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BugFix: Treat same scan point at 0 and 360 deg correctly #67

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Feb 20, 2019
Merged

BugFix: Treat same scan point at 0 and 360 deg correctly #67

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13 changes: 8 additions & 5 deletions arc/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1308,8 +1308,6 @@ def nearly_equal(a, b, sig_fig=5):

def determine_rotor_symmetry(rotor_path, label, pivots):
"""
** This is a temporary function, will soon be incorporated in Arkane instead**

Determine the rotor symmetry number from the potential scan given in :list:`energies` in J/mol units
Assumes the list represents a 360 degree scan
str:`label` is the species name, used for logging and error messages
Expand Down Expand Up @@ -1339,8 +1337,13 @@ def determine_rotor_symmetry(rotor_path, label, pivots):
worst_peak_resolution, worst_valley_resolution = 0, 0
for i, e in enumerate(energies):
# identify peaks and valleys, and determine worst resolutions in the scan
ip1 = cyclic_index_i_plus_1(i, len(energies))
im1 = cyclic_index_i_minus_1(i)
ip1 = cyclic_index_i_plus_1(i, len(energies)) # i Plus 1
im1 = cyclic_index_i_minus_1(i) # i Minus 1
if i == 0 and energies[im1] == e:
# If the first and last scan points have same energy, change im1
im1 -= 1
logging.debug('im1: {0}, ip1: {1}, em1: {2}, e: {3}, ep1: {4}'.format(
im1, ip1, energies[im1], e, energies[ip1]))
if e > energies[im1] and e > energies[ip1]:
# this is a local peak
if any([diff > worst_peak_resolution for diff in [e - energies[im1], e - energies[ip1]]]):
Expand All @@ -1355,7 +1358,7 @@ def determine_rotor_symmetry(rotor_path, label, pivots):
# something seriously wrong with the scan
if len(peaks) != len(valleys):
logging.error('Rotor of species {0} between pivots {1} does not have the same number'
' of peaks and valleys.'.format(label, pivots))
' of peaks ({2}) and valleys ({3}).'.format(label, pivots, len(peaks), len(valleys)))
return len(peaks) # this works for CC(=O)[O]
min_peak = min(peaks)
max_peak = max(peaks)
Expand Down