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Re: [lammps-users] question
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Re: [lammps-users] question


From: ehsan gowdini <ehsangowdini@...24...>
Date: Fri, 13 Apr 2018 14:48:27 +0430

I read manual but I not found charmm dihedral style that compatible
with EAM and L-J pair style
my system that I work on it is a gold nano cluster based on graphene
sheet and I want to measure thermodynamics properties during heating
from 200 to 1800 kelvin and cooling from 1800 to 200 kelvin
 I set EAM potential between gold nano particle and Lennard-Jones
potential between graphene and gold nano particles

I want to see when temperature increase, my system potential energy
how much change



On 4/13/18, Axel Kohlmeyer <akohlmey@...24...> wrote:
> ...and why do you need dihedrals with EAM and LJ potentials?
>
> On Fri, Apr 13, 2018 at 5:11 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>> On Fri, Apr 13, 2018 at 4:39 AM, ehsan gowdini <ehsangowdini@...24...>
>> wrote:
>>> Hi dear all
>>>
>>> I want to calculate my system potential energy from 200 to 1800 kelvin
>>> I use EAM and L-J potential for my system but I see this error
>>>
>>> ERROR: Dihedral charmm is incompatible with Pair style
>>> (../dihedral_charmm.cpp:402)
>>> Last command: minimize        0 0 100000 1000000
>>>
>>>
>>> what is your guide to solve this ( change pair style ? what pair style?
>>> ....)
>>
>> how about reading the documentation?
>> http://lammps.sandia.gov/doc/dihedral_charmm.html
>>
>> axel.
>>
>>>
>>> best
>>>
>>> Ehsan
>>>
>>>
>>> this is my input command
>>>
>>>
>>> units           real
>>> atom_style      full
>>>
>>> neighbor        1 bin
>>> neigh_modify    delay 2 every 1
>>>
>>> bond_style      harmonic
>>> angle_style     charmm
>>> dihedral_style  charmm
>>>
>>>
>>> read_data       256b.data
>>> pair_style     hybrid lj/cut 14.0 eam
>>> dihedral_coeff  1 3.1 2 180 0.5
>>>
>>> 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
>>>
>>> pair_modify     mix arithmetic
>>>
>>> kspace_style    none
>>>
>>>
>>>
>>>
>>> group           CA type 1
>>>
>>> fix             1 CA setforce 0.0 0.0 0.0
>>>
>>> thermo          200
>>> thermo_style    custom step temp pe etotal press vol ke enthalpy evdwl
>>> epair ebond eangle edihed
>>>
>>> minimize        0 0 100000 1000000
>>>
>>> special_bonds   charmm
>>> dump            npt all dcd 5000 ionized-npt.dcd
>>> fix             2 all npt temp 298.0 298.0 100.0 y 1.0 1.0 500
>>> run             4000000
>>> unfix           2
>>> undump          npt
>>>
>>> fix             3 all nvt temp 298.0 298.0 100.0
>>> fix             4 all shake 1e-6 500 0 m 1.0 a 17
>>> velocity        all create 180.0 12345678 rot yes mom yes dist gaussian
>>> velocity        CA create 0.0 12345678  rot yes mom yes dist gaussian
>>>
>>> timestep        0.5
>>>
>>> restart         10 ionized.restart1 ionized.restart2
>>> dump            1 all dcd 5000 ionized.dcd
>>> #dump_modify    1 image yes scale yes
>>>
>>> run             10000000
>>>
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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.
>