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
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
- 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)
OBS-URL: https://build.opensuse.org/request/show/699758
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=7
- 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/642286
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=1
- 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/642129
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=1
