thermoanalysis

External thermochemistry analysis implemented in pure python for all frequency calculations that can be parsed by cclib and provide the required attributes (atomcoords, vibfreqs, scfenergies, atommasses, mult).

The program is inspired by the nice GoodVibes script from the Patton group.

Requirements

python3.6+
cclib
h5py
numpy
pytest
tabulate

Installation

python setup.py install

Until cclib 1.6.2 is released a patch (Correct parsing of vibrational frequencies with ORCA 4.1.x) has to be applied to cclib correctly parse frequency calculations done with recent ORCA versions (4.1+).

Running tests

# Can be executed from any directory after installation of thermoanalysis
pytest --pyargs thermoanalysis

Usage

thermo [log] --temp [298.15] --pg [c1]

Sample output

$ thermo 05_dmso_hf_orca_freq.out --temps 298.15 398.15 11
Using QRRHO-approach for vibrational entropies.
ZPE = 0.083938 au / particle (independent of T)
U_vib and U_tot already include the ZPE.
All quantities given in au / particle except T (given in K).
     T         U_el    U_therm        U_tot            H    TS_tot            G
------  -----------  ---------  -----------  -----------  --------  -----------
298.15  -548.679124   0.089954  -548.589170  -548.589170  0.035958  -548.625128
308.15  -548.679124   0.090262  -548.588863  -548.588863  0.037504  -548.626367
318.15  -548.679124   0.090576  -548.588549  -548.588549  0.039067  -548.627616
328.15  -548.679124   0.090895  -548.588229  -548.588229  0.040647  -548.628876
338.15  -548.679124   0.091221  -548.587903  -548.587903  0.042244  -548.630147
348.15  -548.679124   0.091553  -548.587571  -548.587571  0.043857  -548.631428
358.15  -548.679124   0.091891  -548.587233  -548.587233  0.045487  -548.632720
368.15  -548.679124   0.092235  -548.586889  -548.586889  0.047133  -548.634022
378.15  -548.679124   0.092585  -548.586539  -548.586539  0.048794  -548.635334
388.15  -548.679124   0.092941  -548.586184  -548.586184  0.050472  -548.636656
398.15  -548.679124   0.093303  -548.585822  -548.585822  0.052166  -548.637988
Dumped thermo-data to '05_dmso_hf_orca_freq_thermo.h5'.

Some remarks

Even though it does not (yet) implement all features of the original GoodVibes the present implementation is not restricted to Gaussian logs as GoodVibes. In principle all frequency calculations that can be parsed by cclib are supported. Parsing of files that can't be handled by cclib can easily be achived by reimplenting the set_data(log_fn)-method in subclass of QCData.

Imaginary frequencies are neglected in the thermochemistry calculations.

berhane / thermoanalysis