CH2O coordinate manifolds and their analysis for the paper "A global view of reactive coordinate manifolds from nonlinear dimensionality reduction"

This dataset contains the the following data created for the paper "A global view of reactive coordinate manifolds from nonlinear dimensionality reduction" by Dmitrij Rappoport.

The data was generated using the manic open-source code that is publicly accessible at https://bitbucket.org/rappoport/manic/.

All the data in this dataset is for the CH2O coordinate manifold

Data listing:

MCMC chains (using uniform sampling, average-distance weighted sampling, Jacobian-norm weighted sampling)
- mcmc/uniform-sampling
- mcmc/ave-distance-weighted
- mcmc/jacobian-norm-weighted

MLE dimension estimates (from uniform sampling, average-distance weighted sampling, Jacobian-norm weighted sampling)
- mle/uniform-sampling
- mle/ave-distance-weighted
- mle/jacobian-norm-weighted

Isomap embeddings for d = 2, 3, 4, 6 (from uniform sampling, average-distance weighted sampling, Jacobian-norm weighted sampling)
- isomap/uniform-sampling
- isomap/ave-distance-weighted
- isomap/jacobian-norm-weighted

LLE embeddings for d = 2 (from uniform sampling)
- isomap/uniform-sampling

Embedding of critical points of the CH2O PES in coordinate manifolds (from uniform sampling, average-distance weighted sampling, Jacobian-norm weighted sampling)
- isomap-nystrom/uniform-sampling
- isomap-nystrom/ave-distance-weighted
- isomap-nystrom/jacobian-norm-weighted