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NEWS
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=================
= ESPRESSO NEWS =
=================
ESPResSo 4.2.1
==============
This release provides a number of corrections for the ESPResSo 4.2 line.
We recommend that this release be used for all production simulations.
The interface has not been changed between ESPResSo 4.2.0 and 4.2.1.
However, some bugs were discovered which can affect simulation results.
Please find the list of changes below. The numbers in brackets refer to
ticket numbers on https://github.com/espressomd/espresso
Added functionality
-------------------
* P3M and DipolarP3M can now be used with the hybrid decomposition cell
system with 1 MPI rank (#4678).
* Lattice-Boltzmann can now be used with the N-square and hybrid
decomposition cell systems with 2 or more MPI ranks (#4676).
Changed requirements
--------------------
* The nbconvert version requirement was bumped to 6.5.1 to patch an XSS
vulnerability (#4658).
Improved documentation
----------------------
* The user guide now documents how to improve the reproducibility of
simulations that have checkpointing enabled (#4677).
* The user guide now reflects that the lattice-Boltzmann profile observables
can be used in parallel (#4583).
* The active matter tutorial now uses an adequate engine dipole for the
swimmer particle (#4585).
* The error analysis tutorials have been improved (#4597).
* The tutorials can now be used in VS Code Jupyter (both the desktop and web
versions) and the mathematical formula are now correctly displayed (#4531).
* All ESPResSo-specific CMake options are now documented in the installation
chapter of the user guide (#4608).
* Python package installation instructions no longer feature package version
numbers; instead, `requirements.txt` is used as a constraint file (#4638).
* MMM1D algorithms now properly document their parameter names (#4677).
* Reaction methods now cite the relevant literature (#4681).
* Caveats for chain analysis methods are now documented (#4698).
* Minor formatting issues in Sphinx and typos in Python docstrings were
addressed (#4608).
Interface changes
-----------------
* A new boolean property `System.virtual_sites.override_cutoff_check` was
introduced to allow disabling the cutoff range checks from virtual sites
(#4623).
Removed functionality
---------------------
* The unused and untested `Analysis.v_kappa()` method was removed (#4534).
Improved testing
----------------
* Improve unit testing of core functionality: P3M, MMM1D, OIF, virtual sites,
script interface factory (#4631).
Bug fixes
---------
* The checkpointing mechanism now properly restores the particle quaternion
and all derived quantities (#4637). Release 4.2.0 introduced a regression
that caused checkpoint files to overwrite the particle quaternion/director
by a unit vector pointing along the z direction, when the `DIPOLES` feature
was part of the myconfig file. This lead to incorrect trajectories when
reloading a simulation from a checkpoint file, if the particle director
played a role in the simulation (ex: relative virtual sites, Gay-Berne
potential, anisotropic particles, active particles, etc.). In addition,
the angular velocity in body frame was restored with the wrong orientation.
Since the default myconfig file contains `DIPOLES`, most ESPResSo users
were affected.
* The checkpointing mechanism now properly restores LB boundaries (#4649).
Release 4.2.0 introduced a regression where reloading LB populations
would accidentally reset LB boundary flags.
* The checkpointing mechanism now restores P3M and DipolarP3M solvers without
triggering a re-tune (#4677). In previous releases, the checkpointing code
would automatically re-tune these algorithms during a reload, causing tiny
deviations in the forces that were problematic for trajectory reproducibility.
* Brownian dynamics now integrates the rotational dynamics of rotatable
particles whose position is fixed in 3D space (#4548).
* Langevin dynamics now properly integrates particles with anisotropic
friction (#4683, #4690).
* A regression that caused virtual sites to incorrectly count their image box
when crossing a periodic boundary has been fixed (#4564, #4707).
* Particles can no longer be created or updated with a negative mass or a
null mass (#4679).
* Particles created without a user-specified type can now participate in
reactions (#4589).
* When a Monte Carlo displacement move is rejected, the original particle
velocity is now restored (#4589).
* Reaction methods now raise an exception when accidentally calling
`method.reaction(steps=20)` instead of `method.reaction(reaction_steps=20)`
(#4666). Since 4.2.0 the `steps` argument was ignored, in which case the
default value `reaction_steps=1` would used by the core. Note that in the
next minor release of ESPResSo, the `reaction_steps` argument will be
renamed to `steps`.
* Reaction methods now rebuild the list of free particle ids every time
`WidomInsertion::calculate_particle_insertion_potential_energy()` and
`ReactionAlgorithm::do_reaction()` are called (#4609). This was needed to
allow multiple concurrent reactions, as well as avoiding subtle bugs when
both the user and a reaction method tried to create a new particle with
an id that used to belong to a deleted particle.
