LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] question about potential energy
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] question about potential energy


From: ehsan gowdini <ehsangowdini@...24...>
Date: Wed, 18 Apr 2018 16:58:05 +0430

you right

this is complete script


units           real
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)


now what is yours suggestion ?


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
>>
>> ------------------------------------------------------------------------------
>> 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.
>