[QE-users] Freezing Intermediate Images in NEB Calculation
Achintya Kumar
kumar.achintya14 at gmail.com
Mon Jul 1 19:26:46 CEST 2019
Dear Thomas
Thanks for your quick response
Further, I have calculated Polarization-Total Energy curve(W curve) by
displacing atoms manually, now, I want to produce same curve from NEB.
But the images that I am getting by NEB are inconsistent with the manually
displaced atoms one.
So can I compare these two or not?
Thanks and Regards
On Mon, Jul 1, 2019 at 5:21 PM Thomas Brumme <thomas.brumme at uni-leipzig.de>
wrote:
> Dear Achintya,
>
> so, you want to simulate the layer sliding in SnSe in a phospherene-like
> structure.
> And you get a barrier height of 1.25 eV. Does this make sense? I don't
> know.
> Maybe should ask this specific question if you want to know the answer.
> Maybe
> you can find some published data on this kind of transition? Maybe your
> colleagues can help. The input looks ok. Only suggestion I have: use
> climbing
> image NEB which usually gives better transition states.
>
> Regards
>
> Thomas
>
> On 7/1/19 1:37 PM, Achintya Kumar wrote:
>
> Dear Thomas
> My input and output files are attached
> BEGIN
>
> BEGIN_PATH_INPUT
> &PATH
> restart_mode='from_scratch'
> string_method='neb',
> ds=2.D0,
> opt_scheme="broyden",
> num_of_images=15,
> nstep_path = 60,
> k_max=0.3D0,
> k_min=0.20D0,
> path_thr=0.1D0,
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
> prefix="snse"
> outdir="./outdir",
> pseudo_dir="/cad/QE/pseudopotentials/upf_files",
> /
> &SYSTEM
> ibrav= 0,
> celldm(1)=1.889725989,
> nat= 4,
> ntyp= 2,
> ecutwfc= 40.0D0,
> ecutrho= 200.0D0,
> occupations= "fixed",
> /
> &ELECTRONS
> conv_thr = 1.D-6,
> mixing_beta = 0.5D0,
> /
> &IONS
> /
> ATOMIC_SPECIES
> Sn 118.71 Sn.pbe-dn-kjpaw_psl.0.2.UPF
> Se 78.960 Se.pbe-n-kjpaw_psl.0.2.UPF
> CELL_PARAMETERS (alat= 1.88972599)
> 4.393133495 0.000000000 0.000000000
> 0.000000000 4.245162285 0.000000000
> 0.000000000 0.000000000 25.000000000
>
> K_POINTS automatic
> 14 14 1 0 0 0
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS angstrom
> Sn -0.27090369 0.000000000 11.151283650
> Se 0.27090369 0.000000000 13.851931775
> Sn -2.467470438 2.122581143 13.848716350
> Se 2.467470438 2.122581143 11.148068225
> INTERMEDIATE_IMAGE
> ATOMIC_POSITIONS angstrom
> Sn 0.000000000 0.000000000 11.151283650
> Se 0.000000000 0.000000000 13.851931775
> Sn 2.196566748 2.122581143 13.848716350
> Se 2.196566748 2.122581143 11.148068225
> LAST_IMAGE
> ATOMIC_POSITIONS angstrom
> Sn 0.27090369 0.000000000 11.151283650
> Se -0.27090369 0.000000000 13.851931775
> Sn 2.467470438 2.122581143 13.848716350
> Se -2.467470438 2.122581143 11.148068225
> END_POSITIONS
> END_ENGINE_INPUT
>
> END
> #############################################################
> activation energy (->) = 1.251588 eV
> activation energy (<-) = 1.251588 eV
>
> image energy (eV) error (eV/A) frozen
>
> 1 -17182.1943011 0.998235 T
> 2 -17182.4628221 0.079139 F
> 3 -17181.6722586 0.069784 F
> 4 -17181.2913646 0.124247 F
> 5 -17181.0750253 0.130701 F
> 6 -17181.2203018 0.125583 F
> 7 -17182.2031417 0.146372 F
> 8 -17182.0989949 0.080510 F
> 9 -17181.3352176 0.093461 F
> 10 -17180.9427134 0.045147 F
> 11 -17181.0428918 0.172851 F
> 12 -17181.6282545 0.148683 F
> 13 -17181.7506510 0.946514 F
> 14 -17182.4631851 0.193101 F
> 15 -17182.1943013 0.997393 T
>
> path length = 32.289 bohr
> inter-image distance = 2.306 bohr
>
>
> ---------------------------------------------------------------------------
>
>
> neb: reached the maximum number of steps
>
> NEB : 9h37m CPU 10h36m WALL
>
>
> This run was terminated on: 22:39:42 14Jun2019
>
>
> =------------------------------------------------------------------------------=
> JOB DONE.
