Molecular Dynamics in C

This one is for learning.

This is the C version of this code base. I will try in the future to expand to other languages. Practice makes perfect.

Usage

This project requires the clang compiler and cmake.

To build:

• Create a build directory in the same directory as this readme file
• Execute "cmake -DCMAKE_BUILD_TYPE=Release ../" (change Release to Debug optionally)
• Then execute "make ."
• The executable "molecular_dynamics_c" should be in your build directory (move to bin or wherever you want)
• The executables "commonTest", "classicalTest", and "quantumTest" should also appear (for checking if tests pass)

To Run:

• Have a valid structure
• Make a key file (see keyReader.h for keywords or grab one from examples/keyExamples/)
• Input four arguments "molecular_dynamics_c "command" "structure" "key" (or "molecular_dynamics_c help" for help menu)

My Goals (Theory)

• Explain all the theory and reference heavily so this is educational for other people.

Classical

• See what the simplest AMOEBA engine possible could look like.
• Do NPT, NVT, NVE simulations.
• Perform perturbative FE calculations via MBAR/BAR.
• Write a PB solver.

Quantum

• Learn about foundational quantum chemistry algorithms (Hartree-Fock & Post) and theory following: https://github.com/jjgoings/McMurchie-Davidson
• Write the simplest possible DFT engine that can produce multipole components for AMOEBA.

My Goals (Programming)

• Learn the c programming language (no external libraries except perhaps OpenMP and CUDA)
• Write code that can be very simply parallelized on CPU and GPU by planning ahead.