Dear Lammps-users
I had an issue while trying to calculate the viscosity of water Using RNEMD - the script below-
There is a strange fluctuation in the dVx at several points in the simulation, where the dVx was lower than the steps before and after it by a factor of 10,000 - a section of the output is below the script- this causes a huge change in the resultant accumulative viscosity
can you help me with this please?
Muller-Plathe via fix viscosity
settings
variable x equal 99.3839
variable y equal 99.3839
variable z equal 99.3839
problem setup
units real
boundary p p p
atom_style full
atom_modify map array
pair_style lj/cut/coul/cut 12
bond_style harmonic
angle_style harmonic
dihedral_style opls
read_data ./data.gro2lam
neighbor 1.9 bin
special_bonds lj/coul 0.0 0.0 0.5
pair_modify shift no tail yes mix geometric
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300 97287
fix 1 all nve
fix 2 all langevin 300 300 1.0 498094
equilibration run
thermo 1000
run 5000
turn on Muller-Plathe driving force and equilibrate some more
velocity all scale 300
fix 4 all viscosity 100 x y 20
compute layers all chunk/atom bin/1d y center 4.969 units reduced
fix 5 all ave/chunk 20 50 1000 layers vx file profile.mp.3d
#equilibration run
variable dVx equal f_5[11][3]-f_5[1][3]
thermo 1000
thermo_style custom step temp epair etotal press f_4 v_dVx
run 10000
data gathering run
reset fix viscosity to zero flux accumulation
unfix 4
fix 4 all viscosity 100 x y 20
variable visc equal -(f_4/(2*(step-15000)(lxlz)))/(v_dVx/(ly/2))
fix vave all ave/time 1000 1 1000 v_visc ave running start 16000
thermo_style custom step temp f_4 v_dVx v_visc f_vave
run 500000
---------------------Log.lammps output---------------------
Per MPI rank memory allocation (min/avg/max) = 86.56 | 87.04 | 87.7 Mbytes
Step Temp f_4 v_dVx v_visc f_vave
419000 299.82445 -365.36663 -5.7438505e-06 -0.39362558 -0.070851354
420000 299.74964 -366.26734 2.7892209e-06 0.81058618 -0.068680325
421000 299.7882 -367.16928 -2.1509892e-06 -1.0510927 -0.071094115
422000 299.15376 -368.07082 2.3053985e-05 0.098068589 -0.0706795
423000 299.58143 -369.00934 1.0363854e-09 2181.6991 5.263721
424000 299.91542 -369.90874 -1.6336994e-05 -0.13840063 5.2505451
425000 299.93793 -370.82428 1.8357635e-05 0.12317045 5.2380697
426000 299.38568 -371.72269 6.4811841e-06 0.34886856 5.2262027
427000 300.46583 -372.63419 -1.0551138e-05 -0.21430145 5.2130296