IR spectm for NaCl under PBC

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Victor Volkov

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Jan 23, 2022, 1:58:05 PMJan 23
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Dear colleagues:
here is the normal mode analysis I could manage by now for NaCl under PBC.

There is only one unit cell: previously, I reported that I could not configure CP2K to reproduce NaCl structure using multiple cells 2 2 2.
There are strange distortions, which I did confirm to sustain under different CUTOFF values (1000 and 600), and regardless if dispersion is switched off or not.

When a single cell under PBC, optimization leads to the “right” structure, when ESP 10^-12.

However, the negative(imaginary) frequencies are many and they are very large.
I may anticipate that the “miss performance” is enhanced due to the PBC.

Eventhough the results are "devastating",
:-)
nonetheless, I find this might be very good, very helpful – I got an idea.

Dear Dr. Hutter,
is it possible that CP2K may have an “issue” about positioning a structure
in respect to both, in respect to the FT grind and in respect to the PBC.
Perhaps, there could be a relative mismatch phenomenon, which could stimulate artificial transition states with negative frequencies?

May be, what I observe is that PBC on the unit cell helps to sense this better?


Thank you for your time and for any comments.

With best regards,
Sincerely
Victor
NaCl_fr.inp
NaCl_fr.out
NaCl_fr.mol

fabia...@gmail.com

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Jan 24, 2022, 8:22:29 AMJan 24
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Dear Victor,

You need a much tighter convergence criterion for the optimization prior to the vibrational analysis. You increased MAX_FORCE to 5e-3 (guessing from the output), instead you have to decrease it to at least 1e-5, maybe even lower.
CP2K prints the forces for the replica in the output. The forces under "Minimum Structure - Energy and Forces:" should be more or less 0 and considerably differ between the other images. Currently you are computing the vibrational analysis from almost pure noise.

Cheers,
Fabian

Victor Volkov

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Jan 24, 2022, 11:02:48 AMJan 24
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Dear Fabian;
excellent!
Great learning.
Thank you.
With best regards,
:-)
Victor

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Victor Volkov

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Jan 25, 2022, 11:14:28 AMJan 25
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Dear Fabian:
sorry to bother once more.

Learning from your comments, I optimized the structure (please, see the attached outut)
under
    MAX_DR    8.0E-06
    RMS_DR    4.0E-06    
    MAX_FORCE 1.0E-06
    RMS_FORCE 1.0E-07

This is to run vibrational analysis using the input, as attached.

In DFT, I do instruct to prinnt moments (as you may see),
but
CP2K reports an error- to be unable to read the moments.

I wonder if such unexpected "blindness"
is present because the input contains
   &KPOINTS
   SCHEME  MONKHORST-PACK  8 8 8
   FULL_GRID  .TRUE.
   &END KPOINTS

I include this definition trying to acount the Brullion space structure.
May be this is outside of the scope.

I wish to understand a bit how CP2K vibrational analysis
accounts (or not) dfinitions of
multiple cell, k-points and periodicity.

I be thankful if you comment.
Victor

NaCl_1GPWdiag.out
NaCl_1GPWdiag_F.inp

hut...@chem.uzh.ch

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Jan 26, 2022, 4:26:37 AMJan 26
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Hi

The vibrational analysis module is most useful for molecular systems
(molecular crystals) calculated at the Gamma point. In this case
you can also calculate IR intensities through dipole derivatives.
For k-point calculations the dipoles are not available and no
IR intensities are possible. In addition you only get the
Gamma point phonon.
For systems like NaCl, what you usually want is a full phonon spectra.
In this case you should use specialized software like phonopy
that interfaces to CP2K (and many other codes).

regards

Juerg Hutter
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie E-mail: hut...@chem.uzh.ch
Universität Zürich
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------

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To: cp...@googlegroups.com
From: "Victor Volkov"
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Date: 01/25/2022 05:14PM
Subject: Re: [CP2K:16499] Re: IR spectm for NaCl under PBC
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[attachment "NaCl_1GPWdiag.out" removed by Jürg Hutter/at/UZH]
[attachment "NaCl_1GPWdiag_F.inp" removed by Jürg Hutter/at/UZH]

Victor Volkov

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Jan 26, 2022, 5:40:27 AMJan 26
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Dear Dr.Hutter
good moring in Milchbuck

>For k-point calculations the dipoles are not available and no IR intensities are possible.
>In addition you only get the Gamma point phonon.

Thank you for the kind answer.

> For systems like NaCl, what you usually want is a full phonon spectra.

I target normal modes in LixMnyOz systems to explain
changes of Raman modes at cathode of en electric element
upon a phase transitions, which i could induce using a laser field. 
NaCl is a test ground to understand.

