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.

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.)

*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.

*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 \(\xi\).

*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`

.

*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.

*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.