10
0
mirror of https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local synced 2024-10-31 19:23:42 +01:00
EMSL_Basis_Set_Exchange_Local/README.md

122 lines
4.3 KiB
Markdown
Raw Normal View History

2014-11-12 14:36:12 +01:00
EMSL_Basis_Set_Exchange_Local
=============================
2014-12-04 15:07:19 +01:00
[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/TApplencourt/EMSL_Basis_Set_Exchange_Local?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
2014-11-12 14:36:12 +01:00
2014-11-12 18:34:25 +01:00
Create of Local Copy of the famous [EMSL Basis Set Exchange](https://bse.pnl.gov/bse/portal) and use it easily with the API.
2014-11-12 16:36:38 +01:00
2015-03-17 17:28:31 +01:00
* Make a slight copy (40Mo Sqlite3 database) of the EMSL Basis Set Exchange website. Currently avalaible format are :
2015-03-17 17:43:54 +01:00
* Gamess-us, Gaussian94 and NEWCHEM;
2015-01-12 16:01:52 +01:00
* API for scripting;
* Quick local access without delay;
2015-01-13 10:09:57 +01:00
* Only need [Python](https://www.python.org/)
2014-11-12 16:36:38 +01:00
2015-03-18 13:27:09 +01:00
##Dependencies
2014-11-19 17:31:00 +01:00
* Python >2.6
2015-01-13 10:07:13 +01:00
###### Optional
If you plan to download manually some database -not using the pre existing one- you need :
2015-01-13 10:09:57 +01:00
* [Request](http://docs.python-requests.org/en/latest/) python module. ```$pip install requests``` (do it in a virtual env or with sudo)
2014-11-19 17:31:00 +01:00
##Installation
2015-01-13 10:09:57 +01:00
* Download the git repertory (```$git clone https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local.git``` for example)
2015-01-13 10:01:33 +01:00
* That all! You can now, use ```EMSL_api.py```
2014-11-19 17:31:00 +01:00
2014-11-12 17:41:06 +01:00
##Usage
2014-11-12 16:36:38 +01:00
```
EMSL Api.
Usage:
2015-03-11 10:36:05 +01:00
EMSL_api.py list_basis [--basis=<basis_name>...]
[--atom=<atom_name>...]
[--db_path=<db_path>]
[--average_mo_number]
2015-01-12 16:01:52 +01:00
EMSL_api.py list_atoms --basis=<basis_name>
2015-03-11 10:36:05 +01:00
[--db_path=<db_path>]
2015-01-12 16:01:52 +01:00
EMSL_api.py get_basis_data --basis=<basis_name>
[--atom=<atom_name>...]
[--db_path=<db_path>]
[--with_l]
[(--save [--path=<path>])]
EMSL_api.py list_formats
EMSL_api.py create_db --db_path=<db_path>
--format=<format>
[--no-contraction]
2014-11-12 16:36:38 +01:00
EMSL_api.py (-h | --help)
EMSL_api.py --version
Options:
-h --help Show this screen.
--version Show version.
--no-contraction Basis functions are not contracted
<db_path> is the path to the SQLite3 file containing the Basis sets.
2015-01-12 16:01:52 +01:00
By default is $EMSL_API_ROOT/db/Gausian_uk.db
2015-03-11 10:36:05 +01:00
Example of use:
./EMSL_api.py list_basis --atom Al --atom U
./EMSL_api.py list_basis --atom S --basis 'cc-pV*' --average_mo_number
./EMSL_api.py list_atoms --basis ANO-RCC
./EMSL_api.py get_basis_data --basis 3-21++G*
2014-11-12 16:36:38 +01:00
```
2015-01-12 16:01:52 +01:00
##Demonstration
![](http://fat.gfycat.com/WelcomePerkyChrysomelid.gif)
(For a beter quality see the [Source](https://asciinema.org/api/asciicasts/15380))
2014-11-12 17:41:06 +01:00
##To do
2015-03-17 17:28:31 +01:00
For now we can only parse `Gamess-us, Gaussian94 and NEWCHEM` (Thanks to @mattbernst for Gaussian94 and NEWCHEM) basis set type file.
###I need more format!
I realy simple. Just read the few explanation bellow.
2015-03-17 17:43:54 +01:00
You just need to provide a function who will split the basis data who containt all the atoms in atom only tuple.
2015-03-17 17:28:31 +01:00
Sommething like this:
```python
def parse_basis_data_gaussian94(data, name, description, elements, debug=True):
"""Parse the Gaussian94 basis data raw html to get a nice tuple.
The data-pairs item is actually expected to be a 2 item list:
[symbol, data]
e.g. ["Ca", "#BASIS SET..."]
N.B.: Currently ignores ECP data!
@param data: raw HTML from BSE
@type data : unicode
@param name: basis set name
@type name : str
@param des: basis set description
@type des : str
@param elements: element symbols e.g. ['H', 'C', 'N', 'O', 'Cl']
@type elements : list
@return: (name, description, data-pairs)
@rtype : tuple
"""
```
Then just add the function in `src.parser_handler.format_dict`. You are ready to go!
2014-11-12 17:41:06 +01:00
Feel free to fork/pull request.
##Disclaimer
2014-11-12 17:41:50 +01:00
It'is not a official API. Use it with moderation.
2014-11-12 17:41:06 +01:00
2015-03-17 17:28:31 +01:00
In papers where you use the basis sets obtained from the Basis Set Exchange please site this:
2014-11-20 16:31:26 +01:00
>The Role of Databases in Support of Computational Chemistry Calculations
>
>>--<cite>Feller, D.; J. Comp. Chem., 17(13), 1571-1586, 1996.</cite>
>Basis Set Exchange: A Community Database for Computational Sciences
>
>>--<cite>Schuchardt, K.L., Didier, B.T., Elsethagen, T., Sun, L., Gurumoorthi, V., Chase, J., Li, J., and Windus ; T.L.
>>J. Chem. Inf. Model., 47(3), 1045-1052, 2007, doi:10.1021/ci600510j.</cite>
And don't forget:
2014-11-12 17:41:06 +01:00
>These documents may be freely distributed and used for non-commercial, scientific and educational purposes.
2014-11-12 17:41:20 +01:00
>-- <cite>http://www.pnl.gov/notices.asp</cite>
2014-11-12 17:41:06 +01:00