Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of pyscal

pyscal - 2.10.21

What's Changed

  • Rdf normalisation fix by @stekajack in https://github.com/pyscal/pyscal/pull/148
  • fixed the ase.py file so that the read_snap works by @saswatnayak1998 in https://github.com/pyscal/pyscal/pull/150
  • Fix ase read by @srmnitc in https://github.com/pyscal/pyscal/pull/151

New Contributors

  • @stekajack made their first contribution in https://github.com/pyscal/pyscal/pull/148
  • @saswatnayak1998 made their first contribution in https://github.com/pyscal/pyscal/pull/150

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.20...2.10.21

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 2 years ago

pyscal - 3.0.0.dev.7

What's Changed

  • Add multicomponent SRO by @srmnitc in https://github.com/pyscal/pyscal/pull/113
  • add averaged keyword by @srmnitc in https://github.com/pyscal/pyscal/pull/117
  • Mask by @srmnitc in https://github.com/pyscal/pyscal/pull/118
  • Mask by @srmnitc in https://github.com/pyscal/pyscal/pull/119
  • Disorder by @srmnitc in https://github.com/pyscal/pyscal/pull/120
  • update plm implementation by @srmnitc in https://github.com/pyscal/pyscal/pull/121
  • Disorder by @srmnitc in https://github.com/pyscal/pyscal/pull/122
  • Solids by @srmnitc in https://github.com/pyscal/pyscal/pull/123
  • Rdf by @srmnitc in https://github.com/pyscal/pyscal/pull/124
  • Angular by @srmnitc in https://github.com/pyscal/pyscal/pull/125
  • initial draft of voronoi by @srmnitc in https://github.com/pyscal/pyscal/pull/127

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.15...3.0.0.dev.7

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 2 years ago

pyscal - 3.0.0.dev.6

Full Changelog: https://github.com/pyscal/pyscal/compare/3.0.0.dev.2...3.0.0.dev.6

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 3 years ago

pyscal - 3.0.0.dev.2

Full Changelog: https://github.com/pyscal/pyscal/compare/3.0.0.dev.1...3.0.0.dev.2

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 3 years ago

pyscal - 2.10.20

What's Changed

  • Move visualization to show() by @jan-janssen in https://github.com/pyscal/pyscal/pull/134
  • Test release by @srmnitc in https://github.com/pyscal/pyscal/pull/146

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.18...2.10.20

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 3 years ago

pyscal - 3.0.0.dev.1

What's Changed

  • add custom lattice creation by @srmnitc in https://github.com/pyscal/pyscal/pull/138
  • update doc building by @srmnitc in https://github.com/pyscal/pyscal/pull/139
  • Docs v3 by @srmnitc in https://github.com/pyscal/pyscal/pull/140
  • update examples by @srmnitc in https://github.com/pyscal/pyscal/pull/141
  • update docs by @srmnitc in https://github.com/pyscal/pyscal/pull/142
  • Remap operations by @srmnitc in https://github.com/pyscal/pyscal/pull/143
  • Add gb creation by @srmnitc in https://github.com/pyscal/pyscal/pull/144

Full Changelog: https://github.com/pyscal/pyscal/compare/3.0.0.dev.0...3.0.0.dev.1

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 3 years ago

pyscal - 3.0.0.dev.0

What's Changed

  • Add multicomponent SRO by @srmnitc in https://github.com/pyscal/pyscal/pull/113
  • add averaged keyword by @srmnitc in https://github.com/pyscal/pyscal/pull/117
  • Mask by @srmnitc in https://github.com/pyscal/pyscal/pull/118
  • Mask by @srmnitc in https://github.com/pyscal/pyscal/pull/119
  • Disorder by @srmnitc in https://github.com/pyscal/pyscal/pull/120
  • update plm implementation by @srmnitc in https://github.com/pyscal/pyscal/pull/121
  • Disorder by @srmnitc in https://github.com/pyscal/pyscal/pull/122
  • Solids by @srmnitc in https://github.com/pyscal/pyscal/pull/123
  • Rdf by @srmnitc in https://github.com/pyscal/pyscal/pull/124
  • Angular by @srmnitc in https://github.com/pyscal/pyscal/pull/125
  • initial draft of voronoi by @srmnitc in https://github.com/pyscal/pyscal/pull/127
  • Update atom backend by @srmnitc in https://github.com/pyscal/pyscal/pull/135
  • Separate operations by @srmnitc in https://github.com/pyscal/pyscal/pull/136
  • Add symmetry by @srmnitc in https://github.com/pyscal/pyscal/pull/137

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.15...3.0.0.dev.0

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 3 years ago

pyscal - 2.10.18

What's Changed

  • Remove plotly by @srmnitc in https://github.com/pyscal/pyscal/pull/133

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.17...2.10.18

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 3 years ago

pyscal - 2.10.17

What's Changed

  • make ipywidgets optional by @srmnitc in https://github.com/pyscal/pyscal/pull/132

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.16...2.10.17

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 3 years ago

pyscal - 2.10.16

What's Changed

  • Add multicomponent SRO by @srmnitc in https://github.com/pyscal/pyscal/pull/113
  • add iter methods in traj by @srmnitc in https://github.com/pyscal/pyscal/pull/131

Full Changelog: https://github.com/pyscal/pyscal/compare/2.10.15...2.10.16

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 3 years ago

pyscal - 2.10.15

Changes

  • Update documentation
  • Update dependencies in setup.py
  • Use pybind11 extension instead of cmake

Bug fixes

  • fix local keyword in entropy parameter calculation

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 4 years ago

pyscal - 2.10.14

Bug fixes

  • Remove wrong import in plotly

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 5 years ago

pyscal - 2.10.13

Changes

  • If species is not specified, output in poscar format will use pyscal function instead of ase backend

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 5 years ago

pyscal - 2.10.12

New features

  • remap_atoms method helps in removing ghost atoms and remapping atoms to the system box.
  • add_atoms method which can add additional atoms to the systems.

