Dear lammps users,
I am working on simulation of montmorillonite clay in water box.
The system consists of 4x4x3 supercell with 40 interlayer water in each layer and 5700 water surrounding the clay with total of 5780 water molecules. I need to study the MSD of water and also to compare the MSD of surrounding water and interlayer water separately.
I am using restart files for continuing simulations. With compute msd/chunk, I am getting 5780 msd values at each timeframe (5000 timesteps) in each trajectory.
Does the msd/chunk give square displacement at each timestep with respect to original timestep at which compute msd/chunk was invoked?
or does it give wrt to previous timestep?
The input script is as follows
Intialization
units real
dimension 3
boundary p p p
atom_style full
Atom Definition
#read_data mont-morewat-btw-lyr-eq.lmpdat
read_restart mont-morewat-btw-lyr-eq-npt.*.lmp
include CLAYFF-mont-wat.frc
Settings
group clay type 1 2 5 6
group water type 3 4
#velocity all create 298 123456 rot yes mom yes dist gaussian
#fix 1 all nvt temp 298 298 100 tchain 1
#using NPT ensemble at 1atm pressure with 298K temp
fix 1 all npt temp 298 298 100 iso 1 1 1000
#fix the center of mass for CLAY
fix COM clay recenter INIT INIT INIT units box
#constraint bonds which are attached to type 1 atom i.e. h*
fix 2 all rattle 0.0001 50 0 t 3
#to get angular velocities of molecules and MSD
compute cc1 water chunk/atom molecule
compute omega water omega/chunk cc1
fix 3 water ave/time 5000 1 5000 c_omega[*] file omega-3.out mode vector
compute msd water msd/chunk cc1
fix 4 water ave/time 5000 1 5000 c_msd[*] file msd-3.out mode vector
compute rdf all rdf 5000 4 2 4 4 4 5 4 6 5 3 # oxygen-oxygen
fix rdf all ave/time 5000 1 5000 c_rdf[*] file rdf-3.out mode vector
timestep 0.1
Output
thermo_style multi
thermo_modify flush yes
thermo 5000
dump NPT all custom 5000 eq3-npt.dump id mol type q mass x y z
dump trj all atom 5000 eq3-npt.lammpstrj
restart 100000 mont-morewat-btw-lyr-eq-npt.*.lmp
Run the simulation
run 1000000
Using the restart file generated in previous run, I have run 9 continuous trajectories.
How can I get MSD value for each trajectory and hence the diffusion coef?
Note: I have generated velocities during equilibration and continuing same
Kindly suggest…