Highly versatile open-source software package for performing and analyzing scientific Molecular Dynamics and many-particle simulations of coarse-grained atomistic or bead-spring models used in soft matter research in physics, chemistry, and molecular biology.
Highly versatile open-source software package for performing and analyzing scientific Molecular Dynamics and many-particle simulations of coarse-grained atomistic or bead-spring models used in soft matter research in physics, chemistry, and molecular biology.
Highly versatile software package for performing and analyzing scientific Molecular Dynamics and many-particle simulations of coarse-grained atomistic or bead-spring models.
Open-source Python package for building and managing coarse-grained models of polyelectrolytes, peptides, proteins, and hydrogels in ESPResSo.
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Claim ESPResSoESPResSo has transitioned toward wider GPU support by adding infrastructure for the Kokkos C++ performance portability library. This update establishes CPU as the default execution space while preparing the framework for CUDA-based GPU acceleration. The changes include adjustments to toolchain compiler flags for combined C++/CUDA compilation and the addition of functionality to query the compiler toolchain used for builds.
The ESPResSo software team corrected an issue in the DPD (Dissipative Particle Dynamics) pressure calculation where excluded particle pairs were incorrectly contributing to the DPD virial. By moving force accumulation inside the particle exclusion loop, the fix ensures that excluded pairs do not contribute to the pressure tensor, aligning the computation with intended physical constraints. A new test suite was included to verify the fix.
The software team updated the pressure tensor analysis conventions in ESPResSo. The previous DPD stress observable was replaced with a more consistent DPD pressure function, resolving issues where the system incorrectly returned the negative and transpose of the pressure tensor. These changes ensure consistency across internal observables and provide a more accurate contribution of dissipative and noise-derived forces to the total pressure tensor.
The fractal dimension analysis tool within ESPResSo was updated to correctly handle mandatory input parameters. Previously, the fractal_dimension argument was advertised as optional within the Cluster analysis docstring, creating discrepancies for users. The fix enforces 'dr' as a required parameter and adds error handling to prevent improper function calls.
A noise term was added to the Dissipative Particle Dynamics (DPD) pressure calculation in ESPResSo. Previously, the pressure calculation only accounted for dissipative forces. The update incorporates the random (stochastic) component of DPD forces, achieving full consistency between force calculation and noise-weighted pressure calculations, as validated by new statistical tests.
