baoab-constraints

Code for numerical experiments using Langevin Dynamics with constraints

callgraph

Tool for printing call graphs

cl-buchberger

Buchberger's algorithm in Common Lisp. Moved to https://git.sr.ht/~jmbr/cl-buchberger

cl-mpi

Fork of cl-mpi by M. Heisig. This fork provides bindings for the full MPI specification. Moved to https://git.sr.ht/~jmbr/cl-mpi

colvars-gaussian-processes

Use Gaussian processes as collective variables in molecular simulations with NAMD. Moved to https://git.sr.ht/~jmbr/colvars-gaussian-processes

committor

Solver for the committor equation using the finite element method. Uses FEniCS and a potential of mean force obtained by colvars.

dfftpack

A repackaging of DFFTPACK providing C/C++ header files and ready to be built using CMake.

diffusion-maps

Fast computation of diffusion maps and geometric harmonics in Python. Moved to https://git.sr.ht/~jmbr/diffusion-maps

eigensolver

Library for computing eigenvectors of large sparse matrices using ARPACK and SuiteSparse

gentlest_ascent_dynamics_on_manifolds

Gentlest ascent dynamics on manifolds

gnostic

Rule-based task execution system. Moved to https://git.sr.ht/~jmbr/gnostic

go-replicants

Molecular simulator for proteins that uses Go-type potentials

halberd

Load balancer detection tool. Moved to https://git.sr.ht/~jmbr/halberd

incf-cl

A collection of convenience functions and macros for Common Lisp. Moved to https://git.sr.ht/~jmbr/incf-cl

inferior-maple-mode

Simple Maple command-line interface for Emacs

jmbr

lambda-dynamics-quadrature

Model system for validating lambda dynamics implementations. Moved to https://git.sr.ht/~jmbr/lambda-dynamics-quadrature

laplace-beltrami-eigensolver

Calculates the eigendecomposition of the Laplace-Beltrami operator on charts of Riemannian manifolds. Moved to https://git.sr.ht/~jmbr/laplace-beltrami-eigensolver

latex2anki

Convert decks of flashcards written in LaTeX to Anki. Moved to https://git.sr.ht/~jmbr/latex2anki

lbfgs

L-BFGS Software for Large-scale Unconstrained Optimization by Jorge Nocedal

libeve

Genetic algorithm library written in C. Moved to https://git.sr.ht/~jmbr/libeve

libpme6

C++ implementation of the smooth Particle-Mesh Ewald algorithm for dispersive forces. Moved to https://git.sr.ht/~jmbr/libpme6

make-project

Boilerplate generator for Common Lisp projects

maxima-interface

Simple interface between Common Lisp and Maxima. Moved to https://git.sr.ht/~jmbr/maxima-interface

miles

Milestoning tool

regex-trace

Trace macro with regular expression support

sbcl-notes

Notes written while working my way through the sources of SBCL.

school-on-molecular-kinetics

Jupyter notebooks prepared for the CECAM School on Molecular Kinetics in Lausanne, Switzerland (August 2016)

simple-milestoning

Simple example of Milestoning

staying-the-course-code