mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-12-22 12:23:39 +01:00
Suport of --average_number_mo
This commit is contained in:
Thomas Applencourt
parent
57c4ac024d
commit
70553f1779
16
EMSL_api.py
16
EMSL_api.py
@ -6,6 +6,7 @@
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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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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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@ -62,7 +63,7 @@ if __name__ == '__main__':
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if not(arguments['create_db']):
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db_path, db_path_changed = checkSQLite3(db_path)
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except:
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sys.exit(1)
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raise
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# _ _ _ ______ _
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# | | (_) | | | ___ \ (_)
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@ -75,10 +76,17 @@ if __name__ == '__main__':
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e = EMSL_local(db_path=db_path)
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elts = arguments["--atom"]
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l = e.get_list_basis_available(elts)
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for name, des, n in l:
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print name, "(", n, ")", "|", des
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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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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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else:
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for name, des in l:
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print "{0} | {1}".format(name, des)
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# _ _ _ _____ _ _
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# | | (_) | | | ___| | | |
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@ -377,44 +377,120 @@ class EMSL_dump:
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self.create_sql(array_basis)
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class EMSL_local:
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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=[]):
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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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c.execute("""SELECT DISTINCT name,description, LENGTH(data)- LENGTH(REPLACE(data, X'0A', ''))
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FROM output_tab""")
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data = c.fetchall()
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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 name,description, LENGTH(data)- LENGTH(REPLACE(data, X'0A', ''))
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FROM output_tab WHERE elt=?"""] * len(elts)
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cmd = " INTERSECT ".join(cmd) + ";"
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cmd = """SELECT DISTINCT name,description
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FROM output_tab"""
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c.execute(cmd, elts)
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data = c.fetchall()
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cmd += " WHERE" + cmd_ele + " AND " + cmd_basis
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data = [i[:] for i in data]
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c.execute(cmd)
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info = c.fetchall()
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conn.close()
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return data
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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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c.execute(
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"SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE", {
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"name_us": basis_name})
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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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@ -424,10 +500,20 @@ class EMSL_local:
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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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@ -440,6 +526,7 @@ class EMSL_local:
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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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@ -476,6 +563,7 @@ class EMSL_local:
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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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