[Pw_forum] Si diamond-cubic to beta-Sn transformation
Dayrl, Looking at your output, it seems that you are very far from the minimum energy beta-Sn structure: entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 42.95 0.00079257 0. 0. 116.59 0.00 0.00 0. 0.00079725 0.0001 0.00117.28 0.00 0. 0.0001 -0.00071388 0.00 0.00 -105.01 If you find the actual minimum energy structure for beta-Sn you'll get a much smaller difference in energy. I recently did this calculation using Si.pbe-n-van.UPF, rather than Si.pw91-n-van.UPF, and got an energy difference of 0.29 eV/atom, rather in better agreement with VASP and other published results. Ideally, all ultrasoft pseudopotentials should give the same result, but unfortunately they often don't. On 10/05/2010 02:36 PM, Daryl Chrzan wrote: > Colleagues, > > I am working through a problem that I have assigned to my Computational > Materials Science class - computation of the transition pressure for the > diamond-cubic to beta-Sn structures in diamond using pw.x. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Input files were stripped on the previous message. Here they are as part of the message: Diamond Cubic: calculation='scf' restart_mode='from_scratch', prefix='silicon', tstress= .true. tprnfor= .true. pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' / ibrav=0, celldm(1)=7.29052, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / diagonalization='cg' mixing_mode='plain' mixing_beta=0.7, conv_thr=3.0d-7, / ATOMIC_SPECIES Si 28.086 Si.pw91-n-van.UPF ATOMIC_POSITIONS crystal Si -0.125 0.125 -0.250 0 0 0 Si 0.125 -0.125 0.250 0 0 0 K_POINTS automatic 12 12 12 0 0 0 CELL_PARAMETERS -0.5 0.5 0.707107 0.5 -0.5 0.707107 0.5 0.5 -0.707107 Beta-Sn: calculation='scf' restart_mode='from_scratch', prefix='silicon', tstress= .true. tprnfor= .true. pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' / ibrav=0, celldm(1)=9.13116, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / diagonalization='cg' mixing_mode='plain' mixing_beta=0.7, conv_thr=3.0d-7, / ATOMIC_SPECIES Si 28.086 Si.pw91-n-van.UPF ATOMIC_POSITIONS crystal Si -0.125 0.125 -0.250 0 0 0 Si 0.125 -0.125 0.250 0 0 0 K_POINTS automatic 12 12 12 0 0 0 CELL_PARAMETERS -0.5 0.5 0.2735 0.5 -0.5 0.2735 0.5 0.5 -0.2735 Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Colleagues, I am working through a problem that I have assigned to my Computational Materials Science class - computation of the transition pressure for the diamond-cubic to beta-Sn structures in diamond using pw.x. The problem I have is that pw.x produces answers that are inconsistent with those produced by VASP, and those published in the literature. I have used similar ultrasoft pseudopotentials in both calculations (both based on PW91 correlation). There may be differences, between the two cases, but I have tried a number of pseudopotentials in pw.x and find essentially the same results). I have installed the QE software version 4.2.1 using both gfortran and ifort, using entirely internal libraries and with MKL (32 bit) libraries, both openMPI and single processor mode, and the tests of pw.x all conclude successfully). The software is installed on a Mac OSX 10.6 laptop. I have compiled in 32 and 64 bit mode for gfortran. If memory serves me correctly, all produce essentially the same results. Though I have generated a number of discrepancies, I think the most simple manifestation is the difference in total energy per atom for the equilibrium structures as predicted by VASP. More specifically, I find: (1) Diamond cubic structure in VASP. Relaxed structure (pressure ~ 0). K=Point mesh is 12 x 12 x 12, symmetrized. The lattice parameter comes out to be 5.456 Ang. Ultrasoft pseudopotential, PW91 exchange-correlation, cutoff chosen to be 400 eV. Total energy of relaxed cell = -10.80 eV. (2) Diamond cubic structure run using beta-Sn POSCAR with c/a = sqrt(2). Produces the same lattice parameter and the same total energy per relaxed cell = -10.866649 eV. (3) Beta-Sn structure also relaxed using the same potential yields a lattice parameter a = 4.832 Ang, and the ratio c/a = 0.547. Using the same k-point mesh (perhaps not completely converged, but close enough for our purposes) one finds a total energy of this phase to be -10.191998 eV. (4) Using these numbers, and noting that there are two atoms per unit cell, one finds that the energy difference per atom between the structures is given by E(BetaSn Si)- E(DC Si) = (-10.191998+10.80)/2 eV/atom = 0.34 eV/atom This value is in very good agreement with published results. We can now take these structural parameters and run pw.x from QE to compute the energy difference. I will use the beta-Sn unit cell for both calculations (the natural diamond cubic cell produces essentially the same results). I also used a MP grid 12x12x12 and an energy cutoff of 400 eV (12*400 eV for the charge density). (5) The total energy of the beta-Sn structure, per atom, predicted by QE is -130.192 eV. The total energy of the dc structure, per atom, predicted by QE is -130.982 eV. The difference in energy is, therefore, 0.79 eV/atom, more than a factor of two larger than predicted by VASP. I've attached the input files and the output files for your perusal. Sorry about the size of this message. Any