0 0 > S 7.584834508 2.189562825 2.3306235650 0 0 0 > S 9.481040920 1.094787544 5.4413927710 0 0 0 > Zn 7.584833803 2.189563233 6.2239919760 0 0 0 > Zn 9.481041626 1.094787136 9.3347611820 0 0 0 > S 7.584834508 2.189562825 8.5521622020 0 0 0 > S 9.481040920 1.094787544 11.662931408 0 0 0 > Zn 7.584833803 2.189563233 12.445530613 0 0 0 > Zn 9.481041626 1.094787136 15.556299819 0 0 0 > S 7.584834508 2.189562825 14.773700839 0 0 0 > S 9.481040920 1.094787544 17.884470045 0 0 0 > Zn 7.584833803 2.189563233 18.667069250 0 0 0 > Zn 9.481041626 1.094787136 21.777838456 > S 7.584834508 2.189562825 20.995239476 > S 9.481040920 1.094787544 24.106008682 > Zn 7.584833803 2.189563233 24.888607887 > S 7.584834508 2.189562825 27.216778113 > Zn 7.584837479 4.379116941 3.1132225450 0 0 0 > S 5.688630361 5.473892630 2.3306235650 0 0 0 > S 7.584836773 4.379117349 5.4413927710 0 0 0 > Zn 5.688629656 5.473893038 6.2239919760 0 0 0 > Zn 7.584837479 4.379116941 9.3347611820 0 0 0 > S 5.688630361 5.473892630 8.5521622020 0 0 0 > S 7.584836773 4.379117349 11.662931408 0 0 0 > Zn 5.688629656 5.473893038 12.445530613 0 0 0 > Zn 7.584837479 4.379116941 15.556299819 0 0 0 > S 5.688630361 5.473892630 14.773700839 0 0 0 > S 7.584836773 4.379117349 17.884470045 0 0 0 > Zn 5.688629656 5.473893038 18.667069250 0 0 0 > Zn 7.584837479 4.379116941 21.777838456 > S 5.688630361 5.473892630 20.995239476 > S 7.584836773 4.379117349 24.106008682 > Zn 5.688629656 5.473893038 24.888607887 > S 5.688630361 5.473892630 27.216778113 > Zn 5.688633332 7.663446746 3.1132225450 0 0 0 > S 3.792426214 8.758222435 2.3306235650 0 0 0 > S 5.688632626 7.663447154 5.4413927710 0 0 0 > Zn 3.792425509 8.758222843 6.2239919760 0 0 0 > Zn 5.688633332 7.663446746 9.3347611820 0 0 0 > S 3.792426214 8.758222435 8.5521622020 0 0 0 > S 5.688632626 7.663447154 11.662931408 0 0 0 > Zn 3.792425509 8.758222843 12.445530613 0 0 0 > Zn 5.688633332 7.663446746 15.556299819 0 0 0 > S 3.792426214 8.758222435 14.773700839 0 0 0 > S 5.688632626 7.663447154 17.884470045 0 0 0 > Zn 3.792425509 8.758222843 18.667069250 0 0 0 > Zn 5.688633332 7.663446746 21.777838456 > S 3.792426214 8.758222435 20.995239476 > S 5.688632626 7.663447154 24.106008682 > Zn 3.792425509 8.758222843 24.888607887 > S 3.792426214 8.758222435 27.216778113 > K_POINTS automatic > 3 3 1 0 0 0 > > > -- > > > *************************************** Amin Torabi > Ph.D. Student > Chemistry Dept. > Western University > London, On Canada, N6A 5B7 > Phone: 519-661-2111 Ext: 87871 > **************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- *************************************** Amin Torabi Ph.D. Student Chemistry Dept. Western University London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120813/0763596a/attachment-0001.htm From aakimov at z.rochester.edu Mon Aug 13 20:24:07 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Mon, 13 Aug 2012 14:24:07 -0400 (EDT) Subject: [Pw_forum] zns/zno surface In-Reply-To: Message-ID: <1535034855.13301.1344882247895.JavaMail.root@z.rochester.edu> Dear Amin, Sure it is better to saturate both surfaces - that is why i suggested to put the hydrogens on the dangling bond on each surface. In my understanding it is not realistic to have some unsaturated (dangling) bonds, especially on the surface (which is exposed lets say to the air). The bulk surface (in your case bottom) is not exposed to reactive components, so it maybe ok from the chemical point of view not to saturate them. However, from the computational point of view, that may(and will) lead to different charge density. To cure this you can put hydrogens on all unsaturated surface atoms. Best regards, Alexey ----- Original Message ----- From: "Amin Torabi" To: "PWSCF Forum" Sent: Monday, August 13, 2012 7:27:35 AM Subject: Re: [Pw_forum] zns/zno surface Dear Alexey, How could a calculation without saturation be fine? My understanding is that an unsaturated bottom layer will produce a spurious dipole moment which can be large, and can interact with the corresponding dipole moment in other unit cells. On Sat, Aug 11, 2012 at 1:12 PM, Alexey Akimov < aakimov at z.rochester.edu > wrote: Dear Amin, If you want to saturate bottom (and maybe even top) sulfur/oxygen atoms I would try to put hydrogens on them. This way you can localize electron density on the sulfur/oxigen atoms and avoid dangling bonds. In reality you of course will not see unsaturated O/S atoms on the surface - they will be protonated anyway or carry some other groups on them. However it may be fine to do calculations even without such saturation (especially for the bottom layer). ----- Original Message ----- From: "Amin Torabi" < mtorabi at uwo.ca > To: "PWSCF Forum" < pw_forum at pwscf.org > Sent: Friday, August 10, 2012 9:22:55 AM Subject: [Pw_forum] zns/zno surface Dear PWSCF experts, I am willing to find out how doping of oxygen in a surface of ZnS (wurtzite) changes its band structure. I have a slab model composed of 8 layers of ZnS, in which 2 sulfur atoms are replace with oxygen, and a 15 Angstrom vacuum on top of the surface. I am relaxing only the first two layers. Now, my question is the sulfur or oxygen atoms on the top level resembles the surface that I am interested in; however, the sulfur (or zinc) atoms at the bottom are artifact of the model. How should I saturate them? Can you please take a look on my input file and let me know if you have any suggestion? Thanks &CONTROL calculation = 'relax' prefix = 'orig' pseudo_dir = '/home/p/' outdir = './tmp' tstress = .true tprnfor = .true / &SYSTEM ibrav = 12 A = 11.3772 B = 11.3772 C = 40.0 cosAB = -0.5 nat = 153 ntyp = 3 ecutwfc = 30 ecutrho = 300 occupations = 'smearing' degauss = 0.01 smearing = 'gauss' / &ELECTRONS mixing_mode = 'local-TF' mixing_beta = 0.3 / &IONS / ATOMIC_SPECIES Zn 65.409 Zn.pbe-van.UPF S 32.066 S.pbe-van_bm.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS angstrom Zn 1.896209796 1.094779514 3.1132225450 0 0 0 S 0.000002678 2.189555203 2.3306235650 0 0 0 S 1.896209090 1.094779922 5.4413927710 0 0 0 Zn 0.000001973 2.189555611 6.2239919760 0 0 0 Zn 1.896209796 1.094779514 9.3347611820 0 0 0 S 0.000002678 2.189555203 8.5521622020 0 0 0 S 1.896209090 1.094779922 11.662931408 0 0 0 Zn 0.000001973 2.189555611 12.445530613 0 0 0 Zn 1.896209796 1.094779514 15.556299819 0 0 0 S 0.000002678 2.189555203 14.773700839 0 0 0 S 1.896209090 1.094779922 17.884470045 0 0 0 Zn 0.000001973 2.189555611 18.667069250 0 0 0 Zn 1.896209796 1.094779514 21.777838456 S 0.000002678 2.189555203 20.995239476 S 1.896209090 1.094779922 24.106008682 Zn 0.000001973 2.189555611 24.888607887 S 0.000002678 2.189555203 27.216778113 Zn 0.000005649 4.379109319 3.1132225450 0 0 0 S -1.896201469 5.473885008 2.3306235650 0 0 0 S 0.000004943 4.379109727 5.4413927710 0 0 0 Zn -1.896202174 5.473885416 6.2239919760 0 0 0 Zn 0.000005649 4.379109319 9.3347611820 0 0 0 S -1.896201469 5.473885008 8.5521622020 0 0 0 S 0.000004943 4.379109727 11.662931408 0 0 0 Zn -1.896202174 5.473885416 12.445530613 0 0 0 Zn 0.000005649 4.379109319 15.556299819 0 0 0 S -1.896201469 5.473885008 14.773700839 0 0 0 S 0.000004943 4.379109727 17.884470045 0 0 0 Zn -1.896202174 5.473885416 18.667069250 0 0 0 Zn 0.000005649 4.379109319 21.777838456 S -1.896201469 5.473885008 20.995239476 S 0.000004943 4.379109727 24.106008682 Zn -1.896202174 5.473885416 24.888607887 S -1.896201469 5.473885008 27.216778113 Zn -1.896198498 7.663439124 3.1132225450 0 0 0 S -3.792405616 8.758214813 2.3306235650 0 0 0 S -1.896199204 7.663439532 5.4413927710 0 0 0 Zn -3.792406321 8.758215221 6.2239919760 0 0 0 Zn -1.896198498 7.663439124 9.3347611820 0 0 0 S -3.792405616 8.758214813 8.5521622020 0 0 0 S -1.896199204 7.663439532 11.662931408 0 0 0 Zn -3.792406321 8.758215221 12.445530613 0 0 0 Zn -1.896198498 7.663439124 15.556299819 0 0 0 S -3.792405616 8.758214813 14.773700839 0 0 0 S -1.896199204 7.663439532 17.884470045 0 0 0 Zn -3.792406321 8.758215221 18.667069250 0 0 0 Zn -1.896198498 7.663439124 21.777838456 S -3.792405616 8.758214813 20.995239476 S -1.896199204 7.663439532 24.106008682 Zn -3.792406321 8.758215221 24.888607887 S -3.792405616 8.758214813 27.216778113 Zn 5.688625711 1.094783325 3.1132225450 0 0 0 S 3.792418593 2.189559014 2.3306235650 0 0 0 S 5.688625005 1.094783733 5.4413927710 0 0 0 Zn 3.792417888 2.189559422 6.2239919760 0 0 0 Zn 5.688625711 1.094783325 9.3347611820 0 0 0 S 3.792418593 2.189559014 8.5521622020 0 0 0 S 5.688625005 1.094783733 11.662931408 0 0 0 Zn 3.792417888 2.189559422 12.445530613 0 0 0 Zn 5.688625711 1.094783325 15.556299819 0 0 0 S 3.792418593 2.189559014 14.773700839 0 0 0 S 5.688625005 1.094783733 17.884470045 0 0 0 Zn 3.792417888 2.189559422 18.667069250 0 0 0 Zn 5.688625711 1.094783325 21.777838456 S 3.792418593 2.189559014 20.995239476 S 5.688625005 1.094783733 24.106008682 Zn 3.792417888 2.189559422 24.888607887 S 3.792418593 2.189559014 27.216778113 Zn 3.792421564 4.379113130 3.1132225450 0 0 0 S 1.896214446 5.473888819 2.3306235650 0 0 0 S 3.792420858 4.379113538 5.4413927710 0 0 0 Zn 1.896213741 5.473889227 6.2239919760 0 0 0 Zn 3.792421564 4.379113130 9.3347611820 0 0 0 S 1.896214446 5.473888819 8.5521622020 0 0 0 S 3.792420858 4.379113538 11.662931408 0 0 0 Zn 1.896213741 5.473889227 12.445530613 0 0 0 Zn 3.792421564 4.379113130 15.556299819 0 0 0 S 1.896214446 5.473888819 14.773700839 0 0 0 S 3.792420858 4.379113538 17.884470045 0 0 0 Zn 1.896213741 5.473889227 18.667069250 0 0 0 Zn 3.792421564 4.379113130 21.777838456 S 1.896214446 5.473888819 20.995239476 O 3.792420858 4.379113538 23.706008682 Zn 1.896213741 5.473889227 24.888607887 O 1.896214446 5.473888819 26.816778113 Zn 1.896217417 7.663442935 3.1132225450 0 0 0 S 0.000010299 8.758218624 2.3306235650 0 0 0 S 1.896216711 7.663443343 5.4413927710 0 0 0 Zn 0.000009594 8.758219032 6.2239919760 0 0 0 Zn 1.896217417 7.663442935 9.3347611820 0 0 0 S 0.000010299 8.758218624 8.5521622020 0 0 0 S 1.896216711 7.663443343 11.662931408 0 0 0 Zn 0.000009594 8.758219032 12.445530613 0 0 0 Zn 1.896217417 7.663442935 15.556299819 0 0 0 S 0.000010299 8.758218624 14.773700839 0 0 0 S 1.896216711 7.663443343 17.884470045 0 0 0 Zn 0.000009594 8.758219032 18.667069250 0 0 0 Zn 1.896217417 7.663442935 21.777838456 S 0.000010299 8.758218624 20.995239476 S 1.896216711 7.663443343 24.106008682 Zn 0.000009594 8.758219032 24.888607887 S 0.000010299 8.758218624 27.216778113 Zn 9.481041626 1.094787136 3.1132225450 0 0 0 S 7.584834508 2.189562825 2.3306235650 0 0 0 S 9.481040920 1.094787544 5.4413927710 0 0 0 Zn 7.584833803 2.189563233 6.2239919760 0 0 0 Zn 9.481041626 1.094787136 9.3347611820 0 0 0 S 7.584834508 2.189562825 8.5521622020 0 0 0 S 9.481040920 1.094787544 11.662931408 0 0 0 Zn 7.584833803 2.189563233 12.445530613 0 0 0 Zn 9.481041626 1.094787136 15.556299819 0 0 0 S 7.584834508 2.189562825 14.773700839 0 0 0 S 9.481040920 1.094787544 17.884470045 0 0 0 Zn 7.584833803 2.189563233 18.667069250 0 0 0 Zn 9.481041626 1.094787136 21.777838456 S 7.584834508 2.189562825 20.995239476 S 9.481040920 1.094787544 24.106008682 Zn 7.584833803 2.189563233 24.888607887 S 7.584834508 2.189562825 27.216778113 Zn 7.584837479 4.379116941 3.1132225450 0 0 0 S 5.688630361 5.473892630 2.3306235650 0 0 0 S 7.584836773 4.379117349 5.4413927710 0 0 0 Zn 5.688629656 5.473893038 6.2239919760 0 0 0 Zn 7.584837479 4.379116941 9.3347611820 0 0 0 S 5.688630361 5.473892630 8.5521622020 0 0 0 S 7.584836773 4.379117349 11.662931408 0 0 0 Zn 5.688629656 5.473893038 12.445530613 0 0 0 Zn 7.584837479 4.379116941 15.556299819 0 0 0 S 5.688630361 5.473892630 14.773700839 0 0 0 S 7.584836773 4.379117349 17.884470045 0 0 0 Zn 5.688629656 5.473893038 18.667069250 0 0 0 Zn 7.584837479 4.379116941 21.777838456 S 5.688630361 5.473892630 20.995239476 S 7.584836773 4.379117349 24.106008682 Zn 5.688629656 5.473893038 24.888607887 S 5.688630361 5.473892630 27.216778113 Zn 5.688633332 7.663446746 3.1132225450 0 0 0 S 3.792426214 8.758222435 2.3306235650 0 0 0 S 5.688632626 7.663447154 5.4413927710 0 0 0 Zn 3.792425509 8.758222843 6.2239919760 0 0 0 Zn 5.688633332 7.663446746 9.3347611820 0 0 0 S 3.792426214 8.758222435 8.5521622020 0 0 0 S 5.688632626 7.663447154 11.662931408 0 0 0 Zn 3.792425509 8.758222843 12.445530613 0 0 0 Zn 5.688633332 7.663446746 15.556299819 0 0 0 S 3.792426214 8.758222435 14.773700839 0 0 0 S 5.688632626 7.663447154 17.884470045 0 0 0 Zn 3.792425509 8.758222843 18.667069250 0 0 0 Zn 5.688633332 7.663446746 21.777838456 S 3.792426214 8.758222435 20.995239476 S 5.688632626 7.663447154 24.106008682 Zn 3.792425509 8.758222843 24.888607887 S 3.792426214 8.758222435 27.216778113 K_POINTS automatic 3 3 1 0 0 0 -- *************************************** Amin Torabi Ph.D. Student Chemistry Dept. Western University London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- *************************************** Amin Torabi Ph.D. Student Chemistry Dept. Western University London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From davemeel at yahoo.com Tue Aug 14 03:50:01 2012 From: davemeel at yahoo.com (David Miller) Date: Mon, 13 Aug 2012 18:50:01 -0700 (PDT) Subject: [Pw_forum] Problem with parallel phonon calculation using image method Message-ID: <1344909001.2544.YahooMailNeo@web121101.mail.ne1.yahoo.com> Hello, I am trying to perform phonon calculation using image method of parallelization. ?So, the following is what I do: (i) SCF calculation for 5-atom tetragonal PbTiO3 system. First, I relaxed the system, performed a SCF calculation using 64 processors.? Next, I performed Phonon (at Gamma) calculation using the following input: Phonons of PVDF-beta ?&inputph ? amass(1) = 207.21 ? amass(2) = 47.867 ? amass(3) = 15.9994 ? outdir = '.' ? prefix = 'pto' ? tr2_ph = 1e-18 ? fildyn = 'pto.dyn' ? epsil = .true. ? trans = .true. ?/ ?0.0 0.0 0.0 and running it as?aprun -N 8 -n 128 ./ph.x -npool 4 < ph.in > ph.out The above completed successfully and I have ph.out and pto.dyn files. Next, I tried the image method with the same file as above but with the following command: aprun -N 8 -n 640 ./ph.x -nimage 10 -npool 4 < ph.in > ph.out 10 images because it has 10 irreducible represetations at Gamma point. The INPUT_PH.txt in 4.3.2 version reads the following: *************************** ? ?On parallel machines the q point and the irreps calculations can be split ? ?automatically. The procedure is the following: ? ?1) run pw.x with nproc processors and npools pools. ? ?2) run ph.x with nproc*nimage processors, npools pools and nimage images. ? ?3) run ph.x with the same input and recover=.true. on nproc processors ? ? ? and npools pools and only one image. ? ?During the first ph.x run the phonon code split the total amount of ? ?work into nimage copies. Each image runs with different q and/or ? ?representations. ?The second run of ph.x is the final run that ? ?collects all the data calculated by the images and writes the files ? ?with the dynamical matrices. ***************************** However, all I get in the ph.out is the following: ? ?? **************************************** ? ? ?Program PHONON v.5.0 ? ? ? starts on 10Aug2012 at 22: 0:37 ? ? ?This program is part of the open-source Quantum ESPRESSO suite ? ? ?for quantum simulation of materials; please cite ? ? ? ? ?"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ? ? ? ? ? URL http://www.quantum-espresso.org", ? ? ?in publications or presentations arising from this work. More details at ? ? ?http://www.quantum-espresso.org/quote.php ? ? ?Parallel version (MPI), running on ? 640 processors ? ? ?path-images division: ?nimage ? ?= ? 10 ? ? ?K-points division: ? ? npool ? ? = ? ?4 ? ? ?R & G space division: ?proc/pool = ? 16 ? ? ?Ultrasoft (Vanderbilt) Pseudopotentials Application 16682117 exit codes: 143 Application 16682117 resources: utime 0, stime 0 ******************************************** Several files are generated? directories _ph0 through _ph9 are empty and files out.1_0 through out.9_0 are all empty.? I wonder what am I doing wrong ? Thanks, David -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120813/7f26bdd0/attachment-0001.htm From tube77 at gmail.com Tue Aug 14 07:59:46 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Tue, 14 Aug 2012 00:59:46 -0500 Subject: [Pw_forum] set_irr.f90 in v5.0 Message-ID: Dear, PW users I wonder if there is a progress or fix on the issue posted as below, http://www.democritos.it/pipermail/pw_forum/2012-July/024657.html I'm having the exactly same problem when I run the ph.x which did not happen in v4.3. I've tried to play around the threshold in set_irr.f90 (both line 258 and 282 with 1.d-3, 1.d-2, 1.d-5) but it didn't help. What I could do was to set 'search_sym=.false.' then ph.x ran without error. But then mpi error happens when I run the matdyn.x to plot the dispersion.. I have no idea if this relates with the 'search_sym=.false.' I run the working input files and parallel scheme previously used in v.4.3 as shown below. Thank you. pw.x ========================= &control calculation = 'scf', restart_mode = 'from_scratch', prefix = '$NAME', pseudo_dir = '$PSEUDO_DIR/', outdir = '$OUT_DIR/', wf_collect = .TRUE. tstress = .TRUE. tprnfor = .TRUE. etot_conv_thr = 1.d-5 forc_conv_thr = 1.d-4 / &system ibrav = 0, celldm(1) = 2.687 nat = 2, ntyp = 1, ecutwfc = 45.0, ecutrho = 450.0, occupations = 'smearing', smearing = 'mp', degauss = 0.03, / &electrons diagonalization = 'cg', mixing_mode = 'plain', mixing_beta = 0.7, conv_thr = 1.0d-8, / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF CELL_PARAMETERS 0.86602500 1.50000000 0.00000000 -0.86602500 1.50000000 0.00000000 0.00000000 0.00000000 8.66602500 ATOMIC_POSITIONS (alat) C 0.000000000 1.000000000 0.000000000 C 0.000000000 2.000000000 0.000000000 K_POINTS automatic 8 8 1 0 0 0 ====================== ph.x ====================== &inputph tr2_ph = 1.d-14, prefix = '$NAME', outdir = '$OUT_DIR/', fildyn = '$NAME.dyn', ldisp = .true., nq1 = 8, nq2 = 8, nq3 = 1, amass(1) = 12.0107, ====================== q2r.x ====================== &input fildyn = '$NAME.dyn' flfrc = '$NAME.881.fc' zasr = 'simple' ====================== matdyn.x ====================== &input asr = 'crystal' amass(1) = 12.0107, flfrc = '$NAME.881.fc' flfrq = '$NAME.freq' flvec = 'matdyn.modes' q_in_band_form=.TRUE. / 4 0.000000 0.000000 0.000000 50 !G 0.288675 0.166666 0.000000 30 !M 0.192450 0.333333 0.000000 50 !K 0.000000 0.000000 0.000000 50 !G ====================== JISEOK KIM, Ph.D. Postdoctoral Research Associate Department of Materials Science and Engineering University of Texas at Dallas 800 W. Campbell Rd. RL10 Richardson, TX 75080 (413)386-6285 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120814/60a63e7e/attachment.htm From dalcorso at sissa.it Tue Aug 14 10:29:35 2012 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 14 Aug 2012 10:29:35 +0200 Subject: [Pw_forum] set_irr.f90 in v5.0 In-Reply-To: References: Message-ID: <1344932975.2124.9.camel@ulisse.cm.sissa.it> I think this is not a QE problem. In the definition of the direct lattice vectors > 0.86602500 1.50000000 0.00000000 > -0.86602500 1.50000000 0.00000000 > 0.00000000 0.00000000 8.66602500 there are too few digits in 0.86602500. This creates rotation matrices that confuse the symmetry routines for the classification of the modes. 0.86602500 -> 0.866025403 fixes the problem. HTH, Andrea On Tue, 2012-08-14 at 00:59 -0500, Jiseok Kim wrote: > Dear, PW users > > > I wonder if there is a progress or fix on the issue posted as below, > > > http://www.democritos.it/pipermail/pw_forum/2012-July/024657.html > > > I'm having the exactly same problem when I run the ph.x which did not > happen in v4.3. > I've tried to play around the threshold in set_irr.f90 (both line 258 > and 282 with 1.d-3, 1.d-2, 1.d-5) but it didn't help. > What I could do was to set 'search_sym=.false.' then ph.x ran without > error. > But then mpi error happens when I run the matdyn.x to plot the > dispersion.. > I have no idea if this relates with the 'search_sym=.false.' > > > I run the working input files and parallel scheme previously used in > v.4.3 as shown below. > Thank you. > > > > > pw.x > ========================= > &control > calculation = 'scf', > restart_mode = 'from_scratch', > prefix = '$NAME', > pseudo_dir = '$PSEUDO_DIR/', > outdir = '$OUT_DIR/', > wf_collect = .TRUE. > tstress = .TRUE. > tprnfor = .TRUE. > etot_conv_thr = 1.d-5 > forc_conv_thr = 1.d-4 > / > &system > ibrav = 0, > celldm(1) = 2.687 > nat = 2, > ntyp = 1, > ecutwfc = 45.0, > ecutrho = 450.0, > occupations = 'smearing', > smearing = 'mp', > degauss = 0.03, > / > &electrons > diagonalization = 'cg', > mixing_mode = 'plain', > mixing_beta = 0.7, > conv_thr = 1.0d-8, > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > CELL_PARAMETERS > 0.86602500 1.50000000 0.00000000 > -0.86602500 1.50000000 0.00000000 > 0.00000000 0.00000000 8.66602500 > ATOMIC_POSITIONS (alat) > C 0.000000000 1.000000000 0.000000000 > C 0.000000000 2.000000000 0.000000000 > K_POINTS automatic > 8 8 1 0 0 0 > ====================== > > > > > ph.x > ====================== > &inputph > tr2_ph = 1.d-14, > prefix = '$NAME', > outdir = '$OUT_DIR/', > fildyn = '$NAME.dyn', > ldisp = .true., > nq1 = 8, > nq2 = 8, > nq3 = 1, > amass(1) = 12.0107, > ====================== > > > q2r.x > ====================== > &input > fildyn = '$NAME.dyn' > flfrc = '$NAME.881.fc' > zasr = 'simple' > ====================== > > > > > matdyn.x > ====================== > &input > asr = 'crystal' > amass(1) = 12.0107, > flfrc = '$NAME.881.fc' > flfrq = '$NAME.freq' > flvec = 'matdyn.modes' > q_in_band_form=.TRUE. > / > 4 > 0.000000 0.000000 0.000000 50 !G > 0.288675 0.166666 0.000000 30 !M > 0.192450 0.333333 0.000000 50 !K > 0.000000 0.000000 0.000000 50 !G > ====================== > > > > > > > JISEOK KIM, Ph.D. > Postdoctoral Research Associate > Department of Materials Science and Engineering > University of Texas at Dallas > 800 W. Campbell Rd. RL10 > Richardson, TX 75080 > (413)386-6285 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From csatya11 at gmail.com Tue Aug 14 15:18:39 2012 From: csatya11 at gmail.com (Satyananda Chab) Date: Tue, 14 Aug 2012 18:48:39 +0530 Subject: [Pw_forum] 110-direction Vs 110-point calculation Message-ID: Dear Users, I am trying to calculate the full phonon spectrum of a ferromagnetic alloy but the results that I found are not matching with literature. So I want to know (1) How to assign 110-direction for a grid calculation? (2)Whether calculating phonon spectrum from Gamma to X point along 110 direction is the same as that of a single point calculation at 110 point for this particular point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody throw me some light on these questions, i will be very happy. Thanking you in advance SATYANAND CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com me as that of a single point calculation at 110 point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody of you throw me some light, i will be very happy. Thanking you in advance SATYA NANDA CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120814/d4c05229/attachment.htm From flux_ray12 at 163.com Tue Aug 14 17:46:59 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 14 Aug 2012 23:46:59 +0800 (CST) Subject: [Pw_forum] 110-direction Vs 110-point calculation In-Reply-To: References: Message-ID: <6e72a617.216fb.13925d10759.Coremail.flux_ray12@163.com> Dear S. Chab: Definitely, I am not clear about your system. Which is the 4x4x4 M-P mesh? for k-points or q-points? If it is for k-points, then I think it is too small. But any way, I think the convergence test and well relaxation should be done before phonon calculation. For the [110] direction, which means the path from Gamma to X, in your system. X is just a point in FBZ and corresponds to (110) or (1/2, 1/2, 0) based on different cells. Of course, you can directly calculate frequencies by specifying a series of q-points along [110] direction in ph.x. But, running the whole phonon dispersion at converged q-mesh and only draw Gamma->X out is better choice. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-14 21:18:39,"Satyananda Chab" wrote: Dear Users, I am trying to calculate the full phonon spectrum of a ferromagnetic alloy but the results that I found are not matching with literature. So I want to know (1) How to assign 110-direction for a grid calculation? (2)Whether calculating phonon spectrum from Gamma to X point along 110 direction is the same as that of a single point calculation at 110 point for this particular point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody throw me some light on these questions, i will be very happy. Thanking you in advance SATYANAND CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com me as that of a single point calculation at 110 point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody of you throw me some light, i will be very happy. Thanking you in advance SATYA NANDA CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120814/0ce1f11c/attachment.htm From wparker at anl.gov Tue Aug 14 18:40:07 2012 From: wparker at anl.gov (William Parker) Date: Tue, 14 Aug 2012 11:40:07 -0500 Subject: [Pw_forum] Problem with parallel phonon calculation using image method In-Reply-To: <1344909001.2544.YahooMailNeo@web121101.mail.ne1.yahoo.com> References: <1344909001.2544.YahooMailNeo@web121101.mail.ne1.yahoo.com> Message-ID: <1EEFF91A-0C11-4120-834F-585B66EC6E89@anl.gov> Hello David, If the phonon calculation without images is correct ("aprun -N 8 -n 128 ./ph.x -npool 4 < ph.in > ph.out"), your SCF calculation ran on 128 (not 64) processors, and you need 1280 processors to do 10 images ("aprun -N 8 -n 1280 ./ph.x -nimage 10 -npool 4 < ph.in > ph.out"). Can you verify that? --William On Aug 13, 2012, at 8:50 PM, David Miller wrote: > Hello, > > I am trying to perform phonon calculation using image method of parallelization. So, the following is what I do: > > (i) SCF calculation for 5-atom tetragonal PbTiO3 system. First, I relaxed the system, performed a SCF calculation using 64 processors. > > > Next, I performed Phonon (at Gamma) calculation using the following input: > > Phonons of PVDF-beta > &inputph > amass(1) = 207.21 > amass(2) = 47.867 > amass(3) = 15.9994 > outdir = '.' > prefix = 'pto' > tr2_ph = 1e-18 > fildyn = 'pto.dyn' > epsil = .true. > trans = .true. > / > 0.0 0.0 0.0 > > and running it as aprun -N 8 -n 128 ./ph.x -npool 4 < ph.in > ph.out > > The above completed successfully and I have ph.out and pto.dyn files. > > Next, I tried the image method with the same file as above but with the following command: > > aprun -N 8 -n 640 ./ph.x -nimage 10 -npool 4 < ph.in > ph.out > > 10 images because it has 10 irreducible represetations at Gamma point. The INPUT_PH.txt in 4.3.2 version reads the following: > > *************************** > On parallel machines the q point and the irreps calculations can be split > automatically. The procedure is the following: > > 1) run pw.x with nproc processors and npools pools. > 2) run ph.x with nproc*nimage processors, npools pools and nimage images. > 3) run ph.x with the same input and recover=.true. on nproc processors > and npools pools and only one image. > > During the first ph.x run the phonon code split the total amount of > work into nimage copies. Each image runs with different q and/or > representations. The second run of ph.x is the final run that > collects all the data calculated by the images and writes the files > with the dynamical matrices. > ***************************** > > However, all I get in the ph.out is the following: > > **************************************** > Program PHONON v.5.0 starts on 10Aug2012 at 22: 0:37 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/quote.php > > Parallel version (MPI), running on 640 processors > path-images division: nimage = 10 > K-points division: npool = 4 > R & G space division: proc/pool = 16 > > Ultrasoft (Vanderbilt) Pseudopotentials > Application 16682117 exit codes: 143 > Application 16682117 resources: utime 0, stime 0 > ******************************************** > > Several files are generated > > directories _ph0 through _ph9 are empty and files out.1_0 through out.9_0 are all empty. > > I wonder what am I doing wrong ? > > Thanks, > > David > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ********************************************************* William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From davemeel at yahoo.com Wed Aug 15 16:39:50 2012 From: davemeel at yahoo.com (David Miller) Date: Wed, 15 Aug 2012 07:39:50 -0700 (PDT) Subject: [Pw_forum] Problem with parallel phonon calculation using image method In-Reply-To: <1344909001.2544.YahooMailNeo@web121101.mail.ne1.yahoo.com> References: <1344909001.2544.YahooMailNeo@web121101.mail.ne1.yahoo.com> Message-ID: <1345041590.19113.YahooMailNeo@web121105.mail.ne1.yahoo.com> actually, I typed wrong command in my earlier mail. My SCF calculation was indeed performed using 64 processors as: aprun -N 8 -n 64 ./ph.x -npool 4 < ph.in > ph.out Next, I tried the image method for phonons using: aprun -N 8 -n 640 ./ph.x -nimage 10 -npool 4 < ph.in > ph.out Thanks, David _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120815/deb2995e/attachment.htm From iyad.ne at gmail.com Wed Aug 15 19:27:09 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Wed, 15 Aug 2012 13:27:09 -0400 Subject: [Pw_forum] phonon calculations do not converge In-Reply-To: References: Message-ID: Hi Wiliam, I used tr2_ph = 1.0d-10, it did not converge either after 100 steps. The |ddv_scf|^ values are about ~ E-07. However, when I used tr2_ph = 1.0d-14, the |ddv_scf|^ values are diverging strongly ~E+20 and even more. Kindest Regards, On Fri, Aug 10, 2012 at 5:16 PM, William Parker wrote: > Hi Iyad, > > How strong is the failure to converge at (0, 