started writing something for the simulation of hs_wca particles, still many issues to resolve
written a basic routine to generate initial hard spheres configurations starting from LJ minimum configurations
major rewrite of generate packing classes for the basin volume method
introduced fixes to _write_opengl_input to place all particles in the box
implemented generate_jammed_packing script and inlined some functions to improve performance of modified fire
added reset function to modify fire to resume to constructor state and implemented cpp of CheckSameMinimum test
corrected typos
added __init__.py for monte_carlo
started a re-structuring of pele/optimize to make all optimizers from the same gradient optimizer class, this allows for passable c gradient optimizers objects within python. Performance improvements to modified_fire and finished configuration test CheckSameMinimum
started writing bv potential and written cpp code for RecordDisp2Histogram action, needs to be wrapped
critical bug fixes, implemented configure_bv_mcrunner
rewritten harmonic potential and distance2 histogram as a template class that takes different distance policies
written a possible implementation of hessian in simple pairwise potential and copied test suit from main pele repository
started adding tests
added numerical hessian to hessian test, bug in hessian, return -nan
implemented hessian in pair-wise potential, hessian function needs to be written for all potentials
raise an error if hessian is called when unimplemented
added _mcrunner for basin volume and _configure_bv_mcrunner, started writing script to compute districution of eigenvalues for a particular jammed structure
improved hessian implementation, now potential is called once for each pair
now generate_random_packings analyses jammed structure and determines whether there is any rattler. The structure file is now saved as .xyzdr, to include information about whether it's a rattler or not. The opengl file is also saved assigning a different colour to the rattlers. configure_bv_mcrunner hs been adapted to read .xyzdr file and create a rattlers array passable to the bv_mcrunner