This module implements routines for exploring the energy landscape. This primarily consists of using DoubleEndedConnect to find connected pathways of minimum -> transition state -> minimum between two minima.
Double ended transition state searches are the main technique we use for exploring the energy landscape. We attempt to try to find a connected series of minima and transition states between two end point minima.
| DoubleEndedConnect(min1, min2, pot, mindist, ...) | Find a connected network of minima and transition states between min1 and min2 |
The connect manager is a tool to organize which minima from a database are selected for double ended connect jobs.
| ConnectManager(database[, strategy, ...]) | class to manage which minima to try to connect |
| TSGraph(database[, minima, no_edges]) | Wrapper to represent a database object as a graph |
| database2graph(db[, Emax]) | make a networkx graph from a database |
| smoothPath(path, mindist[, density, ...]) | return a smooth (interpolated) path |
These are some core routines used by this module. The user probably won’t need to call them, but will want to know about them. Parameters for these routines can be changed by passing dictionaries to DoubleEndedConnect.
| LocalConnect(pot, mindist[, tsSearchParams, ...]) | a class to do a single local connect run, i.e. NEB + transition state search |
More core routines can be found in the documentation for the transition_states module