mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-06-12 08:15:26 +02:00
Topologie, Doc, and glob
This commit is contained in:
Thomas Applencourt
parent
70553f1779
commit
8a756a465a
13
EMSL_api.py
13
EMSL_api.py
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@ -7,6 +7,7 @@ Usage:
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EMSL_api.py list_basis [--atom=<atom_name>...]
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[--db_path=<db_path>]
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[--average_mo_number]
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[--basis=<basis_name>...]
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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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@ -41,8 +42,8 @@ import sys
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import os
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from src.docopt import docopt
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from src.EMSL_utility import EMSL_dump
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from src.EMSL_utility import EMSL_local, checkSQLite3
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from src.EMSL_dump import EMSL_dump
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from src.EMSL_local import EMSL_local, checkSQLite3
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if __name__ == '__main__':
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@ -79,14 +80,16 @@ if __name__ == '__main__':
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amn = arguments["--average_mo_number"]
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l = e.get_list_basis_available(elts, average_mo_number=amn)
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l = e.get_list_basis_available(elts,
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arguments["--basis"],
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average_mo_number=amn)
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if amn:
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for name, des, avg in l:
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print "{0} ({2}) | {1}".format(name, des, avg)
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print "- '{}' ({}) || {:<50}".format(name, avg, des)
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else:
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for name, des in l:
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print "{0} | {1}".format(name, des)
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print "- {} || {:<50}".format(name, des)
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# _ _ _ _____ _ _
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# | | (_) | | | ___| | | |
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328
src/EMSL_utility.py → src/EMSL_dump.py
Executable file → Normal file
328
src/EMSL_utility.py → src/EMSL_dump.py
Executable file → Normal file
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@ -1,63 +1,8 @@
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# -*- coding: utf-8 -*-
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import sqlite3
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import re
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import sys
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import os
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import sys
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import re
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import time
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debug = True
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def checkSQLite3(db_path):
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from os.path import isfile, getsize
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# Check if db file is readable
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if not os.access(db_path, os.R_OK):
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print >>sys.stderr, "Db file %s is not readable" % (db_path)
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raise IOError
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if not isfile(db_path):
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print >>sys.stderr, "Db file %s is not... a file!" % (db_path)
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raise IOError
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if getsize(db_path) < 100: # SQLite database file header is 100 bytes
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print >>sys.stderr, "Db file %s is not a SQLite file!" % (db_path)
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raise IOError
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with open(db_path, 'rb') as fd:
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header = fd.read(100)
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if header[:16] != 'SQLite format 3\x00':
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print >>sys.stderr, "Db file %s is not in SQLiteFormat3!" % (db_path)
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raise IOError
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# Check if the file system allows I/O on sqlite3 (lustre)
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# If not, copy on /dev/shm and remove after opening
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except sqlite3.OperationalError:
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print >>sys.stdrerr, "I/O Error for you file system"
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print >>sys.stderr, "Try some fixe"
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new_db_path = "/dev/shm/%d.db" % (os.getpid())
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os.system("cp %s %s" % (db_path, new_db_path))
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db_path = new_db_path
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else:
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changed = False
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return db_path, changed
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# Try again to check
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except:
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print >>sys.stderr, "Sorry..."
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os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
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raise
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else:
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print >>sys.stderr, "Working !"
