Energy Landscape Exploration

This is an attempt at describing the methods used in the double ended connect algorithm. For instructions on how to use it see the module documention and the documentation of functions therin. Also, there are examples in the examples/ folder describing how to use these routines.

Double ended transition state search

• Local Connect Algorithm
• Structure Alignment (pele.mindist)

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 transition states between two minima. The end result might look like:

                         TS2
            TS1        /    \
          /    \      /      \
         /       Min1         \
MinStart                       \
                                MinEnd

The global algorithm looks like this:

while MinStart and MinEnd are not connected:
    min1, min2 = get_next_minima_pair()
    local_connect(min1, min2)

The algorithm has two parts: get_next_minima_pair, and local_connect (psuedo-code names). get_next_minima_pair selects a pair of known, but, unconnected minima (min1 and min2) to try to connect. The algorithm which chooses this minima pair is designed to find the optimial path as quickly as possible between MinStart and MinEnd. Local connect does a nudged elastic band run between min1 and min2 in order to get transition state candidates. It then refines the transition state candidates to find actual transition states to the required tolerance. It then falls off each side of the transition state and minimized in order to find the pair of minima which the transition state connects.

See landscape for more complete documentation