print

The print util allows the display through console of some key properties of the gaussian output files. There options are:

potential 

Prints the Potential energy. Defaults to the 'Done' of l502 or l508

usage: pyssianutils print potential [-h] [-l] [-o OUTFILE]
                                    [--method {oniom,mp2,mp2scs,mp4,ccsdt,default}]
                                    [-v]
                                    files [files ...]

Positional Arguments

files: Gaussian Output File(s)

Named Arguments

-l, --listfile

When enabled instead of considering the files provided as the gaussian output files considers the file provided as a list of gaussian output files

Default: False

-o, --outfile

File to write the Data. If it exists, the data will be appended. If none is provided it will be printed to stdout

--method

Possible choices: oniom, mp2, mp2scs, mp4, ccsdt, default

When not provided it will attempt (and may fail) to guess the method used for the calculation to correctly read the potential energy. Otherwise it defaults to the Energy of the 'SCF Done:'

Default: default

-v, --verbose

if enabled it will raise an error anytime it is unable to find the energy of the provided file

Default: False

Usage

The simplest way to use the print potential utils is to extract the potential energy of a single molecule:

$ pyssianutils print potential File1.log
File1.log     -11111

We can also specify multiple files manually:

$ pyssianutils print potential File1.log File2.log
File1.log     -11111
File2.log     -22222
$ pyssianutils print potential File*.log
File1.log     -11111
File2.log     -22222
File3.log     -33333

Another option is to provide a file where each line points to a gaussian output. pyssianutils will respect the order of the file, which may be useful for some users. For example lets assume a file name Files.txt with the contents:

Path/To/Files/File1.log
Path/To/Files/File3.log
Path/To/Files/File2.log

We can pass this file to pyssianutils with the -l flag:

$ pyssianutils print potential -l Files.txt
Path/To/Files/File1.log     -11111
Path/To/Files/File3.log     -33333
Path/To/Files/File2.log     -22222

Finally the --verbose or -v option will raise an error for files that do not have a potential energy and will stop the execution.

thermo 

Prints the Potential energy, Zero point energy, Enthalpy and Free energy from a gaussian frequency calculation. By default the Potential energy is the value of the 'Done'

usage: pyssianutils print thermo [-h] [-l] [-o OUTFILE]
                                 [--method {oniom,mp2,mp2scs,mp4,ccsdt,default}]
                                 [--only-stem] [-v]
                                 files [files ...]

Positional Arguments

files: Gaussian Output File(s)

Named Arguments

-l, --listfile

When enabled instead of considering the files provided as the gaussian output files considers the file provided as a list of gaussian output files

Default: False

-o, --outfile

File to write the Data. If it exists, the data will be appended. If none is provided it will be printed to stdout

--method

Possible choices: oniom, mp2, mp2scs, mp4, ccsdt, default

When not provided it will attempt (and may fail) to guess the method used for the calculation to correctly read the potential energy. Otherwise it defaults to the Energy of the 'SCF Done:'

Default: default

--only-stem

only show the file stem instead of the full path

Default: False

-v, --verbose

if enabled it will raise an error anytime it is unable to find the thermochemistry of the provided file

Default: False

Usage

The simplest way to use the print thermo utils is to extract the thermochemistry of a single calculation:

$ pyssianutils print thermo File1.log
File             E         Z         H         G
File1.log     -11111    -11111    -11111    -11111

If the thermochemistry is not available but the potential energy is available, only the potential energy will be shown

$ pyssianutils print thermo File1*.log
File               E         Z         H         G
File1.log       -11111    -11111    -11111    -11111
File1_SP.log    -11111

Hint

As with the potential util. We can specify multiple files either manually or using a file that contains one filepath per line.

Finally the --only-stem flag allows to shorten full filepaths to only the filenames, without the suffix:

Path/To/Files/File3.log
Path/To/Files/File2.log

We can pass this file to pyssianutils with the -l flag:

$ pyssianutils print thermo Path/To/Files/File1.log Path/To/Files/File1_SP.log --only-stem
File               E         Z         H         G
File1           -11111    -11111    -11111    -11111
File1_SP        -11111

which, without the flag would instead output

$ pyssianutils print thermo Path/To/Files/File1.log Path/To/Files/File1_SP.log
File                             E         Z         H         G
Path/To/Files/File1.log       -11111    -11111    -11111    -11111
Path/To/Files/File1_SP.log    -11111

summary 

Prints the Potential energy, Zero point energy, Enthalpy and Free energy from a gaussian frequency calculation. By default the Potential energy is the value of the 'Done'

usage: pyssianutils print summary [-h] [-l] [-o OUTFILE] [--with-sp]
                                  [--pattern PATTERN]
                                  [--method {oniom,mp2,mp2scs,mp4,ccsdt,default,default}]
                                  [--method-sp {oniom,mp2,mp2scs,mp4,ccsdt,default}]
                                  [--only-stem] [-v]
                                  files [files ...]

Positional Arguments

files: Gaussian Output File(s)

Named Arguments

-l, --listfile

When enabled instead of considering the files provided as the gaussian output files considers the file provided as a list of gaussian output files

Default: False

-o, --outfile

File to write the Data. If it exists, the data will be appended. If none is provided it will be printed to stdout

--with-sp

if enabled it will try to match the pattern provided to compute the SP corrections from the files that match the pattern to provide the final energies

Default: False

--pattern

pattern used when matching the SP files, defaults to 'SP'

Default: 'SP'

--method

Possible choices: oniom, mp2, mp2scs, mp4, ccsdt, default, default

When not provided it will attempt (and may fail) to guess the method used for the calculation to correctly read the potential energy. Otherwise it defaults to the Energy of the 'SCF Done:'

Default: default

--method-sp

Possible choices: oniom, mp2, mp2scs, mp4, ccsdt, default

When not provided it will attempt (and may fail) to guess the method used for the SP calculation to correctly read the potential energy. Otherwise it defaults to the Energy of the 'SCF Done:'

Default: default

--only-stem

only show the file stem instead of the full path

Default: False

-v, --verbose

if enabled it will raise an error anytime it is unable to find the thermochemistry of the provided file

Default: False

Usage

The simplest way to use the print summary utils is to extract the thermochemistry of a single calculation:

$ pyssianutils print summary File1.log
File             E         Z         H         G
File1.log     -11111    -11111    -11111    -11111

If the thermochemistry is not available but the potential energy is available, only the potential energy will be shown

$ pyssianutils print summary File1*.log
File               E         Z         H         G
File1.log       -11111    -11111    -11111    -11111
File1_SP.log    -11111

Note

For all terms and purposes print summary behaves like print thermo while the --with-sp is not specified.

When the --with-sp flag is enabled, the util will attempt to find files matching the name with a specific pattern at the end of the file stem (which may be specified with the --pattern flag. For the files in which it finds a match it will display the E(SP) and the G(SP) computed as

\[G_{SP} = E_{SP} + (G - E)\]

Therefore, going back to the previous example:

$ pyssianutils print summary File1*.log --with-sp
File        File_SP            E         Z         H         G       E(SP)     G(SP)
File1.log   File1_SP.log    -11111    -11111    -11111    -11111    -11111    -11111

print

potential

Positional Arguments

Named Arguments

Usage

thermo

Positional Arguments

Named Arguments

Usage

summary

Positional Arguments

Named Arguments

Usage

potential 

thermo 

summary 