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README.md |
EMSL_Basis_Set_Exchange_Local
Create of Local Copy of the famous EMSL Basis Set Exchange and use it easily with the API.
- Make a slight copy (40Mo Sqlite3 database) of the EMSL Basis Set Exchange website. Currently avalaible format are :
- Gamess-us, Gaussian94 and NEWCHEM;
- API for scripting;
- Quick local access without delay;
- Only need Python
##Dependencies * Python >2.6
Optional
If you plan to download manually some database -not using the pre
existing one- you need : * Request python
module. $pip install requests
(do it in a virtual env or
with sudo)
##Installation * Download the git repertory
($git clone https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local.git
for example) * That all! You can now, use EMSL_api.py
##Usage
EMSL Api.
Usage:
EMSL_api.py list_basis [--basis=<basis_name>...]
[--atom=<atom_name>...]
[--db_path=<db_path>]
[--average_mo_number]
EMSL_api.py list_atoms --basis=<basis_name>
[--db_path=<db_path>]
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]
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.
By default is $EMSL_API_ROOT/db/Gausian_uk.db
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*
##Demonstration
(For a beter quality see the Source)
##To do 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.
You just need to provide a function who will split the basis data who containt all the atoms in atom only tuple.
Sommething like this:
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!
Feel free to fork/pull request.
##Disclaimer It’is not a official API. Use it with moderation.
In papers where you use the basis sets obtained from the Basis Set Exchange please site this: >The Role of Databases in Support of Computational Chemistry Calculations > >>–Feller, D.; J. Comp. Chem., 17(13), 1571-1586, 1996.
Basis Set Exchange: A Community Database for Computational Sciences
–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.
And don’t forget: >These documents may be freely distributed and used for non-commercial, scientific and educational purposes. >– http://www.pnl.gov/notices.asp