[CP2K:10546] Huge difference in adsorption energies between CP2K and VASP with PBE

Sharma SRK Chaitanya Yamijala sharma... at gmail.com
Wed Jul 18 22:06:05 UTC 2018


Hi Gabriele,

Thanks a lot for trying to help me. Can I send all these files to you off
the list?

Also, can you send any references of the papers which published the
adsorption energies with ZnO(10-10) using CP2K. I really, couldn't find
anything for CO on ZnO from the google scholar search!

Are you by any chance the first author of this paper? "Solvent-Induced
Proton Hopping at a Water–Oxide Interface"

Thanks,
Sharma.





--------------------------------------------------------------------
SRK *Chaitanya* Sharma, Yamijala.
http://www.bmwong-group.com/group-members/


On Wed, Jul 18, 2018 at 2:08 PM, Gabriele <gabri... at gmail.com> wrote:

> Hi,
>
> You can use MT with a vacuum region larger than the slab thickness and a
> centered cell. You can also use an orthorhombic cell for this system. It
> should not make up for 0.4 eV of difference though.
>
> Previous adsorption studies on ZnO(10-10) using DZVP-MOLOPT did not show
> more than a few meV difference in adsorption energies compared to plane
> wave codes.
>
> Can you please upload the inputs, output and .restart file only for the
> calculation at 0.5ML coverage on the 6x3 cell, that for a clean slab and a
> CO molecule in vacuum?
>
> Cheers,
> Gabriele
>
>
> On Wednesday, July 18, 2018 at 7:53:04 PM UTC+2, Sharma SRK Chaitanya
> Yamijala wrote:
>>
>> Hi Gabriele,
>>
>> Thanks for your suggestions. I too have thought about the vacuum space
>> and I have already submitted some jobs with higher vacuum (Till now, I have
>> used 15 Ang vacuum. Now, I have submitted with 20 Ang vacuum space along
>> with TZV2P basis) and I will try to update them when they complete. Can you
>> please suggest which Poisson solvers are best for the XY periodicity and
>> may I know whether there is any possibility to include such
>> dipole-correction schemes with CP2K?
>>
>> Regarding 2x1 cell, yes, I have indeed started with this cell but I
>> couldn't optimize this cell using CP2K (even with 10x10x1 k-mesh) and 1000
>> Ry cutoff. It always goes to very high energies right from the first
>> geometry cycle (I have started from an already optimized geometry. Also,
>> the same geometry, when extended to form 4x4 or 6x3 runs fine with CP2K.
>> So, I believe the problem of convergence could be because of the k-point
>> related issues for the non-cubic cells in CP2K). So, I switched to a 4x4
>> cell, directly (which I could optimize).
>>
>> Regarding coverages, yes, I have performed many coverage dependent
>> studies on a 6x3 cell (with DZVP basis) and I found the energy per
>> adsorbate to be almost the same for all of them (-0.83 eV for 9 COs to
>> -0.86 eV for 1 CO). A 6x3 cell with 9 COs will be equivalent to a 2x1 cell
>> with 1 CO (we confirmed this by calculating the energy per adsorbate values
>> for 2x1 (-0.265 eV) and 6x3 (-0.267 eV) cells using VASP. With VASP, I
>> could converge both 2x1 cell and 6x3 cells).
>>
>> Thanks,
>> Sharma.
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------
>> SRK *Chaitanya* Sharma, Yamijala.
>> http://www.bmwong-group.com/group-members/
>>
>>
>> On Wed, Jul 18, 2018 at 2:06 AM, Gabriele <gabr... at gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I had a look at the  paper you mentioned http://iopscience.io
>>> p.org/article/10.1088/0953-8984/15/2/112/pdf. It seems that the number
>>> you gave is 0.32 eV. This is for a 2x1 structure, which is 1/2ML coverage
>>> as quoted in the table. 1ML coverage is defined by 1 CO molecule adsorbed
>>> per surface Zn atom. However, the coverage in your input structure is much
>>> smaller, i.e. 1/16ML, as there is only one CO molecule per 16 ZnO surface
>>> unit cells. Is the input you posted the same input you used to get the
