- Update to 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. No further bug
fix releases will be provided for the 4.2 line.
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).
- Removed upstreamed patches:
- fix-broken-fft-check.patch
- boost-1.74.patch
- numpy-1.24.patch
- rpath.patch
- missing_size_t.patch
- hdf5.patch
- setuptools.patch
OBS-URL: https://build.opensuse.org/request/show/1080211
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=17
- Update to 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.
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).
- Give up on building on 32bit architectures (gh#espressomd/espresso#4537).
- Fix rpath in provided libraries and shebang in pypresso.
OBS-URL: https://build.opensuse.org/request/show/990492
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=14
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.
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
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=32
- enable hdf5 support
- python3-numpy & python3-h5md are needed at runtime
- add 3427.patch to fix tests on i586
- Update to 4.1.2:
- The interface has not been changed between ESPResSo 4.1.1 and
4.1.2.
- General corrections and improvements:
- Remove correlation between the rotational noise and
translational noise in the Langevin thermostat (#3355)
- Fix a bug that may cause the wrong temperature to be set by
the Langevin and DPD thermostats in the first time step
after the system was altered from the Python level, e.g.,
by changing particles or interactions (#3341)
- Fix a bug that caused the DPD thermostat to generate an
incorrect velocity distribution when used together with the
Langevin thermostat (#3352)
- Fix a bug in MMM2D and ELC with potential boundary
conditions, where one of the correction factors was
over-counted resulting in wrong energies (#3310)
- Fix a bug that caused the wrong bonds to be deleted when
removing particles from the system (#3356)
- Fix an ambiguity in `ParticleSlice`: the values in the
square brackets refer to particle ids, not array indices
(#3367). This means the ill-defined syntax
`system.part[0:-1]` is no longer valid. See the User Guide
section on Setting up particles for more information.
- Remove the mass prefactor in the `ComForce` observable and
use the correct Particle ids in the
`ParticleAngularVelocities` and `ParticleBodyVelocities`
observables (#3380)
- Fix a rounding error that caused debug builds of ESPResSo
running with multiple MPI threads to crash when a particle
was placed exactly on the boundary between two cells
(#3377)
- Fix `espressomd.has_features()` for the corner case where
the list of all compiled-in features is passed as argument,
returning ``False`` instead of ``True`` (#3318)
- Refactor the random number generator code (#3349)
- Documentation and tutorials corrections and improvements:
- Improve documentation of Monte Carlo methods (#3254, #3330)
- Build system and platform-related corrections and
improvements:
- List all Python dependencies in `requirements.txt` with the
supported version numbers (#3300). Please note that most of
them are optional.
- Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the
command lines of parallel tests (#3221)
- Add the `-oversubscribe` flag to the command lines of
parallel tests running with OpenMPI v2.X to avoid exiting
early from a Python test configured without `MAX_NUM_PROC`
on a machine with a hyperthreaded CPU where OpenMPI is
configured such that the number of threads cannot exceed
the number of cores (#3335)
- Refactor the CI, maintainer, Doxygen and pypresso shell
scripts to make them more portable and support filepaths
containing whitespaces (#3326, #3373)
- Fix a nvcc compiler warning on the empty config (#3329)
- Improved testing:
- Add a test for ELC and MMM2D using analytic expressions of
the force and energy (#3331)
- Sped-up seven Python tests (#3319)
- Fix a test that broke on s390x architectures with Fedora 31
(#3312)
- Fix tests that broke on i586 architectures with OpenSUSE
Tumbleweed (#3327, #3358)
- Version bump to 4.1.1
* Restore checkpointing mechanism for the steepest descent and NPT
integrators, LB and NPT thermostats (#3245)
* Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and
lower are no longer supported (#3236)
* Fix `Integrator.set_isotropic_npt()`: remove the silent conversion of
the incorrect input parameter `direction=[0,0,0]` to `[1,1,1]` in the
core; the function now throws an exception for fixed-volume boxes;
this change is unlikely to break pypresso scripts since not providing
a value to `direction` or providing `[1,1,1]` were the two standard
ways to set up a box with all directions allowed to rescale (#3253)
* Fix `Integrator.set_vv()`: this function failed to set the velocity
Verlet integrator if the NPT integrator was active; this is now
resolved (#3274)
* Fix the random segmentation fault triggered by the removal of a
particle with a bond or a virtual site relationship to another
particle (#3288)
* Fix `system.part.writevtk()`: the function now writes down all
particles when using `types="all"` (#3290)
* Disable the deprecated and broken ENGINE shear torque calculation
feature; the feature will be completely removed from the core in
the upcoming 4.2 release (#3277)
* Fix unit conversion for the LB fluid viscosity (#3287)
- Version bump to 4.0.2
*Corrections for bugs that may harm simulation results:
* A sign error in tabulated interactions was corrected such that
the force equals the negative gradient of the potential.
