Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions
The DDEC method is described in the following publication and references therein.
Thomas A. Manz and David S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials", J. Chem. Theory Comput., Vol. 8 (2012) 2844-2867. DOI
The program can be run using either Matlab or Fortran source codes, which yield identical numbers. The Fortran code is parallelized with OpenMP and runs much faster than the Matlab code.