inputht

Generates a gaussian input files from the last geometry of gaussian output files or from the geometry of gaussian input files or a .xyz file using a Header and/or Tail Files which contain everything but the geometry and spin/charge ( which must be provided for .xyz files)

usage: pyssianutils inputht [-h] [-l] [-m MARKER | --no-marker] [-o OUTDIR]
                            [--step STEP] [-H HEADER] [-T TAIL]
                            [--charge CHARGE] [--spin SPIN] [--suffix SUFFIX]
                            files [files ...]

Positional Arguments

files

Gaussian Input/Output Files

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

-m, --marker

Text added to the filename to differentiate

the original file from the newly created one. For example, myfile.com may become myfile_marker.com

Default: 'new'

--no-marker

The file stems are kept

Default: False

-o, --outdir

Where to create the new files, defaults to the

current directory

Default: ''

--step

Will attempt to access the ith optimization step of

a gaussian output file to extract its geometry on all files provided. 'initial geometry'='1'

-H, --header

Header File that contains the queue, memory as well

as the gaussian calculation instructions. The output will start at the charge-spin line

-T, --tail

Tail File that contains the extra options, such as

pseudopotentials, basis sets

--charge

Net charge of the whole system

Default: 0

--spin

spin of the system

Default: 1

--suffix

Input suffix used for gaussian files, e.g. ".com"

Default: '.com'

Usage

The util inputht comes from Input from Head and Tail were both, head and tail refer to the top and bottom of a file. In general, in gaussian input files the geometry is placed in the middle of the file, where the actual calculation requested is in the top of the file and some extra input is placed at the bottom of the file. Thus, normally we find similar file headers for all optimizations to minima, optimizations to ts, single points... and the same for the file tails. inputht works on the basis of having stored two files, one with the header and one with the tail, and generating a gaussian input file from those.

Lets say we have the files:

minima.head

%nprocshared=2
%mem=4GB
#p opt freq pbepbe genecp nosymm

basis.tail

-C -O -N -H 0
6-31+g(d,p)
****

This type of setup allows the modification of the basis set with relative ease, and will not lead to an error if one of the atom types specified in the basis set section is missing.

We can now create a gaussian input by providing files containing geometries. For example, if we use gaussview, we can draw a specific geometry, check the charge and spin and save the file as example1.gjf without any specifics of the calculation. To generate the gaussian with the actual theory and keywords that we have selected:

$ pyssianutils inputht example1.gjf -H minima.head -T basis.tail --no-marker --suffix .com
example1.gjf

This command will generate a file named example1.com which will contain the charge, spin and geometry of example1.gjf, it will start with the contents of minima.head and it will end with the contents of basis.tail. If the --no-marker is not used, the generated file will have a "marker" in the file name. With the default marker the name would have been example1_new.com. The --suffix flag is not necessary in this specific case (as its default value is ".com") but controls the suffix of the generated files.

We can also specify multiple files instead of a single one:

$ pyssianutils inputht example*.gjf -H minima.head -T basis.tail --no-marker --suffix .com
example1.gjf
example2.gjf
example3.gjf
[...]

We may instead be interested in re-using a previous gaussian optimization for different reasons. We just need to provide the files.

$ pyssianutils inputht example*.log -H minima.head -T basis.tail --marker run2
example1.log
example2.log
example3.log
[...]

Here we specified --marker run2 to avoid overwriting the input files of the already existing input files from the outputs that we provided. By default the last geometry of the optimization will be used, and the charge and spin used in the calculation will be considered.

If we want to generate an input from a geometry that is not the last one of the calculation we can also do it with the --step keyword.

$ pyssianutils inputht example1.log -H minima.head -T basis.tail --step 10 --marker step10
example1.log

We can force a specific value of charge and spin by specifying the --charge and --spin flags:

$ pyssianutils inputht example1.gjf -H minima.head -T basis.tail --charge 0 --spin 1
example1.gjf

Attention

note that charge-spin consistency is not checked at this stage, so if you specified a wrong combination, the gaussian calculation will error out almost instantly.

Finally, if we generated the geometries with a different software, we can also use .xyz files.

$ pyssianutils inputht example1.xyz -H minima.head -T basis.tail --charge 0 --spin 1
example1.xyz

Note

However note that the --charge and --spin flags become specially relevant for .xyz files. Otherwise the default values will be used.

Two final remarks to consider is that if we want to provide a file listing all the files with the geometries that we want to use, we can simply use the --listfile flag and use the file with the list as input. The second remark is that we can mix the different types of file containing a geometry within the same command. In other words:

$ pyssianutils inputht example1.com example2.log example3.xyz -H minima.head -T basis.tail
example1.com
example2.log
example3.xyz

This command will yield correct inputs, but note that example3.xyz will have the default charge and spin, and specifying the --charge and --spin would instead force them into example1.com and example2.log.