README.md

Mirheo

Computational Microfluidics

Mirheo is a GPU high-performance and high-throughput code aimed at simulation of flows at milli- and microscales. The code uses Dissipative Particle Dynamics method to describe the liquid and its interaction with cells and rigid bodies.

For more information, please refer to the online documentation: http://mirheo.readthedocs.io/

If you want to cite this repository, please use the reference of the corresponding paper [1]:

@article{alexeev2020a,
author = {Dmitry Alexeev and Lucas Amoudruz and Sergey Litvinov and Petros Koumoutsakos},
doi = {10.1016/j.cpc.2020.107298},
journal = {Computer Physics Communications},
month = {mar},
pages = {107298},
publisher = {Elsevier {BV}},
title = {Mirheo: High-performance mesoscale simulations for microfluidics},
url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/alexeev2020a.pdf},
year = {2020}
}

Installation

git clone --recursive https://github.com/cselab/Mirheo
cd Mirheo
make install

Publications

[1] D. Alexeev, L. Amoudruz, S. Litvinov, and P. Koumoutsakos, “Mirheo: high-performance mesoscale simulations for microfluidics," Comput. Phys. Commun., p. 107298, 2020 10.1016/j.cpc.2020.107298

[2] A. Economides, G. Arampatzis, D. Alexeev, S. Litvinov, L. Amoudruz, L. Kulakova, C. Papadimitriou, and P. Koumoutsakos, “Hierarchical bayesian uncertainty quantification for a model of the red blood cell," Phys. Rev. Appl., vol. 15, iss. 3, 2021. 10.1103/physrevapplied.15.034062

Gallery

Single ABF in a blood suspension	Swarm of ABFs in a blood bifurcation

Changelog

unreleased

• Add extended DPD interactions for visco-elastic fluids (see Ten Bosh 99)
• Add EMA plugin
• Add smooth-velocity-based visco-elastic DPD interactions
• Add compilation option to disable stacktrace (when lib-bfd is not available)
• Add sinusoid forcing term (for kolmogorov forcing)

v1.6.1

• Add ChainObjectVector to model polymers
• Add FENE interactions for ChainObjectVector
• Add Four-roll mill force plugin
• Add plugin to dump ChainObjectVector as polylines
• Allow deformable object vectors to be bounced from walls
• bug fixes
  • No duplicate ObjectVector interactions when interacting with itself through pairwise interactions

v1.6.0

• remove support for config/snapshot. Use checkpoint/restart instead.
• Add growing repulsive LJ pairwise interaction.
• Shardlow integrator: randomize loop order.

v1.5.2

• Add magnetic dipole-dipole interactions plugin
• interface changes
  • Rename magneticOrientation plugin to externalMagneticTorque.
  • Stats plugin: restart now adds to the previously written stats instead of overwriting the file.
  • Object Stats plugin: restart now adds to the previously written stats instead of overwriting the file.
  • Object Stats plugin: takes a filename instead of the path. This allows to avoid to create a directory and is more flexible.
  • Velocity control plugin: restart now adds to the previously written stats instead of overwriting the file.

v1.5.1

• Add particle averager plugin
• Add binding (spring) interaction between particle vectors
• Add Shardlow integrator for membranes
• Add pairwise Morse potential
• Docs: Add ADE model and add the corresponding reference.
• interface changes
  • remove setSpecificPair from pairwise interactions. The same effect can be obtained by creating more pairwise interactions instead.
  • wall force collector plugin: use csv format for output.
  • wall force collector plugin: add optional "detailed" dump.
  • Shape Bouncers: warnings are now optional, disabled by default.
  • Add cupy-compatible bindings to per particle and per object channels.
  • Add DomainInfo and time states to the bindings.
  • Add MIRHEO_DEBUG_LEVEL environment variable.
  • stats plugin: reordered filename and every arguments. Add optional list of pvs to compute stats from.
• bug fixes
  • RDF plugin: fixed a bug that occured when the max distance was more than a third of the subdomain.

v1.5.0

• Add MSD plugin.
• update pybind11 submodule.
• update variant submodule (now supports nvcc-10.2).
• Cmake options are prepended with MIR_
• add support for multistage simulations: run may be invoked multiple times
• add Mirheo::deregisterIntegrator and Mirheo::deregisterPlugin
• interface changes
  • the dt parameter was moved from the Mirheo constructor to the run, makeFrozenWallParticles and makeFrozenRigidParticles methods
• internal changes
  • MirState::dt may now be accessed only through MirState::getState and only during Mirheo::run.

v1.4.1

• Add Rdf plugin.
• Add developer documentation of plugins.

