Tutorial 0: Using the Tutorial

The IMPETUS + Tutorial and Model Files are available to download. The provided .tar files include the library for IMPETUS, the tutorial simulation files, main.cpp, and a makefile. It is recommended that users compile the program using OpenMPI as other compilers are not guaranteed to work.

Selecting the Tutorial Files:

The tutorial demonstrates how to build three different types of simulations: a basic molecular dynamics simulation using “CellSpace” MID, diffusion in a continuum field using “InteractiveField” MID, and a chemotaxis model where particles obey to particle dynamics equations and at the same time can detect the concentration continuum field by coupling a “CellSpace” and an “InteractiveField”. All tutorial files are located in the folder named “Tutorials”. To access different tutorials, adjust the included header file in main.cpp. Additional instructions are shown in the main.cpp file. There are four tutorial files:

·         1a) Simple NVE molecular dynamics simulation:

Tutorials/tutorialSimpleMD/simple.h

·         1b) NVE molecular dynamics simulation of a liquid:

Tutorials/tutorialSimpleMD/liquid.h

·         2) Solving the diffusion equation with the continuum field

Tutorials/tutorialHeat/heat.h

·         3) Simulating Chemotaxis

Tutorials/tutorialChemotaxis/chemotaxis.h

Compiling the Simulation:

We provide a makefile to compile the simulation. Confirm that the programs 'make' and OpenMPI are installed in your system. The user is responsible for providing the path to the OpenMPI compiler in the Makefile. If the IMPETUS library is not in the same folder, the user is also required to change the path of the IMPETUS library to the correct location.

·         To compile the program, use the command:

            make

·         Optionally, the user can clear up the object files by using make clean before make:

            make clean

            make

If the user is planning to use an MPI "machinefile", please modify the file named nodefile accordingly. After compilation, the command to run the program should look similar to:

      /home/shared/openmpi/bin/mpirun -n 8 -machinefile nodefile bin/impetus-run.exe