PTEROSOR/QuAcK
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skipping cap-calculation, if no cap data is provided

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lburth 2025-05-02 16:02:32 +02:00
parent 9063eb7a77
commit 34e872d0cc
1 changed files with 46 additions and 42 deletions
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88
PyDuck.py
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@ -191,49 +191,53 @@ def create_psi4_basis(basis_dict):
# CAP definition
if use_cap:
f = open(working_dir+'/cap_data/'+args.xyz, 'r')
lines = f.read().splitlines()
line = lines[1]
tmp = line.split()
onset_x = float(tmp[0])
onset_y = float(tmp[1])
onset_z = float(tmp[2])
eta_opt = float(tmp[3])
f.close()
f = open(working_dir+'/input/eta_opt.dat', 'w')
f.write(" {} ".format(str(eta_opt)))
f.close()
print(f"CAP eta = {eta_opt}")
# xyz file
with open(working_dir + "/mol/" + xyz, "r") as f:
lines = f.readlines()
try:
f = open(working_dir+'/cap_data/'+args.xyz, 'r')
lines = f.read().splitlines()
line = lines[1]
tmp = line.split()
onset_x = float(tmp[0])
onset_y = float(tmp[1])
onset_z = float(tmp[2])
eta_opt = float(tmp[3])
f.close()
num_atoms = int(lines[0].strip())
atoms = [line.strip() for line in lines[2:2+num_atoms]]
if unit == 'Bohr':
bohr_coordinates = 'true'
else:
bohr_coordinates = 'false'
sys_dict = {
"molecule": "inline",
"geometry": "\n".join(atoms), # XYZ format as a string
"basis_file": create_psi4_basis(basis_dict),
"bohr_coordinates": bohr_coordinates
}
cap_system = pyopencap.System(sys_dict)
if not(cap_system.check_overlap_mat(ovlp, "pyscf")):
raise Exception(
"Provided cap basis does not match to the pyscf basis.")
cap_dict = {"cap_type": "box",
"cap_x": onset_x,
"cap_y": onset_y,
"cap_z": onset_z,
"Radial_precision": "16",
"angular_points": "590",
"thresh": 15}
pc = pyopencap.CAP(cap_system, cap_dict, norb)
cap_ao = pc.get_ao_cap(ordering="pyscf")
f = open(working_dir+'/input/eta_opt.dat', 'w')
f.write(" {} ".format(str(eta_opt)))
f.close()
print(f"CAP eta = {eta_opt}")
# xyz file
with open(working_dir + "/mol/" + xyz, "r") as f:
lines = f.readlines()
f.close()
num_atoms = int(lines[0].strip())
atoms = [line.strip() for line in lines[2:2+num_atoms]]
if unit == 'Bohr':
bohr_coordinates = 'true'
else:
bohr_coordinates = 'false'
sys_dict = {
"molecule": "inline",
"geometry": "\n".join(atoms), # XYZ format as a string
"basis_file": create_psi4_basis(basis_dict),
"bohr_coordinates": bohr_coordinates
}
cap_system = pyopencap.System(sys_dict)
if not(cap_system.check_overlap_mat(ovlp, "pyscf")):
raise Exception(
"Provided cap basis does not match to the pyscf basis.")
cap_dict = {"cap_type": "box",
"cap_x": onset_x,
"cap_y": onset_y,
"cap_z": onset_z,
"Radial_precision": "16",
"angular_points": "590",
"thresh": 15}
pc = pyopencap.CAP(cap_system, cap_dict, norb)
cap_ao = pc.get_ao_cap(ordering="pyscf")
except Exception:
print("No CAP-data provided for this molecule. Skipping CAP calculation...")
use_cap = False
def write_matrix_to_file(matrix, size, file, cutoff=1e-15):
f = open(file, 'w')