* When all particles are cleared, the reaction methods type map is now also
cleared (#4645). In the past, it was possible to attempt a reaction on
particles that had just been cleared from the system, which would raise
an exception. This bug affected all ESPResSo releases since 4.0.
* The `System.part.pairs()` method now returns the correct particle pairs
when particle ids aren't both contiguous and starting from 0 (#4628).
The regression was introduced in release 4.2.0.
* The auto-exclusions feature no longer adds spurious exclusions to particle
ids in the range [1, distance] (#4654). This bug would potentially break
the physics of the system and potentially raise an exception in a system
with non-contiguous particle ids. This regression was introduced in release
2.2.0b.
* The structure factor analysis code no longer double-counts particles when
the same particle type is provided twice (#4534).
* The minimal distance distribution analysis code no longer has an arbitrary
cutoff distance when the simulation box is aperiodic (open boundaries);
this would cause spurious artifacts to appear in the histogram at
`r = np.sum(system.box_l)` when particles were further apart than this
arbitrary distance (#4534).
* The cluster analysis functions are now disabled for systems with
Lees-Edwards periodic boundaries, since the cluster analysis position
wrapping code doesn't properly handle the shear offset (#4698).
* The chain analysis methods now raise an error when the number of chains or
beads per chain is invalid (#4708).
* The observable tests now longer rely on deprecated numpy options that were
removed in numpy 1.24 (#4635).
* The visualizer `*_arrows_type_materials` options now have an effect on
arrow materials (#4686).
* The visualizer exception handling mechanism has been made less brittle
(#4686).
* The visualizer no longer raises exception when the optional dependency
`freeglut` isn't installed (#4691).
* The visualizer can randomly freeze when using collision detection or bond
breakage; a temporary workaround has been introduced that fixes the issue
for simulations that use only 1 MPI rank (#4686).
* The `__dir__()` method of script interface objects no longer raises an
exception (#4674).
* Compilation and testsuite issues involving missing or incorrect feature
guards were addressed (#4562, #4648).
* The build system no longer silently ignores invalid external feature
definitions in `myconfig.hpp` and CMake files (#4608). This issue would
only affect feature developers, as well as users of very old compilers,
and would lead to ESPResSo builds missing features.
Under the hood changes
----------------------
* The Clang 14 and AppleClang 14 compilers are now supported (#4601).
* Several Clang 14 compiler diagnostics have been addressed (#4606).
* Boost 1.81 and later versions are now supported (#4655).
* Compiler errors on non-x86 architectures were addressed (#4538).
* Test tolerances were adjusted for non-x86 architectures (#4708).
* The pypresso script now prints a warning when running with MCA binding
policy "numa" on NUMA architectures that are not supported in singleton
mode by Open MPI 4.x (#4607).
* The config file generator has been rewritten to properly handle external
features and compiler errors (#4608).
* Security hardening for GitHub Workflows (#4577, #4638) and Codecov (#4600).
* Deployment of the user guide to GitHub Pages now relies on cloud providers
to fetch JavaScript dependencies (#4656).
ESPResSo 4.2.0
==============
This is a feature release, i.e., new functionality is added to ESPResSo.
New thermostats, cell systems and boundary conditions have been introduced
to simulate systems with Stokesian Dynamics, Brownian Dynamics, strongly
inhomogeneous particle sizes or translation-invariant shear flow. The
interface underwent (non-silent) changes, therefore scripts will have to
be slightly adapted. Most notably, particle access by id and particle
slices have a new syntax, and electrostatic/magnetostatic layer correction
and reaction methods have a different setup. All errors are also now
emitted as Python exceptions and are recoverable with minimal effort.
An additional focus of this release is the simplification of both the C++ core
and the Python script interface to facilitate future extensions of ESPResSo.
The testing of ESPResSo's functionality has been extended considerably.
We recommend that this release be used for all production simulations.
No further bug fix releases will be provided for the 4.1 line, and not
all fixes are present in ESPResSo 4.1.4.
Please carefully read the detailed list of changes below before using this
release. Issues can be reported at https://github.com/espressomd/espresso.
Added functionality
-------------------
* `P3MGPU` now supports energy and pressure calculation via the CPU
kernels (#4506).
* `ELC` now works with `P3MGPU` (#4506).
* The LB grid now supports slicing operations (#4195) and LB slices are
equality comparable (#4268).
* Lees-Edwards boundary conditions can be used for particle-based
simulations (#4457). Lattice-Boltzmann support will be added in
the 4.3.0 release.
* The non-bonded energy of a single particle can be calculated (#4401).
* The list of close neighbors of a single particle can be extracted (#4401).
* Brownian Dynamics simulations can be carried out with the newly added
Brownian integrator and Brownian thermostat (#1842).
* Stokesian Dynamics simulations can be carried out with the newly added
Stokesian integrator and Stokesian thermostat (#3790, #3987).
