1. PAMoC
  2. User's Manual, Click here to get a list of volumes,
    and eventually click an item to change the current volume.
  3. Introduction,Click here to get a list of chapters,
    and eventually click an item to change the current chapter.
  4. None.All sections are embedded in this page.

Introduction

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.

  1. Properties
  2. Structural Editing
  3. Graphics facilities to visualise the results

The results are presented with a clear, structured and attractive lay-out of the text in the output files.

How to cite

The required citation for this manual is:

Barzaghi, M. “Electron Density Analysis with PAMoC − Online User's Manual”, RV-2021, 2021. URL: https://pamoc.it.

PAMoC output will display the references relevant to the property computed, when necessary.

PAMoC on the WWW

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):

https://www.pamoc.it

which is actually the official web-site of PAMoC.

Site history

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:

 
PAMoC History and Release Notes

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.

Version or
Revision Date		 Description
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 radial integration 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:
  • moving from the computing facilities of the ISTM to the home computer [equipped with an Intel® CoreTM i7 3770 processor (8M Cache, up to 3.90 GHz)]
  • moving from Red Hat Enterprise Linux operating system to the UBUNTU Linux distribution.
  • moving from the Portland Group, Inc. (PGI) Fortran compilers to the GNU Fortran Compiler (gfortran).
  • revising the Fortran code thoroughly (a first compilation of the code by gfortran showed up a number of errors and a lot of diagnostic messages).
  • At the ISTM no one is in charge of the maintenance of the PAMoC code and the Online User's Manual (though the PAMoC website, including the download page will be hosted by the ISTM website till november 2014).
It was also an opportunity that gave birth to a new version of PAMoC. But the development of this new version was subject to some constraints:
  • Upgrading and mantaining PAMoC is no longer part of a job, but it has become simply a hobby.
  • Since family and social obligations have the highest priority, Pamoc developments are expected to be somewhat diluted over time.
but with some benefits
  • All the bureaucratic crap associated with public research are no longer a sword of Damocles and they ended up on the back burner.
  • PAMoC developments may follow different priority criteria, such as an elegant restyling, completeness of the design, care and deepening of the details, curiosity and fun. It can even happen that a page of the manual, with a clear, structured and attractive lay-out of the text, is published on the web before the drafting of the corresponding piece of code.
As a first step, all the interactive pieces of code have been extracted from PAMoC and developed independently in the form of interactive user interfaces.
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:
  • Reading most common versions of VALRAY binary data files.
  • Reading AIMPAC wavefunction files (.wfn).
  • Reading most of the XD ascii files.
  • 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.
The User's Manual is published online on the web site of the ISTM.
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.
 

Conventions and Notations

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.