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Re: [lammps-users] question about potential energy
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Re: [lammps-users] question about potential energy


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 18 Apr 2018 08:35:53 -0400

On Wed, Apr 18, 2018 at 8:28 AM, ehsan gowdini <ehsangowdini@...24...> wrote:
> you right
>
> this is complete script

no, it cannot be run, since you omitted the data file. but please read on.

>
>
> units           real

you *must* use metal units for the EAM potential files bundled with
LAMMPS. see the documentation.

> dimension       3
> boundary        p p p
> atom_style      full
>
>
> neighbor            2.0 bin
> neigh_modify    delay 2 every 1
>
>
> bond_style      harmonic
> angle_style     charmm
> dihedral_style  none
> improper_style  harmonic

>
> read_data       256b.data
>
>
> pair_style      eam
> pair_coeff * * Au
> pair_coeff 2*2 2*2 Au_u3.eam
>
> pair_style      lj/cut 14.0
> pair_coeff * * 1 1
> pair_coeff 1 1 0.10492547 1.7155
> pair_coeff * * 1 2
> pair_coeff 1 2 0.048427138 1.41964710735663
>
> run_style       verlet
>
> group           CA type 1
>
> fix             1 CA setforce 0.0 0.0 0.0
>
>
> # ---------- Run Minimization ---------------------
> reset_timestep 0
>
> min_style cg
> minimize 1e-25 1e-25 5000 10000
>
>
> thermo            200
> thermo_style    custom step temp pe etotal press vol ke enthalpy evdwl
> epair ebond eangle edihed
>
> #-----------------dynamic run in new temperature
> dump              nvt all xyz 1000 ionized-nvt.xyz
> fix               2 all nvt temp 298.0 298.0 100.0
> timestep              2.0
> run               200000
>
> unfix             2
> undump            nvt
>
> dump              nvt1 all xyz 1000 ionized-nvt1.xyz
> fix               3 all nvt temp 398.0 398.0 100.0
> timestep              2.0
> run               200000
>
> unfix             3
> undump            nvt1
>
>
>
> before I use this simulation by LAMMPS I worked by NAMD and CHARMM force field
> I simulated this multi-component system by NAMD but NAMD not support
> to use EAM potential for metalic systems and result that I give by
> NAMD is not true
> then I use lammps for my simulatin
>
> L-J parameters that I write in script all of them is in Kcal/mole (for
> epsilon ) and angstrom(for sigma)

but you are ignoring that CHARMM has a different definition for sigma
than what LAMMPS uses and CHARMM force field files do not store sigma
but sigma/2.

>
>
> now what is yours suggestion ?

my suggestion remains the same!
do *not* even try to simulate a multi-component system unless you have
figured out how to correctly simulate each component separately. and
then you will first also have to switch the CHARMM based simulation to
use metal units and reproduce the previously verified results for real
units. only after you have successfully completed all these steps you
should advance to building and testing a simple multi-component system
(with both parts so far apart, so that the resulting energies should
be the sum of the two individual systems).

this is all common sense and stuff that you should discuss with your
adviser and not the mailing list. these are not LAMMPS issues, but
issues of knowing how to setup and perform MD simulations correctly in
general.

axel.

>
>
> On 4/18/18, Axel Kohlmeyer <akohlmey@...24...> wrote:
>> On Wed, Apr 18, 2018 at 6:19 AM, ehsan gowdini <ehsangowdini@...24...>
>> wrote:
>>> Hi all user
>>>
>>> in my simulation I use the EAM potential for metal-metal interaction
>>> and Lennard-Jones potential for carbon-metal interaction
>>>
>>> I use these command for them
>>>
>>>
>>> 1)
>>> pair_style      eam
>>> pair_coeff 2*2 2*2 Au_u3.eam
>>>
>>> pair_style      lj/cut 14.0
>>> pair_coeff * * 1 1
>>> pair_coeff 1 1 0.10492547 1.7155
>>> pair_coeff * * 1 2
>>> pair_coeff 1 2 0.048427138 1.41964710735663
>>>
>>>
>>> 2)
>>> pair_style     hybrid lj/cut 14.0 eam
>>> pair_coeff      2*2 2*2 eam Au_u3.eam
>>> pair_coeff      1 2 lj/cut 0.048427138 1.41964710735663
>>> pair_coeff      1 1 lj/cut 0.10492547 1.7155
>>>
>>>
>>> simulation done at 298 Kelvin
>>> but in both of two way , metal crystal being vapor
>>>
>>> when i look at the output file I see the potential energy is very high
>>> such 1192000
>>>
>>> what and where is my mistake?
>>
>> since you only provide a small part of your input, you force people to
>> guess and you cannot expect reliable responses. most likely, there are
>> other problems with your input deck.
>>
>> entry 1) is flat out garbage.
>>
>> the LJ parameters for entry 2) don't look right either. they appear to
>> be in kcal/mol instead of eV and the sigma values don't look
>> reasonable either.
>> based on seeing such basic errors already on something that is this
>> simple to get right, there are good chances, that there are many more
>> problems.
>> MD simulations follow the GI-GO (= garbage in, garbage out) principle,
>> so you have to get *everything* right, to have a meaningful
>> simulation. since you seem to have trouble with a multi-component
>> system, it is strongly advised to try and set up each component in a
>> separate simulation first and figure out how to do this to reproduce
>> already published data for the potential parameters in use.
>>
>> axel.
>>
>>> best
>>>
>>> Ehsan
>>>
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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.