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
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
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)
  • hpmc interaction_matrix
  • special_pair framework
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
  • integreate.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
  • 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
James Antonaglia, University of Michigan
  • pair.mie
Carl Simon Adorf, University of Michigan
  • Analyzer callback
  • metadata output
  • Frenkel-Ladd bug fixes
Paull 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, Univeristy 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
Isass Bruss, Chengyu Dai, University of Michigan
  • force.active
  • update.constraint_ellipsoid
Bryan Vansaders, University of Michigan
  • Constant stress mode to integrate.npt.
  • map_overlaps() in hpmc.
Vyas Ramasubramani, University of Michigan
  • init.read_gsd bug fixes
Nathan Horst
  • Language and figure clarifying the dihedral angle definition.
Bryan VanSaders, University of Michigan
  • constrain.oneD
Ludwig Schneider, Georg-August Univeristy Goettingen
  • Constant stress flow: hoomd.md.update.mueller_plathe_flow

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
  • 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
  • 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 collaberation 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
Vyas Ramasubramani, University of Michigan
  • hpmc.util.tune fixes for tuning by type

DEM developers

The following people contributed to the hoomd.dem package.

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

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,
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.

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
              University of Illinois at Urbana-Champaign
              http://www.ks.uiuc.edu/

Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the Software), to deal with
the Software without restriction, including without limitation the rights to
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of the Software, and to permit persons to whom the Software is furnished to
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Redistributions of source code must retain the above copyright notice,
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ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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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:

Copyright (c) 2002, Frank Vanden Berghen<br>
All rights reserved.<br>
Redistribution and use in source and binary forms, with or without
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 - Redistributions of source code must retain the above copyright
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 - Neither the name of the Frank Vanden Berghen nor the
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      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY
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ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Saru is used for random number generation - Used under the following license:

Copyright (c) 2008 Steve Worley < m a t h g e e k@(my last name).com >

Permission to use, copy, modify, and distribute this software for any
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WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
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OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Some CUDA API headers are included in the HOOMD-blue source code for code compatibility in CPU only biulds - Used under the following license:

Copyright 1993-2008 NVIDIA Corporation.  All rights reserved.

NOTICE TO USER:

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Consistent with 48 C.F.R.12.212 and 48 C.F.R. 227.7202-1 through
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FFTs on the CPU reference implementation of PPPM are performed using kissFFT from http://sourceforge.net/projects/kissfft/, used under the following license:

Copyright (c) 2003-2010 Mark Borgerding

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
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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.

ModernGPU source code is embedded in HOOMD’s package and is used for various tasks: http://nvlabs.github.io/moderngpu/:

Copyright (c) 2013, 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 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.

num_util is embedded in HOOMD’s package:

Copyright 2006  Phil Austin (http://www.eos.ubc.ca/personal/paustin)
Distributed under the Boost Software License, Version 1.0. (See
accompanying file LICENSE_1_0.txt or copy at
http://www.boost.org/LICENSE_1_0.txt)
\endverbatim

CUB 1.4.1 source code is embedded in HOOMD’s package and is used for various tasks: http://nvlabs.github.io/cub/:

Copyright (c) 2011, Duane Merrill.  All rights reserved.
Copyright (c) 2011-2015, 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 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.

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:

Copyright (c) 2015, Michael P. Howard. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
    1. Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.

    2. 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.

    3. 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.

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

Copyright (c) 2014-2016 The Regents of the University of Michigan

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.

pybind11 is used to provide python bindings for C++ classes. Used under the BSD license:

Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>, All rights reserved.

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modification, are permitted provided that the following conditions are met:

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   list of conditions and the following disclaimer.

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cereal is used to serialize C++ objects for transmission over MPI. Used under the BSD license:

Copyright (c) 2014, Randolph Voorhies, Shane Grant
All rights reserved.

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DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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Libraries

HOOMD-blue links to the following libraries: