[CP2K-user] [CP2K:19039] Re: TiO2 slab not converging
Jürg Hutter
hutter at chem.uzh.ch
Fri Jun 30 11:33:13 UTC 2023
Hi
I generalized the CP2K CIF parser, so that _atom_site_label is no longer required to be the first of
the _atom_site descriptors.
Thanks for reporting.
JH
________________________________________
From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntadilalufungula at uantwerpen.be>
Sent: Thursday, June 29, 2023 11:41 AM
To: cp2k
Subject: Re: [CP2K:19030] Re: TiO2 slab not converging
So I dug a bit deeper into why the CIF from ASE could not be properly read by CP2K even though it looks correct and apparently something goes wrong when CP2K reads in the CIF file. I noticed this because the same problem happened when I took a molecule in a 25x25x25 Å box from a CIF (created by Critic2, see attachment 3mppa.cif) which could be read by CP2K and used ASE to alter the vacuum size and center the molecule and suddenly the resulting CIF could no longer be properly read by CP2K (i.e., I got errors stating atoms are too close). I noticed that even when just reading in and writing out the CIF with ASE (see attachment 3mppa-ase.cif) already showed atoms too close to one another when read into CP2K:
Atom Kind Element X Y Z Z(eff) Mass
1 1 H 1 7.070300 9.682957 5.879925 1.0000 1.0079
2 2 O 8 7.070300 9.423014 6.500614 6.0000 15.9994
3 1 H 1 7.070300 5.945227 5.744394 1.0000 1.0079
4 2 O 8 7.070300 6.657800 6.398468 6.0000 15.9994
5 3 P 15 7.070300 8.447808 5.896924 5.0000 30.9738
6 2 O 8 7.070300 8.566346 4.554013 6.0000 15.9994
7 1 H 1 7.070300 9.631506 8.443233 1.0000 1.0079
8 1 H 1 7.070300 7.722120 8.375391 1.0000 1.0079
9 4 C 6 7.070300 8.978791 8.136181 4.0000 12.0107
10 4 C 6 7.070300 9.143231 6.759885 4.0000 12.0107
11 1 H 1 7.070300 10.392672 6.492497 1.0000 1.0079
12 5 S 16 7.070300 9.397121 10.419543 6.0000 32.0650
13 1 H 1 7.070300 8.473533 6.425727 1.0000 1.0079
14 4 C 6 7.070300 9.608639 8.784895 4.0000 12.0107
15 1 H 1 7.070300 10.868673 8.560234 1.0000 1.0079
16 1 H 1 7.070300 8.934066 8.505103 1.0000 1.0079
17 1 H 1 7.070300 9.995695 10.760287 1.0000 1.0079
*** WARNING in particle_methods.F:677 :: The distance between the atoms 2 ***
*** and 10 is only 0.381 angstrom and thus smaller than the threshold of ***
*** 0.500 angstrom ***
*** WARNING in particle_methods.F:677 :: The distance between the atoms 7 ***
*** and 14 is only 0.342 angstrom and thus smaller than the threshold of ***
*** 0.500 angstrom ***
*** WARNING in particle_methods.F:677 :: The distance between the atoms 9 ***
*** and 16 is only 0.372 angstrom and thus smaller than the threshold of ***
*** 0.500 angstrom ***
Notice that all the x-coordinates are the same, even though the fractional x-coordinates in the CIF are different for all atoms... I noticed that by switching the order of the lines "_atom_site_type_symbol" and "_atom_site_label" in the CIF (see 3mppa-ase-edited.cif) CP2K could correctly read in the CIF file without a hitch.
