mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-12-22 04:13:43 +01:00
Anthony Scemama
commit
13b8c56766
43
README.md
43
README.md
@ -5,30 +5,39 @@ EMSL_Basis_Set_Exchange_Local
|
||||
Create of Local Copy of the famous [EMSL Basis Set Exchange](https://bse.pnl.gov/bse/portal) and use it easily with the API.
|
||||
|
||||
* Make a slight copy (40Mo Sqlite3 database) of the EMSL Basis Set Exchange website (One database for all the basis set of one format);
|
||||
* API for scripting ;
|
||||
* Quick local access without delay ;
|
||||
* Only need [Python](https://www.python.org/) and [Request](http://docs.python-requests.org/en/latest/) module.
|
||||
* API for scripting;
|
||||
* Quick local access without delay;
|
||||
* Only need [Python](https://www.python.org/)
|
||||
|
||||
##Dependancy
|
||||
##Dependency
|
||||
* Python >2.6
|
||||
* Request ```pip install requests```
|
||||
|
||||
###### Optional
|
||||
If you plan to download manually some database -not using the pre existing one- you need :
|
||||
* [Request](http://docs.python-requests.org/en/latest/) python module. ```$pip install requests``` (do it in a virtual env or with sudo)
|
||||
|
||||
##Installation
|
||||
* Download the git (```$ git clone https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local.git``` for example)
|
||||
* ```cd``` into & run ```$ ./setup.py```
|
||||
* ```source EMSL_api.rc```
|
||||
* Done ! You can now, use ```EMSL_api.py``` or use all the python fonction inside ```./src```
|
||||
* 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 get_list_basis <db_path>
|
||||
EMSL_api.py get_list_elements <db_path> <basis_name>
|
||||
EMSL_api.py get_basis_data <db_path> <basis_name> <elts>...
|
||||
EMSL_api.py get_list_formats
|
||||
EMSL_api.py create_db <db_path> <format> [--no-contraction]
|
||||
EMSL_api.py list_basis [--atom=<atom_name>...]
|
||||
[--db_path=<db_path>]
|
||||
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
|
||||
|
||||
@ -38,7 +47,13 @@ Options:
|
||||
--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
|
||||
```
|
||||
##Demonstration
|
||||
|
||||
|
||||
|
||||
(For a beter quality see the [Source](https://asciinema.org/api/asciicasts/15380))
|
||||
|
||||
##To do
|
||||
For now we can only parse Gaussian-US basis set type file. (Look at ```./src/EMSL_utility.py#EMSL_dump.basis_data_row_to_array```)
|
||||
|
||||
@ -19,6 +19,29 @@ for i in data:
|
||||
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
|
||||
|
||||
|
||||
def install_with_pip(name):
|
||||
|
||||
ins = False
|
||||
d = {'y': True,
|
||||
'n': False}
|
||||
|
||||
while True:
|
||||
choice = raw_input('Do you want to install it ? [Y/N]')
|
||||
try:
|
||||
ins = d[choice.lower()]
|
||||
break
|
||||
except:
|
||||
print "not a valid choice"
|
||||
|
||||
if ins:
|
||||
try:
|
||||
import pip
|
||||
pip.main(['install', name])
|
||||
except:
|
||||
print "You need pip, (http://pip.readthedocs.org/en/latest/installing.html)"
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
def cond_sql_or(table_name, l_value):
|
||||
|
||||
l = []
|
||||
@ -36,8 +59,13 @@ class EMSL_dump:
|
||||
self.format = format
|
||||
self.contraction = str(contraction)
|
||||
|
||||
import requests
|
||||
self.requests = requests
|
||||
try:
|
||||
import requests
|
||||
except:
|
||||
print "You need the requests package"
|
||||
install_with_pip("requests")
|
||||
finally:
|
||||
self.requests = requests
|
||||
|
||||
def set_db_path(self, path):
|
||||
"""Define the database path"""
|
||||
@ -132,7 +160,7 @@ class EMSL_dump:
|
||||
data = data.replace("D+", "E+")
|
||||
