GoodVibes computes quasi-harmonic thermochemical corrections from electronic structure calculations (Gaussian, ORCA, NWChem, QChem, xTB, ASE). It corrects the poor description of low-frequency vibrations by the rigid-rotor harmonic oscillator (RRHO) treatment using the approaches of Grimme and Truhlar.
Features
Grimme quasi-RRHO (mRRHO) and Truhlar quasi-harmonic entropy corrections
Head-Gordon quasi-harmonic enthalpy correction
Variable temperature and concentration thermochemistry
Automated vibrational frequency scaling factor lookup (~200 levels of theory)
Single-point energy corrections (link jobs or separate files)
Boltzmann-weighted populations and N-way stereoselectivity (
--label)Potential energy surface analysis with YAML-defined pathways, stoichiometric sums (
2*A + B), and Gconf correctionsStructured JSON output (
--json) for downstream pipelinesSymmetry-corrected entropy via pymsym point-group detection
Solvent standard-state concentration and free-space corrections
JSON caching for fast re-analysis (
--cache-save/--cache-read)Duplicate structure detection (
--dedup) and energy-sorted output (--sort)Supports Gaussian, ORCA, NWChem, QChem, xTB, and ASE output files
Installation
Requires Python >= 3.9.
pip install goodvibes
Or with uv:
uv pip install goodvibes
Or from conda-forge:
conda install -c conda-forge goodvibes
For development (editable install):
pip install -e .
Quick Start
goodvibes <output_file(s)> -q
The -q flag applies quasi-harmonic corrections (Grimme entropy + Head-Gordon enthalpy). Use -h for the full list of options.
Supported Programs
GoodVibes reads output files from:
Gaussian (09, 16)
.log/.out– optimization, frequency, single-point, link jobs, ONIOM, VPT2 anharmonicORCA (5, 6)
.out– optimization, frequency, single-point, DLPNO-CCSD(T)NWChem
.out– optimization, frequency, single-pointQChem (6)
.out/.qcin– optimization, frequency, single-point, linked jobsxTB
.out– frequency calculations (ORCA/xTB integration compatible)ASE (Atomic Simulation Environment)
.extxyz– extended XYZ format with energy & frequency data
The program is auto-detected from the output file contents. Additional file extensions can be registered with --custom_ext.
Documentation
Full documentation is available on Read the Docs.
Examples
Example 1: Grimme-type quasi-harmonic correction with a cut-off of 150 cm-1
goodvibes examples/methylaniline.out -f 150
Structure E ZPE H T.S T.qh-S G(T) qh-G(T)
*********************************************************************************************************
o methylaniline -326.664901 0.142118 -326.514489 0.039668 0.039465 -326.554157 -326.553954
*********************************************************************************************************
The output shows both standard harmonic and quasi-harmonic corrected thermochemical data (in Hartree). The corrected enthalpy and entropy values are always less than or equal to the harmonic value.
Example 2: Quasi-harmonic thermochemistry with a larger basis set single point energy correction link job
goodvibes examples/ethane_spc.out --spc link
Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
***********************************************************************************************************************
o ethane_spc -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
***********************************************************************************************************************
This calculation contains a multi-step job: an optimization and frequency calculation with a small basis set followed by (–Link1–) a larger basis set single point energy. Note the use of the --spc link option. The standard harmonic and quasi-harmonic corrected thermochemical data are obtained from the small basis set partition function combined with the larger basis set single point electronic energy. In this example, GoodVibes automatically recognizes the level of theory used in the frequency calculation, B3LYP/6-31G(d), and applies the Truhlar group scaling factors of 0.991 (harmonic, used for Hvib and Svib) and 0.977 (ZPE). Use -v 1.0 to suppress all scaling, or --zpe-vscal Y to override only the ZPE factor.
