[QE-users] Crystal structure changes while doing vc-relax calculation.

Tue Feb 1 14:58:48 CET 2022

Dear Vivek,
cell_dofree='ibrav' only works if you specified a value of ibrav>0 to begin with. If you don't know it, you can try to find it reading the description in INPUT_PW.html or with the scan_ibrav.x tool:

$ ~/espresso.BASE/PW/tools/scan_ibrav.x
Enter the unit of measur (angstrom, bohr) or alat in bohr units, or alat in Ang
strom units, followed by ' A'
19.820415
alat (bohr) 19.820415
Enter the cell basis vectors (one per line)
1.0000000000 0.0000000000 0.0000000000
0.0000000000 0.4999999999 0.0000000000
0.0000000000 0.0000000000 1.0845493931
Requested axes in Bohr units:
at1 19.820415 0.000000 0.000000
at2 0.000000 9.910207 0.000000
at3 0.000000 0.000000 21.496219

Scanning ibrav 1
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav 2
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 3
The best cell with this ibrav is not good enough (chisq=0.1E+03)

Scanning ibrav -3
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 4
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav 5
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav -5
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 6
The best cell with this ibrav is not good enough (chisq=0.5E+02)

Scanning ibrav 7
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 8
Minimization succeeded (chisq= 0. )
ibrav = 8
celldm( 1) = 19.820415000
celldm( 2) = 0.500000000
celldm( 3) = 1.084549393
at1 19.820415 0.000000 0.000000
at2 0.000000 9.910207 0.000000
at3 0.000000 0.000000 21.496219

...

Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ (https://link.getmailspring.com/link/78F32A0F-3925-4A88-B3C2-DCE9B9225768@getmailspring.com/0?redirect=http%3A%2F%2Fwww.impmc.upmc.fr%2F~paulatto%2F&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D) - https://anharmonic.github.io/ (https://link.getmailspring.com/link/78F32A0F-3925-4A88-B3C2-DCE9B9225768@getmailspring.com/1?redirect=https%3A%2F%2Fanharmonic.github.io%2F&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Feb 1 2022, at 1:52 pm, Vivek Christhunathan <vivekppn at gmail.com> wrote:
> Hello Everyone,
>
> I'm bringing attention to a topic that has previously been discussed in this forum. I too faced the same type of problem when I try to do structural relaxation for CaWO4 (2x1x1 supercell), that its crystal structure changed from Tetragonal to Orthorhombic. I tried all the following forum's suggestions to get rid of this problem.
>
> As per their suggestion, I tried using the following tags in my input file,
>
> >ion_dynamics = 'damp'
> >and
> >cell_dynamics = "damp-pr"
> >which should respect the constraint.
>
> And also I tried using cell_dofree=‘ibrav'. but still lattice parameter values a and b are not the same. Still, its structure changes from Tetragonal to Orthorhombic.
> >You can open Modules/cell_base.f90 and at line 84 change
> >LOGICAL :: enforce_ibrav = .FALSE.! True if ibrav ...
> >to
> >LOGICAL :: enforce_ibrav = .TRUE.! True if ibrav ...
> >(do not forget to recompile pw.x) to use cell_dofree="ibrav" together with any >other cell_dofree
>
> Since I'm utilizing the Government's supercomputer cluster, I'm not sure how I'd make these adjustments to the QE code. Can I get your suggestion regarding this?
> >Should be present in the available patches for v.6.4.1: file
> backports-6.4.1.diff
> <https://github.com/QEF/q-e/releases/download/qe-6.4.1/backports-6.4.1.diff (https://link.getmailspring.com/link/78F32A0F-3925-4A88-B3C2-DCE9B9225768@getmailspring.com/2?redirect=https%3A%2F%2Fgithub.com%2FQEF%2Fq-e%2Freleases%2Fdownload%2Fqe-6.4.1%2Fbackports-6.4.1.diff&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)>
> in https://github.com/QEF/q-e/releases (https://link.getmailspring.com/link/78F32A0F-3925-4A88-B3C2-DCE9B9225768@getmailspring.com/3?redirect=https%3A%2F%2Fgithub.com%2FQEF%2Fq-e%2Freleases&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
> Could you please advise me on how to proceed with this link?
>
> I have included calculations input and output for your perusal.
>
> If you could share your thoughts on this issue, that would be quite helpful.
>
> Input:
>
> &control
> calculation = 'vc-relax'
> restart_mode = 'restart'
> prefix = 'CaWO4'
> tstress = .true.
> tprnfor = .true.
> pseudo_dir = './'
> outdir = './outCaWO4'
> wf_collect=.true.
> forc_conv_thr = 1d-4
> etot_conv_thr = 1D-4
> !disk_io = 'medium'
> max_seconds = 7200,
> /
>
> &system
> ibrav = 0
> celldm(1) = 19.820415
> nat = 48
> ntyp = 3
> ecutwfc = 65.0
> ecutrho = 780.0
> occupations= 'smearing'
> smearing= 'gaussian'
> degauss= 0.02
> /
>
> &electrons
> mixing_beta = 0.2,
> conv_thr = 1.0d-6,
> electron_maxstep = 50000,
> /
>
> &IONS
> ion_dynamics = 'damp'
>
> /
>
> &cell
> cell_factor = 3.0d0
> cell_dynamics = 'damp-pr'
> !cell_dofree= 'ibrav'
> /
>
> ATOMIC_SPECIES
> Ca 40.08 Ca.pbe-spn-rrkjus_psl.1.0.0.UPF
> W 183.84 W.pbe-spn-rrkjus_psl.1.0.0.UPF
> O 16.00 O.pbe-n-rrkjus_psl.1.0.0.UPF
>
> CELL_PARAMETERS (alat)
> 1.0000000000 0.0000000000 0.0000000000
> 0.0000000000 0.4999999999 0.0000000000
> 0.0000000000 0.0000000000 1.0845493931
>
> ATOMIC_POSITIONS (crystal)
> Ca 0.000000000 0.250000000 0.625000000
> Ca 0.500000000 0.250000000 0.625000000
> Ca 0.000000000 0.750000000 0.375000000
> Ca 0.500000000 0.750000000 0.375000000
> Ca 0.250000000 0.750000000 0.125000000
> Ca 0.750000000 0.750000000 0.125000000
> Ca 0.250000000 0.250000000 0.875000000
> Ca 0.750000000 0.250000000 0.875000000
> W 0.000000000 0.250000000 0.125000000
> W 0.500000000 0.250000000 0.125000000
> W 0.000000000 0.750000000 0.875000000
> W 0.500000000 0.750000000 0.875000000
> W 0.250000000 0.750000000 0.625000000
> W 0.750000000 0.750000000 0.625000000
> W 0.250000000 0.250000000 0.375000000
> W 0.750000000 0.250000000 0.375000000
> O 0.074850000 0.009300000 0.209700003
> O 0.574850023 0.009300000 0.209700003
> O 0.425150007 0.990700006 0.790300012
> O 0.925150037 0.990700006 0.790300012
> O 0.175150007 0.990700006 0.709699988
> O 0.675150037 0.990700006 0.709699988
> O 0.324849993 0.009300000 0.290300012
> O 0.824849963 0.009300000 0.290300012
> O 0.370350003 0.399699986 0.459699988
> O 0.870350003 0.399699986 0.459699988
> O 0.129649997 0.600300014 0.540300012
> O 0.629649997 0.600300014 0.540300012
> O 0.379649997 0.600300014 0.959699988
> O 0.879649997 0.600300014 0.959699988
> O 0.120350003 0.399699986 0.040299997
> O 0.620350003 0.399699986 0.040299997
