Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / readdy/readdy issues and pull requests

#232 - Release ReaDDy on PyPI

Issue - State: open - Opened by blairlyons 6 months ago - 1 comment

#231 - Fission rate constant

Issue - State: closed - Opened by kaa-git over 1 year ago - 4 comments

#230 - Custom potentials for topologic particles

Issue - State: open - Opened by LisaYMD over 1 year ago - 2 comments

#229 - Pybind11 via submodule

Pull Request - State: closed - Opened by clonker over 2 years ago

#228 - catch2 v2 -> v3

Pull Request - State: closed - Opened by clonker over 2 years ago

#227 - set random seed for batch job

Issue - State: open - Opened by mheldman over 2 years ago - 6 comments

#226 - compile cpu kernel directly into library

Pull Request - State: closed - Opened by clonker almost 3 years ago

#225 - Topology reactions not recorded

Issue - State: closed - Opened by zichenzachwang almost 3 years ago - 1 comment

#224 - compile-time index loop unroll

Pull Request - State: closed - Opened by clonker about 3 years ago

#223 - Fix frozen dict implementation

Pull Request - State: closed - Opened by clonker about 3 years ago

#222 - Migrate CI to mambabuild over conda-build

Issue - State: closed - Opened by clonker about 3 years ago
Labels: enhancement

#221 - compiler support for standard library features on macos

Pull Request - State: closed - Opened by chrisfroe about 3 years ago - 1 comment

#220 - Unable to open file from killed simulation run

Issue - State: closed - Opened by jansteinkuehler over 3 years ago - 6 comments

#219 - Remove some submodule dependencies for easier conda-forge integration

Pull Request - State: closed - Opened by clonker over 3 years ago

#218 - Cleanup

Pull Request - State: closed - Opened by clonker over 3 years ago

#217 - cmake cleanup

Pull Request - State: closed - Opened by clonker over 3 years ago

#216 - Recentre atoms based on centre-of-mass of topology

Issue - State: open - Opened by debeshmandal over 3 years ago - 8 comments

#215 - Get trajectory length from Trajectory instance

Pull Request - State: closed - Opened by clonker over 3 years ago

#214 - remove variant, can be introduced easier with custom integrator

Pull Request - State: closed - Opened by clonker over 3 years ago

#213 - Libstructure

Pull Request - State: closed - Opened by clonker over 3 years ago

#212 - Fixes

Pull Request - State: closed - Opened by clonker over 3 years ago

#211 - compartments in simulation loop

Pull Request - State: closed - Opened by clonker over 3 years ago

#210 - Cleanup

Pull Request - State: closed - Opened by clonker over 3 years ago

#209 - Buildsys

Pull Request - State: closed - Opened by clonker over 3 years ago

#208 - Unify compartments and harmonic potentials via geometries

Pull Request - State: closed - Opened by clonker over 3 years ago

#207 - capsule compartment

Pull Request - State: closed - Opened by clonker over 3 years ago

#206 - read back older file versions

Pull Request - State: closed - Opened by clonker over 3 years ago

#205 - Diffusion constant can be vec3

Pull Request - State: closed - Opened by clonker over 3 years ago

#204 - CI finalize

Pull Request - State: closed - Opened by clonker over 3 years ago

#203 - Azure pipelines

Pull Request - State: closed - Opened by clonker over 3 years ago

#202 - h5py modifications

Pull Request - State: closed - Opened by clonker over 3 years ago

#201 - make PyVertex comparable

Pull Request - State: closed - Opened by clonker almost 4 years ago

#200 - Problems while trying to get the index of a vertex neighbor

Issue - State: closed - Opened by miglesias92 almost 4 years ago - 4 comments

#199 - Self reactions

Pull Request - State: closed - Opened by clonker almost 4 years ago

#198 - Association reaction of identical particles

Issue - State: open - Opened by kaa-git almost 4 years ago - 19 comments

#197 - Simulation run problems

Issue - State: closed - Opened by kaa-git almost 4 years ago - 5 comments

#196 - Problem with particles unique ids and vertexes indexes

Issue - State: closed - Opened by miglesias92 about 4 years ago - 3 comments

#195 - Hierarchical Grids for Polydisperse Systems

Issue - State: open - Opened by ilyasku about 4 years ago - 2 comments

#194 - fix python api for structural reactions

Pull Request - State: closed - Opened by clonker about 4 years ago

#193 - Manual compile and install lead to CPU kernel missing

Issue - State: closed - Opened by ilyasku about 4 years ago - 3 comments

#192 - Rate function spatial reaction

Pull Request - State: closed - Opened by ilyasku about 4 years ago - 7 comments

#191 - Spatial Topology Reactions with Rate Function

Issue - State: closed - Opened by ilyasku about 4 years ago - 7 comments

#189 - pip compatible setup

Pull Request - State: closed - Opened by clonker over 4 years ago

#188 - PyPI release / help with install on local testing

Issue - State: closed - Opened by evamaxfield over 4 years ago - 2 comments

#187 - Handle removal of edges gracefully

Pull Request - State: closed - Opened by clonker over 4 years ago

#186 - fix separate vertex

Pull Request - State: closed - Opened by clonker over 4 years ago

#185 - Test MPI observables

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#184 - Towards a RAII Kernel implementation

Issue - State: open - Opened by clonker almost 5 years ago
Labels: long-term

#183 - Observable refactoring and implementations for MPI Kernel

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#182 - MPI fixes and cleanup, update json library

