PAMoC, an acronym for Properties of Atoms and Molecules in Crystals, is a complete system of programs for the analysis of both experimental and theoretical electron density distributions on an equal footing. 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.
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 basic functionality of the package is outlined below.
The results are presented with a clear, structured and attractive lay-out of the text in the output files.
The required citation for this manual is:
PAMoC output will display the references relevant to the property computed, when necessary.
The latest version of the PAMoC manual, including program updates, can be found at the following URL (Uniform Resource Locator, colloquially termed a web address):
which is actually the official web-site of PAMoC.
Other web-sites have been in use over the past few years, and some of them, or at least fragments thereof, can still be active or traceable.
The following list may serve as a disambiguation:
This report is not intended to be exhaustive, but simply to provide the reader with the opportunity to decide whether to make a new download. The release of PAMoC which is available for download is yellow highlighted.
|2019||The site “Electron Density Analysis with PAMoC” is restyled according to the guidelines expressed in the Kyle Siegrist's site Random|
|2018||New features: …|
|2017||New features: …|
|2016||New features: PAMoC can evaluate atomic charges by the Electronegativity Equalization Method.|
|2015||Updated features: the
code is rewritten to include several Gaussian quadrature rules
(Legendre, Laguerre, generalized Laguerre, Hermite, Chebyshev,
Gill-Chien) and different transformations of the radial coordinate
(Becke, Ahlrichs, Gill's MultiExp, Knowles Log-k, Handy),
in addition to the only quadrature scheme (Euler-Maclaurin with Handy
grid) in the “2010-07-27” version.|
Updated features: the grid pruning scheme is restyled and the SG0 grid by Gill and Chien is included.
|2014||New features: …|
|2013||New features: …|
|2012||2012 is the year of author's retirement.
From the summer of this year, a profound revision of the PAMoC code is
being undertaken by the author (who names it the
RV, ie Retirement
Version, due to the coincidence with the beginning of his retirement).
This fact had some consequences:
|2010-07-27||PAMoC, Version 2010-07-27, is made available for download on the web (gzipped, ELF 32-bit LSB executable, Intel 80386, version 1, statically linked, not stripped).|
|2010-07-23||New features: CRYSTAL-XX print-output files are seen by PAMoC as a new type of IDF.|
|2010-05-25||New features: CIF's files are seen by PAMoC as a new type of IDF. In addition, the interactive section of PAMoC can generate CIF's files.|
|2010-05-05||For the first time, PAMoC is made available for download
on the web (gzipped, ELF 32-bit LSB executable, Intel 80386,
version 1, dynamically linked (uses shared libs), not stripped).
The package comprises:
|1996||The PAMoC code originates from merging of three independent
codes developed at the CSRSRC
in Milano in the late 80's and early 90's: EXTREME (CSRSRC
Version by Mario Barzaghi, 1989), PROAIM (CSRSRC Version by
Mario Barzaghi, 1989), and proXray (by Mario Barzaghi and
Felicita Merati, 1993).|
EXTREME/CSRSRC and PROAIM/CSRSRC were locally-modified versions of Bader's codes which implement quantum theory of atoms in molecules to theoretical (ab-initio) electron charge distributions. The proXray program was aimed to apply Bader's quantum theory of atoms in molecules and crystals to experimental electron charge distributions. It was interfaced to the VALRAY code (R.F. Stewart and M.A. Spackman), and also implemented Spackman's model (1986) for calculation of intermolecular interaction energies.
Throughout the manual the following notations will be used. The “Lucida Sans Typewriter” monospaced font family denotes keywords recognized by PAMoC. These have to be typed as shown, but may be in upper or lower case. Keywords which have the same meaning and produce the same action are enclosed in parentheses "()" with a vertical bar "|" as the delimiter, i.e. ( keyword1 | keyword2 | … | keywordN ). A double vertical bar "||" is used to delimite two mutually exclusive options. Parentheses "( )" can be omitted if no ambiguity occurs. Keywords may require one or more parameters: italic text embedded in brackets "< >" is used for parameters and options which should be replaced with actual values. Brackets "< >" usually indicate a set of parameters and options and can be omitted if no ambiguity occurs. Square brackets "[ ]" denote optional keywords and options.