COBRAMM SimPhoNy Wrapper

SimPhoNy wrapper for the COBRAMM engine developed at UNIBO.

The COBRAMM SimPhoNy wrapper enables modelling the electronic (UV-VIS) linear absorption (LA) spectrum of a solvated neutral molecule in its singlet ground state. The QM/MM COBRAMM engine developed at UNIBO is employed. COBRAMM performs hybrid QM/MM calculations by linking the Gaussian (QM) and Amber (MM) software packages.

An explicit atomistic MM model (Amber force field) is used for the solvent, while an explicit atomistic QM model (DFT/TDDFT) is used for the solvated chromophore. A classical equilibration of the solvent-solute system followed by a QM/MM optimization with Wigner sampling and QM/MM excited state calculations is employed to generate the LA spectrum and its bandshape. Vibrational progressions are not considered at this stage. The wrapper makes available to the user three different schemes of increasing complexity and computational time (Low, Medium, High) that do set parameters for MD simulations (boxsize, cutoff, initial optimization steps, time step of the MD run, heating time, time of the final equilibration steps) and QM/MM simulations (solvent droplet radius, mobile layer radius, number of samples produced in the Wigner sampling) of increasing complexity, accuracy and computational cost. Have a look at the documentation for further information and the workflow details.

Contact: Marco Garavelli (UNIBO)

Installation

This wrapper requires a working installation of COBRAMM 2.3. Please follow the installation guide and make sure that you have added the required directories to the PATH environment variable as described on it.

After that, clone the wrapper repository

git clone https://gitlab.cc-asp.fraunhofer.de/simphony/wrappers/cobrammwrapper.git

install the wrapper

pip install cobrammwrapper

and install the ontology.

pico install cobrammwrapper/cobramm.ontology.yml

Documentation

Visit the COBRAMM Wrapper's documentation to learn how to use the wrapper. You may also have a look at the examples folder for additional examples.

The documentation may also be built and displayed locally running the commands below.

pip install -r docs/requirements.txt
sphinx-autobuild --host 127.0.0.1 docs build

Testing

If you wish to verify that the wrapper is working as expected, you can run its test suite. Install the wrapper first and, after the installation:

1. Go inside the tests folder cd tests
2. Execute the command python -m unittest

This will run all tests in the test suite, and it will take approximately 1 hour to run them all. If you prefer you can just run one of them by specifying the name of the file.

python -m unittest test_engine.py

The suite is composed of three different tests

• test_end_to_end: It is intended to test the end to end interaction between application, wrapper and the simulation engine.
• test_session: It comprises both integration tests related to the interaction with the simulation engine and unit tests of the methods that are part of the SimPhoNy wrapper API.
• test_engine: This test suite contains unit tests for the simulation engine.