1/6, 1/6)? Perhaps a less > tight tr2_ph value of, say, 1.0d-10 would get you where you need to be. > > --William > > On Aug 10, 2012, at 12:29 PM, Iyad AL-QASIR wrote: > > > Dear PW_Forum, > > > > I am running phonon calculations for FeSi (a narrow band gap > semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 > q-points ran successfully and got good phonon values. However when I reach > the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. > I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. > > > > Below are my input files: > > > > &control > > calculation='scf', > > restart_mode='from_scratch', > > title='FeSi', > > outdir='./', > > prefix='FeSi', > > pseudo_dir='./', > > / > > &system > > ibrav=1, > > celldm(1)=8.4165, > > nat=8, ntyp=2, > > ecutwfc=60.0, > > ecutrho= 720.0, > > / > > &electrons > > conv_thr=1.0d-9, > > mixing_mode='plain', > > mixing_beta=0.7, > > diagonalization='david', > > / > > ATOMIC_SPECIES > > Fe 55.847 Fe.pw91-sp-van_ak.UPF > > Si 28.086 Si.pw91-n_van.UPF > > ATOMIC_POSITIONS > > Fe 0.134855265 0.134855265 0.134855265 > > Fe 0.634855265 0.365144735 0.865144735 > > Fe 0.865144735 0.634855265 0.365144735 > > Fe 0.365144735 0.865144735 0.634855265 > > Si 0.839976366 0.839976366 0.839976366 > > Si 0.339976366 0.660023634 0.160023634 > > Si 0.160023634 0.339976366 0.660023634 > > Si 0.660023634 0.160023634 0.339976366 > > K_POINTS {automatic} > > 10 10 10 0 0 0 > > *********************************** > > phonons of FeSi > > &inputph > > tr2_ph=1.0d-14, > > prefix='FeSi', > > amass(1)=55.847, > > amass(2)=28.086, > > outdir='./' > > fildyn='FeSi.dyn', > > trans=.true., > > ldisp=.true., > > nq1=6, nq2=6, nq3=6 > > recover=.true., > > alpha_mix(1)=0.30 > > > > Any comments and suggestions are welcomed. > > > > Thanks > > IYAD > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > ********************************************************* > William D. Parker phone: (630) 252-4834 > Computational Postdoctoral Fellow fax: (630) 252-4798 > MSD-212, Rm. C-215 > Argonne National Laboratory > 9700 S. Cass Ave. > Argonne, IL 60439 > ********************************************************* > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ___________________________ IYAD I. AL-QASIR, PhD Postdoc Research Associate X-Ray and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division Oak Ridge National Lab Oak Ridge, TN -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120815/48abc622/attachment.htm From mgtmentink at lbl.gov Wed Aug 15 19:38:13 2012 From: mgtmentink at lbl.gov (Matthijs Mentink) Date: Wed, 15 Aug 2012 10:38:13 -0700 Subject: [Pw_forum] phonon calculations do not converge In-Reply-To: References: Message-ID: Hi Iyad, Have you considered introducing some broadening in the pwscf calculation? It helps. Be careful not to go overboard though. You could try introducing some broadening (like 1e-3 Ry or so) and see if it converges. If that works than you can see how far you can reduce broadening while still having the phonon calculations converge. cheers, Matthijs On Wed, Aug 15, 2012 at 10:27 AM, Iyad AL-QASIR wrote: > Hi Wiliam, > > I used tr2_ph = 1.0d-10, it did not converge either after 100 steps. The > |ddv_scf|^ values are about ~ E-07. > > However, when I used tr2_ph = 1.0d-14, the |ddv_scf|^ values are diverging > strongly ~E+20 and even more. > > Kindest Regards, > > > > > On Fri, Aug 10, 2012 at 5:16 PM, William Parker wrote: > >> Hi Iyad, >> >> How strong is the failure to converge at (0, 1/6, 1/6)? Perhaps a less >> tight tr2_ph value of, say, 1.0d-10 would get you where you need to be. >> >> --William >> >> On Aug 10, 2012, at 12:29 PM, Iyad AL-QASIR wrote: >> >> > Dear PW_Forum, >> > >> > I am running phonon calculations for FeSi (a narrow band gap >> semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 >> q-points ran successfully and got good phonon values. However when I reach >> the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. >> I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. >> > >> > Below are my input files: >> > >> > &control >> > calculation='scf', >> > restart_mode='from_scratch', >> > title='FeSi', >> > outdir='./', >> > prefix='FeSi', >> > pseudo_dir='./', >> > / >> > &system >> > ibrav=1, >> > celldm(1)=8.4165, >> > nat=8, ntyp=2, >> > ecutwfc=60.0, >> > ecutrho= 720.0, >> > / >> > &electrons >> > conv_thr=1.0d-9, >> > mixing_mode='plain', >> > mixing_beta=0.7, >> > diagonalization='david', >> > / >> > ATOMIC_SPECIES >> > Fe 55.847 Fe.pw91-sp-van_ak.UPF >> > Si 28.086 Si.pw91-n_van.UPF >> > ATOMIC_POSITIONS >> > Fe 0.134855265 0.134855265 0.134855265 >> > Fe 0.634855265 0.365144735 0.865144735 >> > Fe 0.865144735 0.634855265 0.365144735 >> > Fe 0.365144735 0.865144735 0.634855265 >> > Si 0.839976366 0.839976366 0.839976366 >> > Si 0.339976366 0.660023634 0.160023634 >> > Si 0.160023634 0.339976366 0.660023634 >> > Si 0.660023634 0.160023634 0.339976366 >> > K_POINTS {automatic} >> > 10 10 10 0 0 0 >> > *********************************** >> > phonons of FeSi >> > &inputph >> > tr2_ph=1.0d-14, >> > prefix='FeSi', >> > amass(1)=55.847, >> > amass(2)=28.086, >> > outdir='./' >> > fildyn='FeSi.dyn', >> > trans=.true., >> > ldisp=.true., >> > nq1=6, nq2=6, nq3=6 >> > recover=.true., >> > alpha_mix(1)=0.30 >> > >> > Any comments and suggestions are welcomed. >> > >> > Thanks >> > IYAD >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> ********************************************************* >> William D. Parker phone: (630) 252-4834 >> Computational Postdoctoral Fellow fax: (630) 252-4798 >> MSD-212, Rm. C-215 >> Argonne National Laboratory >> 9700 S. Cass Ave. >> Argonne, IL 60439 >> ********************************************************* >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > ___________________________ > IYAD I. AL-QASIR, PhD > Postdoc Research Associate > > X-Ray and Neutron Scattering and Spectroscopy Group > Materials Science and Technology Division > Oak Ridge National Lab > Oak Ridge, TN > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120815/cae5d14f/attachment.htm From iyad.ne at gmail.com Wed Aug 15 20:46:32 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Wed, 15 Aug 2012 14:46:32 -0400 Subject: [Pw_forum] phonon calculations do not converge In-Reply-To: References: Message-ID: Hello Matt, Can I introduce some broadening, keeping in mind this structure is semiconductor no metallic? Thanks IYAD On Wed, Aug 15, 2012 at 1:38 PM, Matthijs Mentink wrote: > Hi Iyad, > > Have you considered introducing some broadening in the pwscf calculation? > It helps. Be careful not to go overboard though. You could try introducing > some broadening (like 1e-3 Ry or so) and see if it converges. If that works > than you can see how far you can reduce broadening while still having the > phonon calculations converge. > > cheers, > > Matthijs > > > On Wed, Aug 15, 2012 at 10:27 AM, Iyad AL-QASIR wrote: > >> Hi Wiliam, >> >> I used tr2_ph = 1.0d-10, it did not converge either after 100 steps. The >> |ddv_scf|^ values are about ~ E-07. >> >> However, when I used tr2_ph = 1.0d-14, the |ddv_scf|^ values are >> diverging strongly ~E+20 and even more. >> >> Kindest Regards, >> >> >> >> >> On Fri, Aug 10, 2012 at 5:16 PM, William Parker wrote: >> >>> Hi Iyad, >>> >>> How strong is the failure to converge at (0, 1/6, 1/6)? Perhaps a less >>> tight tr2_ph value of, say, 1.0d-10 would get you where you need to be. >>> >>> --William >>> >>> On Aug 10, 2012, at 12:29 PM, Iyad AL-QASIR wrote: >>> >>> > Dear PW_Forum, >>> > >>> > I am running phonon calculations for FeSi (a narrow band gap >>> semiconductor) using QE-5.0. I am using a 6x6x6 q-vectors mesh. The first 4 >>> q-points ran successfully and got good phonon values. However when I reach >>> the 5th point(0 1/6 1/6). The self-consistent calculations do not converge. >>> I tried to reduce alpha_mix(1) to 0.3 but still have the same problem. >>> > >>> > Below are my input files: >>> > >>> > &control >>> > calculation='scf', >>> > restart_mode='from_scratch', >>> > title='FeSi', >>> > outdir='./', >>> > prefix='FeSi', >>> > pseudo_dir='./', >>> > / >>> > &system >>> > ibrav=1, >>> > celldm(1)=8.4165, >>> > nat=8, ntyp=2, >>> > ecutwfc=60.0, >>> > ecutrho= 720.0, >>> > / >>> > &electrons >>> > conv_thr=1.0d-9, >>> > mixing_mode='plain', >>> > mixing_beta=0.7, >>> > diagonalization='david', >>> > / >>> > ATOMIC_SPECIES >>> > Fe 55.847 Fe.pw91-sp-van_ak.UPF >>> > Si 28.086 Si.pw91-n_van.UPF >>> > ATOMIC_POSITIONS >>> > Fe 0.134855265 0.134855265 0.134855265 >>> > Fe 0.634855265 0.365144735 0.865144735 >>> > Fe 0.865144735 0.634855265 0.365144735 >>> > Fe 0.365144735 0.865144735 0.634855265 >>> > Si 0.839976366 0.839976366 0.839976366 >>> > Si 0.339976366 0.660023634 0.160023634 >>> > Si 0.160023634 0.339976366 0.660023634 >>> > Si 0.660023634 0.160023634 0.339976366 >>> > K_POINTS {automatic} >>> > 10 10 10 0 0 0 >>> > *********************************** >>> > phonons of FeSi >>> > &inputph >>> > tr2_ph=1.0d-14, >>> > prefix='FeSi', >>> > amass(1)=55.847, >>> > amass(2)=28.086, >>> > outdir='./' >>> > fildyn='FeSi.dyn', >>> > trans=.true., >>> > ldisp=.true., >>> > nq1=6, nq2=6, nq3=6 >>> > recover=.true., >>> > alpha_mix(1)=0.30 >>> > >>> > Any comments and suggestions are welcomed. >>> > >>> > Thanks >>> > IYAD >>> > >>> > >>> > _______________________________________________ >>> > Pw_forum mailing list >>> > Pw_forum at pwscf.org >>> > http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> ********************************************************* >>> William D. Parker phone: (630) 252-4834 >>> Computational Postdoctoral Fellow fax: (630) 252-4798 >>> MSD-212, Rm. C-215 >>> Argonne National Laboratory >>> 9700 S. Cass Ave. >>> Argonne, IL 60439 >>> ********************************************************* >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> ___________________________ >> IYAD I. AL-QASIR, PhD >> Postdoc Research Associate >> >> X-Ray and Neutron Scattering and Spectroscopy Group >> Materials Science and Technology Division >> Oak Ridge National Lab >> Oak Ridge, TN >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ___________________________ IYAD I. AL-QASIR, PhD Postdoc Research Associate X-Ray and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division Oak Ridge National Lab Oak Ridge, TN -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120815/1711e896/attachment-0001.htm From csatya11 at gmail.com Wed Aug 15 22:16:12 2012 From: csatya11 at gmail.com (Satyananda Chab) Date: Thu, 16 Aug 2012 01:46:12 +0530 Subject: [Pw_forum] (no subject) Message-ID: Dear Gao Zhe, CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea Thanks for your kind response. I am calculating phonons for 4X4X4 q-mesh for Ni2MnGa. But my calculations doesnot match previous papers. Is there any chance of getting by increasing to 6X6X6 or 8X8X8 q mesh? How can we give direction to a particular q1Xq2Xq3 mesh? Is this assigning direction related with matdyn.in file? Regards, Sayananda Chab Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120816/c24410dc/attachment.htm From giannozz at democritos.it Thu Aug 16 21:42:45 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Aug 2012 21:42:45 +0200 Subject: [Pw_forum] non-existed variables In-Reply-To: References: Message-ID: On Aug 7, 2012, at 21:02 , Ruibin Liu wrote: > There are three examples, H2O, NH4+ and N2 in the dipole example of > qe-4.3.2, > and their input files include several variables like do_ee, nelec, > nelup and neldw > in the SYSTEM nalists. What do those variables mean? whatever they mean, it is no longer important: they have been removed. Apparently an obsolete example was left P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 10:08:48 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 10:08:48 +0200 Subject: [Pw_forum] k points weights In-Reply-To: <20120727093954.Horde.mRhpZs1vlIJQElPap7kyGQA@webmail.bath.ac.uk> References: <20120727093954.Horde.mRhpZs1vlIJQElPap7kyGQA@webmail.bath.ac.uk> Message-ID: On Jul 27, 2012, at 10:39 , Davide Tiana wrote: > As remembered in many QE tutorials, weights are meaningless in NSCF > calculations such as band ones. yes and no, actually. 'nscf' calculation. The output data is meant to be used in subsequent calculations performing integrals over the BZ (e.g. dos); symmetry is applied and occupancies are calculated (using weights among other things) as for the 'scf' case 'band' calculation. Tthe output data is meant to be used only for visualization; symmetry is not applied, occupancies need not to be calculated, weights are in principle not used. Since the latest release, however, weights are used in the 'band' case as well to re-compute occupancies, because there is a specific case in which data to be exported to another code (not part of QE) have to be calculated using 'band' and not 'nscf', for reasons related to the way symmetries are handled. So, in conclusion: while weights in 'band' calculations are in most cases meaningless, it is a good idea not to fill them with absurd numbers (e.g. all zero or negative or very large) because the code could complain when calculating occupancies P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 10:45:09 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 10:45:09 +0200 Subject: [Pw_forum] plotrho.x refuses plotting charge ! In-Reply-To: References: Message-ID: <18E46C12-A03E-47E9-BE5B-4E319D97FE1E@democritos.it> On Aug 2, 2012, at 16:43 , Masoud wrote: > plotrho.x in some cases refuses plotting electron density contour map > and just plots the black circles showing atom's cores. this may happen when values for contour lines are out of the range of values in the file to be plotted > It is weird since with the same input file on another computer system > I can get the right map copy the data file ('A2-p.rho.dat' in your example) from the other computer, plot it on the computer where you say it doesn't work. Then see what happens P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 10:49:30 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 10:49:30 +0200 Subject: [Pw_forum] hibrid functionals In-Reply-To: <7986df2d174870b3a45258704d300df0.squirrel@webmail.roma2.infn.it> References: <5018EBCF.4040300@sissa.it> <7986df2d174870b3a45258704d300df0.squirrel@webmail.roma2.infn.it> Message-ID: <3708D2DC-9058-41FF-8A36-3173B3B6BFE1@democritos.it> On Aug 1, 2012, at 11:35 , Adriano Mosca Conte wrote: > in the last version of espresso I read that, among functionals, > there are > also hybrid ones, like B3LYP. I did not find further information > about it > on the manual. there is something in examples/EXX_example/ > How do they work? safely but slowly > Is it sufficient to generate a pseudo with a b3lyp functional there is currently no way to do this. You can use a BLYP PP. > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 11:07:24 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 11:07:24 +0200 Subject: [Pw_forum] Difference in implementation in matdyn.x between versions 4.2.1 and 5.0.0? In-Reply-To: References: Message-ID: Try with v.5.0.1. Note the following in Doc/release-notes: Fixed in 5.0.1 version * Funny frequencies from matdyn.x if masses were read from file P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 12:25:57 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 12:25:57 +0200 Subject: [Pw_forum] cp.x output: .pos In-Reply-To: References: Message-ID: On Aug 6, 2012, at 18:11 , xiaochuan Ge wrote: > Before before what date? the last change that may have affected the way files *.pos are printed should be this one (6 years ago!): http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=% 2F&view=rev&revision=2919 You may try to set nice_output_file=.false. in print_out.f90 to see what happens P. > the structrue of this file is: > > step number and time of the snapshot 1 > coordinates of all the atoms > step number and time of the snapshot 2 > coordinates of all the atoms > ...... > > That is, different snapshots are separated by an extra line which > indicates the step number and the time of this snapshot. But with > the newest version that I compiled on cineca-plx, this extra line > disappears. Now all the snapshots are mixed together, which is > quite inconvenient for me to check some information. I checked the src > of the printout_base.f90, it seems that nothing has been changed > for this file. Is there anyone knows what happened, and how could I > make a easy change to the code in order to recover the previous > function? > > Thanks in advance. > =================== > Ge Xiaochuan(Giovanni) > 3rd year PHD Student > Condensed Matter > SISSA,Italy > =================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 12:27:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 12:27:39 +0200 Subject: [Pw_forum] cp.x output: .pos In-Reply-To: References: Message-ID: On Aug 17, 2012, at 12:25 , Paolo Giannozzi wrote: > You may try to set nice_output_file=.false. oops, it is nice_output_files='true' --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From rainbee1988 at gmail.com Fri Aug 17 19:34:00 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Fri, 17 Aug 2012 13:34:00 -0400 Subject: [Pw_forum] non-existed variables In-Reply-To: References: Message-ID: The input file of Nitrogen scf calculation is like this: &CONTROL prefix = "N", pseudo_dir = "/home/degironc/QE/espresso/pseudo", outdir = "/home/degironc/tmp", / &SYSTEM ibrav = 1, celldm(1) = 24.0 nat = 1, ntyp = 1, ecutwfc = 30.D0, ecutrho = 120.D0, do_ee = .true. nspin = 2, nelec = 5, nelup = 4, neldw = 1 / &ELECTRONS conv_thr = 1.D-7, mixing_beta = 0.7D0, / &EE which_compensation='martyna-tuckerman' / ATOMIC_SPECIES N 1.00 N.pbe-paw_kj.UPF ATOMIC_POSITIONS {bohr} N 0.000 0.0 0.0 0 0 0 K_POINTS Gamma How to alter the variables in SYSTEM card to get right input file? Ruibin On Thu, Aug 16, 2012 at 3:42 PM, Paolo Giannozzi wrote: > > On Aug 7, 2012, at 21:02 , Ruibin Liu wrote: > > > There are three examples, H2O, NH4+ and N2 in the dipole example of > > qe-4.3.2, > > and their input files include several variables like do_ee, nelec, > > nelup and neldw > > in the SYSTEM nalists. What do those variables mean? > > whatever they mean, it is no longer important: they have been > removed. Apparently > an obsolete example was left > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120817/9d9f11e3/attachment.htm From rainbee1988 at gmail.com Fri Aug 17 19:46:40 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Fri, 17 Aug 2012 13:46:40 -0400 Subject: [Pw_forum] Input file for Cd6Se6 Message-ID: Dear all, When I tried to do a scf calculation for a Cd6Se6(NH3)6 system with this input file: ... prefix='Cd6Se6_6NH3' / &system ibrav = 1, celldm(1) =24.0, nat= 36, ntyp= 4, ecutwfc = 25.0, ecutrho = 200.0 / &electrons diagonalization='david' electron_maxstep = 50, conv_thr = 1.0e-6 mixing_beta = 0.7 / ATOMIC_SPECIES Cd 112.40 Cd.pbe-n-van.UPF Se 78.96 Se.pbe-van.UPF N 14.00674 N.pbe-van_bm.UPF H 1.00794 H.pbe-van_bm.UPF ATOMIC_POSITIONS { Angstrom } Cd 2.335662 -0.652860 -1.245236 Se 0.716568 -2.822854 -1.607832 Cd -1.744362 -1.695189 -1.236658 Se -2.813270 0.793267 -1.589989 Cd -0.604088 2.359223 -1.226735 Se 2.084317 2.042734 -1.598912 Cd 1.743905 1.694974 1.235198 Se -0.716656 2.822664 1.606488 Cd -2.336652 0.652370 1.243401 Se -2.084941 -2.043265 1.597360 Cd 0.603464 -2.360008 1.224830 Se 2.812401 -0.793480 1.589509 N -3.297002 -3.210191 -2.268159 N 1.142941 -4.439357 2.305111 N -4.420213 1.256882 2.274861 N 3.297027 3.208308 2.268243 N 4.433771 -1.251357 -2.251640 N -1.142051 4.445355 -2.294325 H -1.974619 4.288210 -2.861996 H -1.316482 5.110528 -1.541044 H -0.336172 4.714041 -2.858666 H -4.254951 2.101743 2.821691 H -5.065279 1.424795 1.502699 H -4.719730 0.474392 2.856237 H -2.757672 -3.864131 -2.835206 H -3.771885 -3.679104 -1.496722 H -3.942383 -2.655039 -2.829719 H 1.976965 -4.276392 2.869023 H 0.338563 -4.702490 2.874197 H 1.315512 -5.112052 1.558141 H 3.938159 2.652630 2.834135 H 3.776822 3.673792 1.497784 H 2.757064 3.865287 2.831160 H 4.739488 -0.467945 -2.828494 H 5.065281 -1.414646 -1.467255 H 4.283188 -2.097776 -2.800224 K_POINTS Gamma qe told me there is 'illegal instruction'. What is the problem? How to fix it? Thanks, Ruibin Graduate student Department of Chemistry Duke University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120817/f4df29f4/attachment.htm From giannozz at democritos.it Fri Aug 17 19:47:47 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 19:47:47 +0200 Subject: [Pw_forum] non-existed variables In-Reply-To: References: Message-ID: On Aug 17, 2012, at 19:34 , Ruibin Liu wrote: > > How to alter the variables in SYSTEM card to get right input file? replace "do_ee=.true." with "assume_isolated='martyna-tuckerman'" as explained in the documentation and in the examples of the latest version P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 19:49:27 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 19:49:27 +0200 Subject: [Pw_forum] Input file for Cd6Se6 In-Reply-To: References: Message-ID: On Aug 17, 2012, at 19:46 , Ruibin Liu wrote: > > When I tried to do a scf calculation for a Cd6Se6(NH3)6 system with > this input file > [...] > qe told me there is 'illegal instruction'. What is the problem? How > to fix it? bad compilation. The same question was answered a few days ago. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 17 22:25:40 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Aug 2012 22:25:40 +0200 Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: <48885545.196582.1343775111266.JavaMail.root@asems02.its.rochester.edu> References: <48885545.196582.1343775111266.JavaMail.root@asems02.its.rochester.edu> Message-ID: <93DFED01-A8B8-4371-A36C-D005D816E44D@democritos.it> About the first point: are you referring to MD on the ground state ("Born-Oppenheimer" MD), done with PWscf (not Car-Parrinello)? I think that the restart does the correct thing, i.e. use the Verlet algorithm as if the run was not interrupted, but there might be some subtle differences in how the threshold for convergence is calculated, that are more than sufficient to have the two MD simulations diverge. About the difference between nstep and the number of steps actually performed: it shouldn't be difficult to follow variable "nstep" and see why this happen P. On Aug 1, 2012, at 24:51 , Alexey Akimov wrote: > I tried to perform md simulations in Quantum Espresso in 2 > different ways: > 1) simply run a single continuous trajectory (e.g. 10 steps) > 2) run first step of MD as a new calculation (restart_mode = > from_scratch, default) > and run all other (remaining 9) steps as restarts (restart_mode = > restart), doing this for every step > > As a result after a few steps the total energies, atomic forces and > position started to deviate between two approaches. > > I suspect that some information from the previous step may be > dropped during the restart (e.g. by using the first-order Euler > scheme instead of the Verlet algorithm), eventually leading to such > divergence. So my question is: what is restart algorithm for MD in > quantum espresso and is there any possibility to use method 2 (see > above) without accumulation of the integration errors? > > Also can someone clarify why if i specify nstep = 1 in my input > file (request to perform a single MD step), the program actually > makes 2 MD steps? > > > Thank you, > Alexey > > > > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From rainbee1988 at gmail.com Sat Aug 18 01:35:16 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Fri, 17 Aug 2012 19:35:16 -0400 Subject: [Pw_forum] Input file for Cd6Se6 In-Reply-To: References: Message-ID: Thank you for answering again. In general, how to solve this problem? On Fri, Aug 17, 2012 at 1:49 PM, Paolo Giannozzi wrote: > > On Aug 17, 2012, at 19:46 , Ruibin Liu wrote: > > > > When I tried to do a scf calculation for a Cd6Se6(NH3)6 system with > > this input file > > [...] > > qe told me there is 'illegal instruction'. What is the problem? How > > to fix it? > > bad compilation. The same question was answered a few days ago. > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120817/3ed9e61e/attachment.htm From dwick004 at ucr.edu Sat Aug 18 01:40:02 2012 From: dwick004 at ucr.edu (Darshana Wickramaratne) Date: Fri, 17 Aug 2012 16:40:02 -0700 Subject: [Pw_forum] Input file for Cd6Se6 In-Reply-To: References: Message-ID: Hi Ruibin Here is a post on the forum pertaining to a similar problem. http://www.democritos.it/pipermail/pw_forum/2006-March/003854.html The best solution would be to have your sys admin recompile QE distribution. -- Darshana Wickramaratne PhD Candidate Department of Electrical Engineering, University of California - Riverside On Fri, Aug 17, 2012 at 4:35 PM, Ruibin Liu wrote: > Thank you for answering again. In general, how to solve this problem? > > On Fri, Aug 17, 2012 at 1:49 PM, Paolo Giannozzi wrote: > >> >> On Aug 17, 2012, at 19:46 , Ruibin Liu wrote: >> > >> > When I tried to do a scf calculation for a Cd6Se6(NH3)6 system with >> > this input file >> > [...] >> > qe told me there is 'illegal instruction'. What is the problem? How >> > to fix it? >> >> bad compilation. The same question was answered a few days ago. >> >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > *Liu, Ruibin* > Department of Chemistry > Duke University > Durham, NC, 27708 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120817/d2990304/attachment.htm From giannozz at democritos.it Sat Aug 18 19:38:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Aug 2012 19:38:21 +0200 Subject: [Pw_forum] cp.x output: .pos In-Reply-To: References: Message-ID: On Aug 17, 2012, at 12:27 , Paolo Giannozzi wrote: > > On Aug 17, 2012, at 12:25 , Paolo Giannozzi wrote: > >> You may try to set nice_output_file=.false. > > oops, it is nice_output_files='true' wrong again: nice_output_files=.true. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Aug 18 21:00:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Aug 2012 21:00:58 +0200 Subject: [Pw_forum] cp.x output: .pos In-Reply-To: References: Message-ID: On Aug 6, 2012, at 18:11 , xiaochuan Ge wrote: > That is, different snapshots are separated by an extra line which > indicates the step number and the time of this snapshot. But with > the newest version that I compiled on cineca-plx, this extra line > disappears. In CPV/src/printout_base.f90, locate lines 220 and 221: IF( PRESENT( nfi ) .AND. PRESENT( tps ) ) THEN ELSE IF( PRESENT( what ) ) THEN insert the following line: WRITE( iunit, 30 ) nfi, tps between the two lines above. It has been removed by mistake, as it is evident from the absence of any instruction between IF and ELSE P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From aakimov at z.rochester.edu Sun Aug 19 00:09:27 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sat, 18 Aug 2012 18:09:27 -0400 (EDT) Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: <93DFED01-A8B8-4371-A36C-D005D816E44D@democritos.it> Message-ID: <1659304069.79652.1345327767542.JavaMail.root@z.rochester.edu> Dear Paolo, Thank you for your kind reply (I already though that nobody will ever answer this :) ). 1) about first part - yes, i meant BOMD calculations. So are you saying that the difference arises because of the convergence criteria for the electronic problem at restart and during continuous MD run are different? In that case will setting the threshold for this problem to very small value help to prevent such divergence (perhaps for the cost of extra iterations)? Also I tried used the potential and wavefunction interpolation during MD simulation (i hope to accelerate calculations) in MD simulations. Do you think this can interfere with the MD restart algorithm? 