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#181 - Fix random number engine

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#180 - Diffusion Patterns Repeating

Issue - State: closed - Opened by ilyasku almost 5 years ago - 6 comments
Labels: bug

#179 - Github actions workflow

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#178 - Custom simulation loop

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#177 - MPI Synchronization

Pull Request - State: closed - Opened by chrisfroe almost 5 years ago

#176 - Refactoring to use new graph library

Pull Request - State: closed - Opened by clonker almost 5 years ago

#175 - Each topology is limited to one reaction per time step

Issue - State: closed - Opened by ilyasku about 5 years ago - 3 comments

#174 - MPI domains, and timer with json output

Pull Request - State: closed - Opened by chrisfroe about 5 years ago

#173 - Integration test for topology reactions

Pull Request - State: closed - Opened by chrisfroe about 5 years ago

#172 - fix collection of dihedral terms

Pull Request - State: closed - Opened by clonker about 5 years ago

#171 - Network fusion

Pull Request - State: closed - Opened by ilyasku over 5 years ago - 8 comments

#170 - Breaking bonds and caching edges

Pull Request - State: closed - Opened by chrisfroe over 5 years ago

#169 - Reworked simulation progress bar handling, some cleanup

Pull Request - State: closed - Opened by clonker over 5 years ago

#168 - make_checkpoints function

Issue - State: closed - Opened by JoulesJ over 5 years ago - 4 comments

#167 - Context and simulation workflow also in c++ top level

Pull Request - State: closed - Opened by chrisfroe over 5 years ago

#166 - Some cleanup and MPI kernel preparations

Pull Request - State: closed - Opened by chrisfroe over 5 years ago

#165 - [utils] Draw simulation box optionally when converting to xyz

Pull Request - State: closed - Opened by chrisfroe over 5 years ago

#164 - spherical barrier with negative height should be allowed

Pull Request - State: closed - Opened by clonker over 5 years ago

#162 - Reaction counts for topology reactions

Pull Request - State: closed - Opened by clonker over 5 years ago - 1 comment

#161 - Disabling show_progress leads to segmentation fault

Issue - State: closed - Opened by tlkaufmann over 5 years ago - 4 comments

#160 - Checkpointing in separate files

Pull Request - State: closed - Opened by clonker over 5 years ago

#159 - Change ColorID in `convert_trajectory_to_xyz`

Issue - State: closed - Opened by tlkaufmann over 5 years ago - 4 comments

#158 - Bugfix in CPU UncontrolledApproximation reaction handler

Pull Request - State: closed - Opened by chrisfroe over 5 years ago - 1 comment

#157 - Michaelis-Menten benchmark results not consistent in parallel kernel="CPU"

Issue - State: closed - Opened by satya-arjunan over 5 years ago
Labels: bug

#156 - Growing Polymer with Constant Concentration

Issue - State: closed - Opened by JoulesJ almost 6 years ago - 4 comments

#155 - bugfix spatial topology reactions

Pull Request - State: closed - Opened by chrisfroe almost 6 years ago

#154 - [topology reactions / append particle] fix failed state

Pull Request - State: closed - Opened by clonker almost 6 years ago

#153 - Append particle topology reaction recipe action

Pull Request - State: closed - Opened by clonker almost 6 years ago

#152 - Refactor and preparations for first-passage time integrator

Pull Request - State: closed - Opened by chrisfroe almost 6 years ago

#151 - change unit testing framework to Catch2

Pull Request - State: closed - Opened by clonker about 6 years ago

#150 - replace google test with catch2

Issue - State: closed - Opened by clonker about 6 years ago
Labels: suggestion

#149 - remove performance timer

Pull Request - State: closed - Opened by clonker about 6 years ago

#148 - Checkpointing

Pull Request - State: closed - Opened by clonker about 6 years ago

#147 - Trajectory with topology observable data...

Pull Request - State: closed - Opened by clonker over 6 years ago

#146 - Cylinder potentials

Pull Request - State: closed - Opened by chrisfroe over 6 years ago - 1 comment

#145 - fixed a call to remove edge that was delegating to add edge

Pull Request - State: closed - Opened by clonker over 6 years ago

#144 - allow non-negative force constants for harmonic bonds

Pull Request - State: closed - Opened by clonker over 6 years ago

#143 - Fix in topology-topology fusion

Pull Request - State: closed - Opened by clonker over 6 years ago

#142 - recipe can now change particle positions

Pull Request - State: closed - Opened by clonker over 6 years ago

#141 - Method to set particle positions

Issue - State: closed - Opened by ejisaac over 6 years ago - 1 comment

#140 - Improve unit handling

Pull Request - State: closed - Opened by chrisfroe over 6 years ago

#139 - clean state model

Pull Request - State: closed - Opened by clonker over 6 years ago

#138 - fix #135

Pull Request - State: closed - Opened by clonker over 6 years ago

#137 - Modifying access to reaction rates

Pull Request - State: closed - Opened by clonker over 6 years ago

#135 - Encountering strange behavior with Topology-Topology spatial reaction

Issue - State: closed - Opened by ejisaac over 6 years ago - 1 comment

#134 - Functions to set reaction rates

Issue - State: closed - Opened by ejisaac over 6 years ago - 2 comments

#133 - Relicense

Pull Request - State: closed - Opened by clonker over 6 years ago