(#2519,2520)
* The flow field of the CPU lattice-Boltzmann implementation was
deleted when aspects of the molecular dynamics cell grid were
changed; E.g., when interactions, the skin or the parallelization
setup were changed. ESPResSo now terminates with an error, when this
happens. To avoid this, please setup the CPU lattice-Boltzmann after
all other aspects of the system. The GPU LB is not affected in the
4.0 release, but was affected in the current development branch.
(#2728, #2736)
* Corrected the force acting on LB Boundaries for the case of
agrid and density not equal to 1 (#2624).
* Corrected the cutoff calculation for the soft sphere interaction. In
the previous implementation, the offset parameter was ignored.
(#2505)
* The "three point coupling" of particles to the lattice-Boltzmann
method has been removed. While it works in most environments, for
some compilers the calculation gives wrong values. This is likely
caused by undefined behavior. A corrected implementation is
available in ESPResSo's development branch. It cannot be safely
backported to 4.0.2, because the code has diverged too far. (#2516,
#2517) Users who did not explicitly activate this coupling via
couple="3pt" are not affected.
* The velocity of existing particles was changed when setting or
changing the simulation time step (#2480)
* Further changes:
* Fixed the electrokinetic Python interface (#2486)
* Correction to the installation instructions for mac (#2510)
* Corrected file permissions (#2470)
* Minor corrections and extensions to the test suite (#2477, #2552)
* Fixed a dead-lock in the dipolar Barnes Hutt method on the GPU for
recent NVIDIA cards such as RTX 2080 (#2719).
* Restored Mayavi visualizer's API-compatibility with OpenGL
visualizer (#2751)
- Version bump to 4.0.1
* Many small bugfixes
- Drop 2255.patch, 2259.patch and 2265.patch - merged upstream
- added change from request #639007
- rename package to python3-espressomd
- install COPYING for all packages
- change license to GPL-3.0-or-later
- added sonum define
- Version bump to 4.0.0
- Rename pacakge to python-espressomd
- Dropped 1830.patch - merged upstream
- Dropped doc package - under rework in 4.0.0
- New features:
- Reaction ensemble methods for the modelling of chemical reactions, including constant pH and Wang-Landau schemes.
- Polarisable particles via the Drude-oscillator scheme.
- Steepest-descent energy minimization scheme.
- Methods for active particles (swimmer_reaction, dipolar swimmers).
- GPU-accelerated P3M method for electrostatic interactions.
- GPU-accelerated direct summation and Barnes-Hutt schemes for dipolar interactions under open boundary conditions.
- Support for the electrostatic and magnetostatics method provided by the ScaFaCoS library.
- Immersed boundary method for soft immersed objects in an LB fluid.
- Virtual sites acting as inertialess tracers in an LB fluid usable as part of the immersed boundary method or independently.
- New bonded quartic and Coulomb interactions.
- Possibility to tune the skin parameter.
- Support for saving to the h5md file format for molecular dynamics data.
- Connection to the MD Analysis Python package.
- A rotate_system command was added, which rotates the particle positions around the system’s center of mass.