data = data.replace("D-", "E-")
|
||||
|
||||
data = data[b + 5:e-1].split('\n\n')
|
||||
data = data[b + 5:e - 1].split('\n\n')
|
||||
|
||||
for (elt, data_elt) in zip(elts, data):
|
||||
|
||||
@ -193,7 +221,7 @@ class EMSL_dump:
|
||||
q_out.put(([name, url, des, elts], basis_data))
|
||||
q_in.task_done()
|
||||
except:
|
||||
print name,url,des
|
||||
print name, url, des
|
||||
raise
|
||||
|
||||
def enqueue():
|
||||
|
||||
118
src/elts_abrev.dat
Normal file
118
src/elts_abrev.dat
Normal file
@ -0,0 +1,118 @@
|
||||
1 - H - Hydrogen
|
||||
2 - He - Helium
|
||||
3 - Li - Lithium
|
||||
4 - Be - Beryllium
|
||||
5 - B - Boron
|
||||
6 - C - Carbon
|
||||
7 - N - Nitrogen
|
||||
8 - O - Oxygen
|
||||
9 - F - Fluorine
|
||||
10 - Ne - Neon
|
||||
11 - Na - Sodium
|
||||
12 - Mg - Magnesium
|
||||
13 - Al - Aluminum
|
||||
14 - Si - Silicon
|
||||
15 - P - Phosphorus
|
||||
16 - S - Sulfur
|
||||
17 - Cl - Chlorine
|
||||
18 - Ar - Argon
|
||||
19 - K - Potassium
|
||||
20 - Ca - Calcium
|
||||
21 - Sc - Scandium
|
||||
22 - Ti - Titanium
|
||||
23 - V - Vanadium
|
||||
24 - Cr - Chromium
|
||||
25 - Mn - Manganese
|
||||
26 - Fe - Iron
|
||||
27 - Co - Cobalt
|
||||
28 - Ni - Nickel
|
||||
29 - Cu - Copper
|
||||
30 - Zn - Zinc
|
||||
31 - Ga - Gallium
|
||||
32 - Ge - Germanium
|
||||
33 - As - Arsenic
|
||||
34 - Se - Selenium
|
||||
35 - Br - Bromine
|
||||
36 - Kr - Krypton
|
||||
37 - Rb - Rubidium
|
||||
38 - Sr - Strontium
|
||||
39 - Y - Yttrium
|
||||
40 - Zr - Zirconium
|
||||
41 - Nb - Niobium
|
||||
42 - Mo - Molybdenum
|
||||
43 - Tc - Technetium
|
||||
44 - Ru - Ruthenium
|
||||
45 - Rh - Rhodium
|
||||
46 - Pd - Palladium
|
||||
47 - Ag - Silver
|
||||
48 - Cd - Cadmium
|
||||
49 - In - Indium
|
||||
50 - Sn - Tin
|
||||
51 - Sb - Antimony
|
||||
52 - Te - Tellurium
|
||||
53 - I - Iodine
|
||||
54 - Xe - Xenon
|
||||
55 - Cs - Cesium
|
||||
56 - Ba - Barium
|
||||
57 - La - Lanthanum
|
||||
58 - Ce - Cerium
|
||||
59 - Pr - Praseodymium
|
||||
60 - Nd - Neodymium
|
||||
61 - Pm - Promethium
|
||||
62 - Sm - Samarium
|
||||
63 - Eu - Europium
|
||||
64 - Gd - Gadolinium
|
||||
65 - Tb - Terbium
|
||||
66 - Dy - Dysprosium
|
||||
67 - Ho - Holmium
|
||||
68 - Er - Erbium
|
||||
69 - Tm - Thulium
|
||||
70 - Yb - Ytterbium
|
||||
71 - Lu - Lutetium
|
||||
72 - Hf - Hafnium
|
||||
73 - Ta - Tantalum
|
||||
74 - W - Tungsten
|
||||
75 - Re - Rhenium
|
||||
76 - Os - Osmium
|
||||
77 - Ir - Iridium
|
||||
78 - Pt - Platinum
|
||||
79 - Au - Gold
|
||||
80 - Hg - Mercury
|
||||
81 - Tl - Thallium
|
||||
82 - Pb - Lead
|
||||
83 - Bi - Bismuth
|
||||
84 - Po - Polonium
|
||||
85 - At - Astatine
|
||||
86 - Rn - Radon
|
||||
87 - Fr - Francium
|
||||
88 - Ra - Radium
|
||||
89 - Ac - Actinium
|
||||
90 - Th - Thorium
|
||||
91 - Pa - Protactinium
|
||||
92 - U - Uranium
|
||||
93 - Np - Neptunium
|
||||
94 - Pu - Plutonium
|
||||
95 - Am - Americium
|
||||
96 - Cm - Curium
|
||||
97 - Bk - Berkelium
|
||||
98 - Cf - Californium
|
||||
99 - Es - Einsteinium
|
||||
100 - Fm - Fermium
|
||||
101 - Md - Mendelevium
|
||||
102 - No - Nobelium
|
||||
103 - Lr - Lawrencium
|
||||
104 - Rf - Rutherfordium
|
||||
105 - Db - Dubnium
|
||||
106 - Sg - Seaborgium
|
||||
107 - Bh - Bohrium
|
||||
108 - Hs - Hassium
|
||||
109 - Mt - Meitnerium
|
||||
110 - Ds - Darmstadtium
|
||||
111 - Rg - Roentgenium
|
||||
112 - Cn - Copernicium
|
||||
113 - Uut - Ununtrium
|
||||
114 - Fl - Flerovium
|
||||
115 - Uup - Ununpentium
|
||||
116 - Lv - Livermorium
|
||||
117 - Uus - Ununseptium
|
||||
118 - Uuo - Ununoctium
|
||||
Loading…
Reference in New Issue
Block a user