Lammps 問題集錦

一、Results of time averaging in a variable?

Hi - I’d like to run an equilibration NPT, take the average box shape, and then use it to run an NVE, in a single lammps input file.  Is there any way to get the results of the time averaged box shape (e.g. as computed by 「fix ave/time」) in a variable, so I can use it in a change box command?  All I’ve been able to get from the documentation and searching the mailing list is how to write it to a file.

 

thanks,

Noam

 

On Nov 6, 2017, at 9:33 AM, Axel Kohlmeyer <akohlmey@gmail.com> wrote:

 

​from the fix ave/time documentation:

 

​Restart, fix_modify, output, run start/stop, minimize info:

 

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

 

**This fix produces a global scalar or global vector or global array which can be accessed by various output commands. The values can only be accessed on timesteps that are multiples of Nfreq since that is when averaging is performed.**

二、ERROR: Dihedral charmm is incompatible with Pair style

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? ....)

 

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

------------------------------------------------ 

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

-----------------------------------------------------

...and why do you need dihedrals with EAM and LJ potentials?