insight you can lend will be more than appreciated. Thank you, Daryl C. Chrzan Professor, Materials Science and Engineering University of California Berkeley, CA 94720 and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 ph./fax: 510 643 1624 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0005.htm -- next part -- A non-text attachment was scrubbed... Name: Si.DC.in Type: application/octet-stream Size: 705 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0004.obj -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0006.htm -- next part -- A non-text attachment was scrubbed... Name: Si.BetaSn.in Type: application/octet-stream Size: 699 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0005.obj -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0007.htm -- next part -- A non-text attachment was scrubbed... Name: Si.BetaSn.out Type: application/octet-stream Size: 77595 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0006.obj -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/d4c6dbf1/attachment-0008.htm -- next part -- A non-text attachment
[Pw_forum] problem with Xspectra
Dear Min Wu, the pseudopotentials to be used for the absorbing atom in Xspectra are those having the label _gipaw, two examples are: Fe.pbe-sp-mt_gipaw.UPF Fe.star1s-pbe-sp-mt_gipaw.UPF The first one has no core-hole and has full gipaw informations while the second one has core-hole and full gipaw informations. Gipaw informations mean many things. What you need to know is that GIPAW informations include the presence of the all-electron wavefunction for the 1s core state. Now when you run a simulation you first need to calculate the charge density in the presence of a core-hole and thus use pseudo Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x scf calculation using this pseudo. In a second step you need to calcuate the Xanes cross section and this is done by the Xspectra code. In the calculation of the matrix element appearing in the Xanes cross-section (Fermi golden rule) the initial 1s state IN THE ABSENCE of a core hole is needed. This information is contanined in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). Thus you simply extract this wavefunction using the script given with the Xspectra disribution and you put the name of the file produced by the script in the input file of the Xspectra program. You cannot use the 1s core function with the core hole simply because this is wrong as the matrix element inthe cross section involves the product between the initial and final states and the initial state has no core hole. M. > Message: 1 > Date: Tue, 05 Oct 2010 00:42:50 +0800 > From: "wumindt2" > Subject: [Pw_forum] problem with Xspectra > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Hi, > > I'm a new user of Xspectra. > > In the Xspectra example given in the pwscf code, it calculates the > XAS using the pseudopotential > without core hole level. In this case, we need to extract the core > wavefunction from the GIPAW > pseudopotential when we run the xspectra.x. > > Now there are pseudopotentials with core hole, normally named as > *.star1s*.UPF. So here is > my question, after the SCF calculation, do we still need to extract > the core wavefunction from the > peusopotential of the absorbing atom? > > If the answer is yes, then why we choose the core wavefunction from > the pseudopotential as the ground > state, rather than the core wavefunction after the SCF calculation? > > Thanks! > > Min Wu > 2010-10-4 This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] Displacements corresponding to -ve Phonon modes
On Oct 4, 2010, at 3:07 PM, Bipul Rakshit wrote: > Dear PWSCF users, > > I am doing Phonon of KO2 compound. I find some -ve phonon modes at gamma > point. (After applying ASR also) > Following is the dynamical matrix formed by the phonon programme during the > run. > I just want to study the displacement corresponding to -ve modes. So Is it > enough to plot the eigen vectors given below corresponding to each mode. > Strange things what I feel in these eigen vectors are the 'K' is also moving > almost with the same magnitude as 'O' Not so strange for zone-center acoustic modes (their frequency is zero exactly because they correspond to a rigid translation) > and there is no imaginary part of eigen vectors though the frequencies are > -ve. why should there be any? what do you mean by "-ve"? 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/a31206af/attachment.htm
[Pw_forum] problem with Xspectra
Hi, I'm a new user of Xspectra. In the Xspectra example given in the pwscf code, it calculates the XAS using the pseudopotential without core hole level. In this case, we need to extract the core wavefunction from the GIPAW pseudopotential when we run the xspectra.x. Now there are pseudopotentials with core hole, normally named as *.star1s*.UPF. So here is my question, after the SCF calculation, do we still need to extract the core wavefunction from the peusopotential of the absorbing atom? If the answer is yes, then why we choose the core wavefunction from the pseudopotential as the ground state, rather than the core wavefunction after the SCF calculation? Thanks! Min Wu 2010-10-4 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101005/9e5fe0f8/attachment.htm
