Hi lammps users,
I want to calculate shear viscosity using the fix deform-nvt/sllod method and I am trying to work with a simple system first (benzene, 343 molecules). But I found that when I use a strain rate of 0.1 (unit is “real”), I get a good velocity profile but the temperature set at 300K goes to over 8000K and stays there. When I use a smaller strain rate of 0.01, temperature hovers around 300K as it should but the velocity profile looks bad. I have experimented with timestep between 0.5fs to 1fs which is reasonable for the system I have. The system is already well-equilibrated as I have previously done GK thermal conductivity on it and nothing seems out of place. Please, is there anything else I can do to control the high temperature (in the case of high strain rate) as that gives the better profile? I have attached my input file and the plots I generated. Thank you.
variable T equal 300 # Simulated Temperature [K]
variable tempname equal 300 # Temperature Name in Files
variable dt equal 1.0 # timestep
variable srate equal 0.01 # Strain rate
Setup Parameter
units real
dimension 3
boundary p p p
atom_style full
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes page 1000000
kspace_style pppm 1.0e-6
pair_style lj/charmm/coul/long 10.00 10.10
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_restart benzene-300-2.lammps-run05
Allow box to move from cube
change_box all triclinic
timestep ${dt}
velocity all scale $T
shear rate defined relative to perpendicular dimension
variable xyrate equal ${srate}/ly
fix 1 all nvt/sllod temp $T T 100.0 fix 2 all deform 1 xy erate {xyrate} remap v
compute layers all chunk/atom bin/1d y center 0.05 units reduced
fix 4 all ave/chunk 100 1 1000 layers vx file profile.nemd.3d-${srate}
#compute temp after deforming box
compute tilt all temp/deform
data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 10 100 1000 v_visc ave running file visc-avg-${srate}
thermo 1000
thermo_style custom step temp pe etotal press pxy v_visc f_vave
thermo 1000
thermo_style custom step temp pe etotal press pxy v_visc f_vave
thermo_modify temp tilt
run 2000000