2) about nstep - do you suggest to look into code? i just though this might have some faster explanation without digging into code. I think it might be good if someone could make it in accord with the naive expectation that nstep = 1 will make only one MD step, not 2. I suspect that the code performs 1 extra step at the end of simulation. In case of long trajectory e.g. nstep=100 this will not make a difference, but if i want to do the sequence : 1 MD step - (do something) - restart and do one more step - etc..., then 1 extra MD step at each calculation will double the computational expenses. So is it possible to change such behavior e.g. in next versions? Thank you, Alexey ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Friday, August 17, 2012 1:25:40 PM Subject: Re: [Pw_forum] MD restart algorithm in Quantum Espresso About the first point: are you referring to MD on the ground state ("Born-Oppenheimer" MD), done with PWscf (not Car-Parrinello)? I think that the restart does the correct thing, i.e. use the Verlet algorithm as if the run was not interrupted, but there might be some subtle differences in how the threshold for convergence is calculated, that are more than sufficient to have the two MD simulations diverge. About the difference between nstep and the number of steps actually performed: it shouldn't be difficult to follow variable "nstep" and see why this happen P. On Aug 1, 2012, at 24:51 , Alexey Akimov wrote: > I tried to perform md simulations in Quantum Espresso in 2 > different ways: > 1) simply run a single continuous trajectory (e.g. 10 steps) > 2) run first step of MD as a new calculation (restart_mode = > from_scratch, default) > and run all other (remaining 9) steps as restarts (restart_mode = > restart), doing this for every step > > As a result after a few steps the total energies, atomic forces and > position started to deviate between two approaches. > > I suspect that some information from the previous step may be > dropped during the restart (e.g. by using the first-order Euler > scheme instead of the Verlet algorithm), eventually leading to such > divergence. So my question is: what is restart algorithm for MD in > quantum espresso and is there any possibility to use method 2 (see > above) without accumulation of the integration errors? > > Also can someone clarify why if i specify nstep = 1 in my input > file (request to perform a single MD step), the program actually > makes 2 MD steps? > > > Thank you, > Alexey > > > > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From akohlmey at gmail.com Sun Aug 19 07:10:51 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sun, 19 Aug 2012 07:10:51 +0200 Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: <1659304069.79652.1345327767542.JavaMail.root@z.rochester.edu> References: <93DFED01-A8B8-4371-A36C-D005D816E44D@democritos.it> <1659304069.79652.1345327767542.JavaMail.root@z.rochester.edu> Message-ID: On Sun, Aug 19, 2012 at 12:09 AM, Alexey Akimov wrote: > Dear Paolo, > > Thank you for your kind reply (I already though that nobody will ever answer this :) ). > 1) about first part - yes, i meant BOMD calculations. So are you saying that the difference arises because of the convergence criteria for the electronic problem at restart and during continuous MD run are different? In that case will setting the threshold for this problem to very small value help to prevent such divergence (perhaps for the cost of extra iterations)? Also I tried used the potential and wavefunction interpolation during MD simulation (i hope to accelerate calculations) in MD simulations. Do you think this can interfere with the MD restart algorithm? convergence criteria are the same , but only the wavefunction, not the potential is saved, since the latter can be constructed from the former. the issue is a principal one. there will *always* be differences and the trajectories will diverge (usually exponentialls), since you are using floating point math, which is not like real math. floating point math does not commute, i.e. the result depends on the order of operations and floating point math does not have infinite accuracy. this is already a problem in classical MD, but in BOMD it is worse, since one typically does not save the forces to a restart, but recomputes them, which explains the additional SCF step at the beginning of a run. add to this the fact that MD is a chaotic process (coupled differential equation), the divergence is inevitable unless you use fixed point math and only use NVE dynamics (no thermostat). tightening the convergence will reduce the divergence initially, but since it is an exponential process, it is a useless enterprise. when using extrapolation, divergence will be larger, since the amount of history will determine your initial guess and there will some little "memory" of the initial guess (which is why extrapolation is a good thing, as it improves energy conservation and allows using a less tight convergence). but the not fully deterministic nature of restarting an MD is really not a problem, since the trajectory after the restart is statistically mechanically equivalent to the one from the uninterrupted run. for *proper* analysis you would actually need both and the huge number of other equivalent runs to average over and have a good sample of the ensemble. > 2) about nstep - do you suggest to look into code? i just though this might have some faster explanation without digging into code. I think it might be good if someone could make it in accord with the naive expectation that nstep = 1 will make only one MD step, not 2. I suspect that the code performs 1 extra step at the end of simulation. In case of long trajectory e.g. nstep=100 this will not make a difference, but if i want to do the sequence : 1 MD step - (do something) - restart and do one more step - etc..., then 1 extra MD step at each calculation will double the computational expenses. So is it possible to change such behavior e.g. in next versions? no. restarting is a bad idea in this case as you'd double the number of SCF calculations. you better integrate your "do something" into the QE-code. axel. > > Thank you, > Alexey > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Friday, August 17, 2012 1:25:40 PM > Subject: Re: [Pw_forum] MD restart algorithm in Quantum Espresso > > About the first point: are you referring to MD on the ground state > ("Born-Oppenheimer" MD), done with PWscf (not Car-Parrinello)? > I think that the restart does the correct thing, i.e. use the Verlet > algorithm as if the run was not interrupted, but there might be > some subtle differences in how the threshold for convergence is > calculated, that are more than sufficient to have the two MD > simulations diverge. > > About the difference between nstep and the number of steps actually > performed: it shouldn't be difficult to follow variable "nstep" and > see why > this happen > > P. > On Aug 1, 2012, at 24:51 , Alexey Akimov wrote: > >> I tried to perform md simulations in Quantum Espresso in 2 >> different ways: >> 1) simply run a single continuous trajectory (e.g. 10 steps) >> 2) run first step of MD as a new calculation (restart_mode = >> from_scratch, default) >> and run all other (remaining 9) steps as restarts (restart_mode = >> restart), doing this for every step >> >> As a result after a few steps the total energies, atomic forces and >> position started to deviate between two approaches. >> >> I suspect that some information from the previous step may be >> dropped during the restart (e.g. by using the first-order Euler >> scheme instead of the Verlet algorithm), eventually leading to such >> divergence. So my question is: what is restart algorithm for MD in >> quantum espresso and is there any possibility to use method 2 (see >> above) without accumulation of the integration errors? >> >> Also can someone clarify why if i specify nstep = 1 in my input >> file (request to perform a single MD step), the program actually >> makes 2 MD steps? >> >> >> Thank you, >> Alexey >> >> >> >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From aakimov at z.rochester.edu Sun Aug 19 22:05:55 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sun, 19 Aug 2012 16:05:55 -0400 (EDT) Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: Message-ID: <361244964.81900.1345406755584.JavaMail.root@z.rochester.edu> Dear Axel, Thanks you for clarifying the issues. So if i understand your point correctly, the divergence is because of the roundup errors (floating point operation) and not because of the algorithmistic problems - that is good to know. Yes, i see you point about the statistical meaning of the md trajectories - so as long as the divergence is not an artefact of the integration scheme (e.g. because of the lack of time-reversibility or symplecticity) that should not be a problem then for my purposes. Also thank you for clarifying the meaning of the extra step - so it is one extra step in the beginning (perhaps to restart the algorithm), not at the end of the restarted trajectory as i initially though. I think storing the current (and perhaps previous) forces along with the other information needed for restart would help to solve this problem and avoid doing this extra step at restart. W Thank you, Alexey ----- Original Message ----- From: "Axel Kohlmeyer" To: "PWSCF Forum" Sent: Saturday, August 18, 2012 10:10:51 PM Subject: Re: [Pw_forum] MD restart algorithm in Quantum Espresso On Sun, Aug 19, 2012 at 12:09 AM, Alexey Akimov wrote: > Dear Paolo, > > Thank you for your kind reply (I already though that nobody will ever answer this :) ). > 1) about first part - yes, i meant BOMD calculations. So are you saying that the difference arises because of the convergence criteria for the electronic problem at restart and during continuous MD run are different? In that case will setting the threshold for this problem to very small value help to prevent such divergence (perhaps for the cost of extra iterations)? Also I tried used the potential and wavefunction interpolation during MD simulation (i hope to accelerate calculations) in MD simulations. Do you think this can interfere with the MD restart algorithm? convergence criteria are the same , but only the wavefunction, not the potential is saved, since the latter can be constructed from the former. the issue is a principal one. there will *always* be differences and the trajectories will diverge (usually exponentialls), since you are using floating point math, which is not like real math. floating point math does not commute, i.e. the result depends on the order of operations and floating point math does not have infinite accuracy. this is already a problem in classical MD, but in BOMD it is worse, since one typically does not save the forces to a restart, but recomputes them, which explains the additional SCF step at the beginning of a run. add to this the fact that MD is a chaotic process (coupled differential equation), the divergence is inevitable unless you use fixed point math and only use NVE dynamics (no thermostat). tightening the convergence will reduce the divergence initially, but since it is an exponential process, it is a useless enterprise. when using extrapolation, divergence will be larger, since the amount of history will determine your initial guess and there will some little "memory" of the initial guess (which is why extrapolation is a good thing, as it improves energy conservation and allows using a less tight convergence). but the not fully deterministic nature of restarting an MD is really not a problem, since the trajectory after the restart is statistically mechanically equivalent to the one from the uninterrupted run. for *proper* analysis you would actually need both and the huge number of other equivalent runs to average over and have a good sample of the ensemble. > 2) about nstep - do you suggest to look into code? i just though this might have some faster explanation without digging into code. I think it might be good if someone could make it in accord with the naive expectation that nstep = 1 will make only one MD step, not 2. I suspect that the code performs 1 extra step at the end of simulation. In case of long trajectory e.g. nstep=100 this will not make a difference, but if i want to do the sequence : 1 MD step - (do something) - restart and do one more step - etc..., then 1 extra MD step at each calculation will double the computational expenses. So is it possible to change such behavior e.g. in next versions? no. restarting is a bad idea in this case as you'd double the number of SCF calculations. you better integrate your "do something" into the QE-code. axel. > > Thank you, > Alexey > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Friday, August 17, 2012 1:25:40 PM > Subject: Re: [Pw_forum] MD restart algorithm in Quantum Espresso > > About the first point: are you referring to MD on the ground state > ("Born-Oppenheimer" MD), done with PWscf (not Car-Parrinello)? > I think that the restart does the correct thing, i.e. use the Verlet > algorithm as if the run was not interrupted, but there might be > some subtle differences in how the threshold for convergence is > calculated, that are more than sufficient to have the two MD > simulations diverge. > > About the difference between nstep and the number of steps actually > performed: it shouldn't be difficult to follow variable "nstep" and > see why > this happen > > P. > On Aug 1, 2012, at 24:51 , Alexey Akimov wrote: > >> I tried to perform md simulations in Quantum Espresso in 2 >> different ways: >> 1) simply run a single continuous trajectory (e.g. 10 steps) >> 2) run first step of MD as a new calculation (restart_mode = >> from_scratch, default) >> and run all other (remaining 9) steps as restarts (restart_mode = >> restart), doing this for every step >> >> As a result after a few steps the total energies, atomic forces and >> position started to deviate between two approaches. >> >> I suspect that some information from the previous step may be >> dropped during the restart (e.g. by using the first-order Euler >> scheme instead of the Verlet algorithm), eventually leading to such >> divergence. So my question is: what is restart algorithm for MD in >> quantum espresso and is there any possibility to use method 2 (see >> above) without accumulation of the integration errors? >> >> Also can someone clarify why if i specify nstep = 1 in my input >> file (request to perform a single MD step), the program actually >> makes 2 MD steps? >> >> >> Thank you, >> Alexey >> >> >> >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From ptao10b at imr.ac.cn Mon Aug 20 04:08:06 2012 From: ptao10b at imr.ac.cn (Peng Tao) Date: Mon, 20 Aug 2012 10:08:06 +0800 (GMT+08:00) Subject: [Pw_forum] The files for lambda.x are missing! Message-ID: <1993055.2645.13941c978e7.Coremail.ptao10b@imr.ac.cn> Dear all, In my e-ph calculation of an one-dimensional system, I find there is no file of " elph.***.***.*** ". So I cannot apply lambda.x to it. And other files such as " a2Fq2r.* ", " a2Fmatdyn.* " and "a2F.dos*" are already generated. Could any expert help me? Thanks a lot. Best regards, Peng Tao -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120820/ffdd1fba/attachment.htm From giannozz at democritos.it Mon Aug 20 09:26:20 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 20 Aug 2012 09:26:20 +0200 Subject: [Pw_forum] MD restart algorithm in Quantum Espresso In-Reply-To: <1659304069.79652.1345327767542.JavaMail.root@z.rochester.edu> References: <1659304069.79652.1345327767542.JavaMail.root@z.rochester.edu> Message-ID: <2E733DF0-9914-4B72-9AAC-2B468142FF3D@democritos.it> On Aug 19, 2012, at 24:09 , Alexey Akimov wrote: > 1) about first part - yes, i meant BOMD calculations. So are you > saying that the difference arises because of the convergence > criteria for the electronic problem at restart and during > continuous MD run are different? actually the convergence threshold on self consistency is the same, but the starting threshold for diagonalization differs in a restarted run from that of a continuous run. I have verified (see attached) that apart from this small difference, the restart works properly. You can perform one step at the time by setting nstep=0. While I agree that this is a funny behavior, I think that there are more important things to be fixed in BOMD right now P. -------------- next part -------------- A non-text attachment was scrubbed... Name: md.tar.gz Type: application/x-gzip Size: 10088 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120820/00d8f862/attachment-0001.bin -------------- next part -------------- > I suspect that the code performs 1 extra step at the end of > simulation. In case of long trajectory e.g. nstep=100 this will not > make a difference, but if i want to do the sequence : 1 MD step - > (do something) - restart and do one more step - etc..., then 1 > extra MD step at each calculation will double the computational > expenses. So is it possible to change such behavior e.g. in next > versions? > > Thank you, > Alexey > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Friday, August 17, 2012 1:25:40 PM > Subject: Re: [Pw_forum] MD restart algorithm in Quantum Espresso > > About the first point: are you referring to MD on the ground state > ("Born-Oppenheimer" MD), done with PWscf (not Car-Parrinello)? > I think that the restart does the correct thing, i.e. use the Verlet > algorithm as if the run was not interrupted, but there might be > some subtle differences in how the threshold for convergence is > calculated, that are more than sufficient to have the two MD > simulations diverge. > > About the difference between nstep and the number of steps actually > performed: it shouldn't be difficult to follow variable "nstep" and > see why > this happen > > P. > On Aug 1, 2012, at 24:51 , Alexey Akimov wrote: > >> I tried to perform md simulations in Quantum Espresso in 2 >> different ways: >> 1) simply run a single continuous trajectory (e.g. 10 steps) >> 2) run first step of MD as a new calculation (restart_mode = >> from_scratch, default) >> and run all other (remaining 9) steps as restarts (restart_mode = >> restart), doing this for every step >> >> As a result after a few steps the total energies, atomic forces and >> position started to deviate between two approaches. >> >> I suspect that some information from the previous step may be >> dropped during the restart (e.g. by using the first-order Euler >> scheme instead of the Verlet algorithm), eventually leading to such >> divergence. So my question is: what is restart algorithm for MD in >> quantum espresso and is there any possibility to use method 2 (see >> above) without accumulation of the integration errors? >> >> Also can someone clarify why if i specify nstep = 1 in my input >> file (request to perform a single MD step), the program actually >> makes 2 MD steps? >> >> >> Thank you, >> Alexey >> >> >> >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From annetindele at yahoo.fr Mon Aug 20 14:05:01 2012 From: annetindele at yahoo.fr (anne etindele) Date: Mon, 20 Aug 2012 13:05:01 +0100 (BST) Subject: [Pw_forum] About pseudopotential In-Reply-To: <1345463878.16436.YahooMailNeo@web29602.mail.ird.yahoo.com> References: <1345463878.16436.YahooMailNeo@web29602.mail.ird.yahoo.com> Message-ID: <1345464301.31596.YahooMailNeo@web29602.mail.ird.yahoo.com> Dear? all I am interested on the determination of the total energy of C60. I have used the pseudopotential I found in the "pseudopotential" folder of Quantum espresso. I realised that the value of total energy of atoms obtained with pw.x is different from the one with ld1.x for the atom itself. finally the total energy of C60 is really far from the the value obtained with quantum chemistry code like Gaussian. I would like to know if there is a way to get the real total energy of systems when we use pseudopotential? ? Anne Justine ETINDELE PhD Student, University of Douala ( CAMEROON) Descente Mont Essec P.O. Box 24157 Douala Cameroon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120820/298f032f/attachment.htm From akohlmey at gmail.com Mon Aug 20 14:14:23 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 20 Aug 2012 14:14:23 +0200 Subject: [Pw_forum] About pseudopotential In-Reply-To: <1345464301.31596.YahooMailNeo@web29602.mail.ird.yahoo.com> References: <1345463878.16436.YahooMailNeo@web29602.mail.ird.yahoo.com> <1345464301.31596.YahooMailNeo@web29602.mail.ird.yahoo.com> Message-ID: On Mon, Aug 20, 2012 at 2:05 PM, anne etindele wrote: > Dear all > > I am interested on the determination of the total energy of C60. > I have used the pseudopotential I found in the "pseudopotential" folder of > Quantum espresso. > I realised that the value of total energy of atoms obtained with pw.x is > different from the one with ld1.x for the atom itself. finally the total > energy of C60 is > really far from the the value obtained with quantum chemistry code like > Gaussian. > > I would like to know if there is a way to get the real total energy of > systems > when we use pseudopotential? no. the total energy is a useless property, even with when doing all-electron calculations with gaussian. the only meaningful properties are energy *differences*. even gaussian doesn't compute the *real* total energy; it completely neglects the energy that holds the atom cores together (or the individual nucleons for that matter). cheers, axel. > > Anne Justine ETINDELE > PhD Student, > > University of Douala ( CAMEROON) > Descente Mont Essec > P.O. Box 24157 Douala > Cameroon > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From spiga.filippo at gmail.com Tue Aug 21 07:02:51 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 21 Aug 2012 13:02:51 +0800 Subject: [Pw_forum] GPU-accelerated PWscf Test Drive (provided by NVIDIA and partners) opens today Message-ID: Dear Quantum ESPRESSO users and developers, I want to advertise and share with you an NVIDIA initiative called "GPU Test Drive". NVIDIA along with Amazon and 21 other providers is offering FREE and exclusive test-drive to experience running your computational chemistry simulations faster with GPUs in dedicated small HPC systems and/or in cloud environments. The latest GPU-accelerated applications are pre-loaded so you don?t need setup any hardware or software. Simply log on and run apps as usual, NO GPU PROGRAMMING EXPERIENCE IS REQUIRED. NVIDIA (and eventually me if necessary) will provide support do get you in and run. *** GPU-accelerated PWscf v5.0 is available starting from today! *** That's really a great and unique opportunity for each one of you want to try/evaluate/benchmark the GPU accelerated code BUT does not have a machine equipped with GPU (M2070/M2090 GPUs designed for high performance scientific calculations). NVIDIA is going to work with its commercial partners in order to have always available the latest version of the GPU code. The service will provide the environment for both serial and parallel calculations (in this case, up to 4 nodes dual-socket and 8 GPUs in total). If you are interested, you only need to fill the form and wait NVIDIA to contact you in order to setup an access. Feel free to spread the news to any potential interested user that you know. Once again (I like to stress that), this is COMPLETELY FREE OF CHARGE initiative. Regards, Filippo -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120821/119e03ef/attachment.htm From spiga.filippo at gmail.com Tue Aug 21 10:25:47 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 21 Aug 2012 16:25:47 +0800 Subject: [Pw_forum] GPU-accelerated PWscf Test Drive (provided by NVIDIA and partners) opens today In-Reply-To: References: Message-ID: Dear Quantum ESPRESSO users and developers, following my previous email, here the link where you can access the test drive: http://www.nvidia.com/object/gpu-test-drive.html?cid=gputestdrive Enjoy. F. On Aug 21, 2012, at 1:02 PM, Filippo Spiga wrote: > Dear Quantum ESPRESSO users and developers, > > I want to advertise and share with you an NVIDIA initiative called "GPU Test Drive". NVIDIA along with Amazon and 21 other providers is offering FREE and exclusive test-drive to experience running your computational chemistry simulations faster with GPUs in dedicated small HPC systems and/or in cloud environments. The latest GPU-accelerated applications are pre-loaded so you don?t need setup any hardware or software. Simply log on and run apps as usual, NO GPU PROGRAMMING EXPERIENCE IS REQUIRED. NVIDIA (and eventually me if necessary) will provide support do get you in and run. > > *** GPU-accelerated PWscf v5.0 is available starting from today! *** > > That's really a great and unique opportunity for each one of you want to try/evaluate/benchmark the GPU accelerated code BUT does not have a machine equipped with GPU (M2070/M2090 GPUs designed for high performance scientific calculations). NVIDIA is going to work with its commercial partners in order to have always available the latest version of the GPU code. The service will provide the environment for both serial and parallel calculations (in this case, up to 4 nodes dual-socket and 8 GPUs in total). > > If you are interested, you only need to fill the form and wait NVIDIA to contact you in order to setup an access. Feel free to spread the news to any potential interested user that you know. > > Once again (I like to stress that), this is COMPLETELY FREE OF CHARGE initiative. -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120821/ff60e26a/attachment.htm From karandeepster at gmail.com Tue Aug 21 16:39:04 2012 From: karandeepster at gmail.com (karan deep) Date: Tue, 21 Aug 2012 20:09:04 +0530 Subject: [Pw_forum] confusion in ev.x Message-ID: Dear users I am quite confused by the naming used in ev.x after going through ev.f90 i conclude that Birch function used in this program is P(V) equation and for istate=1 i.e birch 1st order is actually a 3rd order Birch-Murnaghan equation of state as mentiontioed in WIKIPEDIA page http://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state Please correct me if i m wrong. Karandeep Research Scholar Physics Department, IIT, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120821/87f55ced/attachment.htm From w2agz at w2agz.com Tue Aug 21 21:01:16 2012 From: w2agz at w2agz.com (W2AGZ) Date: Tue, 21 Aug 2012 12:01:16 -0700 Subject: [Pw_forum] QE 5.0 Release Confusion Message-ID: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> I'm attempting to install and configure QE 5.0xxx. Unlike in the past, this recent release is segmented into separate packages, e.g., QE(PW, PlotPhon, etc.), PHonon, PWcond, etc., each with its separate examples and basic codes. I can manage the "raw" QE-PW package OK, but how do I configure and run all the rest? E.g., "makes" and "make.sys" for phonons? Oh.BTW.there's a problem with the build of the NEB package. gzip: ../archive/neb-5.0.1.tar.gz: not in gzip format tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors make[1]: *** [uncompress-neb] Error 2 make[1]: Leaving directory `/home/pmpgrant/Desktop/espresso-5.0.1/install' make: *** [neb] Error 2 Paul Grant, W2AGZ Technologies IBM Research Staff Member Emeritus Staff Associate, JPL/NASA/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120821/05b1c4ea/attachment.htm From aakimov at z.rochester.edu Tue Aug 21 23:55:03 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Tue, 21 Aug 2012 17:55:03 -0400 (EDT) Subject: [Pw_forum] question about spinors In-Reply-To: <1004228088.12155.1345576578806.JavaMail.root@z.rochester.edu> Message-ID: <24843099.15056.1345586103760.JavaMail.root@z.rochester.edu> Dear all, I try to understand the format of the wavefunction in case of spin-polarization (nspin=4, spinorb=.true. (or something similar)) without digging into code (what may take some longer time). First of all I print the wavefunction in the ascii format (text) using the post-processing utilities, that is the coefficients c_ig in expansion: psi_i = sum_over_g {c_ig * exp(u*g*r)} (assuming Gamma-point case, so k=0). So when i compute overlap of 2 orbitals it is delta_ij (Kronecker) (almost) for non-spin polarized case or with spin-polarized case but without spin-orbit. However, in spin-orbit case i have something like: = 1, = 0, = 1, etc. Also the eigenvalues of the even orbitals look the same as those of odd orbitals (e.g. e_1 = e2, e3 = e4, etc.) So my question is what are the even wavefunctions, why their overlap is not 1, but is 0 while for odd orbitals the normal expectation of overlap being close to 1 is satisfied? More specifically, what is the interpretation of the output wavefunctions (bands) in such calculations? I tried to look tutorial and presentations about spin-orbit coupling calculations in QE. They say about spinors, but what is what in the output and how the (ortho)normalization is expressed in term of the outputs? Thank you, Alexey -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From wangfenggong at gmail.com Wed Aug 22 02:52:49 2012 From: wangfenggong at gmail.com (Fenggong Wang) Date: Tue, 21 Aug 2012 20:52:49 -0400 Subject: [Pw_forum] Dipole correction of PW Message-ID: <1259C03B-366A-4C7A-AD1D-D4FFA41D18FA@gmail.com> Dear Everyone: After searching a lot on the dipole correction of PW and reading the corresponding literature, I still have some confusions about the dipole correction. Could anyone answer me? It seems basically we need the following keywords: tefield=.true. dipfield=.true. edir= emaxpos= eopreg= eamp= I don't understand the keyword of eamp. The default one is 0.001. However, if we just need the dipole correction without adding any additional external electric filed, the eamp should be set to 0. Is it correct? Or the eamp should be set to an electric filed just compensating the dipole field? If we use the default value of 0.001, does it mean we add both the dipole correction and an external electric field? Anyone has any idea on how to set this value? Thank you very much. Fenggong From magerode at gmail.com Wed Aug 22 08:54:27 2012 From: magerode at gmail.com (DENIS MAGERO) Date: Wed, 22 Aug 2012 09:54:27 +0300 Subject: [Pw_forum] QE 5.0 Release Confusion In-Reply-To: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> References: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> Message-ID: On 21 August 2012 22:01, W2AGZ wrote: Dear Paul Grant, Go to the quantum espresso and change your directory to achieve. check the size of the neb.tar.gz file. If its 0 in size, then download another neb.tar.gz from the quantum espresso website, copy it to the archieve in Quantum espresso and compile the neb again. It should work perfectly. the error is caused because of a zero sized neb.tar.gz file. Best regards. -- Dennis Magero, M.Sc Student, Computational group, Chepkoilel University College, ELDORET KENYA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/ae7cadc8/attachment-0001.htm From spiga.filippo at gmail.com Wed Aug 22 10:39:20 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Wed, 22 Aug 2012 16:39:20 +0800 Subject: [Pw_forum] QE 5.0 Release Confusion In-Reply-To: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> References: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> Message-ID: Dear all, another user wrote to me about a similar issue. In my case is the "atomic-5.0.tar.gz" package... if test ! -d ../atomic; then \ (gzip -dc ../archive/atomic-5.0.tar.gz | (cd ../ ; tar -xvf -)) ; fi gzip: ../archive/atomic-5.0.tar.gz: not in gzip format tar: This does not look like a tar archive tar: Error exit delayed from previous errors make[1]: *** [uncompress-ld1] Error 2 make[1]: Target `ld1' not remade because of errors. I haven't investigated yet but? it seems there is something weird with the packages? Cheers, F. On Aug 22, 2012, at 3:01 AM, "W2AGZ" wrote: > Oh?BTW?there?s a problem with the build of the NEB package? > > gzip: ../archive/neb-5.0.1.tar.gz: not in gzip format > tar: This does not look like a tar archive > tar: Exiting with failure status due to previous errors > make[1]: *** [uncompress-neb] Error 2 > make[1]: Leaving directory `/home/pmpgrant/Desktop/espresso-5.0.1/install' > make: *** [neb] Error 2 -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/d04bf759/attachment.htm From lmartinsamos at gmail.com Wed Aug 22 10:40:48 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 22 Aug 2012 10:40:48 +0200 Subject: [Pw_forum] [Q-e-developers] QE 5.0 Release Confusion In-Reply-To: References: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> Message-ID: DEar All, the problem is related with the change in the address of the plugins inside qe-forge. We should be able to solve it today!! thank you for your understanding Layla 2012/8/22 Filippo Spiga > Dear all, > > another user wrote to me about a similar issue. In my case is the > "atomic-5.0.tar.gz" package... > > if test ! -d ../atomic; then \ > (gzip -dc ../archive/atomic-5.0.tar.gz | (cd ../ ; tar -xvf -)) ; > fi > > gzip: ../archive/atomic-5.0.tar.gz: not in gzip format > tar: This does not look like a tar archive > tar: Error exit delayed from previous errors > make[1]: *** [uncompress-ld1] Error 2 > make[1]: Target `ld1' not remade because of errors. > > I haven't investigated yet but? it seems there is something weird with the > packages? > > Cheers, > F. > > > On Aug 22, 2012, at 3:01 AM, "W2AGZ" wrote: > > Oh?BTW?there?s a problem with the build of the NEB package?