>>> values of the adsorption energies reported above? Did you indeed adsorb 8
>>> CO molecules in a 2x1 periodicity?
>>>
>>> On a probably less important note, the paper you quoted has also applied
>>> a dipole correction. Although CO has a small dipole, this might play a
>>> role, so you might want to consider removing the periodicity along z or
>>> check the results running also a larger vacuum region.
>>>
>>> Cheers,
>>> Gabriele
>>>
>>>
>>> On Tuesday, July 17, 2018 at 9:46:32 PM UTC+2, Sharma SRK Chaitanya
>>> Yamijala wrote:
>>>
>>>> Dear Prof. Hutter,
>>>>
>>>> Here are the results with TZVP, TZV2P basis. For Zn, I got the basis
>>>> from BASIS_MOLOPT_UCL and for all the other atoms, from BASIS_MOLOPT.
>>>>
>>>> Clearly, the results with larger basis seem better (though not yet
>>>> matching with the literature reported values). Could you please suggest
>>>> anything else which I could change to improve these adsorption energies? I
>>>> am trying to get the correct binding energies because I would like to use
>>>> CP2K to study the desorption dynamics of these adsorbates (using MD runs).
>>>> If the binding energies are not reasonable (without BSSE), then the results
>>>> with the MD will be less meaningful (Here, I am supposing that there is no
>>>> way to include BSSE while running MD).
>>>>
>>>> Seeking your advice,
>>>> Sincerely,
>>>> Sharma.
>>>>
>>>> in 4x4 cell with dispersion
>>>> 1CO (DZVP) -589.596
>>>> 1CO (TZVP) -589.879
>>>> 1CO (TZV2P) -589.951
>>>> 1CO2 (DZVP) -1027.520
>>>> 1CO2 (TZVP) -1027.697
>>>> 1CO2 (TZV2P) -1027.710
>>>>
>>>>
>>>> (opt param: A=3.28, C=5.293) with dispersion
>>>> 4x4 + DZVP -266793.347
>>>> 4x4 + TZVP -266798.943
>>>> 4x4 + TZV2P -266799.744
>>>>
>>>>
>>>> Basis Set effect Total energy (eV) Adsorption energy (eV)
>>>> 4x4+1CO (DZVP) -267383.806 -0.863
>>>> 4x4+1CO (TZVP) -267389.552 -0.730
>>>> 4x4+1CO (TZV2P) -267390.371 -0.676
>>>> 4x4+1CO2 (DZVP) -267821.300 -0.434
>>>> 4x4+1CO2 (TZVP) -267827.040 -0.399
>>>> 4x4+1CO2 (TZV2P) -267827.857 -0.404
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --------------------------------------------------------------------
>>>> SRK *Chaitanya* Sharma, Yamijala.
>>>> http://www.bmwong-group.com/group-members/
>>>>
>>>>
>>>> On Mon, Jul 16, 2018 at 11:07 AM, Sharma SRK Chaitanya Yamijala <
>>>> shar... at gmail.com> wrote:
>>>>
>>>>> Dear Prof. Hutter,
>>>>>
>>>>> Thank you very much for your help. Following the last equations which
>>>>> you wrote for energy, I have E1(uncorrected adsorption energy) =
>>>>> -0.863 eV and E2 (counterpoise correction) = +1.0669. So, from the
>>>>> way the BSSE corrected adsorption energy is defined, I am getting *+0.204
>>>>> eV* which suggests that the *adsorption is thermodynamically not
>>>>> feasible*. I am getting negative values with VASP and FHIAIMS.
>>>>>
>>>>> However, I would like to point that, when I consider the results of a
>>>>> BSSE calculation (majorly the one-body contribution results) and calculate
>>>>> the counterpoise correction (E2 = ((4)-(5)) +((6)-(7))), then I obtain *zero
>>>>> correction* to the adsorption energy (because the energy of 4 = 5 and
>>>>> 6 = 7). Even following eq13 of this
>>>>> <http://vergil.chemistry.gatech.edu/notes/cp.pdf> document by Prof.
>>>>> Sherrill, I am obtaining basically zero correction. Thus, I believe the
>>>>> printed value of counterpoise correction in the CP2K output is (1 - 5 - 7)
>>>>> and not ((4)-(5)) +((6)-(7))).
>>>>>
>>>>> My runs with TZVP calculation are not finished yet and I will try to
>>>>> update the results when they are finished. If you get time, could you
>>>>> please suggest anything else which I may need to change in the input
>>>>> or anything you feel suspicious in the input?
>>>>>
>>>>> Here are the energies for all the terms which you have mentioned in
>>>>> the earlier email.
>>>>>
