v0.10.0

Version 0.10.0

New XTC Parser

• Now using molly for faster reading of XTC files. Requires the molly feature to be active, otherwise the standard xdrfile library is used. With molly iterating through XTC files is ~50% faster compared to xdrfile.
• Implemented an efficient "partial-frame" XTC reader using molly. It attempts to only read atoms of a specified group while ignoring the rest of the atoms. See GroupXtcReader and System::group_xtc_iter for more information.
• GroupXtcReader implements a new trait TrajGroupReadOpen.

Integration with the chemfiles Library

• All trajectory file formats supported by chemfiles can be now read using System::traj_iter<ChemfilesReader>. However, only XTC, TRR, TNG, DCD, Amber NetCDF, and LAMMPSTRJ are independently tested by groan_rs. Be careful when working with other file formats since these may not work properly.
• To enable integration with chemfiles, you have to enable the chemfiles feature. If you do this, you need to have cmake version LOWER than 4.0.

More Precise Center of Geometry/Mass Calculations

• IMPORTANT Breaking changes:
  • Implemented the Refined Bai-Breen algorithm similar to the pseudo-center of mass recentering algorithm described in https://arxiv.org/abs/2501.14578.
  • Methods AtomIteratorWithBox::get_center and AtomIteratorWithBox::get_com using the original Bai-Breen algorithm have been RENAMED to AtomIteratorWithBox::estimate_center and AtomIteratorWithBox::estimate_com, respectively.
  • Similarly, System::group_get_center and System::group_get_com have been renamed to System::group_estimate_center and System::group_estimate_com.
  • New functions called AtomIteratorWithBox::get_center, AtomIteratorWithBox::get_com, System::group_get_center, System::group_get_com use the Refined Bai-Breen algorithm which consists of 1) calculating the pseudo-center of geometry of the selected atoms, 2) making the group whole in the simulation box, 3) naive calculation of center of geometry or mass in the simulation box.
  • The refined Bai-Breen algorithm is much more precise than the original Bai-Breen algorithm but only works for groups that are smaller than half the simulation box. It is also ~50% slower than the original Bai-Breen algorithm.
  • All internal groan_rs methods now use the Refined Bai-Breen algorithm, with the exception of System::atoms_center and System::atoms_center_mass which continue to use the original Bai-Breen algorithm but are recommended to only be used for visual centering.

CellGrid

• Implemented a CellGrid (also known as cell lists) structure for efficient pairwise distance calculations within a cutoff.
• New atom iterator, UnorderedAtomIterator, has been implemented.
• System::guess_bonds has been reimplemented using a CellGrid making it much more efficient, especially for large systems.
• Breaking change: System::guess_bonds_parallel has been removed. (But the new System::guess_bonds is now much faster than System::guess_bonds_parallel has been.)

Hydrogen Bond Analysis

• Implemented a way to identify hydrogen bonds (HBondAnalysis) in a trajectory. The analysis can be performed with any trajectory reader (HBondTrajRead::hbonds_analyze).

Changes to Trajectory Iteration

• Breaking change: TrajReadOpen trait has been renamed to TrajFullReadOpen. The original TrajReadOpen trait now requires implementing the initialize method which can be used to construct either TrajFullReadOpen structure

Changes to System::traj_iter_map_reduce (as is tradition)

• Breaking changes:
  • The Data structure in System::traj_iter_map_reduce no longer needs to implement Add. Instead, it needs to implement ParallelTrajData which requires the user to specify how the data structures should be reduced (merged). ParallelTrajData also allows the user to provide a custom initialize function which accepts thread ID and is automatically called after spawning a thread. This allows the user to implement thread-specific behavior or to properly sort the final results.
  • System::traj_iter_map_reduce can be now provided a group name in case a "partial-frame" iteration should be performed. In such case, the provided Reader structure must be GroupXtcReader.
  • The Reader structure in System::traj_iter_map_reduce still needs to implement TrajReadOpen but it's the new trait (see 'Changes to Trajectory Iteration`).
  • Made error propagation better. If a single thread encounters an error, all other threads will abort within 10 trajectory frames.

Expansion of Utilities for Ignoring PBC

• Introduced NaiveShape trait for geometry filtering ignoring PBC and implemented this trait for Sphere, Rectangular, and Cylinder.
• Implemented ImmutableAtomIterable::filter_geometry_naive and MutableAtomIterable::filter_geometry_naive for geometry filtering of atoms from iterators ignoring PBC and box dimensions.

Other Changes

• Introduced Atom::reset_bonded and System::clear_bonds for simpler removal of bonding information.
• Sodium atoms should be less often misclassified as sulfur when guessing elements.
• Reworked how groups are stored inside a system. Introduced a new Groups structure for storing groups.
• Bug fix: Fixed undefined behavior in xdrfile jumping which lead to TRR files being read incorrectly when using clang.
• Bug fix: Fixed incorrect parsing of some TPR files generated with Gromacs 2025.