From 70553f17794da7a99d3f329a4c558c9cc0549298 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 10 Mar 2015 19:30:11 +0100 Subject: [PATCH] Suport of --average_number_mo --- EMSL_api.py | 16 ++++-- src/EMSL_utility.py | 128 +++++++++++++++++++++++++++++++++++++------- 2 files changed, 120 insertions(+), 24 deletions(-) diff --git a/EMSL_api.py b/EMSL_api.py index cfb027a..4454163 100755 --- a/EMSL_api.py +++ b/EMSL_api.py @@ -6,6 +6,7 @@ Usage: EMSL_api.py list_basis [--atom=...] [--db_path=] + [--average_mo_number] EMSL_api.py list_atoms --basis= [--db_path=] EMSL_api.py get_basis_data --basis= @@ -62,7 +63,7 @@ if __name__ == '__main__': if not(arguments['create_db']): db_path, db_path_changed = checkSQLite3(db_path) except: - sys.exit(1) + raise # _ _ _ ______ _ # | | (_) | | | ___ \ (_) @@ -75,10 +76,17 @@ if __name__ == '__main__': e = EMSL_local(db_path=db_path) elts = arguments["--atom"] - l = e.get_list_basis_available(elts) - for name, des, n in l: - print name, "(", n, ")", "|", des + amn = arguments["--average_mo_number"] + + l = e.get_list_basis_available(elts, average_mo_number=amn) + + if amn: + for name, des, avg in l: + print "{0} ({2}) | {1}".format(name, des, avg) + else: + for name, des in l: + print "{0} | {1}".format(name, des) # _ _ _ _____ _ _ # | | (_) | | | ___| | | | diff --git a/src/EMSL_utility.py b/src/EMSL_utility.py index 0fb2bf3..ed4323c 100755 --- a/src/EMSL_utility.py +++ b/src/EMSL_utility.py @@ -377,44 +377,120 @@ class EMSL_dump: self.create_sql(array_basis) -class EMSL_local: +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 + """ def __init__(self, db_path=None): self.db_path = db_path - def get_list_basis_available(self, elts=[]): - + def get_list_basis_available(self, elts=[], average_mo_number=False): + """ + return all the basis name who contant all the elts + """ conn = sqlite3.connect(self.db_path) c = conn.cursor() + # 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 + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + # G e t i n g B a s i s _ i d # + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # if not elts: - - c.execute("""SELECT DISTINCT name,description, LENGTH(data)- LENGTH(REPLACE(data, X'0A', '')) - FROM output_tab""") - data = c.fetchall() - + cmd = """SELECT DISTINCT name, description FROM basis_tab""" + c.execute(cmd) + info = c.fetchall() else: - cmd = ["""SELECT name,description, LENGTH(data)- LENGTH(REPLACE(data, X'0A', '')) - FROM output_tab WHERE elt=?"""] * len(elts) - cmd = " INTERSECT ".join(cmd) + ";" - + cmd_ele = ["SELECT DISTINCT basis_id FROM data_tab WHERE elt=?"] * len(elts) + cmd = " INTERSECT ".join(cmd_ele) + ";" c.execute(cmd, elts) - data = c.fetchall() - data = [i[:] for i in data] + 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)) - conn.close() + if average_mo_number: + cmd = """SELECT DISTINCT name,description,data + FROM output_tab""" - return data + else: + cmd = """SELECT DISTINCT name,description + FROM output_tab""" + + cmd += " WHERE" + cmd_ele + " AND " + cmd_basis + + c.execute(cmd) + info = c.fetchall() + + conn.close() + + # ~#~#~#~#~#~#~ # + # P a r s i n g # + # ~#~#~#~#~#~#~ # + + dict_info = {} + # dict_info[name] = [description, nb_mo, nb_ele] + + if average_mo_number: + + for name, description, data in info: + nb_mo = 0 + nb_ele = 0 + for line in data.split("\n")[1:]: + str_l = line.split()[0] + try: + nb_mo += string_to_nb_mo(str_l) + nb_ele += 1 + except BaseException: + pass + + try: + dict_info[name][1] += nb_mo + dict_info[name][2] += 1 + except: + dict_info[name] = [description, nb_mo, nb_ele] + + # ~#~#~#~#~#~ # + # R e t u r n # + # ~#~#~#~#~#~ # + + if average_mo_number: + return[[k, v[0], 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() - c.execute( - "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE", { - "name_us": basis_name}) + str_ = "SELECT DISTINCT elt from output_tab WHERE name=:name_us COLLATE NOCASE" + c.execute(str_, {"name_us": basis_name}) data = c.fetchall() @@ -424,10 +500,20 @@ class EMSL_local: return data def get_basis(self, basis_name, elts=None, with_l=False): - + """ + Return the data from the basis set + """ import re def get_list_type(l_line): + """ + Return the begin and the end of all the type of orbital + Usefull for tranforming the L in S, P + 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(l_line): @@ -440,6 +526,7 @@ class EMSL_local: pass l[-1].append(i + 1) + print l return l # __ _ @@ -476,6 +563,7 @@ class EMSL_local: 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 get_list_type(l_line_raw):