>>>>> System      Geometry from      Basis     Energy (eV)
>>>>>
>>>>> 1  A+B          A+B                    A+B      -267383.806
>>>>> 2      A               A                        A           -589.596
>>>>> 3      B               B                        B      -266793.347
>>>>> 4      A           A+B                        A           -589.596 (Take
>>>>> the A geometry from A+B and do a single point calculation)
>>>>> 5      A           A+B                   A+B            -589.596
>>>>> (From one body contribution result of BSSE calculation)
>>>>> 6      B           A+B                       B       -266793.143
>>>>> (Take the B geometry from A+B and do a single point calculation)
>>>>> 7      B           A+B                   A+B       -266793.143 (From
>>>>> one body contribution result of BSSE calculation)
>>>>>
>>>>> Thanks,
>>>>> Sharma.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --------------------------------------------------------------------
>>>>> SRK *Chaitanya* Sharma, Yamijala.
>>>>> http://www.bmwong-group.com/group-members/
>>>>>
>>>>>
>>>>> On Sat, Jul 14, 2018 at 9:28 AM, <hut... at chem.uzh.ch> wrote:
>>>>>
>>>>>> Hi
>>>>>>
>>>>>> assuming you did all calculations correctly, you should have the
>>>>>> following 7 energies ready
>>>>>>
>>>>>> System      Geometry from      Basis
>>>>>>
>>>>>> 1  A+B          A+B            A+B
>>>>>> 2  A            A              A
>>>>>> 3  B            B              B
>>>>>> 4  A            A+B            A
>>>>>> 5  A            A+B            A+B
>>>>>> 6  B            A+B            B
>>>>>> 7  B            A+B            A+B
>>>>>>
>>>>>> The uncorrected adsorption energy is     :  E1 = (1) - (2+3)
>>>>>>
>>>>>> Counterpoise correction energy is        :  E2 = ((4)-(5)) +((6)-(7))
>>>>>>
>>>>>> BSSE corrected adsorption energy is      :  Ea = E1 + E2
>>>>>>
>>>>>>
>>>>>> E1 is too negative because of BSSE.
>>>>>> Counterpoise correction is positive because larger basis stabilises
>>>>>> systems.
>>>>>> Typically the counterpoise correction is 0-50% of the non-corrected
>>>>>> energy
>>>>>> (depending on the system and the basis)
>>>>>>
>>>>>> regards
>>>>>>
>>>>>> Juerg
>>>>>>
>>>>>> --------------------------------------------------------------
>>>>>> Juerg Hutter                         Phone : ++41 44 635 4491
>>>>>> Institut für Chemie C                FAX   : ++41 44 635 6838
>>>>>> Universität Zürich                   E-mail: hut... at chem.uzh.ch
>>>>>> Winterthurerstrasse 190
>>>>>> <https://maps.google.com/?q=Winterthurerstrasse+190+%0D%0ACH-8057+Z%C3%BCrich,+Switzerland&entry=gmail&source=g>
>>>>>> CH-8057 Zürich, Switzerland
>>>>>> ---------------------------------------------------------------
>>>>>>
>>>>>> -----cp... at googlegroups.com wrote: -----
>>>>>> To: cp... at googlegroups.com
>>>>>> From: "Sharma SRK Chaitanya Yamijala"
>>>>>> Sent by: cp... at googlegroups.com
>>>>>> Date: 07/14/2018 01:59AM
>>>>>> Subject: Re: [CP2K:10528] Huge difference in adsorption energies
>>>>>> between CP2K and VASP with PBE
>>>>>>
>>>>>> I just want to add that, the energy of the CO obtained through the
>>>>>> one body contributions (listed in the output of a BSSE calculation) and the
>>>>>> energy of the optimized CO (in the same cell size but without the slab) is
>>>>>> found to be exactly the same. To me, this suggests the current basis should
>>>>>> be accurate enough as one should expect a larger effect of the BSSE on CO
>>>>>> rather than on slab (as slab contributes to the large portion of basis
>>>>>> functions of the total system). Kindly, let me know if my logic is wrong.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --------------------------------------------------------------------
>>>>>> SRK Chaitanya Sharma, Yamijala.
>>>>>> http://www.bmwong-group.com/group-members/
>>>>>>
>>>>>>
