Simulation Sciences Laboratory - Biophysics application project
Emiliano Ippoliti
Programme
The Biophysics application project of the SiSc Lab focuses on a parallel molecular dynamics (MD) program of a Lennard-Jones fluid. A key point of any MD code consists in updating the positions of the atoms of the system. We will consider three approaches for this:
Basic knowledge required for the course
Mathematics
• Functions, Taylor expansions, series
• Basic differential and integral calculus
• Vector analysis, matrix algebra
Physics
• Basic thermodynamics: Temperature, ideal gas, kinetic gas theory, laws of thermodynamics
• Classical newtonian mechanics
Computer Science
• Basic working knowledge of linux/unix operating systems
• Basic programming knowledge in Fortran77
Course material
Programme
The Biophysics application project of the SiSc Lab focuses on a parallel molecular dynamics (MD) program of a Lennard-Jones fluid. A key point of any MD code consists in updating the positions of the atoms of the system. We will consider three approaches for this:
• A simple approach: the atom-decomposition algorithm
• A counterintuitive (yet efficient) approach: the force-decomposition algorithm
• A state-of-the-art approach: the spatial-decomposition algorithm
The students will be asked to implement one or more of these approaches into a minimal MPI molecular dynamics program code. We will analyze how the performance of each approach depends on the size of the system investigated.Basic knowledge required for the course
Mathematics
• Functions, Taylor expansions, series
• Basic differential and integral calculus
• Vector analysis, matrix algebra
Physics
• Basic thermodynamics: Temperature, ideal gas, kinetic gas theory, laws of thermodynamics
• Classical newtonian mechanics
Computer Science
• Basic working knowledge of linux/unix operating systems
• Basic programming knowledge in Fortran77
Course material