- Phase out recommonmark in favour of myst to generate the documentation
- Improve the test suite
- Add a script that can be used to compute the S(q) of an oxDNA trajectory
- Improve the MSD computation and update the associated docs
- Add more methods to remove bonded neighbours [b1d541549b64fa0e06a648603f2096ef97496f0e]
- Add a method to quickly initialise the topology of chain systems [af5424ef386722c16a91bc36b74cea80fed8be31]
- Add an oxDNA-related example
- Add observables to compute the self and coherent intermediate scattering functions
- Add fast sin and cos functions
- Add an oxDNA topology parser for DNA/RNA
- Keep the topology info when filtering systems with FilterByFunction and use System's method to copy the topology from filtered systems
- Minor API changes to WaveVectorList [5f943fe7af484a06c861936250f5ad7295e7bdb6]
- Make the code compilable on older compilers [91f96878f201b0bc708a47cd4382ab67364b4c8c]
- Make the lib compatible with python >= 3.11
- Add a new observable to compute autocorrelations
- Add python bindings for Particle's remove_neighbour method
- Document some previously undocumented python bindings
- Strengthen the parsing of LAMMPS data files and fix a typo in the docs [a427f667a0c0ee6c269eb14cad39616efbec5328]
- Fix a bug whereby removing a particle wouldn't update its bonded neighs
- Fix issue 5
- Fix a minor bug in the structure factor observable [01a2c901ac6184ee347c0247644a05ad395de2b4]
v. 0.5.0 [213b13a]
- Add heuristics to help determining the file type in the LAMMPS -> cogli1 converter
- Add an observable to compute the gyration radius of molecules (GyrationRadius)
- Reorganise the test folder and add new tests
- Add the `select` method to obtain a list of particles from a set or a System
- Add a way to automatically set up the topology in oxDNA-based parsers
- Add support for Groups to the cogli exporter
- Add bindings for add a method to check for overlaps to the CellLists class
- Add `print_detailed_polymer_topology` to the utils module
- Export more Topology methods
- Add documentation to many undocumented bindings
- Bugfixing
- Fix a bug that affected oxDNA parsers that didn't set bonded neighbours
- Fix the behaviour of the `reset()` method of two observables
- Fix a bug that prevented compilation when both python2 and 3 are present
v. 0.4.0 [8d97eb3]
- Add a few converter executables (oxDNA -> cogli, oxDNA -> LAMMPS, LAMMPS -> cogli)
- Add the new `converters` module, which contains utility functions that can be used to easily convert between different formats
- Add the new `traj` module, which contains some utility functions that speed up the creation of trajectory objects
- Improve the documentation coverage
- Add the possibility of using b-factors to compute form factors
- Fix a bug in the LAMMPS exporter whereby topology links were sometimes written with wrong indexes
v. 0.3.1 [f604419]
- Fix one of the tests
- Strengthen the LAMMPS data file exporter so that it can manage systems with non-integer types and non-positive-defined indexes
- Make the LAMMPS data file parser handle the case of a data file not having an empty line at the end
- Make the LAMMPS dump parser not print a warning when it encounters an empty dump file (which always happens when initialising a trajectory from a file)
- Remove the compiled documentation from the source tree
v. 0.3.0 [c8cbbb7]
- By default neighbour finders will not consider neighbours particles that share bonds (i.e. that are bonded neighbours).
- Add a has_bonded_neighbour method to Particle
- The LAMMPS data file parser and exporter now support the "molecular" style
- The LAMMPS dump file parser has been completely revamped and now auto-detects the atom/particle properties listed in the dump file.
- Bugfixing
- Fix a bug whereby parsing of strings having fields separated by multiple spaces would fail
v. 0.2.0 [6dfcb24]
- Add the "mass" and "charge" fields to particles
- Add support for the "full" atom_style in LAMMPS-related classes
- Make it possible to use a data file to initialise a LAMMPS dump conf
- Add first class support for angles and dihedrals
- Add support for bonds, angles and dihedrals of different types
- Use a custom class to manage neighbours as done for bonded neighbours
- Add a method to init the orientation vectors of oxDNA confs
- Add a new observables that compute cluster sizes (ClusterList)
- Add an observable to compute the radial distribution function (RDF)
- Add a method to use PBC to reconstruct molecules
- Add a method to copy particles (Particle::make_copy)
- Make the logger use stderr instead of stdout
- Performance improvements (remove dependencies and use better algorithms all over the code), especially for parsing
- Add an example featuring parsing and analysis of a LAMMPS data file
- Add a method to the Topology class (`remove_unappliable_links`) to remove from an already-initialised topology all those links (bonds, angles and
dihedrals) that involve particles that are not present in the given system
- Bugfixing
- Fix a bug whereby Topology::bonds would not work on Python
- Fix a bug of the cogli1 exporter
- Remove some huge memory leaks due to a circular dependency
- Fix a bug that would add particles with random indexes to a System
v. 0.1.0 [f4f90ef]
- This is the first beta version
- Add a new parser to build systems out of PatchyParticles configurations
- Add a method to the oxDNA topology Default's class to get the number of particles of species A
- Add flexibility to the LAMMPS parser
- Improve the flexibility of the cogli2 exporter
- Fix a bug whereby parsers would not complain about unreadable files
- Fix a bug whereby the structure factor observable would not take averages in the right way
- Update the documentation
v. 0.0.3 [b5dc92c]
- Add the MapParticle filter, which takes a list of lists that specify the ids
of particles whose centre of mass will be used as a new particle
- Add the FilterById filter, which takes a list of indexes and build systems
where only those particles with a listed index are present
- Add the `set_include_system` method to BaseTrajectory to selectively include
systems in a trajectory
- Remove boost from the dependencies. boost::math remains a requirement only for
the BondOrderParameters observable
- Improve the documentation coverage
v. 0.0.2 [31322e8]
- Add a test that checks the LAMMPS conf and topology parser and exporter
- Add the write_topology and write_trajectory methods to BaseExporter
- Remove Boost's `signal` from the dependencies
- Fix compilation on Ubuntu 20.04 and add some documentation
- Add an observable that computes the structure factor (and can optionally return a "destructured" structure factor)
- Add an oxDNA exporter and improve the oxDNA parser
- Dramatically improve the performance of System::available_index()
- Add to the README updated info about the required libraries/packages
- Add a mechanism to manage the version number
- Bugfixing
v. 0.0.1 [19c49e8]
- First release