PQEnalyzer 0.8.0

A package that help analyze PQ energy and parameter output.

PQEnalyzer

Energy and parameter analyzer for PQ molecular dynamics trajectories.

Installation

Install with pip:

pip install PQEnalyzer

Usage

Open the GUI by passing one or more supported input files to the gui mode. PQEnalyzer detects PQ energy, QMCFC energy, and box files automatically:

pqenalyzer gui pq_output.en

Open the terminal interface for simulation monitoring:

pqenalyzer tui pq_output.en

Read QMCFC output:

pqenalyzer gui --qmcfc pq_output.en

Force PQ energy parsing:

pqenalyzer gui --pq pq_output.en

Plot PQ box parameters from a .box file:

pqenalyzer gui examples/box-01.box

Use --box when a box file does not use the conventional .box suffix.

Multiple input files can be plotted together when they expose the same parameters and units:

pqenalyzer gui md-01.en md-02.en md-03.en

The tui mode opens a full-screen terminal dashboard with file status, per-parameter latest/mean/min/max values, compact trends, file-change watching, and focused terminal charts. Use up/j and down/k to select a parameter, enter to open its chart, esc to return to the dashboard, q to quit, r to refresh manually, and w to pause or resume watching. Focused charts include statistics overlays: m toggles mean, n toggles median, c toggles cumulative average, s toggles self-correlation mean, x toggles difference, and a toggles running average.

In GUI mode, Live Monitor opens a raw overview with one panel per parameter. Auto-Refresh watches the loaded file for changes and redraws open plots when new simulation output is written. Disable Auto-Refresh to pause file watching. Double-click a monitor panel to open a focused plot for that parameter. Statistics and time-series overlay controls apply to the selected focused plot, while the monitor stays raw for simulation monitoring.

Input Files

PQEnalyzer reads energy output through PQAnalysis. Each .en file is expected to have its matching .info sidecar file next to it.

PQEnalyzer also reads PQ box files through PQAnalysis. Box files are expected to contain step x y z alpha beta gamma columns. The plotted parameters are BOX-X, BOX-Y, BOX-Z, ALPHA, BETA, GAMMA, and BOX-VOLUME.

When multiple files are supplied, their parsed parameter mappings and units must match. Files with different columns or incompatible units are rejected before plotting.

Difference plots additionally require both files to have the same simulation-time axis.

Development

Install the package with test dependencies:

pip install -e ".[test]"

Run the default test suite:

python -m pytest -q

Benchmark tests require pytest-benchmark. If it is not installed, benchmark tests are skipped by default.