[Pw_forum] Negative frequencies from ph.x
Dear QE users, The problem of negative frequencies from ph.x was discussed several times on the PWSCF Forum. From what I read in the archives, the negative frequencies were due to too small number of k-points, or too small energy cutoff, or non-zero forces acting on atoms (i.e. non-equilibrium geometry). Unfortunately, I am still getting negative frequencies for my system (FCC cell, 34 Si atoms, semiconductor with ~0.7 eV gap). The results were practically the same for: number of k-points: 1 (gamma point), 10, and 8x8x8 points (=29 k-points) ecutwcf = 25, 30, and 55 Ry, and ecutrho = 4*ecutwfc In all cases, the geometry was optimized so the total force was 0.02 Ry/au, and the max. force acting on an atom was 0.0044 Ry/au. Therefore, all atoms were in equilibrium positions, but yet about 10 first phonon frequencies were negative, and phonon dos (calculated with nq1=nq2=nq3=4) was wrong. I noticed that ionic forces acting on atoms were large, ~0.7 Ry/atom, but these forces were compensated by opposite sign local forces. Is it possible that during perturbation calculations, these two opposite forces are not evaluated accurately, giving unstable system and negative frequencies? Any suggestions? Thank you very much. JG
[Pw_forum] Does symmetry depend on ecutrho-sec. 5.0.0.20 of the user guide
Hello, I am sorry for posting this question before reading sec. 5.0.0.20 of the pw.x user guide. JG
[Pw_forum] Does symmetry depend on ecutrho?
Hello, Does symmetry determined by pw.x depend on euctwfc/ecutrho? I am attaching two input files, T_30.in and T_50.in. With ecutwfc=30, ecutrho=120 (file T_30.in), pw.x correctly finds 48 symmetry operations, whereas with ecutwfc=50, ecutrho=200 (file T_50.in) only 24 symmetry operations are found. Any suggestions why? Best regards, JG -- next part -- &CONTROL title = 'scf run Fd3m coordinates', calculation = 'scf' outdir = '/home/gryko/tmp', wfcdir = '/home/gryko/tmp', pseudo_dir = '/home/gryko/PSEUDO', prefix = 'Si34_E50', lkpoint_dir = .false., tstress = .true., tprnfor = .true., restart_mode = 'from_scratch', verbosity = 'high', wf_collect = .TRUE., / &SYSTEM ecutwfc = 50 , ecutrho = 200 , exxdiv_treatment = 'gygi-baldereschi' , ibrav=2, celldm(1)=27.63, nat=34, ntyp=1, / &ELECTRONS mixing_mode = 'plain' mixing_beta = 0.6 conv_thr = 1.0d-10 / ATOMIC_SPECIES Si 28.0855 Si.vbc.UPF ATOMIC_POSITIONS alat Si 0.000 0.000 0.000 Si 0.750 0.250 0.750 Si 0.906 0.906 0.906 Si 0.094 0.594 0.406 Si 0.594 0.406 0.094 Si 0.406 0.094 0.594 Si 0.656 0.156 0.844 Si 0.344 0.344 0.344 Si 0.156 0.844 0.656 Si 0.844 0.656 0.156 Si 0.942 0.942 0.754 Si 0.754 0.942 0.942 Si 0.942 0.754 0.942 Si 0.692 0.192 0.996 Si 0.692 0.004 0.808 Si 0.504 0.192 0.808 Si 0.058 0.558 0.254 Si 0.254 0.058 0.558 Si 0.558 0.254 0.058 Si 0.308 0.308 0.496 Si 0.808 0.504 0.192 Si 0.004 0.808 0.692 Si 0.558 0.442 0.246 Si 0.246 0.558 0.442 Si 0.442 0.246 0.558 Si 0.192 0.808 0.504 Si 0.308 0.496 0.308 Si 0.996 0.692 0.192 Si 0.442 0.058 0.746 Si 0.746 0.442 0.058 Si 0.058 0.746 0.442 Si 0.808 0.692 0.004 Si 0.192 0.996 0.692 Si 0.496 0.308 0.308 K_POINTS gamma -- next part -- &CONTROL title = 'scf run Fd3m coordinates', calculation = 'scf' outdir = '/home/gryko/tmp', wfcdir = '/home/gryko/tmp', pseudo_dir = '/home/gryko/PSEUDO', prefix = 'Si34_E30', lkpoint_dir = .false., tstress = .true., tprnfor = .true., restart_mode = 'from_scratch', verbosity = 'high', wf_collect = .TRUE., / &SYSTEM ecutwfc = 30 , ecutrho = 120 , exxdiv_treatment = 'gygi-baldereschi' , ibrav=2, celldm(1)=27.63, nat=34, ntyp=1, / &ELECTRONS mixing_mode = 'plain' mixing_beta = 0.6 conv_thr = 1.0d-10 / ATOMIC_SPECIES Si 28.0855 Si.vbc.UPF ATOMIC_POSITIONS alat Si 0.000 0.000 0.000 Si 0.750 0.250 0.750 Si 0.906 0.906 0.906 Si 0.094 0.594 0.406 Si 0.594 0.406 0.094 Si 0.406 0.094 0.594 Si 0.656 0.156 0.844 Si 0.344 0.344 0.344 Si 0.156 0.844 0.656 Si 0.844 0.656 0.156 Si 0.942 0.942 0.754 Si 0.754 0.942 0.942 Si 0.942 0.754 0.942 Si 0.692 0.192 0.996 Si 0.692 0.004 0.808 Si 0.504 0.192 0.808 Si 0.058 0.558 0.254 Si 0.254 0.058 0.558 Si 0.558 0.254 0.058 Si 0.308 0.308 0.496 Si 0.808 0.504 0.192 Si 0.004 0.808 0.692 Si 0.558