Alternatively, if a single point energy calculation has been performed separately, provided both file names share a common root e.g. ethane.out and ethane_TZ.out then use of the --spc TZ option is appropriate. This will give identical results as above.
goodvibes examples/ethane.out --spc TZ
Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
***********************************************************************************************************************
o ethane -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
***********************************************************************************************************************
Example 3: Changing the temperature (from standard 298.15 K to 1000 K) and concentration (from standard state in gas phase, 1 atm, to standard state in solution, 1 mol/l)
goodvibes examples/methylaniline.out --temp 1000 --conc 1.0
Structure E ZPE H T.S T.qh-S G(T) qh-G(T)
*********************************************************************************************************
o methylaniline -326.664901 0.142118 -326.452307 0.218212 0.216559 -326.670519 -326.668866
*********************************************************************************************************
This correction from 1 atm to 1 mol/l is responsible for the addition 1.89 kcal/mol to the Gibbs energy of each species (at 298K). It affects the translational entropy, which is the only component of the molecular partition function to show concentration dependence. In the example above the correction is larger due to the increase in temperature.
Example 4: Analyzing the Gibbs energy across an interval of temperatures 300-1000 K with a stepsize of 100 K, applying a (Truhlar type) cut-off of 100 cm-1
goodvibes examples/methylaniline.out --ti '300,1000,100' --qs truhlar -f 120
Structure Temp/K H T.S T.qh-S G(T) qh-G(T)
******************************************************************************************************
o methylaniline 300.0 -326.514399 0.040005 0.039842 -326.554404 -326.554241
o methylaniline 400.0 -326.508735 0.059816 0.059596 -326.568551 -326.568331
o methylaniline 500.0 -326.501670 0.082625 0.082349 -326.584296 -326.584020
o methylaniline 600.0 -326.493429 0.108148 0.107816 -326.601577 -326.601245
o methylaniline 700.0 -326.484222 0.136095 0.135707 -326.620317 -326.619930
o methylaniline 800.0 -326.474218 0.166216 0.165772 -326.640434 -326.639990
o methylaniline 900.0 -326.463545 0.198300 0.197800 -326.661845 -326.661346
o methylaniline 1000.0 -326.452307 0.232169 0.231614 -326.684476 -326.683921
******************************************************************************************************
Note that the energy and ZPE are not printed in this instance since they are temperature-independent. The Truhlar-type quasi-harmonic correction sets all frequencies below 120 cm-1 to a value of 100. Constant pressure is assumed, so that the concentration is recomputed at each temperature.
Example 5: Analyzing the Gibbs Energy using scaled vibrational frequencies
goodvibes examples/methylaniline.out -v 0.95
Structure E ZPE H T.S T.qh-S G(T) qh-G(T)
*********************************************************************************************************
o methylaniline -326.664901 0.135012 -326.521265 0.040238 0.040091 -326.561503 -326.561356
*********************************************************************************************************
The frequencies are scaled by a factor of 0.95 before they are used in the computation of the vibrational energies (including ZPE) and entropies.
Example 6: Writing Cartesian coordinates
goodvibes examples/HCN*.out --xyz
Optimized cartesian-coordinates found in files HCN_singlet.out and HCN_triplet.out are written to GoodVibes_output.xyz
Example 7: Analyzing multiple files at once
goodvibes examples/*.out --cpu
Structure E ZPE H T.S T.qh-S G(T) qh-G(T)
*********************************************************************************************************
o Al_298K -242.328708 0.000000 -242.326347 0.017670 0.017670 -242.344018 -242.344018
o Al_400K -242.328708 0.000000 -242.326347 0.017670 0.017670 -242.344018 -242.344018
o H2O -76.368128 0.020772 -76.343577 0.021458 0.021458 -76.365035 -76.365035
o HCN_singlet -93.358851 0.015978 -93.339373 0.022896 0.022896 -93.362269 -93.362269
o HCN_triplet -93.153787 0.012567 -93.137780 0.024070 0.024070 -93.161850 -93.161850
o allene -116.569605 0.053913 -116.510916 0.027618 0.027621 -116.538534 -116.538537
o benzene -232.227201 0.101377 -232.120521 0.032742 0.032745 -232.153263 -232.153265
o ethane -79.830421 0.075238 -79.750770 0.027523 0.027525 -79.778293 -79.778295
o isobutane -158.458811 0.132380 -158.319804 0.034241 0.034252 -158.354046 -158.354056
o methylaniline -326.664901 0.142118 -326.514489 0.039668 0.039535 -326.554157 -326.554024
o neopentane -197.772980 0.160311 -197.604824 0.036952 0.036966 -197.641776 -197.641791
*********************************************************************************************************
TOTAL CPU 0 days 2 hrs 29 mins 28 secs
Wildcard characters (*) can be used to specify all output files in a directory.
