Introduction

PAMoC, an acronym for Properties of Atoms and Molecules in Crystals, is a complete system of programs for the analysis of experimental and theoretical electron charge density distributions. It can be used for the study of such diverse fields as organic and inorganic chemistry, crystallography, pharmacochemistry and biochemistry.

PAMoC is dedicated to providing easy-to-learn and easy-to-use electron density analysis tools for chemistry researchers. As distinct from other commonly used packages, the emphasis is on providing a tool to extract the biggest amount of information from a given set of experimental or theoretical results with the least effort for the user, so that working with PAMoC is quite easy and exciting even to the unexperienced user.

An interface data file (IDF), is all what is needed to run a PAMoC job. A number of output data files from other packages are recognized by PAMoC as an IDF, e.g. VALRAY binary data files, AIMPAC wavefunction files, Crystallographic Information Files (CIFs), CRYSTAL print-output files, etc.
The results are presented with a clear, structured and attractive lay-out of the text in the output files. Graphical facilities are also provided.

The heart of the program consists of the modules which implement Bader's Quantum Theory of Atoms in Molecules (QTAIM) based on the quantum chemical topology (QCT) of the electron density, and Spackman's experimental charge density approach (ECDA) to intermolecular non-bonded interaction energies. These are accompanied by a full set of supporting programs. The package comprises:

• Molecular electrostatic outer moments (charge through hexadecapole).
• Electrostatic inner moments at nuclear centres and at any given point (Potential, Electric Field, and Electric Field Gradient).
• Nuclear centred Distributed Multipole Analysis (DMA: Mulliken, Stone, Becke, Hirshfeld's stockholder partitioning, Bader's QCT atoms, and Stewart's pseudoatoms).
• Experimental charge density approach to energies of nonbonded interactions between molecules (Spackman's ECDA).
• Topological analysis of scalar fields: charge distribution (Bader's QTAIM).
• Bond path analysis (Bader's QTAIM).
• Computation of errors on the experimental electron density and the properties derived therefrom using the full variance-covariance matrix.
• Various utilities allowing geometry manipulations, general housekeeping operations.
• Graphics facilities to visualise the results.

PAMoC can be used in the background as well as in an interactive way.

The program is written mostly in standard Fortran-77 and it is suited for an Unix environment. It is compiled by using the GNU gfortran compiler under UBUNTU 16.04 operating system. The release of the program, described in this manual, is ported and tested on a personal computer equipped with an Intel^® Core^TM i7 3770 processor (8M Cache, up to 3.90 GHz). There is a comprehensive user's manual, which includes installation instructions. The manual is available in HTML for mounting on a Worldwide Web server.

Current limitations:

• The calculation of errors has some severe limitations at the moment, namely: only contributions from the multipole populations are currently taken into account (i.e. not kappa's or coordinates).
• Only Slater-type (single or multiple) radial functions must have been used for all multipoles in the least-squares fitting of the experimental charge density in a crystal (i.e. no Laguerre's).
• Only s, p , d, and f gaussian primitives must have been used in computing ab initio charge densities.