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

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

SEE ALSO