v1.4.0

• add basic structure for the development documentation
• particle checker plugin dumps all particle fields when triggered
• add experimental and partial support for saving a snapshot of the whole Mirheo state
• add __main__.py commands run and compile_opt
• add classical (non-repulsive) 12-6 Lennard-Jones interaction
• add support for specifying Mirheo's unit system (based on pint)
• add energy minimization integrator (gradient descent)
• add VACF computation plugin
• interface changes
  • grow_until parameter in membrane forces must be used with initial_length_fraction (which was hardcoded to 0.5)
  • pass particle mass in mirheo::makeFrozenWallParticles and mirheo::makeFrozenRigidParticles
  • use csv format for plugin outputs instead of txt. This allows to access more easily a given field from python.
• internal changes
  • rename LJParams to RepulsiveLJParams, while LJParams is now used for the ordinary LJ force
  • renamed most private variables: now should have a trailing _
  • enabled -Wshadow_`
• bug fix: avoid division by zero and nan in several places:
  • SDPD kernel
  • root finder (concerns bounce back)
• bug fixes:
  • file wrapper: move constructor (added corresponding unit test)
  • file wrapper: flushOnClose was not active for special streams

v1.3.3

• Do not create checkpoint folder when not needed
• bug fix restart for rigid object vector in multi-rank
• bug fix restart: initial processor assignment; shift relies on redistribution
• bug fix repulsive LJ: missing factor; add an additional check so the force is continuous at rc
• internal changes
  • state is private
  • add -Wconversion for .cpp files (not .cu for now because of thrust)

v1.3.2

• bug fix: pass substep with random fluctuations had bias rng
• prepend macros with MIRHEO_
• interface changes:
  • average flow plugins: does not need type
  • changed channel names to a more consistent version
  • add list of reserved channel names into docs
• internal changes:
  • more modern CMakeLists
  • remove unneeded includes
  • reduce compilation time: do not include std::chrono
  • reduce compilation time: do not bind all plugin classes

v1.3.1

• interface changes
  • substep integrator now takes a list of interactions
  • ObjStats plugin dumps additional type id field if activated
  • dump particles plugin does not need type infos
  • dump particles plugin supports object and rod data
  • remove dump particles rod plugin as it would now be redundant
• add membrane with type id IC
• add filtered membrane forces, which can be used in coordination with the type ids field
• make Mirheo more usable as a library:
  • changed the directory structure
  • added namespace mirheo

v1.3.0

• Add double precision support can be compiled with CMAKE_FLAGS="-DDOUBLE_PRECISION=ON" mir.make

• bug fixes:

  • fixed cell lists sizes with domain sizes not multiple of rc
  • fix in reverse force exchanger
  • objectBelonging: split all persistent channels instead of positions and velocities only

• add PlaneOutletPlugin for removing particles that cross a given plane

• add ParticlePortal plugin that transfers standalone particles from one Mirheo instance to another

• add ObjectDeleter helper class for removing marked objects

Work in progress:

• adding ObjectPortal plugin that transfers objects from one Mirheo instance to another
• adding ObjectsToParticles plugin that destroys objects and transforms them into standalone particles once a condition is met

v1.2.1

• support for different bounce kinds: every bouncer can be used with:

  • bounce back
  • bounce maxwell

• Interface changes:

  • need bounce kernel parameter for every bouncer

v1.2.0

• Interface changes:

  • add function to log compile time options; this can be useful to make sure what was run exactly
  • generic Pairwise forces; removed all old pairwise classes from the interface
  • use kBT everywhere instead of kbt
  • use number_density instead of density
  • rename mirheo class coordinator to Mirheo

• internal changes

  • refactored pairwise interaction drivers
  • more consistent naming

v1.1.2

• internal changes:
  • enable and fix warnings
  • fix initialization bugs
  • use forked cselab/cuda_variant
  • refactor interaction manager: one for each interaction stage

v1.1.1

• interface changes: new field requireShift in restart files. Newer versions will not be able to read older restart files.
• add unit tests for restart
• internal changes:
  • refactored restart for particle vectors
  • fix: test for ROV
  • fix: correctly assigns and shift data during restart IC

v1.1.0

• interface changes:
  • no checkpointEvery in registerParticleVector or belongingChercker
• internal changes:
  • refactoring of packers
  • add persistent channels support for rod bisegment data
  • allow silent log
  • pack arguments: logInfo and checkpointInfo for better readability
• add unit tests for packers:
  • redistribute (particles, objects, rods)
  • exchange (particles, objects)
• test for bounce back reverse exchange:
  • rigid
  • membrane mesh
  • rigid mesh

v1.0.0

• rename to Mirheo
• add spin based state update for rods with polymorphic states (not validated yet)
• fix was a possible deadlock for many nodes / many objects suspensions; see commit 4b65e00eba8cf163db3e99e1730e6f16c12fcd26
• add Capsule Rigid Vectors together with bonce back and belonging checkers
• tests: renaming, semantic

