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Re: [lammps-users] Reg. anatase nanorod structure stabilization
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Re: [lammps-users] Reg. anatase nanorod structure stabilization


From: ABHINAV SHUKLA <as37@...7325...>
Date: Thu, 12 Apr 2018 19:10:48 +0530

I am extremely sorry. I'll take care of it from next time.

Sincerely,
Abhinav




On Thu, Apr 12, 2018 at 7:06 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
please always reply to the mailing list and not only individual people. thanks, axel.


On Thu, Apr 12, 2018 at 9:35 AM, ABHINAV SHUKLA <as37@...7325...> wrote:
Dear Axel,

Thanks a lot for your suggestions and advice. I'll work on the pointers you mentioned and run the tests.

Sorry for any inconvenience.

Regards,
Abhinav




On Thu, Apr 12, 2018 at 2:27 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Wed, Apr 11, 2018 at 5:02 PM, ABHINAV SHUKLA <as37@...7325...> wrote:
​​
Dear all,

I am trying to stabilize a cross nanorod system of anatase. However during equilibration atoms are getting off the nanorods (screenshots attached for reference). It would be of great help if somebody can explain the reason behind it. 

​the reason is your input. LAMMPS will read and execute the computations (e.g. evaluate the forces and update velocities and positions) for the atom positions and force field parameters you provide it with.
what you see is what happens for the particular settings, geometry and parameters you input.

so now you have to ask yourself (and run the corresponding tests):
- is the geometry correct? what happens, if you use just one read_data command instead of two?
- is the force field correct? are the parameters suitable to model a system like yours (or only bulk crystals where atoms cannot "escape")?
​- is your relaxation/equilibration/simulation protocol correct?

it is very unlikely, that somebody here has the time to look into it, and it *is* part of the job of doing simulations to test, validate and debug all input and settings. basically, for as long as LAMMPS is doing what it says in the documentation, it should be doing, then any problem is your problem. if there is a conflict or contradiction, then the mailing list is a place to ask people for help.

a couple of obvious things as a starting point to consider:
a) most people do a minimization first; and b) there is no point in using a barostat on such a system.​

​axel.​

 

Following is the input script:

#--------------initialization
dimension 3
units metal
atom_style full
newton on
boundary p s p 

#-----------system 
region simbox block -300 300 -300 300 -100 300
create_box      2 simbox 
read_data nr1.xyz add append 
read_data nr2.xyz add append

set type 1 charge 2.196
set type 2  charge -1.098

#------------int​​eratomic potential
pair_style buck/coul/cut 8.0
pair_coeff   1 1   31393.4364 0.154 5.2929
pair_coeff   1 2   17106.4193 0.194 12.7031
pair_coeff   2 2   11886.2131 0.234 30.4873

neighbor 2.0 bin 
neigh_modify every 1 delay 0 check yes

timestep 0.001
thermo 100
thermo_style custom step cpu temp ke pe etotal pyy lx ly lz
dump config all custom 200 anatase.config.* id type x y z vx vy vz
dump_modify config format line "%8d %5d %25.18g %25.18g %25.18g %20.13g %20.13g %20.13g"

velocity all create 300 12345 mom yes rot no

#------------NVT
fix 2 all nvt temp 300.0 300.0 1.0
run 50000
unfix 2

#----------NPT
fix 1 all npt temp 300.0 300.0 0.1 x 1.0 1.0 1.0 z 1.0 1.0 1.0
run 50000
unfix 1

#------------NVE
fix 3 all nve
run 50000
unfix 3



--
Thanks & Regards,
Abhinav Shukla



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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.



--
Regards,
Abhinav Shukla
Senior Year Undergraduate 
Indian Institute of Technology Bhubaneswar
Odisha, India -752050
Contact No. : +91-7077095192


Disclaimer: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.



--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Regards,
Abhinav Shukla
Senior Year Undergraduate 
Indian Institute of Technology Bhubaneswar
Odisha, India -752050
Contact No. : +91-7077095192


Disclaimer: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.