v0.8.3

Bug fixes

• Fixed bug in make_lattice that gave wrong density for D!=3 and rho!=None.
• Fixed bug in calc_dynmamics when using Lees-Edwards boundary conditions.

New features

• New examples:
  • water.py : Simulation of the SPC/Fw model
  • active_ornstein_uhlenbeck.py : Purely repulsive active particles forming dense clusters (MIPS).
  • zbl.py : Simulation of Cu using universal Ziegler–Biersack–Littmark (ZBL) potential.
  • lennard_jones_argon.py : Lennard-Jones conversion from Argon units to real units
  • lennard_jones_argon_real_units.py : Simulation of Lennard-Jones Argon using real units
  • LJchain_continue.py : Continuation of LJ chains simulation.
  • isomorph_forcemethod.py : An isomorph is traced out using the force method
  • analyze_NVT_thermodynamics.py : Calculates thermodynamical properties of a constant NVT simulation.
  • analyze_NpT_thermodynamics.py Calculates thermodynamical properties of a constant NpT simulation.
• New Pair-potentials:
  • LJ_coulomb_sf
  • Universal ZBL Potential
  • Gaussian-core model
  • Yukawa,
  • Exponential repulsion
  • harmonic repulsion
  • Hertzian repulsion
• Interactions
  • Embedded atom methhod (EAM) potential with parameters for 16 elements, based on Zhou, Johnsonm, Wadley, Phys. Rev. B 69, 144113 (2004)
  • Smooth Cubic spline truncations (gamdpy.apply_cubic_spline_cutoff)
  • Smooth Gromacs style truncations (gamdpy.apply_gromacs_cutoff)
  • Harmonic bond angle potential
  • Possibility to partially exclude pairs interactions as for example for atoms 1,4 of dihedral interactions.
  • Neighbor List for big systems, Linked-List, now works in 2 and 3 dimensions
• Integrator for Active Ornstein-Uhlenbeck Particle (gamdpy.ActiveOUP)
• Mechanism for integators to save their internal state for the purpose of correctly restarting an interrupted simulation (for NVT and NPT_Langevin so far).
• Compression of simulation box implemented as a method in class Simulation ( Simulation.compress() )
• Tools for unit conversions (gp.conversion_factors)
• Tools for analyzing thermodynamics fluctuations