jeargle / moldyne Goto Github PK
View Code? Open in Web Editor NEWExperimental molecular dynamics and monte carlo simulator in julia.
Experimental molecular dynamics and monte carlo simulator in julia.
Moldyne should be runnable through a command-line executable.
Dihedrals connect 4 bonded atoms and have a sinusoidal form.
Code from the Week5 homework for coursera course on Computational Statistical Mechanics. It's in python, but port to julia.
This should probably be either part of a simulation output file or its own output file. For MD it will need locations and velocities for all atoms.
Code from the Week4 homework for coursera course on Computational Statistical Mechanics. It's in python, but port to julia.
Code from the Week3 homework for coursera course on Computational Statistical Mechanics. It's in python, but port to julia.
Code from the Week1 homework for coursera course on Computational Statistical Mechanics. It's in python, but port to julia.
The Monte Carlo code was written separately and needs to be pulled into the Moldyne core.
Angles are between 3 bonded atoms and should be simple harmonic oscillators.
Write a parser for CHARMM force field files. Initially, just read in atom types along with VdW parameters and charges.
Julia seems more appropriate for this kind of compute-heavy scientific application.
Code from the Week2 homework for coursera course on Computational Statistical Mechanics. It's in python, but port to julia.
Read in a file with parameters for a simulation run. It should have things like the starting structure file, the timestep duration, and the number of timesteps.
Switch over from comments to julia docstrings for documentation.
Update docstrings to be more like the examples in https://docs.julialang.org/en/v1/manual/documentation/ .
"""
...
# Arguments
- `n::Integer`: the number of elements to compute.
- `dim::Integer=1`: the dimensions along which to perform the computation.
...
"""
Simple electrostatics are pairwise between non-bonded atoms and follow Coulomb's law.
Add interatomic bonded terms. Bonds should just be simple harmonic oscillators added to pairs of atoms.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.