/*
* Simpatico - Simulation Package for Polymeric and Molecular Liquids
*
* Copyright 2010-2012 David Morse (morse@cems.umn.edu)
* Distributed under the terms of the GNU General Public License.
*/

Simpatico is a C++ package for Monte Carlo (MC), Molecular Dynamics 
(MD) and hybrid MD/MC simulations of classical mechanical models of
polymeric and molecular liquids. It contains:

- Programs for Monte Carlo (MC) and molecular dynamics (MD) 
  simulations on a single processor, named mcSim and mdSim.

- A program for parallel MD simulations, named ddSim.

The parallel MD program ddSim uses a domain (or spatial) 
decomposition algorithm for parallelization.
   
Getting the Source Code:
------------------------

Simpatico source code may be obtained either by downloading 
a tar filefrom the github project web page
<http://dmorse.github.com/simpatico/index.html> 
or by using git to cloning a working tree from
<https://github.com/dmorse/simpatico>.
Either method gets you a current copy of the master branch from 
the git repository.

If you download a tarball, the tar file will be named something
like dmorse-simpatico-id.tar, where "id" denotes a denotes a 
hexadecimal identifier for the most recent commit to the git 
repository.  When you extract the tar file (tar -xvf), the 
source files will be extracted into a directory with the same 
name, dmorse-simpatico-id/.  To recreate the same directory 
structure as that used in the repository, in which the root 
directory is named simpatico/, you may want to rename this root 
directory to simpatico/, before running the ./setup script.
To unpack the tar file and move the directory, enter:

   > tar -xvf dmorse-simpatico-id.tar
   > mv  dmorse-simpatico-id simpatico

from the directory that will contain the simpatico root
directory. If you mv the root directory after running the 
setup script (see below), you must rerun the script. 

Documentation:
--------------

Web pages that provide both user and developer documentation for
Simpatico is prepared using the Doxygen utility (www.doxygen.org). 
Doxygen creates html web pages that are deposited in the directory 
doc/html/ of the working tree. These pages are created from 
comments extracted from the C++ source code, and from a set of 
text files in the directory doc/manual/. These text files, which 
have the file extension *.dox, contain the text for a set of 
introductory documentation pages, and are readable in any text 
editor. 

A recent copy of the documentation is available online, at
<http://dmorse.github.com/simpatico/index.html>.

After getting a copy of the source code (either by download or by 
cloning the git repository), you can use dOxygen to generate a 
local copy of the html documentation within the simpatico/doc/html 
directory of the source code tree.  This requires that dOxygen 
be installed on your computer and that the executable be in a 
directory in your PATH. The basic instructions (after dOxygen is 
installed) are:

  - cd to the simpatico/doc directory
  - Enter "make html"

This should create a large set of html files in the 
simpatico/doc/html directory. To begin reading the documentation, 
point a browser at the file simpatico/doc/html/index.html.

Compiling:
----------

The code is standard C++ and must be compiled from source. 
Multi-processor programs (ddSim and multi-processor versions of 
mcSim and mdSim) require an MPI library. By default, the build
system requires access to a python interpreter, though this
dependence can be removed. Complete instructions for compiling 
various versions of Simpatico are given in the text file 
simpatico/doc/manual/user/compile.dox, or in the corresponding 
html web page in the doc/html directory.

Short instructions for compiling the default single-processor 
versions of mcSim and mdSim (for the impatient) are:

- Add the simpatico/tools/python directory to your PYTHONPATH
  environment variable.

- cd to the simpatico root directory

- Enter "./setup" to run a setup script

- Enter "make mcMd"

The resulting executables, named "mcSim" and "mdSim", will be 
installed in the simpatico bin/ directory. Further instructions
for compiling multi-processor programs, and for enabling or
disabling various compile-time features, are given in the text
and html documentation.