[QE-users] Applying assume_isolated="2D" to modified anatase surface
Pietro Davide Delugas
pdelugas at sissa.it
Thu Dec 1 13:45:22 CET 2022
Hello
These are your axes
0.000000000000000 3.000000000000000 0.000000000000000
1.000000000000000 -0.000000000000000 -2.539341738883929
8.550000000000001 0.000000000000000 0.000000000000000
And this is the complaint of the code
2D CODE WILL NOT WORK, 2D MATERIAL NOT IN X-Y PLANE!!
Your surface is in the ZY plane. You need to reorient your system so that the surface stays in the XY plane.
You might still have problems, though, because the out of plane lattice vector is not orthogonal to the surface.
Pietro
From: users <users-bounces at lists.quantum-espresso.org> On Behalf Of Léon Luntadila Lufungula
Sent: Thursday, December 1, 2022 12:13 PM
To: users at lists.quantum-espresso.org
Subject: [QE-users] Applying assume_isolated="2D" to modified anatase surface
Dear QE users,
I recently learned that you have to apply a dipole correction when adsorbing molecules onto a surface when working under PBC. I know you can do this manually via the dipfield option, but the assume_isolated=”2D” option should have the same effect with the added benefit of truncating the Coulomb interaction in the z-direction. I have tried to re-do one of my calculations with this option enabled but I get the following error:
2D CODE WILL NOT WORK, 2D MATERIAL NOT IN X-Y PLANE!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine vloc_of_g (1):
2D cutoff is smaller than pseudo cutoff radius: increase interlayer distance (or see Modules/read_pseudo.f90)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Can somebody tell me how I can get this to work in my system? I don’t see how my material is not in the X-Y plane when looking at my structure. Could it be a problem because my cell is not orthogonal?
I don’t know if attachments work, so I’ll add my input description here (I only added the assume_isolated=”2D” flag compared to the original calculation):
&CONTROL
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a101-3mppa-md1-2d'
pseudo_dir = '/data/antwerpen/206/vsc20615/temp/quantumespresso/PSEUDOPOTENTIALS'
outdir = '/scratch/antwerpen/206/vsc20615/quantumespresso/a101-3mppa-md1-2d'
nstep = 200
verbosity = 'high'
/
&SYSTEM
ibrav = 0
A = 3.77449
nat = 125
ntyp = 6
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
vdw_corr = "grimme-d2"
assume_isolated = "2D"
! nr1 = 180
! nr2 = 160
! nr3 = 480
/
&ELECTRONS
electron_maxstep = 500
diagonalization = 'david'
conv_thr = 1.0d-10
mixing_beta = 0.70
/
&IONS
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF
H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
P 30.973761 P.wc-n-kjpaw_psl.1.0.0.UPF
S 32.0600 S.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Ti 0.000000000 0.000000000 0.026316000 0 0 0
Ti 0.666667000 0.000000000 0.026316000 0 0 0
Ti 0.333333000 0.000000000 0.026316000 0 0 0
Ti 0.166667000 0.500000000 0.026316000 0 0 0
Ti 0.500000000 0.500000000 0.026316000 0 0 0
Ti 0.833333000 0.500000000 0.026316000 0 0 0
Ti 0.000824658 0.992331197 0.264938249
Ti 0.334135046 0.995049704 0.264624893
Ti 0.667613401 0.992398327 0.264893895
Ti 0.168926625 0.489197175 0.261993802
Ti 0.499777376 0.489341171 0.261832125
Ti 0.834286595 0.493562288 0.264858957
Ti 0.000057357 0.987892876 0.144759568
Ti 0.333795375 0.994450512 0.144007883
Ti 0.667723487 0.987841633 0.144749798
Ti 0.167624322 0.486336635 0.144288179
Ti 0.833927173 0.487390518 0.144773288
Ti 0.500148725 0.486358394 0.144260258
Ti 0.000460100 0.237804472 0.170484800
Ti 0.667233312 0.237885209 0.170448961
Ti 0.333852171 0.235526018 0.175041344
Ti 0.168398115 0.741530329 0.169439965
Ti 0.499182489 0.741792231 0.169370400
Ti 0.833844439 0.738095532 0.170226827
Ti 0.000000000 0.250000000 0.055556000 0 0 0
Ti 0.333333000 0.250000000 0.055556000 0 0 0
Ti 0.666667000 0.250000000 0.055556000 0 0 0
Ti 0.166667000 0.750000000 0.055556000 0 0 0
Ti 0.833333000 0.750000000 0.055556000 0 0 0
Ti 0.500000000 0.750000000 0.055556000 0 0 0
Ti -0.000849135 0.241620902 0.283991654
