LCPQ/EMSL_Basis_Set_Exchange_Local
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Add format in db

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This commit is contained in:
Thomas Applencourt 2015-03-16 19:10:55 +01:00
parent 84a7bc70f7
commit ec0fc43bf8
5 changed files with 136 additions and 155 deletions
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14
EMSL_api.py
View File

@ -5,14 +5,12 @@
Usage:
EMSL_api.py list_basis [--basis=<basis_name>...]
--format=<format>
[--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>
--format=<format>
[--atom=<atom_name>...]
[--db_path=<db_path>]
[(--save [--path=<path>])]
@ -77,7 +75,7 @@ if __name__ == '__main__':
# \_____/_|___/\__| \____/ \__,_|___/_|___/
if arguments["list_basis"]:
e = EMSL_local(db_path=db_path, format=arguments["--format"])
e = EMSL_local(db_path=db_path)
elts = arguments["--atom"]
@ -100,7 +98,7 @@ if __name__ == '__main__':
# | | | / __| __| | __|| |/ _ \ '_ ` _ \ / _ \ '_ \| __/ __|
# | |___| \__ \ |_ | |___| | __/ | | | | | __/ | | | |_\__ \
# \_____/_|___/\__| \____/|_|\___|_| |_| |_|\___|_| |_|\__|___/
if arguments["list_atoms"]:
elif arguments["list_atoms"]:
e = EMSL_local(db_path=db_path)
basis_name = arguments["--basis"]
@ -113,8 +111,8 @@ if __name__ == '__main__':
# | ___ \/ _` / __| / __| / _` |/ _` | __/ _` |
# | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
# \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
if arguments["get_basis_data"]:
e = EMSL_local(db_path=db_path, format=arguments["--format"])
elif arguments["get_basis_data"]:
e = EMSL_local(db_path=db_path)
basis_name = arguments["--basis"][0]
elts = arguments["--atom"]
@ -144,7 +142,7 @@ if __name__ == '__main__':
# | | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __|
# | |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
# \_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
if arguments["list_formats"]:
elif arguments["list_formats"]:
e = EMSL_dump()
for i in e.get_list_format():
print i
@ -155,7 +153,7 @@ if __name__ == '__main__':
# | | | '__/ _ \/ _` | __/ _ \ / _` | '_ \
# | \__/\ | | __/ (_| | || __/ | (_| | |_) |
# \____/_| \___|\__,_|\__\___| \__,_|_.__/
if arguments["create_db"]:
elif arguments["create_db"]:
db_path = arguments["--db_path"]
format = arguments["--format"]

BIN
db/Gamess-us.db
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6
src/EMSL_dump.py
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@ -189,6 +189,10 @@ class EMSL_dump:
REFERENCES basis_tab(basis_id)
);''')
c.execute('''CREATE TABLE format_tab(format TEXT)''')
c.execute('''INSERT INTO format_tab VALUES (?)''', [self.format])
conn.commit()
c.execute(''' CREATE VIEW output_tab AS
SELECT basis_id,
name,
@ -229,8 +233,6 @@ class EMSL_dump:
basis_data = self.parser(text, name, des, elts,
self.debug)
except:
if self.debug:
raise
time.sleep(0.1)
attemps += 1
else:

