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am1reparam

AM1 to High-level Reparameterization via the Genetic Algorithm. Began working on this summer 2015.

ani-1xnr

Machine learning interatomic potential for condensed-phase reactive chemistry

ani-tools

awesome-readme

A curated list of awesome READMEs

baserenderengine

cpp2011testing

cuda_num_integration_2

A CUDA numerical integrator. I wrote this to practice writing in C/C++ and CUDA during the summer of 2014. It's a simple Simpson's rule integrator along with a kernel I wrote for array reduction. This is an early program I wrote when learning C/C++, my skills have greatly improved since this time. I have alos learned how to properly implement error handling since this time.

cuda_remc_v2

This was a class project from the spring of 2014 semester for my computation chemistry course at UF. At this time I was just learning C/C++ and CUDA. The program builds an Ising spin glass model then uses Monte-Carlo (MC) sampling and Replica Exchange (RE) to search the sample space at many temperatures. See Comp_Chem_Proj.pdf in the repository for more detail. This is an early program I wrote when learning C/C++, my skills, in terms of using the object oriented nature of C++, optimization methods, and CUDA have greatly improved since this time.

dnntsdatafiletomdcrd

exampleopenblas

forceparser

Python -- Work in progress

fortrantesting

Justin learning some fortran and C/C++ mixing techniques. Summer 2015.

g09dnntsbuilder

This program was designed to calculate the data points needed to train the artificial neural network potential energy surface. The program is still in use in the current project. It is written in C/C++ and links to the Gaussian 09 software package to carryout the ab-initio quantum calculations.

gnuvectorizationtesing

Here, I was just playing around with how to properly vectorize loops to take advantage of modern processor's AVX units. This program is a bit useless, it was mainly for playing around with how the GNU compiler does certain things. Summer 2015.

harmonicmd

A 1D Harmonic Molecular Dynamics program for studying changes in the RMSD of atomic positions during an MD simulation. Began writing this in 2014, still making modifications every now any then.

hfscfcisprogram

A home built Hartree-Fock Self Consistent Field program with the Configuration Interaction Singles method for calculating excited states. I built this for class projects. It was early in my understanding of C/C++. The inital HF-SCF program was written fall 2014 while the CIS part was written spring 2015.

internal-to-cartesian

Python

internalcoordinatesapi

molcoordsys

mpitesting

neuralnetintaddition

My first attempt at building a neural net of sigmoid neurons to compute n+1 given n for any integer n. This is a self project to help with my understanding of how neural nets work in practice. Derivatives are calculated using a simple gradient descent algorithm. This program builds a training set of 32-bit integers, converts them to binary, converts the binary digits to double precision which it uses as input to the neural net. The output is expected to be a double point number between 0 and 1, and if the number is < 0.5 it is converted to a 0, if > 0.5 it is converted to 1 then the binary digits can be converted back to a 32 bit int. For the training set I generate a set of random 32 bit integers. Summer 2015.

openglengine

An in-the-works OpenGL Engine with some dev tools. Currently the terrain generation tool is in the works. I haven't had a lot of time to devote to this as I've been busy on my Ph.D.

pycharmprojects

PycharmProjects Folder

qr-tests-1us0

Helix example for testing quantum refinement

quac

QUAC ("quantitative analysis of chatter" or any related acronym you like) is a package for acquiring and analyzing social Internet content. Docs are online at http://reidpr.github.io/quac.

solarrenderengine

An OpenGL engine that randomly generates a solar system to roam around in. It is rather useless, as it was just a exercise in programming OpenGL. Originally I built the engine to use classical physics for the motion of the bodies, however, once I added asteroids this became computationally intractable, so, I switched to a simple rigid rotation scheme. In time I would like to solve the physics problem by using CUDA to carryout the physics calculations. Example images are located in the ExampleImages folder. December 2014.

sshtunnelhandler

A C/C++ program to maintain a reverse SSH tunnel to a server. It's basically just a wrapper to the ssh command that reconnects upon disconnection. I wrote this because my internet is not very reliable where my ssh server is located.