[CP2K-user] [CP2K:11473] Re: Water-bilayer/Metal interface - Ab intio MD

[Anna Anic]

Hi,

Thank you for all the help/suggestions. So I decided to simply run the
simulation with a fully solvated box. I also included smearing, as this is
a metallic system. To set the timestep equal to 1fs  I used the deuterium
mass for the hydrogen atoms  (I also tried with the normal H-atom and 0.5
fs timestep). The calculations always start with no problem but also always
stop at a certain MD step. The error file says it is a segmentation fault,
but I have no clue what this implies: is it my input file, or some
compilation error (I never compiled cp2k on my own). I included my geometry
file - frame.xyz the cp2k.in/out  and the error file. Would appreciate any
suggestions.

Greetings,
Anna

Am Sa., 20. Apr. 2019 um 11:29 Uhr schrieb Anna Anic <aan... at gmail.com>:

> Hi,
>
> Thank you for all the help/suggestions. So I decided to simply run the
> simulation with a fully solvated box. I also included smearing, as this is
> a metallic system. To set the timestep equal to 1fs  I used the deuterium
> mass for the hydrogen atoms  (I also tried with the normal H-atom and 0.5
> fs timestep). The calculations always start with no problem but also always
> stop at a certain MD step. The error file says it is a segmentation fault,
> but I have no clue what this implies: is it my input file, or some
> compilation error (I never compiled cp2k on my own). I included my geometry
> file - frame.xyz the cp2k.in/out, the trajectrory.xyz, force.xyz and the
> error file. Would appreciate any suggestions.
>
> Greetings,
> Anna
>
> Am Fr., 22. März 2019 um 19:28 Uhr schrieb Travis <polla... at gmail.com>:
>
>> Hi,
>>
>> The potentials you apply are only zero at their nodes (z=8 and z=55) and
>> they are non-zero everywhere else in your box, explaining the windswept
>> appearance of your water hydrogens. You would need to supply a cube file
>> with these potentials evaluated numerically at each grid point for z < 8
>> and z > 55 and zero in between. Even so, the bilayer will decompose before
>> making contact with the barrier, so I'm not sure this approach is better
>> than just simulating with the aqueous phase as you did previously. You can
>> also simulate with 2D PBC using the wavelet solver and place a 2 nm slab of
>> water on only one side of the oxide (then a bit of vacuum for the densities
>> to trail to ~0 near the boundary in the non-periodic axis), see page 66 of
>> https://tel.archives-ouvertes.fr/tel-01839221/document for an example of
>> what this setup looks like.
>>
>> -T
>>
>>
>>
>> On Thursday, March 21, 2019 at 3:52:02 PM UTC-4, Anna Anic wrote:
>>
>>> PS: I appended the corresponding output file and force.xyz
>>> This was just a 30 min. test run to check if the parameters work
>>>
>>>
>>> Am Do., 21. März 2019 um 20:43 Uhr schrieb Anna Anic <a... at gmail.com>:
>>>
>>>> Dear Marcella,
>>>>
>>>> Thank you very much for the quick response.
>>>> To answer your questions:
>>>> 1. Before I did the MD part I performed energy convergence test for the
>>>> slab thickness and size, then a geometry optimization for the bulk and slab
>>>> with and without adsorbate with a 20 Angstrom thick vacuum level
>>>>
>>>> But I just realized that the coordinates in the input file are not from
>>>> the optimized structure. But I think that the water bilayer still should
>>>> not behave like this
>>>>
>>>> 2. All structures converged during these calculations and surface free
>>>> energies (SFE) are similar to reference values from other works
>>>> 3. I did not calculate the binding energy for water molecules. Is this
>>>> relevant if the SFE values seem to be oke?
>>>> 4. The layers of the water molecules should represent the water
>>>> structure in the Double Layer of an electrode/electrolyte interface. I took
>>>> the geometry of the bilayer from a paper, that claims that the water at the
>>>> interface is ice-like. I want to check if it stays that way (probably not)
>>>> and sample as many water orientations (as this changes the work function)
>>>> as possible.
>>>> 5. Concerning the MD part I did not anneal the structure slowly. But I
>>>> did the same calculation with a fully solvated system, so the whole vacuum
>>>> region was filled with water, and the movement of the water molecules
>>>> seemed reasonable.
>>>> What temperature steps for the anneling would you suggest ?
>>>> And do you maybe have some example input block for that?
>>>>
>>>> In general, do you think that the external potential with the parabolic
>>>> function is oke to keep the water molecules within a certain region from
>>>> the surface?
>>>>
>>>>
>>>>
>>>> Greetings,
>>>> Anna
>>>>
>>>>
>>>> Am Do., 21. März 2019 um 17:00 Uhr schrieb Marcella Iannuzzi <
>>>> ma... at gmail.com>:
>>>>
>>>>>
>>>>> Dear Anna,
>>>>>
>>>>>
>>>>> which type of calculations did you carry out in preparation of the MD
>>>>> run?
>>>>> Is your DFT model reproducing the correct lattice structure?
>>>>> Did you optimise the slab and check that the electronic structure of
>>>>> the bulk and at the surface is what expected from reference data?
>>>>> I do not know this specific system, but the parameters in the DFT
>>>>> section seem to be not very well tuned. Is the SCF converging? Do you get
>>>>> reasonable forces?
>>>>>
>>>>> Did you model the adsorption of individual water molecules to evaluate
>>>>> the binding energy and compare to references?
>>>>> Should the layer of molecules be ice-like or do you want to simulate
>>>>> liquid water?
>>>>> If the coordinates are obtained from some structural data or geometry
>>>>> optimisation, did you anneal slowly from 0K to the final temperature?
>>>>> Why are you running NPE? Did you already thermalised at constant
>>>>> volume?
>>>>>
>>>>> Kind regards
>>>>> Marcella
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thursday, March 21, 2019 at 3:55:19 PM UTC+1, Anna Anic wrote:
>>>>>>
>>>>>> Hey everybody,
>>>>>>
>>>>>> I am trying to do Ab-initio MD for a metal-water interface. I am
>>>>>> using a symmetric slab and positioned a bilayer of water at both surface
>>>>>> sites.
>>>>>> Now, if I run the simulation my water layer just decomposes into the
>>>>>> vacuum region. That is why I would like to implement an vacuum potential
>>>>>> barrier at some point in the z-direction to prevent my water from just
>>>>>> "flying away".
>>>>>> I tried using the &EXTERNAL_POTENTIAL keyword and defined a harmonic
>>>>>> function as a barrier.
>>>>>> But when I run the simulation the hydrogen atoms from the
>>>>>> H2O-bilayer  are "blown away".
>>>>>> The question is, what did I do wrong? Is the idea legit? Does anyone
>>>>>> have a proposal how to fix the problem or how to do it differentey.
>>>>>>
>>>>>> Greetings,
>>>>>>
>>>>>> Anna
>>>>>>
>>>>>> (I attached my input file,geometry and trajectory )
>>>>>>
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