* Bonded interactions can now be automatically broken when the bond length
exceeds a critical value (#4456). This feature can be combined with
collision detection to model reversible bonds (#4464).
* A new cell system `HybridDecomposition` was introduced to speed up
simulations with inhomogeneous particle interaction ranges (#4373).
* Shapes can be merged into meta-shapes (#3493, #3538).
* The `HollowConicalFrustum` can now be sliced open, made thick and rotated
to model quarter pipes in any orientation (#4179). The main application is
in the construction of complex microchannel geometries via `LBBoundaries`.
* A parametric weight function was added to the DPD interaction (#3570).
* H5MD output files now support a unit system (#3751).
* H5MD output files now support custom specifications to control which
particle and box properties to write to disk (#4480).
* The `H5md` class is now checkpointable and usable in an interactive
Python session (#3751).
* MDAnalysis integration now provides bond information (#3801).
Changed requirements
--------------------
* The minimal version of all dependencies was increased (#3375, #3687,
#3878, #3984, #3994, #4115, #4312, #4337, #4489): Python 3.8, Cython
0.29.14, CMake 3.16, Boost 1.69, Sphinx 2.3.0, and Python packages
versions are pinned on versions available in the Ubuntu 20.04 repository.
* CMake no longer emits a warning about the deprecated `distutils` Python
package, which is also no longer a requirement (#4433).
* CUDA 11 support was added (#3870).
* CUDA 8 and CUDA 9 support was removed (#3984).
* AMD GPU support via ROCm (HCC and HIP-Clang compilers) was removed (#3966).
* library `libcuda` is no longer a dependency in CUDA builds (#4095).
* Installation instructions for ESPResSo on Microsoft Windows via WSL are
now available (#4348).
* LaTeX is no longer a requirement for building the Sphinx documentation
and running the tutorials (#3256, #3395).
Feature configuration at compile time
-------------------------------------
* GPU support is now opt-in (#3582). Pass the CMake flags `-DWITH_CUDA=ON`
to compile CUDA code and optionally `-DWITH_CUDA_COMPILER=<compiler>` to
select the CUDA compiler: NVCC (default), Clang.
* Optional features HDF5, ScaFaCoS and Stokesian Dynamics are now opt-in
(#3735, #4112). If they are requested with their `-DWITH_<FEATURE>=ON`
flag and their dependencies are not found, CMake will raise an error.
In the older 4.1 build system, CMake would silently ignore these features
when their dependencies were not found, causing confusion as to what was
exactly compiled.
* Experimental support for fast-math mode was added (#4318). Some features
might break depending on the compiler used to build ESPResSo. Please
quantify the numerical stability of your simulations before enabling
fast-math mode in production.
* The `LANGEVIN_PER_PARTICLE` feature was renamed to
`THERMOSTAT_PER_PARTICLE` (#4057).
* The magnetostatic extension `DLC` now depends on feature `DIPOLES`
instead of `DP3M`, since FFTW is not a dependency of `DLC` (#4238).
* The electrostatic extension `ICC` now depends on feature `ELECTROSTATICS`
instead of `P3M`, since FFTW is not a dependency of `ICC` (#4238).
* The `MMM1D_MACHINE_PREC` feature was added to enable Chebychev series for
MMM1D on CPU without the need to define the (now removed)
`BESSEL_MACHINE_PREC` macro (#4311).
* The `EXPERIMENTAL_FEATURES` feature was removed (#4482).
Improved documentation
----------------------
* Tutorials have been renamed and organized by difficulty level (#3993).
* Tutorials Lennard-Jones, electrostatics, lattice-Boltzmann, raspberry
electrophoresis and constant-pH have been improved (#3408, #3881, #3914,
#3893, #4302, #4262).
* Tutorial lattice-Boltzmann was split into three tutorials: polymer
diffusion, Brownian motion and Poiseuille flow (#4052, #4329).
* The active matter tutorial was rewritten into a Jupyter notebook
(#3395, #4304).
* An error analysis tutorial was added (#4174).
* Tutorials now use the `exercise2` plugin to hide solutions (#3872);
since this plugin only exists for the classic Jupyter Notebook,
a conversion script is provided for JupyterLab users (#4522).
* The user guide now includes a button on Python code samples to hide
terminal output and Python prompt symbols (`>>>` and `...`), so as to
facilitate copy-pasting examples directly in the terminal (#4386).
* The user guide now uses a responsive theme for mobile/tablet users (#4504).
* The user guide chapter on thermostats was moved to the chapter on
integrators, since they are tightly coupled (#4080).
* Mentions to non-existent functions were removed from the user guide (#4482).
* Scientific publications referenced in comment lines in the core have been
converted to BibTeX citations and integrated into Doxygen blocks to make
them accessible in the Doxygen HTML documentation (#3304).
* The Reaction Field electrostatic method is now documented (#4218).
