Getting Started

This guide walks you through downloading, running, and inspecting the results of your first MKMCXX simulation.

1. Obtaining the Software

To begin using MKMCXX, download the software package and unpack it on your machine. The package contains a single executable file in its bin folder:

• Windows: mkmcxx.exe
• Unix/Linux/macOS: mkmcxx

Note

No installation is required; you can run the executable directly. The binaries are designed to be portable and self-contained, allowing you to execute them immediately after download, without the need for additional setup, configuration, or dependencies.

In addition to the software, you will need a flat text editor to create and edit MKMCXX input files:

• Unix/Linux: vim or nano are usually preinstalled.
• Windows: We recommend using Notepad++ or Visual Studio Code.

2. Running the Program

Performing a simulation works somewhat different on Windows as compared to Unix. Please read the respective instructions below.

Windows

To run a built-in example simulation using MKMCXX, follow these steps:

1. Navigate to the Installation Directory
   Go to the folder where you unpacked the MKMCXX software package.

2. Open the Examples Folder
   Inside the main directory, open the examples folder.
   This folder contains several subfolders, each with a different simulation example.

3. Choose an Example
   Open one of the subfolders. You should see a file named input.mkm inside.

4. Open a Terminal in That Folder

5. Right-click in the folder (not on a file).

6. Select "Open in Terminal" (or similar option, depending on your system).

7. Run the Simulation
   In the terminal window, enter the following command to start MKMCXX with the provided input file:

   ..\..\bin\mkmcxx.exe -i input.mkm
   

   Tip

   Make sure the path to mkmcxx.exe is correct relative to the example folder you are in.

Once executed, MKMCXX will begin processing the simulation defined in input.mkm. You can explore and modify the input file to experiment with different simulation setups.

Unix/Linux/macOS

To run a built-in example simulation using MKMCXX on Linux, follow these steps:

1. Open a Terminal

2. Navigate to the Installation Directory
   Change to the directory where you unpacked the MKMCXX software package. For example:

   cd ~/Downloads/mkmcxx
   

3. Go to the Examples Folder Navigate into the examples directory:

   cd examples
   

4. Choose an Example Each subfolder contains a different simulation. For example:

   cd basic-reaction
   

   Inside, you should see a file named input.mkm.

5. Run the Simulation From within the example folder, execute MKMCXX using the relative path to the binary:

   ../../bin/mkmcxx -i input.mkm
   

   Tip

   Ensure that the binary has execute permissions. If needed, run:

   chmod +x ../../bin/mkmcxx
   

After running the command, MKMCXX will process the simulation defined in input.mkm. You can modify this file to explore different simulation setups.

3. Viewing the Results

The results of the simulation are written in a separate folder. The name of the folder starts with SR_, indicative for a sequencerun. Upon opening the SR_*** folder, you will see a list of folders for each temperature at which a simulation has been performed as well as a graphs and range folder. In the graph folder, you can find automatically generated graphs of your simulation. In the other folders, you will find the corresponding data files of your simulation. Below, two graphs are shown that can be found in the graphs/range.