**** > ** ** > gzip: ../archive/neb-5.0.1.tar.gz: not in gzip format**** > tar: This does not look like a tar archive**** > tar: Exiting with failure status due to previous errors**** > make[1]: *** [uncompress-neb] Error 2**** > make[1]: Leaving directory `/home/pmpgrant/Desktop/espresso-5.0.1/install' > **** > make: *** [neb] Error 2 > > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > _______________________________________________ > Q-e-developers mailing list > Q-e-developers at qe-forge.org > http://qe-forge.org/mailman/listinfo/q-e-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/16faa7c3/attachment.htm From kangbugy at lycos.co.kr Wed Aug 22 11:16:28 2012 From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=) Date: Wed, 22 Aug 2012 18:16:28 +0900 Subject: [Pw_forum] =?utf-8?q?=27*****=27_in_output_files?= Message-ID: <311d4076e563720b5e6d4d14aa30fe24$5c6718fd@pcmail3.nate.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/7e3e5024/attachment.htm From giovanni.pizzi at epfl.ch Wed Aug 22 15:06:12 2012 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Wed, 22 Aug 2012 15:06:12 +0200 Subject: [Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm Message-ID: <5034D944.4020601@epfl.ch> Dear all, I believe there is a bug in QE 5.0 (pw.x) that occurs when using ibrav=0 and defining 'a' instead of 'celldm(1)'. In this case, celldm is not set and remains equal to zero. (This behavior was different in 4.3.2, where instead the celldm(1) value was set from the 'a' value.) This doesn't seem to create problems in the pw.x calculation. However, in the matdyn files generated by ph.x, the celldm(1) is set to zero. When the matdyn files are then given to q2r.x, the code crashes, complaining of a wrong celldm value. In particular this is what happens in q2r.x: 1. the first q point is read (matdyn1) using the routine read_dyn_from_file; celldm(1) is set to 0 2. the code calls the routine latgen: this routine sets celldm(1) to the a value different from zero (moreover this value may be wrong if 'a' in the input file was not set to the length of the first lattice vector) 3. the code reads the second q point (matdyn2) and compares the celldm value read from file (which is zero) with the old value (which was set to a value different from zero at step 2): being different, the code stops. I think that to correct it, one should replace the following lines (cell_base.f90, lines 152 and following) IF( celldm( 1 ) /= 0.0_DP ) THEN alat = celldm( 1 ) ELSE IF ( a /= 0.0_dp ) THEN alat = a / bohr_radius_angs ELSE alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 ) END IF at(:,:) = at(:,:) / alat with IF( celldm( 1 ) /= 0.0_DP ) THEN alat = celldm( 1 ) ELSE IF ( a /= 0.0_dp ) THEN alat = a / bohr_radius_angs celldm( 1 ) = alat ELSE alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 ) celldm( 1 ) = alat END IF at(:,:) = at(:,:) / alat Let me know what you think. Best, Giovanni Pizzi -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 319 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31159 From lmartinsamos at gmail.com Wed Aug 22 15:07:52 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 22 Aug 2012 15:07:52 +0200 Subject: [Pw_forum] path for automatic download of plugins Message-ID: Dear all, after the qe-forge migration, the path for the automatic download of plugins such as yambo, want, PHonon, NEB ... has changed. In order to recover this facility, you are invited to follow the instruction below: 1) download plugins_list-5.0 ( http://qeforge.qe-forge.org/gf/download/frsrelease/116/335/plugins_list-5.0) or plugins_list-5.0.1 ( http://qeforge.qe-forge.org/gf/download/frsrelease/116/336/plugins_list-5.0.1) depending on the version you want to patch 2) mv the downloaded file in directory espresso-5.0/install or espresso-5.0.1/install 3) change the name of the downloaded file with plugins_list or you can download from scratch espresso-5.0.tar.gz or espresso-5.0.1.tar.gz and re-install everything. Attention the gipaw release 5.0 has been deleted (see description section in page http://qeforge.qe-forge.org/gf/project/qe-gipaw/ ). sorry for the inconvenience, best regards Layla and Erica -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/442c8317/attachment.htm From giannozz at democritos.it Wed Aug 22 15:40:20 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Aug 2012 15:40:20 +0200 Subject: [Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm In-Reply-To: <5034D944.4020601@epfl.ch> References: <5034D944.4020601@epfl.ch> Message-ID: <6BD243AA-AD4A-47FD-984E-300E7D510975@democritos.it> On Aug 22, 2012, at 15:06 , Giovanni Pizzi wrote: > Let me know what you think. I think that variable celldm should disappear ... Thank you anyway for the report P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From prasenjit.jnc at gmail.com Wed Aug 22 15:47:14 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 22 Aug 2012 19:17:14 +0530 Subject: [Pw_forum] restart flag for nmr calculation using gipaw Message-ID: Dear all, I am doing an nmr calculation with gipaw. I need to restart the calculation because of restriction in the max cpu hour. However, in the manual for the gipaw input file, I could not find any flag to restart a calculation from the point where it has stopped. Is it possible to restart the nmr calculation using gipaw.x. If so how? With regards, Prasenjit -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/9733165d/attachment.htm From giovanni.pizzi at epfl.ch Wed Aug 22 15:52:54 2012 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Wed, 22 Aug 2012 15:52:54 +0200 Subject: [Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm In-Reply-To: <6BD243AA-AD4A-47FD-984E-300E7D510975@democritos.it> References: <5034D944.4020601@epfl.ch> <6BD243AA-AD4A-47FD-984E-300E7D510975@democritos.it> Message-ID: <5034E436.5090904@epfl.ch> On 08/22/2012 03:40 PM, Paolo Giannozzi wrote: > I think that variable celldm should disappear ... Thank you anyway for > the report Ok. But then, to fix the problem, one should define celldm(1) in pw.x as I was suggesting, or change q2r.x so that it doesn't use celldm? Best, Giovanni From giannozz at democritos.it Wed Aug 22 15:56:17 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Aug 2012 15:56:17 +0200 Subject: [Pw_forum] QE 5.0 Release Confusion In-Reply-To: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> References: <014101cd7fcf$57d88d60$0789a820$@w2agz.com> Message-ID: <9AE8EE1F-307F-4BC0-97F1-917B865DC9DC@democritos.it> On Aug 21, 2012, at 21:01 , W2AGZ wrote: > how do I configure and run all the rest? > configure once, then make all-the-rest > BTW?there?s a problem with the build of the NEB package? > this has already been answered, but, BTW, such a problem may also appear if a machine has no direct internet connection; in that case the downoad fails and a zero-size file is left as a souvenir. Not sure whether there is a simple and safe solution to this (e.g. remove file if a nonzero status is returned) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 22 16:00:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Aug 2012 16:00:15 +0200 Subject: [Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm In-Reply-To: <5034E436.5090904@epfl.ch> References: <5034D944.4020601@epfl.ch> <6BD243AA-AD4A-47FD-984E-300E7D510975@democritos.it> <5034E436.5090904@epfl.ch> Message-ID: On Aug 22, 2012, at 15:52 , Giovanni Pizzi wrote: > Ok. But then, to fix the problem, one should define celldm(1) in > pw.x as > I was suggesting, or change q2r.x so that it doesn't use celldm? the latter is the best solution, but requires some care. Moreover there can be more cases like this. So for the time being it is safer to choose the former P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pourazar2012 at gmail.com Wed Aug 22 16:06:29 2012 From: pourazar2012 at gmail.com (yavar pour azar) Date: Wed, 22 Aug 2012 07:06:29 -0700 Subject: [Pw_forum] How I can simulate charged slab with surface charge by QE Message-ID: Dear QE users 1-I want to simulate the charged oxide semiconductor slab, with desired surface charge. if choosing different values for the "tot_charge=...." is enough, for do this? or there is more consideration............. I think if we introduce excess charges by "tot_charge" utility in slab , after scf they should be localize on the surface, as the "surface charge" is this true? Thanks in advance. Yavar Taghipour Azar Physics Group, AEOI Tehran, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/eeb01bd2/attachment.htm From giannozz at democritos.it Wed Aug 22 17:27:59 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Aug 2012 17:27:59 +0200 Subject: [Pw_forum] question about spinors In-Reply-To: <24843099.15056.1345586103760.JavaMail.root@z.rochester.edu> References: <24843099.15056.1345586103760.JavaMail.root@z.rochester.edu> Message-ID: <975E4391-9A59-44E6-B662-1DDD74218886@democritos.it> On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: > I try to understand the format of the wavefunction in case of spin- > polarization > (nspin=4, spinorb=.true. (or something similar)) KS orbitals for the spin-orbit case have coefficient on a basis of NPW plane waves with spin up, NPW plane waves with spin down. The dimension of the orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the middle. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 22 17:28:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 22 Aug 2012 17:28:58 +0200 Subject: [Pw_forum] Dipole correction of PW In-Reply-To: <1259C03B-366A-4C7A-AD1D-D4FFA41D18FA@gmail.com> References: <1259C03B-366A-4C7A-AD1D-D4FFA41D18FA@gmail.com> Message-ID: On Aug 22, 2012, at 2:52 , Fenggong Wang wrote: > After searching a lot on the dipole correction of PW and reading > the corresponding > literature, I still have some confusions about the dipole correction. did you look at examples? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wangfenggong at gmail.com Thu Aug 23 03:40:32 2012 From: wangfenggong at gmail.com (Fenggong Wang) Date: Wed, 22 Aug 2012 21:40:32 -0400 Subject: [Pw_forum] Dipole correction of PW In-Reply-To: References: <1259C03B-366A-4C7A-AD1D-D4FFA41D18FA@gmail.com> Message-ID: <6B5C0E7A-3A86-4F5A-87F3-F7EDB6465B62@gmail.com> Yes. Thanks. I got it. Fenggong Wang Postdoctoral Researcher ----------------------------------------------- Department of Chemistry University of Pennsylvania 231 South 34th Street, Box 314, Room 263A Philadelphia, PA 19104-6323 e-mail: wangfenggong at gmail.com; fenggong at sas.upenn.edu On Aug 22, 2012, at 11:28 PM, Paolo Giannozzi wrote: > > On Aug 22, 2012, at 2:52 , Fenggong Wang wrote: > >> After searching a lot on the dipole correction of PW and reading >> the corresponding >> literature, I still have some confusions about the dipole correction. > > did you look at examples? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120822/f0e273f2/attachment-0001.htm From davide.ceresoli at istm.cnr.it Thu Aug 23 09:22:04 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Thu, 23 Aug 2012 09:22:04 +0200 Subject: [Pw_forum] restart flag for nmr calculation using gipaw In-Reply-To: References: Message-ID: <5035DA1C.6070601@istm.cnr.it> Dear Prasenjit, by default gipaw should restart interrupted calculation. You can check if "prefix.recoverNN" files are present in the scratchdir. If you want instead to start from scratch, you must manually remove those files. Davide On 08/22/2012 03:47 PM, Prasenjit Ghosh wrote: > Dear all, > > I am doing an nmr calculation with gipaw. I need to restart the calculation > because of restriction in the max cpu hour. > However, in the manual for the gipaw input file, I could not find any flag to > restart a calculation from the point where it has stopped. > Is it possible to restart the nmr calculation using gipaw.x. If so how? > > With regards, > > Prasenjit > > -- > PRASENJIT GHOSH, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 -- +--------------------------------------------------------------+ Davide Ceresoli CNR Institute of Molecular Science and Technology (CNR-ISTM) c/o University of Milan, via Golgi 19, 20133 Milan, Italy Email: davide.ceresoli at istm.cnr.it Phone: +39-02-50314276, +39-347-1001570 (mobile) Skype: dceresoli +--------------------------------------------------------------+ From prasenjit.jnc at gmail.com Thu Aug 23 09:33:44 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 23 Aug 2012 13:03:44 +0530 Subject: [Pw_forum] restart flag for nmr calculation using gipaw In-Reply-To: <5035DA1C.6070601@istm.cnr.it> References: <5035DA1C.6070601@istm.cnr.it> Message-ID: Dear Davide, Thanks for the reply. The recover files are there and the calculations have started from the k-point where it stopped earlier. With regards, Prasenjit On 23 August 2012 12:52, Davide Ceresoli wrote: > Dear Prasenjit, > by default gipaw should restart interrupted calculation. > You can check if "prefix.recoverNN" files are present in the > scratchdir. If you want instead to start from scratch, you > must manually remove those files. > > Davide > > > On 08/22/2012 03:47 PM, Prasenjit Ghosh wrote: > > Dear all, > > > > I am doing an nmr calculation with gipaw. I need to restart the > calculation > > because of restriction in the max cpu hour. > > However, in the manual for the gipaw input file, I could not find any > flag to > > restart a calculation from the point where it has stopped. > > Is it possible to restart the nmr calculation using gipaw.x. If so how? > > > > With regards, > > > > Prasenjit > > > > -- > > PRASENJIT GHOSH, > > IISER Pune, > > First floor, Central Tower, Sai Trinity Building > > Garware Circle, Sutarwadi, Pashan > > Pune, Maharashtra 411021, India > > > > Phone: +91 (20) 2590 8203 > > Fax: +91 (20) 2589 9790 > > -- > +--------------------------------------------------------------+ > Davide Ceresoli > CNR Institute of Molecular Science and Technology (CNR-ISTM) > c/o University of Milan, via Golgi 19, 20133 Milan, Italy > Email: davide.ceresoli at istm.cnr.it > Phone: +39-02-50314276, +39-347-1001570 (mobile) > Skype: dceresoli > +--------------------------------------------------------------+ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120823/3289dcb6/attachment.htm From eariel99 at gmail.com Thu Aug 23 18:34:13 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 23 Aug 2012 18:34:13 +0200 Subject: [Pw_forum] differences in vdW_kernel_table Message-ID: Hi, I generated the file vdW_kernel_table with version 5.0.1 and it is different from the filecoming with the 4.3.2. Should they be different ? The first numbers that are different are 1.91402358203250E+07 vs 1.87278875106385E+07 -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120823/bd306dda/attachment.htm From elie.moujaes at hotmail.co.uk Thu Aug 23 20:46:24 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 23 Aug 2012 19:46:24 +0100 Subject: [Pw_forum] Negative frequencies at really low threshold convergence Message-ID: Dear all, I am doing some phonon calculations at the gamma point for a system of 8 atoms . In the scf calculations I used an ultrasoft pseudopotential so I chose my ecutrho= 8* ecutwfc and also in the ph.x calculations tr2_ph was set to 1 *10^(-19) but I still get that the three first values of the frequencies are negative. Does this confirm the instability of the system? SCF INPUT: &system ibrav=0, celldm(1)= 9.008277, nat=8, ntyp= 2, ecutwfc =32, ecutrho=256, occupations='smearing', smearing='mv', degauss=0.02 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, mixing_mode='plain', diago_david_ndim=2,.....etc PH INPUT: &inputph tr2_ph=1.0d-19,prefix='Graphyne',fildvscf='Graphydvscf',recover=.true.,trans=.true.,amass(1)=12.0107,amass(2)=1.00794,outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/Graphyne/GRAPHYNEDIR/',fildyn='Graphy.dynG' /0.0 0.0 0.0 The output i got is : omega( 1) = -11.303890 [THz] = -377.057178 [cm-1] omega( 2) = -11.228798 [THz] = -374.552397 [cm-1] omega( 3) = -1.493780 [THz] = -49.827127 [cm-1] omega( 4) = 1.499866 [THz] = 50.030148 [cm-1] omega( 5) = 2.192955 [THz] = 73.149113 [cm-1] omega( 6) = 11.690342 [THz] = 389.947822 [cm-1]....... Thanks for the help Elie MouhaesUniversity of NottinghamNG7 2RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120823/0190ae50/attachment.htm From aakimov at z.rochester.edu Fri Aug 24 03:38:35 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Thu, 23 Aug 2012 21:38:35 -0400 (EDT) Subject: [Pw_forum] question about spinors In-Reply-To: <975E4391-9A59-44E6-B662-1DDD74218886@democritos.it> Message-ID: <831907319.49466.1345772315829.JavaMail.root@z.rochester.edu> Dear Paolo, I'm not sure that i completely understand what you mean by empty coefficients. Also what is npwx, how is it different from npw? Let say npw = 3 and npwx = 4 (very small basis :)) then the overlap of orbital i and orbital j will be: c_i0^* * c_j0 + c_i1^* * c_j1 + c_i2^* * c_j2 + c_i3^* * c_j3 (four terms as npwx). If, as you say, some coefficients are empty (lets say c_i3 and c_j3) we still have some non-zero terms. I'm not sure if the previous sentence have any sense at all, so sorry if this is something terribly wrong :) - that is why i'm asking. (^* - means complex conjugate) Also am i correct that the spin-up and spin-down orbitals are orthogonal not because of the artificial convention = 0, but rather by construction of the corresponding plane wave expansions (given by coefficients c_gi )? What i mean is that in localized orbitals e.g. Gaussians the spatial parts of the alpha and beta orbitals are practically the same (exactly in restricted HF or KS approaches), but the orthogonality is then introduced by convention: psi_i_alpa = phi_i * sigma_alpha, psi_j_beta = phi_j * sigma_beta => = * , so even if != 0 the orbitals are still orthogonal because = 0 by convention. So in spin-orbital case do we still need to consider these artificial sigma_alpha, sigma_beta spin-functions or the orthogonality is already included in "spatial" part (so = 0 for alpha and beta spin-orbitals)? Thank you, Alexey ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, August 22, 2012 8:27:59 AM Subject: Re: [Pw_forum] question about spinors On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: > I try to understand the format of the wavefunction in case of spin- > polarization > (nspin=4, spinorb=.true. (or something similar)) KS orbitals for the spin-orbit case have coefficient on a basis of NPW plane waves with spin up, NPW plane waves with spin down. The dimension of the orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the middle. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From yuewen.fang at gmail.com Fri Aug 24 03:51:27 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Fri, 24 Aug 2012 09:51:27 +0800 Subject: [Pw_forum] How to modify the input file when testing virtual crystal pseudopotential? Message-ID: Dear all, i generate a virtual crystal pseudopotential of N and O (named virtual-NO.UPF) and I want do dope the SrRuO3 system by using this mixing pseudopotential, but how to modify the input file especially the ATOMIC_SPECIES and ATOMIC_POSITIONS? the primitive input file of ATOMIC_SPECIES and ATOMIC_POSITIONS of SrRuO3 Sr 87.62 Sr.pbe-sp-van.UPF Ru 101.07 Ru.pbe-n-van.UPF O 15.9994 O.pbe-van_ak.UPF how to modify this line? ATOMIC_POSITIONS {crystal} Sr 0.000000000 0.000000000 0.0 Ru 0.500000000 0.500000000 0.5 O 0.500000000 0.000000000 0.5 should i modify these positions or replace the O positions in some way? O 0.000000000 0.500000000 0.5 O 0.500000000 0.500000000 0.0 -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/f7e814d2/attachment.htm From giannozz at democritos.it Fri Aug 24 12:06:56 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Aug 2012 12:06:56 +0200 Subject: [Pw_forum] Negative frequencies at really low threshold convergence In-Reply-To: References: Message-ID: On Aug 23, 2012, at 20:46 , Elie M wrote: > I still get that the three first values of the frequencies are > negative. > Does this confirm the instability of the system? likely, but you should first of all verify the effect of applying the Acoustic Sum Rule. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 24 12:12:48 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Aug 2012 12:12:48 +0200 Subject: [Pw_forum] How I can simulate charged slab with surface charge by QE In-Reply-To: References: Message-ID: <295626E3-845E-4F6F-B9CF-7717AAD7973C@democritos.it> On Aug 22, 2012, at 16:06 , yavar pour azar wrote: > I think if we introduce excess charges by "tot_charge" utility in > slab , > after scf they should be localize on the surface, as the "surface > charge" > is this true? maybe, Or maybe not: all you can do is to add charge to the system, but you cannot force the charge to go where you like it to go P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 24 12:20:30 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Aug 2012 12:20:30 +0200 Subject: [Pw_forum] confusion in ev.x In-Reply-To: References: Message-ID: <29052B36-D58C-4F91-82DC-A4E95CE36059@democritos.it> On Aug 21, 2012, at 16:39 , karan deep wrote: > Birch function used in this program is P(V) equation and for > istate=1 i.e birch 1st order > is actually a 3rd order Birch-Murnaghan equation of state as > mentioned in WIKIPEDIA > page I took the so-called "Birch 1st and 2nd order" and "Keane" equations of state from some geophysics paper many years ago. Nobody has ever complained since (which doesn't mean much about their correctness, tough). I cannot check those papers now because I am away from my desk. Clearly these formulae do not look like those of Wikipedia, but I am not sure how many variants of Birch-Murnaghan equations of states exist, and how reliable is Wikipedia on this subject. People working in geophysics are kindly requested to comment P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gabriele.sclauzero at epfl.ch Fri Aug 24 12:57:54 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Fri, 24 Aug 2012 12:57:54 +0200 Subject: [Pw_forum] question about spinors In-Reply-To: <831907319.49466.1345772315829.JavaMail.root@z.rochester.edu> References: <831907319.49466.1345772315829.JavaMail.root@z.rochester.edu> Message-ID: <2F3CE19A-2F0F-4D83-8CD9-BD30DE571DEF@epfl.ch> > Dear Paolo, > > I'm not sure that i completely understand what you mean by empty coefficients. Also what is npwx, how is it different from npw? I think this is due to the fact that wave functions at different k-points can have different number of plane waves if the basis set cut-off is expressed in terms of the kinetic energy of the plane wave ~ |k+G|^2. Still, it's more practical to use the same array (of size npwx>npw) for storing the wave function (one k-point at a time). Also G-vector parallelization might introduce this kind of issue. > Also am i correct that the spin-up and spin-down orbitals are orthogonal not because of the artificial convention = 0, but rather by construction of the corresponding plane wave expansions (given by coefficients c_gi )? I would not call this is an artificial convention... it's the way you write the wavefunction (space+spin components) that allows you to do this, which is turn depends on the Hamiltonian that you consider. Anyway I think this is correct, although you should be aware that when you take the norm of a two-component spinor you need to sum over the two components, i.e. < Psi_i | Psi_j > = < Psi_i,1 | Psi_j,1 > + < Psi_i,2 | Psi_j,2 >, where 1 and 2 denote first and second component, resp. > or the orthogonality is already included in "spatial" part (so = 0 for alpha and beta spin-orbitals)? Not really in the 3D spatial part, but rather in the "relations" between the first and second component. I mean, the overlap between first components and that between the second components can both be nonzero, but the sum might be zero. This is the most general case, when you have spin-orbit and/or non-collinear magnetization. If the ground state has collinear magnetization you can always rotate the magnetic axis such that each wave function has Psi_1 or Psi_2 which is zero everywhere (and you get the same result, which should be the same as in LSDA). HTH GS > Thank you, > Alexey > > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Wednesday, August 22, 2012 8:27:59 AM > Subject: Re: [Pw_forum] question about spinors > > > On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: > >> I try to understand the format of the wavefunction in case of spin- >> polarization >> (nspin=4, spinorb=.true. (or something similar)) > > KS orbitals for the spin-orbit case have coefficient on a basis of > NPW plane > waves with spin up, NPW plane waves with spin down. The dimension of the > orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the > middle. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/e466e3fc/attachment.htm From ramzialaya at hotmail.fr Fri Aug 24 15:42:50 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Fri, 24 Aug 2012 14:42:50 +0100 Subject: [Pw_forum] (no subject) Message-ID: Dear all: I will study the structural properties of zinc blende ternary alloys. The calculation will be performed on a supercell 16 atoms (1 * 1 * 2). My question is as follows: How do I define my input parameters (ibrav, celldm). Thank you.Regards. **************************************************************************************************************************************************************************** Ramzi Alaya E-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/91911dfc/attachment.htm From akohlmey at gmail.com Fri Aug 24 15:51:50 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 24 Aug 2012 15:51:50 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: On Fri, Aug 24, 2012 at 3:42 PM, ramzi alaya wrote: > Dear all: > > I will study the structural properties of zinc blende ternary alloys. The > calculation will be performed on a supercell 16 atoms (1 * 1 * 2). My > question is as follows: > How do I define my input parameters (ibrav, celldm). preferably with a text editor. read the documentation, study the existing examples and tutorials and just write it. easy as pie. good luck, axel. > > Thank you. > Regards. > > > > > **************************************************************************************************************************************************************************** > Ramzi Alaya > > E-mail : ramzialaya at hotmail.fr > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From elie.moujaes at hotmail.co.uk Fri Aug 24 16:18:54 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Fri, 24 Aug 2012 15:18:54 +0100 Subject: [Pw_forum] Negative frequencies at really low threshold convergence In-Reply-To: References: , Message-ID: Professor Paulo, thanks for your reply. Will do that. Elie > From: giannozz at democritos.it > Date: Fri, 24 Aug 2012 12:06:56 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Negative frequencies at really low threshold convergence > > > On Aug 23, 2012, at 20:46 , Elie M wrote: > > > I still get that the three first values of the frequencies are > > negative. > > Does this confirm the instability of the system? > > likely, but you should first of all verify the effect of applying the > Acoustic Sum Rule. