The PyVisA application¶

PyVisA is the analysis and visualization tool for PyRETIS simulations. It consists of two components:

A compressor that reads raw simulation output, checks consistency, and stores the data in a compressed .hdf5 binary file.
A visualizer (GUI) that loads compressed or raw data and produces interactive plots, cluster analyses, and PCA results. The GUI requires PyQt5, which must be installed separately (see installation).

The general syntax is:

pyvisa [-h] [-i INPUT] [-V] [-cmp] [-data DATA] [-recalculate] [-oo]

where the arguments are described in Table 46.

Example use¶

Compress raw simulation output into a .hdf5 file:
```
pyvisa -i out.rst -cmp
```
Compress using only order parameter files (faster, smaller output):
```
pyvisa -i out.rst -cmp -oo
```
Open the visualization GUI from a compressed file:
```
pyvisa -i simulation.hdf5
```
Open the GUI from the original input file, loading a specific ensemble:
```
pyvisa -i out.rst -data 000
```
Recalculate order parameters and collective variables:
```
pyvisa -i retis.rst -recalculate
```

Table 46 Description of input arguments for PyVisA.¶
Argument	Description
-h, –help	Show the help message and exit.
-i INPUT, –input INPUT	Location of the input file (`.rst` or `.hdf5`).
-V, –version	Show the version number and exit.
-cmp, –pyvisa_compressor	Run the compressor tool to generate a `.hdf5` file from raw simulation output.
-data DATA, –pyvisa-data DATA	Select a subset of data to load. Use `all` for all data, or a folder name (e.g. `000`) for a single ensemble.
-recalculate, –pyvisa-recalculate	Recalculate order parameter and collective variable data using the current `orderp.py`.
-oo, –only_order	Use only data from `order.txt` files when compressing (faster, skips energy data).