[CP2K-user] [CP2K:17721] Re: Large discrepancy in xTB results from CP2K vs DFTB+
Xavier Bidault
jazzquark at gmail.com
Wed Sep 21 01:16:35 UTC 2022
Hi Jürg,
I went further with the tests today, now varying COULOMB_SR_CUT (see
pictures below). Actually, I like the idea of depending neither on
COULOMB_SR_CUT
nor on system size with COULOMB_SR_EPS = 1e-3, even though the resulting
volume is 12.7% underestimated. But I would appreciate your insights on why
it behaves like this (for COULOMB_SR_EPS = 1e-3). You talked earlier about
per-element cutoffs. Is that it? And if so, are these per-element cutoffs
parameters of xTB as published?
[image: image.png][image: image.png][image: image.png]
Thanks,
Xavier
On Tue, Sep 20, 2022 at 5:53 AM Jürg Hutter <hutter at chem.uzh.ch> wrote:
> Hi
> I can only guess here. The stress tensor might be a weak point of this
> type of spherical cutoff
> implementation of long-ranged forces. Subtle changes of symmetry (size of
> your computational box,
> k-points) together with the cutoff radius might cause changes in the
> stress tensor.
> regards
> JH
>
> ________________________________________
> From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Xavier
> Bidault <jazzquark at gmail.com>
> Sent: Tuesday, September 20, 2022 4:06 AM
> To: cp2k at googlegroups.com
> Subject: Re: [CP2K:17714] Re: Large discrepancy in xTB results from CP2K
> vs DFTB+
>
> I just tried with GMAX = 75 or 125 for replication 2x1x2 and
> COULOMB_SR_EPS = 1e-5, same result as above (lower energy than the unit
> cell and 3x2x3 supercell, lower volume and lower beta angle).
> So the problem may not be the Ewald part.
> Is there any known issue with small COULOMB_SR_EPS?
>
> On Mon, Sep 19, 2022 at 8:39 PM Xavier Bidault <jazzquark at gmail.com
> <mailto:jazzquark at gmail.com>> wrote:
> Hi Jürg,
>
> I have a funny behavior with COULOMB_SR_EPS though, with the size of the
> system (replication of the unit cell to supercell). See the figures below.
> For COULOMB_SR_EPS = 1e-2 to 1e-4, there is no variation with the system
> size, which is good. (Naively?)
> For COULOMB_SR_EPS >= 1e-5, there is a deviation, but only for the
> replication 2x1x2 of the supercell. I have checked with denser k-points
> 2x2x2 but the behavior is the same.
> Would that mean that COULOMB_SR_EPS = 1e-4 is the optimal value?
> What could explain this behavior for small COULOMB_SR_EPS??
> The automatic Ewald? The only difference is the G-space max. Miller index:
> 1x1x1 supercell -> 45 75 45
> 2x1x2 supercell -> 75 75 125
> 3x2x3 supercell -> 125 125 135
> Could that be it?
> Let me know what you think.
> [image.png][image.png][image.png]
> Thanks,
> Xavier
>
> On Mon, Sep 19, 2022 at 2:49 AM Jürg Hutter <hutter at chem.uzh.ch<mailto:
> hutter at chem.uzh.ch>> wrote:
> Hi
>
> thank you for the quick tests. It seems to me that the small
> COULOMB_SR_EPS has the
> effect that all cutoff values are determined by COULOMB_SR_CUT (20 bohr).
> This is the reason all your results for 10^-5 and smaller are identical.
> I will further investigate how to treat the 1/r^3 terms more efficiently,
> but this
> will not have a high priority.
>
> best regards
>
> JH
>
> ________________________________________
> From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <
> cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Xavier
> Bidault <jazzquark at gmail.com<mailto:jazzquark at gmail.com>>
> Sent: Sunday, September 18, 2022 9:47 PM
> To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>
> Subject: Re: [CP2K:17710] Re: Large discrepancy in xTB results from CP2K
> vs DFTB+
>
> Hi again,
>
> I found the documentation online for COULOMB_SR_EPS and COULOMB_SR_CUT.
> You'll find below more complete results of simulations using the last CP2K
> update (git:d529ce5) and variable-cell optimization of beta-HMX (unit cell
> and 3x2x3 k-points).
