Thx Axel,

I have run program for ZrO2 and i want to run program for doped ZrO2 (YSZ). I do not know how add Y to my program. Should I use fraction for Y and Zr and add vacancy of Oxygen?

# MD Calculation of doped-ZrO2

units metal

atom_style charge

dimension 3

boundary p p p

variable a0 equal 5

lattice custom ${a0} a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0 0.5 0.5 basis 0.5 0 0.5 basis 0.5 0.5 0 basis 0 0 0 basis 0 0.5 0.5 basis 0.5 0 0.5 basis 0.5 0.5 0 basis 0.25 0.25 0.25 basis 0.75 0.75 0.75 basis 0.75 0.75 0.25 basis 0.25 0.25 0.75 basis 0.75 0.25 0.75 basis 0.25 0.75 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.25

dimension 3

boundary p p p

region box block 0 4 0 4 0 4

create_box 3 box

create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 3 basis 10 3 basis 11 3 basis 12 3 basis 13 3 basis 14 3 basis 15 3 basis 16 3

# Create groups

group Zr type 1 #A for cations

group Y type 2 #B for cations

group O type 3 #C for anions

set group 1 charge 2.4

set group 2 charge 2.4

set group 3 charge -1.2

set group 1 type/fraction 1 0.8 2150

set group 2 type/fraction 2 0.2 1353

set group 3 type/fraction 3 0.9 4652

# Set masses

variable 1 equal 91.224# Zr

variable 2 equal 88.915 # Y

variable 3 equal 15.999 # O

variable V equal vol

variable dt equal 0.0015

variable T equal 200

variable P equal 0.0

variable kB equal 8.6173423e-5 # [eV/K] Boltzman constant

variable eV2J equal 1.60217646e-19

variable A2m equal 1.0e-10

variable ps2s equal 1.0e-12

variable convert equal {eV2J}/{A2m}/${ps2s}

variable CL equal 10000 # correlation length

variable SI equal 1 # sample interval

variable DI equal {CL}*{SI} # dump interval

# setup problem

velocity all create $T 27281 units box

pair_style buck/coul/long 10.0 10

pair_coeff 1 3 1986.8 0.3511 20.40

pair_style buck/coul/long 10.0 10

pair_coeff 3 3 22746.3 0.1490 45.83

pair_style buck/coul/long 10.0 10

pair_coeff 1 1 0.0 1.0 0.0

pair_style buck/coul/long 10.0 10

pair_coeff 2 3 1885.75 0.3399 20.34

pair_style buck/coul/long 10.0 10

pair_coeff 2 2 0.0 1.0 0.0

pair_style buck/coul/long 10.0 10

pair_coeff 1 2 0.0 1.0 0.0

kspace_style ewald 1.0e-4

# equilibrization and thermalization

fix NPT all npt temp $T $T 0.15 iso $P $P 1.5

run 2000000

# thermal conductivity calculation

unfix NPT

fix NPT all npt temp $T $T 0.15 iso $P $P 1.5

reset_timestep 0

compute myKE all ke/atom

compute myPE all pe/atom

compute myStress all stress/atom NULL virial

compute flux all heat/flux myKE myPE myStress

variable Jx equal c_flux[1]/vol

variable Jy equal c_flux[2]/vol

variable Jz equal c_flux[3]/vol

variable scale equal 1/${kB}/$T/$T/V*{SI}*{dt}
variable k11 equal trap(f_JJ[3])*{scale}*{convert}
variable k22 equal trap(f_JJ[4])*{scale}*{convert}
variable k33 equal trap(f_JJ[5])*{scale}*${convert}

run 2000000

variable k equal (v_k11+v_k22+v_k33)/3.0

variable ndens equal count(all)/vol

print “average thermal conductivity: $k [W/mK] @ T K, {ndens} /A^3”

Thanks Axel

I want to run this program and use write_data to create a read data file.

why read a data file, if you can create the system right away?

Also I have used:

units metal

atom_style charge

that script is just one part of program.

it is *extremely* irritating and frustrating when people post incomplete and non-functioning input script code. you are just inviting people to give you incorrect advice.

I do not understand how to make fraction?

a fraction of what? where and how and with what command, and why do you want/need to do this?

Is it need to put vacancy?

how should anybody be able to answer this question?

in general, the quality and usefulness of responses to your question crucially depends on the quality and clarity of the information you provide and how well formulated your questions are. you are so far doing a bad job in that regard and thus there is only very little help that can be given.

axel.