Calculating Pathways

Having found a transition state it is possible to find the corresponding minima (and pathway) by displacing the transition state along the transition vector in both senses and starting minimisations for each point. To make a complete path the data from one of these searches must be reversed and the results for the other side of the path appended to it. Shell scripts to do this automatically for all the transition states in a given directory, and to perform miscellaneous analysis of the pathways, exist for various potentials. The PATH keyword should now be used to calculate complete pathways given a transition state geometry in odata. Characteristics of the path, such as barrier heights, distances and the cooperativity index, are then produced automatically, along with a file containing the energy as a function of integrated path length (in EofS) and an xyz file containing the specified number of frames on each side of the path (in path.xyz).

Pathways are calculated by starting a minimisation of some sort after stepping off the transition state specified in odata. Using MODE values of 1 and -1 will give the two sides of the path. With SEARCH 0 (or 3) or LBFGS minimisation the resulting pathway will only be an approximation to a true gradient line. For search type 6 (or 7) and RKMIN or BSMIN the results should be close to the true steepest-descent path. Note that gradient lines are properties of the potential energy surface alone, and do not depend upon masses. Mass weighting, or calculating pathways in the fictitious space with a kinetic metric,[82] has now been implemented, but not in the BFGS minimisation or hybrid EF/BFGS routines.

From svn revision 24173 it is possible to follow a transition state search by a pathway calculation automatically. The transition state search can be specified by BFGSTS, including NOIT and NOHESS, or full eigenvector-following using SEARCH 2. The default minimisation uses eigenvector-following if no other method is specfied. Otherwise the paths can be calculated by specifying BFGSMIN, PMPATH, BBRSDM, RKMIN, or BSMIN. Example input and output can be found at http://www-wales.ch.cam.ac.uk/examples/OPTIM/. The following input is for a gradient-only hybrid eigenvector-following transition state search with pathways calculated using LBFGS energy minimisation:

MAXBFGS	0.2 0.2
DUMPALLPATHS
PATH	1000 0.0
MAXSTEP	0.1
MAXMAX	0.2
TRAD	0.2
BFGSTS	100 3 25 0.001
UPDATES	10 10
NOHESS
BFGSMIN	1.0D-7
CONVERGE	1.0D-4 1.0D-7
PUSHOFF	0.02
STEPS	200
BFGSSTEPS	5000
POINTS
etc.

The DUPALLPATHS keyword results in a path.info file being created, which can be read into a discrete path sampling database for PATHSAMPLE using the ADDPATH keyword for that program.