PyPI 官网下载 | goodvibes-3.0.1.tar.gz

GoodVibes === [](https://travis-ci.org/luchini18/GoodVibes) [](https://badge.fury.io/py/goodvibes) [](https://conda.anaconda.org/patonlab) [](https://anaconda.org/patonlab/goodvibes) [](https://zenodo.org/badge/latestdoi/54848929) A Python program to compute corrections to thermochemical data from frequency calculations at a given temperature/concentration, corrected for the effects of vibrational scaling-factors and available free space in solvent. Developed by [Robert Paton](https://orcid.org/0000-0002-0104-4166), [Ignacio Funes-Ardoiz](https://orcid.org/0000-0002-5843-9660), and members of the [Paton Research Group, Colorado State](http://patonlab.com/): [Guilian Luchini](https://orcid.org/0000-0003-0135-9624), [Juan V. Alegre-Requena](https://orcid.org/0000-0002-0769-7168), and [Yanfei Guan](https://orcid.org/0000-0003-1817-0190) . Integration with Travis CI testing by [Jaime Rodríguez-Guerra](https://orcid.org/0000-0001-8974-1566) with additions from Guilian Luchini. All (electronic, translational, rotational and vibrational) partition functions are recomputed and will be adjusted to any temperature or concentration. These default to 298.15 Kelvin and 1 atmosphere. The program will attempt to parse the level of theory and basis set used in the calculations and then try to apply the appropriate vibrational (zpe) scaling factor. Scaling factors are taken from the [Truhlar group database](https://t1.chem.umn.edu/freqscale/index.html). #### Quasi-Harmonic Approximation Two types of quasi-harmonic approximation are readily applied. The first is vibrational entropy: below a given cut-off value vibrational normal modes are not well described by the rigid-rotor-harmonic-oscillator (RRHO) approximation and an alternative expression is instead used to compute the associated entropy. The quasi-harmonic vibrational entropy is always less than or equal to the standard (RRHO) value obtained using Gaussian. Two literature approaches have been implemented. In the simplest approach, from [Cramer and Truhlar](http://pubs.acs.org/doi/abs/10.1021/jp205508z),¹ all frequencies below the cut-off are uniformly shifted up to the cut-off value before entropy calculation in the RRHO approximation. Alternatively, as proposed by [Grimme](http://onlinelibrary.wiley.com/doi/10.1002/chem.201200497/full),² entropic terms for frequencies below the cut-off are obtained from the free-rotor approximation; for those above the RRHO expression is retained. A damping function is used to interpolate between these two expressions close to the cut-off frequency. The second type of quasi-harmonic approximation available is applied to the vibrational energy used in enthalpy calculations. Similar to the entropy corrections, the enthalpy correction implements a quasi-harmonic correction to the RRHO vibrational energy computed in DFT methods. The quasi-harmonic enthalpy value as specified by [Head-Gordon](https://pubs.acs.org/doi/10.1021/jp509921r)³ will be less than or equal to the uncorrected value using the RRHO approach, as the quasi-RRHO value of the vibrational energy used to compute the enthalpy is damped to approach a value of 0.5RT, opposed to the RRHO value of RT. Because of this, the quasi-harmonic enthalpy correction is appropriate for use in systems and reactions resulting in a loss of a rotational or translational degree of freedom. #### Symmetry GoodVibes is able to detect a probable symmetry point group for each species and apply a symmetry correction to the entropy (S_sym) by finding a molecule's internal symmetry number using atom connectivity, and external symmetry with the help of the external open source C program, "Brute Force Symmetry Analyzer" developed by S. Patchkovskii. These numbers are combined to give a symmetry number, n, and S_sym is then defined as -Rln(n), which is applied to the GoodVibes calculated entropy. *Note: this option may not function properly on some versions of Windows.* #### Checks A computational workflow can become less effective without consistency throughout the process. By using the `--check` option, GoodVibes will enforce a number of pass/fail checks on the input files given to make sure uniform options were used. Checks employed are: ###### Gaussian Output Checks * Same version of Gaussian used across all output files * Same solvation state/gas phase used across all output files * Same level of theory and basis set used * Same charge and multiplicity used * Check if standard concenctration of 1 atm was used in calculation * Check for duplicate structures or enantiomeric conformers based on E, H, qh_T.S and qh_G with a cutoff of 0.1 kcal/mol * Check for potential calculation error in linear molecules by Gaussian * Check for transition states (one imaginary frequency in output file) * Check if empirical dispersion is used and consistent across all output files ###### Single Point Calculation Checks * Same version and program used for all single point calculations * Same solvation model used across output files * Same level of theory used across all output files * Same charge and multiplicity used * Same geometry coordinates for SPC and associated geometry optimized and frequency calculation output file * Check if empirical dispersion is used and consistent across all output files #### Installation * With pypi: `pip install goodvibes` * With conda: `conda install -c patonlab goodvibes` * Manually Cloning the repository https://github.com/bobbypaton/GoodVibes.git and then adding the location of the GoodVibes directory to the PYTHONPATH environment variable. * Run the script with your Gaussian output files (the program expects .log or .out extensions). It has been tested with Python 2 and 3 on Linux, macOS and Windows **Correct Usage** ```python python -m goodvibes [-q] [--qs grimme/truhlar] [--qh] [-f cutoff_freq] [--fs S_cutoff_freq] [--fh H_cutoff_freq] [--check] [-t temperature] [-c concentration] [--ti 't_initial, t_final, step'] [--ee] [--cosmo cosmo_filename] [--cosmoint cosmo_filename,initial_temp,final_temp] [-v frequency_scale_factor] [--vmm mm_freq_scale_factor][--ssymm] [--spc link/filename] [--boltz] [--dup][--pes pes_yaml] [--nogconf] [--graph graph_yaml] [--cpu] [--imag] [--invertifreq] [--freespace solvent_name] [--output output_name] [--media solvent_name] [--xyz] [--csv] [--custom_ext file_extension] <output_file(s)> ``` * The `-h` option gives help by listing all available options, default values and units, and proper usage. * The `-q` option turns on quasi-harmonic corrections to both entropy and enthalpy, defaulting to the Grimme method for entropy and the Head-Gordon enthalpy correction. * The `--qs` option selects the approximation for the quasi-harmonic entropic correction: `--qs truhlar` or `--qs grimme` request the options explained above. Both avoid the tendency of RRHO vibrational entropies towards infinite values for low frequencies. If not specified this defaults to Grimme's expression. * The `--qh` option selects the approximation for the quasi-harmonic enthalpy correction. Calling this argument requests the enthalpy correction option explained above. This replaces harmonic energy contributions with a quasi-RRHO vibrational energy term. If not specified the Head-Gordon expression is defaulted. * The `-f` option specifies the frequency cut-off for both entropy and enthalpy calculations (in wavenumbers) i.e. `-f 10` would use 10 cm^-1 when calculating thermochemical values. The default value is 100 cm^-1. N.B. when set to zero all th