[CP2K-user] [CP2K:14229] Re: SCF convergence issues
Marcella Iannuzzi
marci... at gmail.com
Tue Nov 17 08:26:46 UTC 2020
Dear Ryan
I don't know the electronic properties of your system. I would be surprised
if it has a metallic character.
There might be some problem of charge delocalisation at the boundaries of
the QM region.
Can you simulate with DFT only the isolated single molecule and the unit
cell of the molecular crystal with PBC?
Best
Marcella
On Monday, November 16, 2020 at 10:23:53 PM UTC+1 r... at nyu.edu wrote:
> Dear Marcella,
>
> I have done as you suggested, and tested a few different basis sets on a
> system with no MM charges, putting the same basis set on all QM atoms. In
> short, none of the basis sets I've tested so far seem to impact the SCF
> behavior.
> I am using the MOLOPT basis sets with pseudopotentials in my QM region.
>
> Under the hypothesis that there could be some unwanted charge transfer
> occurring in my system, I tested the smallest basis (MOLOPT SZV-SR), but to
> no avail.
>
> Under the hypothesis that any possible charge transfer might need extra
> basis functions to be properly described/converged, I also tested the
> largest basis (MOLOPT TZV2PX); also to no avail.
>
> Do you think there is any chance a molecular crystal (with strong hydrogen
> bond networks) could benefit from smearing?
> I am admittedly not very familiar with different smearing methods, but
> know that they are mostly only prescribed for metals/conductor systems.
>
> Sincerely,
> Ryan Rogers
> r... at nyu.edu
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> On Mon, Nov 16, 2020 at 5:52 AM Marcella Iannuzzi <ma... at gmail.com>
> wrote:
>
>>
>> Dear Ryan
>>
>> The behaviour of the SCF is indeed very bad.
>> If possible, I would try to focus on the QM part only, simplify the model
>> as much as you can, for instance using only one type of basis sets, and get
>> it converged.
>> Kind regards
>> Marcella
>>
>>
>>
>> On Saturday, November 14, 2020 at 12:25:51 AM UTC+1 r... at nyu.edu wrote:
>>
>>> Dear Marcella,
>>>
>>> Thank you very much for your suggestion. I tested removing the MM
>>> region, but unfortunately see similar behavior.
>>> My configurations are generated from pure MM simulations with a custom
>>> force field which could possibly be allowing certain atoms to get a little
>>> too close. However, as the thermalized atom positions only vary (for the
>>> most part) by a few tenths of an Angstrom, no problematic close contacts
>>> can be found visually.
>>>
>>> I've pasted below an example of the first SCF cycle from such a job,
>>> showing that the "Total energy" starts off much lower than I'm expecting
>>> (usually on the order of -2,000 +/- 500). During the SCF, the "Total
>>> energy" drops very low. When a job like this is allowed to continue, it
>>> won't crash on its own, but the "Total charge density on r-space grids"
>>> will become too large after 2-3 SCF cycles.
>>>
>>> Is there any advice about how to handle atoms that are potentially
>>> "close" but not chemically "wrong"? These could potentially include
>>> hydrogen-bonding pairs like O-H, N-H, etc.
>>>
>>> Any help is greatly appreciated in advance!
>>>
>>> Sincerely,
>>> Ryan Rogers
>>> r... at nyu.edu
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>
>>> ################################################################################
>>> SCF WAVEFUNCTION OPTIMIZATION
>>>
>>> ----------------------------------- OT
>>> ---------------------------------------
>>> Minimizer : DIIS : direct inversion
>>> in the iterative subspace
>>> using 7 DIIS vectors
>>> safer DIIS on
>>> Preconditioner : FULL_ALL : diagonalization, state selective
>>> Precond_solver : DEFAULT
>>> stepsize : 0.15000000 energy_gap :
>>> 0.00100000
>>> eps_taylor : 0.10000E-15 max_taylor :
>>> 4
>>> ----------------------------------- OT
>>> ---------------------------------------
>>>
>>> Step Update method Time Convergence Total energy
>>> Change
>>>
>>> ------------------------------------------------------------------------------
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 1 OT DIIS 0.15E+00 66.7 0.13322879 -8451.7456190410
>>> -8.45E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 2 OT DIIS 0.15E+00 65.4 0.13364185 -10643.9042780022
