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Re: [lammps-users] Fwd: Problem with fix rigid
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Re: [lammps-users] Fwd: Problem with fix rigid


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 12 Oct 2017 01:07:32 -0400



On Wed, Oct 11, 2017 at 8:38 PM, Ali Mirmohammadi <saam85@...24...> wrote:
Dear users,

It seems that my following email was missed. Any suggestion on that?

​no, it wasn't missed. it was just that nobody has responded.

​please understand, that posting to this mailing list does not entitle you to get a response.
this mailing list is a voluntary effort, which means that people may choose to not respond. possible reasons for that are:
- they don't have the time
- they don't understand what you are asking
- they don't know a good response
- they think, you should just follow the instructions in the manual or search through the mailing list archive
- they think, you should try out what your can figure out yourself and then report back with the details and errors, if any.
- they think, what you are asking for makes no sense
- they don't care

you increase your chances by making it more attractive to answer through providing a more detailed description and showing that you did some research as to why, what you are asking about, might happen. quite a bit of what you are asking about has appeared in similar form in other discussions (quite often, actually).

...and after giving you a lecture on mailing list etiquette i have the following comments:
- your input doesn't specify units, even though it looks like your input was meant for "metal" units
- you build a starting geometry with an unrelaxed interface. that means atoms at the interface will have very high potential energy -> deformation
   try doing a minimization before starting the MD. you even may have to quench multiple times
- "temperature" is not well defined for a single particle. think of a harmonic oscillator where the "temperature" will oscillate between 0 and 2x the average.
- your starting conditions may also be responsible for the drift in your system. this can be removed with the velocity command (or if it is intrinsic in your setup using fix momentum. the former is preferred)
- while not likely a reason in your case, it is usually beneficial to make a test with the latest LAMMPS version to verify if your observation is not due to a bug that has already been fixed.

axel.


 

Thanks in advance,
Ali
---------- Forwarded message ----------
From: Ali Mirmohammadi <saam85@...24...>
Date: Sun, Oct 8, 2017 at 3:30 PM
Subject: Problem with fix rigid
To: lammps-users@...33....396...sourceforge.net


Dear All,

I am trying to relax a system including silver particle immersed in a water box. I have two problems when I use fix rigid command for nanoparticle. Firstly, the particle moves diagonally until it exits the simulation box and enters from the other edge during the simulation. Secondly, although the temperature of the whole systems is maintained at target temperature, temperature of the particle is fluctuating significantly. In case that I uncomment the rigid command, two mentioned problems are gone but the shape of the particle changes strangely and it is not sphere anymore after relaxation period. That is why I think I have to use rigid command anyway. I have tried this with different fix rigid commands such as rigid/nve, rigid/nvt and so on but no improvement observed.

Any advice and suggestions will be greatly appreciated.  

The input script is as below and I am using the Jan 2016 version of LAMMPS.

variable T equal 300
variable dt equal 0.001

# setup problem
dimension 3
boundary p p p
atom_style full
read_data       spce5nm.data
velocity all create $T 1016891 mom yes rot yes dist gaussian

region          sph1 sphere 25 25 25 7.2 units box
delete_atoms    region sph1 bond yes mol yes

# Create Empty Sphere #
region          sph11 sphere 25 25 25 6.68 units box
lattice         fcc 4.09
create_atoms    3 region sph11 units lattice
pair_style      hybrid/overlay lj/cut/coul/long 9.8 9.8 eam lj/class2 9.8 
kspace_style    pppm 0.0001

# 1:Oxygen, 2:Hydrogen, 3:Silver #

pair_coeff    1 1 lj/cut/coul/long 0.0067366153 3.166
pair_coeff    * 2 lj/cut/coul/long 0.0000 0.0000
pair_coeff    2 3 lj/class2 0.0000 0.0000

pair_coeff    2 3 lj/class2 0.005617 2.52# Ag-H interaction (Piotr Zarzycki)
pair_coeff         1 3 lj/class2 0.033 3.0855# Ag-O interaction (Heinz for 9-6 LJ)#
pair_coeff         3 3 eam agu6  


bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none

bond_coeff 1 1000 1.0
angle_coeff 1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 0.5
neighbor        2.0 bin
neigh_modify delay 0 every 1 check yes
#################################################
# Group difinition #

group           hydrogen type 2
group           oxygen type 1
group           water  type 1 2
group           particle1 region sph11

compute         watertemp water temp
compute         Agtemp1  particle1  temp

#########################################################
# equilibration and thermalization

fix 1 water shake 0.0001 200 0 b 1 a 1

fix 0 particle1 rigid molecule

#fix 0 particle1 rigid/npt molecule temp $T $T 0.1 iso 1.013 1.013 0.1

run 0                             # temperature may not be 300K
velocity all scale $T          # now it should be
fix 2 water nvt temp $T $T 0.1 drag 0.2
timestep ${dt}
thermo_style   custom step temp c_watertemp c_Agtemp1 etotal press vol
thermo 100
dump 1 all xyz 500 nvtnew1.xyz 
run 500000



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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.