[CP2K-user] [CP2K:14172] Re: SCF convergence issues
Ryan Rogers
rr... at nyu.edu
Fri Nov 13 23:25:34 UTC 2020
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
rr... at nyu.edu <trr... at email.uark.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
################################################################################
On Thu, Nov 5, 2020 at 10:20 AM Женя Елизарова <zhene... 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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