>>> -2.19E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 3 OT DIIS 0.15E+00 65.7 0.15497766 -13025.7969156521
>>> -2.38E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 4 OT DIIS 0.15E+00 65.5 0.14868108 -14464.8777105315
>>> -1.44E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 5 OT SD 0.15E+00 65.5 0.17759857 -14843.1753581151
>>> -3.78E+02
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 6 OT DIIS 0.15E+00 65.8 0.32256964 -13383.1417204580
>>> 1.46E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 7 OT DIIS 0.15E+00 65.6 0.19569799 -14813.0440620911
>>> -1.43E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 8 OT DIIS 0.15E+00 65.3 0.24452346 -15865.0025958057
>>> -1.05E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 9 OT DIIS 0.15E+00 65.5 0.26678603 -14795.2757334147
>>> 1.07E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 10 OT DIIS 0.15E+00 65.7 0.36307397 -17004.3658543152
>>> -2.21E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 11 OT DIIS 0.15E+00 65.6 0.48782211 -17176.2139668702
>>> -1.72E+02
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 12 OT DIIS 0.15E+00 65.5 0.45773260 -15669.9100288352
>>> 1.51E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 13 OT DIIS 0.15E+00 65.5 0.66194382 -18842.9056350951
>>> -3.17E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 14 OT DIIS 0.15E+00 65.6 0.63269527 -16132.4918799441
>>> 2.71E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 15 OT DIIS 0.15E+00 65.7 0.73064928 -16834.2508612376
>>> -7.02E+02
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 16 OT DIIS 0.15E+00 65.5 1.15829587 -27460.2661838299
>>> -1.06E+04
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 17 OT DIIS 0.15E+00 65.7 0.70782891 -15281.5935133825
>>> 1.22E+04
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 18 OT DIIS 0.15E+00 65.7 0.98480536 -20548.0516400897
>>> -5.27E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 19 OT DIIS 0.15E+00 65.6 1.39954759 -33842.8143338371
>>> -1.33E+04
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 20 OT DIIS 0.15E+00 65.6 1.33809404 -29354.7460547364
>>> 4.49E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 21 OT DIIS 0.15E+00 65.4 1.62600866 -36147.2741396100
>>> -6.79E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 22 OT DIIS 0.15E+00 65.6 1.21990609 -24956.2600892884
>>> 1.12E+04
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 23 OT DIIS 0.15E+00 65.6 1.32400959 -27440.1826004675
>>> -2.48E+03
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 24 OT DIIS 0.15E+00 65.5 1.81006425 -42812.1680574805
>>> -1.54E+04
>>> Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>>> 25 OT DIIS 0.15E+00 65.7 0.89367434 -18701.9345340245
>>> 2.41E+04
>>>
>>> Leaving inner SCF loop after reaching 25 steps.
>>>
>>>
>>> Electronic density on regular grids: -1218.0000000005
>>> -0.0000000005
>>> Core density on regular grids: 1217.9999999992
>>> -0.0000000008
>>> Total charge density on r-space grids: -0.0000000013
>>> Total charge density g-space grids: -0.0000000013
>>>
>>> Overlap energy of the core charge distribution:
>>> 0.00009990728015
>>> Self energy of the core charge distribution:
>>> -4772.82460287547656
>>> Core Hamiltonian energy:
>>> 2367.11980010682919
>>> Hartree energy:
>>> -15786.54494725671611
>>> Exchange-correlation energy:
>>> -509.06361063631039
>>> Dispersion energy:
>>> -0.62127327012014
>>> QM/MM Electrostatic energy:
>>> 0.00000000000000
>>>
>>> Total energy:
>>> -18701.93453402451269
>>>
>>> outer SCF iter = 1 RMS gradient = 0.89E+00 energy = -18701.
>>> 9345340245 <(934)%20534-0245>
>>> ################################################################################
>>>
>>>
>>>
>>> On Thu, Nov 5, 2020 at 10:20 AM Женя Елизарова <zh... at gmail.com>
>>> wrote:
>>>
>>>> I see.
>>>> Actually, I would like to know is it possible to run a single point
>>>> energy calculation of the QM subsystem without the removal of the MM part,
>>>> not in relation to the previous posts (in general)?
>>>>
>>>>
>>>> Best wishes,
>>>> Evgenia
>>>>
>>>> четверг, 5 ноября 2020 г. в 19:08:44 UTC+3, Marcella Iannuzzi:
>>>>
>>>>>
>>>>> Dear Evgenia Elizarova
>>>>>
>>>>> Is this question related to the previous posts in this conversation?
>>>>> If yes, what I meant is to remove all the MM part and just carry out a
>>>>> DFT calculation of the QM part.
