5. Running RPMDrate

Once the input file and exposed the Fortran potential function to Python have been set up, everything is ready to run the RPMD calculation. To do this, invoke the main rpmdrate.py script, passing the input file, temperature, and number of beads as command-line arguments:

$ python rpmdrate.py examples/H+CH4/input.py Temp Nbeads

where Temp is the temperature and Nbeads is the number of ring polymer beads. RPMDrate is also designed to exploit multiprocessor systems. To specify the number of processors, use the -p flag. For example, the following indicates that eight processors are available for RPMDrate to use:

$ python rpmdrate.py examples/H+CH4/input.py Temp Nbeads 1 -p Nprocs

where Nprocs is the number of requested processors.

5.1. Browsing RPMDrate output files

RPMDrate generates a large number of output files for each calculation. These are sorted into subfolders Temp/Nbeads by temperature and number of beads, so that the same input file can be used by multiple RPMD calculations. RPMDrate will also use these output files for restarting incomplete jobs, to avoid repeating already-finished steps in the calculation. (Biased sampling and transmission coefficient calculations are the most time consuming steps. During these steps, the program creates a series of checkpoints which allow RPMDrate to be safely stopped at any point in its execution and then to be restarted later.)

  1. Initial configurations for umbrella integration

The computed initial umbrella configurations are saved to umbrella_configurations.dat in the top-level directory, as these configurations can be used in subsequent calculations. This file contains the Cartesian coordinates in atomic units for each configuration.

  1. Biased sampling

The computed values for the mean \(\overline{\xi }\) and variance \(\sigma^2\) of the reaction coordinate are saved to a set of files named umbrella_sampling_*.dat after each trajectory run, where * represents the position of center of the window along the reaction coordinate \(\xi\).

  1. Potential of mean force

The potential of mean force as a function of the reaction coordinate is saved to the file potential_of_mean_force.dat.

  1. Transmission coefficient

The computed value of the transmission coefficient (recrossing factor) is saved to a file named recrossing_factor_*.dat, where * represents the value of the reaction coordinate \(\xi\) at which this factor was computed.

  1. Ring polymer rate coefficient

The final value of the RPMD rate coefficient, along with a summary of the various intermediate values used to compute it, is saved to a file named rate_coefficient_*.dat, where * represents the value of the reaction coordinate \(\xi\) at which the transmission coefficient was computed. Note that the same value of the reaction coordinate \(\xi\) is used to obtain the centroid-density quantum transition state theory rate coefficient and the recrossing factor.