All the TRIPLES keywords have been retired, i.e. TRIPLES, ADDTRIPLES, STARTTRIPLES. These should be removed from all pathdata files in the future. All path.info files produced by OPTIM are now in the triples format, whether generated by DUMPPATH or DUMPALLPATHS. This change means that the getallpaths subroutine is used to read all path.info files, and that the getnewpath routine is obsolete.
DIJINITSTART and DIJINITCONT can now have an additional argument to specify the number of entries in the sorted list of metric values that is dumped in file pairdist.
The NGT keyword has been added for a new graph transformation procedure. This routine can calculate , and for both and , as well as committor probabilities, in one call. This is now the recommended way to calculate rate constants.
The DIJINIT keyword has been replaced by two separate keywords, namely DIJINITSTART and DIJINITCONT, to simplify the generation of initial paths.
DIJINITSTART is intended for automatic setup of the min.A, min.B, min.data, ts.data, points.ts and points.min files from initial odata.start and odata.finish files. In contrast to the previous philosophy, DIJINITSTART will overwrite database files if they already exist. Hence it is possible to wipe an existing database with this keyword.
DIJINITCONT is intended for continuation of initial path searches that have not yet completed. It can also be used to start a run if the required database entries for two end points have been created by hand. DIJINITCONT will check that the required files are present in the current working directory, and stop if they are not.
The MFPT calculation for the fastest steady-state path (ignoring recrossings) in a DIJKSTRA calculation has been changed to the graph transformation approach.
The printing of rate constants at the end of a GT calculation has been changed to make it clear which values are calculated assuming that detailed balance holds. An extra summary line with the non-detailed balance rate constants is printed at the end.
After each cycle over the available CPU's PATHSAMPLE will now check to see if the file pathdata.change exists in the current working directory. If it does, then pathdata.change is copied to pathdata and all parameters are reread using keyword. This feature is designed to allow for change of parameters during a run without the need to kill and requeue a job. Attempts to change variables that affect declarations of array bounds will cause the program to crash.
David Wales 2018-01-18