Rewrite particle serialization mechanism #4637
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The Drude particle parameters were incorrect and created particles with negative mass, which would produce NaN values during force calculation, break the LB thermostat, and require workarounds when setting up the H5MD writer.
christophlohrmann
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Dec 22, 2022
reinaual
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Dec 23, 2022
jngrad
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Dec 23, 2022
Fixes espressomd#4633 Release 4.2.0 introduced a regression that causes checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the `DIPOLES` feature is part of the myconfig file. This leads to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director plays a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). Since the default myconfig file contains `DIPOLES`, most ESPResSo users are affected. Description of changes: - write new checkpointing logic to avoid overwriting the particle director with the particle dipole moment - add checks to verify particle properties are correctly reloaded from a checkpoint file - fix regressions in the checkpointing tests
jngrad
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Dec 23, 2022
Fixes espressomd#4633 Release 4.2.0 introduced a regression that causes checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the `DIPOLES` feature is part of the myconfig file. This leads to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director plays a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). Since the default myconfig file contains `DIPOLES`, most ESPResSo users are affected. Description of changes: - write new checkpointing logic to avoid overwriting the particle director with the particle dipole moment - add checks to verify particle properties are correctly reloaded from a checkpoint file - fix regressions in the checkpointing tests
jngrad
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Dec 23, 2022
Fixes espressomd#4633 Release 4.2.0 introduced a regression that causes checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the `DIPOLES` feature is part of the myconfig file. This leads to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director plays a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). Since the default myconfig file contains `DIPOLES`, most ESPResSo users are affected. Description of changes: - write new checkpointing logic to avoid overwriting the particle director with the particle dipole moment - add checks to verify particle properties are correctly reloaded from a checkpoint file - fix regressions in the checkpointing tests
kodiakhq bot
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Feb 24, 2023
Partial fix for #4614 Partial fix for #4617 Follow-up to #4637 Description of changes: - reaction methods are now fully parallel and no longer rely on MpiCallbacks - reaction methods are no longer entangled with the particle management code - the Monte Carlo acceptance probability is now implemented in Python - API changes: - it is no longer possible to change the reaction constant of an existing reaction with `gamma <= 0` - `ReactionAlgorithm.reaction()` now takes `steps` instead of `reaction_steps` as argument - when setting up a MC method with two or more reactions, a runtime error is raised if a reaction accidentally overwrites the default charge of a specific type with a different value - under-the-hood changes: - the `particle_data.cpp` source file was removed - the `EspressoSystemStandAlone` class no longer relies on MpiCallbacks - frequency of cell system invalidation during Monte Carlo trial moves has been significantly reduced - the new Python interface of reaction methods is around 40% slower than the original C++ implementation
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Fixes #4633
Release 4.2.0 introduced a regression that causes checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the
DIPOLESfeature is part of the myconfig file. This leads to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director plays a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). Since the default myconfig file containsDIPOLES, most ESPResSo users are affected.Description of changes: