Python library to compute statistical description of chemical systems in real-time without the need to write trajectories to disk. This allows one to collect high resolution distribution functions with roughly 4 orders of magnitude less disk space. In practice 100GB trajectory files have been replaced by 50MB state files.
This library is based around StatComputers which extract the necessary information from a sequence of simulation configurations to compute a specific distribution function. StatComputers are memory efficient in that they extract the minimal information from each configuration. The internal analysis code is implemented in Cython for efficiency. StatComputers are also restartable, in that they can be pickled to disk as part of a simulation restart file.
StatComputers are implemented for the following distribution functions:
- Isotropic pair correlation function (i.e. h(r) = g(r) - 1)
- 2-Dimensional pair correlation function
- 2-Dimensional orientation correlation function
- Bond angle about a common atom distribution
- Mean squared displacement function
- Velocity autocorrelation function
- Reversible bond duration distribution
rtchemstats is Licensed under the permissive Apache Licensed. See included LICENSE file.