[QE-users] Freezing Intermediate Images in NEB Calculation
Thomas Brumme
thomas.brumme at uni-leipzig.de
Mon Jul 1 13:51:27 CEST 2019
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 <mailto: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 <mailto: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
>> <mailto: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 <http://www.max-centre.eu/quantum-espresso>)
>>> users mailing listusers at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>
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>>
>> --
>> 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 <mailto: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 <mailto: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
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