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changed = True
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return db_path, changed
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import sqlite3
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def install_with_pip(name):
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@ -83,17 +28,10 @@ def install_with_pip(name):
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sys.exit(1)
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def cond_sql_or(table_name, l_value):
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l = []
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dmy = " OR ".join(['%s = "%s"' % (table_name, i) for i in l_value])
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if dmy:
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l.append("(%s)" % dmy)
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return l
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class EMSL_dump:
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"""
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This call implement all you need for download the EMSL and save it localy
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"""
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format_dict = {"g94": "Gaussian94",
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"gamess-us": "GAMESS-US",
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@ -116,6 +54,8 @@ class EMSL_dump:
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self.db_path = db_path
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self.format = format
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self.contraction = str(contraction)
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self.debug = True
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try:
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import requests
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except:
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@ -152,7 +92,7 @@ class EMSL_dump:
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"""Download the source code of the iframe who contains the list of the basis set available"""
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url = "https://bse.pnl.gov/bse/portal/user/anon/js_peid/11535052407933/panel/Main/template/content"
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if debug:
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if self.debug:
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import cPickle as pickle
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dbcache = 'db/cache'
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if not os.path.isfile(dbcache):
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@ -211,7 +151,7 @@ class EMSL_dump:
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b = data.find("$DATA")
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e = data.find("$END")
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if (b == -1 or data.find("$DATA$END") != -1):
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if debug:
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if self.debug:
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print data
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raise Exception("WARNING not DATA")
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else:
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@ -229,14 +169,14 @@ class EMSL_dump:
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elt_long_exp = data_elt.split()[0].lower()
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if "$" in data_elt:
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if debug:
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if self.debug:
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print "Eror",
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raise Exception("WARNING bad split")
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if elt_long_th == elt_long_exp:
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d.append([elt, data_elt.strip()])
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else:
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if debug:
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if self.debug:
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print "th", elt_long_th
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print "exp", elt_long_exp
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print "abv", elt
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@ -314,7 +254,7 @@ class EMSL_dump:
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try:
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q_out.put(basis_data)
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except:
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if debug:
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if self.debug:
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print "Fail on q_out.put", basis_data
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raise
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else:
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@ -375,245 +315,3 @@ class EMSL_dump:
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del _data
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self.create_sql(array_basis)
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def string_to_nb_mo(str_l):
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assert len(str_l) == 1
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d = {"S": 3,
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"P": 5,
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"D": 7,
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"F": 9,
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"L": 8}
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if str_l in d:
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return d[str_l]
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# ord("G") = 72 and ord("Z") = 87
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elif 72 <= ord(str_l) <= 87:
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# orf("G") = 72 and l = 4 so ofset if 68
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return 2 * (ord(str_l) - 68) + 1
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else:
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raise BaseException
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class EMSL_local:
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"""
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All the method for using the EMSL db localy
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"""
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def __init__(self, db_path=None):
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self.db_path = db_path
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def get_list_basis_available(self, elts=[], average_mo_number=False):
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"""
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return all the basis name who contant all the elts
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"""
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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# If not elts just get the disctinct name
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# Else: 1) fetch for geting the run_id available
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# 2) If average_mo_number:
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# * Get name,descripption,data
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# * Then parse it
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# Else Get name,description
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# 3) Parse it
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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# G e t i n g B a s i s _ i d #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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if not elts:
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cmd = """SELECT DISTINCT name, description FROM basis_tab"""
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c.execute(cmd)
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info = c.fetchall()
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else:
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cmd_ele = ["SELECT DISTINCT basis_id FROM data_tab WHERE elt=?"] * len(elts)
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cmd = " INTERSECT ".join(cmd_ele) + ";"
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c.execute(cmd, elts)
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dump = [i[0] for i in c.fetchall()]
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cmd_basis = " ".join(cond_sql_or("basis_id", dump))
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cmd_ele = " ".join(cond_sql_or("elt", elts))
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if average_mo_number:
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cmd = """SELECT DISTINCT name,description,data
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FROM output_tab"""
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else:
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cmd = """SELECT DISTINCT name,description
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FROM output_tab"""
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cmd += " WHERE" + cmd_ele + " AND " + cmd_basis
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c.execute(cmd)
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info = c.fetchall()
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conn.close()
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# ~#~#~#~#~#~#~ #
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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dict_info = {}
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# dict_info[name] = [description, nb_mo, nb_ele]
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if average_mo_number:
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for name, description, data in info:
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nb_mo = 0
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nb_ele = 0
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for line in data.split("\n")[1:]:
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str_l = line.split()[0]
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try:
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nb_mo += string_to_nb_mo(str_l)
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nb_ele += 1
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except BaseException:
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pass
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try:
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dict_info[name][1] += nb_mo
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dict_info[name][2] += 1
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except:
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dict_info[name] = [description, nb_mo, nb_ele]
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# ~#~#~#~#~#~ #
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# R e t u r n #
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# ~#~#~#~#~#~ #
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if average_mo_number:
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return[[k, v[0], v[1] / v[2]] for k, v in dict_info.iteritems()]
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else:
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return [i[:] for i in info]
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def get_list_element_available(self, basis_name):
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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str_ = "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE"
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c.execute(str_, {"name_us": basis_name})
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data = c.fetchall()
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data = [str(i[0]) for i in data]
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conn.close()
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return data
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def get_basis(self, basis_name, elts=None, with_l=False):
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"""
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Return the data from the basis set
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"""
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import re
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def get_list_type(l_line):
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"""
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Return the begin and the end of all the type of orbital
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Usefull for tranforming the L in S, P
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output : [ [type, begin, end], ...]
