Version history

This is a list of the main updates in the different versions of Pysic. Descriptions of all incremental changes can be found in the commit log (see also the develop version).

The version number is available in Pysic as the variable:

pysic.version

Version 0.6

• Added support for dividing the system to subsystems and allowing the use of different calculators on the subsystems. This allows hybrid QM/MM calculations. See HybridCalculator, SubSystem, Interaction.

Version 0.5

• Added hdf5 archiving module pysic.utility.archive.
• Added the Comb potential for Si/SiO

Version 0.4.8

• Fixed compatibility with syntax changes in ASE 3.7.0.
• Added piping of ChargeRelaxation objects.
• Added a potentiostat as a ChargeRelaxation type.
• Added a constrained optimization as a ChargeRelaxation type.
• Added utility functions such as get_neighbor_distances(), expand_symbols_string()

Version 0.4.7

• Added wrapping of several Calculators in ASE

Version 0.4.6

• Code optimization: updates in the memory allocation and computation routines in the Fortran core for better performance.
• Added a warning system (pysic.utility.error.Warning)
• Added support for pairwise bond order factors (in addition to per-atom factors), see Atomic and pairwise factors.
• Numerous bug fixes, see the github commit log for details.

Version 0.4.5

• Added the CompoundPotential class for representing complicated potentials.
• Added the SuttonChenPotential class describing the Sutton-Chen potential.
• Added the Shifted power potential
• Interface enhancements. E.g., it is possible to pass lists of potentials to methods like pysic.calculator.Pysic.add_potential(), or pass ProductPotential objects to other ProductPotential objects.
• Efficiency fixes. E.g., when bond order factors are created in the core, it is checked that duplicates are not created.

Version 0.4.4

• Added the ability to calculate products of local potentials (see pysic.interactions.local.ProductPotential)
• Added the Charged-pair potential
• Separated the old charged exponential potential to Exponential potential and Charge dependent exponential potential
• Changed the Bond bending potential to allow more general expressions.
• Added the Absolute charged-pair potential

Version 0.4.3

• Major restructuring of the Python source code
• Provided a Makefile for compiling
• Added calculation of the stress tensor with the method pysic.calculator.Pysic.get_stress()
• Added the Tabulated potential
• Added the Tabulated scaling function
• Added the Tabulated bond order factor
• Bug fix: Fixed an issue with core initialization where changing the size of the supercell would lead to a conflict in neighbor list updating (the list update was tried before the cell update but failed due to the cell having been changed).
• Bug fix: Fixed an issue with the parallel neighbor list building algorithm which did not properly broadcast the calculated lists to all cpus.

Version 0.4.2

• Restructured the interaction evaluation loops in the Fortran core (potentials (Potentials.f90))
• Added support for 4-body potentials
• Added the Dihedral angle potential
• Added the Buckingham potential
• Added the Power decay potential
• Added the Power decay bond order factor
• Added the Square root scaling function
• Bug fix: fixed a memory issue in Ewald summation CoulombSummation
• Bug fix: fixed an issue with periodic boundaries in FastNeighborList
• Bug fix: fixed an issue with special parameter values in Tersoff bond order factor evaluation
• Bug fix: fixed an issue where the cutoff of a bond order factor could overwrite a longer cutoff a potential
• Bug fix: fixed an indexing error in evaluation of 3-body interaction which gave to incorrect forces
• Bug fix: fixed and indexing error in neighbor offsets in FastNeighborList

Version 0.4.1

• Implemented an order \(\mathcal{O}(n)\) neighbor finding algorithm in Fortran (see pysic.calculator.FastNeighborList)

Version 0.4

• Implemented the Ewald summation of \(\frac{1}{r}\) potentials (see pysic.interactions.coulomb.CoulombSummation)
• The framework allows for the addition of other summation methods later on, but for now only standard Ewald is available

Version 0.3

• Implemented framework for charge relaxation (see pysic.charges.relaxation.ChargeRelaxation)
• Implemented the Damped dynamics charge relaxation algorithm.
• Implemented the Charge dependent exponential potential potential.

Version 0.2

• Implemented bond order factors (see pysic.interactions.bondorder.Coordinator and pysic.interactions.bondorder.BondOrderParameters) for scaling of potential energy according to local bond structure.
• Implemented a more robust method for tracking the status of the Fortran core (see pysic.core.CoreMirror). This makes it less likely that wrong results are produced due to the changes in the user interface not propagating to the core.

Version 0.1

• First publicly available version
• Python interface
  • pysic
  • pysic.calculator.Pysic
  • pysic.interactions.local.Potential
  • pysic_utility
• Framework for handling pair- and three-body potentials
• ASE compatibility
  • pysic.calculator.Pysic.get_forces()
  • pysic.calculator.Pysic.get_potential_energy()