Atom Kind Element X Y Z Z(eff) Mass
1 1 H 1 8.143430 6.455697 4.999966 1.0000 1.0079
2 2 O 8 7.924816 7.137164 5.661084 6.0000 15.9994
3 3 H 1 4.999975 6.306894 6.438132 1.0000 1.0079
4 4 O 8 5.599253 7.025016 6.709042 6.0000 15.9994
5 5 P 15 7.104662 6.474360 6.880102 5.0000 30.9738
6 6 O 8 7.204353 4.999949 6.935846 6.0000 15.9994
7 7 H 1 8.100160 9.270007 7.237998 1.0000 1.0079
8 8 H 1 6.494353 9.195522 7.971859 1.0000 1.0079
9 9 C 6 7.551222 8.932889 8.129596 4.0000 12.0107
10 10 C 6 7.689517 7.421824 8.281361 4.0000 12.0107
11 11 H 1 8.740305 7.128253 8.426234 1.0000 1.0079
12 12 S 16 7.903040 11.439841 9.116297 6.0000 32.0650
13 13 H 1 7.126297 7.054944 9.153051 1.0000 1.0079
14 14 C 6 8.080929 9.645126 9.361478 4.0000 12.0107
15 15 H 1 9.140625 9.398466 9.518603 1.0000 1.0079
16 16 H 1 7.513608 9.337936 10.250780 1.0000 1.0079
17 17 H 1 8.406445 11.813951 10.314334 1.0000 1.0079
Perhaps someone with more knowledge about the process of reading in a CIF file in CP2K can take a look at the code and where/why it does not work if the two labels are in the original order and maybe fix this in an upcoming version?
Best,
Léon
On Wednesday, 28 June 2023 at 16:52:05 UTC+2 Léon Luntadila Lufungula wrote:
Hi Matthias,
Thanks a lot, now it does not throw the error anymore. I'll keep you updated if this fixes the convergence issues but I suspect it will. Again, thanks for the help!
All the best,
Léon
On Wednesday, 28 June 2023 at 16:37:28 UTC+2 Krack Matthias wrote:
Hi Léon
Try
&CELL
A 10.2988004684 0.0000000000 0.0000000000
B 0.0000000000 11.3549995422<tel:(354)%20999-5422> 0.0000000000
C 0.0000000000 0.0000000000 49.3899002075
&END CELL
&COORD
O 9.300228691 0.000000000 19.999946640
O 9.300228691 3.784962059 19.999946640
O 9.300228691 7.570037822 19.999946640
. . . further 69 O atoms
36 Ti atoms
&END COORD
HTH
Matthias
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntad... at uantwerpen.be>
Date: Wednesday, 28 June 2023 at 16:29
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:19022] Re: TiO2 slab not converging
Hi Matthias,
So I opened the CIF file in VESTA and did Export Data > VASP file > Save > Cartesian coordinates > Output current unit cell and this resulted in the file shown below, but I don't see how this will "easily" cut&paste into a CP2K input file as the atom labels are missing...
"O72 Ti36"
1.0
10.2988004684 0.0000000000 0.0000000000
0.0000000000 11.3549995422<tel:(354)%20999-5422> 0.0000000000
0.0000000000 0.0000000000 49.3899002075
O Ti
72 36
Cartesian
9.300228691 0.000000000 19.999946640
9.300228691 3.784962059 19.999946640
9.300228691 7.570037822 19.999946640
4.151034406 1.892992021 20.000439738
4.151034406 5.677953911 20.000439738
4.151034406 9.463029336 20.000439738
7.074658142 1.892992021 20.879580124
7.074658142 5.677953911 20.879580124
7.074658142 9.463029336 20.879580124
1.923610010 0.000000000 20.880567792
1.923610010 3.784962059 20.880567792
1.923610010 7.570037822 20.880567792
5.583803656 0.000000000 21.468802556
5.583803656 3.784962059 21.468802556
5.583803656 7.570037822 21.468802556
0.433682486 1.892992021 21.469295653
0.433682486 5.677953911 21.469295653
0.433682486 9.463029336 21.469295653
3.357409004 1.892992021 22.348436040
3.357409004 5.677953911 22.348436040
3.357409004 9.463029336 22.348436040
8.505058213 0.000000000 22.349423707
8.505058213 3.784962059 22.349423707
8.505058213 7.570037822 22.349423707
0.392487277 0.000000000 23.519964286
0.392487277 3.784962059 23.519964286
0.392487277 7.570037822 23.519964286
5.542093345 1.892992021 23.520458855
5.542093345 5.677953911 23.520458855
5.542093345 9.463029336 23.520458855
8.465716774 1.892992021 24.399597769
8.465716774 5.677953911 24.399597769
8.465716774 9.463029336 24.399597769
3.314668949 0.000000000 24.400586909
3.314668949 3.784962059 24.400586909
3.314668949 7.570037822 24.400586909
6.974965416 0.000000000 24.988818729
6.974965416 3.784962059 24.988818729
6.974965416 7.570037822 24.988818729
1.824741540 1.892992021 24.989807868
1.824741540 5.677953911 24.989807868
1.824741540 9.463029336 24.989807868
4.748467944 1.892992021 25.868455157
4.748467944 5.677953911 25.868455157
