<commit_before>= SPCE2

* http://github.com/q10/SPCE2

SPCE is a program that simulates the behavior of ions in water interfaces according 
to the SPC/E model of water and ion solvation.  This is a Monte Carlo 
simulation program.  SPCE2 is a complete rewrite of the original SPCE program, 
with emphasis on speed, code parallelizibility, re-usability, testability.

= Install:

== Requirements:

* git
* g++
* make

== Instructions:

Pull code from GitHub:

    $ git pull <EMAIL>:q10/SPCE2.git

Then compile everything from inside the SPCE program folder into a binary:

    $ make

The following make flags are available:

    $ make          // default options (-O2 optimization applied)
    $ make o3       // -O3 optimization applied
    $ make o2       // -O2 optimization applied
    $ make o1       // -O1 optimization applied
    $ make o0       // no optimizations applied
    $ make remove   // delete the compiled executable SPCE
    $ make clean    // removes SPCE executable and *.o and *~ files everywhere

= Usage:

Simply run the following command on terminal:

    $ ./SPCE

== Flags:

The following program flags are allowed for a customized simulation.

-r:: Specify the system configuration file to import
-w:: Specify the name of the file to export the system configuration
-v:: Specify the name of the VMD (.lammpstrj) file to export the system configuration

All customizations must be specified in the config file that is to be used by the -r flag

Example Usage:

    $ ./SPCE -r=sample.config -w=output.config -v=output.lammpstrj

= Development:

* Source hosted at {GitHub}[https://github.com/q10/SPCE2].
* Report issues on {GitHub Issues}[https://github.com/q10/SPCE2/issues]

Pull requests are very welcome! Make sure your patches are well tested. Please 
create a topic branch for every separate change you make.

= License:

SPCE2 is licensed under the the New BSD License and may be freely redistributed 
under the terms specified in the {LICENSE}[https://github.com/q10/SPCE2/blob/master/LICENSE] file.<commit_msg>config_reader under rewrite but everything else is fine - re-architected simulation template class, hoepfully for the last time<commit_after>= SPCE2

* http://github.com/q10/SPCE2

SPCE is a program that simulates the behavior of ions in water interfaces according 
to the SPC/E model of water and ion solvation.  This is a Monte Carlo 
simulation program.  SPCE2 is a complete rewrite of the original SPCE program, 
with emphasis on speed, code parallelizibility, re-usability, testability.

= Install:

== Requirements:

* git
* g++
* make

== Instructions:

Pull code from GitHub:

    $ git pull <EMAIL>:q10/SPCE2.git

Then compile everything from inside the SPCE program folder into a binary:

    $ make

The following make flags are available:

    $ make          // default options (-O2 optimization applied)
    $ make o3       // -O3 optimization applied
    $ make o2       // -O2 optimization applied
    $ make o1       // -O1 optimization applied
    $ make o0       // no optimizations applied
    $ make mbar   // builds the MBAR program used to assemble data collected from umbrella sampling
    $ make remove   // delete the compiled executable SPCE
    $ make clean    // removes SPCE executable and *.o and *~ files everywhere

= Usage:

Simply run the following command on terminal:

    $ ./SPCE

Sample qsub scripts and metascripts that run SPCE on a grid engine, wait, and post-process data  are also available in the top level directory.

= Flags:

Flags are not implemented by default, to give the end users more choice in coding their simulation.  However, a ConfigReader class is provided that will build an example WaterSystem with customizations specified in a config file.  Please read the config output format to see how to take advantage of this.

= Development:

* Source hosted at {GitHub}[https://github.com/q10/SPCE2].
* Report issues on {GitHub Issues}[https://github.com/q10/SPCE2/issues]

Pull requests are very welcome! Make sure your patches are well tested. Please 
create a topic branch for every separate change you make.

= License:

SPCE2 is licensed under the the New BSD License and may be freely redistributed 
under the terms specified in the {LICENSE}[https://github.com/q10/SPCE2/blob/master/LICENSE] file.
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