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implemented S100, S131, P103, P150 basis sets
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@kousuke-nakano
kousuke-nakano committed May 15, 2024
1 parent 2487587 commit a478d29
Showing 1 changed file with 45 additions and 5 deletions.
50 changes: 45 additions & 5 deletions turbogenius/pyturbo/basis_set.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
turbo_prim_orb_type_num,
turbo_cont_orb_type_num,
return_orbchr,
turbo_conv_cont_to_prim_orb_type_num,
)
from turbogenius.pyturbo.utils.env import pyturbo_root

Expand Down Expand Up @@ -482,8 +483,13 @@ def contracted_to_uncontracted(self) -> None:
# shell
shell_factor.append(None)
shell_ang_mom.append(shell_ang_mom_n)
# shell_ang_mom_turbo_notation.append(
# turbo_prim_orb_type_num(return_orbchr(shell_ang_mom_n))
# )
shell_ang_mom_turbo_notation.append(
turbo_prim_orb_type_num(return_orbchr(shell_ang_mom_n))
turbo_conv_cont_to_prim_orb_type_num(
shell_ang_mom_turbo_notation_n
)
)

self.nucleus_index = nucleus_index
Expand Down Expand Up @@ -532,6 +538,7 @@ def parse_basis_sets_from_gamess_format_files(

return cls.parse_basis_sets_from_texts(texts=texts, format="gamess")

'''
@classmethod
def parse_basis_sets_from_eCEPP_format_files(
cls, files: Optional[list] = None
Expand All @@ -556,6 +563,7 @@ def parse_basis_sets_from_eCEPP_format_files(
texts.append(text)
return cls.parse_basis_sets_from_texts(texts=texts, format="eCEPP")
'''

@classmethod
def parse_basis_sets_from_texts(
Expand Down Expand Up @@ -591,14 +599,15 @@ def parse_basis_sets_from_texts(

if format == "gamess":
basis_set = Basis_set.parse_basis_set_info_from_gamess_format_text(text)
elif format == "eCEPP":
basis_set = Basis_set.parse_basis_set_info_from_eCEPP_format_text(text)
# elif format == "eCEPP":
# basis_set = Basis_set.parse_basis_set_info_from_eCEPP_format_text(text)
else:
logger.error(f"format = {format} is not implemented")
raise NotImplementedError
# storing
nucleus_index += [nuc_i] * basis_set.shell_num
shell_ang_mom += basis_set.shell_ang_mom
shell_ang_mom_turbo_notation += basis_set.shell_ang_mom_turbo_notation
shell_factor += [1.0] * basis_set.shell_num
shell_index += list(np.array(basis_set.shell_index) + shell_num)
exponent += basis_set.exponent_list
Expand All @@ -610,6 +619,7 @@ def parse_basis_sets_from_texts(
shell_num += basis_set.shell_num
prim_num += basis_set.prim_num

"""
for i, ang_mom in enumerate(shell_ang_mom):
if shell_index.count(i) > 1:
contraction = True
Expand All @@ -624,6 +634,7 @@ def parse_basis_sets_from_texts(
shell_ang_mom_turbo_notation.append(
turbo_prim_orb_type_num(orb_type_chr=return_orbchr(ang_mom=ang_mom))
)
"""

return cls(
nucleus_index=nucleus_index,
Expand All @@ -646,6 +657,7 @@ class Basis_set:
Attributes:
shell_ang_mom (list): One-to-one correspondence between shells and angular momenta. Dimensions=shell_num.
shell_ang_mom_turbo_notation (list): TurboRVB notations.
shell_index (list): One-to-one correspondence between primitives and shell index. Dimensions=prim_num.
exponent_list (list): Exponents of the primitives. Dimensions=prim_num.
coefficient_list (list): Coefficients of the primitives (real part). Dimensions=prim_num.
Expand All @@ -655,13 +667,16 @@ class Basis_set:
def __init__(
self,
shell_ang_mom: Optional[list] = None,
shell_ang_mom_turbo_notation: Optional[list] = None,
shell_index: Optional[list] = None,
exponent_list: Optional[list] = None,
coefficient_list: Optional[list] = None,
coefficient_imag_list: Optional[list] = None,
):
if shell_ang_mom is None:
shell_ang_mom = []
if shell_ang_mom_turbo_notation is None:
shell_ang_mom_turbo_notation = []
if shell_index is None:
shell_index = []
if exponent_list is None:
Expand All @@ -673,12 +688,14 @@ def __init__(

