[CP2K:10243] Re: rewrite cp2k cube file for Henkelman's code

[Ada Sedova]

Oh wow, excellent!  How does one post-process?

On Tue, May 1, 2018 at 4:06 PM, Matt W <mattwa... at gmail.com> wrote:

> The code is
>
>          IF (dft_control%qs_control%gapw) THEN
>             CALL pw_transfer(rho0_s_gs%pw, wf_r%pw)
>             IF (dft_control%qs_control%gapw_control%nopaw_as_gpw) THEN
>                CALL pw_axpy(rho_core%pw, wf_r%pw)
>             END IF
>          ELSE
>             CALL pw_transfer(rho_core%pw, wf_r%pw)
>          END IF
>
>
> So for GPW it will add in a Gaussian charge with value +Zeffective centred
> on the atoms the same as is done when calculating electrostatics (see
> original paper).
>
> It is quite possible to post process the results of a trajectory to add in
> an atom centred density.
>
> Matt
>
> On Tuesday, May 1, 2018 at 8:54:09 PM UTC+1, Ada Sedova wrote:
>>
>> 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 <matt... 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
>>>>>>>>>
>>>>>>>> --
>>>>>>>> You received this message because you are subscribed to a topic in
>>>>>>>> the Google Groups "cp2k" group.
>>>>>>>> To unsubscribe from this topic, visit
>>>>>>>> https://groups.google.com/d/topic/cp2k/IVj1WAxCAYs/unsubscribe.
>>>>>>>> To unsubscribe from this group and all its topics, send an email to
>>>>>>>> cp2k+... at googlegroups.com.
>>>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>>>> Visit this group at https://groups.google.com/group/cp2k.
>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>> You received this message because you are subscribed to a topic in the
>>>>> Google Groups "cp2k" group.
>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/to
>>>>> pic/cp2k/IVj1WAxCAYs/unsubscribe.
>>>>> To unsubscribe from this group and all its topics, send an email to
>>>>> cp2k+... at googlegroups.com.
>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>> Visit this group at https://groups.google.com/group/cp2k.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>
>>>> --
>>> You received this message because you are subscribed to a topic in the
>>> Google Groups "cp2k" group.
>>> To unsubscribe from this topic, visit https://groups.google.com/d/to
>>> pic/cp2k/IVj1WAxCAYs/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> cp2k+... at googlegroups.com.
>>> To post to this group, send email to cp... at googlegroups.com.
>>> Visit this group at https://groups.google.com/group/cp2k.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
> You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/cp2k/IVj1WAxCAYs/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at https://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20180501/bcfe6d1a/attachment.htm>