4.748467944 9.463029336 25.868455157
9.896220587 0.000000000 25.869935922
9.896220587 3.784962059 25.869935922
9.896220587 7.570037822 25.869935922
1.783546255 0.000000000 27.040476500
1.783546255 3.784962059 27.040476500
1.783546255 7.570037822 27.040476500
6.933152591 1.892992021 27.040476500
6.933152591 5.677953911 27.040476500
6.933152591 9.463029336 27.040476500
9.856776020 1.892992021 27.919615415
9.856776020 5.677953911 27.919615415
9.856776020 9.463029336 27.919615415
4.705727889 0.000000000 27.921099124
4.705727889 3.784962059 27.921099124
4.705727889 7.570037822 27.921099124
8.366024662 0.000000000 28.508839318
8.366024662 3.784962059 28.508839318
8.366024662 7.570037822 28.508839318
3.215800326 1.892992021 28.509825513
3.215800326 5.677953911 28.509825513
3.215800326 9.463029336 28.509825513
6.139527190 1.892992021 29.388472802
6.139527190 5.677953911 29.388472802
6.139527190 9.463029336 29.388472802
0.988478905 0.000000000 29.389953567
0.988478905 3.784962059 29.389953567
0.988478905 7.570037822 29.389953567
7.442016174 0.000000000 20.734373862
7.442016174 3.784962059 20.734373862
7.442016174 7.570037822 20.734373862
2.292821888 1.892992021 20.734868432
2.292821888 5.677953911 20.734868432
2.292821888 9.463029336 20.734868432
5.215518701 1.892992021 21.614008818
5.215518701 5.677953911 21.614008818
5.215518701 9.463029336 21.614008818
0.065397382 0.000000000 21.614996485
0.065397382 3.784962059 21.614996485
0.065397382 7.570037822 21.614996485
8.833075420 0.000000000 24.254391507
8.833075420 3.784962059 24.254391507
8.833075420 7.570037822 24.254391507
3.683880827 1.892992021 24.254886077
3.683880827 5.677953911 24.254886077
3.683880827 9.463029336 24.254886077
6.606680461 1.892992021 25.134024991
6.606680461 5.677953911 25.134024991
6.606680461 9.463029336 25.134024991
1.456456432 0.000000000 25.135014131
1.456456432 3.784962059 25.135014131
1.456456432 7.570037822 25.135014131
10.224134052 0.000000000 27.774409152
10.224134052 3.784962059 27.774409152
10.224134052 7.570037822 27.774409152
5.074939767 1.892992021 27.774903722
5.074939767 5.677953911 27.774903722
5.074939767 9.463029336 27.774903722
7.997739707 1.892992021 28.654537206
7.997739707 5.677953911 28.654537206
7.997739707 9.463029336 28.654537206
2.847515371 0.000000000 28.655031776
2.847515371 3.784962059 28.655031776
2.847515371 7.570037822 28.655031776
On Wednesday, 28 June 2023 at 16:15:00 UTC+2 Krack Matthias wrote:
Hi Léon
You can export cell and coordinates as a POSCAR file in VESTA and from that file you can easily cut&paste CP2K’s &CELL and &COORD section.
HTH
Matthias
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntad... at uantwerpen.be>
Date: Wednesday, 28 June 2023 at 16:10
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:19020] Re: TiO2 slab not converging
Hi Matthias,
Thanks a lot for the tip! The output when using the pre-compiled binary shows that some atoms are indeed too close together, which is probably the cause of the bad convergence. Is there an easy way to fix this?
I made the slabs with ASE so I'm quite surprised that it did not make the slabs correctly. Here is the script I used to make them with ASE, perhaps you can see where I made a mistake, resulting in the faulty CIF files...
from ase.io<http://ase.io> import read, write
from ase.visualize import view
from ase.build.surfaces_with_termination import surfaces_with_termination
from ase.build.tools import sort
ana = read('anatase_opt_tzvp.pdb')
for N in range(2,13):
s = surfaces_with_termination(ana, (1,0,1), N, vacuum=20, termination='O')
s = s[1]
s = s.repeat((1,3,1))
s = sort(s, tags=s.positions[:, 2])
name = f'a101-{N}-layer'
write(f'{name}.cif', s)
Léon
On Wednesday, 28 June 2023 at 15:58:25 UTC+2 Krack Matthias wrote:
Hi Léon
You are using CP2K version 8.2. Newer CP2K versions perform a distance check for CP2K/Quickstep by default (see also this input keyword<https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/PRINT/INTERATOMIC_DISTANCES.html#CHECK_INTERATOMIC_DISTANCES>) when the system is smaller than 2000 atoms and prints a warning if a small distance is found.
