fromage (FRamewOrk for Molecular AGgregate Excitations) is a library designed to support investigation of photophenomena in molecular crystals. Among the features are:

• Cross-program ONIOM-style calculations with different electrostatic embedding methods

• Location of energy minima and minimal energy conical intersections

• Command line geometry manipulation tools

• Evaluation of exciton coupling values using multiple schemes (under development)

The current version is 1.0

To cite the use of the program, please use:

Rivera, M., Dommett, M., Sidat, A., Rahim, W., Crespo‐Otero, R. fromage: A library for the study of molecular crystal excited states at the aggregate scale. J Comput Chem 2020; 1– 14. https://doi.org/10.1002/jcc.26144

And if you are using one of the ONIOM implementations:

Rivera, M., Dommett, M., Crespo-Otero, R. ONIOM(QM:QM′) Electrostatic Embedding Schemes for Photochemistry in Molecular Crystals. J. Chem. Theory Comput. 2019; 15, 4, 2504-2516 https://doi.org/10.1021/acs.jctc.8b01180

General

• 1. Program overview and install
• 2. Essential glossary
• 3. Tutorial for geometry optimisation
• 4. License
• 5. Contact
• 6. References

Theoretical background

• 1. ONIOM cluster models
  • 1.1. Embedded Cluster
  • 1.2. Ewald Embedded Cluster
  • 1.3. Self-Consistent Ewald Embedded Cluster
• 2. Ewald point charge fitting
• 3. Minimal Energy Conical Intersection optimisation
• 4. Population analysis
  • 4.1. Methods
  • 4.2. Crystal or molecular

Program documentation

• 1. Interfaces
• 2. Input file description
  • 2.1. config file
  • 2.2. fromage.in file
• 3. Structure manipulation in fromage
  • 3.1. The Atom object
  • 3.2. The Mol object
  • 3.3. The Dimer object
  • 3.4. IO
• 4. Miscellaneous scripts
  • 4.1. Assign charges
  • 4.2. Population statistics
  • 4.3. Pick a molecule
  • 4.4. Manipulate unit cell .xyz files
  • 4.5. Analyse dimers in aggregate geometries
  • 4.6. Voronoi volume evaluation
  • 4.7. Exciton coupling evaluation
  • 4.8. Exciton classification
• 5. fromage
  • 5.1. fromage package

References and indices

• References

• Index

• Module Index

• Search Page