# Gallery

Reproducible reaction-profile figures. Each is rebuilt by
`python goodvibes/examples/gallery/build_gallery.py` from compact files in the
repository (reaction-profile documents with embedded conformers, and a CSV
table); no program output is needed. The inputs, the code of every figure and
the commands are in
[`goodvibes/examples/gallery`](https://github.com/patonlab/GoodVibes/tree/master/goodvibes/examples/gallery).

## Δqh-G with every conformer

![Aza-borocyclization Δqh-G profile with conformers](gallery/azabor_dft.png)

One computed series at 298.15 K from about 100 Gaussian outputs, transition
states labelled above their bar, each conformer drawn around its species'
level, and a barrier annotation.

## One profile at four temperatures

![The same profile at 273, 298, 373 and 423 K](gallery/azabor_temperatures.png)

The embedded structures re-evaluated at each temperature without the output
files: `goodvibes-profile plot goodvibes/examples/profiles/azabor_profile.json --temperatures 273.15,298.15,373.15,423.15 -o scan.png`.

## ΔE, ΔH and Δqh-G on one axes

![ΔE, ΔH and Δqh-G of one profile](gallery/azabor_quantities.png)

Three quantities of the same structures as three series.

## Competing transition states, one panel each

![R and S transition states in two panels](gallery/aminox_branches.png)

Two pathways from one reactant pair (`layout: panels`), ΔE dotted and
Δqh-G solid, barriers marked.

## A CSV table of relative energies

![A profile drawn from a CSV table](gallery/declared_csv.png)

`goodvibes-profile plot goodvibes/examples/profiles/levels.csv -o levels.png`: a hand-typed table is a profile.
The values are illustrative, not from a publication.

## Computed and declared values together

![Computed and declared series on one pathway](gallery/dft_vs_declared.png)

A declared series (hollow markers; illustrative values) next to the computed
Δqh-G on the same points.

## A journal-column preset with error bars

![A declared profile with error bars at the single-column preset](gallery/column_preset_uncertainty.png)

`minimal.yaml` with illustrative ± uncertainties added, drawn at the
`single-column` preset. Saved as SVG, the figure keeps its text editable and
embeds the drawn document.

```python
from goodvibes import load_profile

prof = load_profile("goodvibes/examples/profiles/minimal.yaml")
prof.series[0].uncertainty = {"main": {"TS1": 1.5, "Int": 0.8, "TS2": 1.2, "P": 1.0}}
prof.plot(preset="single-column", label_points=True).save("fig.svg", "fig.pdf")
```

In a document the uncertainties sit under the series as `uncertainty:`, next
to `levels:`; `goodvibes-profile plot profile.yaml -o fig.svg --preset
single-column` then draws the same figure.