v0.17.0

• add CylinderRigidObjectVectors (CROVs)
• add bounce back on rods and CROVs
• add belonging checker for rods and CROVs
• tests belonging checkers
• internal changes:
  • do not rely on hash for mpi tags in plugins
  • generic kernels in belonging and bounce for RigidObjectVectors with analytical shapes

v0.16.3

• fix MPI cleanup
• fix restart in pvs now supports extra data
• fix checkpoint in pvs also shifts the extra data
• fix dump plugins for xyz, ply and grid h5 timestamp based on simulation time (hence continues after restart)
• fix float4 data is correctly dumped in checkpoint
• minor fix stats plugin works for 0 particles
• interface changes anchor particle plugin accepts multiple anchors
• add pin rod extremity plugin

v0.16.2

• fix cleanup streams
• fix more robust filename creation
• fix more robust parameter passing to rod forces factory
• interace chanes rod forces:
  • change omega0 to kappa0
  • remove k_visc
  • split k_bounds into k_s_center and k_s_frame
  • can optionally save energies and polymorphic states
• extend rod IC
• implement polymorphic states

v0.16.1

• add interaction rod-rigid
• fix free communicator in plugins

v0.16.0

• add particleChecker plugin
• interface changes: average flow plugin does not support float8 entries anymore due to internal changes; use float4 instead
• internal changes
  • particles are now separated into 2 arrays: positions and velocities; this will simplify packing/unpacking kernels
  • positions and velocities are stored as other quantities in dataManagers
  • old particles are only positions
  • vertices are only positions

v0.15.0

• output change
  • restart time-stamps are now continuing from the previous simulation
  • output dump files start at t=0
• fix in TextIO::reader
• internal changes:
  • currentStep is long long -> allow longer simulations
  • forces are stored as generic arrays -> simplifies a bit cell lists

v0.14.4

• interface change pass rod width to rod ic
• add bound viscous forces to rod

v0.14.3

• fix issues #38 and #54
• safe check: cannot register or set objects to coordinator after setup

v0.14.2

• interface changes Integrator: SubStepMembrane -> SubStep
• SubStep integrator supports rods
• add anchor_particle plugin
• internal changes:
  • ids are stored in 64 bits integers

v0.14.1

• Add "rod aware" LJ repulsion interactions
• interface change DPD, MDPD and LJ interactions have only one constructor each
• Safer parameters in interaction factory: treat unread parameters

v0.14.0

• Add elastic rod interactions: bounds, bending and torsion
• Add corresponding unit test
• Add corresponding regression tests
• Add particle drap plugin
• fix (minor) dependencies for tools installation

v0.13.0

• compilation changes require c++ 14 and cuda 9.2
• additional extern code include src/extern/mpark
• interface change linear EOS in SDPD needs an extra parameter rho_0
• fix SDPD: correct use of mass density
• checkpoint and restart interaction random state
• internal changes:
  • cleanup some implementations from interfaces
  • adding rod vectors
  • remove xmacros for channel types
  • use mpark::variant for membrane interaction

v0.12.3

• interface changes
  • use checkpoint instead of restart in Ymero coordinator constructor
  • add checkpoint_mode parameter to Ymero coordinator constructor
• checkpoint/restart mechanism is more uniform

v0.12.2

• densities computed from pairwise interactions are now mass density
• internal changes:
  • add fetcher with mass
  • add type trait for self interacting pairwise kernels

v0.12.1

• add support of SDPD/MDPD for objects
• fix belonging checkers for halo objects: needed rigid motions
• fix reverse exchanger data taken from halo for the extra data

v0.12.0

• fix mirheo.restart() will now indeed restart the simulation
• interface change Renamed and moved parameter for MPI communicator in the mirheo constructor
• interface change Density interaction needs a density kernel
• add SDPD interactions
• add more density kernels
• docs: add tutorials
• docs: minor fixes
• internal:
  • tests are more robust to DPD noise
  • proper rng per time step in DPD/MDPD
• add density outlet plugin
• add rate outlet plugin
• add experimental version of density control plugin

v0.11.5

• support for RDMA communication
• membrane fluctuation forces: use uniform distribution instead of gaussian so that it is bounded
• membrane forces: more robust computation of Lim forces
• internal changes:
  • simplify interface of interaction manager
  • pairwise forces can contain only host memory variable and pass a separate handle to gpu
  • pairwise interaction: compiled separately when template instances are created

v0.11.4

• fix Lim shear forces bug: triangle invariant
• fix reset accumulated quantities in Juelicher ADE model
• fix check MPI send requests

v0.11.3

• fix Juelicher bending forces sign
• fix Lim shear forces sign
• add possibility to compute membrane forces in double perecision

