The Computational Chemistry Comparison and Benchmark Database (CCCBDB) contains links to experimental and computational thermochemical data for a selected set of gas-phase atoms and molecules as well as tools for comparing experimental and computational ideal-gas thermochemical properties.
PyQuante is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed.
To make a density map from a 2D set of data, the first step is to compute values for the third dimension. (Gnuplot has no facilities for computing these values automatically.) The simplest way is to make a 2D histogram; the plot is divided in small 2D regions, and the z-values are proportional to the number of points inside these regions. The following Python script will make an histogram from a time series of two dihedral angles.
P. Woodland, J. Odell, V. Valtchev, and S. Young. Proceedings of the 1994 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
, 2, page 125-128. Adelaide, Australia, (April 1994)