Example 8: Entropic Symmetry Correction
goodvibes examples/allene.out examples/benzene.out examples/ethane.out examples/isobutane.out examples/neopentane.out --symm
Structure E ZPE H T.S T.qh-S G(T) qh-G(T) Point Group
**********************************************************************************************************************
o allene -116.569605 0.053913 -116.510916 0.026309 0.026312 -116.537225 -116.537228 D2d
o benzene -232.227201 0.101377 -232.120521 0.030396 0.030399 -232.150917 -232.150919 D6h
o ethane -79.830421 0.075238 -79.750770 0.025831 0.025833 -79.776601 -79.776603 D3d
o isobutane -158.458811 0.132380 -158.319804 0.033204 0.033214 -158.353008 -158.353019 C3v
o neopentane -197.772980 0.160311 -197.604824 0.034606 0.034620 -197.639430 -197.639444 Td
*********************************************************************************************************************************************
Example 9: Potential Energy Surface (PES) Comparison with Accessible Conformer Correction
goodvibes examples/gconf_ee_boltz/*.log --pes examples/gconf_ee_boltz/gconf_aminox_cat.yaml
Structure E ZPE H T.S T.qh-S G(T) qh-G(T)
************************************************************************************************************
o Aminoxylation_TS1_R -879.405138 0.295352 -879.091374 0.063746 0.061481 -879.155120 -879.152855
o Aminoxylation_TS2_S -879.404445 0.295301 -879.090562 0.064366 0.061891 -879.154928 -879.152453
o aminox_cat_conf212_S -517.875165 0.200338 -517.662195 0.051817 0.049814 -517.714012 -517.712009
o aminox_cat_conf280_R -517.877308 0.200869 -517.664171 0.049996 0.048777 -517.714167 -517.712948
o aminox_cat_conf65_S -517.877161 0.200789 -517.664159 0.049790 0.048656 -517.713949 -517.712815
o aminox_subs_conf713 -361.535757 0.095336 -361.433167 0.037824 0.037696 -361.470991 -361.470863
************************************************************************************************************
Gconf correction requested to be applied to below relative values using quasi-harmonic Boltzmann factors
RXN: Reaction (kcal/mol) DE DZPE DH T.DS T.qh-DS DG(T) qh-DG(T)
************************************************************************************************************
o Cat+Subs 0.00 0.00 0.00 0.00 0.00 0.00 0.00
o TS 4.72 -0.46 3.53 -15.85 -16.37 19.39 19.90
************************************************************************************************************
Example 10: Stereoselectivity and Boltzmann populations
goodvibes examples/gconf_ee_boltz/Aminoxylation_TS1_R.log examples/gconf_ee_boltz/Aminoxylation_TS2_S.log --boltz --ee "*_R*:*_S*"
Structure E ZPE H T.S T.qh-S G(T) qh-G(T) Boltz
*******************************************************************************************************************
o Aminoxylation_TS1_R -879.405138 0.295352 -879.091374 0.063746 0.061481 -879.155120 -879.152855 0.605
o Aminoxylation_TS2_S -879.404445 0.295301 -879.090562 0.064366 0.061891 -879.154928 -879.152453 0.395
*******************************************************************************************************************
Selectivity Excess (%) Ratio (%) Ratio Major Iso ddG
*****************************************************************************************
o 20.98 60:40 1.5:1 R 0.25
*****************************************************************************************
CLI Reference
Run goodvibes -h for the full list of options. Key flags:
Flag |
Description |
Default |
|---|---|---|
|
Apply quasi-harmonic corrections (Grimme entropy + Head-Gordon enthalpy) |
off |
|
Frequency cut-off for entropy and enthalpy (cm-1) |
100 |
|
Frequency cut-off for entropy only (cm-1) |
100 |
|
Frequency cut-off for enthalpy only (cm-1) |