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"""
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# Example
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# [[u'S', 1, 5], [u'L', 5, 9], [u'L', 9, 12], [u'D', 16, 18]]"
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l = []
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for i, line in enumerate(l_line):
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m = re.search(p, line)
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if m:
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l.append([m.group(1), i])
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try:
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l[-2].append(i)
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except IndexError:
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pass
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l[-1].append(i + 1)
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print l
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return l
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# __ _
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# /__ _ _|_ _|_ ._ _ ._ _ _ _. |
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# \_| (/_ |_ | | (_) | | | _> (_| |
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# |
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conn = sqlite3.connect(self.db_path)
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c = conn.cursor()
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if elts:
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cmd_ele = "AND " + " ".join(cond_sql_or("elt", elts))
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else:
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cmd_ele = ""
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c.execute('''SELECT DISTINCT data from output_tab
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WHERE name="{basis_name}" COLLATE NOCASE
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{cmd_ele}'''.format(basis_name=basis_name,
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cmd_ele=cmd_ele))
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l_data_raw = c.fetchall()
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conn.close()
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# |_| _. ._ _| | _ || | ||
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# | | (_| | | (_| | (/_ |_
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#
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p = re.compile(ur'^(\w)\s+\d+\b')
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l_data = []
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for data_raw in l_data_raw:
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basis = data_raw[0].strip()
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l_line_raw = basis.split("\n")
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# l_line_raw[0] containt the name of the Atom
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l_line = [l_line_raw[0]]
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for symmetry, begin, end in get_list_type(l_line_raw):
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if not(with_l) and symmetry in "L":
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body_s = []
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body_p = []
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for i_l in l_line_raw[begin + 1:end]:
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# one L => S & P
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a = i_l.split()
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common = "{:>3}".format(a[0])
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common += "{:>15.7f}".format(float(a[1]))
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tail_s = common + "{:>23.7f}".format(float(a[2]))
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body_s.append(tail_s)
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# Is only a whan only 3 elements, coef for p == coef for s
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try:
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tail_p = common + "{:>23.7f}".format(float(a[3]))
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except IndexError:
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tail_p = tail_s
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finally:
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body_p.append(tail_p)
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l_line += [l_line_raw[begin].replace("L", "S")]
