larsbratholm / molstat

Molecular Statistics

Molecular Statistic

A bachelor course in understanding simulations and programming with Python

Setup

See INSTALL.MD

Lecture Plan and Weekly Goals

check virtualization with cpu-z (vt-x/vmx for intel, svm amd)

http://www.cpuid.com/softwares/cpu-z.html

Week 1

Science

• Introduction to simulation thinking

Programming skills

• Variables and datatypes
• Print (output)
• Operators and expressions
• Booleans (if else or)
• Looping and Double looping
• Importing modules (e.g. numpy)

Exercise

• Non-interacting particles
• box boundaries

Week 2

Science

molecular dynamics and LJ-potential

• modelering af gas og væsker
• molecular dynamic = newstons 2. lov - del 1
• lennart-Jones potentialet
• molecular dynamic = newstons 2. lov - del 2
• initalisering
• udregning af kræfter og at tage et skridt
• skridtlængde
• ækvilibering og konstant E vs konstant T

Programming

• functions
• read/write files

Exercise

• Hard sphere model
• histogram

Week 3

Science

• grænseproblemet
• periodiske grænsebetingelser - en skitse
• periodiske grænsebetingelser - en animation
• cutoff - del 1
• cutoff - del 2
• udregning af molekylære egenskaber
• udregning af fri energiændringer - del 1
• udregning af fri energiændringer - del 2

Programming

• none

Exercise

• implement LJ potential
• velo-verlet solver

Week 4

Science

• kraftfelter
• energi minimering

Programming

• advanced numpy

Exercise

• periodic boundary conditions
• conservation of energy
• Instantaneous temperature, pressure

Week 5

Science

• Radial distributionsfunktion
• Diffusion

Programming

• read/write files
• tips and tricks

Exercise

• Data-analysis