[ase-users] BEEF-vdW ensemble mean vs energy

Rune Christensen runch at dtu.dk
Thu Apr 20 10:48:41 CEST 2017 

Hi Manuel

That is only true for balanced reactions. For individual calculations there is an offset. 

In the below I have calculated electronic energies of OH* on Pt111 with the main BEEF-vdW functional and a BEEF ensemble of size 2000.

	OH*@Pt_slab	Pt_slab	H2	H2O		OH*@Pt_slab+H2/2- Pt_slab - H2O
E_U	-65.80235945	-57.14552399	-7.458367	-13.123977		0.73795804
<ENS>	-59.35023216	-50.93147788	-7.411974999	-12.865059		0.74031721
diff	-6.452127285	-6.21404611	-0.046392001	-0.258918005		-0.00235917

The difference between the electronic energy with the BEEF-vdW main functional and the ensemble average is in some cases quite large. However, when you balance the reaction to calculate the adsorption energy (right most column) you will see that the difference is nearly gone. 

Best,
Rune


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Emne: ase-users Digest, Vol 106, Issue 17

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Today's Topics:

   1. Re: Split POSCAR/CONTCAR files (Oscar Xavier Guerrero)
   2. BEEF-vdW ensemble mean vs energy (Manuel ?aric)


----------------------------------------------------------------------

Message: 1
Date: Wed, 19 Apr 2017 11:11:35 -0500
From: Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>
To: fabian <Fabian.T89 at web.de>
Cc: ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] Split POSCAR/CONTCAR files
Message-ID:
        <CAM0Hkbf+icJDMPY1297CkebBfVCAV5Hd3PD33Jk71sPDwJRBqA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

No, you would have to use in:

slab_elms = ['Cu', 'O']
slab_i = [a.index for a in atoms if a.symbol *in slab_elms*]

This is correct only if you have no O in your adsorbate. Otherwise, it
would be better to use height to separate.


2017-04-19 2:56 GMT-05:00 fabian <Fabian.T89 at web.de>:

