GoodVibes Versions Save

Version 3.2 fixes a bug when parsing ORCA Single-point calculations when MiniPrint formatting is used.

References to the "patonlab" GitHub page have been added

This release adds the proper GNU license for the brute force symmetry analyzer code found at this repostory.

Full Changelog: https://github.com/patonlab/GoodVibes/compare/3.1.0...3.1.1

Bug Fixes:

• Fixed issues loading/reading SPC files.
• Issue with --invertifreq default option fixed.
• Better duplicate checking.
• Improved removal of unfinished/failed jobs from further calculation.
• Fix for changing concentration for temperature intervals (thanks @hmayes).
• Fix for checking multiplicities >10 (thanks @arosen93).
• Fixed issue with vibrational scaling factors not being found correctly.
• Windows 10 support for TravisCI
• Issue with --media options working incorrectly with -c option fixed.
• General bug fixes.

What's Changed

• Fix bug in computing values for solvated molecules over a range of temperatures by @hmayes in https://github.com/patonlab/GoodVibes/pull/27
• Fix reading of multiplicities >= 10 by @arosen93 in https://github.com/patonlab/GoodVibes/pull/30
• Adding NWChem compatibility by @sibo in https://github.com/patonlab/GoodVibes/pull/36
• Documentation & Moment of Inertia Parsing by @luchini18 in https://github.com/patonlab/GoodVibes/pull/40
• create entry_point for goodvibes during installation by @fdroessler in https://github.com/patonlab/GoodVibes/pull/41
• auto inverts freqs depending on the job type by @Margoju in https://github.com/patonlab/GoodVibes/pull/42
• Include G4 calculations by @jvalegre in https://github.com/patonlab/GoodVibes/pull/49
• Replace custom output file parsing with cclib by @berquist in https://github.com/patonlab/GoodVibes/pull/43

New Contributors

• @hmayes made their first contribution in https://github.com/patonlab/GoodVibes/pull/27
• @arosen93 made their first contribution in https://github.com/patonlab/GoodVibes/pull/30
• @sibo made their first contribution in https://github.com/patonlab/GoodVibes/pull/36
• @fdroessler made their first contribution in https://github.com/patonlab/GoodVibes/pull/41
• @Margoju made their first contribution in https://github.com/patonlab/GoodVibes/pull/42
• @jvalegre made their first contribution in https://github.com/patonlab/GoodVibes/pull/49
• @berquist made their first contribution in https://github.com/patonlab/GoodVibes/pull/43

Full Changelog: https://github.com/patonlab/GoodVibes/compare/v3.0.0...3.1.0

Entropy symmetry correction not included in 3.0.0!

New functionality including :

• Writes thermochemical data to .CSV
• Quasi-harmonic enthalpy correction implementation (applies to zeolitic systems, as per Head-Gordon et al.)
• Checks for similar level of theory, program version, solvation, detection of potential duplicates, linear molecules, valid transition states, and empirical dispersion for frequency and single-point calculations
• Correction for entropy based on solvent molecule standard concentration
• Correction to free energy related to multiple accessible conformers in potential energy surface
• Graphing of potential energy surface
• Using temperature intervals with potential energy surface calculations
• Using temperature intervals with COSMO-RS interval calculations
• Correction to entropy related to molecular symmetry
• Selectivity calculations for %ee, er, dr
• Ability to convert low-lying imaginary frequencies to positive values
• Method for detecting duplicate structures, exclusion from potential further Boltzmann weighting
• Updated vibrational scaling-factors based on Truhlar's database
• More methods working better together
  • Can use --spc with --cosmo
  • Can use --spc with --cosmo_int
  • Can use --ti with --pes
  • Can use --ti with --spc
  • Added more helpful/relevant error messages
• Minor Pythonic speed enhancements
• Test cases for implemented methods
• More comments!

New functionality including : Writes thermochemical data to .CSV Quasi-harmonic enthalpy correction implementation (applies to zeolitic systems, as per Head-Gordon et al.) Checks for similar level of theory, program version, solvation, detection of potential duplicates, linear molecules, valid transition states, and empirical dispersion for frequency and single-point calculations Correction for entropy based on solvent molecule standard concentration Correction to free energy related to multiple accessible conformers in potential energy surface Graphing of potential energy surface Using temperature intervals with potential energy surface calculations Using temperature intervals with COSMO-RS interval calculations Correction to entropy related to molecular symmetry Selectivity calculations for %ee, er, dr Ability to convert low-lying imaginary frequencies to positive values Method for detecting duplicate structures, exclusion from potential further Boltzmann weighting Updated vibrational scaling-factors based on Truhlar's database More methods working better together

• Can use --spc with --cosmo
• Can use --spc with --cosmo_int
• Can use --ti with --pes
• Can use --ti with --spc Added more helpful/relevant error messages Minor Pythonic speed enhancements Test cases for implemented methods More comments!

Features since last update:

• Imaginary frequency analysis
• Boltzmann weighting
• Selectivity prediction from multiple structures
• Improved printing including CSV option
• Total CPU time from all calculations, including single points
• Single point corrections include Orca output
• reads COSMO-RS solvation free energies
• collected xyz output
• installation via pip install goodvibes
• installation via conda -c patonlab goodvibes

2.0.1

2017-09-04

Added

• Supports external single point energies (Gaussian or Orca)
• Writes Cartesians to xyz file

Updates:

• More pythonic
• Automatically detects level of theory and applies scaling-factor from Truhlar's database
• Fixed monoatomic species
• Supports linked jobs containing single point energies
• GoodVibes.py -h now prints out all available options
• Minor fixes to output formatting