Output from compute voronoi

LAMMPS LAMMPS General Discussion
1

hi i am running a shock simulation on aluminium and it is giving satifactory output for density and velocity obtained using compute ave/chunk command but the value of pressure is larger by a factor of 10, i have calculated pressure as

compute peratom bulk stress/atom NULL
compute vorvol bulk voronoi/atom

variable meanpress atom -(c_peratom[1]+c_peratom[2]+c_peratom[3])/3/c_vorvol[1]
compute cc3 bulk chunk/atom bin/1d z lower ${deltaz} units box

fix pressure_profile bulk ave/chunk {Nevery} {Nrepeat} $ {Nfreq} cc3 v_meanpress file pressure.profile

to find where the error occurs i am trying to ouput values of vorvol but every time i use fix, thermo_style custom or dump command sum or the other error pops up.

can someone point out the mistake i am making while calculating the\ pressure or the how to plot the c_vorvol[1]

also in the meanpress variable the code still runs when i replace c_vorvol[1] with vol, however there is nothing defind as “vol” can someone clarify what this vol is and where it is coming from

2

You post is largely unreadable (please check out the forum guidelines about proper quoting of input files) and just a few command without the context of the remaining input.

what error?

The keyword “vol” is a thermo keyword for custom thermo output: thermo_style command — LAMMPS documentation

3

i am sorry for the ambiguity, i am trying to simulate shock in an aluminum bar using NEMD(non-equilibrium molecular dynamics) method where i have split the simulation box into a piston and a bulk,used EAM as pair style i have then prescribed velocity to the piston and no force, after which i have set up bins to track the passing of the shock wave, using this bins i am plotting the density, pressure and particle velocity along the loading direction, i am able to get satisfactory results for velocity and density but the values of pressure are x10 of the expected domain.

i am calculating the pressure by first using compute stress/atom which gives a (stressvolume per atom) vector with six elements xx,yy,zz,xy,xz,yz, then i calculate hydrostatic pressure using (xx+yy+zz/(3c_vorvol[1]) as defined in stress/atom command page in the LAMMPS manual, but the results are 10x of expected values(ex. 160Gpa instead of 16Gpa),

so i investigated the c_vorvol[1], which is calculated using the compute voronoi/atom command and as far as i have understand calculates the volume per atom in the simulation, which gives me the the value of hydro static pressure variation along the length, with time.

so i think i have to exclude center of mass bias while calculating atomic velocities to compute the thermodynamic properties accurately. how to exculde center of mass bias while calculating the stress/atom as the first term in the formula of stress/atom contains kinetic energy contribution

4

This post has the same formatting issues as the previous ones.

Only for a dense system. Voronoi tesselation is an algorithm that divides the total volume into cells. So if you have vacuum regions in your system, that vacuum will be divided as well and added to the closest atoms. Voronoi diagram - Wikipedia

What you are asking about is not a LAMMPS issue but rather a question of how you are planning your simulation and research. The LAMMPS manual documents in detail what each command does. How to combine this for your purposes is your job, not ours.