Tags: turkiAlturaifi/GoodVibes
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GoodVibes v3.0.0 (patonlab#22) * Save output as CSV * Head-Gordon Enthalpy Correction Implementation * Separated cutoffs for enthalpy and entropy corrections, updated README * Small README updates, resurrected -f option, updated HG reference * Implemented conformer correction to free energy and enantioselectivity * Conformer correction to free energies and enantioselectivity option * trigger travis * Updated vibrational scale factors to v4 * testing tests.. * testing tests pt 2 * rounding vib scale factors, comments * Merged Juanvi's checks manually * updated tests and check fixes * >:( forgot a comma * plz no more commas * qhH tests * separated methods for testing * Found omega and tau in vib_scale_factors * --media option * media thing * media with interval * corrected _SPC instead of _options.spc * dd * Improved Readability * More specific spc options added for printing * Sylistic changes: indented blocks for readability, atmos->ATMOS in tests * Stylistic changes: indent levels are now 4 spaces, consistent throughout file * Adjusted for speed: "line.find(x) > -1" -> "x in line" * Optimizations: add_option (depricated) -> add_argument, some style text wrapping * Tests: Use default version of Xcode for macOS (depricated), added py3.7 * edit travis yaml * one more time * trying some tricky test stuff * travis * travis config * travis config more * executable permission on .travis-install.sh * support for python 3.7 * py3.7 try 2 * opt, scaling factors -> dict, added checks for dispersion, false TSs * bug fix for Link1 in check version * bug fix for Link1 in level of theory * same file but without the print statement at the end * fix bug of ) in check solvent * now GV recognizes HCN and N3 as linear molecules * bug fixed with indentation in checks * duplicate check changed * update dispersion check * fix check messages * fix bug with dispersion check * fix bug in dispersion bug * fix bug empirical disp check * DFT methods and basis sets default to Gaussian values * invert imaginary frequencies * merge conflicts * fixed invert in check * fixed invert stuff and made ee printing more robust * FORCE PUSH * --pes fix when wrong file given * fixed XYZ * merge conflicts * fixed requested args printing * put new arg for check * spc causing headaches * invert * COSMOOOOOOOo * pes fixed * x when spc is not located * add o in scaling factor * beginnings of graphs * fixed bug duplic * fix bug no SPC * ddd * Progress on graph * cool graph changes * Graph and README updates * x when spc is not located 2.0 * fix check duplic SPC * fix duplic SPC - more robust for G16 random input transformations * gconf shenanigans and readme edits * graphing * decimal places * gconf troubles * smol changes * added check for standard concentration * intro test pes * mor tests and csv catch * take out print() * Added testing for PES and media options * logger formatting * tabs? testing for python2.6 / 2.7 * testing some more * quick lil test * last test i swear * Examples, test and graph updates * Options to add grid lines and to remove title * changed how zero structures are parsed in PES * Reformatting PES, graphing conformers * Graphing conformers with Gconf working * tests * graph options * title * indent+comma * updates here n there. T interval for PES, codecov badge :/ * symmetry correction * add some examples (.log files), delete later * Symmetry corrections, add some .log testing file, delete later * relocate symmetry C files, relocate symmetric molecules to the example folder * COSMO in PES T interval, test for interval * Added symmetry libraries for Linux and macOS * Ssymm no longer default - use --ssymm to turn symmetry correction on * --ssymm now cites Patchkovskii, prints point group to user * Added sections to README * '--dup' option added for duplicate checking. Code optimization/formatting * Radii reference, fix for standard conc= error, calc_bbe optimization * bug fixes, diasteromer ratio option added (--dr), * Now grabs ONIOM scaling factors (%ModelSys) when provided option (--vmm) * Readme updates, comment updates * Calculate D3 corrections Co-Authored-By: Paton Lab <[email protected]> * update tests Co-Authored-By: Paton Lab <[email protected]> * ReadMe changes, speed edits, formatting * Check for normal/error termination/currently running jobs and pull them * Better solvation model parsing * solvation parsing II * Better empricial dispersion parsing, small bug fixes * emp dispersion parsing II * Ssymm not compatible (yet) with Windows OS. Prints message to user * Windows support for --ssymm! * commenting * Maintainence for merge