Changes

  • Voronoi vertex_positions are remapped correctly to atomic positions.

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 5 years ago

pyscal - 2.10.10

Changes

  • Format access methods for vertex positions calculated through Voronoi tessellation

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 5 years ago

pyscal - 2.10.9

Bug fixes

  • Bug fixes in trajectory module

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.8

Bug fixes

  • Numerous bug fixes in trajectory module

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.7

Bug fixes

  • Fix for memory error when using large cells

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.6

bug fixes

  • Fix error in Voronoi volume for big triclinic cells

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.5

Bug fixes

  • Fix bug in cell lists if atom coordinate was slightly lesser than 0

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.4

Bug fixes

  • Fix centrosymmetry bug for diamond structure

Changes

  • Move centrosymmetry implementation to the C++ side
  • Deprecate gvm algorithm for centrosymmetry

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.3

Bug fixes

  • Fix for Voronoi volume calculation with triclinic cells

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.1

Bug fix

  • Fix bug in repeating cells for very small cells

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.10.0

Bug fixes

  • Fix bug in a-CNA where lesser number of atoms were correctly identified.
  • Fix bug in c-CNA with selection of wrong cutoff.

New features

  • Identify diamond structure method based on extended CNA
  • Trajectory module which is used fast reading/writing of LAMMPS trajectories
  • Add a setter for Atoms object
  • Add a new method for extracting all atoms including ghost atoms

Changes

  • Simulation box has to be specified before assigning atoms
  • System and Atom are directly accessible from pyscal

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.9.3

This is minor release for bug fixes

Fixes

  • Update poscar read/write backend to ase

Changes

  • Remove is_triclinic keyword from read_inputfile. Boxes are automatically checked.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.9.2

The main changes in this release are described below-

Fixes

  • periodic boundary condition bug removed in poscar read in
  • minor bug fixes in bindings and crystal structures module

Deprecated features

  • frame keyword in read_inputfile removed
  • old box dimension is no longer used. Boxes are now in 3x3 cell vectors

New features

  • repeat method now has option to scale boxes
  • repeat method can also handle triclinic cells
  • add ghost atoms
  • small simulation cells are repeated automatically
  • remap method
  • add a new lightweight visualization module
  • traj_process module is restructured
  • read/write of unknown formats is attempted through ASE backend

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal - 2.8.14

This release introduces a number of changes listed below-

  • add entropy parameters including simple averaged version and switching function averaged version
  • add new examples and improve documentation
  • add new tests to increase coverage to 80%
  • add only_averaged keyword to q calculation
  • add < operator for identification of solid atoms
  • bug fixes in traj_process, atom, system and core
  • additions to misc module- largely untested
  • add convert_ase method for seamless convertion of ase objects
  • lammps wrapper for energy calculation introduced including simple averaging
  • fix zipped writing
  • remove deprecated methods from core
  • redesign of binder interface
  • add diamond neighbor calculation method
  • add repeat method for system
  • add ghost variable for atom to be used in future release

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 5 years ago

pyscal -

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal -

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal - Add windows support

pyscal is supported on windows systems through conda forge installation from this release.

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal -

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal - Add windows support

This release includes windows support

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal - Addition of Centrosymmetry parameter and common neighbor analysis

This release adds a number of new changes to the code: Major changes - Remove pickling support - Add variable conditions for clustering - Add new neighbor method which finds N nearest neighbors - Add centrosymmetry parameter with two algorithms - Add Common Neighbor Analysis and adaptive CNA

Minor changes - traj process: - poscar with selective dynamics can be read in - add write poscar method - split trajectory will automatically remove incomplete snapshots - Add misc module which has methods to compare atomic environments - system - remove stale indicator functions - restructure system code and clean up - atom - remove access functions and implement read_write - restructure atom code and clean up - faster chi params method - documentation updates - remove access functions and implement read write

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal - Minor bugfixes and updates

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 6 years ago

pyscal - Access functions for qlm

Provides access functions for real and imaginary parts of qlm

Scientific Software - Peer-reviewed - C++
Published by srmnitc about 6 years ago

pyscal - Support for mdtraj objects and more access functions

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Support for ASE objects and bug fixes

This version introduces support for loading ASE Atoms object as an input source for pyscal System. Also provides bug fixes for better parsing of POSCAR files.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Support for ASE objects and bug fixes

This version introduces support for loading ASE Atoms object as an input source for pyscal System. Also provides bug fixes for better parsing of POSCAR files.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Addition of short range order parameter and bug fixes

This release includes two major features -

  1. Addition of calculation for Short range order parameter for alloys
  2. Bug fix for Voronoi volume calculation which gives extremely large volumes for particles with negative coordinates on the cell edge.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Introduce fast neighbor calculations with cell lists

This result incorporates cell lists in both brute force and adaptive neighbor methods which leads to an increase in speed for neighbor calculations.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Introduce cell lists

This release contains further updates to the code including the ability to calculate solid atoms based on any q parameters, calculation of chi parameters and introduction of cell lists for improved speed in neighbor calculation.

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - Release for joss paper

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - 2.0.0

Updated version with significant changes to Atom and System

Scientific Software - Peer-reviewed - C++
Published by srmnitc over 6 years ago

pyscal - 1.0.3

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 7 years ago

pyscal - Version 1.0.1

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 7 years ago

pyscal - Version 1.0.0

Scientific Software - Peer-reviewed - C++
Published by srmnitc almost 7 years ago