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/4d3595ce/attachment-0001.htm From baroni at sissa.it Fri Aug 24 17:40:56 2012 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 24 Aug 2012 17:40:56 +0200 Subject: [Pw_forum] Negative frequencies at really low threshold convergence In-Reply-To: References: , Message-ID: <493C2DD9-CC4B-4687-95B2-123FFA828016@sissa.it> Just for the sake of linguistic accuracy, the name is PaOlo. You can address him by name ("Paolo"), or by title ("Prof."), in the latter case the title should be followed by the family name ("Prof. Giannozzi" ;-). Stefano On Aug 24, 2012, at 4:18 PM, Elie M wrote: > Professor Paulo, > > thanks for your reply. Will do that. > > Elie > > > From: giannozz at democritos.it > > Date: Fri, 24 Aug 2012 12:06:56 +0200 > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] Negative frequencies at really low threshold convergence > > > > > > On Aug 23, 2012, at 20:46 , Elie M wrote: > > > > > I still get that the three first values of the frequencies are > > > negative. > > > Does this confirm the instability of the system? > > > > likely, but you should first of all verify the effect of applying the > > Acoustic Sum Rule. > > > > P. > > --- > > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/4102c11c/attachment.htm From aakimov at z.rochester.edu Sat Aug 25 03:06:11 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Fri, 24 Aug 2012 21:06:11 -0400 (EDT) Subject: [Pw_forum] How I can simulate charged slab with surface charge by QE In-Reply-To: <295626E3-845E-4F6F-B9CF-7717AAD7973C@democritos.it> Message-ID: <255570751.62824.1345856771894.JavaMail.root@z.rochester.edu> i would also suggest not to forget about spin-polarization, that is if you simulated neutral system with nspin = 1 (no spin-polarization), in the case of +1 or -1 charge you will have one electron less or more so now should not forget to turn on the spin polarization nspin=2, starting_magnetization(1) = 0.7 (for example) and choose the smearing options. ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Friday, August 24, 2012 3:12:48 AM Subject: Re: [Pw_forum] How I can simulate charged slab with surface charge by QE On Aug 22, 2012, at 16:06 , yavar pour azar wrote: > I think if we introduce excess charges by "tot_charge" utility in > slab , > after scf they should be localize on the surface, as the "surface > charge" > is this true? maybe, Or maybe not: all you can do is to add charge to the system, but you cannot force the charge to go where you like it to go P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From aakimov at z.rochester.edu Sat Aug 25 04:06:22 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Fri, 24 Aug 2012 22:06:22 -0400 (EDT) Subject: [Pw_forum] question about spinors In-Reply-To: <2F3CE19A-2F0F-4D83-8CD9-BD30DE571DEF@epfl.ch> Message-ID: <70176487.62973.1345860382226.JavaMail.root@z.rochester.edu> Dear Gabriele, Thank you for your great comments! So as i understand the key for orbital overlap is additional summation over spin components. This makes a lot sense to what i see - the odd-even alteration of 1 or 0 overlaps. In other words Psi_1 = psi_1,1 , Psi_2 = psi_1,2, ... Psi_2n+1 = psi_n,1, Psi_2n+2 = psi_n,2 and then = = 1, = = 0 (alteration), but + = + = 1, ... (no alteration). That is the orbitals written in the output are actually not 1, 2, 3, ... etc, but rather 1,1, 1,2, 2,1, 2,2, ... etc. (here the second index is the spin-state or more precisely the spinor component). Also if i understand it correctly we should not consider spin-up and spin-down functions separately. Is this right? I would appreciate if someone could give some reference (apart from wikipedia and QE tutorials/presentations) for the spinor algebra. Ok. I see the point with the npwx vs. npw. However i was using a single k-point (gamma), so one would expect that this should not introduce additional complications. You also mentioned that the parallelization can effect this - would storing the entire wavefunction in one file solve such issue (wf_collect = .true.) instead of storing it in different files - one per process? Thank you, Alexey ----- Original Message ----- From: "Gabriele Sclauzero" To: "PWSCF Forum" Sent: Friday, August 24, 2012 3:57:54 AM Subject: Re: [Pw_forum] question about spinors Dear Paolo, I'm not sure that i completely understand what you mean by empty coefficients. Also what is npwx, how is it different from npw? I think this is due to the fact that wave functions at different k-points can have different number of plane waves if the basis set cut-off is expressed in terms of the kinetic energy of the plane wave ~ |k+G|^2. Still, it's more practical to use the same array (of size npwx>npw) for storing the wave function (one k-point at a time). Also G-vector parallelization might introduce this kind of issue. Also am i correct that the spin-up and spin-down orbitals are orthogonal not because of the artificial convention = 0, but rather by construction of the corresponding plane wave expansions (given by coefficients c_gi )? I would not call this is an artificial convention... it's the way you write the wavefunction (space+spin components) that allows you to do this, which is turn depends on the Hamiltonian that you consider. Anyway I think this is correct, although you should be aware that when you take the norm of a two-component spinor you need to sum over the two components, i.e. < Psi_i | Psi_j > = < Psi_i,1 | Psi_j,1 > + < Psi_i,2 | Psi_j,2 >, where 1 and 2 denote first and second component, resp. or the orthogonality is already included in "spatial" part (so = 0 for alpha and beta spin-orbitals)? Not really in the 3D spatial part, but rather in the "relations" between the first and second component. I mean, the overlap between first components and that between the second components can both be nonzero, but the sum might be zero. This is the most general case, when you have spin-orbit and/or non-collinear magnetization. If the ground state has collinear magnetization you can always rotate the magnetic axis such that each wave function has Psi_1 or Psi_2 which is zero everywhere (and you get the same result, which should be the same as in LSDA). HTH GS Thank you, Alexey ----- Original Message ----- From: "Paolo Giannozzi" < giannozz at democritos.it > To: "PWSCF Forum" < pw_forum at pwscf.org > Sent: Wednesday, August 22, 2012 8:27:59 AM Subject: Re: [Pw_forum] question about spinors On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: I try to understand the format of the wavefunction in case of spin- polarization (nspin=4, spinorb=.true. (or something similar)) KS orbitals for the spin-orbit case have coefficient on a basis of NPW plane waves with spin up, NPW plane waves with spin down. The dimension of the orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the middle. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From zhanhit at hotmail.com Sat Aug 25 08:16:25 2012 From: zhanhit at hotmail.com (Franklin Zhan) Date: Sat, 25 Aug 2012 06:16:25 +0000 Subject: [Pw_forum] (no subject) In-Reply-To: References: , Message-ID: Hi, I suggest you read the example 3 which is about structural optimization. I think it helps. Then you might write codes by yourself. Best regards, Franklin > Date: Fri, 24 Aug 2012 15:51:50 +0200 > From: akohlmey at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] (no subject) > > On Fri, Aug 24, 2012 at 3:42 PM, ramzi alaya wrote: > > Dear all: > > > > I will study the structural properties of zinc blende ternary alloys. The > > calculation will be performed on a supercell 16 atoms (1 * 1 * 2). My > > question is as follows: > > How do I define my input parameters (ibrav, celldm). > > preferably with a text editor. > > read the documentation, study the existing examples > and tutorials and just write it. > > easy as pie. > > good luck, > axel. > > > > > > Thank you. > > Regards. > > > > > > > > > > **************************************************************************************************************************************************************************** > > Ramzi Alaya > > > > E-mail : ramzialaya at hotmail.fr > > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie > > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120825/c2f5eb16/attachment-0001.htm From pourazar2012 at gmail.com Sat Aug 25 08:23:25 2012 From: pourazar2012 at gmail.com (yavar pour azar) Date: Fri, 24 Aug 2012 23:23:25 -0700 Subject: [Pw_forum] How I can simulate charged slab with surface charge by QE In-Reply-To: <255570751.62824.1345856771894.JavaMail.root@z.rochester.edu> References: <295626E3-845E-4F6F-B9CF-7717AAD7973C@democritos.it> <255570751.62824.1345856771894.JavaMail.root@z.rochester.edu> Message-ID: Dear Professor Giannozzi, and Dear Alexey thanks for your consideration and suggestion Bests. On Fri, Aug 24, 2012 at 6:06 PM, Alexey Akimov wrote: > i would also suggest not to forget about spin-polarization, that is if you > simulated neutral system with nspin = 1 (no spin-polarization), in the case > of +1 or -1 charge you will have one electron less or more so now should > not forget to turn on the spin polarization nspin=2, > starting_magnetization(1) = 0.7 (for example) and choose the smearing > options. > > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Friday, August 24, 2012 3:12:48 AM > Subject: Re: [Pw_forum] How I can simulate charged slab with surface > charge by QE > > > On Aug 22, 2012, at 16:06 , yavar pour azar wrote: > > > I think if we introduce excess charges by "tot_charge" utility in > > slab , > > after scf they should be localize on the surface, as the "surface > > charge" > > is this true? > > maybe, Or maybe not: all you can do is to add charge to the system, > but you cannot force the charge to go where you like it to go > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120824/e9c33110/attachment.htm From ylli at theory.issp.ac.cn Sat Aug 25 23:57:26 2012 From: ylli at theory.issp.ac.cn (=?utf-8?B?WS4gTC4gTGk=?=) Date: Sun, 26 Aug 2012 5:57:26 +0800 Subject: [Pw_forum] =?utf-8?q?Bug_in_QE_5=2E0_with_ibrav=3D0_and_using_a_i?= =?utf-8?q?nstead_of?= Message-ID: <20120825215726.3279.qmail@ms.hfcas.ac.cn> Hi, I agree with you. I also found this bug as you said. Yanling ----On Wed, 22 Aug 2012 15:06:20 +0200 wrote: ---- > Date: Wed, 22 Aug 2012 15:06:12 +0200 > From: Giovanni Pizzi > Subject: [Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of > celldm > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear all, > I believe there is a bug in QE 5.0 (pw.x) that occurs when using ibrav=0 > and defining 'a' instead of 'celldm(1)'. > In this case, celldm is not set and remains equal to zero. (This > behavior was different in 4.3.2, where instead the celldm(1) value was > set from the 'a' value.) > > This doesn't seem to create problems in the pw.x calculation. > However, in the matdyn files generated by ph.x, the celldm(1) is set to > zero. > When the matdyn files are then given to q2r.x, the code crashes, > complaining of a wrong celldm value. > > In particular this is what happens in q2r.x: > 1. the first q point is read (matdyn1) using the routine > read_dyn_from_file; celldm(1) is set to 0 > 2. the code calls the routine latgen: this routine sets celldm(1) to the > a value different from zero (moreover this value may be wrong if 'a' in > the input file was not set to the length of the first lattice vector) > 3. the code reads the second q point (matdyn2) and compares the celldm > value read from file (which is zero) with the old value (which was set > to a value different from zero at step 2): being different, the code stops. > > I think that to correct it, one should replace the following lines > (cell_base.f90, lines 152 and following) > IF( celldm( 1 ) /= 0.0_DP ) THEN > alat = celldm( 1 ) > ELSE IF ( a /= 0.0_dp ) THEN > alat = a / bohr_radius_angs > ELSE > alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 ) > END IF > at(:,:) = at(:,:) / alat > > with > IF( celldm( 1 ) /= 0.0_DP ) THEN > alat = celldm( 1 ) > ELSE IF ( a /= 0.0_dp ) THEN > alat = a / bohr_radius_angs > celldm( 1 ) = alat > ELSE > alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 ) > celldm( 1 ) = alat > END IF > at(:,:) = at(:,:) / alat > > Let me know what you think. > > Best, > Giovanni Pizzi > > > > -- > Giovanni Pizzi > Post-doctoral Research Scientist > EPFL STI IMX THEOS > MXC 319 (B?timent MXC) > Station 12 > CH-1015 Lausanne (Switzerland) > Phone: +41 21 69 31159 > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 62, Issue 37 > **************************************** > ------ ISSP -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120826/13dee290/attachment.htm From tfcao at theory.issp.ac.cn Sun Aug 26 09:48:33 2012 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Sun, 26 Aug 2012 15:48:33 +0800 Subject: [Pw_forum] =?utf-8?q?STM_simulation?= Message-ID: <20120826074833.19061.qmail@ms.hfcas.ac.cn> Dear QE users It is seems that we can only get the STM image of rectangular cell with the calculation of pp.x. So is it possible to get the STM image of hexagonal cell ? Thank you in advance. * ELSE IF iflag = 3 : THE FOLLOWING VARIABLES ARE OPTIONAL: +-------------------------------------------------------------------- Variables: e1(i), e2(i), e3(i), i=1,3 Type: REAL Description: 3D vectors which determine the plotting parallelepiped (if present, must be orthogonal) e1, e2, and e3 are in alat units ! Reserach laboratory for Computational Material Science. Institute of Solid State Physics, CAS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120826/eff15c3b/attachment.htm From florenceliu86 at gmail.com Mon Aug 27 04:55:31 2012 From: florenceliu86 at gmail.com (florence liu) Date: Mon, 27 Aug 2012 10:55:31 +0800 Subject: [Pw_forum] PAW+PBE0 Message-ID: Dear all, I am trying to perform a PBE0 calculation with PAWs in QE 5.0. However, I get the error messages task # 2 from setup : error # 1 HYBRID XC not implemented for USPP or PAW and task # 6 from setup : error # 1 HYBRID XC not implemented for USPP or PAW Can any body confirm that this combination is indeed not implemented? Or is this error rather a results of some mistakes in my input files? If the combination PBE0+PAW is not possible in the current version of QE, are there any possibilities to use any hybrid functional together with PAW? best wishes, F. Liu TU Munich -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120827/ceba633c/attachment.htm From gabriele.sclauzero at epfl.ch Mon Aug 27 10:04:17 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 27 Aug 2012 10:04:17 +0200 Subject: [Pw_forum] question about spinors In-Reply-To: <70176487.62973.1345860382226.JavaMail.root@z.rochester.edu> References: <70176487.62973.1345860382226.JavaMail.root@z.rochester.edu> Message-ID: <249E1B46-C049-4A66-869C-643F8884AACD@epfl.ch> Hello, Il giorno 25/ago/2012, alle ore 04.06, Alexey Akimov ha scritto: > Dear Gabriele, > > Thank you for your great comments! So as i understand the key for orbital overlap is additional summation over spin components. Just to be a bit more pedantic... I would not call them as that, but rather "spinor components", to avoid confusion. In general, when magnetization is non collinear you cannot identify the first component with "spin-up" and the second with "spin-down", unless the magnetization is collinear and oriented along z. > This makes a lot sense to what i see - the odd-even alteration of 1 or 0 overlaps. In other words Psi_1 = psi_1,1 , Psi_2 = psi_1,2, ... Psi_2n+1 = psi_n,1, Psi_2n+2 = psi_n,2 and then = = 1, = = 0 (alteration), but + = + = 1, ... (no alteration). I've got a bit lost here with your notation, but it seems that you got the point. I think you meant "alternation" here, am I correct? > That is the orbitals written in the output are actually not 1, 2, 3, ... etc, but rather 1,1, 1,2, 2,1, 2,2, ... etc. (here the second index is the spin-state or more precisely the spinor component). I don't know of which output you are talking about here (pp.x?). Anyway, I think that the wave function coefficients for the first and the second component are stored consecutively in the same array (as said by Paolo in the first reply). > Also if i understand it correctly we should not consider spin-up and spin-down functions separately. Is this right? I'm not sure I understand this point correctly, maybe it is related to what I've written above? > I would appreciate if someone could give some reference (apart from wikipedia and QE tutorials/presentations) for the spinor algebra. I do not have any references at hand, but I'm pretty sure that if you look up at "Pauli equation" in any good quantum mechanics book (maybe advanced ones) you'll find what you need. Indeed, the fully-relativistic non collinear KS equation is pretty similar to that one. > Ok. I see the point with the npwx vs. npw. However i was using a single k-point (gamma), so one would expect that this should not introduce additional complications. You also mentioned that the parallelization can effect this - would storing the entire wavefunction in one file solve such issue (wf_collect = .true.) instead of storing it in different files - one per process? It should, but I'm not sure... you can make a small test. GS > > Thank you, > Alexey > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "PWSCF Forum" > Sent: Friday, August 24, 2012 3:57:54 AM > Subject: Re: [Pw_forum] question about spinors > > > > > > > > Dear Paolo, > > I'm not sure that i completely understand what you mean by empty coefficients. Also what is npwx, how is it different from npw? > > > I think this is due to the fact that wave functions at different k-points can have different number of plane waves if the basis set cut-off is expressed in terms of the kinetic energy of the plane wave ~ |k+G|^2. Still, it's more practical to use the same array (of size npwx>npw) for storing the wave function (one k-point at a time). Also G-vector parallelization might introduce this kind of issue. > > > > > Also am i correct that the spin-up and spin-down orbitals are orthogonal not because of the artificial convention = 0, but rather by construction of the corresponding plane wave expansions (given by coefficients c_gi )? > > > I would not call this is an artificial convention... it's the way you write the wavefunction (space+spin components) that allows you to do this, which is turn depends on the Hamiltonian that you consider. > Anyway I think this is correct, although you should be aware that when you take the norm of a two-component spinor you need to sum over the two components, i.e. > < Psi_i | Psi_j > = < Psi_i,1 | Psi_j,1 > + < Psi_i,2 | Psi_j,2 >, where 1 and 2 denote first and second component, resp. > > > > > or the orthogonality is already included in "spatial" part (so = 0 for alpha and beta spin-orbitals)? > > > > Not really in the 3D spatial part, but rather in the "relations" between the first and second component. I mean, the overlap between first components and that between the second components can both be nonzero, but the sum might be zero. This is the most general case, when you have spin-orbit and/or non-collinear magnetization. If the ground state has collinear magnetization you can always rotate the magnetic axis such that each wave function has Psi_1 or Psi_2 which is zero everywhere (and you get the same result, which should be the same as in LSDA). > > > HTH > > > > > GS > > > > > > Thank you, > Alexey > > > ----- Original Message ----- > From: "Paolo Giannozzi" < giannozz at democritos.it > > To: "PWSCF Forum" < pw_forum at pwscf.org > > Sent: Wednesday, August 22, 2012 8:27:59 AM > Subject: Re: [Pw_forum] question about spinors > > > On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: > > > > I try to understand the format of the wavefunction in case of spin- > > > polarization > > > (nspin=4, spinorb=.true. (or something similar)) > > KS orbitals for the spin-orbit case have coefficient on a basis of > NPW plane > waves with spin up, NPW plane waves with spin down. The dimension of the > orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the > middle. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120827/6ce6a49d/attachment.htm From lmartinsamos at gmail.com Mon Aug 27 11:35:16 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 27 Aug 2012 11:35:16 +0200 Subject: [Pw_forum] PAW+PBE0 In-Reply-To: References: Message-ID: Dear Florence, Hybrids with PAW or US are corrently not implemented. It is in the ROAD MAP and we already have some volunteers for the implementation, but we will probalby need to wait 2013. Now you can just run with norm conserving. best regards Layla 2012/8/27 florence liu > Dear all, > I am trying to perform a PBE0 calculation with PAWs in QE 5.0. However, I > get the error messages > > task # 2 > from setup : error # 1 > HYBRID XC not implemented for USPP or PAW > > and > > task # 6 > from setup : error # 1 > HYBRID XC not implemented for USPP or PAW > > Can any body confirm that this combination is indeed not implemented? Or > is this error rather a results of some mistakes in my input files? If the > combination PBE0+PAW is not possible in the current version of QE, are > there any possibilities to use any hybrid functional together with PAW? > > best wishes, > > F. Liu > TU Munich > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120827/b5fa10b5/attachment.htm From fratesi at mater.unimib.it Mon Aug 27 14:53:55 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Mon, 27 Aug 2012 14:53:55 +0200 Subject: [Pw_forum] STM simulation In-Reply-To: <20120826074833.19061.qmail@ms.hfcas.ac.cn> References: <20120826074833.19061.qmail@ms.hfcas.ac.cn> Message-ID: <503B6DE3.8020605@mater.unimib.it> On 08/26/2012 09:48 AM, Cao TF wrote: > Dear QE users > It is seems that we can only get the STM image of rectangular cell with > the calculation of pp.x. So is it possible to get the STM image of > hexagonal cell ? Thank you in advance. You can get the result for any cell shape, written in an internal yet easily readable format in the "filplot" file (specified in the &inputpp namelist), for all points in the real-space grid. Then, just choose a parallelepiped (or rectangle) which embraces the region you want, or use iflag=3 with output_format=5. Guido -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From aakimov at z.rochester.edu Mon Aug 27 15:13:05 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Mon, 27 Aug 2012 09:13:05 -0400 (EDT) Subject: [Pw_forum] question about spinors In-Reply-To: <249E1B46-C049-4A66-869C-643F8884AACD@epfl.ch> Message-ID: <1570523744.70968.1346073185059.JavaMail.root@z.rochester.edu> Dear Gabriele, Thank you for additional clarifications. Best, Alexey ----- Original Message ----- From: "Gabriele Sclauzero" To: "PWSCF Forum" Sent: Monday, August 27, 2012 1:04:17 AM Subject: Re: [Pw_forum] question about spinors Hello, Il giorno 25/ago/2012, alle ore 04.06, Alexey Akimov ha scritto: Dear Gabriele, Thank you for your great comments! So as i understand the key for orbital overlap is additional summation over spin components. Just to be a bit more pedantic... I would not call them as that, but rather "spinor components", to avoid confusion. In general, when magnetization is non collinear you cannot identify the first component with "spin-up" and the second with "spin-down", unless the magnetization is collinear and oriented along z. >>> ok. thank you for pointing this out This makes a lot sense to what i see - the odd-even alteration of 1 or 0 overlaps. In other words Psi_1 = psi_1,1 , Psi_2 = psi_1,2, ... Psi_2n+1 = psi_n,1, Psi_2n+2 = psi_n,2 and then = = 1, = = 0 (alteration), but + = + = 1, ... (no alteration). I've got a bit lost here with your notation, but it seems that you got the point. I think you meant "alternation" here, am I correct? >>> right, alternation That is the orbitals written in the output are actually not 1, 2, 3, ... etc, but rather 1,1, 1,2, 2,1, 2,2, ... etc. (here the second index is the spin-state or more precisely the spinor component). >>> i see. this is the point from the previous sentence. I don't know of which output you are talking about here (pp.x?). Anyway, I think that the wave function coefficients for the first and the second component are stored consecutively in the same array (as said by Paolo in the first reply). >>> yes, i meant the output produced by pp.x. So, as you say the orbitals are written as 1,1, 1,2, 2,1, 2,2, ... etc. Do you mean the first band (and hence its planewave expansion) is 1,1 ("spin-up"), the second band (and its coefficients in output) is 1,2, etc. ? Also if i understand it correctly we should not consider spin-up and spin-down functions separately. Is this right? I'm not sure I understand this point correctly, maybe it is related to what I've written above? >>> yes, you already answered this in the first part. I would appreciate if someone could give some reference (apart from wikipedia and QE tutorials/presentations) for the spinor algebra. I do not have any references at hand, but I'm pretty sure that if you look up at "Pauli equation" in any good quantum mechanics book (maybe advanced ones) you'll find what you need. Indeed, the fully-relativistic non collinear KS equation is pretty similar to that one. Ok. I see the point with the npwx vs. npw. However i was using a single k-point (gamma), so one would expect that this should not introduce additional complications. You also mentioned that the parallelization can effect this - would storing the entire wavefunction in one file solve such issue (wf_collect = .true.) instead of storing it in different files - one per process? It should, but I'm not sure... you can make a small test. GS Thank you, Alexey ----- Original Message ----- From: "Gabriele Sclauzero" < gabriele.sclauzero at epfl.ch > To: "PWSCF Forum" < pw_forum at pwscf.org > Sent: Friday, August 24, 2012 3:57:54 AM Subject: Re: [Pw_forum] question about spinors Dear Paolo, I'm not sure that i completely understand what you mean by empty coefficients. Also what is npwx, how is it different from npw? I think this is due to the fact that wave functions at different k-points can have different number of plane waves if the basis set cut-off is expressed in terms of the kinetic energy of the plane wave ~ |k+G|^2. Still, it's more practical to use the same array (of size npwx>npw) for storing the wave function (one k-point at a time). Also G-vector parallelization might introduce this kind of issue. Also am i correct that the spin-up and spin-down orbitals are orthogonal not because of the artificial convention = 0, but rather by construction of the corresponding plane wave expansions (given by coefficients c_gi )? I would not call this is an artificial convention... it's the way you write the wavefunction (space+spin components) that allows you to do this, which is turn depends on the Hamiltonian that you consider. Anyway I think this is correct, although you should be aware that when you take the norm of a two-component spinor you need to sum over the two components, i.e. < Psi_i | Psi_j > = < Psi_i,1 | Psi_j,1 > + < Psi_i,2 | Psi_j,2 >, where 1 and 2 denote first and second component, resp. or the orthogonality is already included in "spatial" part (so = 0 for alpha and beta spin-orbitals)? Not really in the 3D spatial part, but rather in the "relations" between the first and second component. I mean, the overlap between first components and that between the second components can both be nonzero, but the sum might be zero. This is the most general case, when you have spin-orbit and/or non-collinear magnetization. If the ground state has collinear magnetization you can always rotate the magnetic axis such that each wave function has Psi_1 or Psi_2 which is zero everywhere (and you get the same result, which should be the same as in LSDA). HTH GS Thank you, Alexey ----- Original Message ----- From: "Paolo Giannozzi" < giannozz at democritos.it > To: "PWSCF Forum" < pw_forum at pwscf.org > Sent: Wednesday, August 22, 2012 8:27:59 AM Subject: Re: [Pw_forum] question about spinors On Aug 21, 2012, at 23:55 , Alexey Akimov wrote: I try to understand the format of the wavefunction in case of spin- polarization (nspin=4, spinorb=.true. (or something similar)) KS orbitals for the spin-orbit case have coefficient on a basis of NPW plane waves with spin up, NPW plane waves with spin down. The dimension of the orbitals is 2*NPWX >= 2*NPW, so there can be empty coefficients in the middle. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From ananyamondol3 at gmail.com Mon Aug 27 22:29:07 2012 From: ananyamondol3 at gmail.com (Ananya mondal) Date: Mon, 27 Aug 2012 16:29:07 -0400 Subject: [Pw_forum] pseudopotential for Sodium Message-ID: Dear quantum-espresso users, I'm looking for a PBE type Norm-conserving Troullier Martins pseudopotential pseudopotential for Sodium. Thanks Ananya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120827/d6b38db7/attachment.htm From bfazi90 at gmail.com Mon Aug 27 22:46:54 2012 From: bfazi90 at gmail.com (bf azi) Date: Tue, 28 Aug 2012 01:16:54 +0430 Subject: [Pw_forum] pseudopotential for Vdw Message-ID: Hi Dear all In calculation of Van der waals interaction , Which kind of pseudopotential is better (GGA or LDA)? Bani Adam Faculty of Science Egypt From ananyamondol3 at gmail.com Mon Aug 27 23:11:31 2012 From: ananyamondol3 at gmail.com (Ananya Mondal) Date: Mon, 27 Aug 2012 17:11:31 -0400 Subject: [Pw_forum] pseudopotential for Sodium In-Reply-To: References: Message-ID: Including s and p semicore states in valence. On 8/27/12, Ananya mondal wrote: > Dear quantum-espresso users, > I'm looking for a PBE type Norm-conserving Troullier Martins > pseudopotential pseudopotential for Sodium. > Thanks > Ananya > From yuewen.fang at gmail.com Tue Aug 28 08:03:26 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 28 Aug 2012 14:03:26 +0800 Subject: [Pw_forum] pseudopotential for Sodium In-Reply-To: References: Message-ID: May be you can generate the pp using ld1.x and test it by yourself. But it not very simple Y.-W. Fang 2012/8/28 Ananya Mondal > Including s and p semicore states in valence. > > On 8/27/12, Ananya mondal wrote: > > Dear quantum-espresso users, > > I'm looking for a PBE type Norm-conserving Troullier Martins > > pseudopotential pseudopotential for Sodium. > > Thanks > > Ananya > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120828/78d4b79e/attachment.htm From degironc at sissa.it Tue Aug 28 10:02:02 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 28 Aug 2012 10:02:02 +0200 Subject: [Pw_forum] pseudopotential for Sodium In-Reply-To: References: Message-ID: <503C7AFA.7040807@sissa.it> Dear Ananya. If I remember correctly, in the ps-library distribution there is a Na US pseudopotential with s and p semicore states you can modify the input to make it NC (the US generation is actually a 2-step process in which the NC version is generated first). It's probably going to be a hard pseudo. HTH stefano PS: please don't forget to include your affiliation in your posts. thanks - Stefano de Gironcoli SISSA and DEMOCRITOS On 08/28/2012 08:03 AM, Yue-Wen Fang wrote: > May be you can generate the pp using ld1.x and test it by yourself. But it > not very simple > > Y.