Ubuntu Manpage: goodvibes - Python program to compute corrections to thermochemical data from frequency calculations

Provided by: python3-goodvibes_3.2+dfsg-4_all

NAME

       goodvibes - Python program to compute corrections to thermochemical data from frequency calculations

DESCRIPTION

       usage: goodvibes [-h] [-q] [--qs QS] [--qh] [-f FREQ_CUTOFF]

              [--fs  S_FREQ_CUTOFF]  [--fh H_FREQ_CUTOFF] [-t TEMP] [-c CONC] [--ti TI] [-v SCALE_FACTOR] [--vmm
              MM_SCALE_FACTOR] [--spc SPC] [--boltz] [--cpu] [--d3] [--d3bj] [--atm]  [--xyz]  [--csv]  [--imag]
              [--invertifreq [INVERT]] [--freespace FREESPACE] [--dup] [--cosmo COSMO-RS] [--cosmo_int COSMO-RS]
              [--output  OUTPUT]  [--pes  PES]  [--nogconf]  [--ee  EE]  [--check] [--media MEDIA] [--custom_ext
              CUSTOM_EXT] [--graph GRAPH] [--ssymm] [--bav {global,conf}] [--g4]

   options:
       -h, --help
              show this help message and exit

       -q     Quasi-harmonic  entropy  correction   and   enthalpy   correction   applied   (default   S=Grimme,
              H=Head-Gordon)

       --qs QS
              Type of quasi-harmonic entropy correction (Grimme or Truhlar) (default Grimme)

       --qh   Type of quasi-harmonic enthalpy correction (HeadGordon)

       -f FREQ_CUTOFF
              Cut-off frequency for both entropy and enthalpy (wavenumbers) (default = 100)

       --fs S_FREQ_CUTOFF
              Cut-off frequency for entropy (wavenumbers) (default = 100)

       --fh H_FREQ_CUTOFF
              Cut-off frequency for enthalpy (wavenumbers) (default = 100)

       -t TEMP
              Temperature (K) (default 298.15)

       -c CONC
              Concentration (mol/l) (default 1 atm)

       --ti TI
              Initial temp, final temp, step size (K)

       -v SCALE_FACTOR
              Frequency  scaling factor. If not set, try to find a suitable value in database. If not found, use
              1.0

       --vmm MM_SCALE_FACTOR
              Additional frequency scaling factor used in ONIOM calculations

       --spc SPC
              Indicates single point corrections (default False)

       --boltz
              Show Boltzmann factors

       --cpu  Total CPU time

       --d3   Zero-damped DFTD3 correction will be computed

       --d3bj Becke-Johnson damped DFTD3 correction will be computed

       --atm  Axilrod-Teller-Muto 3-body dispersion correction will be computed

       --xyz  Write Cartesians to a .xyz file (default False)

       --csv  Write .csv output file format

       --imag Print imaginary frequencies (default False)

       --invertifreq [INVERT]
              Make low lying imaginary frequencies positive (cutoff > -50.0 wavenumbers)

       --freespace FREESPACE
              Solvent (H2O, toluene, DMF, AcOH, chloroform) (default none)

       --dup  Remove possible duplicates from thermochemical analysis

       --cosmo COSMO-RS
              Filename of a COSMO-RS .tab output file

       --cosmo_int COSMO-RS
              Filename of a COSMO-RS .tab output file along with a temperature range  (K):  file.tab,'Initial_T,
              Final_T'

       --output OUTPUT
              Change the default name of the output file to GoodVibes_"output".dat

       --pes PES
              Tabulate relative values

       --nogconf
              Calculate a free-energy correction related to multiconfigurational space (default calculate Gconf)

       --ee EE
              Tabulate  selectivity values (excess, ratio) from a mixture, provide pattern for two types such as
              *_R*,*_S*

       --check
              Checks if calculations were done with the same program, level of theory and solvent,  as  well  as
              detects potential duplicates

       --media MEDIA
              Entropy correction for standard concentration of solvents

       --custom_ext CUSTOM_EXT
              List  of  additional file extensions to support, beyond .log or .out, use separated by commas (ie,
              '.qfi, .gaussian'). It can also be specified with environment variable GOODVIBES_CUSTOM_EXT

       --graph GRAPH
              Graph a reaction profile based on free energies calculated.

       --ssymm
              Turn on the symmetry correction.

       --bav {global,conf}
              Choice of how the moment of inertia is computed.  Options = 'global' or 'conf'.'global'  will  use
              the  same  moment  of  inertia  for  all input molecules of 10*10-44,'conf' will compute moment of
              inertia from parsed rotational constants from each Gaussian output file.

       --g4   Use this option when using G4 calculations in Gaussian

              Citation: Luchini, G.; Alegre-Requena, J. V.; Funes-Ardoiz, I.; Paton, R. S. F1000Research,  2020,
              9, 291.  GoodVibes version 3.2 DOI: 10.12688/f1000research.22758.1

NAME

DESCRIPTION

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