v0.11.2

• fix wall thickness is larger when using MDPD
• internal changes:
  • cell lists do not know about special channels
  • add interaction manager to manage interaction channels

v0.11.1

• fix bounce back on multiple nodes for objects
• minor fixes in documentation

v0.11.0

• add Lim model for shear forces on membranes
• add corresponding tests

v0.10.7

• interface change membrane interactions take only one constructor (see docs)
• fix warp reductions: all threads participate
• internal changes:
  • cosmetic changes: more consistent namespace style
  • membrane interaction takes a functor for dihedral computations
  • refactor membrane interactions: take functors for shear and bending forces

v0.10.6

• Internal change: add before cell list plugin task
• fix: pvs exchanger plugin: new particles are now correctly redistributed
• fix: velocity inlet plugin: new particles are now correctly redistributed
• fix: communication of persistent data to empty pvs
• fix: average plugin asynchronous message to postprocessing

v0.10.5

• add displacement plugin
• add radial velocity control plugin
• fix reordering of extra data in celllists
• fix pvsExchanger plugin also copies persistent channels
• add test for pvsExchanger
• add test for displacement plugin
• internal changes:
  • packers can copy to another packer
  • defaultStream in core/utils/cuda_common.h

v0.10.4

• add velocity inlet plugin
• add very simple CPU marching cubes implementation in core
• clean up units

v0.10.3

• add wall force collector plugin
• automated support of multiple GPUs on single nodes
• fix in bounce
• remove deprecate warings for python 3.7

v0.10.2

• Adds support for different stress free shape than original mesh

v0.10.1

• add plugin to save a channel of extra particle data (useful for intermediate quantities such as densities in MDPD)
• fix reordering of persistent extra channels in primary cell lists
• fix use local cell lists instead of primary ones in halo exchanger

v0.10.0

• Add MDPD interaction (walls and solvent fully supported only)
• internal changes:
  • generic pairwise interaction fetching
  • 2-steps interaction support: extended task dependency graph
  • cell lists are aware of which channels to clear, accumulate and reorder
  • wip: more general object reverse exchangers
• interface change: make frozen walls takes a list of interactions
• interface change: make frozen rigid takes a list of interactions

v0.9.7

• support for VOLTA architecture
• internal changes
  • generic pairwise interaction output: accumulators
  • generic pairwise_interaction: pass views
  • cell lists produce views; cellinfos don not know about particles and forces
  • less magic numbers

v0.9.6

• fix: LJ potential had swapped epsilon and sigma

v0.9.5

• separate sdf grid implementation into more general core/field
• field can be initialized from std::function
• pressure plugin uses region

v0.9.4

• fix: stress free state can be used when the cell is grown
• fix: MembraneMesh wrapper needs GPU

v0.9.3

• fix: the stress entries are now cleared before forces; could be cleared more by other interaction handlers
• use mirheo state inside the simulation objects; do not have current time, step and dt separate in simulation

v0.9.2

• add filtered initial conditions: allows custom regions in space to initialise uniform density particles

v0.9.1

• add sphere initial condition
• add plugin to compute total virial pressure from stresses per particle for a given pv

v0.9.0

• Add common YmrState object.
• interface change:
  • the time step is now passed to the coordinator constructor
  • the time step is not passed to any other object

v0.8.0

• add checkpoint for permanent channels
• extra data managers are aware of the type

v0.7.1

• add permanent channels in extra data manager

v0.7.0

• reorganise membrane interaction kernels:
  • bending force kernels now separated from other
  • 2 parameter strctures
• add Juelicher bending model
• add force saver plugin to save forces in channels

v0.6.1

• rename uDeviceX to Ymero
• synchronzation bug fix

v0.6.0

• add plugin for magnetic orientation of rigid bodies

v0.5.1

• make the stress channel name customizable

v0.5.0

• add stress computation + tests
• perf improvement in sdf
• minor perf improvement in pairwise kernels

v0.4.2

• compile some units
• use gtest

v0.4.1

• interface change: wall oscillation: period is in dpd units now

v0.4.0

• add hdf5 support for mesh dump
• allow for extra channels to be dumped together with the mesh

v0.3.1

• add compile time switch for CUDA>9 support
• add extra force plugin

v0.3.0

• proper MPI init and finalize
• communicator can be passed from python

v0.2.1

• add tools python submodule

v0.2.0

• add checkpoint/restart support for object vectors
• dumped in xdmf+hdf5 format: restart files can be viewed

v0.1.4

• add bounce tests
• wip: xdmf support for restart

v0.1.3

• bug fix: bounce back with substep integration
• xdmf reader

v0.1.2

• dump walls in xdmf format
• add tests for bounce back on mesh + rigid ellipsoids

v0.1.1

• sdf fix: merged sdf before splittinf frozen particles

v0.1.0

• set up versioning