Credits¶

HOOMD-blue Developers¶

The following people contributed to the hoomd and hoomd.md packages.

Joshua Anderson, University of Michigan - Lead developer

Alex Travesset, Iowa State University and Ames Laboratory

Rastko Sknepnek, Northwestern

integrate.npt

pair.morse

Carolyn Phillips, University of Michigan

dihedral.table

angle.table

bond.table

pair.dpdlj

pair.dpd

pair.dpd_conservative

integrate.langevin

bond.fene

pair.slj

Initial testing and debugging of HOOMD on Mac OS X systems

Aaron Keys, University of Michigan

update.enforce2d and other updates enabling to 2D simulations

hoomd c++ compilation helper script

binary restart files

integrate.mode_minimize_fire

Andrew Schultz, University at Buffalo

Harmonically Mapped Averaging implementation

Axel Kohlmeyer, David LeBard, Ben Levine, from the ICMS group at Temple University

pair.cgcmm

angle.harmonic

angle.cgcmm

dihedral.harmonic

improper.harmonic

numerous other small contributions enhancing the usability of HOOMD

Igor Morozov, Andrey Kazennov, Roman Bystryi, Joint Institute for High Temperatures of RAS (Moscow, Russia)

pair.eam (original implementation)

Philipp Mertmann, Ruhr University Bochum

charge.pppm

pair.ewald

Stephen Barr, Princeton University

charge.pppm

pair.ewald

Greg van Anders, Benjamin Schultz, University of Michigan

refactoring of ForceCompute

Eric Irrgang, University of Michigan

RPM packaging and daily builds

Ross Smith, University of Michigan

Deb packaging and daily builds

Peter Palm, Jens Glaser, Leipzig University

group functionality in force.constant

misc bug fixes

conversion of bond forces to template evaluator implementation

Jens Glaser, University of Michigan

integrate.npt anisotropic integration (mkt)

pair.force_shifted_lj

Dynamic addition/removal of bonds

Computation of virial and pressure tensor

integrate.nph

Framework for external potentials

external.periodic

ParticleData refactoring

MPI communication

Optimization of MPI communication for strong scaling

Neighborlist and pair force performance improvements (multiple threads per particle)

Enable cell based neighbor list on small boxes

Testing of angle.table and dihedral.table

Replicate command

metadata output

anisotropic particle integrators

Gay-Berne pair potential

pair.reaction_field

Rewrite of rigid body framework

Multi-GPU electrostatics (PPPM)

pair.van_der_waals

hpmc interaction_matrix

special_pair framework

TBB support

randomize integrator variables

GPUArray refactoring

Pavani Medapuram, University of Minnesota

Framework for external potentials

external.periodic

Brandon D. Smith, University of Michigan

full double precision compile time option

integrate.berendsen

pair.tersoff

Trung Dac Nguyen, University of Michigan

integrate.nve_rigid

integrate.bdnvt_rigid

integrate.nvt_rigid

integrate.npt_rigid

integrate.mode_minimize_rigid_fire

associated rigid body data structures and helper functions

integrate.nph_rigid

Ryan Marson, University of Michigan

unwrap_rigid option to dump.dcd

Kevin Silmore, Princeton University

OPLS dihedral

David Tarjan, University of Virginia

performance tweaks to the neighbor list and pair force code

Sumedh R. Risbud, James W. Swan, Massachusetts Institute of Technology

bug fixes for rigid body virial corrections

Michael P. Howard, Princeton University & University of Texas at Austin

Automatic citation list generator

Neighbor list memory footprint reduction

Bounding volume hierarchy (tree) neighbor lists

Stenciled cell list (stencil) neighbor lists

Per-type MPI ghost layer communication

Dynamic load balancing

Wall potentials extrapolated mode

XML dump by particle group

Fix references when disabling/enabling objects

Misc. bug fixes

CUDA9+V100 compatibility

GPU polymorphic object wrapper

Performance improvements to tree neighbor lists

James Antonaglia, University of Michigan

pair.mie

Carl Simon Adorf, University of Michigan

Analyzer callback

metadata output

Frenkel-Ladd bug fixes

Paul Dodd, University of Michigan

pair.compute_energy

Erin Teich, University of Michigan

addInfo callback to dump.pos

Joseph Berleant, University of Michigan

fix python 3.4 segfault

Matthew Spellings, University of Michigan

anisotropic particle integrators

Gay-Berne, dipole pair potentials

GTAR file format

External components in hoomd 2.x

James Proctor, University of Michigan

Refactor external potential framework

Wall potentials

boost python to pybind11 conversion

boost unit_test to upp11 conversion

boost signals to Nano::Signals conversion

Removal of misc boost library calls

Chengyu Dai, University of Michigan

Rewrite integrate.brownian with 3D rotational updates

Rewrite integrate.langevin with 3D rotational updates

Isaac Bruss, Chengyu Dai, University of Michigan

force.active

update.constraint_ellipsoid

Vyas Ramasubramani, University of Michigan

init.read_gsd bug fixes

Reverse communication for MPI

Enable simulation of floppy bodies that can be integrated separately but are ignored by the NeighborList

Enabled use of shared memory for Evaluator structs

Added per-type shape information to anisotropic pair potentials

Fix cutoff rescaling in Gay-Berne potential

Nathan Horst

Language and figure clarifying the dihedral angle definition.