>>>>> Regards
>>>>> Marcella
>>>>>
>>>>> On Thursday, November 5, 2020 at 3:29:42 PM UTC+1 zh... at gmail.com
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> Dear Marcella Iannuzzi
>>>>>>
>>>>>> I've just started to explore opportunities of the cp2k package. I've
>>>>>> done some tutorials about single-point calculations of ethane molecule,
>>>>>> QM/MM simulations, and some more. I am very interested in single point
>>>>>> energy calculation for the QM part of the system. As I understood, I have
>>>>>> to define the force_eval section (method - quickstep), and also I have to
>>>>>> define subsections: dft, subsys, qmmm. Did I understand correctly? Also, i
>>>>>> have some questions.
>>>>>> Do I have to define the MM subsection? In subsys section, I should
>>>>>> define the whole system? How to define for which part of the system run a
>>>>>> single point calculation?
>>>>>> Could you help me, please?
>>>>>>
>>>>>> Best wishes,
>>>>>> Evgenia Elizarova
>>>>>> понедельник, 2 ноября 2020 г. в 11:55:28 UTC+3, Marcella Iannuzzi:
>>>>>>
>>>>>>> Dear Ryan Rogers
>>>>>>>
>>>>>>> There is apparently a problem with the conservation of the charge on
>>>>>>> the QM grid.
>>>>>>>
>>>>>>> Did you try to run a single point energy calculation for the QM part
>>>>>>> alone?
>>>>>>> Kind regards
>>>>>>> Marcella
>>>>>>>
>>>>>>> On Thursday, October 29, 2020 at 7:11:42 PM UTC+1 r... at nyu.edu
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I might add that I have not been able to identify any obvious
>>>>>>>> problems with the configurations (e.g. overlapping or too close atoms,
>>>>>>>> etc.) when I encounter these errors.
>>>>>>>>
>>>>>>>> On Monday, October 26, 2020 at 4:07:46 PM UTC-5 Ryan Rogers wrote:
>>>>>>>>
>>>>>>>>> Dear CP2K community,
>>>>>>>>>
>>>>>>>>> I am having issues in DFT QM/MM force calculations on molecular
>>>>>>>>> crystals of paracetamol (acetaminophen). I am describing here the two
>>>>>>>>> problems I most often experience. I am currently unable to identify the
>>>>>>>>> cause or any pattern in the problems I encounter. The root of the problems
>>>>>>>>> could be something other than what I identify below; I am pointing out the
>>>>>>>>> problematic features in the output that are most obviously to me. All input
>>>>>>>>> and output files are included.
>>>>>>>>>
>>>>>>>>> *1. Total energy falls into "hole" and never converges.
>>>>>>>>> (CP2K_problemTotalE_conf_0636.tar.gz)*
>>>>>>>>> Personal experience tells me to expect a "Total energy" for these
>>>>>>>>> systems on the order of -2,000 (Hartree) and a "Hartree energy" on the
>>>>>>>>> order of +2,000 (Hartree).
>>>>>>>>> In these jobs, I find an initial "Hartree energy" on the order of
>>>>>>>>> >-10,000 (Hartree), which appears to send the SCF wavefunction optimization
>>>>>>>>> down a path of non-convergence, in which the "Total energy" can easily
>>>>>>>>> become on the order of -100,000 (Hartree) before I kill the job.
>>>>>>>>>
>>>>>>>>> *2. Total charge density on grids grows too large.
>>>>>>>>> (CP2K_problemEGrids_conf_0623.tar.gz)*
>>>>>>>>> In these jobs, the Total energy looks reasonable, and the
>>>>>>>>> Convergence looks promising in the few SCF cycles of steps.
>>>>>>>>> However, the total Change never drops below my threshold, and
>>>>>>>>> eventually the "Total charge density on r-space/g-space grids" becomes much
>>>>>>>>> too large.
>>>>>>>>>
>>>>>>>>> My configurations are extracted from MD trajectories, so the atoms
>>>>>>>>> have perturbations from their perfect crystal positions. One confusing
>>>>>>>>> observation is that very similar QM/MM configurations selected from other
>>>>>>>>> frames of the same trajectory often have no problems.
>>>>>>>>> My configurations are constructed from a cluster of several
>>>>>>>>> molecules in the QM region with usually another layer usually 1-2 molecules
>>>>>>>>> thick making up the MM region. (In the attached sample images, the size of
>>>>>>>>> the stick molecules alludes to a larger/smaller basis set used, while the
>>>>>>>>> MM atoms are denoted as points.) Because I am not including integer numbers
>>>>>>>>> of unit cells, I am not using PBC.
>>>>>>>>>
>>>>>>>>> Any advice about both/either problem will be greatly appreciated!
>>>>>>>>>
>>>>>>>>> Sincerely,
>>>>>>>>> Ryan Rogers
>>>>>>>>> r... at nyu.edu
>>>>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>>>>
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