101
src/EMSL_local.py
View File

@ -70,14 +70,14 @@ def cond_sql_or(table_name, l_value, glob=False):
def string_to_nb_mo(str_type):
"""Take a string and return the nb of orbital"""
assert len(str_type) == 1
d = {"S": 1,
"P": 2,
"D": 3}
d = {"S": 3,
"P": 5,
"D": 7,
"SP": 8}
if str_type in d:
return 2 * d[str_type] + 1
return d[str_type]
# ord("F") = 70 and ord("Z") = 87
elif 70 <= ord(str_type) <= 87:
# ord("F") = 70 and l = 4 so ofset if 66
@ -127,36 +127,14 @@ class EMSL_local:
All the method for using the EMSL db localy
"""
def __init__(self, db_path=None, format=None):
def __init__(self, db_path=None):
self.db_path = db_path
self.p = re.compile(ur'^(\w)\s+\d+\b')
self.format = format
def get_list_symetry(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]]"
self.conn = sqlite3.connect(self.db_path)
self.c = self.conn.cursor()
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)
print l
sys.exit()
return l
self.c.execute("SELECT * from format_tab")
self.format = self.c.fetchone()[0]
def get_list_basis_available(self,
elts=[],
@ -173,12 +151,6 @@ class EMSL_local:
# Else Get name,description
# 3) Parse it
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
conn = sqlite3.connect(self.db_path)
c = conn.cursor()
# ~#~#~#~#~#~ #
# F i l t e r #
@ -213,9 +185,9 @@ class EMSL_local:
WHERE elt=? AND {0}""".format(cmd_filter_basis)
cmd = " INTERSECT ".join([str_] * len(elts)) + ";"
c.execute(cmd, elts)
self.c.execute(cmd, elts)
l_basis_id = [i[0] for i in c.fetchall()]
l_basis_id = [i[0] for i in self.c.fetchall()]
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# C r e a t e _ t h e _ c m d #
@ -240,10 +212,8 @@ class EMSL_local:
# F e t c h #
# ~#~#~#~#~ #
c.execute(cmd)
info = c.fetchall()
conn.close()
self.c.execute(cmd)
info = self.c.fetchall()
# ~#~#~#~#~#~#~ #
# P a r s i n g #
@ -254,32 +224,25 @@ class EMSL_local:
dict_info = OrderedDict()
# Description : dict_info[name] = [description, nb_mo, nb_ele]
from src.parser import symmetry_dict
if average_mo_number:
from src.parser import handle_f_dict
try:
f = handle_f_dict[self.format]
l_symmetry = symmetry_dict[self.format]
except KeyError:
str_ = " WARNING Cannot handle counting L function in this format"
print >> sys.stderr, str_
print >> sys.stderr, "You need to add a function in symmetry_dict"
print >> sys.stderr, "for your format ({0})".format(self.format)
sys.exit(1)
for name, description, atom_basis in info:
try:
atom_basis = f([atom_basis], self.get_list_symetry)
atom_basis = "\n\n".join(atom_basis)
except UnboundLocalError:
pass
nb_mo = 0
line = atom_basis.split("\n")
for type_, _, _ in self.get_list_symetry(line):
for type_, _, _ in l_symmetry(line):
nb_mo += string_to_nb_mo(type_)
try:
dict_info[name][1] += nb_mo
dict_info[name][2] += 1.
@ -297,13 +260,6 @@ class EMSL_local:
def get_list_element_available(self, basis_name):
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
conn = sqlite3.connect(self.db_path)
c = conn.cursor()
# ~#~#~#~#~#~ #
# F i l t e r #
# ~#~#~#~#~#~ #
@ -316,14 +272,13 @@ class EMSL_local:
# F e t c h #
# ~#~#~#~#~ #
c.execute(str_, {"name_us": basis_name})
conn.close()
self.c.execute(str_, {"name_us": basis_name})
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return [str(i[0]) for i in c.fetchall()]
return [str(i[0]) for i in self.c.fetchall()]
def get_basis(self,
basis_name, elts=None,
@ -332,26 +287,18 @@ class EMSL_local:
Return the data from the basis set
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
conn = sqlite3.connect(self.db_path)
c = conn.cursor()
# ~#~#~#~#~#~ #
# F i l t e r #
# ~#~#~#~#~#~ #
cmd_filter_ele = " ".join(cond_sql_or("elt", elts)) if elts else "(1)"
c.execute('''SELECT DISTINCT data from output_tab
self.c.execute('''SELECT DISTINCT data from output_tab
WHERE name="{0}"
AND {1}'''.format(basis_name, cmd_filter_ele))
# We need to take i[0] because fetchall return a tuple [(value),...]
l_atom_basis = [i[0].strip() for i in c.fetchall()]
conn.close()
l_atom_basis = [i[0].strip() for i in self.c.fetchall()]
# ~#~#~#~#~#~#~#~ #
# h a n d l e _ f #

