andersx/phd-thesis

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andersx/phd-thesis

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PhD Thesis // Inferential Protein Structure Determination Using Chemical Shifts

libsimdmath

C++ library of fast, approximate math functions, primarily for Intel AVX2.

python-intro

Jupyter Notebooks for Python Introduction, University of Basel, May 2020

Jupyter Notebook

goptimizer

Tool to use the Gaussian 09 geometry optimizer with energy and force supplied by an external program.

mcdock

McDock: Simple Monte Carlo docking algorithm in C++

auto-ts

Template-directed automatic generation of transition state structures.

check-sdf

Script to correct connectivity in SDF files via NBO calculations

errorlearn

ML implementation find errors in molecular-mechanics force fields and semi-empirical QM methods.

fml

Some optimized functions for machine learning, primarily written using OMP parallel F2PY wrappers and parallel MKL calls.

ml-intro

Jupyter Notebooks for ML Intro, University of Basel, May 2020

Jupyter Notebook

ml-dftb3

A Machine-Learning Augmented DFTB3 Method

qmepa890

QM calculated proton affinities of 890 molecules from the QM7 database

qml-ase

ASE interface for QML

libopenmndo

Open-sourced library for semi-empirical MNDO integrals.

ls1-mardyn

Ls1 Mardyn source code

dftb3-delta-machine

Simple Kernel Ridge Regression to calculate PBE0/def2-TZVP energies from DFTB3 calculation. Kernel is written in OpenMP parallel F90, yo.

mkl-discover

Python module to check if libmkl_rt.so is installed.

pymopac

Python interface for MOPAC2016

pymndo99

Python interface for Walter Thiel's MNDO99

dftbfit

Framework for Bayesian inference of DFTB parameters using DFTB+.

boss-representation

Bags of spatial spectra (BOSS); a continuous, differentiable two- and three-body ML representation for molecules

wrapparrep

Wrapper to run MD and MC Parallel Replica dynamics.

qmlmpi

Test for mpi/scalapack with f2py and QML.

cpe-source

Chemical Potential Equalization // DFTB source code

PKM

个人知识管理

beamer-gif

Example of how to embed gifs/videos into latex beamer

pauli-se

Short program to calculate Pauli-repulsion between hydrogen atoms (based on a semi-empirical approximation)

mfls

Make Fortran Less Sucky(tm)

charmm36

CHARMM36/EEF1-SB force fields for PHAISTOS

myrpg

Python/pygame based ARPG (will probably never be finished ever)

dftd3-wrapper

Wrapper for Stephan Grimme's DFT-D3 program (for easy interface to QM programs).

charmm-dftb-py

Wrapper for running DFTB calculations with CHARMM

cpe-gradient-latex

Derivation of the DFTB3/CPE gradient.

nucff

Simple coulombic force field for point charges in Python

jamess

Jimmy's and Anders' Modular Electronic Structure Software

fep-ml

Free-Energy Perturbation with FML