1、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.**
2、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
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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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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
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...and why do you need dihedrals with EAM and LJ potentials?