This manual describes PAMoC, a connected system of programs for retrieving a variety of properties from experimental and theoretical electron charge density distributions. It is designed as a complete reference to all of the program's capabilities. This manual aims to be an exhaustive and concise source of information to help you to become familiar with the application. The PAMoC documentation set is described in this chapter.
This manual is intended for researchers, teachers, and students who are interested in studying the properties of atoms and molecules by analyzing their electron probability density. It can also be of help in the classroom as a supplement to usual textbooks.
The Table of Contents shows how
this manual is organized. The brochure and the
Introduction give an overview of the
general features of PAMoC.
Two chapters, “The I/O system”
and “Data Input”, describe how
to communicate with PAMoC using keywords, environment variables, records and
files. The structure and syntax of specific data input decks are also defined.
The list of keywords and options is the
essential reference for the PAMoC user. A manual page for each keyword describes
in detail the purpose and the data input of the individual program modules,
with the aid of examples of data input and output of results.
The appendices describe details of running the program, and the installation
procedure.
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> 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.
The manual is being written for online use, and is expected
to be read using a browser. Therefore it makes extensive use of hyperlinks.
These may refer to a position in the current manual page or to a different page
of the manual. External links to pages or other resources on the World Wide Web
(WWW) are also frequently used.
In most cases, an unvisited link is presented
in blue, and a visited link is purple.
A hover link (mouse over) is red.
In addition, while the link is being activated (being clicked on), it bumps
down two pixel for a split second, giving the impression of being pushed down
in three-dimensional space.
References are usually signalled by numbers enclosed in brackets, […], at appropriate points in the text. Similarly, notes and external links are signalled by the capital letters N and L, respectively, followed by a number, and enclosed in brackets. All references, notes and external links signalled in a manual page (chapter) are listed in the appropriate sections at the end of the manual page, ordered according to their sequence number.
When the user hovers the mouse pointer over a reference numberThis “hover box” provides a short description of the item being hovered over., a tooltip appears, i.e. a small “hover box” with a short description of the reference being hovered over. The same happens with endnotes and external links.
In a few cases, notes and additional details are presented directly in the text in a hidden form. A small black right-pointing triangle (►) is used as a disclosure widget which indicates a closed status, with hidden additional information. The latter are presented on screen only when the widget is toggled into an “open” state, and the right-pointing triangle rotates to a small black down-pointing triangle (▼).
The latest information on PAMoC, 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:
These sites were hosted by the CNR Institute of Molecular Science and Technologies (ISTM, Milano, Italy) since 2001 and survived till november 2014, two years after the retirement of the author. Then, the PAMoC sites were lost during a restyling process of the ISTM web-site which is still far from being completed.
Hosted by Cloud Cannon, a Dropbox based content menagement system (CMS). Cloud Cannon takes the pain out of uploading and mantaining websites, as it pulls designer web files out of his dropbox. So, any change to this manual will be available on the web in a moment (including errors, of course: the author apologizes in advance for any inconvenience and ensures that he will try to fix that soon).
Hosted by Weebly, a free Web Designer Platform.
Hosted by Google Sites, a free web page-creation tool offered by Google as a part of the Google Apps productivity suite.
The release of PAMoC which is available for download is yellow highlighted. 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.
| Version or Revision Date |
Description |
| 2017 | New features: … |
| 2016 | New features: PAMoC can evaluate atomic charges by the Electronegativity Equalization Method. |
| 2015 | Updated features: the
radial integration
code has been 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 was restyled and the SG0 grid by Gill and Chien was 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 was
undertaken by the author (who called it
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, was 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 | PAMoC for the first time was 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:
|
| 1995 | It is the year of birth of PAMoC. The code has been originated
by merging of three
separate 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 code was intended to apply Bader's quantum theory of atoms in molecules and crystals to experimental electron charge distributions. It was interfaced to the VALRAY code by R.F. Stewart and M.A. Spackman, and it also implemented Spackman's model (1986) for calculation of intermolecular interaction energies. |