>
> =------------------------------------------------------------------------------=
>
> On Mon, Jul 1, 2019 at 4:58 PM Thomas Brumme <thomas.brumme at uni-leipzig.de>
> wrote:
>
>> Dear Achintya,
>>
>> without any info on how you made your NEB calculation, which system using
>> this or that
>> parameter, we cannot judge if it is correct or not. If you don't want to
>> or can't provide these
>> informations, then you need to discuss this with some locals. Your
>> supervisor?
>> In general, if you want to know if an NEB makes sense you need to have an
>> idea of the
>> potential energy surface and look at the final path...
>>
>> Thomas
>>
>> On 7/1/19 12:02 PM, Achintya Kumar wrote:
>>
>> Dear Thomas
>> How can I make sure that my neb calculation is correct or not.
>>
>> On Mon, Jul 1, 2019 at 3:29 PM Achintya Kumar <kumar.achintya14 at gmail.com>
>> wrote:
>>
>>> Dear Thomas
>>> I have done the same thing by splitting my path in two separate paths,
>>> but I was just interested to know whether it is possible or not to fix an
>>> intermediate images.
>>> Thanks for your answer.
>>>
>>> On Mon, Jul 1, 2019 at 1:55 PM Thomas Brumme <
>>> thomas.brumme at uni-leipzig.de> wrote:
>>>
>>>> Dear Achintya,
>>>>
>>>> I think that fixing an intermediate image is not possible as this makes
>>>> no sense.
>>>> If an image is fixed, it is also an end point of an elastic band... So,
>>>> if you just
>>>> split your path in two separate paths you can fix this "intermediate"
>>>> image.
>>>>
>>>> Cheerio
>>>>
>>>> Thomas
>>>>
>>>> On 7/1/19 8:19 AM, Achintya Kumar wrote:
>>>>
>>>> Hello
>>>> How can I kept frozen intermediate images in NEB calculation?
>>>>
>>>> --
>>>> =========================
>>>> Achintya Priydarshi
>>>> Research Scholar
>>>> IIT Kanpur.
>>>> ===========================
>>>>
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>>>> users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>>>
>>>>
>>>> --
>>>> Dr. rer. nat. Thomas Brumme
>>>> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
>>>> Leipzig University
>>>> Phillipp-Rosenthal-Strasse 31
>>>> 04103 Leipzig
>>>>
>>>> Tel: +49 (0)341 97 36456
>>>>
>>>> email: thomas.brumme at uni-leipzig.de
>>>>
>>>>
>>>
>>> --
>>> =========================
>>> Achintya Priydarshi
>>> Research Scholar
>>> IIT Kanpur.
>>> ===========================
>>>
>>
>>
>> --
>> =========================
>> Achintya Priydarshi
>> Research Scholar
>> IIT Kanpur.
>> ===========================
>>
>>
>> --
>> Dr. rer. nat. Thomas Brumme
>> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
>> Leipzig University
>> Phillipp-Rosenthal-Strasse 31
>> 04103 Leipzig
>>
>> Tel: +49 (0)341 97 36456
>>
>> email: thomas.brumme at uni-leipzig.de
>>
>>
>
> --
> =========================
> Achintya Priydarshi
> Research Scholar
> IIT Kanpur.
> ===========================
>
>
> --
> Dr. rer. nat. Thomas Brumme
> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
> Leipzig University
> Phillipp-Rosenthal-Strasse 31
> 04103 Leipzig
>
> Tel: +49 (0)341 97 36456
>
> email: thomas.brumme at uni-leipzig.de
>
>
--
=========================
Achintya Priydarshi
Research Scholar
IIT Kanpur.
===========================
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