* The H5MD feature is now better documented (#4480).
* A Gibbs ensemble sample was added to simulate the exchange of particles
between two ESPResSo systems via the `multiprocessing` Python module (#4243).
* A reaction ensemble sample was added to simulate a complex chemical
reaction involving 5 chemical species (#3778).
Interface changes
-----------------
* The `system.set_random_state_PRNG()` method was removed (#3482).
* The []-operator on `system.part` was removed (#4402). Use
`system.part.by_id(1)` to fetch a specific particle,
`system.part.by_id([1, 3])` to fetch a group of particles, or
`system.part.all()` to fetch all particles. This change was necessary
to resolve the ambiguity of particle slices containing non-contiguous
particle ids.
* The domain decomposition cell system was renamed to regular decomposition
(#4442). The `system.cell_system.set_domain_decomposition()` function
was renamed to `system.cell_system.set_regular_decomposition()`.
* Bonds are now immutable (#4350). Bonds added to the list of bonds can
no longer be overwritten by a bond of a different type, as it could
lead to undefined behavior when the number of bonded partners was
higher in the overwriting bond. Bonds can now be removed from the
list of bonds, after they have been removed from particles.
* Observable parameters are now immutable (#4206, #4211).
* The `Electrokinetics` actor parameters are now immutable (#4327).
* The `LBFluid`, `LBFluidGPU`, `Electrokinetics` and `Species` methods
`print_*()` have been renamed to `write_*()` (#4049).
* The `ELC` actor is no longer an electrostatics extension (#4125, #4506).
The `ELC` actor now takes a `P3M` or a `P3MGPU` actor as argument and
modifies it. Only the `ELC` actor needs to be added to the system list
of actors. The `ELC` actor can now be removed from the list of actors.
* The `DLC` actor is no longer a magnetostatic extension (#4506). The
`DLC` actor now takes a magnetostatic actor as argument and modifies it.
Only the `DLC` actor needs to be added to the system list of actors.
* The NpT thermostat now uses the Philox random number generator and
requires a random seed on first instantiation (#3444).
* The analysis module `energy()` function now returns the lower triangle
of the non-bonded interaction matrix, to be consistent with `pressure()`
and `stress_tensor()` (#3712).
* The analysis module `energy()`, `pressure()` and `pressure_tensor()`
functions now return only two slots for electrostatics and magnetostatics:
short-range contribution in the first slot and long-range contribution +
layer correction in the second slot (#3770).
* The analysis module `pressure()` and `pressure_tensor()` functions no
longer provide a velocity-compensation flag to compute the pressure at
half the time step in NpT simulations (#3756).
* The `espressomd.reaction_ensemble` module was renamed to
`espressomd.reaction_methods` (#4482).
* The argument `temperature` in reaction methods was renamed to `kT`
for clarity (#4305).
* All reaction methods now take keyword arguments instead of positional
arguments (#4451).
* The constant pH method now implements a symmetric proposal probability
instead of an asymmetric proposal probability (#4207).
* The reaction method parameter `exclusion_radius` was renamed to
`exclusion_range` (#4469).
* Reaction method now take an optional parameter `exclusion_radius_per_type`
for better control of the exclusion radius in simulations involving
different particle sizes (#4469).
* The `WidomInsertion.measure_excess_chemical_potential()` method was
replaced by `WidomInsertion.calculate_particle_insertion_potential_energy()`,
which returns the instantaneous value of the excess chemical potential
instead of the accumulated mean and standard error (#4374). The mean value
and standard error of the excess chemical potential must be now be
calculated by `WidomInsertion.calculate_excess_chemical_potential()`.
* Reaction method constraints can now be safely changed from cylindrical
to slab and can be removed (#4310). They will also raise an error when
created with invalid parameters.
* The `mpiio` global variable was removed (#4455). The MPI-IO feature is now
used by creating a local instance with `mpiio = espressomd.io.mpiio.Mpiio()`.
* The MPI-IO feature now raises an exception from which the user can
recover when the simulation script runs on 1 MPI rank, instead of
an unrecoverable fatal error (#4455). This change is meant to help
debugging read/write errors in simulation scripts. On 2 or more MPI
ranks, exceptions still lead to a fatal error.
* The `H5md` class takes new arguments during instantiation (#3785).
* The `system.cell_system.get_pairs_()` method was renamed to
`system.cell_system.get_pairs()` and now supports filtering particle
pairs by type (#4035).
* The polymer setup code was moved from the core to Python (#3477). The
`espressomd.polymer.positions()` function was renamed to
`espressomd.polymer.linear_polymer_positions()` and the
`espressomd.diamond.Diamond` class was converted to function
`espressomd.polymer.setup_diamond_polymer()`. For diamond polymers,
counter-ions must now be added manually by the user.