>you should use specialized software like phonopy that interfaces to CP2K (and many other codes).

Jein: Yes, and No.

I installed and run phonopy under cygwin-windows.
Indeed, usinf CP2K,
phonopy does compute phonon DOS and PDOS.

However, a scientific discussion requires understanding what kind of interatomic displacements
those densities would correspond.
In this respect,
learning how to condition cp2k is the only way
towards practical.

Just to have DOS from phonopy and normal modes from cp2k,
already would be a sufficient playground to impact technology.

However, conditioninig cp2k to generate relevent (no need to be perfect) normal modes
is the important connection.

After 30 years in spectroscopy,
I may say that even computing IR or Raman may not be that important.

Yes, computing such is possible using, for example:


However, IR-Raman is  just a "luxury".

Correlating normal modes to phonon DOS is sufficient to answer many questions

With best regards,
Victor













Victor Volkov

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Jan 26, 2022, 3:12:03 PMJan 26
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Dear Fabian:
please forgive me

If I set
    OPTIMIZER BFGS

    MAX_DR    8.0E-06
    RMS_DR    4.0E-06    
    MAX_FORCE 1.0E-06
    RMS_FORCE 1.0E-07
then the forces are
ATOMIC FORCES in [a.u.]
 # Atom   Kind   Element          X              Y              Z
      1      1      Na          0.00000796     0.00000796     0.00000796
      2      1      Na          0.00000796     0.00001127     0.00001127
      3      1      Na          0.00001127     0.00000796     0.00001127
      4      1      Na          0.00001127     0.00001127     0.00000796
      5      2      Cl          0.00000052     0.00000052     0.00000052
      6      2      Cl          0.00000052     0.00000052     0.00000052
      7      2      Cl          0.00000052     0.00000052     0.00000052
      8      2      Cl          0.00000052     0.00000052     0.00000052
 SUM OF ATOMIC FORCES           0.00004056     0.00004056     0.00004056     0.00007026

and the soectrum is terrible (please, see the attached xxx_F.out)

Then I try to instruct more strict convregence by
    OPTIMIZER BFGS
    MAX_DR    8.0E-07
    RMS_DR    4.0E-07    
    MAX_FORCE 1.0E-07
    RMS_FORCE 1.0E-08

but the forces deteriorate
ATOMIC FORCES in [a.u.]
 # Atom   Kind   Element          X              Y              Z
      1      1      Na          0.00009945     0.00009945     0.00009945
      2      1      Na          0.00025879    -0.00001513    -0.00001513
      3      1      Na         -0.00001519     0.00025872    -0.00001518
      4      1      Na         -0.00001513    -0.00001513     0.00025879
      5      2      Cl          0.00031492     0.00004422     0.00004422
      6      2      Cl          0.00024177     0.00024177     0.00024177
      7      2      Cl          0.00004422     0.00004422     0.00031492
      8      2      Cl          0.00004422     0.00031492     0.00004422
 SUM OF ATOMIC FORCES           0.00097305     0.00097303     0.00097305     0.00168536

I attach the optimization inp and out pair.
I donot see what is wrong?
May be GPW and BFGS are not for such optimizations?  
Thank you.
Victor



On Mon, Jan 24, 2022 at 4:22 PM fabia...@gmail.com <fabia...@gmail.com> wrote:
--
NaCl_1GPWdiag_F.out
NaCl_1GPWdiag.out
NaCl_1GPWdiag.inp

fabia...@gmail.com

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Jan 27, 2022, 4:00:54 AMJan 27
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Dear Viktor,

The output you attached shows for step 28:
  Max. gradient              =         0.0002958006
  Conv. limit for gradients  =         0.0004500000
  Conv. in gradients         =                  YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Fabian

Victor Volkov

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Jan 27, 2022, 5:39:21 AMJan 27
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Dear Fabian:
Dear Dr. Hutter:

is it possible that CP2K is present not to follow the input instructons?

According to my instructions (pleas, see attached)
in the MOTION section there are instructions
    MAX_DR    8.0E-07
    RMS_DR    4.0E-07    
    MAX_FORCE 1.0E-07
    RMS_FORCE 1.0E-08

but
as Fabian has noticed:

The output you attached shows for step 28:
  Max. gradient              =         0.0002958006
  Conv. limit for gradients  =         0.0004500000
  Conv. in gradients         =                  YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Is it possible that there is a bug
that prevents a certain level of precision?

Thank you.
With best regards.