> Dear Oscar,
> Thank you very much for your fast reply! This is exactly what i want to do!
>
>
> If my slab consist of different species , for example Cu and O atoms, is
> it correct to change this line
>
>
> slab_i = [a.index for a in atoms if a.symbol == 'Cu']
>
>
> to
>
>
>
> slab_i = [a.index for a in atoms if a.symbol == 'Cu','O'] ?
>
>
> All the best
>
>
> fabian
>
>
> Am 18.04.2017 um 23:25 schrieb Oscar Xavier Guerrero:
>
> Sorry, in the previous example I forgot to convert from list to an atoms
> object.
>
> This should work:
>
> from ase.io import read, write
> from ase.atoms import Atoms
> atoms = read('CONTCAR')
> # assuming the slab is only composed of Cu and the adsorbate has no Cu
> slab_i = [a.index for a in atoms if a.symbol == 'Cu']
> ads_i = [a.index for a in atoms if a.symbol != 'Cu']
> # you could also use height as the threshold
> th = max(a.z for a in atoms if a.symbol == 'Cu')
> # you can also use constraints to set the th
> slb = {atoms[i].symbol for i in atoms.constraints[0].index}
> th = max(a.z for a in atoms if a.symbol in alb)
>
> slab_i = [a.index for a in atoms if a.z <= th]
> ads_i = [a.index for a in atoms if a.z > th]
>
> # this is a quick fix, maybe there's a better method
> slab = atoms.copy()
> for i in sorted(ads_i, reverse=True):
>     del slab[i]
> ads = atoms.copy()
> for i in sorted(slab_i, reverse=True):
>     del ads[i]
>
> # or you could use Atoms
> slab = Atoms([a for a in atoms if a.index in slab_i])
> ads = Atoms([a for a in atoms if a.index in ads_i])
> cell = atoms.get_cell()
> slab.set_cell(cell)
> ads.set_cell(cell)
> constraint = atoms.constraints[0]
> slab.set_constraints(constraint)
> ads.set_constraints(constraint)
>
> write('slab.vasp', slab, vasp5=True, sort=True, direct=True, format='vasp')
> write('ads.vasp', ads, vasp5=True, sort=True, direct=True, format='vasp')
>
> If you have any questions I'm happy to help.
>
>
> 2017-04-18 15:53 GMT-05:00 Oscar Xavier Guerrero <oscarxavier.ox at gmail.com
> >:
>
>> Hello Fabian,
>>
>> You can read POSCAR/CONTCAR files with ase.io.read, you get an atoms
>> object with all the information the file had. Then you can copy parts of
>> that atoms object into other atoms object. Then use the ase.io.write
>> function to write POSCAR files for each of the new atoms objects. Since you
>> have a slab and an adsorbate, you can use the height as a threshold. It
>> really depends on your systems.
>>
>> Here's an example:
>>
>> from ase.io import read, write
>> atoms = read('CONTCAR')
>> # assuming the slab is only composed of Cu and the adsorbate has no Cu
>> slab = [a for a in atoms if a.symbol == 'Cu']
>> ads = [a for a in atoms if a.symbol != 'Cu']
>> # you could also use height as the threshold
>> th = max(a.z for a in atoms if a.symbol == 'Cu')
>> # you can also use constraints to set the th
>> slb = {atoms[i].symbol for i in atoms.constraints[0].index}
>> th = max(a.z for a in atoms if a.symbol in alb)
>>
>> slab = [a for a in atoms if a.z <= th]
>> ads = [a for a in atoms if a.z > th]
>>
>> write('slab.vasp', slab, vasp5=True, sort=True, direct=True,
>> format='vasp')
>> write('ads.vasp', ads, vasp5=True, sort=True, direct=True, format='vasp')
>>
>> If you have any questions I'm happy to help.
>>
>> P.S. heres my github with some of my scripts. https://github.com/iz
>> xle/VaspTools
>>
>>
>>
>>
>>
>>
>>
>>
>> 2017-04-18 2:52 GMT-05:00 fabian via ase-users <
>> ase-users at listserv.fysik.dtu.dk>:
>>
>>> Dear all,
>>>
>>> I want to perform a series of charge density difference calculations. Therefore i want to split the geometry optimised CONTCAR file
>>> containing the coordinates from the slab and the Molecule into tow files containing only slab or Molecule coordinates. At the moment i am doing this
>>> manually. Can someone give me a hint how to read positions and constraints as well as atom types from the POSCAR/CONTCAR files and later write them into two new POSCAR Files?
>>> I would like to be able to either fix all atomic coordinates or leave the as they are.
>>> Atom types could also be extracted from OUTCAR or POTCAR files. For now it is sufficient to perform the split based on the ATOM tag.
>>> Unfortunately i am completely stuck.
>>>
>>> All the best
>>>
>>> fabian
>>>
>>>
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>
>>
>>
>
>
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Message: 2
Date: Thu, 20 Apr 2017 07:55:39 +0000
From: Manuel ?aric <msaric at fysik.dtu.dk>
To: "ase-users at listserv.fysik.dtu.dk"
        <ase-users at listserv.fysik.dtu.dk>
Subject: [ase-users] BEEF-vdW ensemble mean vs energy
Message-ID:
        <1CA2EC7E0C81D94593070449293978AE1D589FDF at ait-pex02mbx04.win.dtu.dk>
Content-Type: text/plain; charset="Windows-1252"

Hi everyone,

I have a question about something that I'm not sure I quite understand.

Let's say I have a system and I do a calculation with BEEF-vdW.
I can get the ensemble of that system (ens) and the potential energy (e).

Shouldn't the mean of the ensemble (ens) give the potential energy (e)?

mean(ens) == e ???

Cheers,

Manuel


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