[CP2K-user] [CP2K:17737] Re: IR spectm for NaCl under PBC

Victor Volkov volkovskr at gmail.com
Thu Sep 22 15:49:47 UTC 2022
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Dear Matthew:
thank you for the kind answer and the great help.
With best regards,
:-)
Victor

On Thu, Sep 22, 2022 at 4:57 PM Matt Watkins <mattwatkinsuk at gmail.com>
wrote:

> 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
>
> On Wednesday, 21 September 2022 at 19:07:55 UTC+1 volk... at gmail.com wrote:
>
>> 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... at 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... at googlegroups.com <cp... at googlegroups.com> on behalf of
>>> Victor Volkov <volk... at gmail.com>
>>> Sent: Tuesday, September 20, 2022 3:46 PM
>>> To: cp... at 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
>>>
>>>
>>>
>>> On Mon, May 16, 2022 at 1:56 PM Jürg Hutter <hut... at chem.uzh.ch<mailto:
>>> hut... at chem.uzh.ch>> wrote:
>>> 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... at googlegroups.com<mailto:
>>> cp... at 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
>>>
>>> 在2022年3月6日星期日 UTC+8 00:29:21<volk... at gmail.com<mailto:volk... at gmail.com>>
>>> 写道：
>>> 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
>>>
>>>
>>> On Friday, January 28, 2022 at 3:42:08 PM UTC+3 fabia... at gmail.com
>>> <mailto:fabia... at 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 Friday, 28 January 2022 at 09:30:16 UTC+1 volk... at gmail.com<mailto:
>>> volk... at gmail.com> wrote:
>>> 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
>>>
>>>
>>>
>>> On Thu, Jan 27, 2022 at 2:30 PM fabia... at gmail.com<mailto:
>>> fabia... at gmail.com> <fabia... at gmail.com<mailto:fabia... at 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... at gmail.com<mailto:
>>> volk... at 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... at gmail.com<mailto:
>>> fabia... at gmail.com> <fabia... at gmail.com<mailto:fabia... at 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 Wednesday, 26 January 2022 at 21:12:03 UTC+1 volk... at gmail.com
>>> <mailto:volk... at gmail.com> wrote:
>>> 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... at gmail.com<mailto:
>>> fabia... at gmail.com> <fabia... at gmail.com<mailto:fabia... at 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... at gmail.com<mailto:
>>> volk... at 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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