* The particle director can be set from the Python interface (#4053).
* The particle method `vs_auto_relate_to()` can take a particle as
argument instead of a particle id (#4058).
* Particles can be serialized and deserialized in the Python interface with
`particle_dict = p.to_dict()` and `system.part.add(particle_dict)` (#4060).
* It is no longer necessary to manually reshape the output of `Observable`
objects. The `Observable` classes now return multi-dimensional numpy
arrays and the documentation clearly indicates the shape and size of
the calculated data (#3560). The same applies to accumulators and
time series (#3578).
* `Accumulator` and `Correlator` classes now return the data in suitably
shaped multi-dimensional numpy arrays; dependent properties such as lag
times and sample sizes need to be obtained separately by calling methods
`lag_times()` resp. `sample_sizes()` (#3848).
* `Profile` observables provide methods `bin_centers()` and `bin_edges()`
to facilitate plotting (#3608).
* The observable `ComForce` was renamed to `TotalForce`, so as to better
reflect what it actually calculates (#3471).
* The RDF feature was removed from the analysis module and converted to
an Observable class (#3706). Time averages can be obtained using the
`TimeSeries` accumulator.
* All occurrences of "Stress Tensor" in the analysis module, LB module and
EK module were renamed to "Pressure Tensor" to better reflect what is
actually calculated (#3723, #4228).
* The `MeanVarianceCalculator` interface changed (#3996).
* Observables now check their input parameters (#4211, #4255) and raise
an exception when an invalid value is detected (e.g. `min_x > max_x`
in profile-based observables).
* Cylindrical observable classes have an extra `transform_params` argument
to change the orientation of the cylindrical coordinates systems and
control the origin of the phi angle (#4152).
* Incompatible thermostat/integrator combinations raise an exception (#3880).
* The `system.cuda_init_handle.list_devices()` feature is now a function,
and the `system.cuda_init_handle.list_devices_properties()` function
disabled in 4.0.0 was restored (#4095).
* CUDA errors now halt the flow of the program by throwing a Python
exception with a clear error message (#4095).
* Parameter `particle_scales` of coupling-based fields `PotentialField`
and `ForceField` now takes a `dict` object instead of a list of tuples
(#4121).
* The `System` class no longer has a `globals` member (#4276). Global
variables are still accessible from other members of the `System` class.
* Methods from the cluster analysis class `Cluster` no longer returns
`False` when a string passed to `call_method()` doesn't match the name
of a core method; instead `None` is returned (#4234).
* Methods from the cluster analysis class `ClusterStructure`, integrator
classes and interaction classes no longer returns `True` when the
corresponding core method doesn't return a value; instead `None`
is returned (#4234, #4516).
* Several parameters of the `ICC` class are no longer optional: `epsilons`,
`normals`, `areas`, `sigmas` (#4162).
* The electrostatic actors charge neutrality check tolerance can be modified
via `actor.charge_neutrality_tolerance`; this is mostly relevant to actors
coupled to `ICC`, whose induced charges can have values spanning several
orders of magnitude (#4506).
* Electrostatic and magnetostatic methods that support tuning now have a
`timings` argument to control the number of integration loops to run
during tuning (#4276).
* The Drude helpers (global variables and free functions) have been
gathered into a checkpointable class `DrudeHelpers`, which now relies
on particle handles instead of particle ids (#4353).
* ScaFaCoS integration now supports activating an electrostatics ScaFaCoS
actor at the same time as a magnetostatics ScaFaCoS actor (#4036).
* The list of actors can no longer end up in an invalid state: updating
an electrostatic or magnetostatic actor with an invalid parameter now
automatically restores the original parameter; inserting an invalid
electrostatic or magnetostatic actor in the list of actors now
automatically removes the actor from the list of active actors,
even when the exception happens during tuning (#4506).
* The `LBBoundaries` slip velocity check was lowered to Mach 0.35, or 0.2 in
LB units (#4376).
* The OpenGL visualizer allows changing the radius of LB velocity arrows,
documents all LB-related keyword arguments, and no longer suffers from
a division-by-zero error that used to trigger a runtime warning for
fluid inside boundaries (#4376).
* The `Electrokinetics` class got an optional `ext_force_density` parameter
for consistency with other LB implementations (#4203).
* MDAnalysis integration now checks if the MDAnalysis package version is
supported (#4386).
Removed functionality
---------------------
* The `ENGINE` shear torque calculation feature deprecated in 4.1.1 was
removed (#3277).
* The `MEMBRANE_COLLISION` and `OifOutDirection` features were removed
(#3418).
* The `AFFINITY` feature was removed (#3225).
* The unused and untested `UMBRELLA` feature was removed (#4032, #4079).
* The unused and untested `VIRTUAL_SITES_COM` feature was removed (#3250).