You can download a pre-compiled binary of CP2K 2023.1 here<https://github.com/cp2k/cp2k/releases/download/v2023.1/cp2k-2023.1-Linux-gnu-x86_64.ssmp>, which is sufficient for that initial check.
HTH
Matthias
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntad... at uantwerpen.be>
Date: Wednesday, 28 June 2023 at 15:46
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:19017] Re: TiO2 slab not converging
Hi Matthias,
Thanks for you reply!
I looked at my CIF file in various visualization software and it looked okay there. Is there a way to check this via CP2K to be sure?
I also have some preliminary results of some ongoing calculations with DIIS/FULL_ALL and DIIS/FULL_SINGLE_INVERSE and these seem to be a bit faster than CG but reaching convergence is still a big issue (see attachments).
Best,
Léon
On Wednesday, 28 June 2023 at 15:35:32 UTC+2 Krack Matthias wrote:
Hi Léon
Did you check the set of atomic coordinates read from the cif file for close contacts possibly caused by the periodic boundary conditions?
Best
Matthias
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntad... at uantwerpen.be>
Date: Wednesday, 28 June 2023 at 14:16
To: cp2k <cp... at googlegroups.com>
Subject: [CP2K:19014] Re: TiO2 slab not converging
I forgot to add the cif file which is read with the input, so here it is if someone needs it.
On Wednesday, 28 June 2023 at 13:54:37 UTC+2 Léon Luntadila Lufungula wrote:
Update:
I tried to optimize a 3-layer slab with altered SCF cycle settings (inner loop: 15 steps, outer loop: 45 steps) and still it does not converge. The convergence goes towards 2E-7 after 22 outer SCF cycles, but then doesn't seem to get lower (see attachment a101-3-layer-jobID_188.out). I tried to restart the calculation with altered EPS_SCF (= 1E-6) and then the restarted SCF cycle converges as the convergence was already below 1E-6. Unfortunately, after that the SCF again seems to only very slowly converge, after 27 outer SCF steps it's still only at 8E-5 convergence (see attachment a101-3-layer-jobID_189.out). Can anybody please help me out? I feel like the calculation is not converging properly, as after nearly 2 hours it still hasn't converged one SCF cycle but I don't know what might be wrong orhow to fix it... Requiring 300+ steps to reach SCF convergence seems quite high to me and makes me start to think there is something fundamentally wrong with my input. If anyone could look at my inputs and tell me what's wrong with them, I would be forever thankful!
Kind regards,
Léon
P.S. Could the TZVP basis set pose a problem? I often see people use DZVP-SR for similar calculations, but my promotor and co-promotor both told me that TZVP is required for proper energetics and should be used in production runs.
On Wednesday, 28 June 2023 at 10:04:07 UTC+2 Léon Luntadila Lufungula wrote:
Dear all,
I am trying to determine the ideal slab thickness for an anatase (101) slab but my SCF cycles are not converging. I optimized the cutoffs for the anatase bulk and did a CELL_OPT calculation on the unit cell to get the converged structure. From this optimized unit cell, I then used ASE to build the (101) slabs with a 20 Å vacuum width and thicknesses varying from 2 to 12 layers. During the GEO_OPT calculation I keep the bottom layer frozen to act as the bulk. I started the 2-layer calculation yesterday but when I looked at the output today, I see that the SCF cycle fails at every step of the geometry optimization (see output in attachment). Is there something wrong with my setup (too tight convergence criteria, wrong SCF setup, ...), or is it because a 2-layer structure is perhaps too small? The changes in energy go to 1E-5 - 1E-6 but never reach the convergence criteria of 1E-7 even after 300 steps (inner cycle: 10 steps, outer cycle 30 steps). I would guess that it could converge if I would increase the maximum number of steps, but 300 steps already seems quite a lot to me, although I could be wrong...
If anyone could share their thoughts on the situation so I can continue my work, I would greatly appreciate the help! Thanks in advance!
Best regards,
Léon
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