I’m using a toy system to scan through a PES using SAPT. I wa able to run the calculation using XYZ coordinates and now I’m trying internal coordinates. This is my input:
import psi4
import numpy as np
psi4.core.set_output_file("output.dat", True)
psi4.set_memory("2 GB")
psi4.set_num_threads(4)
distance = np.linspace(1.8, 2.7, 10)
FeOOOOOAc_geometry = """
2 1
Fe1
O2 Fe1 2.12340
H3 O2 0.96366 Fe1 116.54762
O4 Fe1 2.11960 O2 87.61370 H3 91.31735
H5 O4 0.96282 Fe1 122.16867 O2 136.53594
O6 Fe1 2.12087 O2 92.36700 H3 271.28429
H7 O6 0.96289 Fe1 122.30420 O2 42.47875
H8 O2 0.96304 Fe1 122.21963 H3 134.32578
H9 O4 0.96362 Fe1 116.04157 O2 2.89923
H10 O6 0.96349 Fe1 116.18109 O2 176.45484
O11 Fe1 2.12083 O2 92.11855 H3 183.35462
H12 O11 0.96300 Fe1 122.24567 O2 315.84590
O13 Fe1 2.12030 O2 87.92043 H3 3.36278
H14 O13 0.96292 Fe1 122.02769 O2 223.43284
H15 O11 0.96370 Fe1 116.45738 O2 90.15002
H16 O13 0.96353 Fe1 116.37977 O2 89.57353
--
-1 1
O17 H10 2.17380 O6 117.33005 Fe1 5.01757
O18 Fe1 {0} O2 164.03932 H3 92.29818
C19 O17 1.30726 H10 146.31209 O6 356.52467
C20 C19 1.48970 O17 113.16753 H10 179.18582
H21 C20 1.08148 C19 109.47134 O17 26.12026
H22 C20 1.09220 C19 109.47125 O17 146.12022
H23 C20 1.08939 C19 109.47098 O17 266.12015
units angstrom
symmetry c1
no_reorient
"""
for R in distance:
print(R)
FeOOOOOAc = psi4.geometry(FeOOOOOAc_geometry.format(R))
psi4.set_options({'maxiter': 2000})
psi4.energy('sapt0/def2-tzvp', molecule=FeOOOOOAc)
print("=="*80)
And the error is this:
1.8
Traceback (most recent call last):
File "/home/henrique/bin/anaconda3/envs/psi4/bin/psi4", line 287, in <module>
exec(content)
File "<string>", line 57, in <module>
File "/home/henrique/bin/anaconda3/envs/psi4/lib//python3.7/site-packages/psi4/driver/molutil.py", line 252, in geometry
molecule = core.Molecule.from_dict(molrec['qm'])
RuntimeError:
Fatal Error: Illegal value Fe1 in atom specification on line
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1557940846948/work/psi4/src/psi4/libmints/molecule.cc on line: 2319
The most recent 5 function calls were:
psi::Molecule::get_anchor_atom(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
psi::Molecule::add_unsettled_atom(double, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)
Printing out the relevant lines from the Psithon --> Python processed input file:
symmetry c1
no_reorient
"""
for R in distance:
print(R)
--> FeOOOOOAc = psi4.geometry(FeOOOOOAc_geometry.format(R))
psi4.set_options({'maxiter': 2000})
psi4.energy('sapt0/def2-tzvp', molecule=FeOOOOOAc)
print("=="*80)
I’m using Psi4 1.3.2 from Anaconda.