https://github.com/berquist/td

Parsing and plotting of excited state calculations from Gaussian/Turbomole/ORCA.

https://github.com/berquist/td

Repository

Parsing and plotting of excited state calculations from Gaussian/Turbomole/ORCA.

https://github.com/berquist/td/blob/master/

# td

Parser for excited state calculations done with **Gaussian 09** (*td* keyword), **TURBOMOLE** (*escf* and *ricc2* module) and **ORCA** calculations.

The script tries to determine the program type from the supplied log file. For TURBOMOLE
calculations it expects *escf.out* or *ricc2.out* file names.

The script uses a slightly modified version of Sergey Astanin's **tabulate** module (https://bitbucket.org/astanin/python-tabulate) and **peakdetect** from Sixten Bergman. Thanks to them.

## Installation
Clone this repository with ``git clone https://github.com/eljost/td.git`` and run
``python setup.py install`` in the cloned directory.

The **argcomplete** module (https://pypi.python.org/pypi/argcomplete) has to be configured separately. When using **argcomplete** *td* looks for files with *.out* and *.log* extensions.

## Usage
Display the help message with all available commands:

	td -h

Common usage examples are the generation of broadened spectra from calculated excitation energies and oscillator strenghts according to http://dev.gaussian.com/uvvisplot/ and this paper https://dx.doi.org/10.1002/chir.20733. Spectra can be generated in two ways: Not normalized ( in l mol cm) or normalized with the brightest  peak set to 1 (/_max). The spectrum is printed to STDOUT.

### Easy plotting of UV absorption spectra

    td.py [log] --plot [nm or ev] [--peaks] [--plotalso [additional logs to plot]]


### Verbose MO names 
Verbose MO names can optionally be loaded from a *mos.json* file with the following format:

	{
		"[MO number] [MO irrep] : "[verbose name]",
		e.g.,
		"61 a'" : "d",
		"39 a\"" : "d"
		
		! The last entry must NOT have a comma at the end
	}

The *mos.json* file must reside next to the parsed log file.

### Spectrum generation

td exports the spectrum (x) for x in two different units: *nm* and *eV*. The first two blocks hold the spectrum and the oscillator strength impulses in *nm*, the third and fourth blocks hold the same data in *eV*. Within *gnuplot* the data blocks can be easily accessed by with the *index [id]* command.

#### Normalized spectrum with (/~max~) on the ordinate:

	./td [fn] --spectrum [from in nm] [to in nm]  > [outfn]
	
#### Non-normalized spectrum with  on the ordinate:

	./td [fn] --spectrum [from in nm] [to in nm] --nnorm > [outfn]
	
#### Oscillator strength scale on the ordiante
When used with the argument  *\-\-e2f* the molecular extinction coefficients on the ordinate will be converted to an oscillator strength scale.

	./td [fn] --spectrum [from in nm] [to in nm] --e2f --nnorm > [outfn]
	
#### Dealing with different multiplicities
A constant shift in a.u. can be added to the excitation energies with `--enoffset`. This may be useful when one has a calculation with triplet-triplet excitation energies and wants to relate these energies to the corresponding singlet groundstate energy. Additionally all oscillator strengths can be zeroed with `--zeroosc`.

### Filtering

To investigate a **Gaussian 09** excited state optimization it may be useful to split the output in chunks, where chunks should correspond to the number of calculated roots at every step of the optimization:

	./td [fn] --chunks [roots]

Only show transitions with an oscillator strength greater than or equal to a supplied threshold and sort by oscillator strength:
	
	./td [fn] --fthresh [thresh] --sf

### Exporting
Several export-formats are available:

| Format | Argument | Comment |
| --------- | ------------- | ------------- |
| booktabs | \-\-booktabs | To be used in .tex-documents (doesn't export transitions and weights yet).|
| raw | \-\-raw | Export without any formatting. |
| docx | \-\-docx | Export to an .docx-document. Needs python-docx-module. |
| tiddlywiki | \-\-tiddly | Export as a tiddlywiki-table. |
| csv | \-\-csv | Export as CSV. |

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