apallath

torch_models

Basic deep learning models in PyTorch.

WHAM

Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches.

stringmethod

Python implementation of the string method to compute the minimum energy path between two points on any 2-dimensional energy landscape.

gcmc

C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble.

sl-correlation-scripts

MATLAB scripts for calculating correlations for fluctuations at solid-liquid interface, using LAMMPS MD simulation datta

parallel_algos

Implementations of high performance shared and distributed memory parallel algorithms using OpenMP and MPI in C [work in progress].

postmetad

Python package for post-processing PLUMED metadynamics and OPES simulations.

INDUSAnalysis

Python package to analyze molecular simulation data generated using GROMACS-INDUS.

keras_sklearn_models

Basic tf2/keras deep learning models on image data and sklearn machine learning models on tabular data.

pyves

Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.

acad-council-website

Website for IITGN Academic Council 2017-18

apallath

apallath.github.io

autoencoders_project

bootstrapping_tutorial

Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data.

comp

Solutions to Programming Contest/Practice Problems

crossref_miner

A simple tool to fetch citations using the Crossref REST API.

ENM531

GameOfLife

Conway's Game of Life on a rectangular 2D grid with OpenMP parallelization.

gemini_penn

gemini_penn is an (unofficial) fork of the Gemini beamerposter theme with the University of Pennsylvania logo, colors, and fonts

hexagdly

Process hexagonally sampled data with PyTorch

multiagent_timetable_scheduling

Implementation of a multi-agent based algorithm for solving a simplified version of the University Timetabling Problem, using Simulated Annealing, in NetLogo

network_flow

Implementation of selected flow algorithms and programming contest problems (TopCoder and ACM-ICPC)

paperfetcher

paperfetcheR-Notebooks

R-Notebooks demonstrating how to use paperfetcher in R through reticulate.

paperfetcheR-starter

R script templates to help you get started with handsearching and citation searching using paperfetcher.

paperfetcher-web-app

pgcc

Website for Penn Graduate Consulting Club

prog_practices_demo

Repository accompanying the Patel Group tutorial on good programming practices.

pyib

PyTorch & OpenMM implementations of information bottleneck based approaches for learning and biasing reaction coordinates in molecular simulations.