[CP2K-user] [CP2K:17752] Re: Large discrepancy in xTB results from CP2K vs DFTB+

Xavier Bidault jazzquark at gmail.com
Sat Sep 24 15:53:05 UTC 2022
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Hi Jürg,

I would appreciate your insights about the per-element cutoffs. See my
previous email. Is it a feature of xTB or CP2K?

Thank you,
Xavier

On Tue, Sep 20, 2022 at 8:16 PM Xavier Bidault <jazzquark at gmail.com> wrote:

> 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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