-W. Fang > > > 2012/8/28 Ananya Mondal > >> Including s and p semicore states in valence. >> >> On 8/27/12, Ananya mondal wrote: >>> Dear quantum-espresso users, >>> I'm looking for a PBE type Norm-conserving Troullier Martins >>> pseudopotential pseudopotential for Sodium. >>> Thanks >>> Ananya >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120828/04c5991b/attachment.htm From jerome.cuny at hotmail.fr Tue Aug 28 14:37:32 2012 From: jerome.cuny at hotmail.fr (=?iso-8859-1?B?auly9G1lIGN1bnk=?=) Date: Tue, 28 Aug 2012 14:37:32 +0200 Subject: [Pw_forum] Generation of H and O GIPAW PP Message-ID: Dear quantum-espresso users, I would like to share with you a problem I have for which I hope you could help me. I am trying to generate H and O norm-conserving PP to calculate the NMR properties of water molecules using the GIPAW module. I am using the 4.3.2 version of both quantum-espresso and gipaw (I join to this e-mail the make.sys file I used for the compilation). My problem is that, even if the generation of the PPs seems fine, their use by the gipaw module leads to bad results. I consider as good results the results I obtain using the H and O PP provided in the example folder of the gipaw module (see file water-nmr_1.log). Using the input file H.pbe-tm_good.in for the PP generation of H, the result I obtain for one water molecule in a box is not too bad (see water-nmr_1_good.log) However, my problem appear when I want to use as local part of the PP, the p orbital (see H.pbe-tm_bad.in and water-nmr_1_bad.log). Strangely, when I do this, I always obtain a contribution to the total chemical shit coming from some core orbitals! The same problem occur when I generate the O PP (in that case I use as input, the data I found in a presentation on GIPAW, see fig O_PP_Slide.tiff) as the core contribution become really different from the one of the reference calculation. So, does somebody see what I do wrong in my PP generation? Or, of course, is there any other source of error that could lead to this problem? I have checked the previous postings on the subject (GIPAW+PP) and I have not find one that answered my question. If I missed the good one, I am sorry. Best Regards, J?r?me Cuny ETH-Zurich/USI-Campus -------------------------------------------------------------------- J?r?me Cuny Department of Chemistry and Applied Biochemistry ETH-Zurich USI-Campus, Via Giuseppe Buffi 13 Computational Sciences/Parrinello 6900 Lugano, Switzerland Tel : +41 (0) 58666-4802 Fax : +41 (0) 58666-4817 -------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: O_PP_Slide.tiff Type: image/tiff Size: 123568 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0001.tiff -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys Type: application/octet-stream Size: 4708 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0005.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: H.pbe-tm_good.in Type: application/octet-stream Size: 447 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0006.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: H.pbe-tm_bad.in Type: application/octet-stream Size: 476 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0007.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: water-nmr_1.log Type: application/octet-stream Size: 7316 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0008.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: water-nmr_1_good.log Type: application/octet-stream Size: 7232 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/f2dc9636/attachment-0009.obj From giannozz at democritos.it Tue Aug 28 15:09:32 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 28 Aug 2012 15:09:32 +0200 Subject: [Pw_forum] differences in vdW_kernel_table In-Reply-To: References: Message-ID: <1346159372.3233.20.camel@fe12lx.fisica.uniud.it> On Thu, 2012-08-23 at 18:34 +0200, Eduardo Ariel Menendez Proupin wrote: > I generated the file vdW_kernel_table with version 5.0.1 and it is different > from the file coming with the 4.3.2. Should they be different ? they shouldn't, but apparently the kernel is given by an integral that is numerically unstable at small values of q, so you may get slightly different numbers with different machines/compilers/phases of the moon. This shouldn't however affect the final results: those large numbers you get are multiplied by very small densities. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From davide.ceresoli at istm.cnr.it Tue Aug 28 15:12:35 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Tue, 28 Aug 2012 15:12:35 +0200 Subject: [Pw_forum] Generation of H and O GIPAW PP In-Reply-To: References: Message-ID: <503CC3C3.8090801@istm.cnr.it> Dear J?r?me, the two output files you attached do not show large differences, The core contribution is only for oxygen, in both cases. What can lead to wrong/inaccurate results is the linear dependence between GIPAW projectors (in your "not-good" calculation). Moreover, I strongly advise to generate always two projectors per angular momentum in the &test section. I've never tried to generate hydrogen with 'p' locality. Maybe someone else can comment. In any case, I'm attaching original the input files for the hydrogen and oxygen pseudopotentials. You can try to add to them. Best wishes, Davide On 08/28/2012 02:37 PM, j?r?me cuny wrote: > Dear quantum-espresso users, > > I would like to share with you a problem I have for which I hope you could help me. > > I am trying to generate H and O norm-conserving PP to calculate the NMR > properties of water molecules using the GIPAW module. > I am using the 4.3.2 version of both quantum-espresso and gipaw (I join to this > e-mail the make.sys file I used for the compilation). > > My problem is that, even if the generation of the PPs seems fine, their use by > the gipaw module leads to bad results. > I consider as good results the results I obtain using the H and O PP provided in > the example folder of the gipaw module (see file water-nmr_1.log). > > Using the input file H.pbe-tm_good.in for the PP generation of H, the result I > obtain for one water molecule in a box is not too bad (see water-nmr_1_good.log) > > However, my problem appear when I want to use as local part of the PP, the p > orbital (see H.pbe-tm_bad.in and water-nmr_1_bad.log). Strangely, when I do > this, I always obtain a contribution to the total chemical shit coming from some > core orbitals! The same problem occur when I generate the O PP (in that case I > use as input, the data I found in a presentation on GIPAW, see fig > O_PP_Slide.tiff) as the core contribution become really different from the one > of the reference calculation. > > So, does somebody see what I do wrong in my PP generation? Or, of course, is > there any other source of error that could lead to this problem? > > I have checked the previous postings on the subject (GIPAW+PP) and I have not > find one that answered my question. If I missed the good one, I am sorry. > > Best Regards, > > J?r?me Cuny > ETH-Zurich/USI-Campus > > -------------------------------------------------------------------- > J?r?me Cuny > Department of Chemistry and Applied Biochemistry > ETH-Zurich > USI-Campus, Via Giuseppe Buffi 13 > Computational Sciences/Parrinello > 6900 Lugano, Switzerland > Tel : +41 (0) 58666-4802 Fax : +41 (0) 58666-4817 > -------------------------------------------------------------------- > > -------------- next part -------------- &input title = 'H' prefix = 'h' zed = 1 dft = 'PBE' rel = 0 iswitch = 3 beta = 0.2 xmin = -8.0, dx = 0.01 nld = 3, rlderiv = 2.2, eminld = -5.0, emaxld = 5.0, deld = 0.005 / 2 1S 1 0 0.5 1 2S 2 0 0.0 1 &inputp pseudotype = 1 lloc = 0 tm = .true. file_pseudopw = 'H.pbe-tm-new-gipaw.UPF' lgipaw_reconstruction = .true. upf_v1_format = .true. author = 'D.C.' / 1 1S 1 0 0.5 0.00 0.90 0.90 &test ecutmin = 60 ecutmax = 120 decut = 10 / 2 1S 1 0 0.50 0.00 0.90 0.90 2S 2 0 0.00 0.00 0.90 0.90 -------------- next part -------------- &input title = 'O' prefix = 'o' zed = 8 dft = 'PBE' rel = 1 iswitch = 3 beta = 0.2 xmin = -8.0, dx = 0.01 nld = 3, rlderiv = 2.0, eminld = -5.0, emaxld = 5.0, deld = 0.005 / 5 1S 1 0 2.0 1 2S 2 0 2.0 1 2P 2 1 4.0 1 3S 3 0 0.0 1 3P 3 1 -1.0 1 &inputp pseudotype = 1 lloc = 1 tm = .true. file_pseudopw = 'O.pbe-tm-new-gipaw.UPF' lgipaw_reconstruction = .true. upf_v1_format = .true. author = 'D.C.' / 2 2S 1 0 2.0 0.00 1.40 1.40 2P 2 1 4.0 0.00 1.40 1.40 &test ecutmin = 60 ecutmax = 120 decut = 10 / 4 2S 1 0 2.00 0.00 1.40 1.40 3S 2 0 0.00 0.00 1.40 1.40 2P 2 1 4.00 0.00 1.40 1.40 3P 3 1 0.00 -0.10 1.40 1.40 From nazari at iasbs.ac.ir Tue Aug 28 15:23:31 2012 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Tue, 28 Aug 2012 17:53:31 +0430 Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality In-Reply-To: <1570523744.70968.1346073185059.JavaMail.root@z.rochester.edu> References: <1570523744.70968.1346073185059.JavaMail.root@z.rochester.edu> Message-ID: <8d82cfa104a1cc5caa501d1340ea3998.squirrel@mail.iasbs.ac.ir> Dear All, Would you please let me know if the kohen -sham?orbitals ,which are obtained by pp.x,? are normalized, orthogonalized or orthonormalized? Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120828/6a1a252f/attachment.htm From ananyamondol3 at gmail.com Tue Aug 28 19:33:01 2012 From: ananyamondol3 at gmail.com (Ananya Mondal) Date: Tue, 28 Aug 2012 13:33:01 -0400 Subject: [Pw_forum] pseudopotential for Sodium In-Reply-To: <503C7AFA.7040807@sissa.it> References: <503C7AFA.7040807@sissa.it> Message-ID: Hi Gironcoli & Fang, Thanks for your reply. I am facing some problem to generate the PP from the atomic code. here is my inputs. pseudotype=1 &input title='Na', zed=11.0, rel=1, config='[Ne] 3s1 3p0 3d-2', iswitch=3, dft='PBE' / &inputp pseudotype=1, file_pseudopw='Na.pbe-tm.UPF', author='ADC', lloc=2, tm=.true. zval=9.0 / 5 2S 1 0 2.00 0.00 1.50 1.80 0.0 3S 2 0 1.00 0.00 1.50 1.80 0.0 2P 2 1 6.00 0.00 1.50 2.00 0.0 3P 3 1 0.00 0.00 1.50 2.00 0.0 3D 3 2 -2.00 0.30 2.00 2.00 0.0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ld1_readin : error # 1 Two wavefunctions for the same l %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... pseudotype=2, &input title='Na', zed=11.0, rel=1, config='[Ne] 3s1 3p0 3d-2', iswitch=3, dft='PBE' / &inputp pseudotype=2, file_pseudopw='Na.pbe-tm.UPF', author='ADC', lloc=2, tm=.true. zval=9.0 / 5 2S 1 0 2.00 0.00 1.50 1.80 0.0 3S 2 0 1.00 0.00 1.50 1.80 0.0 2P 2 1 6.00 0.00 1.50 2.00 0.0 3P 3 1 0.00 0.00 1.50 2.00 0.0 3D 3 2 -2.00 0.30 2.00 2.00 0.0 WARNING! Expected number of nodes: 1= 2- 0- 1, number of nodes found: 2. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from run_pseudo : error # 1 Errors in PS-KS equation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... On 8/28/12, Stefano de Gironcoli wrote: > Dear Ananya. > > If I remember correctly, in the ps-library distribution > > there is a Na US pseudopotential with s and p semicore states > > you can modify the input to make it NC (the US generation is actually a > 2-step process in which the NC version is generated first). > > It's probably going to be a hard pseudo. > > HTH > > stefano > > PS: please don't forget to include your affiliation in your posts. thanks > > - > Stefano de Gironcoli > SISSA and DEMOCRITOS > > On 08/28/2012 08:03 AM, Yue-Wen Fang wrote: >> May be you can generate the pp using ld1.x and test it by yourself. But >> it >> not very simple >> >> Y.-W. Fang >> >> >> 2012/8/28 Ananya Mondal >> >>> Including s and p semicore states in valence. >>> >>> On 8/27/12, Ananya mondal wrote: >>>> Dear quantum-espresso users, >>>> I'm looking for a PBE type Norm-conserving Troullier Martins >>>> pseudopotential pseudopotential for Sodium. >>>> Thanks >>>> Ananya >>>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > From sxr109320 at utdallas.edu Tue Aug 28 21:53:31 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Tue, 28 Aug 2012 14:53:31 -0500 (CDT) Subject: [Pw_forum] Join to group , confirmation # Message-ID: <137083830.643670.1346183611644.JavaMail.root@zem1.utdallas.edu> Hi , -- Best Regards, Saeedeh Ravandi From sxr109320 at utdallas.edu Tue Aug 28 21:53:20 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Tue, 28 Aug 2012 14:53:20 -0500 (CDT) Subject: [Pw_forum] Question about InAs Message-ID: <1517012342.643656.1346183600379.JavaMail.root@zem1.utdallas.edu> Hi , I am trying to see InAs band structure Hybride fucntions: What I have done is using these pseudos; In.pbe-d-rrkjus.UPF and As.pbe-n-van.UPF and have automatic 24x24x24 k-points in my scf calculation and try to see band structure , what I found is not resealable. Do you have any idea , how I can PEB0 oe B3LYP in my calculations ?? -- Best Regards, Saeedeh Ravandi From jerome.cuny at hotmail.fr Tue Aug 28 22:14:42 2012 From: jerome.cuny at hotmail.fr (=?iso-8859-1?B?auly9G1lIGN1bnk=?=) Date: Tue, 28 Aug 2012 22:14:42 +0200 Subject: [Pw_forum] Generation of H and O GIPAW PP In-Reply-To: <503CC3C3.8090801@istm.cnr.it> References: , <503CC3C3.8090801@istm.cnr.it> Message-ID: Dear Davide, I have just tried the PPs you sent me and they works perfectly. I also understand what I was doing wrong in my initial input. So thanks a lot for the help. However, in my initial e-mail I forget to send the output corresponding to the bad H PP, where a core contribution appears. I send it to you now (as well as the corresponding PP generation input). Maybe that will help a future pwscf user for not doing the same wrong thing as me. Best Regards, J?r?me Cuny Date: Tue, 28 Aug 2012 15:12:35 +0200 From: davide.ceresoli at istm.cnr.it To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Generation of H and O GIPAW PP Dear J?r?me, the two output files you attached do not show large differences, The core contribution is only for oxygen, in both cases. What can lead to wrong/inaccurate results is the linear dependence between GIPAW projectors (in your "not-good" calculation). Moreover, I strongly advise to generate always two projectors per angular momentum in the &test section. I've never tried to generate hydrogen with 'p' locality. Maybe someone else can comment. In any case, I'm attaching original the input files for the hydrogen and oxygen pseudopotentials. You can try to add to them. Best wishes, Davide On 08/28/2012 02:37 PM, j?r?me cuny wrote: > Dear quantum-espresso users, > > I would like to share with you a problem I have for which I hope you could help me. > > I am trying to generate H and O norm-conserving PP to calculate the NMR > properties of water molecules using the GIPAW module. > I am using the 4.3.2 version of both quantum-espresso and gipaw (I join to this > e-mail the make.sys file I used for the compilation). > > My problem is that, even if the generation of the PPs seems fine, their use by > the gipaw module leads to bad results. > I consider as good results the results I obtain using the H and O PP provided in > the example folder of the gipaw module (see file water-nmr_1.log). > > Using the input file H.pbe-tm_good.in for the PP generation of H, the result I > obtain for one water molecule in a box is not too bad (see water-nmr_1_good.log) > > However, my problem appear when I want to use as local part of the PP, the p > orbital (see H.pbe-tm_bad.in and water-nmr_1_bad.log). Strangely, when I do > this, I always obtain a contribution to the total chemical shit coming from some > core orbitals! The same problem occur when I generate the O PP (in that case I > use as input, the data I found in a presentation on GIPAW, see fig > O_PP_Slide.tiff) as the core contribution become really different from the one > of the reference calculation. > > So, does somebody see what I do wrong in my PP generation? Or, of course, is > there any other source of error that could lead to this problem? > > I have checked the previous postings on the subject (GIPAW+PP) and I have not > find one that answered my question. If I missed the good one, I am sorry. > > Best Regards, > > J?r?me Cuny > ETH-Zurich/USI-Campus > > -------------------------------------------------------------------- > J?r?me Cuny > Department of Chemistry and Applied Biochemistry > ETH-Zurich > USI-Campus, Via Giuseppe Buffi 13 > Computational Sciences/Parrinello > 6900 Lugano, Switzerland > Tel : +41 (0) 58666-4802 Fax : +41 (0) 58666-4817 > -------------------------------------------------------------------- > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120828/baef3677/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: water-nmr_1_bad.log Type: application/octet-stream Size: 7232 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/baef3677/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: H.pbe-tm_bad.in Type: application/octet-stream Size: 476 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120828/baef3677/attachment-0003.obj From aakimov at z.rochester.edu Tue Aug 28 22:36:15 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Tue, 28 Aug 2012 16:36:15 -0400 (EDT) Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality In-Reply-To: <8d82cfa104a1cc5caa501d1340ea3998.squirrel@mail.iasbs.ac.ir> Message-ID: <753983661.102089.1346186175848.JavaMail.root@z.rochester.edu> Dear Fariba, The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not orthonormalized in general, because of the pseudo-potentials and projection techniques (PAW). However, practically, you may safely assume they are orthogonal and almost normalized (self-overlaps are not far from 1.0). This is especially true for norm-conserving PP (by construction, the wavefunctions supposed to preserve norm), and, in slightly smaller extent, for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to reconstruct full wavefunction from the projection, so it is S|psi>. If i remember it correctly, the ortogonality will then be for = delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. Please anyone correct me if i'm wrong at some point. Thank you, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Tuesday, August 28, 2012 6:23:31 AM Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality Dear All, Would you please let me know if the kohen -sham orbitals ,which are obtained by pp.x, are normalized, orthogonalized or orthonormalized? Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From masoudnahali at gmail.com Wed Aug 29 01:42:58 2012 From: masoudnahali at gmail.com (Masoud) Date: Wed, 29 Aug 2012 01:42:58 +0200 Subject: [Pw_forum] Question about InAs Message-ID: Dear Saeede What is the unreasonable point ? If you meant the band gap energy you should have compared the band gap energy of your system with some other systems then see the trends ! have you checked it out ? Also, Indium arsenide's band gap is too small and DFT may not predict it as accurate as you desire. Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Tue, Aug 28, 2012 at 10:14 PM, Saeedeh S Ravandi wrote: > > > Hi , > > I am trying to see InAs band structure Hybride fucntions: > What I have done is using these pseudos; In.pbe-d-rrkjus.UPF and > As.pbe-n-van.UPF and have automatic 24x24x24 k-points in my scf calculation > and try to see band structure , what I found is not resealable. Do you have > any idea , how I can PEB0 oe B3LYP in my calculations ?? > > > > > -- > Best Regards, > Saeedeh Ravandi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/e47a9364/attachment.htm From nazari at iasbs.ac.ir Wed Aug 29 07:43:52 2012 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 29 Aug 2012 10:13:52 +0430 Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <753983661.102089.1346186175848.JavaMail.root@z.rochester.edu> References: <753983661.102089.1346186175848.JavaMail.root@z.rochester.edu> Message-ID: <80737a36883c74092aed47a93dd019fe.squirrel@mail.iasbs.ac.ir> ?Dear Alexey ?Would you please let me know how the S|psi>? is obtained? ?with pp.x . I need orthonormal kohn-sham orbitals. ?Regards ?Fariba Nazari IASBS ? > Dear Fariba, > > The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not > orthonormalized in general, because of the pseudo-potentials and > projection techniques (PAW). However, practically, you may safely assume > they are orthogonal and almost normalized (self-overlaps are not far from > 1.0). This is especially true for norm-conserving PP (by construction, the > wavefunctions supposed to preserve norm), and, in slightly smaller extent, > for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to > reconstruct full wavefunction from the projection, so it is S|psi>. If i > remember it correctly, the ortogonality will then be for = > delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. > Please anyone correct me if i'm wrong at some point. > > Thank you, > Alexey > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 6:23:31 AM > Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality > > > > > Dear All, > > Would you please let me know if the kohen -sham orbitals ,which are > obtained by pp.x, are normalized, orthogonalized or orthonormalized? > > Regards > Fariba Nazari > IASBS > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/4c5c4a0f/attachment.htm From giannozz at democritos.it Wed Aug 29 08:16:07 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Aug 2012 08:16:07 +0200 Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <80737a36883c74092aed47a93dd019fe.squirrel@mail.iasbs.ac.ir> References: <753983661.102089.1346186175848.JavaMail.root@z.rochester.edu> <80737a36883c74092aed47a93dd019fe.squirrel@mail.iasbs.ac.ir> Message-ID: On Aug 29, 2012, at 7:43 , nazari at iasbs.ac.ir wrote: > Would you please let me know how the S|psi> is obtained with pp.x you need to modify the code > I need orthonormal kohn-sham orbitals. in order to do what? KS orbitals obey a generalized orthonormality relation <\psi_i|S|\psi_j> = \delta_{ij} with ultrasoft pseudopotentials or PAW. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nazari at iasbs.ac.ir Wed Aug 29 08:25:09 2012 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Wed, 29 Aug 2012 10:55:09 +0430 Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: References: <753983661.102089.1346186175848.JavaMail.root@z.rochester.edu> <80737a36883c74092aed47a93dd019fe.squirrel@mail.iasbs.ac.ir> Message-ID: <46c5c92a893f91dd763d81d5125dd1c0.squirrel@mail.iasbs.ac.ir> >> Would you please let me know how the S|psi> is obtained with pp.x > > you need to modify the code? ??? ??? Which part of the code. Would you please let me know the? name of files that? should be? changed? >> I need orthonormal kohn-sham orbitals. > > in order to do what?? ??? I wish to??find the localized orbitals. Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/bfb2b2de/attachment.htm From davide.ceresoli at istm.cnr.it Wed Aug 29 09:47:50 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Wed, 29 Aug 2012 09:47:50 +0200 Subject: [Pw_forum] Generation of H and O GIPAW PP In-Reply-To: References: , <503CC3C3.8090801@istm.cnr.it> Message-ID: <503DC926.4040300@istm.cnr.it> Dear J?r?me, I think the atomic code got confused by your input and classified the 1S as a core state. This is done in ld1_setup.f90, from line 100. I'll check the code with your input and see if I can fix it. Best, Davide On 08/28/2012 10:14 PM, j?r?me cuny wrote: > Dear Davide, > > I have just tried the PPs you sent me and they works perfectly. I also > understand what I was doing wrong in my initial input. > So thanks a lot for the help. > > However, in my initial e-mail I forget to send the output corresponding to the > bad H PP, where a core contribution appears. I send it to you now (as well as > the corresponding PP generation input). Maybe that will help a future pwscf user > for not doing the same wrong thing as me. > > Best Regards, > > J?r?me Cuny > From karandeepster at gmail.com Wed Aug 29 11:24:41 2012 From: karandeepster at gmail.com (karan deep) Date: Wed, 29 Aug 2012 14:54:41 +0530 Subject: [Pw_forum] confusion in ev.x Message-ID: Thanks for reply but i m now sure that it is a third order birch-murnaghan equation. it needs correction it is also given in this paper Achieves of material science and emerging. vol 45, 2010, 108-113. Karandeep Research Scholar Physics Department, IIT, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/49572534/attachment.htm From vijayamirtharajit at gmail.com Wed Aug 29 11:47:17 2012 From: vijayamirtharajit at gmail.com (Vijay Amirtharaj A) Date: Wed, 29 Aug 2012 15:17:17 +0530 Subject: [Pw_forum] dapl_post_req resource ERR: dtos pending Message-ID: Hi, all users getting this kind of error. Error-1: ----------- node9.local:29311: node9.local:29313: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 node13.local:10441: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 node13.local:10442: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 node13.local:10443: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 node8.local:15066: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 339 tl 340 rank 39 in job 1 node17.local_54584 caused collective abort of all ranks exit status of rank 39: killed by signal 9 ===================== Error - 2: ------------ node24.local:11692: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 227 tl 228 node13.local:31886: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 136 tl 137 node13.local:31889: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 136 tl 137 node24.local:11694: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 227 tl 228 rank 50 in job 1 node45.local_50595 caused collective abort of all ranks exit status of rank 50: killed by signal 9 rank 19 in job 1 node45.local_50595 caused collective abort of all ranks exit status of rank 19: killed by signal 9 rank 17 in job 1 node45.local_50595 caused collective abort of all ranks exit status of rank 17: killed by signal 9 ======================== Error - 3 ---------- node22.local:10954: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 111 tl 112 rank 20 in job 1 node45.local_41415 caused collective abort of all ranks exit status of rank 20: killed by signal 9 ==================== Error - 4: iter # 7 total cpu time : 790.8 secs av.it.: 6.1 thresh= 0.786E-05 alpha_mix = 0.700 |ddv_scf|^2 = 0.902E-09 node4.local:4634: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 362 tl 363 rank 36 in job 2 node47.local_44548 caused collective abort of all ranks exit status of rank 36: killed by signal 9 =============== Error - 5: ------------- node22.local:2564: node19.local:19251: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 289 tl 290 dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 289 tl 290 rank 24 in job 1 node35.local_45835 caused collective abort of all ranks exit status of rank 24: killed by signal 9 ------------ Here with i have attached my make.sys file. Please guide me. -- Regards Vijay Amirtharaj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/840cd265/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: make-sys Type: application/octet-stream Size: 4755 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120829/840cd265/attachment.obj From giannozz at democritos.it Wed Aug 29 11:58:19 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Aug 2012 11:58:19 +0200 Subject: [Pw_forum] dapl_post_req resource ERR: dtos pending In-Reply-To: References: Message-ID: <2BA25106-46E8-4F11-9799-E37E7EAC01EB@democritos.it> On Aug 29, 2012, at 11:47 , Vijay Amirtharaj A wrote: > all users getting this kind of error it is a problem of your computer, not of QE P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vijayamirtharajit at gmail.com Wed Aug 29 12:41:03 2012 From: vijayamirtharajit at gmail.com (Vijay Amirtharaj A) Date: Wed, 29 Aug 2012 16:11:03 +0530 Subject: [Pw_forum] dapl_post_req resource ERR: dtos pending In-Reply-To: <2BA25106-46E8-4F11-9799-E37E7EAC01EB@democritos.it> References: <2BA25106-46E8-4F11-9799-E37E7EAC01EB@democritos.it> Message-ID: Hi Paolo, I am not able to find out,what is the problem in my computer. Did you have any idea or if you want any more information. i will give. Thanks, Vijay On Wed, Aug 29, 2012 at 3:28 PM, Paolo Giannozzi wrote: > > On Aug 29, 2012, at 11:47 , Vijay Amirtharaj A wrote: > > > all users getting this kind of error > > it is a problem of your computer, not of QE > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/9dd11648/attachment.htm From akohlmey at gmail.com Wed Aug 29 13:20:32 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 29 Aug 2012 13:20:32 +0200 Subject: [Pw_forum] dapl_post_req resource ERR: dtos pending In-Reply-To: References: <2BA25106-46E8-4F11-9799-E37E7EAC01EB@democritos.it> Message-ID: On Wed, Aug 29, 2012 at 12:41 PM, Vijay Amirtharaj A wrote: > Hi Paolo, > > I am not able to find out,what is the problem in my computer. Did you have > any idea or if you want any more information. i will give. spending <5 mins on a google search reveals that this error message is related to infinband or rather the openfabrics distribution. this is a *lowlevel* MPI related issue and - as paolo rightfully mentioned - has *nothing* to do with Q-E. so it is either a hardware problem or a machine configuration problem or a 'whatever else' problem. if you cannot figure out how to fix these kind of issues or get proper help for it in the proper places, you may want to investigate options for early retirement, since i doubt that there is anything we can do for your here. ;-) cheers, axel. > > Thanks, > Vijay > On Wed, Aug 29, 2012 at 3:28 PM, Paolo Giannozzi > wrote: >> >> >> On Aug 29, 2012, at 11:47 , Vijay Amirtharaj A wrote: >> >> > all users getting this kind of error >> >> it is a problem of your computer, not of QE >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From aakimov at z.rochester.edu Wed Aug 29 15:19:08 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Wed, 29 Aug 2012 09:19:08 -0400 (EDT) Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <80737a36883c74092aed47a93dd019fe.squirrel@mail.iasbs.ac.ir> Message-ID: <1339392117.107177.1346246348700.JavaMail.root@z.rochester.edu> Dear Fariba, I think you can get S|psi> without modifying the code. Here is an input for pp.x: &inputpp prefix = 'x', outdir = './', pseudo_dir = 'path-to-your-PP-directory', psfile(1) = 'C.pbe-van_bm.UPF', psfile(2) = 'H.pbe-van_bm.UPF', single_file = .FALSE., ascii = .TRUE., uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as long as i understand this should work at least for US-PPs / In addition, if you need localized orbitals, you might look in the direction of maximally localized wannier functions, ELF, or, if you want to plot MOs, you can use the pp.x to make .xsf files with the charge density corresponding to necessary KS orbitals. Best regards, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Tuesday, August 28, 2012 10:43:52 PM Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality Dear Alexey Would you please let me know how the S|psi> is obtained with pp.x . I need orthonormal kohn-sham orbitals. Regards Fariba Nazari IASBS > Dear Fariba, > > The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not > orthonormalized in general, because of the pseudo-potentials and > projection techniques (PAW). However, practically, you may safely assume > they are orthogonal and almost normalized (self-overlaps are not far from > 1.0). This is especially true for norm-conserving PP (by construction, the > wavefunctions supposed to preserve norm), and, in slightly smaller extent, > for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to > reconstruct full wavefunction from the projection, so it is S|psi>. If i > remember it correctly, the ortogonality will then be for = > delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. > Please anyone correct me if i'm wrong at some point. > > Thank you, > Alexey > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 6:23:31 AM > Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality > > > > > Dear All, > > Would you please let me know if the kohen -sham orbitals ,which are > obtained by pp.x, are normalized, orthogonalized or orthonormalized? > > Regards > Fariba Nazari > IASBS > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From fratesi at mater.unimib.it Wed Aug 29 15:24:29 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Wed, 29 Aug 2012 15:24:29 +0200 Subject: [Pw_forum] Memory usage by pw.x Message-ID: <503E180D.4030000@mater.unimib.it> Dear all, I'm trying to quantify the memory usage by pw.x: at the beginning of the SCF cycle the message "per-process dynamical memory:" reports the memory allocated at that time (clib/memstat.c), but this value is significantly less than the one I can see by monitoring the process by the "top" command, as more memory is allocated afterwards. Let me guess that calling again memstat later on, eg in c_bands, could provide one a more precise estimate, but maybe you can suggest a better approach, or correct me if I'm completely wrong. Thank you in advance, Guido -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From sxr109320 at utdallas.edu Wed Aug 29 15:20:32 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Wed, 29 Aug 2012 08:20:32 -0500 (CDT) Subject: [Pw_forum] Pw_forum Digest, Vol 62, Issue 50 In-Reply-To: Message-ID: <1538185568.657991.1346246432114.JavaMail.root@zem1.utdallas.edu> Hi Masoud , Yes , I have already checked the band gap for InAs in other articles , what they have for LDA (not even PBE) Celldem=6.06 BHR is 0.259 ev band gap. what I have is 0.014 ev !! theses are my input file ,probably , I do mistake somewhere . I have used same pseudo for In and As In.pz-bhs.UPF . My goal is not just having band gap with LDA , is also calculate it for Hybrid Functional. please , help me , ----- Original Message ----- From: pw forum-request To: pw forum Sent: Wed, 29 Aug 2012 02:41:36 -0500 (CDT) Subject: Pw_forum Digest, Vol 62, Issue 50 Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. Re: kohen -sham orbitals ortogonality and ortonormality (Alexey Akimov) 2. Re: Question about InAs (Masoud) 3. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) 4. Re: kohn -sham orbitals ortogonality and ortonormality (Paolo Giannozzi) 5. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Aug 2012 16:36:15 -0400 (EDT) From: Alexey Akimov Subject: Re: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality To: PWSCF Forum Message-ID: <753983661.102089.1346186175848.JavaMail.root at z.rochester.edu> Content-Type: text/plain; charset=utf-8 Dear Fariba, The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not orthonormalized in general, because of the pseudo-potentials and projection techniques (PAW). However, practically, you may safely assume they are orthogonal and almost normalized (self-overlaps are not far from 1.0). This is especially true for norm-conserving PP (by construction, the wavefunctions supposed to preserve norm), and, in slightly smaller extent, for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to reconstruct full wavefunction from the projection, so it is S|psi>. If i remember it correctly, the ortogonality will then be for = delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. Please anyone correct me if i'm wrong at some point. Thank you, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Tuesday, August 28, 2012 6:23:31 AM Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality Dear All, Would you please let me know if the kohen -sham orbitals ,which are obtained by pp.x, are normalized, orthogonalized or orthonormalized? Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu ------------------------------ Message: 2 Date: Wed, 29 Aug 2012 01:42:58 +0200 From: Masoud Subject: Re: [Pw_forum] Question about InAs To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear Saeede What is the unreasonable point ? If you meant the band gap energy you should have compared the band gap energy of your system with some other systems then see the trends ! have you checked it out ? Also, Indium arsenide's band gap is too small and DFT may not predict it as accurate as you desire. Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Tue, Aug 28, 2012 at 10:14 PM, Saeedeh S Ravandi wrote: > > > Hi , > > I am trying to see InAs band structure Hybride fucntions: > What I have done is using these pseudos; In.pbe-d-rrkjus.UPF and > As.pbe-n-van.UPF and have automatic 24x24x24 k-points in my scf calculation > and try to see band structure , what I found is not resealable. Do you have > any idea , how I can PEB0 oe B3LYP in my calculations ?? > > > > > -- > Best Regards, > Saeedeh Ravandi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/e47a9364/attachment.html ------------------------------ Message: 3 Date: Wed, 29 Aug 2012 10:13:52 +0430 From: nazari at iasbs.ac.ir Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: "PWSCF Forum" Message-ID: <80737a36883c74092aed47a93dd019fe.squirrel at mail.iasbs.ac.ir> Content-Type: text/plain; charset="utf-8" ?Dear Alexey ?Would you please let me know how the S|psi>? is obtained? ?with pp.x . I need orthonormal kohn-sham orbitals. ?Regards ?Fariba Nazari IASBS ? > Dear Fariba, > > The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not > orthonormalized in general, because of the pseudo-potentials and > projection techniques (PAW). However, practically, you may safely assume > they are orthogonal and almost normalized (self-overlaps are not far from > 1.0). This is especially true for norm-conserving PP (by construction, the > wavefunctions supposed to preserve norm), and, in slightly smaller extent, > for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to > reconstruct full wavefunction from the projection, so it is S|psi>. If i > remember it correctly, the ortogonality will then be for = > delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. > Please anyone correct me if i'm wrong at some point. > > Thank you, > Alexey > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 6:23:31 AM > Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality > > > > > Dear All, > > Would you please let me know if the kohen -sham orbitals ,which are > obtained by pp.x, are normalized, orthogonalized or orthonormalized? > > Regards > Fariba Nazari > IASBS > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/4c5c4a0f/attachment-0001.htm ------------------------------ Message: 4 Date: Wed, 29 Aug 2012 08:16:07 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: PWSCF Forum Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed On Aug 29, 2012, at 7:43 , nazari at iasbs.ac.ir wrote: > Would you please let me know how the S|psi> is obtained with pp.x you need to modify the code > I need orthonormal kohn-sham orbitals. in order to do what? KS orbitals obey a generalized orthonormality relation <\psi_i|S|\psi_j> = \delta_{ij} with ultrasoft pseudopotentials or PAW. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ------------------------------ Message: 5 Date: Wed, 29 Aug 2012 10:55:09 +0430 From: nazari at iasbs.ac.ir Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: "PWSCF Forum" Message-ID: <46c5c92a893f91dd763d81d5125dd1c0.squirrel at mail.iasbs.ac.ir> Content-Type: text/plain; charset="utf-8" >> Would you please let me know how the S|psi> is obtained with pp.x > > you need to modify the code? ??? ??? Which part of the code. Would you please let me know the? name of files that? should be? changed? >> I need orthonormal kohn-sham orbitals. > > in order to do what?? ??? I wish to??find the localized orbitals. Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/bfb2b2de/attachment-0001.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 62, Issue 50 **************************************** -- Best Regards, Saeedeh Ravandi From giannozz at democritos.it Wed Aug 29 18:14:08 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Aug 2012 18:14:08 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: <503E180D.4030000@mater.unimib.it> References: <503E180D.4030000@mater.unimib.it> Message-ID: <82B3D8B1-D76E-426F-93B2-34BB06B3263B@democritos.it> Hi Guido > I'm trying to quantify the memory usage by pw.x good luck. Understand how much memory a code really uses is highly nontrivial, due to the way modern operating systems work (shared libraries, files kept in RAM, ...) > at the beginning of the SCF cycle the message "per-process > dynamical memory:" reports the memory allocated at that time > (clib/memstat.c), but this value is significantly less than the one > I can see by monitoring the process by the "top" command, as > more memory is allocated afterwards. Let me guess that calling > again memstat later on, eg in c_bands, could provide one a more > precise estimate, but maybe you can suggest a better approach > I cannot P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From spiga.filippo at gmail.com Wed Aug 29 21:59:18 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Wed, 29 Aug 2012 21:59:18 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: <503E180D.4030000@mater.unimib.it> References: <503E180D.4030000@mater.unimib.it> Message-ID: <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> On Aug 29, 2012, at 3:24 PM, Guido Fratesi wrote: > Let me guess that > calling again memstat later on, eg in c_bands, could provide one a more > precise estimate, but maybe you can suggest a better approach, or > correct me if I'm completely wrong. I think you need to put several calls in several part of the code in order to have an understanding how much memory is going to be allocated. It will likely happen that the memory occupancy increases than decreases than increases again and so on. It is possible to incorporate a memory monitoring within the clock module BUT the amount of output that can be printed is huge! What about tracking the maximum and the minimum recorded within an entire SCF loop by sampling the memory occupancy where a clock (start or stop) is triggered? Cheers, Filippo -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/cf053c5a/attachment-0001.htm From florenceliu86 at gmail.com Thu Aug 30 03:10:21 2012 From: florenceliu86 at gmail.com (florence liu) Date: Thu, 30 Aug 2012 09:10:21 +0800 Subject: [Pw_forum] vdw-df2 Message-ID: Dear all, i have been looking through the file Modules/funct.f90 and i have found something which confuses me a little. according to the file the vdw-df2 functional is "defined" as "sla+pw+rpb+vdw2". however the corresponding reference (Lee et al., Phys. Rev. B 82, 081101 (2010)) mentions that the the revPBE exchange is replaced by the PW86 exchange. Doesn't that mean that the vdw-df2 should rather be "nox+pw+rw86+vdw2" ? or am i totally wrong? best wishes, florence TU Munich -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/dd27b2e2/attachment.htm From aryjunior at gmail.com Thu Aug 30 03:33:47 2012 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 29 Aug 2012 22:33:47 -0300 Subject: [Pw_forum] vdw-df2 In-Reply-To: References: Message-ID: Hi, everything is ok in Modules/funct.f90 from QE-4.3.2. There is a typo in the comment. else if ('VDW-DF2' .EQ. TRIM(dftout) ) then ! Special case vdW-DF2 call set_dft_value (iexch, 0) call set_dft_value (icorr, 4) call set_dft_value (igcx, 13) call set_dft_value (igcc, 0) call set_dft_value (inlc, 2) dft_defined = .true. else if ('VDW-DF' .EQ. TRIM(dftout)) then ! Special case vdW-DF call set_dft_value (iexch, 1) call set_dft_value (icorr, 4) call set_dft_value (igcx, 4) call set_dft_value (igcc, 0) call set_dft_value (inlc, 1) dft_defined = .true. All the best, Ary Junior Universidade Federal de Juiz de Fora - Brasil On Wed, Aug 29, 2012 at 10:10 PM, florence liu wrote: > Dear all, > i have been looking through the file Modules/funct.f90 and i have found > something which confuses me a little. > according to the file the vdw-df2 functional is "defined" as > "sla+pw+rpb+vdw2". however the corresponding reference (Lee et al., Phys. > Rev. B 82, 081101 (2010)) mentions that the the revPBE exchange is replaced > by the PW86 exchange. Doesn't that mean that the vdw-df2 should rather be > "nox+pw+rw86+vdw2" ? or am i totally wrong? > > best wishes, > > florence > > TU Munich > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- http://lattes.cnpq.br/8221674673413336 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/4d477405/attachment.htm From somayehfotohi at yahoo.com Thu Aug 30 08:23:01 2012 From: somayehfotohi at yahoo.com (somayeh fotohi) Date: Wed, 29 Aug 2012 23:23:01 -0700 (PDT) Subject: [Pw_forum] parallel processing Message-ID: <1346307781.16507.YahooMailNeo@web126101.mail.ne1.yahoo.com> dear all? I have two problems in quantum espresso. I work a simple structure of graphene.(60 atom) I run my program in cluster with 32 core (4 node) and use? below command for running: export PATH=/opt/espresso/openmpi-1.4.2-install/bin:/opt/intel/composer_xe_2011_sp1.11.339/bin/intel64:$PATH export OMP_NUM_THREADS=1 /opt/espresso/openmpi-1.4.2-install/bin/mpirun -hostfile .nodelist60 -np 32 /opt/espresso/espresso-5.0/bin/pw.x -npool 8 < 60.scf.in > 60.scf.out output file was reported: ?General routines ???? calbec?????? :?? 1832.29s CPU?? 2261.50s WALL (?? 20586 calls) ???? fft????????? :???? 21.02s CPU??? 105.36s WALL (???? 130 calls) ???? ffts???????? :????? 1.83s CPU????? 4.52s WALL (????? 29 calls) ???? fftw???????? :?? 1026.00s CPU?? 2618.48s WALL (?? 33010 calls) ???? interpolate? :????? 6.29s CPU???? 13.35s WALL (????? 29 calls) ???? davcio?????? :????? 0.01s CPU? 23906.83s WALL (????? 88 calls) ? ???? Parallel routines ???? fft_scatter? :??? 295.81s CPU?? 1939.74s WALL (?? 33169 calls) ???? EXX routines ? ????PWSCF??????? :???? 2h 8m CPU?????? 10h48m WALL as you seen , difference between CPU and WALL is very much and? run of program is finished after 12 hours approximately. what can i do for reduce WALL time? another problem is : when i use 32 cores or 16 cores,the speed dose not change considerably. I do not know the parallel of cores is done? badly or must change the parameter for improving run time and performance. can any one help me? thanks for advance. Best Regards somayeh fotoohi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/4dec2e31/attachment.htm From giannozz at democritos.it Thu Aug 30 08:38:05 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Aug 2012 08:38:05 +0200 Subject: [Pw_forum] parallel processing In-Reply-To: <1346307781.16507.YahooMailNeo@web126101.mail.ne1.yahoo.com> References: <1346307781.16507.YahooMailNeo@web126101.mail.ne1.yahoo.com> Message-ID: <65D8338A-CA33-470D-9DAF-3C5990121923@democritos.it> On Aug 30, 2012, at 8:23 , somayeh fotohi wrote: > I have two problems in quantum espresso. no, you have one: you haven't read the user guide > davcio : 0.01s CPU 23906.83s WALL ( 88 calls) this is I/O: more than 6h are spent reading and writing files. Either your file system is very strange, or you are using a NFS-mounted file system (very bad idea). > when i use 32 cores or 16 cores, the speed does not change > considerably maybe 32 cores are already too many for your system and/or for your communication hardware P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nazari at iasbs.ac.ir Thu Aug 30 10:09:20 2012 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Thu, 30 Aug 2012 12:39:20 +0430 Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <1339392117.107177.1346246348700.JavaMail.root@z.rochester.edu> References: <1339392117.107177.1346246348700.JavaMail.root@z.rochester.edu> Message-ID: <6f96edb3168001569fc4fb965381758d.squirrel@mail.iasbs.ac.ir> Dear? Alexey ?Thank? you . I have cheked? your suggestion?and it works. ?One more question : IS it possible that the? obtanied files have cube format.? ?? ?Best Regards Fariba Nazari IASBS > Dear Fariba, > > I think you can get S|psi> without modifying the code. Here is an input > for pp.x: > > &inputpp > prefix = 'x', > outdir = './', > pseudo_dir = 'path-to-your-PP-directory', > psfile(1) = 'C.pbe-van_bm.UPF', > psfile(2) = 'H.pbe-van_bm.UPF', > single_file = .FALSE., > ascii = .TRUE., > uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as > long as i understand this should work at least for US-PPs > / > > In addition, if you need localized orbitals, you might look in the > direction of maximally localized wannier functions, ELF, or, if you want > to plot MOs, you can use the pp.x to make .xsf files with the charge > density corresponding to necessary KS orbitals. > > > Best regards, > Alexey > > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 10:43:52 PM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > > Dear Alexey > > Would you please let me know how the S|psi> is obtained with pp.x . I need > orthonormal kohn-sham orbitals. > Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >> orthonormalized in general, because of the pseudo-potentials and >> projection techniques (PAW). However, practically, you may safely assume >> they are orthogonal and almost normalized (self-overlaps are not far >> from >> 1.0). This is especially true for norm-conserving PP (by construction, >> the >> wavefunctions supposed to preserve norm), and, in slightly smaller >> extent, >> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >> reconstruct full wavefunction from the projection, so it is S|psi>. If i >> remember it correctly, the ortogonality will then be for >> = >> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >> Please anyone correct me if i'm wrong at some point. >> >> Thank you, >> Alexey >> >> ----- Original Message ----- >> > From: nazari at iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 6:23:31 AM >> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >> >> >> >> >> Dear All, >> >> Would you please let me know if the kohen -sham orbitals ,which are >> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >> >> Regards >> Fariba Nazari >> IASBS >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/1a02f8a9/attachment.htm From aakimov at z.rochester.edu Thu Aug 30 15:50:26 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Thu, 30 Aug 2012 09:50:26 -0400 (EDT) Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <6f96edb3168001569fc4fb965381758d.squirrel@mail.iasbs.ac.ir> Message-ID: <1999476497.125891.1346334626145.JavaMail.root@z.rochester.edu> Dear Fariba, That is nice to know. Also i just found, that the example of the input i sent in the previous letter is not for pp.x, but rather for pw_export.x - that is for producing |psi> and S|psi>. For printing orbitals you of course need pp.x. Also i'm not sure what output files you mean - those with psi and Spsi (pw_export.x) can be produced in either binary or text format - that is it. If you imply orbitals (the charge density for given band) - i think they may be written in cube format (output_format = 6, just look in Doc/INPUT_PP.txt in you QE distribution for more details) Best regards, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Thursday, August 30, 2012 1:09:20 AM Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality Dear Alexey Thank you . I have cheked your suggestion and it works. One more question : IS it possible that the obtanied files have cube format.? Best Regards Fariba Nazari IASBS > Dear Fariba, > > I think you can get S|psi> without modifying the code. Here is an input > for pp.x: > > &inputpp > prefix = 'x', > outdir = './', > pseudo_dir = 'path-to-your-PP-directory', > psfile(1) = 'C.pbe-van_bm.UPF', > psfile(2) = 'H.pbe-van_bm.UPF', > single_file = .FALSE., > ascii = .TRUE., > uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as > long as i understand this should work at least for US-PPs > / > > In addition, if you need localized orbitals, you might look in the > direction of maximally localized wannier functions, ELF, or, if you want > to plot MOs, you can use the pp.x to make .xsf files with the charge > density corresponding to necessary KS orbitals. > > > Best regards, > Alexey > > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 10:43:52 PM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > > Dear Alexey > > Would you please let me know how the S|psi> is obtained with pp.x . I need > orthonormal kohn-sham orbitals. > Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >> orthonormalized in general, because of the pseudo-potentials and >> projection techniques (PAW). However, practically, you may safely assume >> they are orthogonal and almost normalized (self-overlaps are not far >> from >> 1.0). This is especially true for norm-conserving PP (by construction, >> the >> wavefunctions supposed to preserve norm), and, in slightly smaller >> extent, >> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >> reconstruct full wavefunction from the projection, so it is S|psi>. If i >> remember it correctly, the ortogonality will then be for >> = >> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >> Please anyone correct me if i'm wrong at some point. >> >> Thank you, >> Alexey >> >> ----- Original Message ----- >> > From: nazari at iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 6:23:31 AM >> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >> >> >> >> >> Dear All, >> >> Would you please let me know if the kohen -sham orbitals ,which are >> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >> >> Regards >> Fariba Nazari >> IASBS >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From fratesi at mater.unimib.it Thu Aug 30 15:54:35 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 30 Aug 2012 15:54:35 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> Message-ID: <503F709B.4070807@mater.unimib.it> > What about tracking the maximum and the minimum recorded within an > entire SCF loop by sampling the memory occupancy where a clock (start or > stop) is triggered? I tried this possibility, defining the routines below in clocks.f90 and the variable max_ram_kb (stored for laziness in "mytime"). Then, I call set_max_tracked_ram at every start/stop of a clock. I would expect this to work, since for example h_psi is called within the diagonalization cycles where workspaces and (I expect) most arrays have been already allocated. Yet in my test, the max memory printed by top is 2.3GB within the first step of the SCF cycle, but the standard call to memstat in electrons.f90 returned 744.1 Mb and the one tracked as described above 1168.572 Mb (maximum reached earlier than that 744.1 Mb). I report here the subroutines I used, they are trivial but... SUBROUTINE set_max_tracked_ram () USE mytime, ONLY : max_ram_kb IMPLICIT NONE INTEGER :: kilobytes CALL memstat ( kilobytes ) IF ( kilobytes > max_ram_kb+50 ) THEN max_ram_kb = kilobytes CALL write_max_tracked_ram () END IF END SUBROUTINE set_max_tracked_ram ! SUBROUTINE write_max_tracked_ram () USE io_global, ONLY : stdout USE mytime, ONLY : max_ram_kb IMPLICIT NONE WRITE( stdout, 9001 ) max_ram_kb/1000.0 9001 FORMAT(/' XXX per-process dynamical memory: ',f7.1,' Mb' ) END SUBROUTINE write_max_tracked_ram Guido -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From sxr109320 at utdallas.edu Thu Aug 30 15:54:03 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Thu, 30 Aug 2012 08:54:03 -0500 (CDT) Subject: [Pw_forum] InAs Pseudo HSE In-Reply-To: Message-ID: <2143665415.684691.1346334843397.JavaMail.root@zem1.utdallas.edu> Dear Developers , Thanks for your previous help , I could get my band gap in LDA and PBE, As I have checked , should I use PBE pseudo for HSE as well ? and do I need to use this part ? cos It starts giving me error in out put file input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2 , I am not sure how I have to choose Pseudo ? Thanks ----- Original Message ----- From: pw forum-request To: pw forum Sent: Wed, 29 Aug 2012 02:41:36 -0500 (CDT) Subject: Pw_forum Digest, Vol 62, Issue 50 Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. Re: kohen -sham orbitals ortogonality and ortonormality (Alexey Akimov) 2. Re: Question about InAs (Masoud) 3. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) 4. Re: kohn -sham orbitals ortogonality and ortonormality (Paolo Giannozzi) 5. Re: kohn -sham orbitals ortogonality and ortonormality (nazari at iasbs.ac.ir) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Aug 2012 16:36:15 -0400 (EDT) From: Alexey Akimov Subject: Re: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality To: PWSCF Forum Message-ID: <753983661.102089.1346186175848.JavaMail.root at z.rochester.edu> Content-Type: text/plain; charset=utf-8 Dear Fariba, The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not orthonormalized in general, because of the pseudo-potentials and projection techniques (PAW). However, practically, you may safely assume they are orthogonal and almost normalized (self-overlaps are not far from 1.0). This is especially true for norm-conserving PP (by construction, the wavefunctions supposed to preserve norm), and, in slightly smaller extent, for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to reconstruct full wavefunction from the projection, so it is S|psi>. If i remember it correctly, the ortogonality will then be for = delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. Please anyone correct me if i'm wrong at some point. Thank you, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Tuesday, August 28, 2012 6:23:31 AM Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality Dear All, Would you please let me know if the kohen -sham orbitals ,which are obtained by pp.x, are normalized, orthogonalized or orthonormalized? Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu ------------------------------ Message: 2 Date: Wed, 29 Aug 2012 01:42:58 +0200 From: Masoud Subject: Re: [Pw_forum] Question about InAs To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear Saeede What is the unreasonable point ? If you meant the band gap energy you should have compared the band gap energy of your system with some other systems then see the trends ! have you checked it out ? Also, Indium arsenide's band gap is too small and DFT may not predict it as accurate as you desire. Best Wishes, m ---------------------------------------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Tue, Aug 28, 2012 at 10:14 PM, Saeedeh S Ravandi wrote: > > > Hi , > > I am trying to see InAs band structure Hybride fucntions: > What I have done is using these pseudos; In.pbe-d-rrkjus.UPF and > As.pbe-n-van.UPF and have automatic 24x24x24 k-points in my scf calculation > and try to see band structure , what I found is not resealable. Do you have > any idea , how I can PEB0 oe B3LYP in my calculations ?? > > > > > -- > Best Regards, > Saeedeh Ravandi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/e47a9364/attachment.html ------------------------------ Message: 3 Date: Wed, 29 Aug 2012 10:13:52 +0430 From: nazari at iasbs.ac.ir Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: "PWSCF Forum" Message-ID: <80737a36883c74092aed47a93dd019fe.squirrel at mail.iasbs.ac.ir> Content-Type: text/plain; charset="utf-8" ?Dear Alexey ?Would you please let me know how the S|psi>? is obtained? ?with pp.x . I need orthonormal kohn-sham orbitals. ?Regards ?Fariba Nazari IASBS ? > Dear Fariba, > > The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not > orthonormalized in general, because of the pseudo-potentials and > projection techniques (PAW). However, practically, you may safely assume > they are orthogonal and almost normalized (self-overlaps are not far from > 1.0). This is especially true for norm-conserving PP (by construction, the > wavefunctions supposed to preserve norm), and, in slightly smaller extent, > for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to > reconstruct full wavefunction from the projection, so it is S|psi>. If i > remember it correctly, the ortogonality will then be for = > delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. > Please anyone correct me if i'm wrong at some point. > > Thank you, > Alexey > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Tuesday, August 28, 2012 6:23:31 AM > Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality > > > > > Dear All, > > Would you please let me know if the kohen -sham orbitals ,which are > obtained by pp.x, are normalized, orthogonalized or orthonormalized? > > Regards > Fariba Nazari > IASBS > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/4c5c4a0f/attachment-0001.htm ------------------------------ Message: 4 Date: Wed, 29 Aug 2012 08:16:07 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: PWSCF Forum Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed On Aug 29, 2012, at 7:43 , nazari at iasbs.ac.ir wrote: > Would you please let me know how the S|psi> is obtained with pp.x you need to modify the code > I need orthonormal kohn-sham orbitals. in order to do what? KS orbitals obey a generalized orthonormality relation <\psi_i|S|\psi_j> = \delta_{ij} with ultrasoft pseudopotentials or PAW. