LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] Fwd: Problem with fix rigid
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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


From: Andrew Jewett <jewett@...1937...>
Date: Wed, 18 Oct 2017 14:14:45 -0700

Just a very quick observation that may not be relevant.  (I confess I
did not read your email carefully.)

I assume that what you mean by "temperature" of a particle, you mean
it's kinetic energy.  If that's the case, you should expect it to have
some vaguely Maxwell-Boltzmann like distribution ranging from 0kB*T to
several kB*T.  1000K is not unreasonable at all (assuming temperature
is around 300K)

The kinetic energy of a rigid body with N atoms is different than the
kinetic energy of N atoms.  (There is less atom movement, you'd expect
it to be significantly lower on average.)  The equations you use to
calculate its kinetic energy will be modified.  You will have to dig
into the LAMMPS documentation to make sure that you are invoking the
lammps commands in the correct way so that LAMMPS is computing kinetic
energy of the system correctly (and hence its temperature).

Cheers
Andrew

On Tue, Oct 17, 2017 at 6:23 PM, Ali Mirmohammadi <saam85@...24...> wrote:
> Dear Axel,
>
> Thanks for your response.
>
> I have applied your suggestions and was able to control the particle from
> moving. However, when I want to calculate thermal conductivity using
> Green-Kubo method, since I unfix all ensembles except NVE, I can see too
> much fluctuation in temperature of the particle (in order of 1000 K) and
> consequently high unreliable values for thermal conductivity.
>
> Do you think it could be from lattice spacing or potential between silver
> atoms?
> If I do not turn off the thermostats of the rigid particle, does it yield
> unreliable data? In other words, is it a MUST to unfix all ensembles except
> NVE while using Green-Kubo equation?
>
> Best Regards,
> Ali
>
> On Thu, Oct 12, 2017 at 4:07 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>
>>
>> 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@lists.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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>
>>
>>
>> --
>> 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.
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> lammps-users mailing list
> lammps-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>