# variables
self.shell_ang_mom = shell_ang_mom
self.shell_ang_mom_turbo_notation = shell_ang_mom_turbo_notation
self.shell_index = shell_index
self.exponent_list = exponent_list
self.coefficient_list = coefficient_list
self.coefficient_imag_list = coefficient_imag_list

logger.debug(self.shell_ang_mom)
logger.debug(self.shell_ang_mom_turbo_notation)
logger.debug(self.shell_index)
logger.debug(self.exponent_list)
logger.debug(self.coefficient_list)
Expand Down Expand Up @@ -731,6 +748,7 @@ def parse_basis_set_info_from_gamess_format_file(cls, file: str): # -> cls
text = "".join(text)
return cls.parse_basis_set_info_from_gamess_format_text(text=text)

'''
@classmethod
def parse_basis_set_info_from_eCEPP_format_file(cls, file: str): # -> cls
"""
Expand Down Expand Up @@ -761,6 +779,7 @@ def parse_basis_set_info_from_eCEPP_format_text(cls, text: str): # -> cls
"""
shell_ang_mom = []
shell_ang_mom_turbo_notation = []
shell_index = []
exponent_list = []
coefficient_list = []
Expand Down Expand Up @@ -793,17 +812,28 @@ def parse_basis_set_info_from_eCEPP_format_text(cls, text: str): # -> cls
logger.debug(r_coefficient_list)
r_shell_index = len(shell_ang_mom)
shell_ang_mom.append(ang_mom)
if len(r_coefficient_list) > 1:
ang_mom_turbo_notation = turbo_prim_orb_type_num(
orb_typ_chr=l_str
)
else:
ang_mom_turbo_notation = turbo_cont_orb_type_num(
orb_typ_chr=l_str
)
shell_ang_mom_turbo_notation.append(ang_mom_turbo_notation)
for r_coefficient in r_coefficient_list:
shell_index.append(r_shell_index)
coefficient_list.append(r_coefficient)
return cls(
shell_ang_mom=shell_ang_mom,
shell_ang_mom_turbo_notation=shell_ang_mom_turbo_notation,
shell_index=shell_index,
exponent_list=exponent_list,
coefficient_list=coefficient_list,
coefficient_imag_list=coefficient_imag_list,
)
'''

@classmethod
def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls
Expand All @@ -818,6 +848,7 @@ def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls
"""
shell_ang_mom = []
shell_ang_mom_turbo_notation = []
shell_index = []
exponent_list = []
coefficient_list = []
Expand All @@ -843,7 +874,7 @@ def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls
if num_contraction == 1:
orb_type_chr = str(orb_type)
ang_mom = int(return_ang_mom(orb_type_chr))

ang_mom_turbo_notation = turbo_prim_orb_type_num(orb_type_chr=orb_type)
if len(lines[i + 1].split()) == 3:
# gamess format
stride = 1
Expand All @@ -857,6 +888,7 @@ def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls
coefficient = float(lines[i + 1].split()[stride + 1].replace("D", "E"))

shell_ang_mom.append(ang_mom)
shell_ang_mom_turbo_notation.append(ang_mom_turbo_notation)
shell_index.append(shell_num)
exponent_list.append(exponent)
coefficient_list.append(coefficient)
Expand All @@ -871,8 +903,11 @@ def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls

orb_type_chr = str(orb_type)
ang_mom = int(return_ang_mom(orb_type_chr))

ang_mom_turbo_notation = turbo_cont_orb_type_num(
orb_type_chr=orb_type_chr
)
shell_ang_mom.append(ang_mom)
shell_ang_mom_turbo_notation.append(ang_mom_turbo_notation)

for j in range(1, num_contraction + 1):

Expand Down Expand Up @@ -901,12 +936,14 @@ def parse_basis_set_info_from_gamess_format_text(cls, text: str): # -> cls

return cls(
shell_ang_mom=shell_ang_mom,
shell_ang_mom_turbo_notation=shell_ang_mom_turbo_notation,
shell_index=shell_index,
exponent_list=exponent_list,
coefficient_list=coefficient_list,
coefficient_imag_list=coefficient_imag_list,
)

'''
def to_text_gamess_format(self) -> str:
"""
convert basis set to GAMESS format text
Expand All @@ -933,7 +970,9 @@ def to_text_gamess_format(self) -> str:
text += line
return text
'''

'''
def to_text_nwchem_format(self, element: str) -> str:
"""
convert basis set to GAMESS format text
Expand Down Expand Up @@ -963,6 +1002,7 @@ def to_text_nwchem_format(self, element: str) -> str:
text += line
return text
'''


class Det_Basis_sets(Basis_sets):
Expand Down

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