[Pw_forum] nstep parameter for geometry optimization
Hello, I am trying to optimize geometry of a FCC crystal containing 36 atoms. The optimization runs fine, but pw.x stops after 3 bfgs steps with a message: The maximum number of steps has been reached End of BFGS Geometry Optimization I increased the n step parameter to nstep=1000, but no change. The total force is very small, Total force = 0.000178 (Ry/au), and the largest force acting on atom is approx. 0.29 (Ry/au). Does this mean that forces are too small and optimization must stop at this point? Unfortunately, even with such small forces, a number of vibrational frequencies calculated by the PHONON run is still negative. Any suggestions? Thank you very much, Jan
[Pw_forum] linking quantum espresso with ACML library
Hello, Several day ago I asked about linking Quantum Espresso with the ACML library. In fact this is very simple and all you need to do is to runs configure as: ./configure BLAS_LIBS="-L/opt/acml5.3.0/gfortran64_fma4/lib -lacml" \ FFT_LIBS="-L/$HOME/FFTW3/lib -lfftw3 and other options, such as FC, CC, FCFLAGS. You do not need to add LAPACK_LIBS, as ACML will be used. BLAS_LIB_SWITCH and LAPACK_LIB_SWITCH will be set to external by the configure script. Best regards, JG
[Pw_forum] linking quantum espresso with ACML library
Hello, I would like to ask to clarify how to link Quantum Espresso with ACML library. I have no problem linking with fftw3, but when I try to link with the ACML, it cannot find all subroutines. There several posts on ACML on the Forum, but I still cannot link it. My PC is 8 core AMD 8350 Vishera with 32 GB memory. Thank you very much, Jan Gryko Jacksonville, AL
[Pw_forum] FX8350 and Quantum Espresso
Hello, Does anyone have experience running QE on AMD FX 8350 or FX 8320 eight-core PC? There are several posts on the Forum about Intel 7/AMD dating back to 2009, but I do not see anything about the PC using the newest FX AMD processors. Right now it is possible to build FX8350 (8core, 4 GHz, 16GB memory) for less than $700.00, or with 32 GB memory for additional $150.00. If you use these processors, can you post info on the Forum? Thank you, Best regards, Jan Gryko Jacksonville State Univ. Jacksonville, AL
[Pw_forum] lnscf variable
Hello, Here is an excerpt from the README file in espresso-5.0.2/PHonon/examples/example01 "...make a phonon calculation for X point (input=si.phX.in, output=si.phX.out). Note the option "lnscf=.true.": this instructs the code to perform a needed non-scf calculation first. Note that the q-point (the X point in this case) is read after the namelist inputph." However, the runexample file does not have the lnscf variable. It looks like the scf data are used for the X point. Any comments? Best regards, Jan Gryko Jacksonville State Univ., Alabama
[Pw_forum] wyckoff position builder
Hello, Excellent idea - it will be very nice if Espresso could read crystallographic files, such as .cif or .cel files. Attached are several .cel files that are used by the PowderCell. Download free PowderCell program and run it. PowderCell will read the attached files and display structures and X-ray powder spectra (to load the attached file, click File --> Load). To examine the input file, click Structure --> Edit initial data. You can see all generated positions by clicking Structure-->Info-->Generated positions. Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax - Original Message - From: marsa...@democritos.it To: "pw forum" , "pw users" Sent: Tuesday, May 18, 2010 11:35:11 AM GMT -06:00 US/Canada Central Subject: [Pw_forum] wyckoff position builder Dear all, we are testing a new atomic position builder (including Wyckoff groups), consistent with Quantum ESPRESSO. We would like to test it with some "realistic" systems that you have found during your research (in particular orthorhombic C, trigonal R and monoclinic C). We would need Wychoff group, atom types, multiplicity, wyckoff letter, cell parameters, etc ... and the corresponding file xyz. Thank you very much for your contribution Layla & Riccardo Sabatini -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy This message was sent using IMP, the Internet Messaging Program. ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An embedded and charset-unspecified text was scrubbed... Name: AL2O3-HEX.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment.asc -- next part -- An embedded and charset-unspecified text was scrubbed... Name: GRAPHITE-HEX.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment.txt -- next part -- An embedded and charset-unspecified text was scrubbed... Name: GRAPHITE-RHOMB.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment-0001.asc -- next part -- An embedded and charset-unspecified text was scrubbed... Name: Na6Si34-166_2_from_227_2.cel Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100518/8421031a/attachment-0001.txt
[Pw_forum] ABINIT-QE conversion
I am sorry, I did not attach abinit and QE files with my previous msg. Here they are. Hello, I am trying to convert ABINIT files into QE using QE-ABINIT Perl script. Attached are: Abinit input (Na6Si34.inp) and converted QE file Na6Si34.pw.in. I had to modify Na6Si34.pw.in by adding Na and Si symbols, as the Perl script does not recognize atom types. However, inspecting Na6Si34.pw.in with xcrysden file I see that atomic positions are incorrect. Even correcting CELL_PARAMETERS (last line should be probably 0.5 0.5 0, instead of 0.5 0 0, am I correct?) results in an incorrect structure. I also tried to directly specify trigonal lattice, ibrav = 5 celldm(1) = 19.536 celldm(4) = 0.5 but the resulting atomic positions are also incorrect. The cell coordinates in the ABINIT file are obtained using PowderCell free program, by transforming space group 227,setting 1 into trigonal group 166, setting 2, i.e. transforming cubic a,b,c, axes into A=1/2(b+c), B=1/2(a+c) C=1/2(a+b) and shifting origin by (-1/8, -1/8, -1/8). Reading INPUT_PW Doc file I see that trigonal axes used by QE are v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). Shall I transform my coordinates into the (v1, v2, v3) axes? Thank you for your advice, Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- A non-text attachment was scrubbed... Name: Na6Si34.inp Type: application/octet-stream Size: 3669 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100505/0dbc1f3d/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: Na6Si34.pw.in Type: application/octet-stream Size: 1307 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100505/0dbc1f3d/attachment-0003.obj
[Pw_forum] ABINIT-QE conversion
Hello, I am trying to convert ABINIT files into QE using QE-ABINIT Perl script. Attached are: Abinit input (Na6Si34.inp) and converted QE file Na6Si34.pw.in. I had to modify Na6Si34.pw.in by adding Na and Si symbols, as the Perl script does not recognize atom types. However, inspecting Na6Si34.pw.in with xcrysden file I see that atomic positions are incorrect. Even correcting CELL_PARAMETERS (last line should be probably 0.5 0.5 0, instead of 0.5 0 0, am I correct?) results in an incorrect structure. I also tried to directly specify trigonal lattice, ibrav = 5 celldm(1) = 19.536 celldm(4) = 0.5 but the resulting atomic positions are also incorrect. The cell coordinates in the ABINIT file are obtained using PowderCell free program, by transforming space group 227,setting 1 into trigonal group 166, setting 2, i.e. transforming cubic a,b,c, axes into A=1/2(b+c), B=1/2(a+c) C=1/2(a+b) and shifting origin by (-1/8, -1/8, -1/8). Reading INPUT_PW Doc file I see that trigonal axes used by QE are v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz). Shall I transform my coordinates into the (v1, v2, v3) axes? Thank you for your advice, Jan Gryko Jacksonville State University 232-C Martin Hall Jacksonville, Al 36265 256-782-5218 256-782-5336 fax
