Responding to some of questions I got about how to use COMB3 potential for calculating the ZrH mean square displacement to be used for the diffusion coefficient calculation. I would put it here at once for all of you, below is an full input script you just probably copy it and run after you download the potential model from the above link I previously mentioned, it is up to you how to modify and refine for your HCP structure or other aspects:

####################################################

units metal

boundary p p p

atom_style charge

pair_style comb3 polar_off #for comb3 potential

variable X equal "16"

variable Y equal "10"

variable Z equal "10"

variable T equal "500"

lattice hcp 3.232

region box block 0 $X 0 $Y 0 $Z

create_box 2 box

create_atoms 1 box

create_atoms 2 random 100 878567 box

group zr type 1

group hydrogen type 2

pair_coeff * * ffield.comb3 Zr H #H

neighbor 2 bin

neigh_modify delay 10 check yes

mass 1 91.224

mass 2 1.0079

thermo 500

# Energy minimization and pressure minimization

fix 1 all nve/limit 0.1

thermo_style custom step pe lx ly lz press pxx pyy pzz vol etotal

minimize 1.00e-30 1.00e-30 100000 1000000

unfix 1

fix 1 all box/relax aniso 0.0 vmax 0.1

thermo_style custom step pe lx ly lz press pxx pyy pzz vol etotal

minimize 1.0e-30 1.0e-30 100000 1000000

unfix 1

write_data data_after_E_P_Min_step_1

# Equilibration at desired temperature

timestep 0.0002

velocity all create $T 32145 mom yes rot no

fix 1 all npt temp $T $T 1 iso 0 0 1 drag 1

# Set thermo output

thermo 500

thermo_style custom step lx ly lz press pxx pyy pzz pe temp

run 300000

write_data data_after_T_Min_step_2

unfix 1

reset_timestep 0

timestep 0.0002

fix 1 all nvt temp $T $T 100.0

thermo 100#00

compute 5 hydrogen msd com yes

compute 6 zr msd

thermo_style custom step temp pe press vol etotal

fix 3 hydrogen ave/time 10 5 1000 c_5[1] c_5[2] c_5[3] c_5[4] c_6[4] file $T_MSD_zr_h

run 10000000

unfix 1

unfix 3

write_data data_after_MSD_step_3

Thanks Vladimir, but there is no Zr-H/Zr-He on ctcms website

in that case i am afraid you have to produce your own. but beware that eam potentials are constructed to reproduce metallic character of bonding. btw, there is very old paper by Puskas http://journals.aps.org/prb/abstract/10.1103/PhysRevB.24.3037 regarding embeding of atoms into electron gas. 

Thanks  Drahomir, I intend to attach Zr and H within LAMMPS which I believe is possible.

Dear Afshin Arjhangmehr,

Did you figure out Zr-H and Zr-He potentials ?

Dear Afshin

Maybe you can try atomicrex and/or potfit

http://www.atomicrex.org/

https://www.potfit.net/wiki/doku.php

Best

Can the parameters from these works can be used to make our own potential along with the help from the links provided by Dear Alberto Fraile ?

Dear Afshin

Probably you couldn't find the Zrh, EAM potential yet or at least not a good one. I have found a reasonable (2NN) MEAM potential model which seems to work nicely for several parameters in comparison with the experimental results. This potential were discussed in a paper title as "A comparative study on hydrogen diffusion in amorphous and crystalline metals using a molecular dynamics simulation Byeong-Moon Lee and Byeong-Joo Lee, Metall. Mater. Trans. A 45, 2906-2915 (2014)."

"https://link.springer.com/content/pdf/10.1007%2Fs11661-014-2230-4.pdf"

Another way is to use comb3 potential it may work for specific research aspects but we may consider its simulation cost as it goes higher with a larger number of atoms system ~ power of 3 factor. And here where you can download the potential model from :

https://github.com/lammps/lammps/blob/master/potentials/ffield.comb3

**if you don't know how to use it with lammp i may help you with that too as it is not common for usual atomic collision applications, for input script with MD codes,

Best regards

Responding to some of questions I got about how to use COMB3 potential for calculating the ZrH mean square displacement to be used for the diffusion coefficient calculation. I would put it here at once for all of you, below is an full input script you just probably copy it and run after you download the potential model from the above link I previously mentioned, it is up to you how to modify and refine for your HCP structure or other aspects:

####################################################

units metal

boundary p p p

atom_style charge

pair_style comb3 polar_off #for comb3 potential

variable X equal "16"

variable Y equal "10"

variable Z equal "10"

variable T equal "500"

lattice hcp 3.232

region box block 0 $X 0 $Y 0 $Z

create_box 2 box

create_atoms 1 box

create_atoms 2 random 100 878567 box

group zr type 1

group hydrogen type 2

pair_coeff * * ffield.comb3 Zr H #H

neighbor 2 bin

neigh_modify delay 10 check yes

mass 1 91.224

mass 2 1.0079

thermo 500

# Energy minimization and pressure minimization

fix 1 all nve/limit 0.1

thermo_style custom step pe lx ly lz press pxx pyy pzz vol etotal

minimize 1.00e-30 1.00e-30 100000 1000000

unfix 1

fix 1 all box/relax aniso 0.0 vmax 0.1

thermo_style custom step pe lx ly lz press pxx pyy pzz vol etotal

minimize 1.0e-30 1.0e-30 100000 1000000

unfix 1

write_data data_after_E_P_Min_step_1

# Equilibration at desired temperature

timestep 0.0002

velocity all create $T 32145 mom yes rot no

fix 1 all npt temp $T $T 1 iso 0 0 1 drag 1

# Set thermo output

thermo 500

thermo_style custom step lx ly lz press pxx pyy pzz pe temp

run 300000

write_data data_after_T_Min_step_2

unfix 1

reset_timestep 0

timestep 0.0002

fix 1 all nvt temp $T $T 100.0

thermo 100#00

compute 5 hydrogen msd com yes

compute 6 zr msd

thermo_style custom step temp pe press vol etotal

fix 3 hydrogen ave/time 10 5 1000 c_5[1] c_5[2] c_5[3] c_5[4] c_6[4] file $T_MSD_zr_h

run 10000000

unfix 1

unfix 3

write_data data_after_MSD_step_3

Dear Mosab,

Thank you very much, it is really helpful.