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WIP: Stokesian Dynamics#3445

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biermanncarl wants to merge 179 commits intoespressomd:pythonespressomd/espresso:pythonfrom biermanncarl:sdbiermanncarl/espresso:sdCopy head branch name to clipboard

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Commits on Jun 30, 2019

• [SD] Starting with the new implementation

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• [SD] Stokesian dynamics in the integration loop

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• [SD] Unequal radius, variable viscosity

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• [SD] Communicate new positions and velocities

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• [SD] Interface

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• [SD] Sample for dancing spheres

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• [SD] Adapt to the new MPI communication scheme

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• [SD] Rebase onto latest origin/python

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• [SD] Lubrication corrections and feature bitflags

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Commits on Oct 8, 2019

• Merge remote-tracking branch 'origin/python' into sd

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• [SD] Adapt to new integrators

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• [SD] Associate radius with particle type

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• [SD] Expose bit flags for feature selection

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• [SD] Move implementation to libs/stokesian_dynamics

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• [SD] Test against reference data from Brady's paper

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Commits on Oct 9, 2019

• Formatting suggested by fix_style

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• [SD] Add reference, check Euclidean distance

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• [SD] Communicate rotations to core

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Commits on Oct 11, 2019

• [SD] First take on thermalization

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• [SD] make kT optional

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Commits on Oct 15, 2019

• [SD] thermalization test

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Commits on Dec 16, 2019

• Merge remote-tracking branch 'origin/python' into sd

  

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Commits on Jan 14, 2020

• A few changes regarding PBC check in SD MPI particle transfer

  

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Commits on Jan 23, 2020

• trying parallelization

  

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Commits on Jan 29, 2020

• implemented multithread support for the SD integrator

  

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Commits on Feb 4, 2020

• fixed rotation

  

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Commits on Feb 11, 2020

• some changes

  

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Commits on Feb 20, 2020

• Fixed SD thermalisation, now dependency on temperature and particle

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• Added SD setup test

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• Formatting with fix_style

  

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• More style corrections

  

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Commits on Mar 23, 2020

• fixed rescaling bug, added thrust wrapper

  

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• style corrections

  

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• removed unused stuff from SD test

  

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• temporarily removed style_doxygen from gitlab

  

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• minor change

  

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• Make STOKESIAN_DYNAMICS an external feature

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• Merge branch 'python' into sd

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• Revert "temporarily removed style_doxygen from gitlab"

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Commits on Mar 30, 2020

• fixed merge with recent python branch + introduced non-cuda rng

  

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• Fix regression with feature STOKESIAN_DYNAMICS

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Commits on Mar 31, 2020

• fixed crash when running SD integrator

  

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Commits on Apr 1, 2020

• refactored SD cmake logic and compiler option logic, SD is internal

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• style

  

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• temporarily removed CMake section to add SD GPU code, so that we can

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• temporarily removed CMake section to add SD GPU code, so that we can test CI at least for CPU

  

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Commits on Apr 2, 2020

• suppress compiler warnings in Random123

  

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• addition to commits 965e509 and 149aa2d

  

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Commits on Apr 6, 2020

• get rid of various compiler warnings

  

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• correct dumb mistake

  

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• adding install commands for SD libraries

  

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Commits on Apr 8, 2020

• fixed a_host array legth

  

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• fixed compiler warnings

  

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• added boost to libs SD dependencies

  

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Commits on Apr 9, 2020

• trying to fix OSX linker issue

  

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• Revert "trying to fix OSX linker issue"

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• CMake: use python -m sphinx instead of sphinx-build et al.

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• blacklist Sphinx 3.0.0

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• removed EspressoCore dependency from sd_interface

  

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• Fix sphinx version regex

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• fix sphinx apidoc detection above version 1.7

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• sd_interface.cpp is now part of EspressoCore library

  

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• Merge commit 'refs/pull/3648/head' of https://github.com/espressomd/espresso into sd

  

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Commits on Apr 14, 2020

• fix RNG issue

  

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• fix_style: try python3 -m pre_commit if pre-commit not found

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• Merge commit 'refs/pull/3661/head' of https://github.com/espressomd/espresso into sd

  

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• style

  

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• fix cmake_format or pylint not found

  

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Commits on Apr 15, 2020

• SD: fix issue with rotation on Clang

  

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• SD: started SPHINX documentation

  

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Commits on Apr 16, 2020

• added sd.rst to CMakeLists.txt

  

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• Merge commit 'refs/pull/3666/head' of https://github.com/espressomd/espresso into sd

  

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• fix add_css_file incompatible with Sphinx below 1.8

  

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Commits on Apr 20, 2020

• added MWE to documentation

  

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Commits on Apr 21, 2020

• SD: refactor python interface

  

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Commits on Apr 22, 2020

• remove old code from fix_style.sh

  

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• style

  

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• SD: refactor SD test and update to new interface

  

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Commits on Apr 28, 2020

• SD: fix undefined rotation when omega=0

  

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• SD: adding/correcting code documentation

  