100 |
|
Quasi-harmonic entropy method |
grimme |
|
Apply Head-Gordon enthalpy correction only |
off |
|
Temperature in Kelvin |
298.15 |
|
Temperature interval scan |
– |
|
Concentration in mol/L (solution-phase entropy) |
gas phase |
|
Vibrational frequency scaling factor |
auto |
|
Single-point energy correction (suffix or |
– |
|
Apply symmetry correction to entropy (pymsym) |
off |
|
Print Boltzmann-weighted populations |
off |
|
N-way selectivity bucket (repeatable, fnmatch on basenames) |
– |
|
Selectivity spec via YAML (alternative to |
– |
|
(deprecated) Two-species selectivity, e.g. |
– |
|
YAML-defined reaction pathway analysis (legacy + true YAML auto-detected) |
– |
|
PES tables: use only each species’ lowest qh-G conformer |
off |
|
Write structured results (schema v1.0: thermo, selectivity, pes blocks) |
– |
|
Solvent standard-state concentration correction |
– |
|
Free-space correction for solvent cavity |
– |
|
Invert small imaginary frequencies to positive values |
off |
|
Moment of inertia for free-rotor entropy |
global |
|
Sort output by energy |
– |
|
Remove duplicate structures |
off |
|
Decimal places for energy output |
6 |
|
Save parsed data to JSON cache |
– |
|
Read parsed data from JSON cache |
– |
|
Additional file extensions (comma-separated) |
– |
|
Glob pattern to exclude files |
– |
|
Verify consistency across input files |
off |
|
Print total CPU time |
off |
|
Write Cartesian coordinates to .xyz file |
off |
|
Print imaginary frequencies |
off |
|
Output file base name |
output |
|
Frequency scaling factor for ONIOM MM region |
– |
|
Disable Gconf correction in PES analysis |
off |
|
Graph a reaction profile from free energies |
– |
Dependencies
Python >= 3.9
numpy – numerical computations
pymsym – point group detection and symmetry numbers
rich >= 13 – console table rendering
Optional:
ase >= 3.22 (
goodvibes[ase]) – only needed to parse.extxyzinputspyyaml – needed at runtime when reading new-style PES YAML or
--selectivity FILE.yaml; included in thetestextra
Build requires setuptools >= 64. See pyproject.toml for details.
Contributing
Install for development:
pip install -e .
Run the test suite:
pytest -v
Test data is organized by program:
tests/g16/– Gaussian 16 output filestests/orca6/– ORCA 6 output files (full coverage)tests/orca5/– ORCA 5 output files (lightweight regression layer)tests/qchem6/– QChem 6 output filestests/xtb/– xTB output filestests/ase/– ASE (extended XYZ) test files
Test helpers in tests/conftest.py provide path resolvers (g16path(), orca_path(), orca5_path(), qchem_path(), xtb_path(), ase_path()) and categorized file lists (G16_FREQ_FILES, ORCA_FREQ_FILES, QCHEM_FREQ_FILES, XTB_FREQ_FILES, ASE_FREQ_FILES, etc.) used by parametrized tests.
Citing GoodVibes
Luchini, G.; Alegre-Requena, J. V.; Funes-Ardoiz, I.; Paton, R. S. GoodVibes: Automated Thermochemistry for Heterogeneous Computational Chemistry Data. F1000Research, 2020, 9, 291 DOI: 10.12688/f1000research.22758.1
References
Ribeiro, R. F.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2011, 115, 14556-14562 DOI: 10.1021/jp205508z
Grimme, S. Chem. Eur. J. 2012, 18, 9955-9964 DOI: 10.1002/chem.201200497
Li, Y.; Gomes, J.; Sharada, S. M.; Bell, A. T.; Head-Gordon, M. J. Phys. Chem. C 2015, 119, 1840-1850 DOI: 10.1021/jp509921r
Alecu, I. M.; Zheng, J.; Zhao, Y.; Truhlar, D. G.; J. Chem. Theory Comput. 2010, 6, 2872-2887 DOI: 10.1021/ct100326h
Mammen, M.; Shakhnovich, E. I.; Deutch, J. M.; Whitesides, G. M. J. Org. Chem. 1998, 63, 3821-3830 DOI: 10.1021/jo970944f
Pracht, P.; Grimme, S. Chem. Sci. 2021, 12, 6551-6568 DOI: 10.1039/D1SC00621E
License
GoodVibes is freely available under an MIT License