[CP2K-user] [CP2K:17715] Re: Large discrepancy in xTB results from CP2K vs DFTB+
Jürg Hutter
hutter at chem.uzh.ch
Tue Sep 20 10:53:28 UTC 2022
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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