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Can't handle PySCF custom basis sets in cclib.bridge.cclib2pyscf.makecclib #1851
Description
PySCF allows custom basis sets to be specified in the basis keyword, eg:
from pyscf import dft, gto, lib
def calculate():
# This is DVB.
mol = gto.M(
atom="""
C 1.43386 -0.00000 0.00000
C -1.43386 0.00000 0.00000
C 0.69976 -1.21791 0.00000
C -0.69976 1.21791 0.00000
C -0.70271 -1.21960 0.00000
C 0.70271 1.21960 0.00000
H 1.24445 -2.17211 0.00000
H -1.24445 2.17211 0.00000
H -1.24514 -2.17312 0.00000
H 1.24514 2.17312 0.00000
C -2.93083 0.05118 0.00000
C 2.93083 -0.05118 0.00000
H -3.35520 1.06709 0.00000
H 3.35520 -1.06709 0.00000
C -3.76833 -1.00028 0.00000
C 3.76833 1.00028 0.00000
H -3.41193 -2.03669 0.00000
H 3.41193 2.03669 0.00000
H -4.85625 -0.86201 0.00000
H 4.85625 0.86201 0.00000
""",
basis={
'H': gto.parse('''
#BASIS SET: (3s) -> [1s]
H S
0.3425250914E+01 0.1543289673E+00
0.6239137298E+00 0.5353281423E+00
0.1688554040E+00 0.4446345422E+00
'''),
'C': gto.parse('''
#BASIS SET: (6s,3p) -> [2s,1p]
C S
0.7161683735E+02 0.1543289673E+00
0.1304509632E+02 0.5353281423E+00
0.3530512160E+01 0.4446345422E+00
C SP
0.2941249355E+01 -0.9996722919E-01 0.1559162750E+00
0.6834830964E+00 0.3995128261E+00 0.6076837186E+00
0.2222899159E+00 0.7001154689E+00 0.3919573931E+00
'''),
},
symmetry=True,
# MB
max_memory=400,
)
lib.num_threads(8)
scf_steps = []
def store_intermediate(_locals):
scf_steps.append(
{
"e_tot": _locals["e_tot"],
"norm_gorb": _locals["norm_gorb"],
"conv_tol": _locals["conv_tol"],
"conv_tol_grad": _locals["conv_tol_grad"],
}
)
method = dft.RKS(mol)
method.callback = store_intermediate
method.xc = "b3lyp"
method.kernel()
return {"methods": [method], "scf_steps": [scf_steps]}Which unfortunately results in an error in the parsing routine:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/oliver/Dev/cclib/cclib/bridge/cclib2pyscf.py", line 233, in makecclib
return cclibfrommethods(
File "/home/oliver/Dev/cclib/cclib/bridge/cclib2pyscf.py", line 296, in cclibfrommethods
else ", ".join(set(mol.basis.values())),
TypeError: unhashable type: 'list'The PySCF basis format is just a nested list, eg:
>>> from pyscf import gto
>>> gto.parse('''
... #BASIS SET: (3s) -> [1s]
... H S
... 0.3425250914E+01 0.1543289673E+00
... 0.6239137298E+00 0.5353281423E+00
... 0.1688554040E+00 0.4446345422E+00
... ''')
[[0, [3.425250914, 0.1543289673], [0.6239137298, 0.5353281423], [0.168855404, 0.4446345422]]]Should be easy enough to detect the list and skip those basis sets in the parser.
This probably belongs in regression tests right? Which makes things slightly more complicated as I don't think those support PySCF yet...
Activity
[-]Can't handle PySCF custom bases sets in cclib.bridge.cclib2pyscf.makecclib[/-][+]Can't handle PySCF custom basis sets in cclib.bridge.cclib2pyscf.makecclib[/+]