Molecular Dynamics Simulation with C++

Report

the report can be found in the Report folder here: report

Structure of the project

The main branch is the main branch, it has the most updated codes and the most updated report. And you can run all milestones from this branch. But just in case if some milestone doesn't work, you can switch to the corresponding branch (it starts with ready-milestone*) to run the milestone.
Also there exist two branches to run milestones 7 and 8 on the cluster (it starts with rmilestone*-on-cluster), it's basically the same codes as the ready-milestone* branchs, but different directory structure.

Milestone 08 (main branch) in here: milestone 08 has the parallel version of the code, so you need to compile it with mpic++ compiler. and to use the parallel version you need to run the code with mpirun command. While all other milestones can be compiled and run with g++ compiler.

How to change the parameters of the simulation according the report:

Milestones 4, 5, and 6:

• The parameters exist in the corresponding main.cpp file, you can change the parameters there, and make sure to change the directories as well.

Milestone 7,8:

• The parameters are in a new class called the SimulationData and can be found in the simulation_data.cpp file.
• In the same file,you will need to change the directories for outputs in here and here.
• Note: milestone8 uses the cluster_file as input while milestone7 uses the layer_numbers and atomic_distance to automatically create cluster and use it as input.

How to generate the same graphs as the report:

The output files from each milestone are stored in the output folder, and in each milestone folder inside this output folder there is a python file that can be used to generate the same graphs as the report.

Codes architectures:

Milestone 4-5:

Milestone 6:

Milestone 7:

Milestone 8: