Automated S/T/C calculation

[qzhu2017]

An automated script to run

1. Default xx, yy, zz on tensile/compression, xy, yz, xz on shear,
2. choose different supercell size based on the loading condition?
3. Dump the molecular centers, and PE(eV/molecule)-strain, stress(MPa)-strain curves for quick analysis.

[pedroantoniosantosf]

@qzhu2017
I got a way to dump the values of center-of-mass. It just copy the same value to all atoms in each molecule... But we can just for post-analysis use 1 atom per molecule.

compute         cmol all chunk/atom molecule.      # Define the chunk as a molecule
compute         com all com/chunk cmol                # Calculate the center-of-mass per molecule
compute         vcm all vcm/chunk cmol                # Calculate the center-of-mass velocity per molecule
compute         mychunk all chunk/spread/atom cmol c_com[*] c_vcm[*]         # Values are copied to each atom in the molecule.
dump            1 all custom ${dump_steps} shear.*.dump element id mol type x y z c_mychunk[*]
dump_modify     1 element ${ele_string}

[qzhu2017]

@pedroantoniosantosf
Thanks, I have a somewhat more challenging case.
Here I need to compute both the mass center and velocity for every two molecules (e.g., molecular id [1,2], [3, 4], ...)
I want to output these information to a single file like what we did before.

fix             3 all ave/time 2 100 1000 c_mychunk[*] file center.dat mode vector

Can you help? This will be very useful for our data analysis.

[pedroantoniosantosf]

@qzhu2017
I was trying but I couldn't find the way to do it in lammps. Wouldn't it be possible to do it before, by modifying the lmp.dat file combining the 2 molecules?

[qzhu2017]

Todo

• Simplify lmp.dat (use replicate function)
• quick scan all of folders / html output
• Run jobs in parallel

[qzhu2017]

Todo

If 'xx' calculation is complete, skip the calculation.