Victor




NaCl_1GPWdiag.inp

fabia...@gmail.com

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Jan 27, 2022, 6:30:13 AMJan 27
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cp2k works just fine and does everything you tell it to do. The issue is that you specified MAX_FORCE 1.0E-07  etc. for &GEO_OPT instead of &CELL_OPT...

Victor Volkov

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Jan 27, 2022, 7:29:28 AMJan 27
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Thank you, dear Fabian.
I will study.
With best regards,
sincerely
Victor


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Victor Volkov

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Jan 28, 2022, 3:30:16 AMJan 28
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Dear Fabian:
good morning.

According to your notice
I redefined MAX_FORCE to be under
&MOTION
   &CELL_OPT
However, the cp2k failed convergence - energy was just oscillating.

After studying your replies to other members,
I did two changes in the input.

1.
While keeping the definitions in
&MOTION
   &CELL_OPT
....
in GLOBAL
I changed to
 RUN_TYPE GEO_OPT

The logic of the guess is that apparently &CELL_OPT can not lead.
Then, may be,
GEO should lead, while CELL should be set to follow.

It is not clear, if under such setting STRESS TENSOR would have any meaning.
Perhaps it has not role no more and becomes redundant.

2.
Also, I introduced
CELL_REF

I attach the input.
This is the job I am testing.

Would you have a minute to comment, criticize - I be thankful.

In any way,
thank you for your time,
and nice weekend
:-)
Best!
Victor

 

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NaCl_2GPWdiag.inp

fabia...@gmail.com

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Jan 28, 2022, 7:42:08 AMJan 28
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Dear Viktor,

Several things:
 - If you choose RUN_TYPE GEO_OPT then you should have MOTION&GEO_OPT and not MOTION&CELL_OPT and vice versa.
 - Set EPS_DEFAULT to 1e-12
 - For CELL_OPT: you should have a &CELL_REF section with dimensions approx. 1.3-1.5 times larger (test this!) than &CELL
 - You need MULTIPLE_UNIT_CELL in &CELL_REF too

Cheers,
Fabian

Victor Volkov

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Jan 28, 2022, 7:51:32 AMJan 28
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Thank you dear Fabian
Sincerely
Victor

Victor Volkov

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Feb 5, 2022, 5:29:53 AMFeb 5
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Dear Fabian:
good morning.

Sorry to bother once more.

I used the "experience" with NaCl
to step toward Li2MnO3:
I attach cif, UnitCell xyz, input and current output.

Of course, the spinel is much more demanding: I specified NEL for every ion.

I wish to ask your opinion in respect to your advise to test
&CELL_REF section with dimensions approx. 1.3-1.5 times larger than the  &CELL.

Specifically, I have noticed that for the larger &CELL_REF
the time for an SCF cycle increases
and the efficiency of the convergence decreases.

Currently, for &CELL_REF dimensions 1.5 times larger
I have one SCF cycle done in about 16 hours.

Currently, i am finishing the convergence for NaCL using the same criteria
    MAX_DR    8.0E-07
    RMS_DR    4.0E-07    
    MAX_FORCE 1.0E-07
    RMS_FORCE 1.0E-08
The optimization (I will report to the members once done)
report 24 SCF for every structural update.
Currently the optimization accounts 111 structural updates,
Accounting this, I extrapolate 111*24*16 = 42624 hours = 4.87 years
I would need to optimize the spinel.

As you know,
I am "stubborn enough" to take such a challenge

(For example, this week,
I submitted to ACS Inorg. Chemistry a manuscript
using 2DIR data I measured, when I was a researcher in Uni. Zurich in 2002-2004.
I remember Dr. Hutter when he was much younger. :-)

However, may be you give me an advise if
&CELL_REF could be attuned to be smaller
to account better properties of  DZVP and the nature of the ions in the system?

Of course, trying to improved the performance I will explore
&OT, GAWP, DFT+U options
as well as switching to MULTIPLE 1 1 1.
The latter, however, I see cannot provide any quality for normal modes.

Best,
En Schöne
Victor





 

Li2MnO3_mp-18988_computed.cif
Li2MnO3.out
Li2MnO3.inp
Li2MnO3_UniyCell.xyz

Victor Volkov

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Mar 5, 2022, 11:29:21 AMMar 5
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Dear Fabian:
cannot say that evening is any good.

Relatives are in leveled Starobelsk,
and in Hadich, where the front is incoming.

Science ...

Here,
are the results of calculations of the normal modes fro NaCl.at the Gamma point.
Also, I attach the optimization files.
It seems to me that after increasing the optimization criteria
    MAX_DR    8.0E-07
    RMS_DR    4.0E-07    
    MAX_FORCE 1.0E-07
    RMS_FORCE 1.0E-08

The results are curious.
May be there are some mistakes I did?

