[QE-users] Crystal structure changes while doing vc-relax calculation.
Husak Michal
Michal.Husak at vscht.cz
Wed Feb 9 19:54:04 CET 2022
If you use space group for QE setting, you can enter ONLY the symmetry
independent atoms ... Othervise QE will generate the atoms based on symetry multiple times = overlap.
If your supercell keep the original symetry it will work ...
If your supercell does not have the original symmetry and it realy have
P1 group, QE nor other code can keep the lattice parameters symmetric,
becouse they must differ .... There is no forces/sg symmetry forcing the lattice parameters to keep original symmetry ... P1 is triclinic ...
I am primary a crystallographer (developing just crystallographic GUI for QE), I do not 100% understand QE internal processing - I belive QE try to find symmetry itself and keep it. If none found, none restraines used ....
Can you please:
1) Send me the starting structure in CIF format ?
2) Send me the supercell you need to process in CIF format ?
In such case I can try our CIF -> QE conversion engine and see whatever I can generete what you need ....
Michal Husak
husakm at vscht.cz
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Vivek Christhunathan <vivekppn at gmail.com>
Sent: Wednesday, February 9, 2022 12:44:22 PM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Crystal structure changes while doing vc-relax calculation.
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.
&control
calculation = 'vc-relax'
restart_mode = 'from_scratch'
prefix = 'CaWO4'
pseudo_dir = './'
outdir = './outCaWO4'
max_seconds = 3500,
/
&system
celldm(1) = 19.820415
celldm(2) = 0.500000000
celldm(3) = 1.084549393
space_group = 1
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
/
&cell
cell_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.UPF
ATOMIC_POSITIONS (crystal_sg)
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
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<mailto:v.christhunathan1 at nuigalway.ie>
Phone: +353 899811181, +91 9600752742
[https://docs.google.com/uc?export=download&id=1oPtxd7PT5ljQRnuP-Gdf5upjiKPXk7Fz&revid=0B_S3ZLbRRu26NW1YallITFk1ZHMxaStQaUVoMjZ4M2NqcC9BPQ]
On Mon, Feb 7, 2022 at 3:47 PM Vivek Christhunathan <vivekppn at gmail.com<mailto: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<mailto:v.christhunathan1 at nuigalway.ie>
Phone: +353 899811181, +91 9600752742
[https://docs.google.com/uc?export=download&id=1oPtxd7PT5ljQRnuP-Gdf5upjiKPXk7Fz&revid=0B_S3ZLbRRu26NW1YallITFk1ZHMxaStQaUVoMjZ4M2NqcC9BPQ]
On Thu, Feb 3, 2022 at 3:55 PM Vivek Christhunathan <vivekppn at gmail.com<mailto: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<mailto:v.christhunathan1 at nuigalway.ie>
Phone: +353 899811181, +91 9600752742
[https://docs.google.com/uc?export=download&id=1oPtxd7PT5ljQRnuP-Gdf5upjiKPXk7Fz&revid=0B_S3ZLbRRu26NW1YallITFk1ZHMxaStQaUVoMjZ4M2NqcC9BPQ]
On Thu, Feb 3, 2022 at 2:05 PM Vivek Christhunathan <vivekppn at gmail.com<mailto: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<mailto:v.christhunathan1 at nuigalway.ie>
Phone: +353 899811181, +91 9600752742
[https://docs.google.com/uc?export=download&id=1oPtxd7PT5ljQRnuP-Gdf5upjiKPXk7Fz&revid=0B_S3ZLbRRu26NW1YallITFk1ZHMxaStQaUVoMjZ4M2NqcC9BPQ]
On Tue, Feb 1, 2022 at 12:52 PM Vivek Christhunathan <vivekppn at gmail.com<mailto: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>
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<mailto:v.christhunathan1 at nuigalway.ie>
Phone: +353 899811181, +91 9600752742
[https://docs.google.com/uc?export=download&id=1oPtxd7PT5ljQRnuP-Gdf5upjiKPXk7Fz&revid=0B_S3ZLbRRu26NW1YallITFk1ZHMxaStQaUVoMjZ4M2NqcC9BPQ]
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