PAMoC's execution is controlled by user-prepared data. Input data are provided through:
The user input-file may be prepended by a default procedure or configuration file. PAMoC looks for the following configuration files
at first in the current working directory and then in the home directory. Configuration files are searched in the specified order, but only the first one which is found is read.
An auxiliary input file can be specified by the keyword inp (e.g., on the command line: -inp <aux-input-file>). Data provided on the configuration, standard input and auxiliary input files obey the same syntax rules, so that the three files are interchangeable. However, a hierarchy exists, so that data on the auxiliary input file override those on the configuration file, and data on the standard input file override those on the auxiliary input file.
Input data can be rather complex, like wavefunctions or the results of least-squares multipole refinement of experimental structure factors, so that they are usually stored on disk files, either in binary or ascii text format. However a lot of data are in the form of keywords with optional arguments and options, and can be provided also through the command line or as environment variables. A full list of the available keywords can be found in a separate section of this manual.
The C-shell UNIX command line to run a PAMoC job in background mode has the following syntax:
Syntax rules agree with the following notations. The “Lucida Sans Typewriter” monospaced font family denotes both UNIX commands (including the executable program name, pamoc.exe) and keywords recognized by PAMoC. UNIX commands are given in bold and are case sensitive. PAMoC keywords must be typed as shown, but they can be in upper, lower or mixed case. In addition, keywords are prepended by the minus sign, "-". Keywords which have the same meaning and produce the same action are enclosed in parentheses "( )" with a vertical bar "|" as the delimiter. 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 options. <italic> embedded in angle brackets "< >" is used for variables and options which should be replaced with actual values. Angle brackets "< >" can be omitted if no ambiguity occurs. Square brackets "[ ]" denote optional values.
Every UNIX process runs in a specific environment. An environment consists of a table of environment variables, each with an assigned value. C-shell environment variables are set by the setenv command, and displayed by the printenv or env commands, while the echo command is used to display a specified variabe, individually. The syntax of the command is:
where option is interpreted as a character string. If the string includes blanks (i.e. if it encompasses multiple values), enclose the string in double quotes (" "), e.g.:
At variance from the command line, here keyword must not be prepended with the minus sign "-".
Since input data can be rather complex, they are usually stored on disk files. Three types of data input files are mentioned above, namely the standard input file, the auxiliary input file and the configuration file. Other files can provide additional data input to specific sections of PAMoC and are addressed by specific keywords. Interface data files (IDF's) provide an interface between PAMoC and other computer packages, which are able to produce a representation of the electron density distribution of an isolated molecule or molecular crystal. Currently PAMoC is interfaced to ab initio electronic structure packages and to packages based on multipole refinement of experimental electron densities. Eventually, PAMoC accepts other types of IDF (e.g. CIF, CRYSTAL-XX print-output files, etc.). Of course, the actions that PAMoC will take, depend on the type and content of the IDF, and additional input data may be required.
Print output data are sent to the terminal (standard output) unless they are redirected to a disk file by the user. A print output file can also be specified by the keyword out (e.g., on the command line: -out <print-output-file>). In this case, most print output data are sent to the specified disk file and only a small piece of information may still be sent to the standard output (mainly for debugging purposes). In addition, PAMoC can generate output files either by itself or upon user request through specific keywords.
An interactive procedure, designed primarily for debugging
and testing purposes, was present in the PAMOC code, since its early
development.
Based on a cascade of menus, it was rather self explaining and easy to use.
To activate an interactive session, it was sufficient to launch PAMoC without
redirecting the standard input.
The two parts of the program, the one for batch execution and the one
related to the use of interactive sessions, shared many routines.
Changing one of these subroutines made it necessary to update both sections
of the program.
Unfortunately, urgency reasons (or simply author's laziness) favored the fact
that only the part for batch execution was updated. Thus the number
of bugs in the interactive part began to grow, making the user unhappy.
From the summer of 2012, 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). Since then, all the interactive pieces of code have been extracted from PAMoC and developed independently in the form of interactive user interfaces.