The goal of self-consistent optimization of the reaction path (RP) is usually to obtain an initial guess for Transition State Search or an approximation to the barrier. Methods that use reactant and product structure to compute the RP are often referred to as ’double-ended’ methods or, if the the RP is discretized, ’chain-of-states’ methods. [45–47]
The RP connects reactant and product, its highest point being the transition state. It is a steepest descent path, which means that its tangent t is always parallel to the gradient g. The RP is in actual calculations discretized by a finite number of structures n. The tangents are parallel to the gradients for all structures i = 1,..,n. Assuming normalized tangents tiTti = 1, this can be written as:
|0 = (1 - titiT)g i||(5.5)|
The structure of the optimization is the same as in other TURBOMOLE structure optimizations: As the jobex script drives optimizations by calling statpt/relax as well the SCF and gradient modules.The woelfling-job script drives optimizations by calling woelfling as well as the SCF and gradient modules. The woelfling-job scripts reads the current path from file path.xyz which is the output of the woelfling program. woelfling-job then creates folders to run the calculations of each structure in, gathers coordinates and gradients, and then calls woelfling again.
The aim of RP optimization is usually not to optimize the RP to some accuracy, but to obtain an initial guess for a TS optimization. It is in general not possible to find a convergence criterion (and a corresponding threshold) that guarantees a good initial guess. The maximum number of iterations and the convergence threshold are therefore relatively high and tight. One can extract a TS guess also during the course of the optimization. If the TS search is successful (or not) you can stop (or restart) the RP optimization. Apart from simply killing the program you can add a ’stop’ file in the (scratch) directory, in which the script runs. It will then terminate at the end of the current cycle and can easily be restarted.
Options can be modified using keywords in the $woelfling data-group. The most important options are:
The values above are the default values. If $woelfling is missing, it will be added during the first woelfling run and default values will be set. Most importantly, ncoord is the number of input structures provided, ninter is the number of structures to be used for discretization of the path and maxit is the number of cycles to run. If maxit 0, structures will be rotated/translated to minimize the cartesian distance, for maxit 1 strutures will be used as provided. Using method qg instead of method q, a reaction path will be grown as in the growing string method. To start a RP optimization you need to provide at least a reactant and a product structure ncoord ≥ 2. You may provide more structures if you have a guess for the reaction path. The input structures will be used to compute an initial guess with ninter structures that is then optimized. Reactant and product structure will stay fixed throughout the optimization. All structures have to have the same ordering of atoms!
The input structures are provided in a file coords, which contains merged coord files. All ncoord structures are given in the right order in the typical TURBOMOLE coord format.
Minimum Input/Quick and Dirty
It is usually a good idea to check the initial path before starting the calculation. Once you have prepared the input, simply run woelfling directly and check path.xyz. If it looks reasonable, just run the woelfling-job script.
Unsuccessful Optimization If there is no reasonable TS guess or a frequency calculation does not give the correct number of imaginary frequencies, you can:
If the calculation crashed ’on its own’ it is likely that the SCF failed to converge - improve the corresponding options. If the optimization crashed in the middle of the run, it is most likely that it crashed during a SCF or gradient step, since basically all cpu time is spent there. In that case, remove at least the folder where the SCF and gradient program had been running when the program crashed. The files necessary for woelfling should be intact and you can simply restart it.
Restart - more details If the files are not intact, one can still use the optimized coordinates in one way or the other. There are basically three phases which are explicitely indicated by the number of iterations riter =:
Therefore repeated execution of woelfling will yield the same output (unless new energies/gradients are computed). The woelfling-job script takes care of the file-handling and should enable restart at any time. If files are damaged it will be hard to gather gradients and corresponding hessian- and oldgradient-information. If you have an intact gradients or oldgradients-file (necessary condition: number of lines=(3 + 2 × natoms)×number of structures), name it gradients, set riter in the control-file to 1 and restart. If those file are not intact, you can extract whatever structure information you have obtained and use it to provide a better initial guess: Modify file coords and ncoord in the control-file accordingly, set riter to 0 and restart.