tangelo.problem_decomposition.oniom package
Submodules
tangelo.problem_decomposition.oniom.oniom_problem_decomposition module
Our own n-layered Integrated molecular Orbital and Molecular mechanics (ONIOM) solver. User specifies either the number (if beginning from start of list), or the indices, of atoms which are to be identified as the model system(s), from the larger molecular system.
Main model class for running oniom-calculations. This is analogous to the scf.RHF, etc. methods, requiring however a bit more information. User supplies an atomic-geometry, and specifies the system, as well as necessary models, of increasing sophistication.
- Reference:
The ONIOM Method and Its Applications. Lung Wa Chung, W. M. C. Sameera,
Romain Ramozzi, Alister J. Page, Miho Hatanaka, Galina P. Petrova, Travis V. Harris, Xin Li, Zhuofeng Ke, Fengyi Liu, Hai-Bei Li, Lina Ding and Keiji Morokuma Chemical Reviews 2015 115 (12), 5678-5796. DOI: 10.1021/cr5004419.
- class tangelo.problem_decomposition.oniom.oniom_problem_decomposition.ONIOMProblemDecomposition(opt_dict)
Bases:
ProblemDecomposition- distribute_atoms()
For each fragment, the atom selection is passed to the Fragment object. Depending on the input, the method has several behaviors.
- get_resources()
Estimate the resources required by ONIOM. Only supports fragments solved with quantum solvers. Resources for each fragments are outputed as a dictionary.
- simulate()
Run the ONIOM core-method. The total energy is defined as E_ONIOM = E_LOW[SYSTEM] + sum_i {E_HIGH_i[MODEL_i] - E_LOW_i[MODEL_i]}
- Returns:
float – Total ONIOM energy.