>
> 1) EPS_DEFAULT (1e-n below) dependency (with SCF 1e-8 and default
> COULOMB_SR_EPS 1e-3):
> EPS_DEFAULT(1e-n) Energy(Ha) Volume(A3) beta(°)
> 6 -151.006625427635726 451.587706 101.776164
> 7 -151.006672807135971 451.590652 101.780407
> 8 -151.006676191174904 451.591670 101.780813
> 9 -151.006676832199673 451.591242 101.780877
> 10 -151.006676871358280 451.591222 101.780881
> 11 -151.006676887368030 451.591220 101.780880
>
> -> Good convergence! No more weird variations. EPS_DEFAULT = 1e-8 is
> perfectly usable.
>
> 2) COULOMB_SR_EPS (1e-n below) dependency (with SCF 1e-8 and EPS_DEFAULT
> 1e-8):
> COULOMB_SR_EPS(1e-n) Energy(Ha) Volume(A3) beta(°)
> 2 -151.026393509116332 466.813094 102.291412
> 3 -151.006676191174904 451.591670 101.780813
> 4 -151.001068739435084 467.465511 103.232087
> 5 -150.999031773201608 466.553038 103.882789
> 6 -150.999031773201438 466.553038 103.882789
> 7 -150.999031773201438 466.553038 103.882789
> 8 -150.999031773201438 466.553038 103.882789
> 9 -150.999031773201438 466.553038 103.882789
> 10 -150.999031773201438 466.553038 103.882789
>
> Actually, the default value or 1e-3 is the worst you could choose. I would
> recommend a default value for COULOMB_SR_EPS of 1e-5.
>
> The behavior of xTB at CP2K is much more stable, and I would consider this
> issue solved. I just have to re-run a huge batch of simulations in the next
> 2 weeks with this update before submitting my paper ;-)
>
> Thanks a lot!
> Xavier
>
>
> On Sun, Sep 18, 2022 at 9:50 AM Xavier Bidault <jazzquark at gmail.com
> <mailto:jazzquark at gmail.com><mailto:jazzquark at gmail.com<mailto:
> jazzquark at gmail.com>>> wrote:
> Hi Jürg,
>
> A quick test with EPS_DEFAULT of 1e-10 or 1e-11 yields practically the
> same variable-cell optimization now for bHMX. So that's better, even though
> I'll have to check it up with a larger panel of values and watch
> convergence.
>
> What are the default values you chose for these parameters?
> COULOMB_SR_EPS : atom dependent range
> COULOMB_SR_CUT : maximum range for all atoms
> Are they dependent on the (automatic) Ewald parameters?
> If I want to modify them, what would be the section in the input file?
> Are they "per atom" or global parameters?
>
> Thank you,
> Xavier
>
> On Fri, Sep 16, 2022 at 2:53 AM Jürg Hutter <hutter at chem.uzh.ch<mailto:
> hutter at chem.uzh.ch><mailto:hutter at chem.uzh.ch<mailto:hutter at chem.uzh.ch>>>
> wrote:
> I have updated the Trunk version with a new patch for xTB. This should now
> have the
> electrostatic energy calculated as originally expected. The long-range 1/r
> term is
> handled by an Ewald sum (using SPME) and the remaining terms with an 1/r^3
> contribution
> are cut at an atom dependent distance. The strong dependence of this term
> on the
> requested general accuracy (EPS_DEFAULT) should now be gone.
> The range (*2) of this interaction is controlled by two keywords
> COULOMB_SR_EPS : atom dependent range
> COULOMB_SR_CUT : maximum range for all atoms
> This neglects the long range character of the 1/r^3 terms that might
> affect especially the
> stress tensor.
>
> I hope this helps to stabilize simulations.