Bryan VanSaders, University of Michigan

constrain.oneD

Constant stress mode to integrate.npt.

map_overlaps() in hpmc.

Torque options to force.constant and force.active

Ludwig Schneider, Georg-August Univeristy Goettingen

Constant stress flow: hoomd.md.update.mueller_plathe_flow

Matrix logging and hdf5 logging: hoomd.hdf5.log

Bjørnar Jensen, University of Bergen

Add Lennard-Jones 12-8 pair potential

Add Buckingham/exp-6 pair potential

Add special_pair Coulomb 1-4 scaling

Lin Yang, Alex Travesset, Iowa State University

metal.pair.eam - reworked implementation

Tim Moore, Vanderbilt University

angle.cosinesq

Documentation fixes

Bradley Dice, Avisek Das, University of Michigan

integrator.randomize_velocities()

Bradley Dice, Simon Adorf, University of Michigan

SSAGES support

Bradley Dice, University of Michigan

Documentation improvements

WSL support

Peter Schwendeman, Jens Glaser, University of Michigan

NVLINK optimized multi-GPU execution

Alyssa Travitz, University of Michigan

get_net_force implementation

bond bug fixes

Mike Henry, Boise State University

Documentation improvements

Pengji Zhou, University of Michigan

pair.fourier

Tommy Waltmann, University of Michigan

hoomd.device module

Patrick Lawton, University of Michigan

Documentation changes

Luis Rivera-Rivera, University of Michigan

hoomd.dump.gsd.dump_shape implementation

Alex Yang, Vanderbilt University

hoomd.md.dihedral.harmonic update for phase shift

Geert Kapteijns, University of Amsterdam

Bug fixes.

Simone Ciarella, Wouter Ellenbroek, Eindhoven University of Technology

Add RevCross potential

Charlie Slominski, Caltech

HOOMD-blue as a submodule

HPMC developers¶

The following people contributed to the hoomd.hpmc package.

Joshua Anderson, University of Michigan - Lead developer

Vision

Initial design

Code review

NVT trial move processing (CPU / GPU)

Sphere shape

Polygon shape

Spheropolygon shape

Simple polygon shape

Ellipsoid shape - adaptation of Michael’s Ellipsoid overlap check

2D Xenocollide implementation

2D GJKE implementation

MPI parallel domain decomposition

Scale distribution function pressure measurement

POS writer integration

Bounding box tree generation, query, and optimizations

BVH implementation of trial move processing

SSE and AVX intrinsics

jit.patch.user user defined patchy interactions with LLVM runtime compiled code

Eric Irrgang, University of Michigan

NPT updater

Convex polyhedron shape

Convex spheropolyhedron shape

3D Xenocollide implementation

3D GJKE implementation

Move size autotuner (in collaboration with Ben Schultz)

Densest packing compressor (in collaboration with Ben Schultz)

POS file utilities (in collaboration with Ben Schultz)

Shape union low-level implementation

Sphere union shape (in collaboration with Khalid Ahmed)

Ben Schultz, University of Michigan

Frenkel-Ladd free energy determination

Move size autotuner (in collaboration with Eric Irrgang)

Densest packing compressor (in collaboration with Eric Irrgang)

POS file utilities (in collaboration with Eric Irrgang)

Assign move size by particle type

Ellipsoid overlap check bug fixes

Jens Glaser, University of Michigan

Patchy sphere shape

General polyhedron shape

BVH implementation for countOverlaps

Hybrid BVH/small box trial move processing

Helped port the Sphinx overlap check

Dynamic number of particle types support

Implicit depletants

jit.patch.user_union user defined patchy interactions with LLVM runtime compiled code

Geometric Cluster Algorithm implementation

convex_spheropolyhedron_union shape class

test_overlap python API

Eric Harper, University of Michigan

Misc bug fixes to move size by particle type feature

Initial code for MPI domain decomposition

Khalid Ahmed, University of Michigan

Ported the Sphinx overlap check

Sphere union shape (in collaboration with Eric Irrgang)