Again,
I wish to ask if CP2K has an issue
about the Fourier grid
that may generate imaginary frequencies
if the coords are not properly positioned?

If you do not have energy/time/will,
please,
forgive and disregard the inquiry.

With best regards,
Victor
NaCl_optimization.inp
NaCl_optimization.out
NaCl_optimization.xyz
NaCl_freq.out
NaCl_freq.inp
NaCl_freq.mol

Václav Havel

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May 13, 2022, 9:51:48 PMMay 13
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Dear Viktor,
I have the same question about imaginary frequencies.
Have you tackled the problem of imaginary frequency ?  It seems that just  increasing the optimization criteria  cannot  eliminate  all   imaginary frequencies .

With best regards
Vaclav

Victor Volkov

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May 14, 2022, 4:57:37 AMMay 14
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Dear Vaclav:
good morning.

> It seems that just  increasing the optimization criteria  cannot  eliminate  all   imaginary frequencies .

The issue is not too trivial.
A presence of imaginary friequencies may not be considered as unhappy artifact, always.
They report on displacements characteristic to transition states.
Furthermore, when we study transition states, imaginary frequencies are under attention.

Let us assume we optimize a single acetic acid either without periodic boundary conditions
or in a box under PBC, the size of which is very large, that replica would not affect each other.
Then, if the molecule is well optimized, we should not observe transition states, and, therefore, we should not
observe imaginary frequencies.

Under such condition, CP2K preforms very well: quality of the normal modes are competitive.

However, the value of the package is that it can do condensed matter under periodic boundary conditions. 
This is where Dr. Scuseria limited Gaussian.
(Apparently, it is a historical-remarkable example how a will of one person affected science of millions for decades.)

Trying to optimize NaCl under PBC using criteria of different perfection did not work out for me so far.

I should add that my computational capacity is limited - I compute everything on my private notebook
and do not have any access to any resources controlled by any state or any organization or any business.

Among possible issues,
I anticipate there could be a conceptual one concerning the "FT engine" of CP2K.

Perhaps,  this is why the discussion on the topic does not bring enthusiasm.
Perhaps such attenuation is to see if other initiatives, like Phonopy or Travis could complement.

A significant time of the "political thoughtfulness" has passed - apparently,  the "rock and roll" is dead
to parallel the climax of Gaussian on the matter.

:-)
in respect to the band structure - I hear only the buzz about the VVASP.
:-)

Best
Victor

Jürg Hutter

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May 16, 2022, 6:56:14 AMMay 16
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Hi

just a few thoughts on geometry optimizations and frequency calculations using CP2K.
It might help for the present discussion.

In an ideal setting one expects that the energy of a molecule is constant for translations and rotations.
For periodic systems, the energy should be constant for translations.
In CP2K the XC energy is calculated using equidistant grids (the same for all PW codes) and this
breaks translational invariants and rotational invariants for molecules.
If you calculate the energy for a system while translating it rigidly you will observe a small periodic change
of the energy with a frequency given by the grid spacing. This phenomenon is usually called 'ripples'.
The size of the ripples depends on many parameters (cutoff, pseudopotential, smearing, etc).
The GPW method in CP2K shows rather large ripples, which cause problems in tight geometry optimizations
and frequency calculations. However, forces are consistent with the ripples, so there is no problem
in MD.
For geometry optimizations the optimizer gets "confused" by the ripples and starts to jump back and forth
and might have problems to converge.
In frequency calculations, you will observe non-zero translational and rotational modes. These modes
can have positive or negative frequencies. In CP2K these modes are projected out from the Hessian
assuming they don't couple to the internal molecular modes.
If you want to reduce the ripples in CP2K you can explore some options:
- use GAPW, it will reduce the size considerably
- use smearing of density and gradients (this might have side effects, use with care!)
- some functionals are worse than others (BLYP!)

best regards

Juerg Hutter

________________________________________
From: 'Václav Havel' via cp2k <cp...@googlegroups.com>
Sent: Saturday, May 14, 2022 3:51 AM
To: cp2k
Subject: Re: [CP2K:16978] Re: IR spectm for NaCl under PBC
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/dd5077c3-4bac-4fa0-a81d-ef779f43e157n%40googlegroups.com<https://groups.google.com/d/msgid/cp2k/dd5077c3-4bac-4fa0-a81d-ef779f43e157n%40googlegroups.com?utm_medium=email&utm_source=footer>.