* The unused and untested `EK_DOUBLE_PREC` feature was removed (#4192).
* The unused and untested MD metadynamics feature was removed (#3563).
* The unused and untested `Stomatocyte` shape was removed (#3730).
* The `PdbParser` feature deprecated in 4.1.1 was removed (#3257).
* The incorrectly implemented and untested `HarmonicDumbbellBond`
interaction was removed (#3974, #4079).
* The layered cell system was removed (#3512).
* The unused Wang-Landau reaction ensemble algorithm was removed (#4288).
* The reaction ensemble tutorial deprecated in 4.1.1 was removed (#3256).
* The per-particle temperature feature was removed (#4057).
* The `Current` observable was removed in favor of the `FluxDensityProfile`
observable (#3973).
* The incorrectly implemented analysis function `cylindrical_average` was
removed in favor of the `CylindricalDensityProfile` observable (#3470).
* The `minimize_energy` member of the `System` class was removed (#3390,
#3891). The steepest descent algorithm is now a regular integrator that
is set up via the `system.integrator.set_steepest_descent()` method.
* The MMM2D electrostatics feature was removed (#3340). Electrostatics in
slab geometries can still be achieved by ELC, with significantly better
performance.
* The dipolar direct sum with replica method is now disabled on periodic
systems with zero replica, as it does not apply minimum image convention
(#4061).
* The analysis module `min_dist2()` function was removed and the `dist_to()`
function was merged into `system.distance_vec()` (#3586).
* The analysis module `nbhood()` function slab search mode was removed
(#4516) since it was incorrect (all ESPResSo versions were affected).
* The number of cells for the link cell algorithm can no longer be
constrained to a range of values (#3701).
* The global Mersenne Twister RNG was removed (#3482). All thermostats
are now Philox-based. Local Mersenne Twister RNGs are still used in
the linear polymer position generator (now with proper warmup) and
in the `ReactionAlgorithm` class.
* It is no longer possible to checkpoint an ESPResSo system instance that
contains `Union` shape-based constraints when the simulation is running
with 2 or more MPI ranks. An error will be raised (#4287, #4510).
* It is no longer possible to checkpoint an `Electrokinetics` instance (#4327).
* The unmaintained `lj-demo.py` sample was removed (#4482).
* The unmaintained `mayaviLive` visualizer was removed (#4515).
Improved testing
----------------
* The C++ core of ESPResSo is covered by unit tests and integration tests
at 98% coverage (#4426, #4479, #4489).
* The structure factor code is tested against simple lattices (#4205).
* The MMM1D GPU code is tested (#4064).
* The reaction method core classes are unit tested (#4164).
Performance enhancements
------------------------
* The `Particle` memory footprint was reduced and the MPI serialization
code was improved (#4414). The structure size is now 584 bytes instead
of 640 bytes on maxset configuration (10% reduction). All substructures
in `Particle` are bitwise serializable and dynamic vectors are compact
vectors. The performance gain is about 9% for a LJ liquid on both maxset
and empty configurations, for both 1 000 and 10 000 particles per core.
* Particle creation happens in constant time instead instead of monotonically
increasing with the number of particles already in the system (#4493).
* When only one MPI rank is used, the maximum cutoff of bonded interactions
is ignored when initializing the cell properties, since the bond partners
are always accessible on the same node, regardless of the cell size; if
the system also doesn't have short-range interactions, the short-range
loop is skipped (#4452).
* The `ReactionAlgorithm::do_reaction()` function used by reaction methods
now caches the potential energy of the system and only updates it after
a successful reaction trial move (#4374).
* Reaction methods can delegate the particle neighbor search to the cell
system when evaluating the exclusion range of inserted particles (#4401).
This leads to better performance only on 2 or more MPI ranks.
Bug fixes
---------
* The `transform_vector_cartesian_to_cylinder()` now calculates the correct
phi angle (#4094). The bug was present since ESPResSo 4.0.0 and affected
observables `CylindricalVelocityProfile`, `CylindricalFluxDensityProfile`,
`CylindricalLBVelocityProfile`, `CylindricalLBVelocityProfileAtParticlePositions`,
`CylindricalLBFluxDensityProfileAtParticlePositions`.
* Several memory leaks were fixed in the `TabulatedBond` interactions
(#3961), electrostatics and magnetostatics tuning functions (#4069),
lattice-Boltzmann code (#4108) and Barnes-Hut code (#4404).
* The `system.actors.clear()` method was broken and would only remove half
of the actors since 4.0.0. This is now fixed (#4037).
* The `ClusterStructure` feature did not properly handle box periodicity
since 4.0.0 and would under rare circumstances calculate a center of mass
to be outside a fully periodic simulation, and would incorrectly fold
coordinates in aperiodic systems. This is now fixed (#4363).
