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https://github.com/radi0sus/orca_st
Easily transfer selected states from ORCA output files into tables
https://github.com/radi0sus/orca_st
computational-chemistry dft docx markdown orca orca-quantum-chemistry pandoc python python3 quantum-chemistry spectra spectrum tables td-dft uv-vis uvvis
Last synced: 17 days ago
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Easily transfer selected states from ORCA output files into tables
- Host: GitHub
- URL: https://github.com/radi0sus/orca_st
- Owner: radi0sus
- License: bsd-3-clause
- Created: 2021-09-05T20:18:54.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2021-09-07T15:55:36.000Z (over 3 years ago)
- Last Synced: 2024-01-28T01:53:51.272Z (11 months ago)
- Topics: computational-chemistry, dft, docx, markdown, orca, orca-quantum-chemistry, pandoc, python, python3, quantum-chemistry, spectra, spectrum, tables, td-dft, uv-vis, uvvis
- Language: Python
- Homepage:
- Size: 16.1 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# orca_st
A Python 3 script for (hassle-free) extraction of state informations from [ORCA](https://orcaforum.kofo.mpg.de)
output files. Selection of states and threshold based printing is possible.
Annoyed with Python? Try the [Go Edition](https://github.com/radi0sus/orca_st-go)!
## External modules
`re`
## Quick start
Start the script with:
```console
python3 orca-st.py filename
```
it will show the table in the console. The table will probably exceed the size of
your console window and the table might therefore look unfamiliar.
Start the script with:
```console
python3 orca-st.py filename > filename.md
```
it will save the table in markdown format.
Convert markdown to docx (install [PANDOC](https://pandoc.org) first):
```console
pandoc filename.md -o filename.docx
```
This will convert the markdown file to a docx file. Open it with your favorite
word processor. Convert the file to even more formats such as HTML, PDF or TeX with PANDOC.
## Command-line options
- `filename` , required: filename
- `-s` `S1, S2, ... Sx` , optional: process all or selected states (default is `S = all`)
- `-t` `N`, optional: set a threshold in %. Transitions below the threshold value will not be printed (default is `N = 0`)
- `-nto`, optional: process all or selected states for natural transition orbitals (NTO)
- `-tr`, optional: show 'Transition' in case of ORCA 6 output files
## Code options
You can change the table header in the script (take care of the row size if necessary).
## Remarks
- The data are taken from the section "ABSORPTION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS".
- Only tested with "normal" outputs (including NTO) from TD-DFT calculations.
- Selected transitions that are below the threshold will not be printed in the table. This may result in empty cells.
- If NTO transitions are present int the output file and NTO transitions should be printed, use the `-nto` keyword.
Otherwise, do not use the `-nto` keyword.
- The script used two unicode characters, namely "⁻¹". Please have a look at the script if you experience any issues. The easiest
solution is to replace "⁻¹" with the ascii characters "-1".
## Examples
| State | Energy (cm⁻¹) | Wavelength (nm) | fosc | Selected transitions |
|-------|---------------|-----------------|--------------|---------------------------------------|
| 1 | 23979.9 | 417.0 | 0.010256887 | 54a -> 55a (92.2%) |
| 2 | 31770.2 | 314.8 | 0.074054821 | 53a -> 55a (94.9%) |
| 3 | 34195.7 | 292.4 | 0.009570330 | 52a -> 55a (92.5%) |
| 4 | 34682.0 | 288.3 | 0.004586429 | 51a -> 55a (91.9%) |
| 5 | 36920.0 | 270.9 | 0.015882129 | 50a -> 55a (89.0%) |
| 12 | 46564.6 | 214.8 | 0.022945033 | 52a -> 56a (43.6%), 53a -> 58a (17.8%)|
| 20 | 50438.7 | 198.3 | 0.011430245 | 50a -> 58a (45.2%), 52a -> 59a (24.0%)|
| 25 | 53856.3 | 185.7 | 0.048902902 | 46a -> 55a (20.3%), 47a -> 55a (64.4%)|
| State | Energy (cm⁻¹) | Wavelength (nm) | fosc | Selected transitions (NTO) |
|-------|---------------|-----------------|--------------|-----------------------------------------------------------|
| 20 | 50693.7 | 197.3 | 0.349127321 | 54a -> 55a (38.6%), 53a -> 56a (31.2%), 52a -> 57a (27.7%)|
| 25 | 53666.2 | 186.3 | 0.001229720 | 54a -> 55a (62.0%), 53a -> 56a (29.7%) |
| 30 | 55961.6 | 178.7 | 0.000789896 | 54a -> 55a (93.9%) |