>
> best regards
> JH
>
> ________________________________________
> From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com><mailto:
> cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> <
> cp2k at googlegroups.com<mailto:cp2k at googlegroups.com><mailto:
> cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>> on behalf of Magnus
> Rahm <magnus at compulartech.com<mailto:magnus at compulartech.com><mailto:
> magnus at compulartech.com<mailto:magnus at compulartech.com>>>
> Sent: Wednesday, September 7, 2022 2:20 PM
> To: cp2k
> Subject: Re: [CP2K:17622] Re: Large discrepancy in xTB results from CP2K
> vs DFTB+
>
> Btw, I can confirm that the energy now converges with EPS_DEFAULT also for
> the LiO2 system, although the convergence is perhaps a bit slower (=very
> small EPS_DEFAULT values needed) than what one might have expected (see
> LiO2-EPS_DEFAULT.pdf). The figure I attached in my previous post was made
> with EPS_DEFAULT at the default value, if I use 1e-24 I get a bit closer to
> DFTB+ but still there is a weird slope in the E-V curve (EV-LiO2.pdf).
>
> Furthermore, I had a look at the energy broken down into its different
> contributions as a function of volume (LiO2-energies-split.pdf), and FWIW
> it indicates that the electronic energy is responsible for the unexpected
> slope in the E-V curve (perhaps that was already obvious?).
>
> > Could you remind me how to update CP2K 2022.1 to include this bug fix?
>
> I think the easiest approach is to use Docker (following these
> instructions: https://github.com/cp2k/cp2k/tree/master/tools/docker),
> unless you want to clone the CP2K repo from github and compile from scratch.
>
> Kind regards,
> Magnus Rahm
>
>
> On Wednesday, September 7, 2022 at 2:16:23 AM UTC+2 jazz... at gmail.com
> <mailto:jazz... at gmail.com><mailto:jazz... at gmail.com<mailto:
> jazz... at gmail.com>> wrote:
> Thank you. Could you remind me how to update CP2K 2022.1 to include this
> bug fix?
>
> On Tue, Sep 6, 2022 at 10:36 AM Jürg Hutter <hut... at chem.uzh.ch<mailto:
> hut... at chem.uzh.ch><mailto:hut... at chem.uzh.ch<mailto:hut... at chem.uzh.ch>>>
> wrote:
> Hi
>
> the updates are now on Github (Trunk version).
> This should at least fix the strange behavior for changes of EPS_DEFAULT.
>
> regards
>
> JH
>
> ________________________________________
> From: cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>> <
> cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>>> on behalf of Jürg
> Hutter <hut... at chem.uzh.ch<mailto:hut... at chem.uzh.ch><mailto:
> hut... at chem.uzh.ch<mailto:hut... at chem.uzh.ch>>>
> Sent: Tuesday, September 6, 2022 11:37 AM
> To: cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>>
> Subject: Re: [CP2K:17614] Re: Large discrepancy in xTB results from CP2K
> vs DFTB+
>
> Hi
>
> I think I found the problem. This is in fact a bug in CP2K and is related
> to the damping of
> the "short range" part of the Coulomb term. As mentioned before this short
> range part
> is not short range at all, even diverging in periodic systems. We use a
> damping function
> for this term and the radius is taken from the range of the basis function
> on each atom.
> The bug is now, that this range is not a constant but depends on
> EPS_DEFAULT.
> I will work on a solution, but at least the default settings will cause
> considerable changes
> in the energies of periodic systems.
>
> regards
>
> JH
>
> ________________________________________
> From: cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>> <
> cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>>> on behalf of
> Magnus Rahm <mag... at compulartech.com<mailto:mag... at compulartech.com
> ><mailto:mag... at compulartech.com<mailto:mag... at compulartech.com>>>
> Sent: Monday, September 5, 2022 3:19 PM
> To: cp2k
> Subject: Re: [CP2K:17609] Re: Large discrepancy in xTB results from CP2K
> vs DFTB+
>
> Hi,
>
> Thank you for valuable input! Here's a breakdown of energies for a
> periodic LiO2 system (where CP2K and DFTB+ disagree).
