
RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields
By: Pierre de Buyl, Mu-Jie Huang and Laurens Deprez
References
- Frenkel D Smit B Understanding molecular simulation: From algorithms to applications 2002 2nd edition San Diego, CA Academic Press
- Malevanets A Kapral R Mesoscopic model for solvent dynamics J. Chem. Phys 1999 110 8605 10.1063/1.478857
- Malevanets A Kapral R Solute molecular dynamics in a mesoscale solvent J. Chem. Phys 2000 112 7260 10.1063/1.481289
- Rohlf K Fraser S Kapral R Reactive multiparticle collision dynamics Comput. Phys. Commun 2008 179 132 10.1016/j.cpc.2008.01.027
- Rückner G Kapral R Chemically powered nanodimers Phys. Rev. Lett 2007 98 150603 10.1103/PhysRevLett.98.150603
-
Prohm
C
Gierlak
M
Stark
H
Inertial microfluidics with multi-particle collision dynamics
Eur. Phys. J. E
2012
35
8
80
1292–8941 10.1140/epje/i2012-12080-3 - Lüsebrink D Yang M Ripoll M Thermophoresis of colloids by mesoscale simulations J. Phys. Cond. Matt 2012 24 28 284132 10.1088/0953-8984/24/28/284132
- Allen MP Tildesley DJ Computer Simulation of Liquids 1987 Oxford Clarendon Press
- de Buyl P Colberg PH Höfling F H5MD: A structured, efficient, and portable file format for molecular data Comp. Phys. Commun 2014 185 1546 1553 10.1016/j.cpc.2014.01.018
-
de Buyl
P
fortran_h5md
2015–2016
URL
https://github.com/pdebuyl/fortran_h5md - Wilson G Aruliah DA Brown CT Hong NPC Davis M Guy RT Haddock SHD Huff KD Mitchell IM Plumbley MD White BWEP Wilson P Best practices for scientific computing PLoS Biol 2014 12 e1001745 10.1371/journal.pbio.1001745
-
Git
URL
https://git-scm.com/ -
de Buyl
P
fortran_tester
2015–2016
URL
https://github.com/pdebuyl/fortran_tester - Lee SH Kapral R Friction and diffusion of a brownian particle in a mesoscopic solvent J. Chem. Phys 2004 121 11163 10.1063/1.1815291
-
de Buyl
P
Parsetext
2011–2016
URL
https://github.com/pdebuyl/ParseText -
Jones
E
Oliphant
T
Peterson
P
2001– SciPy: Open source scientific tools for Python
URL
http://www.scipy.org/ - Hunter JD Matplotlib: A 2D graphics environment Computing In Science & Engineering 2007 9 3 90 95 10.1109/MCSE.2007.55
- Collette A Python and HDF5 2013 O’Reilly
- Ramachandran P Varoquaux G Mayavi: 3D visualization of scientific data Comput. Sci. Eng 2011 13 2 40 51 10.1109/MCSE.2011.35
-
Brandl
G
Sphinx
2007–2016
URL
http://www.sphinx-doc.org/ - Noguchi H Kikuchi N Gompper G Particle-based mesoscale hydrodynamic techniques EPL (Europhysics Letters) 2007 78 1 10005 10.1209/0295-5075/78/10005
- Ihle T Kroll DM Stochastic rotation dynamics: A galilean-invariant mesoscopic model for fluid flow Phys. Rev. E 2001 63 20201 10.1103/PhysRevE.63.020201
- Allahyarov E Gompper G Mesoscopic solvent simulations: Multiparticle-collision dynamics of three-dimensional flows Phys. Rev. E 2002 66 36702 10.1103/PhysRevE.66.036702
- Whitmer JK Luijten E Fluid–solid boundary conditions for multiparticle collision dynamics J. Phys. Condens. Matt 2010 22 10 104106 10.1088/0953-8984/22/10/104106
- Lamura A Gompper G Ihle T Kroll DM Multi-particle collision dynamics: Flow around a circular and a square cylinder EPL (Europhysics Letters) 2001 56 319 10.1209/epl/i2001-00522-9
- Andersen HC Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations J. Comp. Phys 1983 52 24 10.1016/0021-9991(83)90014-1
-
Hamilton
CH
Compact hilbert indices 2006 Dalhousie University Technical Report CS-2006–07, URLhttps://www.cs.dal.ca/research/techreports/cs-2006-07 -
Salmon
JK
Moraes
MA
Dror
RO
Shaw
DE
Parallel random numbers: As easy as 1, 2, 3
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, SC ’11
2011
New York, NY, USA
ACM 978-1-4503-0771-0 10.1145/2063384.2063405 pages 16:1–16:12 -
de Buyl
P
random module
2015–2016
URL
https://github.com/pdebuyl/random_module -
Colberg
PH
nano-dimer
2013–2015
URL
https://colberg.org/nano-dimer/ - Howse JR Jones RAL Ryan AJ Gough T Vafabakhsh R Golestanian R Self-motile colloidal particles: From directed propulsion to random walk Phys. Rev. Lett 2007 99 48102 10.1103/PhysRevLett.99.048102
- de Buyl P Kapral R Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion Nanoscale 2013 5 1337 1344 10.1039/c2nr33711h
DOI: https://doi.org/10.5334/jors.142 | Journal eISSN: 2049-9647
Language: English
Submitted on: Aug 17, 2016
Accepted on: Dec 7, 2016
Published on: Jan 11, 2017
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
Keywords:
© 2017 Pierre de Buyl, Mu-Jie Huang, Laurens Deprez, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.