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