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Victor Volkov

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May 16, 2022, 7:33:37 AMMay 16
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Dear Dr. Hutter:
good afternoon.
thank you very much for the kind reply and the instructions.
I will study.
Best regards,
Victor


Victor Volkov

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Sep 20, 2022, 9:46:37 AMSep 20
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Dear Dr. Hutter:
good afternoon.
Sorry to bother with couple questions.

First, I wish to ask you if CP2K, when performing TD-DFT,
can print cubes (for ED and orbitals) using 
"difference density matrix representation"?
Reviewers (possibly from the Q-chem community) inquire this since they consider the representation
to be more helpful in discussion of charge-transfer events at surfaces.

Second, the reviewers point that the GGA-PBE from CP2K is not any adequate in respect to computing charge transfers,
but long-range hybrid corrected functionals would have to be considered.
Would you recommend a sound alternative by CP2K to compare with the results by GGA-PBE?

Thank you.
With best regards,
Sincerely,
Victor



On Mon, May 16, 2022 at 1:56 PM Jürg Hutter <hut...@chem.uzh.ch> wrote:

Jürg Hutter

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Sep 21, 2022, 4:25:09 AMSep 21
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Dear Victor

printing of cube files for ED or excitation orbitals is unfortunately not implemented.

A simple hybrid functional, e.g. PBE0 (truncated HFX for PBC) could be a way to go.
For molecular systems, CAM-B3LYP is probably most popular. There is an example input,
but I have no experience how it performs in TDDFT calculations.

cp2k/tests/QS/regtest-hybrid-4/Ne_hybrid-rcam-b3lyp_tc.inp

regards

Juerg Hutter

________________________________________
From: cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Victor Volkov <volk...@gmail.com>
Sent: Tuesday, September 20, 2022 3:46 PM
To: cp...@googlegroups.com
Subject: Re: [CP2K:17718] Re: IR spectm for NaCl under PBC

Dear Dr. Hutter:
good afternoon.
Sorry to bother with couple questions.

First, I wish to ask you if CP2K, when performing TD-DFT,
can print cubes (for ED and orbitals) using
"difference density matrix representation"?
Reviewers (possibly from the Q-chem community) inquire this since they consider the representation
to be more helpful in discussion of charge-transfer events at surfaces.

Second, the reviewers point that the GGA-PBE from CP2K is not any adequate in respect to computing charge transfers,
but long-range hybrid corrected functionals would have to be considered.
Would you recommend a sound alternative by CP2K to compare with the results by GGA-PBE?

Thank you.
With best regards,
Sincerely,
Victor



From: 'Václav Havel' via cp2k <cp...@googlegroups.com<mailto:cp...@googlegroups.com>>
Sent: Saturday, May 14, 2022 3:51 AM
To: cp2k
Subject: Re: [CP2K:16978] Re: IR spectm for NaCl under PBC

Dear Viktor,
I have the same question about imaginary frequencies.
Have you tackled the problem of imaginary frequency ? It seems that just increasing the optimization criteria cannot eliminate all imaginary frequencies .

With best regards
Vaclav

On Friday, January 28, 2022 at 3:42:08 PM UTC+3 fabia...@gmail.com<mailto:fabia...@gmail.com> wrote:
Dear Viktor,

Several things:
- If you choose RUN_TYPE GEO_OPT then you should have MOTION&GEO_OPT and not MOTION&CELL_OPT and vice versa.
- Set EPS_DEFAULT to 1e-12
- For CELL_OPT: you should have a &CELL_REF section with dimensions approx. 1.3-1.5 times larger (test this!) than &CELL
- You need MULTIPLE_UNIT_CELL in &CELL_REF too

Cheers,
Fabian

On Thu, Jan 27, 2022 at 2:30 PM fabia...@gmail.com<mailto:fabia...@gmail.com> <fabia...@gmail.com<mailto:fabia...@gmail.com>> wrote:
cp2k works just fine and does everything you tell it to do. The issue is that you specified MAX_FORCE 1.0E-07 etc. for &GEO_OPT instead of &CELL_OPT...

On Thursday, 27 January 2022 at 11:39:21 UTC+1 volk...@gmail.com<mailto:volk...@gmail.com> wrote:
Dear Fabian:
Dear Dr. Hutter:

is it possible that CP2K is present not to follow the input instructons?

According to my instructions (pleas, see attached)
in the MOTION section there are instructions
MAX_DR 8.0E-07
RMS_DR 4.0E-07
MAX_FORCE 1.0E-07
RMS_FORCE 1.0E-08

but
as Fabian has noticed:

The output you attached shows for step 28:
Max. gradient = 0.0002958006
Conv. limit for gradients = 0.0004500000
Conv. in gradients = YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Is it possible that there is a bug
that prevents a certain level of precision?