Elizabeth R Chen, University of Michigan

Developed the Sphinx overlap check

Carl Simon Adorf, University of Michigan

meta data output

Samanthule Nola, University of Michigan

Run time determination of max_verts

Paul Dodd, Erin Teich, University of Michigan

External potential framework

Wall overlap checks

Lattice external potential

Erin Teich, University of Michigan

Convex polyhedron union particle type

Vyas Ramasubramani, University of Michigan

hpmc.util.tune fixes for tuning by type

hpmc.update.boxmc fixes for non-orthorhombic box volume moves

Fixed various bugs with wall overlap checks

jit.external.user implementation

Refactored depletant integrators

William Zygmunt, Luis Rivera-Rivera, University of Michigan

Patchy interaction support in HPMC CPU integrators

GSD state bug fixes

DEM developers¶

The following people contributed to the hoomd.dem package.

Matthew Spellings, University of Michigan - Lead developer Ryan Marson, University of Michigan

MPCD developers¶

The following people contributed to the hoomd.mpcd package.

Michael P. Howard, Princeton University & University of Texas at Austin - Lead developer

Design

Cell list and properties

Particle and cell communication

Basic streaming method

Slit streaming method

Slit pore streaming method

SRD and AT collision rules

Virtual particle filling framework

External force framework and block, constant, and sine forces

Bounce-back integrator framework

Source code¶

HOOMD: HOOMD-blue is a continuation of the HOOMD project (http://www.ameslab.gov/hoomd/). The code from the original project is used under the following license:

Highly Optimized Object-Oriented Molecular Dynamics (HOOMD) Open
Source Software License
Copyright (c) 2008 Ames Laboratory Iowa State University
All rights reserved.

Redistribution and use of HOOMD, in source and binary forms, with or
without modification, are permitted, provided that the following
conditions are met:

* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names HOOMD's
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.

Disclaimer

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND
CONTRIBUTORS ``AS IS''  AND ANY EXPRESS OR IMPLIED WARRANTIES,
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THE POSSIBILITY OF SUCH DAMAGE.

Sockets code from VMD is used for the IMDInterface to VMD (http://www.ks.uiuc.edu/Research/vmd/) - Used under the UIUC Open Source License.

Molfile plugin code from VMD is used for generic file format reading and writing - Used under the UIUC Open Source License:

University of Illinois Open Source License
Copyright 2006 Theoretical and Computational Biophysics Group,
All rights reserved.

Developed by: Theoretical and Computational Biophysics Group
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XML parsing is performed with XML.c from http://www.applied-mathematics.net/tools/xmlParser.html - Used under the BSD License:

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Eigen 3.2.5 (http://eigen.tuxfamily.org/) is embedded in HOOMD’s package and is made available under the Mozilla Public License v.2.0 (http://mozilla.org/MPL/2.0/). Its linear algebra routines are used for dynamic load balancing. Source code is available through the [downloads](http://glotzerlab.engin.umich.edu/hoomd-blue/download.html).

A constrained least-squares problem is solved for dynamic load balancing using BVLSSolver, which is embedded in HOOMD’s package and is made available under the following license:

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libgetar is used to read and write GTAR files. Used under the MIT license:

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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

[HIP](https://github.com/ROCm-Developer-Tools/HIP) is included under the following license:

Copyright (c) 2015-2016 Advanced Micro Devices, Inc. All rights reserved.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

[hipCUB](https://github.com/ROCmSoftwarePlatform/hipCUB/blob/develop/LICENSE.txt) is included under the following license:

Copyright (c) 2010-2011, Duane Merrill.  All rights reserved.
Copyright (c) 2011-2018, NVIDIA CORPORATION.  All rights reserved.
Modifications Copyright (c) 2019, Advanced Micro Devices, Inc.  All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
   *  Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
   *  Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
   *  Neither the name of the NVIDIA CORPORATION nor the
      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

HOOMD-blue uses headers from jitify (https://github.com/NVIDIA/jitify) under the following license:

BSD 3-Clause License

Copyright (c) 2017-2019, NVIDIA Corporation All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Libraries¶

HOOMD-blue links to the following libraries:

python - Used under the Python license (http://www.python.org/psf/license/)

cuFFT - Used under the NVIDIA CUDA toolkit license (http://docs.nvidia.com/cuda/eula/index.html)

rocFFT - Used under the MIT license (https://github.com/ROCmSoftwarePlatform/rocFFT)

HOOMD-blue uses the following header-only libraries:

rocPRIM - https://github.com/ROCmSoftwarePlatform/rocPRIM
rocThrust - https://github.com/ROCmSoftwarePlatform/rocThrust