[QE-users] Crystal structure changes while doing vc-relax calculation.
Vivek Christhunathan
vivekppn at gmail.com
Wed Feb 9 12:44:22 CET 2022
Hi Michal,
Thank you very much for your suggestion.
*>crystal_sg and correct space gropu nuber (space_group)>Correct ibrav
will be generated automatically , no need to eneter ...*
The space group number of CaWO4 unit-cell (ICSD no: 18135) is 88 since it
has I41/a space-group, but the Space group number of CaWO4 supercell (2x1x1)
is 1 as it has P1 space-group name (Note: I used VESTA tool make supercell).
I tried with both the sapace-group numbers. I received an error called "Error
in routine check_atoms (1): atoms # 1 and # 62 overlap!" when I used
space_group=88. I think this is because of the space-group changes when we
make supercell from the CaWO4 unit-cell (using VESTA tool).
In v6.4.1, I used space_group=1 for the calculation but again symmetry of
the supercell changes (a≠b). I have included my input for your reference.
*&controlcalculation = 'vc-relax'restart_mode = 'from_scratch'prefix =
'CaWO4'pseudo_dir = './'outdir = './outCaWO4'max_seconds =
3500,/&systemcelldm(1) = 19.820415celldm(2) = 0.500000000celldm(3) =
1.084549393space_group = 1nat = 48ntyp = 3ecutwfc = 65.0ecutrho =
780.0occupations= 'smearing'smearing= 'gaussian'degauss=
0.02/&electronsmixing_beta = 0.2,conv_thr = 1.0d-6,electron_maxstep =
50000,/&IONS/&cellcell_factor = 3.0d0/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.UPFATOMIC_POSITIONS (crystal_sg)Ca
0.000000000 0.250000000 0.625000000Ca 0.500000000
0.250000000 0.625000000Ca 0.000000000 0.750000000
0.375000000Ca 0.500000000 0.750000000 0.375000000Ca
0.250000000 0.750000000 0.125000000Ca 0.750000000
0.750000000 0.125000000Ca 0.250000000 0.250000000
0.875000000Ca 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
0.540300012K_POINTS AUTOMATIC2 2 2 1 1 1 *
Can anyone please explain why my system 'CaWO4 supercell' keep on changing
its symmetry and why I am not able to control it?
Thanks 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 Mon, Feb 7, 2022 at 3:47 PM Vivek Christhunathan <vivekppn at gmail.com>
wrote:
> 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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