>>>>>> On Fri, Jul 13, 2018 at 1:16 PM, Sharma SRK Chaitanya Yamijala <
>>>>>> shar... at gmail.com> wrote:
>>>>>> And I believe the increase in the adsorption energy could be because
>>>>>> of the non-ground-state geometry of the "slab" during the BSSE calculation.
>>>>>> The slab's absolute energy when considered in the monomer basis (for the
>>>>>> ground state geometry) is -9804.47553 au and it is -9804.468056 au for the
>>>>>> geometry in the dimer configuration (i.e. for the slab geometry in the
>>>>>> "slab + CO" optimized geometry).
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --------------------------------------------------------------------
>>>>>> SRK Chaitanya Sharma, Yamijala.
>>>>>> http://www.bmwong-group.com/group-members/
>>>>>>
>>>>>>
>>>>>> On Fri, Jul 13, 2018 at 12:29 PM, Sharma SRK Chaitanya Yamijala <
>>>>>> shar... at gmail.com> wrote:
>>>>>> Dear Prof. Hutter,
>>>>>>
>>>>>> I have performed the BSSE corrections and the results are given
>>>>>> below. Clearly, the BSSE corrected interaction energy is huge (~ 1 eV). If
>>>>>> I consider this CP-corrected energy as the adsorption energy (I have
>>>>>> calculated adsorption energy as Eads = EAB - EA -EB), then it will be too
>>>>>> off from the VASP (-0.466 eV) or FHIAIMs (-0.595 eV) results. As mentioned,
>>>>>> without BSSE the calculated adsorption energy is -0.863 eV. All the
>>>>>> energies given are with Grimme's-D3 dispersion. Kindly, let me know if you
>>>>>> have any comments about this.
>>>>>>
>>>>>> To check the accuracy of my basis set, I have started a run with TZVP
>>>>>> basis (instead of DZVP) for adsorption energy calculation and I will update
>>>>>> here.
>>>>>>
>>>>>> On a different note, the number of basis functions used for the
>>>>>> calculation in FHIAIMS (6172) and CP2K (5660) is roughly the same.
>>>>>>  -----------------------------------------------------------
>>>>>> --------------------
>>>>>>  -
>>>>>>          -
>>>>>>  -                                 BSSE RESULTS
>>>>>>           -
>>>>>>  -
>>>>>>          -
>>>>>>  -                 CP-corrected Total energy:        0.039208
>>>>>>           -
>>>>>>  -
>>>>>>          -
>>>>>>  -                       1-body contribution:    -9804.468056
>>>>>>           -
>>>>>>  -                       1-body contribution:      -21.667247
>>>>>>           -
>>>>>>  -
>>>>>>          -
>>>>>>  -                       2-body contribution:     9826.174511
>>>>>>           -
>>>>>>  -                 BSSE-free interaction energy:     9826.174511
>>>>>>          -
>>>>>>  -----------------------------------------------------------
>>>>>> --------------------
>>>>>>
>>>>>> Thanks,
>>>>>> Sharma.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --------------------------------------------------------------------
>>>>>> SRK Chaitanya Sharma, Yamijala.
>>>>>> http://www.bmwong-group.com/group-members/
>>>>>>
>>>>>>
>>>>>> On Fri, Jul 13, 2018 at 12:31 AM,  <hut... at chem.uzh.ch> wrote:
>>>>>> Hi
>>>>>>
>>>>>>  you are using a DZVP basis, this is rather small. Check the number
>>>>>>  of basis functions. Do the same for the FHIaims calculation
>>>>>>  and compare.
>>>>>>  The cutoff of VASP cannot be compared to a local basis set.
>>>>>>
>>>>>>  regards
>>>>>>
>>>>>>  Juerg Hutter
>>>>>>  --------------------------------------------------------------
>>>>>>  Juerg Hutter                         Phone : ++41 44 635 4491
>>>>>>  Institut für Chemie C                FAX   : ++41 44 635 6838
>>>>>>  Universität Zürich                   E-mail: hut... at chem.uzh.ch
>>>>>>  Winterthurerstrasse 190
>>>>>> <https://maps.google.com/?q=Winterthurerstrasse+190+%0D%0A%C2%A0CH-8057+Z%C3%BCrich,+Switzerland&entry=gmail&source=g>
>>>>>>  CH-8057 Zürich, Switzerland
>>>>>>  ---------------------------------------------------------------
>>>>>>
>>>>>>  -----cp... at googlegroups.com wrote: -----
