[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 was scrub
[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: &control 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/' / &system ibrav=0, celldm(1)=7.29052, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / &electrons 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: &control 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/' / &system ibrav=0, celldm(1)=9.13116, nat=2, ntyp=1, ecutwfc=29.3991, ecutrho=352.789, nbnd=8, smearing = 'gaussian', degauss = 0.02, / &electrons 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
Dear Prof Daryl ! Can you please attach your VASP file also so that I can have a closer look at your VASP file. In fact I did the calculation with your input file and after optimizing the structure I was getting the energy difference of 0.69 ev/atom. I just wanted to see the structures. On Wed, Oct 6, 2010 at 4:09 AM, Daryl Chrzan wrote: > Input files were stripped on the previous message. Here they are as part > of the message: > > Diamond Cubic: > > &control > 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/' > / > &system > ibrav=0, > celldm(1)=7.29052, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > &electrons > 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: > > &control > 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/' > / > &system > ibrav=0, > celldm(1)=9.13116, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > &electrons > 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 mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101007/b758d7c3/attachment.htm
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Daryl Chrzan wrote: > smearing = 'gaussian', > degauss = 0.02, you need occupations='smearing' as well, or else the code will silently default to fixed occupations. There should be a check and a warning, but there isn't any. Using QE in teaching is a great way to find all kinds of problems. I noticed it because this statement looked weird to me: highest occupied, lowest unoccupied level (ev):11.4054 5.2182 and no, the numbers were not printed in revers order. It doesn't make any difference for diamond Si, but it does for beta-Sn Si. I got betatin.out:!total energy = -19.20675112 Ry diamond.out:!total energy = -19.25371607 Ry i.e. 0.32eV/atoms > Beta-Sn: > nat=2 I was convinced that beta-Sn has 4 atoms per unit cell, not 2. I am interested because I also have used QE for teaching, and the diamond to beta-tin transition is a good exercise Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Michael, Thank you for the response. I agree that I am far from the minimum. However, when I do get to the minimum, I end up with a c/a ratio that is far off, and an energy difference of 0.6 eV, about twice what you find. (I have, I believe, accounted for the proper number of atoms, etc.) I have done the calculation with the PAW potential and the PZ-vbc potential and obtained the same results. Obviously I am doing something wrong but I simply cannot see it. I'll try the Si.pbe-n-van.UPF and see if I can reproduce your 0.29 eV energy difference. Did you c/a work out to be around 0.547? Daryl 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
Paolo, The smearing flag solved the problems. Thank you much for the tip (on behalf of myself and my class). I agree this is an excellent teaching exercise. Mark Asta suggested it to me, and it seems perfect. I still believe that there are 2 atoms per unit cell in the beta-Sn structure, so I am a bit confused by your final statement. I suppose this depends on the choice of lattice vectors... Daryl 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
On Oct 8, 2010, at 22:05 , Daryl Chrzan wrote: > I still believe that there are 2 atoms per unit cell in the beta-Sn > structure, so I am a bit confused by your final statement > don't take it too seriously: I interpreted the "4a" positions mentioned in http://cst-www.nrl.navy.mil/lattice/struk/a5.html as meaning that there are 4 atoms in the unit cell, but I am too lazy to go and check the International Tables of Cristallography! P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Not quite: celldm(1) =11.15433936, celldm(3) =0.54170527 On 10/08/2010 03:55 PM, Daryl Chrzan wrote: > Michael, > > Thank you for the response. I agree that I am far from the minimum. > However, when I do get to the minimum, I end up with a c/a ratio that is far > off, and an energy difference of 0.6 eV, about twice what you find. (I have, > I believe, accounted for the proper number of atoms, etc.) > > I have done the calculation with the PAW potential and the PZ-vbc potential > and obtained the same results. Obviously I am doing something wrong but I > simply cannot see it. I'll try the Si.pbe-n-van.UPF and see if I can > reproduce your 0.29 eV energy difference. Did you c/a work out to be around > 0.547? > > Daryl -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC