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l_line += body_s
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l_line += [l_line_raw[begin].replace("L", "P")]
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l_line += body_p
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else:
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l_line += l_line_raw[begin:end]
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l_data.append("\n".join(l_line))
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return l_data
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if __name__ == "__main__":
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e = EMSL_local(db_path="EMSL.db")
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l = e.get_list_basis_available()
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for i in l:
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print i
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l = e.get_list_element_available("pc-0")
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print l
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l = e.get_basis("cc-pVTZ", ["H", "He"])
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for i in l:
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print i
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340
src/EMSL_local.py
Executable file
340
src/EMSL_local.py
Executable file
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@ -0,0 +1,340 @@
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# -*- coding: utf-8 -*-
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import sqlite3
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import re
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import sys
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import os
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def checkSQLite3(db_path):
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"""Check if the db_path is a good one"""
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from os.path import isfile, getsize
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# Check if db file is readable
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if not os.access(db_path, os.R_OK):
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print >>sys.stderr, "Db file %s is not readable" % (db_path)
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raise IOError
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if not isfile(db_path):
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print >>sys.stderr, "Db file %s is not... a file!" % (db_path)
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raise IOError
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if getsize(db_path) < 100: # SQLite database file header is 100 bytes
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print >>sys.stderr, "Db file %s is not a SQLite file!" % (db_path)
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raise IOError
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with open(db_path, 'rb') as fd:
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header = fd.read(100)
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if header[:16] != 'SQLite format 3\x00':
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print >>sys.stderr, "Db file %s is not in SQLiteFormat3!" % (db_path)
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raise IOError
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# Check if the file system allows I/O on sqlite3 (lustre)
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# If not, copy on /dev/shm and remove after opening
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except sqlite3.OperationalError:
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print >>sys.stderr, "I/O Error for you file system"
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print >>sys.stderr, "Try some fixe"
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new_db_path = "/dev/shm/%d.db" % (os.getpid())
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os.system("cp %s %s" % (db_path, new_db_path))
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db_path = new_db_path
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else:
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changed = False
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return db_path, changed
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# Try again to check
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try:
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EMSL_local(db_path=db_path).get_list_basis_available()