Ti 0.334211578 0.229486912 0.294789499
Ti 0.669259871 0.241661770 0.283943878
Ti 0.167941078 0.743027462 0.282833203
Ti 0.500298838 0.743518834 0.282674577
Ti 0.834126861 0.742296000 0.283914549
O 0.000000000 0.792604000 0.050573000 0 0 0
O 0.666667000 0.792604000 0.050573000 0 0 0
O 0.333333000 0.792604000 0.050573000 0 0 0
O 0.166667000 0.292603000 0.050573000 0 0 0
O 0.500000000 0.292603000 0.050573000 0 0 0
O 0.833333000 0.292603000 0.050573000 0 0 0
O 0.000999902 0.783997574 0.290644302
O 0.334194354 0.782131036 0.289864123
O 0.667315797 0.784210346 0.290600729
O 0.165022435 0.285293931 0.288688459
O 0.503402803 0.285414366 0.288633679
O 0.834202275 0.284726475 0.291829067
O 0.000328547 0.782573684 0.166458648
O 0.333763074 0.782094072 0.166486451
O 0.667375878 0.782525490 0.166428258
O 0.167196314 0.280774534 0.168158388
O 0.833857737 0.281487490 0.166486492
O 0.500533758 0.280806577 0.168126558
O 0.000646472 0.446942502 0.148138954
O 0.667028635 0.447056244 0.148130898
O 0.333832262 0.446912009 0.149006038
O 0.167435932 0.948443020 0.148023522
O 0.500160423 0.948420706 0.147970167
O 0.833815451 0.948371263 0.148089448
O 0.000000000 0.457396000 0.031299000 0 0 0
O 0.333333000 0.457396000 0.031299000 0 0 0
O 0.666667000 0.457396000 0.031299000 0 0 0
O 0.166667000 0.957398000 0.031298000 0 0 0
O 0.833333000 0.957398000 0.031298000 0 0 0
O 0.500000000 0.957398000 0.031298000 0 0 0
O 0.000182502 0.455103259 0.265406655
O 0.334217463 0.454182236 0.265386721
O 0.668275913 0.455113562 0.265283540
O 0.167329550 0.952869715 0.266041159
O 0.500976826 0.953007465 0.266063759
O 0.834173758 0.954309912 0.266193670
O 0.167225159 0.528205014 0.079851481
O 0.833501149 0.528933548 0.079684771
O 0.499798809 0.528195196 0.079854300
O 0.000112744 0.028909917 0.079703966
O 0.333513512 0.029310025 0.079609205
O 0.666824884 0.028885840 0.079701780
O 0.168927393 0.552195069 0.311862455
O 0.500571116 0.552647575 0.311599738
O 0.834128121 0.554244676 0.312443095
O 0.001667002 0.053292910 0.312465752
O 0.334125750 0.041489697 0.314643237
O 0.666824841 0.053356919 0.312418201
O 0.167074901 0.534322574 0.197303614
O 0.500957026 0.534453287 0.197252476
O 0.834095888 0.534153834 0.197415660
O 0.000656870 0.033252329 0.197686285
O 0.667173613 0.033248085 0.197668359
O 0.334064313 0.032371261 0.198159864
O 0.001261584 0.194859151 0.119262607
O 0.666176302 0.194863415 0.119249014
O 0.333617170 0.195806181 0.120022086
O 0.166511195 0.693813129 0.119146228
O 0.833748973 0.694242339 0.119183090
O 0.500653091 0.693865672 0.119119289
O 0.000000000 0.207396000 0.002059000 0 0 0
O 0.333333000 0.207396000 0.002059000 0 0 0
O 0.666667000 0.207396000 0.002059000 0 0 0
O 0.166667000 0.707397000 0.002059000 0 0 0
O 0.500000000 0.707397000 0.002059000 0 0 0
O 0.833333000 0.707397000 0.002059000 0 0 0
O -0.002833921 0.208797549 0.233695444
O 0.334081147 0.205057932 0.237064131
O 0.671094794 0.208883738 0.233641915
O 0.165998811 0.710283185 0.232877352
O 0.501855504 0.710591340 0.232747947
O 0.834046683 0.710385014 0.233486355
P 0.337744915 0.299655874 0.389987571
O 0.334392761 0.232493133 0.354696138
O 0.454064087 0.383366154 0.386837757
H 0.475874889 0.456048986 0.354982614
O 0.224881710 0.388759446 0.387378347
H 0.199773273 0.457858542 0.355474070
C 0.338658788 0.171092313 0.445085474
H 0.258917787 0.106622145 0.448843615
H 0.415955064 0.103932102 0.447364310
C 0.343855835 0.236865735 0.480533751
H 0.421119565 0.306204721 0.474551370
H 0.264862358 0.301600934 0.478018945
C 0.351618891 0.124349150 0.526761244
H 0.432463886 0.062465297 0.529674497
H 0.274773960 0.054552295 0.532970920
S 0.354786587 0.207513983 0.567892849
H 0.359959849 0.088820581 0.604398345
CELL_PARAMETERS {alat}
0.000000000000000 3.000000000000000 0.000000000000000
1.000000000000000 -0.000000000000000 -2.539341738883929
8.550000000000001 0.000000000000000 0.000000000000000
K_POINTS {automatic}
2 2 1 1 1 0
Thanks in advance and kind regards,
Léon Luntadila Lufungula
PhD student
University of Antwerp
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