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).

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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).

Example potential-energy trace.

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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).

Example BSF time series.

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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).

Cluster size vs BSF.

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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).

Dissociation events per Δt.

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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).

Cluster-size histogram.

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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).

Sticker vs spacer radial densities.

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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).

Chain-neighbour histogram.

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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).

Example histogram of sticker-bond multiplicities.

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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.

Sticker‑sticker distance distributions.