GoodVibes v3.0.0 (patonlab#22) * Save output as CSV * Head-Gordon Enthalpy Correction Implementation * Separated cutoffs for enthalpy and entropy corrections, updated README * Small README updates, resurrected -f option, updated HG reference * Implemented conformer correction to free energy and enantioselectivity * Conformer correction to free energies and enantioselectivity option * trigger travis * Updated vibrational scale factors to v4 * testing tests.. * testing tests pt 2 * rounding vib scale factors, comments * Merged Juanvi's checks manually * updated tests and check fixes * >:( forgot a comma * plz no more commas * qhH tests * separated methods for testing * Found omega and tau in vib_scale_factors * --media option * media thing * media with interval * corrected _SPC instead of _options.spc * dd * Improved Readability * More specific spc options added for printing * Sylistic changes: indented blocks for readability, atmos->ATMOS in tests * Stylistic changes: indent levels are now 4 spaces, consistent throughout file * Adjusted for speed: "line.find(x) > -1" -> "x in line" * Optimizations: add_option (depricated) -> add_argument, some style text wrapping * Tests: Use default version of Xcode for macOS (depricated), added py3.7 * edit travis yaml * one more time * trying some tricky test stuff * travis * travis config * travis config more * executable permission on .travis-install.sh * support for python 3.7 * py3.7 try 2 * opt, scaling factors -> dict, added checks for dispersion, false TSs * bug fix for Link1 in check version * bug fix for Link1 in level of theory * same file but without the print statement at the end * fix bug of ) in check solvent * now GV recognizes HCN and N3 as linear molecules * bug fixed with indentation in checks * duplicate check changed * update dispersion check * fix check messages * fix bug with dispersion check * fix bug in dispersion bug * fix bug empirical disp check * DFT methods and basis sets default to Gaussian values * invert imaginary frequencies * merge conflicts * fixed invert in check * fixed invert stuff and made ee printing more robust * FORCE PUSH * --pes fix when wrong file given * fixed XYZ * merge conflicts * fixed requested args printing * put new arg for check * spc causing headaches * invert * COSMOOOOOOOo * pes fixed * x when spc is not located * add o in scaling factor * beginnings of graphs * fixed bug duplic * fix bug no SPC * ddd * Progress on graph * cool graph changes * Graph and README updates * x when spc is not located 2.0 * fix check duplic SPC * fix duplic SPC - more robust for G16 random input transformations * gconf shenanigans and readme edits * graphing * decimal places * gconf troubles * smol changes * added check for standard concentration * intro test pes * mor tests and csv catch * take out print() * Added testing for PES and media options * logger formatting * tabs? testing for python2.6 / 2.7 * testing some more * quick lil test * last test i swear * Examples, test and graph updates * Options to add grid lines and to remove title * changed how zero structures are parsed in PES * Reformatting PES, graphing conformers * Graphing conformers with Gconf working * tests * graph options * title * indent+comma * updates here n there. T interval for PES, codecov badge :/ * symmetry correction * add some examples (.log files), delete later * Symmetry corrections, add some .log testing file, delete later * relocate symmetry C files, relocate symmetric molecules to the example folder * COSMO in PES T interval, test for interval * Added symmetry libraries for Linux and macOS * Ssymm no longer default - use --ssymm to turn symmetry correction on * --ssymm now cites Patchkovskii, prints point group to user * Added sections to README * '--dup' option added for duplicate checking. Code optimization/formatting * Radii reference, fix for standard conc= error, calc_bbe optimization * bug fixes, diasteromer ratio option added (--dr), * Now grabs ONIOM scaling factors (%ModelSys) when provided option (--vmm) * Readme updates, comment updates * Calculate D3 corrections Co-Authored-By: Paton Lab <[email protected]> * update tests Co-Authored-By: Paton Lab <[email protected]> * ReadMe changes, speed edits, formatting * Check for normal/error termination/currently running jobs and pull them * Better solvation model parsing * solvation parsing II * Better empricial dispersion parsing, small bug fixes * emp dispersion parsing II * Ssymm not compatible (yet) with Windows OS. Prints message to user * Windows support for --ssymm! * commenting * Maintainence for merge