Reaction Simulation (RS) Documentation

We have written a basic manual, which describes the simulation approach and the usage of RS:

RS Manual (PDF)

Installation guide:

Prerequisites

Operating systems

RS is implemented in the Lua scripting language. Therefore, in standalone mode RS only needs a working Lua interpreter, which is available for every major operating system (Windows, Mac, Unix/Linux).

In combination with SIMION/SDS, RS needs (obviously) a working installation of SIMION, which is a Windows program, is required. Fortunately, SIMION works under the wine runtime environment without major problems. Wine allows to run Windows software under Unix-like operating systems. Thus, to run SIMION/SDS-RS under Unix a working wine installation is needed too.

The open source part of RS is hosted on github. If you plan to contribute to the development of RS or want to stay in touch with the project, a github account would you allow to do this very conveniently. Github is based on the widely used open source version control system git which we also use to manage the RS source code. The github help pages are a very good source for information to become familiar with git and help with the initial git setup.

Get RS source code

Source download without git

Simply download the ZIP file of the RS repository from the source code page. Extract it into a local folder of your choice.

Source checkout with git

To checkout the RS sourcecode with git, clone the RS repository from github:

git clone http://github.com/IPAMS/RS localFolderName

Combine RS code with proprietary code

To combine the open source RS code with the proprietary RS parts (primarily the SDS collision model) you can either copy the SDS parts into the cloned RS folder or link to the installed SDS parts.

Copy SDS into RS folder Copy the following files from the SDS folder (SIMION-Folder/examples/collision_sds) to the RS folder:

  • arraylib.lua
  • collision_sds.lua
  • m_defs.dat
  • mbmr.dat
  • p_defs.dat
  • t_defs.dat
  • textfilelib.lua
  • vx_defs.dat
  • vy_defs.dat
  • vz_defs.dat

Alternatively you can change the SDS import path in RS_collision_sds.lua to the actual SDS path.

For example change the line

local SDS = simion.import('collision_sds.lua', '8.1.1.15.20120807 noinstall')

in RS_collision_sds.lua to

local SDS = simion.import('C:/Program Files/SIMION/examples/collision_sds/collision_sds.lua', '8.1.1.15.20120807 noinstall')

Test installation

After the installation process, the test SIMION project (test.iob) should work without problems. You shold see a bunch of reacting ions drifiting in an uniform electic field after pressing “Fly'em”