* Adding a LB thermostat when any other thermostat was already active would
silently fail since 4.0.0. This is now fixed (#4116).
* Setting the NpT or steepest descent integrators with incorrect parameters
no longer leaves the system in an undefined state (#4026).
* The OpenGL visualizer had a tendency to slow down after pausing and
resuming the simulation, or freezing when using the steepest descent
integrator. This was due to a race condition between two threads that
has been fixed (#4040).
* The OpenGL visualizer no longer raises an exception when activating the
`LB_draw_boundaries` option without any other `LB_draw_*` option (#4479).
* The OpenGL visualizer now correctly updates bond information when the
collision detection and bond breakage features are used (#4502).
* It is no longer possible to accidentally set a non-cubic NpT integrator
with P3M (#4165).
* The NpT integrator used to work with `P3MGPU` even though it didn't
implement long-range energy calculation and therefore couldn't contribute
to the virial; now the long-range energy is calculated and added to the
virial (#4026, #4506).
* Illegal LB node access is now properly caught by exceptions (#3978).
* EK node access no longer accepts floating-point values for node indices
(#4228), and always requires exactly three integers (#4482).
* Accessing the flux property of EK species no longer throws an error
(#4106).
* Accessing the `boundary` field of LB nodes from a `LBFluid` actor when
`LB_BOUNDARIES` is not compiled in now returns 0 instead of a random
integer (#4479).
* The LB grid in the GPU implementation is now automatically resized when
the simulation box size changes (#4191).
* The LB code now throws an error when adding a LB boundary to the
`LBFluid` actor when `LB_BOUNDARIES` is not compiled in, or to the
`LBFluidGPU` actor when `LB_BOUNDARIES_GPU` is not compiled in (#4472).
* The lattice-Boltzmann Python interface no longer ignores runtime errors,
nor converts them to cryptic system errors (#4355).
* The script interface no longer silently ignores runtime errors when
converting Python objects to C++ data types (#4387, #4492).
* The system now throws an error when a non-bonded interaction cutoff is
too large for the local box size in MPI-parallel simulations; in older
releases the error was queued and deferred to the integration loop (#4479).
* The system now throws an error when a virtual site tracks a real particle
too far away for the local box size in MPI-parallel simulations; in older
releases the error was queued and deferred to the integration loop (#4479).
* It is no longer possible for a virtual site to track itself (#4479).
* It is no longer possible for a particle to exclude itself (#4493).
* It is no longer possible to accidentally add the same bond twice on the
same particles (#4058).
* Fatal errors triggered by stale references in virtual sites, invalid
particle ids and null quaternions have become runtime exceptions (#4479).
* Virtual sites now contribute to the rotational kinetic energy of the
system (#4198).
* Particle creation no longer raises `numpy.VisibleDeprecationWarning`
(#4493).
* The EK feature now generates VTK files that are compliant with the VTK 2.0
standard (#4106).
* The `ELC` and `DLC` actors now throw an error when a particle enters the
gap region (#4051).
* The `ELC` actor is now updated when the box size changes in the
z-direction (#4231).
* The `DLC` actor now raises an exception when tuning fails instead of
causing a fatal error (#4238).
* The `MMM1D` actor now raises an exception for incorrect periodicity or
cell system instead of causing a segfault (#4064).
* The `DipolarP3M` checkpointing mechanism was fixed (#3879).
* The `DipolarP3M` method now recalculates the energy correction when the
box length changes (#4506).
* P3M-based actors now sanitize the user-provided `alpha` and `accuracy`
parameters and no longer allow constraining the `alpha` parameter during
tuning (`alpha` was always derived from the other parameters at the end
of tuning) (#4118).
* A buffer overflow in the `DipolarP3M` tuning function lead to random
failures during tuning, this is now fixed (#3879).
* A buffer overflow in the LB code could lead to incorrect results in grids
of size 9x9x9 or larger with open boundaries, this is now fixed (#4078).
* Providing incorrect parameters to the ScaFaCoS actors no longer cause
ESPResSo to crash (#4068).
* FENE, harmonic and quartic bonds now throw an error when the bond length
is zero and the equilibrium bond length is non-zero, since the direction
of the force cannot be determined (#4471).
* Immutable parameters `default_scale`, `particle_scales` and `gamma` of
coupling-based fields `PotentialField`, `ForceField`, `FlowField` and
`HomogeneousFlowField` now throw an error when an attempt is made to
change their value via the class setter, instead of silently ignoring
the new value (#4121).
* The `CylindricalLBFluxDensityProfileAtParticlePositions` observable now
measures the correct quantity (#4152).
* The Boost 1.74 bug was patched (#3978).
* A bug involving an access out of bounds was fixed in the structure factor
code (#4205).
* A bug in the collision detection feature that lead to a harmless warning
being printed to the terminal upon collision was fixed (#4484).
