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pyqchem's Introduction

pyQChem - Input/Output-Tools for Q-Chem

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PyQChem is a Python module designed for an intuitive manipulation of Q-Chem input and output files. It was written with special focus on the features of IPython such as tab completion and easy access to help docstrings via the question mark operator.

Use conda to add the latest release of pqQChem to your environment (recommended),

conda install -c awhauser pyqchem 

or clone and install the current Github development version via

git clone https://github.com/hauser-group/pyQChem.git
cd pyQChem
pip install .

Two IPython notebooks (and support files) are provided as an introduction to basic inputfile handling and outputfile parsing. Example Python scripts that use pyQChem can be found in the 'demos' directory.

Andreas W. Hauser, Matthew Goldey, Ehud Tsivion and Michael Wormit, January 2015

Ralf Meyer and Thomas Heavey, September 2018

pyqchem's People

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pyqchem's Issues

constants.py atomic masses

There are significant differences between the atomic masses in NIST PML database and pyqchem/constants.py:

Z= 3, nist = 7.0160034366   , pyqchem = 6.015122795
Z= 5, nist = 11.00930536    , pyqchem = 10.012937
Z=18, nist = 39.9623831237  , pyqchem = 35.967545106
Z=22, nist = 47.94794198    , pyqchem = 45.9526316
Z=23, nist = 50.94395704    , pyqchem = 49.9471585
Z=24, nist = 51.94050623    , pyqchem = 49.9460442
Z=26, nist = 55.93493633    , pyqchem = 53.9396105
Z=32, nist = 73.921177761   , pyqchem = 69.9242474
Z=34, nist = 79.9165218     , pyqchem = 73.9224764
Z=36, nist = 83.9114977282  , pyqchem = 77.9203648
Z=38, nist = 87.9056125     , pyqchem = 83.913425
Z=42, nist = 97.90540482    , pyqchem = 91.906811
Z=43, nist = 97.9072124     , pyqchem = 96.906365
Z=44, nist = 101.9043441    , pyqchem = 95.907598
Z=46, nist = 105.9034804    , pyqchem = 101.905609
Z=48, nist = 113.90336509   , pyqchem = 105.906459
Z=49, nist = 114.903878776  , pyqchem = 112.904058
Z=50, nist = 119.90220163   , pyqchem = 111.904818
Z=52, nist = 129.906222748  , pyqchem = 119.90402
Z=54, nist = 131.9041550856 , pyqchem = 123.905893
Z=56, nist = 137.905247     , pyqchem = 129.9063208
Z=57, nist = 138.9063563    , pyqchem = 137.907112
Z=58, nist = 139.9054431    , pyqchem = 135.907172
Z=62, nist = 151.9197397    , pyqchem = 143.911999
Z=63, nist = 152.921238     , pyqchem = 150.9198502    
Z=64, nist = 157.9241123    , pyqchem = 151.919791
Z=66, nist = 163.9291819    , pyqchem = 155.924283
Z=68, nist = 165.9302995    , pyqchem = 161.928778
Z=70, nist = 173.9388664    , pyqchem = 167.933897
Z=72, nist = 179.946557     , pyqchem = 175.9414086
Z=73, nist = 180.9479958    , pyqchem = 179.9474648
Z=74, nist = 183.95093092   , pyqchem = 179.946704
Z=75, nist = 186.9557501    , pyqchem = 184.952955
Z=76, nist = 191.961477     , pyqchem = 183.9524891
Z=77, nist = 192.9629216    , pyqchem = 190.960594
Z=78, nist = 194.9647917    , pyqchem = 189.959932
Z=80, nist = 201.9706434    , pyqchem = 195.965833
Z=81, nist = 204.9744278    , pyqchem = 202.9723442
Z=82, nist = 207.9766525    , pyqchem = 203.9730436
Z=86, nist = 222.0175782    , pyqchem = 210.990601
Z=88, nist = 226.0254103    , pyqchem = 223.0185022
Z=90, nist = 232.0380558    , pyqchem = 230.0331338
Z=92, nist = 238.0507884    , pyqchem = 233.0396352
Z=93, nist = 237.0481736    , pyqchem = 236.04657
Z=94, nist = 244.0642053    , pyqchem = 238.0495599

Even after discounting Z=43, 61, 84--89, 93, 94 (for which the NIST database does not give isotopic composition but the most stable isotope) the result suggests maybe the lightest isotope was used instead of the most common, contradicting the comment on line 216 # Relative atomic mass per most common isotope?

QChem opt2man/atom_data.C seems to be using something else (e.g. for Kr it defaults to 86Kr), but that's another issue which probably does not belong here.

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