168
src/parser.py
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@ -1,4 +1,5 @@
import sys
import os
def get_dict_ele():
@ -72,7 +73,98 @@ def parse_basis_data_gamess_us(data, name, des, elts, debug=False):
return [name, des, basis_data]
import os
import re
symmetry_regex = re.compile(ur'^(\w)\s+\d+\b')
def l_symmetry_gamess_us(atom_basis):
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
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(symmetry_regex, line)
if m:
# Cause of L !
read_symmetry = m.group(1)
# L is real L or special SP
# Just check the number of exponant
if read_symmetry == "L" and len(atom_basis[i + 1].split()) == 4:
real_symmetry = "SP"
else:
real_symmetry = read_symmetry
l.append([real_symmetry, i])
try:
l[-2].append(i)
except IndexError:
pass
l[-1].append(i + 1)
return l
def handle_f_gamess_us(l_atom_basis):
"""
Read l_atom_basis and change the SP in L and P
"""
l_data = []
for atom_basis in l_atom_basis:
# Split the data in line
l_line_raw = atom_basis.split("\n")
l_line = [l_line_raw[0]]
# l_line_raw[0] containt the name of the Atom
for symmetry, begin, end in l_symmetry_gamess_us(l_line_raw):
if symmetry == "SP":
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)
tail_p = common + "{:>23.7f}".format(float(a[3]))
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
# ______ _ _ _ _
# | ___| | | | (_) | |
# | |_ _ __ ___ _ __ ___ __ _| |_ __| |_ ___| |_
# | _| '__/ _ \| '_ ` _ \ / _` | __| / _` | |/ __| __|
# | | | | | (_) | | | | | | (_| | |_ | (_| | | (__| |_
# \_| |_| \___/|_| |_| |_|\__,_|\__| \__,_|_|\___|\__|
#
format_dict = {"Gaussian94": None,
"GAMESS-US": parse_basis_data_gamess_us,
@ -91,70 +183,12 @@ format_dict = {"Gaussian94": None,
"AcesII": None}
# _____ _ _ _ _
# | | | | | | | ( | ) | ( | )
# | |_| | __ _ _ __ __| | | ___ V V| | V V
# | _ |/ _` | '_ \ / _` | |/ _ \ | |
# | | | | (_| | | | | (_| | | __/ | |____
# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/
#
#
# / ___| | | | (_) | |
# \ `--. _ _ _ __ ___ _ __ ___ ___| |_ _ __ _ _ __| |_ ___| |_
# `--. \ | | | '_ ` _ \| '_ ` _ \ / _ \ __| '__| | | | / _` | |/ __| __|
# /\__/ / |_| | | | | | | | | | | | __/ |_| | | |_| | | (_| | | (__| |_
# \____/ \__, |_| |_| |_|_| |_| |_|\___|\__|_| \__, | \__,_|_|\___|\__|
# __/ | __/ |
# |___/ |___/
def handle_f_gamess_us(l_atom_basis, list_symetry):
"""
Read l_atom_basis, if "L" orbital before "D" one, split them into S and P
"""
l_data = []
for atom_basis in l_atom_basis:
# Split the data in line
l_line_raw = atom_basis.split("\n")
l_line = [l_line_raw[0]]
# l_line_raw[0] containt the name of the Atom
maybe_good_l = True
for symmetry, begin, end in list_symetry(l_line_raw):
if maybe_good_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)
# Maybe only One coefficient for L function
# I guess it mean S and L are equal
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]
if symmetry not in ["S", "P", "L"]:
maybe_good_l = False
l_data.append("\n".join(l_line))
return l_data
handle_f_dict = {"GAMESS-US": handle_f_gamess_us}
symmetry_dict = {"GAMESS-US": l_symmetry_gamess_us}