Dijkstra test.py

What is it and why is it important?

For large distances in PATHSAMPLE it can happen that many minima are found around the provided A and B minimum, but not between them. At some point this means, there are no entries in pairlist or ts.data that connect A and B. PATHSAMPLE then attempts to connect A and B and will repeat this until it finds a new minimum that reconnects A and B (this is however very unlikely to happen). The script runs a Dijkstra shortest path search over the graph formed by all minima as vertices and the edges are taken as the transition states (with weight 0.0) and the entries of pairlist with weights taken from pairdist.

How do I use it?

./dijkstra_test.py  minA  minB [True/False]

The last argument allows for some additional printing, the default is False. You need networkx and numpy to run the script, so make sure you have loaded these modules (for example module load anaconda/python2/2.4.1).

Where can I find it?

It is in the svn/SCRIPTS/PATHSAMPLE directory