[CP2K-user] [CP2K:19047] Re: TiO2 slab not converging

[Léon Luntadila Lufungula]

Hi Prof. Hutter,

Thanks for solving this issue, it is very much appreciated!

Best,
Léon

On Friday, 30 June 2023 at 13:33:21 UTC+2 Jürg Hutter wrote:

> 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: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Léon 
> Luntadila Lufungula <Leon.luntad... 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 <(354)%20999-5422><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 <(354)%20999-5422><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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