> O 0.324849993 0.509299994 0.709699988
> O 0.824849963 0.509299994 0.709699988
> O 0.175150007 0.490700006 0.290300012
> O 0.675150037 0.490700006 0.290300012
> O 0.425150007 0.490700006 0.209700003
> O 0.925150037 0.490700006 0.209700003
> O 0.074850000 0.509299994 0.790300012
> O 0.574850023 0.509299994 0.790300012
> O 0.120350003 0.899699986 0.959699988
> O 0.620350003 0.899699986 0.959699988
> O 0.379649997 0.100299999 0.040299997
> O 0.879649997 0.100299999 0.040299997
> O 0.129649997 0.100299999 0.459699988
> O 0.629649997 0.100299999 0.459699988
> O 0.370350003 0.899699986 0.540300012
> O 0.870350003 0.899699986 0.540300012
>
> K_POINTS AUTOMATIC
> 2 2 2 1 1 1
>
>
> Output (a scf loop from output file):
>
> atom 48 type 3 force = 0.00003185 -0.00002222 -0.00008890
>
> Total force = 0.000633 Total SCF correction = 0.000137
> SCF correction compared to forces is large: reduce conv_thr to get better values
>
>
> Computing stress (Cartesian axis) and pressure
>
>
> negative rho (up, down): 1.178E+00 0.000E+00
> total stress (Ry/bohr**3) (kbar) P= 0.04
> 0.00000050 -0.00000019 -0.00000004 0.07 -0.03 -0.01
> -0.00000019 0.00000058 -0.00000002 -0.03 0.08 -0.00
> -0.00000004 -0.00000002 -0.00000017 -0.01 -0.00 -0.02
>
>
> number of scf cycles = 14
> number of bfgs steps = 13
>
> enthalpy old = -2905.7085634122 Ry
> enthalpy new = -2905.7085638929 Ry
>
> CASE: enthalpy_new < enthalpy_old
>
> new trust radius = 0.0005206840 bohr
> WARNING! With ibrav=0, cell_dofree='ibrav' does not have any effect.
> new conv_thr = 0.0000000100 Ry
>
> new unit-cell volume = 4353.65352 a.u.^3 ( 645.14488 Ang^3 )
> density = 5.92862 g/cm^3
>
> CELL_PARAMETERS (alat= 19.82041500)
> 1.009431575 0.000035319 0.000001684
> 0.000017655 0.504836574 0.000001702
> 0.000001845 0.000003719 1.097205402
>
> ATOMIC_POSITIONS (crystal)
> Ca 0.000001762 0.249997612 0.625000246
> Ca 0.500002903 0.249995682 0.624999551
> Ca -0.000001762 0.750002388 0.374999754
> Ca 0.499997097 0.750004318 0.375000449
> Ca 0.249995760 0.750002886 0.125000569
> Ca 0.749997044 0.750001219 0.124998286
> Ca 0.250002956 0.249998781 0.875001714
> Ca 0.750004240 0.249997114 0.874999431
> W -0.000007775 0.250005618 0.125011626
> W 0.499993856 0.250003532 0.125006749
> W 0.000007775 0.749994382 0.874988374
> W 0.500006144 0.749996468 0.874993251
> W 0.250000614 0.749987294 0.625009963
> W 0.750012640 0.750006266 0.625006514
> W 0.249987360 0.249993734 0.374993486
> W 0.749999386 0.250012706 0.374990037
> O 0.074741741 0.007038639 0.209937560
> O 0.574740434 0.007045102 0.209936159
> O 0.425259596 0.992954904 0.790063856
> O 0.925258296 0.992961367 0.790062455
> O 0.175252613 0.992959249 0.709941460
> O 0.675260736 0.992953207 0.709933905
> O 0.324739294 0.007046799 0.290066095
> O 0.824747357 0.007040757 0.290058540
> O 0.371508681 0.399412719 0.459931561
> O 0.871509937 0.399409012 0.459929597
> O 0.128490063 0.600590988 0.540070403
> O 0.628491319 0.600587281 0.540068439
> O 0.378491935 0.600589896 0.959931149
> O 0.878493035 0.600590218 0.959930080
> O 0.121506965 0.399409782 0.040069905
> O 0.621508065 0.399410104 0.040068836
> O 0.324753467 0.507030327 0.709936158
> O 0.824758249 0.507031484 0.709937563
> O 0.175241721 0.492968516 0.290062437
> O 0.675246563 0.492969673 0.290063842
> O 0.425243174 0.492974405 0.209938014
> O 0.925241517 0.492963083 0.209937166
> O 0.074758520 0.507036917 0.790062849
> O 0.574756856 0.507025595 0.790062001
> O 0.121518578 0.899409145 0.959930613
> O 0.621518989 0.899409438 0.959931475
> O 0.378481011 0.100590547 0.040068510
> O 0.878481422 0.100590840 0.040069372
> O 0.128480180 0.100591392 0.459933045
> O 0.628486141 0.100588990 0.459929416
> O 0.371513859 0.899410995 0.540070584
> O 0.871519820 0.899408593 0.540066955
>
>
>
> Writing output data file CaWO4.save/
> NEW-OLD atomic charge density approx. for the potential
>
> negative rho (up, down): 1.178E+00 0.000E+00
> extrapolated charge 384.00680, renormalised to 384.00000
>
> total cpu time spent up to now is 3371.9 secs
>
> Self-consistent Calculation
>
> iteration # 1 ecut= 65.00 Ry beta= 0.20
> Davidson diagonalization with overlap
> ethr = 1.00E-06, avg # of iterations = 2.0
>
>
> Thanks in advance.
>
> Kind Regards,
> Vivek C
>
>
>
> __________________________________
> Vivek Christhunathan
> PhD researcher
> Mechanical Engineering
> College of Engineering and Informatics
> Room 2053
> Alice Perry Engineering Building
> National University of Ireland Galway
> Ireland
> E-mail: v.christhunathan1 at nuigalway.ie (https://link.getmailspring.com/link/78F32A0F-3925-4A88-B3C2-DCE9B9225768@getmailspring.com/4?redirect=mailto%3Av.christhunathan1%40nuigalway.ie&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
> Phone: +353 899811181, +91 9600752742
>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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