Data-Analysis Helpers

Note

These lightweight scripts live in /analysis and are meant for quick, single-file previews of key observables.

Exactly one input file is supplied as the first positional argument.

Run them from the project root, for example:

python docs/_static/scripts/plot_PE.py  results/Thermo_run1.dat

Each script prints an informative --help message describing optional flags (e.g. custom column numbers, unit conversions).

Potential-Energy Trace

Script plot_PE.py Input Thermo_<run>.dat (LAMMPS thermo dump) Action Extracts the potential-energy column and plots energy vs step (line plot saved as PE.png).

../_images/PE.png — Example potential-energy trace.

Bonded-Sticker Fraction (BSF) – time series

Script plot_BSF.py Input Thermo_<run>.dat (must include a running bonds column) Action Computes the percentage of newly formed cross-links and plots % stickers bonded vs simulation step (figure saved as BSF_timeseries.png).

../_images/BSF_timeseries.png — Example BSF time series.

Cluster Size vs Bound-Sticker Fraction (scatter)

Script plot_cSizeBSF.py Input one LAMMPS *.DATA snapshot Action Detects connected clusters and scatter-plots cluster size vs bound-sticker fraction for every cluster (figure saved as cSize_BSF_scatter.png).

../_images/cSize_BSF_scatter.png — Cluster size vs BSF.

Sticker Dissociation Events

Script plot_SD.py Input BondData_<run>.dat (3-column cumulative formed / broken counters) Action Converts cumulative counts to per-interval break events and plots a line-style time series (SD.png).

../_images/SD.png — Dissociation events per Δt.

Cluster-Size Distribution

Script plot_cSize.py Input one *.DATA snapshot Action Plots the fraction of chains in each cluster size s (histogram saved as cSize.png).

../_images/cSize.png — Cluster-size histogram.

Radial Sticker / Spacer Density

Script plot_radialDist.py Input one *.DATA snapshot (types 1/3 = stickers, 2/4 = spacers) Action Computes volume-normalised radial density profiles for stickers and spacers (figure saved as RD.png).

../_images/RD.png — Sticker vs spacer radial densities.

Chain-Neighbour Histogram

Script plot_neighCount.py Input one *.DATA snapshot Action Builds a graph whose nodes are chains and whose edges are sticker bonds between different chains; bar-plots the degree distribution (histogram saved as neigh_hist.png).

../_images/neigh_hist.png — Chain-neighbour histogram.

Sticker-Bond Multiplicity per Chain Pair

Script plot_pair_bonds.py Input one *.DATA snapshot Action Builds a MultiGraph in which nodes are chains and each type-1 ⇄ type-3 sticker bond becomes an edge. For every neighbouring chain pair the helper counts the number of parallel edges (i.e. how many sticker bonds connect that pair) and histograms those counts (figure saved as pair_bonds_hist.png).

../_images/pair_bonds_hist.png — Example histogram of sticker-bond multiplicities.

Inter-molecular Sticker-Sticker Distances

Script plot_sticker_dist.py Input one or more *.DATA snapshots Action For every file, measures all pair-wise distances between type-1 and type-3 atoms residing on different molecules; overlays raw-count histograms (sticker_dist.png). bins_w and max_r can be tuned via flags.

../_images/sticker_dist.png — Sticker-sticker distance distributions.