<commit_before># Change Log

All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).

## Next Release (current master)

### New features

* Change the license to the 3-clauses BSD license.
* Chemfiles will now read configuration files (by default in `.chemfilesrc`),
  and use the configuration data to rename atomic types to make sure they
  match element names. The `chemfiles::add_configuration` function can be used
  to add additional configuration files.
* Reading a `Frame` (with `Trajectory::read` or `Trajectory::read_step`) will
  now set the frame step.
* The `Atom` faillible methods (`atomic_number`, `vdw_radius`,
  `covalent_radius` and `full_name`) returns `optional<T>` instead of `T`.
* Functions taking an atomic index parameter can now throw `OutOfBounds` errors
  if the index is out of bounds.
* `Topology::append` is now called `Topology::add_atom`

### Changes in supported formats

* Amber NetCDF format is now activated by default, by embedding the netcdf
  library in chemfiles.
* Added `LAMMPS Data` format, reading [LAMMPS data files].

[LAMMPS data files]: http://lammps.sandia.gov/doc/read_data.html

### C API changes

* Added `chfl_add_configuration` to add more configuration files.
* Renamed `chfl_vector_t` to `chfl_vector3d`; and `chfl_cell_shape_t` to
  `chfl_cellshape`.
* `chfl_atom_atomic_number`, `chfl_atom_vdw_radius` and
  `chfl_atom_covalent_radius` all returns 0 instead of -1 if the atom does not
  have a known value for this property. This allow `chfl_atom_atomic_number`
  to take a `uint64_t*` parameter instead of an `int64_t*`, following all the
  other functions in the C API.
* Added `CHFL_OUT_OF_BOUNDS` variant to `chfl_status`

### Deprecation and removals
<commit_msg>Update changelog<commit_after># Change Log

All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).

## Next Release (current master)

### New features

* Change the license to the 3-clauses BSD license.
* Chemfiles will now read configuration files (by default in `.chemfilesrc`),
  and use the configuration data to rename atomic types to make sure they
  match element names. The `chemfiles::add_configuration` function can be used
  to add additional configuration files.
* Reading a `Frame` (with `Trajectory::read` or `Trajectory::read_step`) will
  now set the frame step.
* The `Atom` faillible methods (`atomic_number`, `vdw_radius`,
  `covalent_radius` and `full_name`) returns `optional<T>` instead of `T`.
* Functions taking an atomic index parameter can now throw `OutOfBounds` errors
  if the index is out of bounds.
* `Topology::append` is now called `Topology::add_atom`
* Added `Frame::distance`, `Frame::angle` and `Frame::dihedral` to get
  geometric information on the system, accounting for periodic boundary
  conditions.  

### Changes in supported formats

* Amber NetCDF format is now activated by default, by embedding the netcdf
  library in chemfiles.
* Added `LAMMPS Data` format, reading [LAMMPS data files].

[LAMMPS data files]: http://lammps.sandia.gov/doc/read_data.html

### C API changes

* Added `chfl_add_configuration` to add more configuration files.
* Renamed `chfl_vector_t` to `chfl_vector3d`; and `chfl_cell_shape_t` to
  `chfl_cellshape`.
* `chfl_atom_atomic_number`, `chfl_atom_vdw_radius` and
  `chfl_atom_covalent_radius` all returns 0 instead of -1 if the atom does not
  have a known value for this property. This allow `chfl_atom_atomic_number`
  to take a `uint64_t*` parameter instead of an `int64_t*`, following all the
  other functions in the C API.
* Added `CHFL_OUT_OF_BOUNDS` variant to `chfl_status`
* Added `chfl_frame_distance`, `chfl_frame_angle`, `chfl_frame_dihedral` and
  `chfl_cell_wrap` to work with periodic boundary conditions. 

### Deprecation and removals

{'fraction_non_alphanumeric': 0.08728943338437979, 'fraction_numerical': 0.00408371618172537, 'mean_word_length': 5.06656346749226, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7003113', 'n_tokens_mistral': 1234, 'n_tokens_neox': 1200, 'n_words': 474}