Frequency calculation with single atom crashes cclib (ORCA) #778
Description
The attached output (cl.zip) file throws an error when parsed:
import cclib
cclib.ccopen("../../data/cl.out").parse()The error:
...
.../cclib/cclib/parser/logfileparser.py in parse(self, progress, fupdate, cupdate)
327 # in data._attrlist will be moved to final data object that is returned.
328 try:
--> 329 self.extract(inputfile, line)
330 except StopIteration:
331 self.logger.error("Unexpectedly encountered end of logfile.")
.../cclib/cclib/parser/orcaparser.py in extract(self, inputfile, line)
1009
1010 nonzero = numpy.nonzero(vibfreqs)[0]
-> 1011 self.first_mode = nonzero[0]
1012 # Take all modes after first
1013 # Mode between imaginary and real modes could be 0
IndexError: index 0 is out of bounds for axis 0 with size 0The problem seems to be the number of frequencies (it's a single atom!):
...
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
------------
NORMAL MODES
------------
...
Could a try...except clause solve it? Some parts of the output are also affected by the fact that it's a single atom, such as entropy calculations, which could also throw new errors:
...
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00065446 Eh 0.41 kcal/mol
Vibrational entropy ... -inf Eh -inf kcal/mol
Rotational entropy ... 0.00000000 Eh 0.00 kcal/mol
Translational entropy ... 0.01740262 Eh 10.92 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... -inf Eh -inf kcal/mol
-------------------
GIBBS FREE ENTHALPY
-------------------
...
The correct behaviour is to consider Vibrational entropy equal to zero and sum all lines again into Final entropy term. (Enthalpies look fine, but the Final Gibbs free enthalpy is also inf in the output....)