[CP2K:10240] Re: rewrite cp2k cube file for Henkelman's code

[Ada Sedova]

Right- I know you said that. The response from David didn't seem to relate
to the original question. You also said you hadn't tried it. The link to
the cp2k forum discussion I added above shows that it does not in fact add
it, if you are not using GAPW.

So, the question is, does it add it or not? It seems from the above, it
does not. Someone familiar with the code would have to determine if this is
true or not. For me, I have tens of picoseconds of simulation for systems
with hundred of atoms, and re-running this to check would be a pain. I
would do it if I knew for sure it would work. I'm trying to monitor the
changing densities.



On Tue, May 1, 2018 at 1:21 PM, Matt W <mattwa... at gmail.com> wrote:

> According to Matt, just running with the TOTAL...etc command will add the
>> core electrons. Are you saying this works? Because a previous thread,
>> linked above, describes this as not working unless you are using GAPW, not
>> just GPW.
>>
>>
> Hi Ada,
>
> no, I said it would a add in a core charge at the nuclei equal to the Z
> effective of the pseudo at the atom centre.
>
> What is required for getting a correct topological description to get AIM
> descriptors? I haven't read up on it.
>
> Adding in an atomic density that does not respond to the valence density
> could be made into a fairly simple post-processing step - is that what is
> needed, the [core] atom density (from an isolated atom) added to the
> density cube file?
>
> Matt
>
>
>
>
>> -Ada
>>
>>
>>
>> On Tue, May 1, 2018 at 9:33 AM, David T <amazi... at gmail.com> wrote:
>>
>>> You are right Matt.
>>> I did it for the 1st time in this article:
>>> https://pubs.acs.org/doi/abs/10.1021/jp901753p
>>>
>>> Sadly Henkelman and VASP persons have started using my Algorithm without
>>> citing it... but that is another story....
>>>
>>>
>>> On Tuesday, 17 April 2018 19:19:13 UTC+1, Matt W wrote:
>>>>
>>>> I _think_ it should add the approximate core charge for GPW (i.e. a
>>>> gaussian with charge +Z centred on the atom), which should be enough for
>>>> the correct topology for AIM.
>>>>
>>>> I'm not speaking from experience though. May well be wrong.
>>>>
>>>> On Tuesday, April 17, 2018 at 7:08:09 PM UTC+1, Ada Sedova wrote:
>>>>>
>>>>> I think that only works if you're using GAPW, though, am I right?
>>>>> Because if you are not calculating the core electrons they won't print? At
>>>>> least that's according to another thread I read on this forum...
>>>>>
>>>>> On Tue, Apr 17, 2018 at 12:49 PM, Matt W <matt... at gmail.com> wrote:
>>>>>
>>>>>> https://manual.cp2k.org/cp2k-5_1-branch/CP2K_INPUT/FORCE_EVA
>>>>>> L/DFT/PRINT/TOT_DENSITY_CUBE.html
>>>>>>
>>>>>> I think.
>>>>>>
>>>>>> On Tuesday, April 17, 2018 at 5:14:12 PM UTC+1, Ada Sedova wrote:
>>>>>>>
>>>>>>> Hi all-
>>>>>>> There was a thread from 2016 about finding a way to add core
>>>>>>> electrons to a cp2k cube file so that Bader analysis can be performed with
>>>>>>> Henkelman's code, which takes cube files, but of the Gaussian format, which
>>>>>>> includes all electrons. There was no definitive solution posted, but a
>>>>>>> suggestion was to hack the Manz DDEC code to add core electrons and print
>>>>>>> out a new cube. The Manz code has gone through some changes and a brief
>>>>>>> look at it did not reveal a rewrite option.
>>>>>>>
>>>>>>> I was wondering if there have been any updates on the ability to use
>>>>>>> Henkelman's with a cp2k cube file. The other option would be to create a
>>>>>>> VASP CHGCAR file from a cp2k cube file, but the core electrons still need
>>>>>>> to be added somehow.
>>>>>>>
>>>>>>> Thanks!
>>>>>>> AS
>>>>>>>
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>>>>>
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