LCPQ/EMSL_Basis_Set_Exchange_Local
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Need format un get_basis_data now. For test ! Need cleaning.

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This commit is contained in:
Thomas Applencourt 2015-03-16 15:46:27 +01:00
parent b6503406f8
commit a773c4ed06
3 changed files with 114 additions and 20 deletions
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11
EMSL_api.py
View File

@ -11,10 +11,12 @@ Usage:
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>])]
[--check=<format>]
[--check]
[--treat_l]
EMSL_api.py list_formats
EMSL_api.py create_db --db_path=<db_path>
--format=<format>
@ -39,7 +41,6 @@ Example of use:
version = "0.3.0"
import sys
import os
from src.docopt import docopt
@ -112,11 +113,13 @@ if __name__ == '__main__':
# | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
# \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
if arguments["get_basis_data"]:
e = EMSL_local(db_path=db_path)
e = EMSL_local(db_path=db_path, format=arguments["--format"])
basis_name = arguments["--basis"][0]
elts = arguments["--atom"]
l_atom_basis = e.get_basis(basis_name, elts, arguments["--check"])
l_atom_basis = e.get_basis(basis_name, elts,
arguments["--treat_l"],
arguments["--check"])
# Add separation between atoms, and a empty last line
str_ = "\n\n".join(l_atom_basis) + "\n"

52
src/EMSL_local.py
View File

@ -98,7 +98,7 @@ def check_gamess(str_type):
if str_type in "S P D".split():
return True
elif str_type > "L":
elif str_type == "L":
raise BaseException
else:
return True
@ -127,11 +127,12 @@ class EMSL_local:
All the method for using the EMSL db localy
"""
def __init__(self, db_path=None):
def __init__(self, db_path=None, format=None):
self.db_path = db_path
self.p = re.compile(ur'^(\w)\s+\d+\b')
self.format = format
def get_list_type(self, atom_basis):
def get_list_symetry(self, atom_basis):
"""
Return the begin and the end of all the type of orbital
input: atom_basis = [name, ]
@ -223,7 +224,9 @@ class EMSL_local:
if average_mo_number:
column_to_fech += ", data"
filter_where = " ({}) AND ({})".format(cmd_filter_ele, cmd_filter_basis)
filter_where = " ({}) AND ({})".format(
cmd_filter_ele,
cmd_filter_basis)
cmd = """SELECT DISTINCT {0}
FROM output_tab
@ -248,10 +251,14 @@ class EMSL_local:
# Description : dict_info[name] = [description, nb_mo, nb_ele]
if average_mo_number:
print "WARNING DO NOT SUPPORT L COUNTING"
print "TREAD L FUNCTION NOT LIKE A SPECIAL ONE"
for name, description, atom_basis in info:
nb_mo = 0
for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
line = atom_basis.split("\n")
for type_, _, _ in self.get_list_symetry(line):
nb_mo += string_to_nb_mo(type_)
try:
@ -299,7 +306,9 @@ class EMSL_local:
return [str(i[0]) for i in c.fetchall()]
def get_basis(self, basis_name, elts=None, check_format=None):
def get_basis(self,
basis_name, elts=None,
handle_f_format="GAMESS-US", check_format=None):
"""
Return the data from the basis set
"""
@ -325,31 +334,46 @@ class EMSL_local:
l_atom_basis = [i[0].strip() for i in c.fetchall()]
conn.close()
# ~#~#~#~#~#~#~#~ #
# h a n d l e _ f #
# ~#~#~#~#~#~#~#~ #
if handle_f_format:
from src.parser import handle_f_dict
try:
f = handle_f_dict[self.format]
except KeyError:
str_ = "You cannot handle f function with {0} format"
print >> sys.stderr, str_.format(self.format)
print >> sys.stderr, "Choose in:"
print >> sys.stderr, handle_f_dict.keys()
sys.exit(1)
else:
l_atom_basis = f(l_atom_basis,self.get_list_symetry)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
d_check = {"gamess": check_gamess,
d_check = {"GAMESS-US": check_gamess,
"NWChem": check_NWChem}
if check_format:
try:
f = d_check[check_format]
f = d_check[self.format]
except KeyError:
str_ = """This format is not handle. Chose one of : {}"""
print >>sys.stderr, str_.format(format(str(d_check.keys())))
sys.exit(1)
for atom_basis in l_atom_basis:
for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
f(type_)
else:
for atom_basis in l_atom_basis:
lines = atom_basis.split("\n")
for type_, _, _ in self.get_list_symetry(lines):
f(type_)
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return l_atom_basis
if __name__ == "__main__":
e = EMSL_local(db_path="EMSL.db")

71
src/parser.py
View File

@ -88,5 +88,72 @@ format_dict = {"Gaussian94": None,
"Dalton": None,
"deMon-KS": None,
"deMon2k": None,
"AcesII": 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}