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except:
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print >>sys.stderr, "Sorry..."
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os.system("rm -f /dev/shm/%d.db" % (os.getpid()))
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raise
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||||
else:
|
||||
print >>sys.stderr, "Working !"
|
||||
changed = True
|
||||
return db_path, changed
|
||||
|
||||
|
||||
def cond_sql_or(table_name, l_value, glob=False):
|
||||
|
||||
opr = "GLOB" if glob else "="
|
||||
|
||||
l = []
|
||||
dmy = " OR ".join(['%s %s "%s"' % (table_name, opr, i) for i in l_value])
|
||||
if dmy:
|
||||
l.append("(%s)" % dmy)
|
||||
|
||||
return l
|
||||
|
||||
|
||||
def string_to_nb_mo(str_l):
|
||||
|
||||
assert len(str_l) == 1
|
||||
|
||||
d = {"S": 3,
|
||||
"P": 5,
|
||||
"D": 7,
|
||||
"F": 9,
|
||||
"L": 8}
|
||||
|
||||
if str_l in d:
|
||||
return d[str_l]
|
||||
# ord("G") = 72 and ord("Z") = 87
|
||||
elif 72 <= ord(str_l) <= 87:
|
||||
# orf("G") = 72 and l = 4 so ofset if 68
|
||||
return 2 * (ord(str_l) - 68) + 1
|
||||
else:
|
||||
raise BaseException
|
||||
|
||||
|
||||
class EMSL_local:
|
||||
"""
|
||||
All the method for using the EMSL db localy
|
||||
"""
|
||||
|
||||
import re
|
||||
|
||||
def __init__(self, db_path=None):
|
||||
self.db_path = db_path
|
||||
self.p = re.compile(ur'^(\w)\s+\d+\b')
|
||||
|
||||
def get_list_type(self, atom_basis):
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, ]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
# Example
|
||||
# [[u'S', 1, 5], [u'L', 5, 9], [u'L', 9, 12], [u'D', 16, 18]]"
|
||||
|
||||
l = []
|
||||
for i, line in enumerate(atom_basis):
|
||||
|
||||
m = re.search(self.p, line)
|
||||
if m:
|
||||
l.append([m.group(1), i])
|
||||
try:
|
||||
l[-2].append(i)
|
||||
except IndexError:
|
||||
pass
|
||||
|
||||
l[-1].append(i + 1)
|
||||
return l
|
||||
|
||||
def get_list_basis_available(self,
|
||||
elts=[],
|
||||
basis=[],
|
||||
average_mo_number=False):
|
||||
"""
|
||||
return all the basis name who contant all the elts
|
||||
"""
|
||||
# If not elts just get the disctinct name
|
||||
# Else: 1) fetch for geting the run_id available
|
||||
# 2) If average_mo_number:
|
||||
# * Get name,descripption,data
|
||||
# * Then parse it
|
||||
# Else Get name,description
|
||||
# 3) Parse it
|
||||
|
||||
# ~#~#~#~ #
|
||||
# I n i t #
|
||||
# ~#~#~#~ #
|
||||
|
||||
conn = sqlite3.connect(self.db_path)
|
||||
c = conn.cursor()
|
||||
|
||||
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||
# G e t i n g B a s i s _ i d #
|
||||
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||
|
||||
if basis:
|
||||
cmd_basis = " ".join(cond_sql_or("name", basis, glob=True))
|
||||
else:
|
||||
cmd_basis = "(1)"
|
||||
|
||||
if not elts:
|
||||
|
||||
if not average_mo_number:
|
||||
cmd = """SELECT DISTINCT name, description
|
||||
FROM basis_tab
|
||||
WHERE {0}"""
|
||||
else:
|
||||
cmd = """SELECT DISTINCT name, description, data
|
||||
FROM output_tab
|
||||
WHERE {0}"""
|
||||
|
||||
cmd = cmd.format(cmd_basis)
|
||||
|
||||
else:
|
||||
str_ = """SELECT DISTINCT basis_id
|
||||
FROM output_tab
|
||||
WHERE elt=? AND {0}""".format(cmd_basis)
|
||||
|
||||
cmd = " INTERSECT ".join([str_] * len(elts)) + ";"
|
||||
c.execute(cmd, elts)
|
||||
|
||||
dump = [i[0] for i in c.fetchall()]
|
||||
cmd_basis = " ".join(cond_sql_or("basis_id", dump))
|
||||
cmd_ele = " ".join(cond_sql_or("elt", elts))
|
||||
|
||||
cmd = """SELECT DISTINCT {0}
|
||||
FROM output_tab
|
||||
WHERE {1}
|
||||
ORDER BY name"""
|
||||
|
||||
if average_mo_number:
|
||||
column = "name, description, data"
|
||||
else:
|
||||
column = "name, description"
|
||||
|
||||
filter_ = cmd_ele + " AND " + cmd_basis
|
||||
|
||||
cmd = cmd.format(column, filter_)
|
||||
|
||||
c.execute(cmd)
|
||||
info = c.fetchall()
|
||||
|
||||
conn.close()
|
||||
|
||||
# ~#~#~#~#~#~#~ #
|
||||
# P a r s i n g #
|
||||
# ~#~#~#~#~#~#~ #
|
||||
|
||||
from collections import OrderedDict
|
||||
dict_info = OrderedDict()
|
||||
# Description : dict_info[name] = [description, nb_mo, nb_ele]
|
||||
|
||||
if average_mo_number:
|
||||
for name, description, data in info:
|
||||
nb_mo = 0
|
||||
for line in data.split("\n")[1:]:
|
||||
str_l = line.split()[0]
|
||||
try:
|
||||
nb_mo += string_to_nb_mo(str_l)
|
||||
except BaseException:
|
||||
pass
|
||||
|
||||
try:
|
||||
dict_info[name][1] += nb_mo
|
||||
dict_info[name][2] += 1.
|
||||
except:
|
||||
dict_info[name] = [description, nb_mo, 1.]