- Added 2255.patch to fix numpy issue on i586
- Added 2259.patch to fix numpy issue on big-endian platforms
- Added 2265.patch to fix test on i586
- add 1830.patch to fix install
- update version 3.3.1+git20180203.f74064d
* many many small fixes
* support for newer cython
- adapt to new openlmi package - source mpivars.h during build
- use individual libboost-*-devel packages instead of boost-devel
- RPM group fixup
- switched to cmake build-system
- build python module
- dropped header as they are for internal use only
- dropped pkg-config files as nothing depends on libs yet
- update version 3.3.1+git20160803.6ed0518.tar.gz
* overhaul of buildsystem
* many many small fixes
- fix boo#985147
* there's a commit that removed redefinition of malloc and realloc
which fixed build for gcc 6. but it's too hard to cherry pick, so
update to the latest git version is a good idea
- there's no --without-mpi option left in configure.ac, so "-openmpi"
sub-package is meaningless now (everything has openmpi support)
and since there's no two main packages any more, "-common" sub-package
is also meaningless now (and it doesn't contains data), merged.
- add sub-package: "-devel", "libEspresso0", "libEspressoTcl0"
- add generate_headers.rb to gather those .hpp that're really used
into "-devel" sub-package
- create pkgconfig files
- add some texlive BuildRequires to build pdf documentation.
- update version 3.3.1+git20160622.6aa229c:
* added edge statistics for meshes used by object-in-fluid
* added pos_folded property
* Adapted simple LB tests to current interface.
* system.part.writevtk()
* redesigned exclusions and added slice input
* Scafacos: Add long range energy to correct place in energy data structure
* Correction to scafacos energy calculation: Check cutoff in near field contrib
* Scafacos: Sort out conditional compilation and cython includes
* Scafacos: methods shared between electrostatics and dipolar calculations
- Update to version 3.3.1
* A lot of changes; please read the NEWS file
- version bumped to 3.3.0
- Highlights of this release include:
- Calculation of the electrokinetic equations via the ELECTROKINETICS feature,
- the Shan/Chen method for multi component lattice Boltzmann fluids,
- the P3M and MMM1D methods can now be computed on a GPU,
- ESPResSo now has a rudimentary Python interface.
For a complete list of the changes in the release, please refer to:
http://download.savannah.gnu.org/releases/espressomd/NEWS
- build openmpi and non-mpi version
- initial commit
OBS-URL: https://build.opensuse.org/request/show/802785
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=17
- Update to 4.1.2:
- The interface has not been changed between ESPResSo 4.1.1 and
4.1.2.
- General corrections and improvements:
- Remove correlation between the rotational noise and
translational noise in the Langevin thermostat (#3355)
- Fix a bug that may cause the wrong temperature to be set by
the Langevin and DPD thermostats in the first time step
after the system was altered from the Python level, e.g.,
by changing particles or interactions (#3341)
- Fix a bug that caused the DPD thermostat to generate an
incorrect velocity distribution when used together with the
Langevin thermostat (#3352)
- Fix a bug in MMM2D and ELC with potential boundary
conditions, where one of the correction factors was
over-counted resulting in wrong energies (#3310)
- Fix a bug that caused the wrong bonds to be deleted when
removing particles from the system (#3356)
- Fix an ambiguity in `ParticleSlice`: the values in the
square brackets refer to particle ids, not array indices
(#3367). This means the ill-defined syntax
`system.part[0:-1]` is no longer valid. See the User Guide
section on Setting up particles for more information.
- Remove the mass prefactor in the `ComForce` observable and
use the correct Particle ids in the
`ParticleAngularVelocities` and `ParticleBodyVelocities`
observables (#3380)
- Fix a rounding error that caused debug builds of ESPResSo
running with multiple MPI threads to crash when a particle
was placed exactly on the boundary between two cells
(#3377)
- Fix `espressomd.has_features()` for the corner case where
the list of all compiled-in features is passed as argument,
returning ``False`` instead of ``True`` (#3318)
- Refactor the random number generator code (#3349)
- Documentation and tutorials corrections and improvements:
- Improve documentation of Monte Carlo methods (#3254, #3330)
- Build system and platform-related corrections and
improvements:
- List all Python dependencies in `requirements.txt` with the
supported version numbers (#3300). Please note that most of
them are optional.
- Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the
command lines of parallel tests (#3221)
- Add the `-oversubscribe` flag to the command lines of
parallel tests running with OpenMPI v2.X to avoid exiting
early from a Python test configured without `MAX_NUM_PROC`
on a machine with a hyperthreaded CPU where OpenMPI is
configured such that the number of threads cannot exceed
the number of cores (#3335)
- Refactor the CI, maintainer, Doxygen and pypresso shell
scripts to make them more portable and support filepaths
containing whitespaces (#3326, #3373)
- Fix a nvcc compiler warning on the empty config (#3329)
- Improved testing:
- Add a test for ELC and MMM2D using analytic expressions of
the force and energy (#3331)
- Sped-up seven Python tests (#3319)
- Fix a test that broke on s390x architectures with Fedora 31
(#3312)
- Fix tests that broke on i586 architectures with OpenSUSE
Tumbleweed (#3327, #3358)
OBS-URL: https://build.opensuse.org/request/show/764825
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=5
- Update to 4.1.2:
- The interface has not been changed between ESPResSo 4.1.1 and
4.1.2.
- General corrections and improvements:
- Remove correlation between the rotational noise and
translational noise in the Langevin thermostat (#3355)
- Fix a bug that may cause the wrong temperature to be set by
the Langevin and DPD thermostats in the first time step
after the system was altered from the Python level, e.g.,
by changing particles or interactions (#3341)
- Fix a bug that caused the DPD thermostat to generate an
incorrect velocity distribution when used together with the
Langevin thermostat (#3352)
- Fix a bug in MMM2D and ELC with potential boundary
conditions, where one of the correction factors was
over-counted resulting in wrong energies (#3310)
- Fix a bug that caused the wrong bonds to be deleted when
removing particles from the system (#3356)
- Fix an ambiguity in `ParticleSlice`: the values in the
square brackets refer to particle ids, not array indices
(#3367). This means the ill-defined syntax
`system.part[0:-1]` is no longer valid. See the User Guide
section on Setting up particles for more information.
- Remove the mass prefactor in the `ComForce` observable and
use the correct Particle ids in the
`ParticleAngularVelocities` and `ParticleBodyVelocities`
observables (#3380)
- Fix a rounding error that caused debug builds of ESPResSo
running with multiple MPI threads to crash when a particle
was placed exactly on the boundary between two cells
OBS-URL: https://build.opensuse.org/request/show/764818
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=11
- Version bump to 4.1.1
* Restore checkpointing mechanism for the steepest descent and NPT
integrators, LB and NPT thermostats (#3245)
* Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and
lower are no longer supported (#3236)
* Fix `Integrator.set_isotropic_npt()`: remove the silent conversion of
the incorrect input parameter `direction=[0,0,0]` to `[1,1,1]` in the
core; the function now throws an exception for fixed-volume boxes;
this change is unlikely to break pypresso scripts since not providing
a value to `direction` or providing `[1,1,1]` were the two standard
ways to set up a box with all directions allowed to rescale (#3253)
* Fix `Integrator.set_vv()`: this function failed to set the velocity
Verlet integrator if the NPT integrator was active; this is now
resolved (#3274)
* Fix the random segmentation fault triggered by the removal of a
particle with a bond or a virtual site relationship to another
particle (#3288)
* Fix `system.part.writevtk()`: the function now writes down all
particles when using `types="all"` (#3290)
* Disable the deprecated and broken ENGINE shear torque calculation
feature; the feature will be completely removed from the core in
the upcoming 4.2 release (#3277)
* Fix unit conversion for the LB fluid viscosity (#3287)
OBS-URL: https://build.opensuse.org/request/show/748973
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=9
