Appendix B. Directory Structure of the AMS Package
**************************************************

Below is the list of major parts of the AMS package.


The bin directory
=================

When the package is installed, the executable files are placed in
$AMSHOME/bin.  The binary executable file is usually called 'ams.exe',
'reaxff.exe', and so on. On Windows  it is ams.3.exe, reaxff.3.exe,
etc. There will also be files called just 'ams' or 'reaxff'. The
latter are shell scripts that execute the corresponding binaries.

You should use the script files, rather than the executables directly.
The script files provide a correct environment, and if needed prepare
for running in parallel and then launch the binary using the correct
mpirun command. See also the sample run scripts and the Examples
document.

The $AMSBIN/setenv.sh and $AMSBIN/start scripts take care of setting
up the environment and starting the binaries. If necessary, it parses
the information provided by a batch system and sets up a machinefile
(or an appfile) and runs tasks in parallel. Edit the file if you need
to customize the way MPI programs are started.


The atomicdata directory
========================

The directory atomicdata/ contains a large amount of data needed by
programs from the AMS package at run time. For example, it contains
basis sets for all atoms. Generally you should  **not** modify any of
the files in this directory.

The basis sets are described in detail in the ADF manual and BAND
manual


The data directory
==================

The directory data/ contains files needed for running the programs and
GUI from the AMS package. No modifications should be made to the files
in this directory.


The examples directory
======================

The directory examples/ contains sample script and output files. The
files with extension .run are shell scripts that also contain embedded
input. Thus, these files should be executed, and not given as input to
AMS.

The example calculations are documented in the ADF Examples
documentation, and BAND Examples documentation.


The src directory
=================

The source files are only visible if you have a copy of the source
code distribution. The source code files found in the program and
library directories and subdirectories thereof have extensions .f,
.f90, .c or .cu and contain FORTAN or C/CUDA code. Other source files
are include files (files with extension .fh or .h). When compiling,
the object files are generated in the folder $AMSHOME/build, and
archived into libraries.

Compilation is done by $AMSBIN/foray, and the configure options are
located in $AMSHOME/Install/-machinetype-/Forayflags.

The Install directory contains a configure script, some data files
which provide generic input for configure (start,  starttcl, and some
more), a portable preprocessor cpp (based on  Mouse cpp) and machine-
specific files that are unpacked into the bin folder (precompiled
packages), or the build folder (precompiled libraries). The machine-
specific folders start with x86 or x86_64.


The Utils directory
===================

The Utils/ directory contains the "run_test" script and two "rc"
scripts. The run_test script can be used to run examples from the
examples/ folder and validate their output. The amsrc.sh and amsrc.csh
can be used instead of the amsbashrc.sh script in case one uses a
C/TC/Z-shell (amsrc.csh), or if bash needs to be avoided (amsrc.sh).


The Doc directory
=================

All the user documentation for AMS is present in html format in
$AMSBIN/Doc.  Documentation is also available on the  SCM website


The scripting directory
=======================

This directory contains some useful scripts that are part of the AMS
package.
