[CP2K-user] [CP2K:16980] Re: IR spectm for NaCl under PBC
Victor Volkov
volkovskr at gmail.com
Sat May 14 08:57:37 UTC 2022
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
On Saturday, May 14, 2022 at 4:51:48 AM UTC+3 10751... at qq.com wrote:
> 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> 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 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 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 <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
>>>>> 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 <
>>>>>> 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
>>>>>>> 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 <
>>>>>>>> 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
>>>>>>>>> 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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