> CP2K:
>
> Core Hamiltonian energy:
> -609.45757320827579
> Repulsive potential energy:
> 2.86335541921533
> Electronic energy:
> -65.73940900376786
> DFTB3 3rd order energy:
> 9.00274299587460
> Dispersion energy:
> -2.00065978643714
> Correction for halogen bonding:
> 0.00000000000000
>
> Total energy:
> -665.33154358339084
>
> outer SCF iter = 1 RMS gradient = 0.49E-06 energy =
> -665.3315435834<tel:(331)%20543-5834>
> outer SCF loop converged in 1 iterations or 10 steps
>
> And the same system with DFTB+ (I don't know this is the best breakdown I
> can get from DFTB+? This info is from detailed.out.):
>
> Fermi level: -0.1574062769 H -4.2832 eV
> Band energy: -254.9890864567 H -6938.6061 eV
> TS: 0.0000000000 H 0.0000 eV
> Band free energy (E-TS): -254.9890864567 H -6938.6061 eV
> Extrapolated E(0K): -254.9890864567 H -6938.6061 eV
> Input / Output electrons (q): 864.0000000000 864.0000000000
>
> Energy H0: -610.3586854777 H -16608.7049 eV
> Energy SCC: 13.1915555608 H 358.9605 eV
> Total Electronic energy: -597.1671299169 H -16249.7444 eV
> Repulsive energy: 0.0000000000 H 0.0000 eV
> Total energy: -597.1671299169 H -16249.7444 eV
> Extrapolated to 0: -597.1671299169 H -16249.7444 eV
> Total Mermin free energy: -597.1671299169 H -16249.7444 eV
> Force related energy: -597.1671299169 H -16249.7444 eV
>
>
> ----------------------------------------------------------------------------------------------------------------
> For reference, here are the equivalent breakdowns for the LiF molecule,
> where the total energies do match quite well.
> CP2K:
>
> Core Hamiltonian energy:
> -5.57594122418510
> Repulsive potential energy:
> 0.00036401843654
> Electronic energy:
> 0.08477836575096
> DFTB3 3rd order energy:
> -0.00385103760005
> Dispersion energy:
> -0.00008325087778
> Correction for halogen bonding:
> 0.00000000000000
>
> Total energy:
> -5.49473312847544
>
> outer SCF iter = 1 RMS gradient = 0.12E-06 energy =
> -5.4947331285
> outer SCF loop converged in 1 iterations or 25 steps
>
> DFTB+
> Fermi level: -0.3434874008<tel:(343)%20487-4008> H
> -9.3468 eV
> Band energy: -3.7493389034 H -102.0247 eV
> TS: 0.0000000000 H 0.0000 eV
> Band free energy (E-TS): -3.7493389034 H -102.0247 eV
> Extrapolated E(0K): -3.7493389034 H -102.0247 eV
> Input / Output electrons (q): 8.0000000444 8.0000000000
>
> Energy H0: -5.5743451431<tel:(574)%20345-1431> H
> -151.6856 eV
> Energy SCC: 0.0807122067 H 2.1963 eV
> Total Electronic energy: -5.4936329365 H -149.4894 eV
> Repulsive energy: 0.0000000000 H 0.0000 eV
> Total energy: -5.4936329365 H -149.4894 eV
> Extrapolated to 0: -5.4936329365 H -149.4894 eV
> Total Mermin free energy: -5.4936329365 H -149.4894 eV
> Force related energy: -5.4936329365 H -149.4894 eV
>
>
> ----------------------------------------------------------------------------------------------------------------
>
> > I recently run variable-cell optimization of various molecular crystals
> and I found xTB at CP2K ultra sensitive to EPS_DEFAULT. Tested from 1e-5 to
> 1e-24 (with EPS_SCF 1e-8), and no convergence happened.
>
> Thank you for sharing this info! I tried a series of calculations with
> LiO2 using varying values of EPS_DEFAULT (using default EPS_SCF) and found
> the same effect; no convergence with EPS_DEFAULT (or perhaps unreasonably
> slow convergence). I attach a figure showing these results, including the
> energy broken down into the different parts as specified in the CP2K
> output. Note the energy scale, the changes with EPS_DEFAULT are really
> quite substantial. In the LiF (non-PBC) case, the corresponding curves look
> completely flat on the same scale. I don't know what to make of this
> result, but perhaps someone else does?