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ------------------------------ Message: 5 Date: Wed, 29 Aug 2012 10:55:09 +0430 From: nazari at iasbs.ac.ir Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality To: "PWSCF Forum" Message-ID: <46c5c92a893f91dd763d81d5125dd1c0.squirrel at mail.iasbs.ac.ir> Content-Type: text/plain; charset="utf-8" >> Would you please let me know how the S|psi> is obtained with pp.x > > you need to modify the code? ??? ??? Which part of the code. Would you please let me know the? name of files that? should be? changed? >> I need orthonormal kohn-sham orbitals. > > in order to do what?? ??? I wish to??find the localized orbitals. Regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120829/bfb2b2de/attachment-0001.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 62, Issue 50 **************************************** -- Best Regards, Saeedeh Ravandi From nazari at iasbs.ac.ir Thu Aug 30 16:10:00 2012 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Thu, 30 Aug 2012 18:40:00 +0430 Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <1999476497.125891.1346334626145.JavaMail.root@z.rochester.edu> References: <1999476497.125891.1346334626145.JavaMail.root@z.rochester.edu> Message-ID: <83f17239bde95246844d8b4d796d517c.squirrel@mail.iasbs.ac.ir> Dear Alexey, ?I understand that the input is for pw_export.x and run with it. I also need the? kohn-Sham orbitals whichare produced by pp.x.? but in ortogonalized form.? is it possible? Regards Fariba Nazari IASBS > Dear Fariba, > > That is nice to know. Also i just found, that the example of the input i > sent in the previous letter is not for pp.x, but rather for > pw_export.x - that is for producing |psi> and S|psi>. For printing > orbitals you of course need pp.x. > Also i'm not sure what output files you mean - those with psi and Spsi > (pw_export.x) can be produced in either binary or text format - that is > it. If you imply orbitals (the charge density for given band) - i think > they may be written in cube format (output_format = 6, just look in > Doc/INPUT_PP.txt in you QE distribution for more details) > > Best regards, > Alexey > > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Thursday, August 30, 2012 1:09:20 AM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > Dear Alexey > > Thank you . I have cheked your suggestion and it works. > One more question : IS it possible that the obtanied files have cube > format.? > > Best Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> I think you can get S|psi> without modifying the code. Here is an input >> for pp.x: >> >> &inputpp >> prefix = 'x', >> outdir = './', >> pseudo_dir = 'path-to-your-PP-directory', >> psfile(1) = 'C.pbe-van_bm.UPF', >> psfile(2) = 'H.pbe-van_bm.UPF', >> single_file = .FALSE., >> ascii = .TRUE., >> uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as >> long as i understand this should work at least for US-PPs >> / >> >> In addition, if you need localized orbitals, you might look in the >> direction of maximally localized wannier functions, ELF, or, if you want >> to plot MOs, you can use the pp.x to make .xsf files with the charge >> density corresponding to necessary KS orbitals. >> >> >> Best regards, >> Alexey >> >> >> ----- Original Message ----- >> > From: nazari at iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 10:43:52 PM >> Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and >> ortonormality >> >> >> >> Dear Alexey >> >> Would you please let me know how the S|psi> is obtained with pp.x . I >> need >> orthonormal kohn-sham orbitals. >> Regards >> Fariba Nazari >> IASBS >> >> >> >> >>> Dear Fariba, >>> >>> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >>> orthonormalized in general, because of the pseudo-potentials and >>> projection techniques (PAW). However, practically, you may safely >>> assume >>> they are orthogonal and almost normalized (self-overlaps are not far >>> from >>> 1.0). This is especially true for norm-conserving PP (by construction, >>> the >>> wavefunctions supposed to preserve norm), and, in slightly smaller >>> extent, >>> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >>> reconstruct full wavefunction from the projection, so it is S|psi>. If >>> i >>> remember it correctly, the ortogonality will then be for >>> >>> = >>> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >>> Please anyone correct me if i'm wrong at some point. >>> >>> Thank you, >>> Alexey >>> >>> ----- Original Message ----- >>> >> > From: nazari at iasbs.ac.ir >>> To: "PWSCF Forum" >>> Sent: Tuesday, August 28, 2012 6:23:31 AM >>> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >>> >>> >>> >>> >>> Dear All, >>> >>> Would you please let me know if the kohen -sham orbitals ,which are >>> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >>> >>> Regards >>> Fariba Nazari >>> IASBS >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner , and is >>> believed to be clean. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> Dr. Alexey V. Akimov >>> >>> Postdoctoral Research Associate >>> Department of Chemistry >>> University of Rochester >>> >>> aakimov at z.rochester.edu >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >>> >>> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/d33f29d1/attachment.htm From giannozz at democritos.it Thu Aug 30 16:24:56 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Aug 2012 16:24:56 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: <503F709B.4070807@mater.unimib.it> References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> Message-ID: <1346336696.27464.8.camel@fe12lx.fisica.uniud.it> On Thu, 2012-08-30 at 15:54 +0200, Guido Fratesi wrote: > Yet in my test, the max memory printed by top is 2.3GB within the first > step of the SCF cycle, but the standard call to memstat in electrons.f90 > returned 744.1 Mb and the one tracked as described above 1168.572 Mb my (limited) understanding is that the internal call to "memstat" reports only the dynamically allocated memory; "top" reports all memory taken by the process, including shared libraries and whatnot. It seems to me that the difference, (2.3-1.2)Gb=1.1Gb, is a lot of memory, but I have no idea how to figure out where all this memory come from (or goes to). This is stuff for OS wizards. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From lorenzo.paulatto at impmc.upmc.fr Thu Aug 30 16:34:03 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 30 Aug 2012 16:34:03 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: <503F709B.4070807@mater.unimib.it> References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> Message-ID: On 30 August 2012 15:54, Guido Fratesi wrote: > Yet in my test, the max memory printed by top is 2.3GB within the first > step of the SCF cycle, but the standard call to memstat in electrons.f90 > returned 744.1 Mb and the one tracked as described above 1168.572 Mb > (maximum reached earlier than that 744.1 Mb). > > Measuring the amount of memory in the "clock" subroutines is far from optimal, as they are usually called before temporary variables are allocated (start)clock) and after they are deallocated (stop_clock). With a command like this: sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find /where/is/espresso -name \*.f90) You can add a call to mem_whatever after *every* allocate in the entire code. This will also modify all your f90 files, so I suggest making a backup first. This should result in a quite accurate report of memory consumption (at the cost of a certain performance hit, I guess). Eventual allocations in c files and external libraries could still escape. I.e. the FFT library could decide to allocate a temporary array of 1GB, you will not see this in the final report. I suggest putting the subroutine mem_whatever somewher in flib/ and without a Module, otherwise you'll be forced to include also a USE in every file, which can be annoying. bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/45925cc4/attachment.htm From sbinnie at sissa.it Thu Aug 30 16:50:54 2012 From: sbinnie at sissa.it (Simon Binnie) Date: Thu, 30 Aug 2012 16:50:54 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> Message-ID: On Thu, 30 Aug 2012 16:34:03 +0200, Lorenzo Paulatto wrote: > On 30 August 2012 15:54, Guido Fratesi wrote: > >> Yet in my test, the max memory printed by top is 2.3GB within the first >> step of the SCF cycle, but the standard call to memstat in electrons.f90 >> returned 744.1 Mb and the one tracked as described above 1168.572 Mb >> (maximum reached earlier than that 744.1 Mb). >> >> > Measuring the amount of memory in the "clock" subroutines is far from > optimal, as they are usually called before temporary variables are > allocated (start)clock) and after they are deallocated (stop_clock). > > With a command like this: > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) > > You can add a call to mem_whatever after *every* allocate in the entire > code. This will also modify all your f90 files, so I suggest making a > backup first. > This should result in a quite accurate report of memory consumption (at > the > cost of a certain performance hit, I guess). You could use valgrind with the 'massif' tool. This should be able to tell you in which routine the memory usage peaks and thus where is best to put your memory check. Running qe under valgrind can be a very slow process though... Simon -- Simon Binnie | Post Doc, Condensed Matter Sector Scuola Internazionale di Studi Avanzati (SISSA) Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it From fratesi at mater.unimib.it Thu Aug 30 17:57:58 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 30 Aug 2012 17:57:58 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> Message-ID: <503F8D86.3000101@mater.unimib.it> This was indeed very useful, thank you. I got 1.9GBMb out of about 2400 On 08/30/2012 04:34 PM, Lorenzo Paulatto wrote: > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy Phone: +39 02 6448 5183 email: fratesi at mater.unimib.it From fratesi at mater.unimib.it Thu Aug 30 18:04:26 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 30 Aug 2012 18:04:26 +0200 Subject: [Pw_forum] Memory usage by pw.x In-Reply-To: References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> Message-ID: <503F8F0A.402@mater.unimib.it> I'm sorry for a previous incomplete message. > sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find > /where/is/espresso -name \*.f90) That was very useful, thank you. I now get 1.9GB out of 2.4, which starts giving some usable estimate, but I do understand that getting the accurate value is very complex. To my purpose, I'll monitor the memory occupancy by a script, which follows below in case someone finds it useful... Guido ================ command=pw.x maxsecs=$((60*60*24)) delay=1 nsteps=$((maxsecs/delay)) echo "#when RAM PID (0 for all $command instances)"} for ((i=0;((i References: <503E180D.4030000@mater.unimib.it> <9DAD4CFF-D105-4CEC-B4D2-0F8ACF557B60@gmail.com> <503F709B.4070807@mater.unimib.it> <503F8F0A.402@mater.unimib.it> Message-ID: guido, On Thu, Aug 30, 2012 at 12:04 PM, Guido Fratesi wrote: > I'm sorry for a previous incomplete message. > >> sed -ri "s/(^ *)(allocate.*$)/\1\2\n\1 CALL mem_whatever()/i" $(find >> /where/is/espresso -name \*.f90) > > That was very useful, thank you. > > I now get 1.9GB out of 2.4, which starts giving some usable estimate, > but I do understand that getting the accurate value is very complex. quantifying memory usage precisely on unix/linux machines with virtual memory management and memory sharing is almost impossible. you have multiple components to worry about: - address space (memory reserved to be used, but initially all mapped to the same copy-on-write location) - resident set size (actual physical memory used) - shared memory (it is not memory that is shared, but more a measure for how much sharing is going on) - swap space. - device memory (from infiniband cards for example) - pinned memory (allocated memory that cannot be swapped, usually used to back device memory) so what is the real memory usage is difficult to determine. address space (VMEM) is usually too large, resident set size (RSS) does not consider memory that is swapped out, so it is often too small. using many MPI tasks drives up the address space for device memory (which doesn't increase real memory usage, but also requires more pinned memory, which makes swapping more likely). multi-threading results in a lot of sharing. ...and tracking allocations in the code only handles explicit allocations, not those incurred by the fortran language on the stack or otherwise. so for all practical purposes you can say that memory use is usually somewhere between VMEM and RSS, but that can be pretty far apart. axel. > To my purpose, I'll monitor the memory occupancy by a script, which > follows below in case someone finds it useful... > Guido > > ================ > > command=pw.x > > maxsecs=$((60*60*24)) > delay=1 > nsteps=$((maxsecs/delay)) > > echo "#when RAM PID (0 for all $command instances)"} > > for ((i=0;((i #timer=`date +%H:%M:%S` > #timer=`date +"%H:%M:%S %s.%N"` > timer=`date +"%s.%N"` > ps -eo comm,rss,pid | > awk -v comm=$command -v timer=$timer ' > BEGIN {tot=0} > ($1==comm) { > tot+=$2; > print timer, $2, $3; > } > END {if (tot) print timer, tot, 0} > ' > sleep 1 > done > > > > -- > Guido Fratesi > > Dipartimento di Scienza dei Materiali > Universita` degli Studi di Milano-Bicocca > via Cozzi 53, 20125 Milano, Italy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From elie.moujaes at hotmail.co.uk Thu Aug 30 19:19:44 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 30 Aug 2012 18:19:44 +0100 Subject: [Pw_forum] q-points in the phonon calculations Message-ID: Dear all, I am doing phonon calculations at the Dirac K point of a graphene allotrope and I am getting two negative frequencies (almost degenerate). I need to confirm something regarding the units of the q-points. Should they be in terms of b1, b2 and b3, the reciprocal lattice vectors or in cartesian coordinates in terms of 2Pi/a? Is this written somewhere in the Guide... Reagrds Elie Moukaesuniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120830/25d6533c/attachment.htm From giannozz at democritos.it Thu Aug 30 20:49:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 30 Aug 2012 20:49:28 +0200 Subject: [Pw_forum] q-points in the phonon calculations In-Reply-To: References: Message-ID: <60C924EF-F00C-4A25-B730-6BFF5666F385@democritos.it> On Aug 30, 2012, at 19:19 , Elie M wrote: > Should they be in terms of b1, b2 and b3, the reciprocal lattice > vectors or in cartesian coordinates in terms of 2Pi/a? the latter you said > Is this written somewhere in the Guide... sure it is P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From aakimov at z.rochester.edu Thu Aug 30 23:58:00 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Thu, 30 Aug 2012 17:58:00 -0400 (EDT) Subject: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality In-Reply-To: <83f17239bde95246844d8b4d796d517c.squirrel@mail.iasbs.ac.ir> Message-ID: <1963004800.138378.1346363880598.JavaMail.root@z.rochester.edu> Dear Fariba, I think pp.x outputs give you just another representation of the orbitals in terms of the charge density. The plane wave expansion coefficients given by pw_export.x is one way to think of the orbitals, the charge density (e.g. cube files) produced by pp.x - is another. The orbitals are still orthogonal to each other (this is by construction, you have checked this with the plane wave expansion). Such orthogonality is of course not rigorous, as i pointed out in earlier messages (psi vs. Spsi), but the deviation is not very big. It is hard to say more without knowing the final goal. Hopefully this can be helpful. Best regards, Alexey ----- Original Message ----- From: nazari at iasbs.ac.ir To: "PWSCF Forum" Sent: Thursday, August 30, 2012 7:10:00 AM Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality Dear Alexey, I understand that the input is for pw_export.x and run with it. I also need the kohn-Sham orbitals whichare produced by pp.x. but in ortogonalized form. is it possible? Regards Fariba Nazari IASBS > Dear Fariba, > > That is nice to know. Also i just found, that the example of the input i > sent in the previous letter is not for pp.x, but rather for > pw_export.x - that is for producing |psi> and S|psi>. For printing > orbitals you of course need pp.x. > Also i'm not sure what output files you mean - those with psi and Spsi > (pw_export.x) can be produced in either binary or text format - that is > it. If you imply orbitals (the charge density for given band) - i think > they may be written in cube format (output_format = 6, just look in > Doc/INPUT_PP.txt in you QE distribution for more details) > > Best regards, > Alexey > > > ----- Original Message ----- > From: nazari at iasbs.ac.ir > To: "PWSCF Forum" > Sent: Thursday, August 30, 2012 1:09:20 AM > Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and ortonormality > > > Dear Alexey > > Thank you . I have cheked your suggestion and it works. > One more question : IS it possible that the obtanied files have cube > format.? > > Best Regards > Fariba Nazari > IASBS > > > > >> Dear Fariba, >> >> I think you can get S|psi> without modifying the code. Here is an input >> for pp.x: >> >> &inputpp >> prefix = 'x', >> outdir = './', >> pseudo_dir = 'path-to-your-PP-directory', >> psfile(1) = 'C.pbe-van_bm.UPF', >> psfile(2) = 'H.pbe-van_bm.UPF', >> single_file = .FALSE., >> ascii = .TRUE., >> uspp_spsi = .TRUE., <--- this produces S|psi> along with the |psi>, as >> long as i understand this should work at least for US-PPs >> / >> >> In addition, if you need localized orbitals, you might look in the >> direction of maximally localized wannier functions, ELF, or, if you want >> to plot MOs, you can use the pp.x to make .xsf files with the charge >> density corresponding to necessary KS orbitals. >> >> >> Best regards, >> Alexey >> >> >> ----- Original Message ----- >> > From: nazari at iasbs.ac.ir >> To: "PWSCF Forum" >> Sent: Tuesday, August 28, 2012 10:43:52 PM >> Subject: Re: [Pw_forum] kohn -sham orbitals ortogonality and >> ortonormality >> >> >> >> Dear Alexey >> >> Would you please let me know how the S|psi> is obtained with pp.x . I >> need >> orthonormal kohn-sham orbitals. >> Regards >> Fariba Nazari >> IASBS >> >> >> >> >>> Dear Fariba, >>> >>> The Kohn-Sham (please, not kohen) orbitals produced by pp.x are not >>> orthonormalized in general, because of the pseudo-potentials and >>> projection techniques (PAW). However, practically, you may safely >>> assume >>> they are orthogonal and almost normalized (self-overlaps are not far >>> from >>> 1.0). This is especially true for norm-conserving PP (by construction, >>> the >>> wavefunctions supposed to preserve norm), and, in slightly smaller >>> extent, >>> for ultra-soft pseudopotentials. For PAW wavefunctions the trick is to >>> reconstruct full wavefunction from the projection, so it is S|psi>. If >>> i >>> remember it correctly, the ortogonality will then be for >>> >>> = >>> delta_ij. However you can obtain S|psi> with pp.x as well as |psi>. >>> Please anyone correct me if i'm wrong at some point. >>> >>> Thank you, >>> Alexey >>> >>> ----- Original Message ----- >>> >> > From: nazari at iasbs.ac.ir >>> To: "PWSCF Forum" >>> Sent: Tuesday, August 28, 2012 6:23:31 AM >>> Subject: [Pw_forum] kohen -sham orbitals ortogonality and ortonormality >>> >>> >>> >>> >>> Dear All, >>> >>> Would you please let me know if the kohen -sham orbitals ,which are >>> obtained by pp.x, are normalized, orthogonalized or orthonormalized? >>> >>> Regards >>> Fariba Nazari >>> IASBS >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner , and is >>> believed to be clean. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> Dr. Alexey V. Akimov >>> >>> Postdoctoral Research Associate >>> Department of Chemistry >>> University of Rochester >>> >>> aakimov at z.rochester.edu >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >>> >>> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner , and is >> believed to be clean. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Dr. Alexey V. Akimov >> >> Postdoctoral Research Associate >> Department of Chemistry >> University of Rochester >> >> aakimov at z.rochester.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Dr. Alexey V. Akimov > > Postdoctoral Research Associate > Department of Chemistry > University of Rochester > > aakimov at z.rochester.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner , and is believed to be clean. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From tube77 at gmail.com Fri Aug 31 10:19:59 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Fri, 31 Aug 2012 03:19:59 -0500 Subject: [Pw_forum] Possible bug(?) in q2r.x when using FFT routine in ESSL Message-ID: Dear, QE users I have been struggling for a while to find out what's going on with q2r.x The problem was that I could not get rid of the error messages below when doing q2r.x. ------------------------------------------------- DCFT3 : 2538-2030 The transform length (ARG NO. 9) is not an allowed value. The next higher allowed value is (2). ------------------------------------------------- I've compiled QE-v5.0.1. on AIX6.1(parallel machine) with 'mpxlf' with ESSL routines. So the 'q2r.x' calls 'cfft3d' and then the 'cfft3d' calls 'dcft3' in ESSL when performing FFT. The problem is this. The 'dcft3' in ESSL only accepts certain values of transforming length as shown in, ------------------------------------------------- http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2Fco m.ibm.cluster.essl.v5r1.essl100.doc%2Fam501_hscft3.htm ------------------------------------------------- so the FFT dimensions (nx, ny, nz), which is read from outputs by ph.x, should be the values in the table. Otherwise, the 'dcft3' crashes. The FFT dimensions (nx, ny, nz) in q2r.x are equivalent to the (nq1, nq2, nq3) in ph.x so that the Monkhorst-pack grid for ph.x should be limited by the values in the table when using the ESSL. For example, the Monkhorst-pack grid (16x16x1) for q-points in the case of two-dimensional supercell, such as graphene, cannot be accepted by the 'dcft3' so we have to avoid using the nq3=1. (For some reason, the 'dcft3' does not allow odd number of FFT dimensions..) So here is a question. I wonder if I can use the different Monkhorst-pack grid for pw.x and ph.x when calculating a phonon dispersion. For example, can I use the (16x16x1) k-points for pw.x and (16x16x2) q-points for ph.x. in the case of graphene or some two dimensional supercell ? I guess it should not be matter but I just want to be sure .. Thank you. Sincerely, JISEOK KIM, Ph.D. Postdoctoral Research Associate Department of Materials Science and Engineering University of Texas at Dallas 800 W. Campbell Rd. RL10 Richardson, TX 75080 (413)386-6285 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120831/9bf23f85/attachment.htm From giannozz at democritos.it Fri Aug 31 10:55:54 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 31 Aug 2012 10:55:54 +0200 Subject: [Pw_forum] Possible bug(?) in q2r.x when using FFT routine in ESSL In-Reply-To: References: Message-ID: <1346403354.6068.21.camel@fe12lx.fisica.uniud.it> The simplest workaround is to move the *.dyn* files to another machine, compute there the force constants in reciprocal space. The ultimate solution is to go into Modules/fft_scalar.f90, edit routine cfft3d in such a way that it can cope with a dimension of length 1. You need to modify line 1238: IF( isign /= 0 ) CALL dcft3( f(1), ldx,ldx*ldy, f(1), ldx,ldx*ldy, & nx,ny,nz, idir, tscale, work(1), lwork) and call dcft2 instead. You will also need to add initialization of dft2 in line 1159, definition of needed arrays somewhere around line 1094. Of course you can use any grid of phonon wave-vectors, but it is a waste of time. P. On Fri, 2012-08-31 at 03:19 -0500, Jiseok Kim wrote: > Dear, QE users > > > I have been struggling for a while to find out what's going on with > q2r.x > The problem was that I could not get rid of the error messages below > when doing q2r.x. > > > ------------------------------------------------- > DCFT3 : 2538-2030 > The transform length (ARG NO. 9) is not an allowed value. The next > higher > allowed value is (2). > ------------------------------------------------- > > > I've compiled QE-v5.0.1. on AIX6.1(parallel machine) with 'mpxlf' with > ESSL routines. > So the 'q2r.x' calls 'cfft3d' and then the 'cfft3d' calls 'dcft3' in > ESSL when performing FFT. > > > The problem is this. > The 'dcft3' in ESSL only accepts certain values of transforming length > as shown in, > > > ------------------------------------------------- > http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2Fcom.ibm.cluster.essl.v5r1.essl100.doc%2Fam501_hscft3.htm > ------------------------------------------------- > > > so the FFT dimensions (nx, ny, nz), which is read from outputs by > ph.x, should be the values in the table. > Otherwise, the 'dcft3' crashes. > > > The FFT dimensions (nx, ny, nz) in q2r.x are equivalent to the (nq1, > nq2, nq3) in ph.x so that the Monkhorst-pack grid for ph.x should be > limited by the values in the table when using the ESSL. > > > For example, the Monkhorst-pack grid (16x16x1) for q-points in the > case of two-dimensional supercell, such as graphene, cannot be > accepted by the 'dcft3' so we have to avoid using the nq3=1. > (For some reason, the 'dcft3' does not allow odd number of FFT > dimensions..) > > > So here is a question. > I wonder if I can use the different Monkhorst-pack grid for pw.x and > ph.x when calculating a phonon dispersion. > For example, can I use the (16x16x1) k-points for pw.x and (16x16x2) > q-points for ph.x. in the case of graphene or some two dimensional > supercell ? > I guess it should not be matter but I just want to be sure .. > > > Thank you. > > > Sincerely, > > > JISEOK KIM, Ph.D. > Postdoctoral Research Associate > Department of Materials Science and Engineering > University of Texas at Dallas > 800 W. Campbell Rd. RL10 > Richardson, TX 75080 > (413)386-6285 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From yuewen.fang at gmail.com Fri Aug 31 14:03:34 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Fri, 31 Aug 2012 20:03:34 +0800 Subject: [Pw_forum] Join to group , confirmation # In-Reply-To: <137083830.643670.1346183611644.JavaMail.root@zem1.utdallas.edu> References: <137083830.643670.1346183611644.JavaMail.root@zem1.utdallas.edu> Message-ID: Hello, you have succeeded in subscribing this mail list and you can post your problems by sending emails to pw_forum at pwscf.org Best Regards Yuewen East China Normal Univ 2012/8/29 Saeedeh S Ravandi > Hi , > > -- > Best Regards, > Saeedeh Ravandi > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120831/b3ac7846/attachment.htm From Matthew.Montemore at Colorado.EDU Fri Aug 31 22:55:25 2012 From: Matthew.Montemore at Colorado.EDU (Matthew M Montemore) Date: Fri, 31 Aug 2012 14:55:25 -0600 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information Message-ID: Hi all, I'm new to QE and recently installed the svn version on a Linux cluster. Unfortunately, I had some strange pseudopotential issues using ld1.x and pslibrary.0.2.5. The upshot is that some of the PPs won't work unless I delete the input information from the file, and others won't work if I do delete the input information. This seems to depend on the author of the particular PP. I saw that adding the input file info is a fairly recent change (http://www.democritos.it/pipermail/pw_forum/2012-July/024717.html). After deleting the input info from the proper PPs, everything seems to work just fine. I checked the numbers in one of the PP files against a file generated by a colleague, and they agree to plenty of decimal places. I can also use my colleague's file with no problems, probably because it doesn't have the input info. I just wanted to make the community aware of this issue and help out anyone having similar problems. However, if anyone thinks that this issue indicates that I'm doing something wrong, please let me know. Matt Montemore University of Colorado Boulder