Thank you.
With best regards.

Victor




On Thu, Jan 27, 2022 at 12:00 PM fabia...@gmail.com<mailto:fabia...@gmail.com> <fabia...@gmail.com<mailto:fabia...@gmail.com>> wrote:
Dear Viktor,

The output you attached shows for step 28:
Max. gradient = 0.0002958006
Conv. limit for gradients = 0.0004500000
Conv. in gradients = YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Fabian

On Mon, Jan 24, 2022 at 4:22 PM fabia...@gmail.com<mailto:fabia...@gmail.com> <fabia...@gmail.com<mailto:fabia...@gmail.com>> wrote:
Dear Victor,

You need a much tighter convergence criterion for the optimization prior to the vibrational analysis. You increased MAX_FORCE to 5e-3 (guessing from the output), instead you have to decrease it to at least 1e-5, maybe even lower.
CP2K prints the forces for the replica in the output. The forces under "Minimum Structure - Energy and Forces:" should be more or less 0 and considerably differ between the other images. Currently you are computing the vibrational analysis from almost pure noise.

Cheers,
Fabian
On Sunday, 23 January 2022 at 19:58:05 UTC+1 volk...@gmail.com<mailto:volk...@gmail.com> wrote:
Dear colleagues:
here is the normal mode analysis I could manage by now for NaCl under PBC.

There is only one unit cell: previously, I reported that I could not configure CP2K to reproduce NaCl structure using multiple cells 2 2 2.
There are strange distortions, which I did confirm to sustain under different CUTOFF values (1000 and 600), and regardless if dispersion is switched off or not.

When a single cell under PBC, optimization leads to the “right” structure, when ESP 10^-12.

However, the negative(imaginary) frequencies are many and they are very large.
I may anticipate that the “miss performance” is enhanced due to the PBC.

Eventhough the results are "devastating",
:-)
nonetheless, I find this might be very good, very helpful – I got an idea.

Dear Dr. Hutter,
is it possible that CP2K may have an “issue” about positioning a structure
in respect to both, in respect to the FT grind and in respect to the PBC.
Perhaps, there could be a relative mismatch phenomenon, which could stimulate artificial transition states with negative frequencies?

May be, what I observe is that PBC on the unit cell helps to sense this better?


Thank you for your time and for any comments.

With best regards,
Sincerely
Victor

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Victor Volkov

unread,
Sep 21, 2022, 6:13:52 AMSep 21
to cp...@googlegroups.com
Dear Dr. Hutter:
thank you for the explanations.
With best regards,
Victor

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Victor Volkov

unread,
Sep 21, 2022, 2:07:55 PMSep 21
to cp...@googlegroups.com
Dear Dr. Hutter:
sorry to bother once again.
I have developed three approaches to explore trying to account the long-range correlations.

According to the first one, I only introduced  
OE_CORR SAOP
into &TDDFPT,
and such calculation runs without complain.

The second approach as you recommended - &BECKE88
The third one employs &AUXILIARY_DENSITY_MATRIX_METHOD

These trials do run but they complain
 *** WARNING in hfx_energy_potential.F:591 :: The Kohn Sham matrix is not 100% occupied.
 *** WARNING in hfx_types.F:1959 :: Periodic Hartree Fock calculation requested without use of a truncated or shortrange potential.

The system is a triclinic segment of graphene with pyrazine.
Would you find a moment to look at the inputs to express your opinion if the functional parameters are not optimal.
I would be grateful.
If neither energy nor will nor time - please, forgive and disregard.

Sincerely,
Victor



On Wed, Sep 21, 2022 at 11:25 AM Jürg Hutter <hut...@chem.uzh.ch> wrote:
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Gpz_td_admm.inp
Gpz_td_B88.inp
Gpz_td_B88.out
Gpz_td_admm.out

Matt Watkins

unread,
Sep 22, 2022, 9:57:23 AMSep 22
to cp2k
The first warning is harmless - see the FAQ
https://www.cp2k.org/faq:hfx_eps_warning
you can check if there is a big sensitivity to EPS_DEFAULT and EPS_PGF_ORB.