>
> Magnus
>
> [X]
> On Monday, September 5, 2022 at 12:18:26 PM UTC+2 jazz... at gmail.com
> <mailto:jazz... at gmail.com><mailto:jazz... at gmail.com<mailto:
> jazz... at gmail.com>> wrote:
> I recently run variable-cell optimization of various molecular crystals
> and I found xTB at CP2K ultra sensitive to EPS_DEFAULT. Tested from 1e-5 to
> 1e-24 (with EPS_SCF 1e-8), and no convergence happened. I just ended up
> with EPS_DEFAULT 1e-10 as a "gut" choice. Also, the behavior of xTB at CP2K
> is doutfull with MD even at ambiant conditions, where the converged volume
> is barely larget than at 0K. Depending on EPS_DEFAULT, it can even be
> smaller at ambient T. Weird. The behavior of DFTB2 at CP2K is far better.
>
> I found that DFTB+ has other issues. xTB at DFTB+ has no convergence issue,
> but the recommended variable-cell optimization algorithm has flaws. The
> unit cell and a supercell does NOT always end up with related lattice
> parameters. The main issue is that some 90° angles are not preserved with
> DFTB+ whereas CP2K does (with no symmetry enforced, obviously). Some
> inconsistencies appears in DFTB+ with a lattice dimensions < 10 angstroms
> in the unit cell versus > 10 angstroms in the supercell. A proper tight
> mesh of k-points does not improve. So I'm afraid that xTB at DFTB+ (or
> DFTB+, actually) cannot be a relevant choice for crystal structure
> predictions, for instance.
>
> xTB may be unreliable with CP2K and DFTB+, but for the different reasons
> above. You can check these weird behaviors with your own crystals of
> interest.
>
> Xavier
>
>
>
> Le lun. 5 sept. 2022, 3:59 AM, Jürg Hutter <hut... at chem.uzh.ch<mailto:
> hut... at chem.uzh.ch><mailto:hut... at chem.uzh.ch<mailto:hut... at chem.uzh.ch>>>
> a écrit :
> Hi
>
> thank you for testing. Could you send a break down of the energies for the
> LiF molecule for
> the two codes? That might help to recognize the source of the difference.
>
> regards
>
> JH
>
> ________________________________________
> From: cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>> <
> cp... at googlegroups.com<mailto:cp... at googlegroups.com><mailto:
> cp... at googlegroups.com<mailto:cp... at googlegroups.com>>> on behalf of
> Magnus Rahm <mag... at compulartech.com<mailto:mag... at compulartech.com
> ><mailto:mag... at compulartech.com<mailto:mag... at compulartech.com>>>
> Sent: Monday, September 5, 2022 8:40 AM
> To: cp2k
> Subject: [CP2K:17599] Re: Large discrepancy in xTB results from CP2K vs
> DFTB+
>
> For the record, the problem is the same in CP2K version 2022.1.
>
> On Thursday, September 1, 2022 at 12:48:35 PM UTC+2 Magnus Rahm wrote:
> Dear all,
>
> I want to use CP2K (version 8.2, trying to get a more recent version
> compiled) together with xTB for a crystal containing Li and O. I get
> strange results already for a simple LiO2 crystal:
>
> * There is a very large discrepancy compared to DFTB+ (version 22.1).
> * Mulliken charges tend to be large, meaning that CHECK_ATOMIC_CHARGES
> stops the SCF. If I turn it off, the system tends to converge
> systematically to values just outside the "chemical range". Mulliken
> charges obtained by DFTB+ are significantly smaller (and within "chemical
> range").
> * The energy-volume curve looks strange and very different from DFTB+.
>
> I have tried converging with respect to system size and the EWALD / ALPHA
> and GMAX parameters, but they have only a marginal impact. I have tried
> similar calculations for a number of periodic systems. Sometimes I get
> agreement, sometimes not. I also tried calculations for CO and NO molecules
> which agree perfectly between CP2K and DFTB+, whereas an artificial LiF
> molecule does not.
>
> A perhaps related issue was reported in
> https://groups.google.com/g/cp2k/c/oFwgGcQuySs but the solutions
> suggested there did not solve my problem.
>
> I attach input scripts for CP2K and DFTB+, as well as a figure showing the
> E-V curve for LiO2 obtained with CP2K and DFTB+. I'm new to CP2K, DFTB+ and
> xTB so I suspect I have made some simple mistake, and any advice is
> appreciated.
>
> Kind regards,
> Magnus Rahm
>
>
>
>
>
>
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