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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 14:49:47 +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, ehsan gowdini <ehsangowdini@...24...> wrote:
> 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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>>>> _______________________________________________
>>>> 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.
>>
>>
>>
>> --
>> 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.
>>
>