What's Changed

• compile cpu kernel directly into library by @clonker in #226
• catch2 v2 -> v3 by @clonker in #228
• Pybind11 via submodule by @clonker in #229
• Update deps by @clonker in #236

Full Changelog: v2.0.11...v2.0.13

What's Changed

• compile cpu kernel directly into library by @clonker in #226
• catch2 v2 -> v3 by @clonker in #228
• Pybind11 via submodule by @clonker in #229

Full Changelog: v2.0.11...v2.0.12

What's Changed

• compile-time index loop unroll by @clonker in #224

Full Changelog: v2.0.10...v2.0.11

What's Changed

• compiler support for standard library features on macos by @chrisfroe in #221
• Fix frozen dict implementation by @clonker in #223

Full Changelog: v2.0.9...v2.0.10

What's Changed

• Remove some submodule dependencies for easier conda-forge integration by @clonker in #219

Full Changelog: v2.0.6...v2.0.7

Patch release

What's Changed

• Diffusion constant can be vec3 by @clonker in #205
• read back older file versions by @clonker in #206
• capsule compartment by @clonker in #207
• Unify compartments and harmonic potentials via geometries by @clonker in #208
• Buildsys by @clonker in #209
• Cleanup by @clonker in #210
• compartments in simulation loop by @clonker in #211
• Fixes by @clonker in #212
• Libstructure by @clonker in #213
• remove variant, can be introduced easier with custom integrator by @clonker in #214
• Get trajectory length from Trajectory instance by @clonker in #215
• cmake cleanup by @clonker in #217
• Cleanup by @clonker in #218

Full Changelog: v2.0.5...v2.0.6

• checkpoints are stored in separate files so corruption is not fatal for the whole simulation (#160)
• reaction counts can be obtained for spatial and structural topology reactions (#162)
• structural topology reactions now need to have a unique name to make them identifiable (#162)
• removed ostream redirect in simulation run loop, could lead to segfault (#162, #161)
• spatial topology reaction counts indexed by name, not descriptor (#163)
• allow spherical barrier with negative height (#164)
• Draw simulation box optionally when converting to xyz (#165)
• Context and simulation workflow also in c++ top level (#167)
• New action BreakBonds that can remove edges in the topology graph, if the potential energy of the corresponding bond exceeds a certain threshold energy (#170)
• Finding all edges in the graph (linked list) is expensive, thus cache all found edges and only update when necessary (#170)
• added graph distance check to topology-topology self-reaction (thanks @ilyasku )
• (corner case) fix collection of dihedral terms (#172)
• Integration test for topology reactions (#173)
• reworked graph library, major refactoring and simplification of codebase (#176)
• custom python simulation loops (#178)
• migrate from travis to github actions (#179)
• use different random number generator with longer period (#181)

• Trajectory with topology observable data can be read back into memory chunk-wise (#147)
• Checkpointing, i.e. make snapshots of the system in regular intervals and save them to file, to continue simulating from there at a later time (#148)
• Remove architecture-invasive timer (#149)
• Change unit testing framework from gtest to Catch2 (#151)
• Refactor and prepations for first-passage time diffusion integrator (#152)
• New topology operation for structural reaction recipes to create a new particle in place and attach it to the topolgy (#153, #154)
• Bugfix in spatial topology reactions ( #155)
• Bugfix in CPU UncontrolledApproximation reaction handler (#158)