[QE-users] Crystal structure changes while doing vc-relax calculation.
Vivek Christhunathan
vivekppn at gmail.com
Mon Feb 7 16:47:45 CET 2022
Hi Lorenzo,
>$scan_ibrav.x
I tried it on my machine, and it printed exactly the same as your prior
message.
I received the following cell parameter values when I run the calculation
with these tags such as ibrav = 8, celldm( 1) = 19.820415000, celldm( 2) =
0.500000000, and celldm( 3) = 1.084549393.
*CELL_PARAMETERS (alat= 19.82041500)*
* 1.013661333 0.000011180 -0.000000334*
* 0.000005590 0.506839078 0.000000525*
* -0.000000363 0.000001138 1.097952283*
And also I received the following cell parameter values when I run the
calculation with these tags such as ibrav = 8, celldm( 1) =
19.820415000, celldm(
2) = 0.500000000, celldm( 3) = 1.084549393, and *cell_dofree = 'ibrav' *(Note:
I included cell_dofree here because ibrav>0).
*ibrav = 8*
* celldm(1) = 20.00638452*
* celldm(2) = 0.50013749*
* celldm(3) = 1.08713582*
*Input lattice vectors:*
* 1.00938273 0.00000000 0.00000000*
* 0.00000000 0.50483015 0.00000000*
* 0.00000000 0.00000000 1.09733611*
*New lattice vectors in INITIAL alat:*
* 1.00938273 0.00000000 0.00000000*
* 0.00000000 0.50483015 0.00000000*
* 0.00000000 0.00000000 1.09733611*
*New lattice vectors in NEW alat (for information only):*
* 1.00000000 0.00000000 0.00000000*
* 0.00000000 0.50013749 0.00000000*
* 0.00000000 0.00000000 1.08713582*
*Discrepancy in bohr = 0.000000 0.000000 0.000000*
* bfgs converged in 11 scf cycles and 10 bfgs steps*
* (criteria: energy < 1.0E-04 Ry, force < 1.0E-03Ry/Bohr, cell <
5.0E-01kbar)*
* End of BFGS Geometry Optimization*
* Final enthalpy = -2905.7085616081 Ry*
*Begin final coordinates*
* new unit-cell volume = 4353.90605 a.u.^3 ( 645.18230 Ang^3 )*
* density = 5.92828 g/cm^3*
*CELL_PARAMETERS (alat= 19.82041500)*
* 1.009382726 0.000000000 0.000000000*
* 0.000000000 0.504830148 0.000000000*
* 0.000000000 0.000000000 1.097336114*
Still I don't get the Tetragonal crystal structure of CaWO4, it only gives
the lattice parameter values a=5.291688 ang and b=5.293143 ang (a≠b).
Note: Tetrahedra
CaWO4 Unit-cell was used to make this CaWO4 supercell. Is there any other
way to relax CaWO4's structure without affecting its symmetry?
And also I'm not sure why ibrav = 8 is required if CaWO4 has a tetragonal
crystal structure. Because ibrav = 8 for Orthorhombic is described in the
QE-input description. It would be great if you could explain this to me.
Thank you very much in advance.
Kind Regards,
Vivek C
__________________________________
Vivek Christhunathan
PhD researcher
Mechanical Engineering
College of Engineering and Informatics
Alice Perry Engineering Building
National University of Ireland Galway
Ireland
E-mail: v.christhunathan1 at nuigalway.ie
Phone: +353 899811181, +91 9600752742
On Thu, Feb 3, 2022 at 3:55 PM Vivek Christhunathan <vivekppn at gmail.com>
wrote:
> Hi Lorenzo,
>
> Thank you very much for your response.
>
> Sorry for the earlier message. I did not get notified on this.
>
> >$ ~/espresso.BASE/PW/tools/scan_ibrav.x
>
> Yes, I will get used to it on this.
>
> As per your suggestion, I will use the following values for my calculation
> and let you know the results.
>
> 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
>
>
> Thanks a million.
>
> 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
> Phone: +353 899811181, +91 9600752742
>
>
>
> On Thu, Feb 3, 2022 at 2:05 PM Vivek Christhunathan <vivekppn at gmail.com>
> wrote:
>
>> Hello Everyone,
>>
>> I could not solve this issue even after trying with v6.8 (the older
>> version was v6.4.1). Still, the CaWO4 (2x1x1 supercell) changes its
>> symmetry from Tetragonal to Orthorhombic while doing structural
>> relaxation. Even I tried with multiple different input parameters.
>>
>> Can I get any suggestions regarding this, please?
>>
>> 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
>> Phone: +353 899811181, +91 9600752742
>>
>>
>>
>> On Tue, Feb 1, 2022 at 12:52 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:
>>> filebackports-6.4.1.diff*
>>>
>>> <https://github.com/QEF/q-e/releases/download/qe-6.4.1/backports-6.4.1.diff>
>>> in https://github.com/QEF/q-e/releases
>>>
>>>
>>> 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
>>> Phone: +353 899811181, +91 9600752742
>>>
>>>
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