Scripts to process and analyze TILD simulation output

Calculate the density profiles in the z direction and fit an error function to the two interfaces:

run_profile.sh:

Bash script that runs the key python scripts

check_profile.sh:

Bash script that checks the quality of density profile phase-coexistence predictions; averages and gets uncertainties

min_gNP.py:

Python script to determine the minimum volume fraction of grafted nanoparticles in the dilute region based on box size -- min_gNP.py -h for info

dmft_slice.py:

Python script that takes an output density file and averages over a chosen plane. -- dmft_slice.py -h for info -- Nx = Number of grid points in x-direction -- Lx = Length of box in x-direction -- Hardcoded output is always 'dens_no-shift_slice.dat' -- Modified from Jason Koski's script.

com2.py:

Shifts input file so that the density file is centered at Lz/2

com.py [input file, typically 'dens_no-shift_slice.dat'] [centered output density]
com2.py is basically the same file as com.py but it shifts the density file to be centered at 0 -- com2.py -h for info -- Modified from Jason Koski's script.

Once in a while in doing my mass analysis, some of the density profiles would be shifted so that the matrix-dense region was more dense in the center of the box. 'fit_curve.py' is best setup to calculate density profiles for [matrix-dense, gnp-dense, matrix-dense] curves. This way, you have both centering scripts incase you run into this problem.

fit_curve.py: fits a density curve to 2 error functions and spits out the matrix-dense volume fraction and the gnp-dense volume fraction

--Note dmft_slice.py spits out the density file as phi vs z/Lz, so always use Lz is 1 -- fit_curve.py -h for info --If you get funky results from this, you likely have to center the density curve using com2.py OR once in a blue moon, you may have to change your initial guess. --Note you’ll need the scripts in the fts folder as well, as they have some functions that are used. -- Modified from Jason Koski's script.

Trajectory analysis

np_properties.py

Analyzes the trajectories. -- np_properties.py -h for info

Visualization

paraview.py:

To look at the density profiles in Sandia’s code Paraview, you can use the attached script, e.g.:

python paraview Nx Ny Nz rhoga.tec rhoga.all -- From Jason Koski

-- Notes Upload tec file press apply color -> real put slice to see a plane iso -> contour

apsantos/fieldanalysis