Jon Bender's repositories
abinit-medusa
A guide for building ABINIT with Intel compilers, MKL, and MPI.
BestPractices
A list of Libraries, blogs, manual, etc. for numerical simulations best practices
calc2DIR
Calculate linear and 2D IR spectrum for a single, uncoupled chromophore
calcIR
Calculate IR Spectra of Water from MD simulation using the maps developed by Jim Skinner's group.
calcIR2
This repository contains a program to calculate the IR spectroscopy of dilute HOD in D2O or H2O.
chemicaljson
Development of the Chemical JSON data representation
CheMPS2
CheMPS2: a spin-adapted implementation of DMRG for ab initio quantum chemistry
Combining-Petsc-and-Slepc-with-MPI
The respository contains a code which has been developed from scratch. The code implements Slepc and Petsc along with parallel computing techniques to understand charge transport and polaron emission in semiconducting polymers
Cyclic-Voltammetry-Simulator
A simple cyclic voltammetry simulator, built as a MATLAB app. Based on Appendix B in Bard & Faulkner.
dftcxx
C++ based DFT program for educational purposes
Exciton-1D
This is a work in progress. We are developing the fundamental differences and similarities between a Polaron and Exciton
FeynDyn
Type an M x M matrix for your open quantum system Hamiltonian, and give a spectral density (analytic or numerical). FeynDyn gives the density matrix dynamics according to the Leggett-Caldeira bath or the Feynman-Vernon bath at any temperature. Can do up to 16 qubits (65536 levels) and infinitely many bath modes. Email dattani.nike@gmail.com for the latest version or any questions.
feynman
Sharp-looking Feynman diagrams in python
harminv
harmonic inversion algorithm of Mandelshtam: decompose signal into sum of decaying sinusoids
linabsspec
Calculates linear absorption spectrum
materials-toolbox
A collection of scripts to help with general comp chem hpc work
minimal-mistakes
:triangular_ruler: A flexible two-column Jekyll theme perfect for building personal sites, blogs, and portfolios.
Modelling-the-Holstein-Hamiltonian-
The repository contains the basic program which shows how to model the Holstein molecular crystal Hamiltonian for a charge/Polaron in a polymer stack employing a multiparticle basis set
mqds
A High-Performance Molecular Quantum Dynamics and Spectroscopy package for general system-bath problems
numopt
A C++ library for performing numerical optimization.
NWChemOutputToJson
Python files for reading NWChem output and converting to Json
PhysicsModels
Physics Models for Nonlinear Optics and Statistical Mechanics
Polaron-Coherence-in-2D-aggregates-using-openmp
We have developed a code which calculates the charge modulation spectra and polaron delocalization lengths both along the polymer backbone and in between stacks for bound and unbound polarons in P3HT films.
PyNergy
A python script to extract transition energies from ABINIT eigen-energy files.
PyTMM
Transfer Matrix Method implemetation & RefractiveIndex.info database browser
RTACalc
MatLab thin film reflection, transmission, absorption calculator based on transfer matrix method. Includes ability to plot dispersion for arbitrary number of films and wavelength-dependent complex dielectric functions.
thesis-phd
A derivation of the formalism for SHG in the length-gauge
TT-Toolbox
The git repository for the TT-Toolbox
TTSOFT
J. Chem. Theory Comput. 13: 4034-4042 (2017)
zotero-storage-scanner
A Zotero plugin to remove the broken & duplicate attachment link of the bibliography