For the 2nd, you need to use a truncated coulomb interaction with periodic boudary conditions (as k-points not available atm with hybrids).
You need a section similar to:

      &HF
        &SCREENING
          EPS_SCHWARZ 5.0E-7
          SCREEN_ON_INITIAL_P .TRUE.
        &END
        &INTERACTION_POTENTIAL
          POTENTIAL_TYPE TRUNCATED
          CUTOFF_RADIUS 6
          T_C_G_DATA ./t_c_g.dat
        &END
        &MEMORY
          MAX_MEMORY 1750*8
          EPS_STORAGE_SCALING 0.1
        &END
        FRACTION 0.25
      &END

the cutoff_radius must be less than half the smallest cell dimension.
Matt

Victor Volkov

unread,
Sep 22, 2022, 11:50:05 AMSep 22
to cp...@googlegroups.com
Dear Matthew:
thank you for the kind answer and the great help.
With best regards,
:-)
Victor

Jürg Hutter

unread,
Sep 23, 2022, 3:32:42 AMSep 23
to cp...@googlegroups.com
Dear Victor

1) SAOP is a method/functional to address the long range potential in TDDFT.
It was implemented ca. 20 years ago, and I don't know if it still works correctly.
This was before we started regression tests.

2) A Coulomb cutoff is needed, e.g. for CAM-B3LYP
GAPW with TDDFT only with a very recent version of CP2K (TRUNK)
&INTERACTION_POTENTIAL
POTENTIAL_TYPE MIX_CL_TRUNC
OMEGA 0.33
SCALE_LONGRANGE 0.94979
SCALE_COULOMB 0.18352
! should be cell L/2 but large enough for the erf to decay
CUTOFF_RADIUS 2.5
T_C_G_DATA t_c_g.dat
&END

3) ADMM is an acceleration method for exact exchange. If you don't have a hybrid functional
it will just be ignored.

regards

JH


________________________________________
From: cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Victor Volkov <volk...@gmail.com>
Sent: Wednesday, September 21, 2022 8:07 PM
To: cp...@googlegroups.com
Subject: Re: [CP2K:17730] Re: IR spectm for NaCl under PBC

Dear Dr. Hutter:
sorry to bother once again.
I have developed three approaches to explore trying to account the long-range correlations.

According to the first one, I only introduced
OE_CORR SAOP
into &TDDFPT,
and such calculation runs without complain.

The second approach as you recommended - &BECKE88
The third one employs &AUXILIARY_DENSITY_MATRIX_METHOD

These trials do run but they complain
*** WARNING in hfx_energy_potential.F:591 :: The Kohn Sham matrix is not 100% occupied.
*** WARNING in hfx_types.F:1959 :: Periodic Hartree Fock calculation requested without use of a truncated or shortrange potential.

The system is a triclinic segment of graphene with pyrazine.
Would you find a moment to look at the inputs to express your opinion if the functional parameters are not optimal.
I would be grateful.
If neither energy nor will nor time - please, forgive and disregard.

Sincerely,
Victor



On Wed, Sep 21, 2022 at 11:25 AM Jürg Hutter <hut...@chem.uzh.ch<mailto:hut...@chem.uzh.ch>> wrote:
Dear Victor

printing of cube files for ED or excitation orbitals is unfortunately not implemented.

A simple hybrid functional, e.g. PBE0 (truncated HFX for PBC) could be a way to go.
For molecular systems, CAM-B3LYP is probably most popular. There is an example input,
but I have no experience how it performs in TDDFT calculations.

cp2k/tests/QS/regtest-hybrid-4/Ne_hybrid-rcam-b3lyp_tc.inp

regards

Juerg Hutter

________________________________________
From: cp...@googlegroups.com<mailto:cp...@googlegroups.com> <cp...@googlegroups.com<mailto:cp...@googlegroups.com>> on behalf of Victor Volkov <volk...@gmail.com<mailto:volk...@gmail.com>>
Sent: Tuesday, September 20, 2022 3:46 PM
To: cp...@googlegroups.com<mailto:cp...@googlegroups.com>
Subject: Re: [CP2K:17718] Re: IR spectm for NaCl under PBC

Dear Dr. Hutter:
good afternoon.
Sorry to bother with couple questions.

First, I wish to ask you if CP2K, when performing TD-DFT,
can print cubes (for ED and orbitals) using
"difference density matrix representation"?
Reviewers (possibly from the Q-chem community) inquire this since they consider the representation
to be more helpful in discussion of charge-transfer events at surfaces.

Second, the reviewers point that the GGA-PBE from CP2K is not any adequate in respect to computing charge transfers,
but long-range hybrid corrected functionals would have to be considered.
Would you recommend a sound alternative by CP2K to compare with the results by GGA-PBE?

Thank you.
With best regards,
Sincerely,
Victor



From: 'Václav Havel' via cp2k <cp...@googlegroups.com<mailto:cp...@googlegroups.com><mailto:cp...@googlegroups.com<mailto:cp...@googlegroups.com>>>
Sent: Saturday, May 14, 2022 3:51 AM
To: cp2k
Subject: Re: [CP2K:16978] Re: IR spectm for NaCl under PBC

Dear Viktor,
I have the same question about imaginary frequencies.
Have you tackled the problem of imaginary frequency ? It seems that just increasing the optimization criteria cannot eliminate all imaginary frequencies .