>>>>>>  To: "cp2k" <cp... at googlegroups.com>
>>>>>>
>>>>>>  From: "Sharma SRK Chaitanya Yamijala"
>>>>>>  Sent by: cp... at googlegroups.com
>>>>>>  Date: 07/12/2018 07:55PM
>>>>>>  Subject: Re: [CP2K:10514] Huge difference in adsorption energies
>>>>>> between CP2K and VASP with PBE
>>>>>>
>>>>>>
>>>>>>  Dear Prof. Hutter,
>>>>>>
>>>>>>  Thanks. I will try the BSSE correction with CP2K. Regarding k-point
>>>>>> sampling, in both the softwares, I have used Gamma point only. Could you
>>>>>> please elobarate your point on "size of basis sets" here? I don't know how
>>>>>> should I compare VASP basis (plane waves) with CP2K (both PW and
>>>>>> Gaussians)? I have converged the CUTOFFs in both the cases such that the
>>>>>> energy differences are < 1 meV.
>>>>>>
>>>>>>  Also, yesterday, I have performed similar calculations with FHIAims
>>>>>> and I have obtained the adsorption energy (withOUT dispersion and BSSE
>>>>>> corrections) as 0.412 eV which is again closer to the VASP result and to
>>>>>> the result in the reference.
>>>>>>
>>>>>>  Seeking your advice.
>>>>>>
>>>>>>  Thanks,
>>>>>>  Sincerely,
>>>>>>  Sharma.
>>>>>>
>>>>>>  On Thursday, July 12, 2018 at 12:11:59 AM UTC-7, jgh wrote:Hi
>>>>>>
>>>>>>  my first guess: you didn't calculate the BSSE correction.
>>>>>>
>>>>>>  other possible contributions: size of basis sets
>>>>>>                                k-point sampling
>>>>>>
>>>>>>  regards
>>>>>>
>>>>>>  Juerg Hutter
>>>>>>  --------------------------------------------------------------
>>>>>>  Juerg Hutter                         Phone : ++41 44 635 4491
>>>>>>  Institut für Chemie C                FAX   : ++41 44 635 6838
>>>>>>  Universität Zürich                   E-mail: hut... at chem.uzh.ch
>>>>>>  Winterthurerstrasse 190
>>>>>> <https://maps.google.com/?q=Winterthurerstrasse+190++%0D%0A%C2%A0CH-8057+Z%C3%BCrich,+Switzerland&entry=gmail&source=g>
>>>>>>  CH-8057 Zürich, Switzerland
>>>>>>  ---------------------------------------------------------------
>>>>>>
>>>>>>  -----cp... at googlegroups.com wrote: -----
>>>>>>  To: cp... at googlegroups.com
>>>>>>  From: "Sharma SRK Chaitanya Yamijala"
>>>>>>  Sent by: cp... at googlegroups.com
>>>>>>  Date: 07/12/2018 01:48AM
>>>>>>  Subject: [CP2K:10507] Huge difference in adsorption energies between
>>>>>> CP2K and VASP with PBE
>>>>>>
>>>>>>  Dear CP2K members,
>>>>>>
>>>>>>  I am calculating the adsorption energies of CO on ZnO (4x4-slab with
>>>>>> 4 layers of ZnO(10-10) surface). The adsorption energy obtained from VASP
>>>>>> is ~ 0.3 eV (without dispersion) and it is ~ 0.45 eV (with
>>>>>> dispSECTION_PARAMETERS TRUEersion). However, when calculating the same
>>>>>> system with CP2K (geometry is re-optimized), I am obtaining the energies
>>>>>> 0.688 eV and 0.863 eV for without and with dispersion correction,
>>>>>> respectively.
>>>>>>
>>>>>>  The literature value is close to the VASP result. Here is the
>>>>>> reference (kindly, see Table 2, C-down, 2x1 cell, Full).
>>>>>>
>>>>>>  B Meyer and D Marx 2003 J. Phys.: Condens. Matter 15 L89
>>>>>>  http://iopscience.iop.org/article/10.1088/0953-8984/15/2/112/pdf
>>>>>>
>>>>>>  Could anyone give an advice on why there is such a discrepancy in
>>>>>> the adsorption energies irrespective of using the same functional?
>>>>>>
>>>>>>  I am attaching the geometry and the input file for your reference.
>>>>>>
>>>>>>  Thanks,
>>>>>>  Sharma.
>>>>>>
>>>>>>  --------------------------------------------------------------------
>>>>>>
>>>>>>  SRK Chaitanya Sharma, Yamijala.
>>>>>>  http://www.bmwong-group.com/group-members/
>>>>>>
>>>>>>
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>>>>>>
>>>>>>  [attachment "1CO_on_opt_4x4_slab.xyz" removed by Jürg Hutter/at/UZH]
>>>>>>  [attachment "zno_bulk.inp" removed by Jürg Hutter/at/UZH]
>>>>>>
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