ESPResSo

Edit Package python3-espressomd

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes.

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Source Files
Filename Size Changed
boost-1.74.patch 0000001435 1.4 KB
espresso-4.2.0.tar.gz 0014000445 13.4 MB
hdf5.patch 0000000410 410 Bytes
missing_size_t.patch 0000000309 309 Bytes
python3-espressomd.changes 0000018963 18.5 KB
python3-espressomd.spec 0000004494 4.39 KB
rpath.patch 0000000358 358 Bytes
Revision 14 (latest revision is 21)
Richard Brown's avatar Richard Brown (RBrownFactory) accepted request 990492 from Matej Cepl's avatar Matej Cepl (mcepl) (revision 14)
- 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.
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