SPECTRE

SPECTRE is a tool to compute optical properties of molecules in any homo- or heterogenous environment.

Requirements

Python

Preferably a version 2.7 during the initial development phase. Later (post 2020 version 3.6+)

Numpy

A version that ships with python. SPECTRE requires nothing fancy functionality-wise.

OpenBabel with Python bindings

Version 2.3 or higher. OpenBabel can be obtained from source on github or through your operating system package manager.

If you choose to install OpenBabel yourself remember to add your installation directory to the PYTHONPATH environment variable.

Ubuntu

On ubuntu the following should work

sudo apt-get install openbabel python-openbabel

FragIt

FragIt can be obtained from github.

Remember to add your installation directory to the PYTHONPATH environment variable.

CalcIt

CalcIt can be obtained from github.

Remember to add your installation directory to the PYTHONPATH environment variable. Remember to export the installation directory to CALCIT so SPECTRE can find it.

pepytools

peptyools can be obtained from github.

Remember to add your installation directory to the PYTHONPATH environment variable.

LoProp for Dalton

LoProp for Dalton can be obtained from github.

Remember to export the installation directory to LOPROP so SPECTRE can find it.

DALTON

Finally, you will need a licensed copy of the DALTON quantum chemistry program. See http://daltonprogram.org/ on how to obtain a license and the source code.

In order for SPECTRE to know where DALTON is you must export the DALTON environment variable that points to the folder where you compiled DALTON. SPECTRE also needs to know where CALCIT is installed (slave.py script imports stuff from calcit) For example

export DALTON=/path/to/where/dalton/was/built

Example

In the example folder type

spectre -v -f pe.ini -c CCN --ex-n 4 ccn.pdb

which will compute a spectrum (excitation energies and oscillator strengths) of the chromophores CCN in the ccn.pdb file. SPECTRE first computes the individual embedding potentials for each molecule in the ccn.pdb file. Hereafter, TDDFT calculations are carried out for each chromohore embedded in the embedding potential from all other molecules. An exciton-model is then constructed taking into account the screening effects of the environment. Finally, a stick-spectrum is written to disk for later post-processing.