|
||||
|
||||
# ~#~#~#~#~#~ #
|
||||
# R e t u r n #
|
||||
# ~#~#~#~#~#~ #
|
||||
|
||||
if average_mo_number:
|
||||
return[[k, v[0], str(v[1] / v[2])] for k, v in dict_info.iteritems()]
|
||||
else:
|
||||
return [i[:] for i in info]
|
||||
|
||||
def get_list_element_available(self, basis_name):
|
||||
|
||||
conn = sqlite3.connect(self.db_path)
|
||||
c = conn.cursor()
|
||||
|
||||
str_ = "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE"
|
||||
c.execute(str_, {"name_us": basis_name})
|
||||
|
||||
data = c.fetchall()
|
||||
|
||||
data = [str(i[0]) for i in data]
|
||||
|
||||
conn.close()
|
||||
return data
|
||||
|
||||
def get_basis(self, basis_name, elts=None, with_l=False):
|
||||
"""
|
||||
Return the data from the basis set
|
||||
"""
|
||||
|
||||
# __ _
|
||||
# /__ _ _|_ _|_ ._ _ ._ _ _ _. |
|
||||
# \_| (/_ |_ | | (_) | | | _> (_| |
|
||||
# |
|
||||
conn = sqlite3.connect(self.db_path)
|
||||
c = conn.cursor()
|
||||
|
||||
if elts:
|
||||
cmd_ele = "AND " + " ".join(cond_sql_or("elt", elts))
|
||||
else:
|
||||
cmd_ele = ""
|
||||
|
||||
c.execute('''SELECT DISTINCT data from output_tab
|
||||
WHERE name="{basis_name}" COLLATE NOCASE
|
||||
{cmd_ele}'''.format(basis_name=basis_name,
|
||||
cmd_ele=cmd_ele))
|
||||
|
||||
l_data_raw = c.fetchall()
|
||||
conn.close()
|
||||
|
||||
# |_| _. ._ _| | _ || | ||
|
||||
# | | (_| | | (_| | (/_ |_
|
||||
#
|
||||
|
||||
l_data = []
|
||||
|
||||
for data_raw in l_data_raw:
|
||||
|
||||
basis = data_raw[0].strip()
|
||||
|
||||
l_line_raw = basis.split("\n")
|
||||
|
||||
# l_line_raw[0] containt the name of the Atom
|
||||
l_line = [l_line_raw[0]]
|
||||
|
||||
for symmetry, begin, end in self.get_list_type(l_line_raw):
|
||||
|
||||
if not(with_l) and symmetry in "L":
|
||||
|
||||
body_s = []
|
||||
body_p = []
|
||||
|
||||
for i_l in l_line_raw[begin + 1:end]:
|
||||
|
||||
# one L => S & P
|
||||
a = i_l.split()
|
||||
|
||||
common = "{:>3}".format(a[0])
|
||||
common += "{:>15.7f}".format(float(a[1]))
|
||||
|
||||
tail_s = common + "{:>23.7f}".format(float(a[2]))
|
||||
body_s.append(tail_s)
|
||||
|
||||
# Is only a whan only 3 elements, coef for p == coef for s
|
||||
try:
|
||||
tail_p = common + "{:>23.7f}".format(float(a[3]))
|
||||
except IndexError:
|
||||
tail_p = tail_s
|
||||
finally:
|
||||
body_p.append(tail_p)
|
||||
|
||||
l_line += [l_line_raw[begin].replace("L", "S")]
|
||||
l_line += body_s
|
||||
|
||||
l_line += [l_line_raw[begin].replace("L", "P")]
|
||||
l_line += body_p
|
||||
else:
|
||||
l_line += l_line_raw[begin:end]
|
||||
|
||||
l_data.append("\n".join(l_line))
|
||||
|
||||
return l_data
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
e = EMSL_local(db_path="EMSL.db")
|
||||
l = e.get_list_basis_available()
|
||||
for i in l:
|
||||
print i
|
||||
|
||||
l = e.get_list_element_available("pc-0")
|
||||
print l
|
||||
|
||||
l = e.get_basis("cc-pVTZ", ["H", "He"])
|
||||
for i in l:
|
||||
print i
|
||||
Loading…
Reference in New Issue
Block a user