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Commits on Apr 29, 2020

• SD: revert unwanted changes

  

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• revert more unwanted change

  

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• SD: add copyright headers, change code documentation

  

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• SD: removed a debug log

  

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• SD: added doxygen to device_matrix

  

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Commits on May 8, 2020

• SD: updated documentation

  

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• SD: add to documentation

  

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• SD: documentation

  

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• SD: remove lubrication from (documented) ESPResSo

  

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• SD: citations

  

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Commits on May 13, 2020

• SD: cleanup of CMake

  

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• SD: remove commented out code

  

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• Update doxygen in libs/stokesian_dynamics/device_matrix.hpp

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• Update documentation of libs/stokesian_dynamics/sd.hpp

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• Update documentation of libs/stokesian_dynamics/sd.hpp

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• SD: minor cleanups

  

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• Revert "SD: cleanup of CMake"

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• SD: STOKESIAN_DYNAMICS_GPU won't be set

  

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• SD: removed debugging code

  

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• SD: removed #ifdef ROTATION

  

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• SD: changes in serialization

  

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• SD: remove #ifdef ROTATION once more

  

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• SD: add header protectors

  

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• SD: removed CXX_14_CONSTEXPR from multi_array.hpp

  

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• SD: update sample dancing.py

  

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Commits on May 14, 2020

• SD: mainly in-code documentation

  

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Commits on May 18, 2020

• SD: in-code documentation

  

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Commits on May 19, 2020

• SD: in-code documentation

  

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• SD: restructured SD solver for clarity

  

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• SD: fix in-code documentation formulas

  

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Commits on May 20, 2020

• SD: raise error upon Lubrication usage

  

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Commits on May 22, 2020

• SD: renamed lubrication_method to approximation_method (now matches the

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• SD: reactivate (and fix) GPU version

  

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• SD: deactivate STOKESIAN_DYNAMICS_GPU again

  

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• SD: deactivate overlap check

  

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• SD: add header protectors

  

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• Merge branch 'python' into sd

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• Remove overload optional argument

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• Revert "SD: deactivate STOKESIAN_DYNAMICS_GPU again"

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• SD: get rid of Clang-sanitizer warnings

  

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• Update src/core/stokesian_dynamics/sd_interface.cpp

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  2 peopleauthored and

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• SD: replace cuda_add_library() with custom add_gpu_library()

  

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• SD: fix possible repeated branch in conditional chain error

  

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• Silence Clang-Tidy warnings from thrust

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Commits on May 28, 2020

• Merge branch 'python' into sd

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• SD: Add missing dependency

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• SD: Add CUDA libraries for the Clang compiler

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Commits on Jun 3, 2020

• SD: add ROCm support

  

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Commits on Jun 4, 2020

• ROCm 3.5 CMake fixes

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• ROCm 3.5 compiler flags need a different variable

  

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• cmake: Make Stokesian Dynamics optional

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• cmake: Make Stokesian Dynamics external

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• cmake: Decouple CMake logic from myconfig.hpp

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• sd: Add support for ROCm 3.3

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Commits on Jun 8, 2020

• Revert "cmake: Decouple CMake logic from myconfig.hpp"

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• Add missing externals

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• Merge branch 'python' into sd

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• docs: Document SD dependencies and CMake flag

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Commits on Jun 12, 2020

• cmake: convert SD to FetchContent project

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• cmake: Use SD with add_subdirectory

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• docs: Fix links and bash variables

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• docs: Explain how to install without network

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• sd: Fix compiler guards

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• CI: Use latest ROCm image with all dependencies

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Commits on Jun 15, 2020

• sd: Fix compiler issue with CUDA 10.1 + thrust 1.9.5

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• sd: Remove license headers

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• sd: Move header files to /src

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• sd: Simplify GPU guards

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• docs: Fix Sphinx issues in SD

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• cmake: Correctly locate CUDA libraries

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• cmake: Remove misplaced flag

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• core: Fix compiler error in NO_ROTATION builds

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• Merge remote-tracking branch 'origin/cmake-deps-inversion' into sd

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• cmake: Dependency inversion

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• Merge branch 'python' into sd

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• Formatting

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• cmake: Fix operator precedence

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Commits on Jun 16, 2020

• SD: Update documentation

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• SD: Add missing license headers

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• SD: Simplify interface code

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• SD: Add CMake version guard for CUDA 10

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• Formatting

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• Merge branch 'python' into sd

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• SD: Test checkpointing mechanism

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• testsuite: Fix MAX_NUM_PROC

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• SD: Split GPU and CPU test

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• SD: Disable GPU test

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• SD: Commit missing files...

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Commits on Jul 1, 2020

• Merge branch 'python' into sd

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• SD: Test CPU version on multiple OSse

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Commits on Jul 2, 2020

• SD: Integrate SD docs into the integrator and thermostat pages

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• SD: Improve sample

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• SD: Test sample

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• SD: Accelerate tests

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• SD: Style fix

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• Formatting

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• SD: Mark GPU implementation as experimental

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• Fix build system

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• SD: Rename integrator and thermostat

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