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Re: [lammps-users] Fluctuation in calculating energy and specific heat
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Re: [lammps-users] Fluctuation in calculating energy and specific heat


From: Muhammad Saeed <saeedphysics96@...24...>
Date: Mon, 23 Apr 2018 19:32:58 +0800

Dear  Dr. Axel Kohlmeyer,

Thank you for your response and suggestions.

I am using LAMMPS version released on 11 Aug 2017, running on Linux platform.
My system is in solid state, a molecule containing C,H, O atoms placed on a graphene sheet.

Could you please suggest some other force-field for this type of system, i.e., containing C,H, and O atoms?
 
I could not find any other potential in LAMMPS potential directory for C,H,O.


Kind Regards

Saeed


On Mon, Apr 23, 2018 at 6:43 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Sun, Apr 22, 2018 at 11:28 PM, Muhammad Saeed
<saeedphysics96@...24...> wrote:
> Dear LAMMPS users,
>
> I am working on "Thermal properties of Self-Assembly monolayers at the
> liquid-solid interface" and want to calculate adsorption energy, enthalpy
> and specific heat with NVT ensembles using LAMMPS. But high fluctuations
> occurs in the temperature (+- 30) and energy of the system during the
> simulations.

...and what version of LAMMPS are you using? and on what platform are
you running? the mailing list guidelines state, that those are crucial
pieces of information.

> Can someone please give me suggestions how to minimize these fluctuations?

some fluctuations are to be expected and depend on the system size.
there are multiple discussions on this subject in the mailing list
archives, and it should also be explained in any good text book on MD,
that for a system in equilibrium, the average over time is equivalent
to the average over the system.

> The input script for adsorption energy is

now, there are multiple problems with this script. please see the
in-line comments below.

> units           real
> atom_style      charge
> variable        t      equal    278
> variable        dt     equal    0.01
> variable        system string   combined
>
> read_data      data.in.combined
>
> pair_style   reax/c NULL
> pair_coeff    * * ./ffield.reax.cho C H O

as it says in the header of the ffield.reax.cho file, this is a force
field for combustion, so it is a *very* bad choice for your project.

>
> velocity        all create \$t 87287
>
> neighbor        1.5 bin
> neigh_modify    once yes

not updating the neighbor lists for a liquid system is also a *very* bad idea.

> fix 1 all box/relax iso 0.0 vmax 0.001

fix box/relax has *no* effect during dynamics runs.

> fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
> fix 3 all nvt temp \$t \$t 0.03

a choice of 0.03fs for tdamp is a *bad* choice with a time step of 0.01fs.

> timestep        \${dt}

a time step of 0.01fs is rather wasteful for the type of your system
at ambient temperatures. with a proper starting geometry and a
suitable force field, you should be able to run a stable, energy
conserving MD with 0.1fs and possibly even larger (0.2 - 0.25fs).

axel.

> thermo          100
>
> run 500000
>
>
>
> Kind Regards
>
> Saeed
>
>
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
kind regards

Muhammad Saeed

Postdoctoral Researcher 
Institute for Advanced Study
Shenzhen University
Nanhai Ave 3688
Shenzhen,Guangdong,
P.R.China, 518060.