* Calling `collision_detection.set_params()` with invalid arguments no
longer leaves the collision detection feature in an indeterminate state;
the previous state is automatically rolled back (#4484).
* Setting the collision detection mode `glue_to_surface` or
`bind_at_point_of_collision` when feature `VIRTUAL_SITES_RELATIVE`
is not compiled in now generates the correct error message (#4484).
* Passing a particle chain-based observable object (`ParticleDistances`,
`BondAngles`, `BondDihedrals`, `CosPersistenceAngles`) that doesn't have
enough particle ids for the calculation (e.g. only 1 particle id when 2
are needed for the bond distance calculation) to a `Correlator` object
no longer causes a memory overflow (#4255).
* Calculating the energy of the system when an IBM object is present no
longer terminates ESPResSo, instead a warning is issued (#4286).
* The `Sphere` shape no longer returns NaN values in the distance vector
for particles located exactly in its center (#4384).
* Runtime errors raised when the maximal bonded interaction range becomes
larger than the simulation box are no longer ignored when dihedral bonds
are added to the list of interactions (#4383).
* Runtime errors about incorrectly initialized electrostatic/magnetostatic
methods are no longer silently ignored at integration start (#4383).
* Runtime errors about incorrectly initialized GPU dipolar direct sum and
Barnes-Hut are no longer silently ignored when the actors are instantiated
(#4404).
* A bug that could potentially lead to stale references in the script
interface was fixed (#4476).
* `TabulatedNonBonded.is_active()` now returns `False` instead of `None`
when the interaction is inactive (#3586).
Under the hood changes
----------------------
* The Python code is now checked with Pylint to prevent the introduction
of unused code and dangerous anti-patterns (#3293, #3203).
* The CMakeLists.txt files are now formatted automatically with
`cmake-format` (#3622).
* The Python code and C++ code were checked with LGTM to detect and fix
coding errors and anti-patterns (#3851, #3856, #4300).
* Compiler warnings and diagnostics from GCC 11, 12, from Clang 10, 12, 13, 14
and from Intel 19.0.4 were addressed (#4084, #4426, #4510, #4526).
* The `Particle` struct was moved to a dedicated header file `Particle.hpp`
to improve separation of concerns in the core (#3251, #3164).
* The `Observable_stat` structs were moved to a dedicated header file
`Observable_stat.hpp` and decoupled from the pressure/energy/coulomb/dipolar
frameworks (#3712) and made stateless (#3723).
* Observables based on particle ids have been rewritten using particle traits
to decouple the `Particle` struct from `Observable` classes (#3667).
* The Python `Integrator` class was split into multiple classes, one for each
integrator, with a structure similar to actor and interaction classes
(#3390). This layout better reflects the structure of integrators in
the core and will make it easier to include new integrators in the future.
This change doesn't break the API.
* The ghost communication infrastructure was simplified (#3216, #3399).
* The LB coupling for the regular decomposition scheme was rewritten (#4470).
* Thermostats are now fully object-oriented in the core to reduce code
duplication (#3438, #3444, #3461).
* Bonded interactions are now fully object-oriented in the core to
facilitate the development of new interactions (#4161).
* Bonded interactions are now communicated between MPI processes
automatically and transparently by the script interface (#4350).
* The custom `MpiCallbacks` framework has been simplified and the callbacks
made more homogeneous (#4383).
* The custom `MpiCallbacks` framework is being progressively replaced by
`boost::mpi` communication (#4506, #4511).
* The `local_particles` global variable is no longer accessible directly
(#3501).
* The Python tests now use specialized assertions to generate more helpful
error messages (#3419).
* The tutorial tests were simplified using AST to parse Jupyter notebooks
(#3408).
* The CMake logic for tutorials has been simplified (#3408, #3486).
* The Cython interface was thoroughly cleaned up from unused imports
(#3496, #3510).
* The `ScriptInterface` framework was rewritten (#3794).
* The `ScriptInterface` framework is now the preferred way to implement
new features. Existing features were converted to `ScriptInterface`
objects: bonded interactions (#4350), bond breakage (#4464), collision
detection (#4484), reaction methods (#4451), MPI-IO (#4455), H5MD (#4480),
cell system (#4511), actors, scafacos, electrostatics and magnetostatics
(#4506). The corresponding Cython files were converted to Python files.
* It is now possible to extend the list of available specifications in the
H5MD feature at the C++ level (#4480).
* The duplicated functions between `P3M` and `DipolarP3M` were factored out
(#3879).
* Statistical tests are no longer executed in coverage and sanitizers
builds (#3999).
* The `Utils::Mpi::gather_buffer()` function was fixed (#4075). The bug
didn't affect ESPResSo.
* Parameters can be passed to CTest at configuration time via the new
`CTEST_ARGS` CMake option (#3862). This replaces the deprecated and