With best regards
Vaclav

On Friday, January 28, 2022 at 3:42:08 PM UTC+3 fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>> wrote:
Dear Viktor,

Several things:
- If you choose RUN_TYPE GEO_OPT then you should have MOTION&GEO_OPT and not MOTION&CELL_OPT and vice versa.
- Set EPS_DEFAULT to 1e-12
- For CELL_OPT: you should have a &CELL_REF section with dimensions approx. 1.3-1.5 times larger (test this!) than &CELL
- You need MULTIPLE_UNIT_CELL in &CELL_REF too

Cheers,
Fabian

On Thu, Jan 27, 2022 at 2:30 PM fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>> <fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>>> wrote:
cp2k works just fine and does everything you tell it to do. The issue is that you specified MAX_FORCE 1.0E-07 etc. for &GEO_OPT instead of &CELL_OPT...

On Thursday, 27 January 2022 at 11:39:21 UTC+1 volk...@gmail.com<mailto:volk...@gmail.com><mailto:volk...@gmail.com<mailto:volk...@gmail.com>> wrote:
Dear Fabian:
Dear Dr. Hutter:

is it possible that CP2K is present not to follow the input instructons?

According to my instructions (pleas, see attached)
in the MOTION section there are instructions
MAX_DR 8.0E-07
RMS_DR 4.0E-07
MAX_FORCE 1.0E-07
RMS_FORCE 1.0E-08

but
as Fabian has noticed:

The output you attached shows for step 28:
Max. gradient = 0.0002958006
Conv. limit for gradients = 0.0004500000
Conv. in gradients = YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Is it possible that there is a bug
that prevents a certain level of precision?

Thank you.
With best regards.

Victor




On Thu, Jan 27, 2022 at 12:00 PM fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>> <fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>>> wrote:
Dear Viktor,

The output you attached shows for step 28:
Max. gradient = 0.0002958006
Conv. limit for gradients = 0.0004500000
Conv. in gradients = YES

So that output is for MAX_FORCE 4.5E-4 and not 1.0E-7. You should also decrease EPS_SCF (to 1e-7 or 1e-8) and probably EPS_DEFAULT.

Fabian

On Mon, Jan 24, 2022 at 4:22 PM fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>> <fabia...@gmail.com<mailto:fabia...@gmail.com><mailto:fabia...@gmail.com<mailto:fabia...@gmail.com>>> wrote:
Dear Victor,

You need a much tighter convergence criterion for the optimization prior to the vibrational analysis. You increased MAX_FORCE to 5e-3 (guessing from the output), instead you have to decrease it to at least 1e-5, maybe even lower.
CP2K prints the forces for the replica in the output. The forces under "Minimum Structure - Energy and Forces:" should be more or less 0 and considerably differ between the other images. Currently you are computing the vibrational analysis from almost pure noise.

Cheers,
Fabian
On Sunday, 23 January 2022 at 19:58:05 UTC+1 volk...@gmail.com<mailto:volk...@gmail.com><mailto:volk...@gmail.com<mailto:volk...@gmail.com>> wrote:
Dear colleagues:
here is the normal mode analysis I could manage by now for NaCl under PBC.

There is only one unit cell: previously, I reported that I could not configure CP2K to reproduce NaCl structure using multiple cells 2 2 2.
There are strange distortions, which I did confirm to sustain under different CUTOFF values (1000 and 600), and regardless if dispersion is switched off or not.

When a single cell under PBC, optimization leads to the “right” structure, when ESP 10^-12.

However, the negative(imaginary) frequencies are many and they are very large.
I may anticipate that the “miss performance” is enhanced due to the PBC.

Eventhough the results are "devastating",
:-)
nonetheless, I find this might be very good, very helpful – I got an idea.

Dear Dr. Hutter,
is it possible that CP2K may have an “issue” about positioning a structure
in respect to both, in respect to the FT grind and in respect to the PBC.
Perhaps, there could be a relative mismatch phenomenon, which could stimulate artificial transition states with negative frequencies?

May be, what I observe is that PBC on the unit cell helps to sense this better?


Thank you for your time and for any comments.

With best regards,
Sincerely
Victor

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Victor Volkov

unread,
Sep 23, 2022, 5:39:17 AMSep 23
to cp...@googlegroups.com
Dear Dr. Hutter:
good morning.
Thank you for the explanations.
Sincerely,
Victor

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