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https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-08-24 21:41:44 +02:00
Need format un get_basis_data now. For test ! Need cleaning.
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11
EMSL_api.py
11
EMSL_api.py
@ -11,10 +11,12 @@ Usage:
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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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--format=<format>
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[--atom=<atom_name>...]
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[--db_path=<db_path>]
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[(--save [--path=<path>])]
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[--check=<format>]
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[--check]
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[--treat_l]
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EMSL_api.py list_formats
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EMSL_api.py create_db --db_path=<db_path>
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--format=<format>
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@ -39,7 +41,6 @@ Example of use:
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version = "0.3.0"
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import sys
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import os
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from src.docopt import docopt
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@ -112,11 +113,13 @@ if __name__ == '__main__':
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# | |_/ / (_| \__ \ \__ \ | (_| | (_| | || (_| |
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# \____/ \__,_|___/_|___/ \__,_|\__,_|\__\__,_|
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if arguments["get_basis_data"]:
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e = EMSL_local(db_path=db_path)
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e = EMSL_local(db_path=db_path, format=arguments["--format"])
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basis_name = arguments["--basis"][0]
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elts = arguments["--atom"]
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l_atom_basis = e.get_basis(basis_name, elts, arguments["--check"])
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l_atom_basis = e.get_basis(basis_name, elts,
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arguments["--treat_l"],
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arguments["--check"])
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# Add separation between atoms, and a empty last line
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str_ = "\n\n".join(l_atom_basis) + "\n"
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@ -98,7 +98,7 @@ def check_gamess(str_type):
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if str_type in "S P D".split():
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return True
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elif str_type > "L":
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elif str_type == "L":
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raise BaseException
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else:
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return True
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@ -127,11 +127,12 @@ class EMSL_local:
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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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def __init__(self, db_path=None, format=None):
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self.db_path = db_path
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self.p = re.compile(ur'^(\w)\s+\d+\b')
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self.format = format
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def get_list_type(self, atom_basis):
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def get_list_symetry(self, atom_basis):
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"""
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Return the begin and the end of all the type of orbital
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input: atom_basis = [name, ]
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@ -223,7 +224,9 @@ class EMSL_local:
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if average_mo_number:
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column_to_fech += ", data"
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filter_where = " ({}) AND ({})".format(cmd_filter_ele, cmd_filter_basis)
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filter_where = " ({}) AND ({})".format(
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cmd_filter_ele,
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cmd_filter_basis)
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cmd = """SELECT DISTINCT {0}
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FROM output_tab
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@ -248,10 +251,14 @@ class EMSL_local:
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# Description : dict_info[name] = [description, nb_mo, nb_ele]
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if average_mo_number:
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print "WARNING DO NOT SUPPORT L COUNTING"
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print "TREAD L FUNCTION NOT LIKE A SPECIAL ONE"
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for name, description, atom_basis in info:
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nb_mo = 0
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for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
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line = atom_basis.split("\n")
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for type_, _, _ in self.get_list_symetry(line):
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nb_mo += string_to_nb_mo(type_)
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try:
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@ -299,7 +306,9 @@ class EMSL_local:
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return [str(i[0]) for i in c.fetchall()]
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def get_basis(self, basis_name, elts=None, check_format=None):
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def get_basis(self,
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basis_name, elts=None,
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handle_f_format="GAMESS-US", check_format=None):
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"""
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Return the data from the basis set
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"""
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@ -325,31 +334,46 @@ class EMSL_local:
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l_atom_basis = [i[0].strip() for i in c.fetchall()]
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conn.close()
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# ~#~#~#~#~#~#~#~ #
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# h a n d l e _ f #
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# ~#~#~#~#~#~#~#~ #
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if handle_f_format:
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from src.parser import handle_f_dict
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try:
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f = handle_f_dict[self.format]
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except KeyError:
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str_ = "You cannot handle f function with {0} format"
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print >> sys.stderr, str_.format(self.format)
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print >> sys.stderr, "Choose in:"
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print >> sys.stderr, handle_f_dict.keys()
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sys.exit(1)
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else:
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l_atom_basis = f(l_atom_basis,self.get_list_symetry)
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# ~#~#~#~#~ #
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# C h e c k #
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# ~#~#~#~#~ #
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d_check = {"gamess": check_gamess,
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d_check = {"GAMESS-US": check_gamess,
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"NWChem": check_NWChem}
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if check_format:
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try:
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f = d_check[check_format]
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f = d_check[self.format]
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except KeyError:
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str_ = """This format is not handle. Chose one of : {}"""
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print >>sys.stderr, str_.format(format(str(d_check.keys())))
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sys.exit(1)
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for atom_basis in l_atom_basis:
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for type_, _, _ in self.get_list_type(atom_basis.split("\n")):
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f(type_)
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else:
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for atom_basis in l_atom_basis:
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lines = atom_basis.split("\n")
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for type_, _, _ in self.get_list_symetry(lines):
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f(type_)
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# ~#~#~#~#~#~ #
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# R e t u r n #
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# ~#~#~#~#~#~ #
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return l_atom_basis
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if __name__ == "__main__":
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e = EMSL_local(db_path="EMSL.db")
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@ -88,5 +88,72 @@ format_dict = {"Gaussian94": None,
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"Dalton": None,
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"deMon-KS": None,
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"deMon2k": None,
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"AcesII": None,
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}
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"AcesII": None}
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# _ _ _ _ _ _ _ _ _
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# | | | | | | | ( | ) | ( | )
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# | |_| | __ _ _ __ __| | | ___ V V| | V V
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# | _ |/ _` | '_ \ / _` | |/ _ \ | |
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# | | | | (_| | | | | (_| | | __/ | |____
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# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/
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#
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#
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def handle_f_gamess_us(l_atom_basis, list_symetry):
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"""
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Read l_atom_basis, if "L" orbital before "D" one, split them into S and P
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"""
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l_data = []
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for atom_basis in l_atom_basis:
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# Split the data in line
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l_line_raw = atom_basis.split("\n")
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l_line = [l_line_raw[0]]
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# l_line_raw[0] containt the name of the Atom
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maybe_good_l = True
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for symmetry, begin, end in list_symetry(l_line_raw):
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if maybe_good_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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# Maybe only One coefficient for L function
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# I guess it mean S and L are equal
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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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if symmetry not in ["S", "P", "L"]:
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maybe_good_l = False
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l_data.append("\n".join(l_line))
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return l_data
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handle_f_dict = {"GAMESS-US": handle_f_gamess_us}
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