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Re: [lammps-users] Tabulated potential + coulombic long range potential
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Re: [lammps-users] Tabulated potential + coulombic long range potential


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 11 Aug 2017 08:02:58 -0400



On Fri, Aug 11, 2017 at 6:10 AM, Meral Sharkas <eng_meral.sh10@...16...> wrote:
Thank you very much Axel for your reply and guidance. 
May i ask plz what does a 'bad geometry' indicates.does  that mean like overlappimg of atoms?

​that is one option.​
 
Also if I am having the unit cell position from the internet not developed by myself is there a chance to have a bad geometry?

​yes.​
 

I understand that this is out of the  scope of the mailing list but I just want to know if it is a problem in how I am using lammps or another problem..

​from remote it is impossible to tell the difference.

axel.​

 

Thank you in advance.

Best,
Meral

On Thu, Aug 10, 2017 at 6:51 PM, Axel Kohlmeyer


On Wed, Aug 9, 2017 at 10:04 AM, Meral Sharkas via lammps-users <lammps-users@...6335.....sourceforge.net> wrote:
Dear lammps users,

I am simulating radiation damage in zircon and according to the literature the potential is ZBL for ranges < 1 A , born mayer huggings <10 A and colombic long range.

I tabulated the short ranges potential an joined the two potentials using a fermi function. When i attempted to use a pair_style hybrid/overlay to overlay the colombic long range potential with the tabulated potential, i got an error of "Lost atoms".

N.b: When creating the tabulated potential, i made all the cutoff distances= 10 A(for zbl and BMH potential)

As a troubleshoot to my problem i tried to simulate the system with just pair_style coul/long, i got NAN results, and when i used pair_style coul/cut i got lost atoms.

​only using coulomb interactions for point particles cannot result in stable dynamics, since coulomb has no short range repulsion. atoms of opposite charge will just end up on top of each other (also known as "classical coulomb catastrophe"). so NaN​ (i.e. divergence) or lost atoms (due to extremely strong forces when atoms get close) are to be expected.

when you get lost atoms for your tabulated potential, chances are, that your tabulation is faulty or your geometry not good. this is something that you have to resolve yourself. that is just part of the job of doing simulations. nobody here will do this work for you.

please note, that building tabulated potentials has become much simpler with LAMMPS with the addition of pair style python. you can simply define a piece-wise defined potential function (and check or derive its force through numerical differentiation) in python, plot and compare it with a standalone code and then put it into LAMMPS, create the tables using the pair_write command. there are several examples provided in the examples/python folder. 

axel.

 

i am wondering what could be the reason of these problems?

Please find a part of my input and if you can help me that would be really appreciated.

******Part of the input file*******

units         metal 
atom_style    charge
boundary      p p p

lattice custom 1 a1 6.607 0 0 a2 0 6.607 0 a3 0 0 5.982 basis 0.0 0.75 0.125 basis 0.0 0.25 0.875 basis 0.5 0.75 0.375 basis 0.5 0.25 0.625 basis 0.0 0.75 0.625 basis 0.0 0.25 0.375 basis 0.5 0.75 0.875 basis 0.5 0.25 0.125 basis 0.0 0.0658 0.1955 basis 0.0 0.9342 0.8045 basis 0.5  0.0658 0.3045 basis 0.5 0.9342 0.6955 basis 0.0 0.5658 0.8045 basis 0.0 0.4342 0.1955 basis 0.5 0.5658 0.6955 basis 0.5 0.4342 0.3045 basis 0.6842 0.25 0.9455 basis 0.8158 0.75 0.4455 basis 0.8158 0.25 0.5545 basis 0.6842 0.75 0.0545 basis 0.1842 0.25 0.5545 basis 0.3158 0.75 0.0545 basis 0.3158 0.25 0.9455 basis 0.1842 0.75 0.4455

region R1 block -1 1 -1 1 -1 1

create_box    3 R1
create_atoms 3 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 3 basis 10 3 basis 11 3 basis 12 3 basis 13 3 basis 14 3 basis 15 3 basis 16 3 basis 17 3 basis 18 3 basis 19 3 basis 20 3 basis 21 3 basis 22 3 basis 23 3 basis 24 3

kspace_style ewald 0.00001
pair_style hybrid/overlay table linear 9999 ewald coul/long 10

pair_coeff    1 1 table zircon21.table ZR-ZR
pair_coeff    1 3 table zircon21.table ZR-O
pair_coeff    2 3  table zircon21.table SI-O
pair_coeff    3 3  table zircon21.table O-O
pair_coeff    1 2  table zircon21.table ZR-SI
pair_coeff    2 2  table zircon21.table SI-SI
pair_coeff    * * coul/long

pair_write 1 3 10000 rsq 0.1 10 energy-forceZRO.txt zr-o 3.8 -1.45
pair_write 2 3 10000 rsq 0.1 10 energy-force.txtSIO si-o 2.0 -1.45
pair_write 3 3 10000 rsq 0.1 10 energy-forceOO.txt o-o -1.45 -1.45 

********Part of the tabulated potential**********
SI-O
N 9999 RSQ 0.001 10
1    0.002    20180.1269905582    13589.3273976564
2    0.003    13386.0395578569    5095.2810331941
3    0.004    9989.56492417    2716.9549052967
4    0.005    7952.1297472636    1697.6776377744

Thanks in advance

Regards,
Meral

 
 

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.