Hi,
I tried the following input using Psi4 1.3.2 release, Git: Rev {HEAD} ecbda83
memory 300 mb
molecule oh {
0 2
O 0.0 0.0 0.047
H 0.0 0.0 -0.732
@O 0.0 0.0 0.102
@H 0.0 0.0 -1.515
@O 0.0 0.0 0.159
@H 0.0 0.0 -2.226
units angstrom
symmetry c1
}
set basis 6-31G
set reference uhf
set scf_type pk
E, wfn = energy(‘scf’, return_wfn=True)
energy(‘scf’)
I got a message
File “”, line 32, in
File /psi4conda/lib//python3.6/site-packages/psi4/driver/molutil.py", line 250, in geometry
geom, enable_qm=True, missing_enabled_return_qm=‘minimal’, enable_efp=True, missing_enabled_return_efp=‘none’)
File /psi4conda/lib//python3.6/site-packages/qcelemental/molparse/from_string.py", line 263, in from_string
**molinit)
File /psi4conda/lib//python3.6/site-packages/qcelemental/molparse/from_arrays.py", line 123, in from_input_arrays
verbose=1)
File /psi4conda/lib//python3.6/site-packages/qcelemental/molparse/from_arrays.py", line 347, in from_arrays
tooclose=tooclose) # yapf: disable
File /psi4conda/lib//python3.6/site-packages/qcelemental/molparse/from_arrays.py", line 586, in validate_and_fill_geometry
[(i, j, dm[i, j]) for i, j in zip(*tooclosem)]))
qcelemental.exceptions.ValidationError: Following atoms are too close: [(2, 0, 0.0474115), (4, 0, 0.0840313), (4, 2, 0.036619799999999994), (6, 2, 0.0701034), (6, 4, 0.0334836)]
It seems the distance is between atom O and ghost atom O. I tried to modify from_arrays, set the value of “tooclose” to 0.03. It led to
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgdma.so 00007F45CE9660DC for__signal_handl Unknown Unknown
libpthread-2.19.s 00007F45D3BF0330 Unknown Unknown Unknown
core.cpython-36m- 00007F45D1FB3207 Unknown Unknown Unknown
core.cpython-36m- 00007F45CF8EE684 Unknown Unknown Unknown
core.cpython-36m- 00007F45CF511FE6 Unknown Unknown Unknown
python3.6 00007F45D4294744 _PyCFunction_Fast Unknown Unknown
python3.6 00007F45D431B57E Unknown Unknown Unknown
python3.6 00007F45D434038A _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D43148E4 Unknown Unknown Unknown
python3.6 00007F45D4315771 Unknown Unknown Unknown
python3.6 00007F45D431B505 Unknown Unknown Unknown
python3.6 00007F45D434038A _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D431553B Unknown Unknown Unknown
python3.6 00007F45D431B505 Unknown Unknown Unknown
python3.6 00007F45D434038A _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D4316289 PyEval_EvalCodeEx Unknown Unknown
python3.6 00007F45D43171A6 Unknown Unknown Unknown
python3.6 00007F45D429454E PyObject_Call Unknown Unknown
python3.6 00007F45D4341A6C _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D4316289 PyEval_EvalCodeEx Unknown Unknown
python3.6 00007F45D43171A6 Unknown Unknown Unknown
python3.6 00007F45D429454E PyObject_Call Unknown Unknown
python3.6 00007F45D4341A6C _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D43148E4 Unknown Unknown Unknown
python3.6 00007F45D4315771 Unknown Unknown Unknown
python3.6 00007F45D431B505 Unknown Unknown Unknown
python3.6 00007F45D4341147 _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D4316289 PyEval_EvalCodeEx Unknown Unknown
python3.6 00007F45D431701C PyEval_EvalCode Unknown Unknown
python3.6 00007F45D43993C4 Unknown Unknown Unknown
python3.6 00007F45D439945D PyRun_StringFlags Unknown Unknown
python3.6 00007F45D433DD2E Unknown Unknown Unknown
python3.6 00007F45D4294681 _PyCFunction_Fast Unknown Unknown
python3.6 00007F45D431B42C Unknown Unknown Unknown
python3.6 00007F45D434038A _PyEval_EvalFrame Unknown Unknown
python3.6 00007F45D4316289 PyEval_EvalCodeEx Unknown Unknown
python3.6 00007F45D431701C PyEval_EvalCode Unknown Unknown
python3.6 00007F45D43993C4 Unknown Unknown Unknown
python3.6 00007F45D43997C1 PyRun_FileExFlags Unknown Unknown
python3.6 00007F45D43999C3 PyRun_SimpleFileE Unknown Unknown
python3.6 00007F45D439D4B3 Py_Main Unknown Unknown
python3.6 00007F45D426602E main Unknown Unknown
libc-2.19.so 00007F45D3831F45 __libc_start_main Unknown Unknown
python3.6 00007F45D4346E0E Unknown Unknown Unknown
Is there any way to surpass the 0.1 atomic distance threshold, at least for atom and ghost atom? It seems ORCA can accept a distance closer than 0.1.
Thank you very much