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Framework Design, Parallelization and Force Computation in Molecular Dynamics  (Make Corrections)  
Thierry Matthey



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Abstract: Factory and Prototypes . . . . . . . . . 43 5.6 Functionalities to compare force algorithms . . . . . . . . . . . . 46 5.7 Implementation and validation of fast electrostatic force algorithms 47 5.7.1 Standard Ewald summation . . . . . . . . . . . . . . . . 47 5.7.2 Particle-mesh based Ewald summation . . . . . . . . . . 48 5.7.3 Multi-grid . . . . . . . . . . . . . . . . . . . . . . . . . . 49 5.8 Practical examples of extendibility and optimization . . . . . . . . 50 5.8.1 Adding a new force... (Update)

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BibTeX entry:   (Update)

@misc{ matthey-framework,
  author = "Thierry Matthey",
  title = "Framework Design, Parallelization and Force Computation in Molecular Dynamics",
  url = "citeseer.ist.psu.edu/589651.html" }
Citations (may not include all citations):
1274   Object-Oriented Software Construction (context) - Meyer - 1997  ACM
1002   Programming Language (context) - Stroustrup - 1997
308   Designing reusable classes (context) - Johnson, Foote - 1988
306   Computer Simulation of Liquids (context) - Allen, Tildesley - 1987  ACM
277   A fast algorithm for particle simulations - Greengard, Rokhlin - 1987  ACM
257   force-calculation algorithm (context) - Barnes, Hut et al. - 1986
254   Elements of Reusable Object-Oriented Software (context) - Gamma, Helm et al. - 1995
235   Classical mechanics (context) - Goldstein - 1980
156   Computer Simulation Using Particles (context) - Hockney, Eastwood - 1981  ACM
120   CHARMM: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
82   Some computer organizations and their effectiveness (context) - Flynn - 1972
57   Fast parallel algorithms for short-range molecular dynamics - Plimpton - 1995  ACM
56   Understanding ActiveX and OLE (context) - Chappell - 1997  ACM
52   Numerical Hamiltonian Problems (context) - Sanz-Serna, Calvo - 1994
51   PVM 3 users guide and reference manual (context) - Geist, Beguelin et al. - 1994
31   Message-passing multi-cell molecular dynamics on the Connect.. - Beazley, Lomdahl - 1994
31   Parallelization of CHARMM for MIMD machines (context) - Brooks, Hodoscek - 1992
29   Parallelizing molecular dynamics using spatial decomposition - Clark, van Hanxleden et al. - 1994
26   Parallelizing molecular dynamics programs for distributed-me.. - Hwang, Das et al. - 1995  ACM
25   NAMD2: Greater scalability for parallel molecular dynamics - Kale, Skeel et al. - 1999
22   The Art of Molecular Dynamics Simulation (context) - Rapaport - 1995
21   design: generic programming and design patterns applied (context) - Alexandrescu - 2001
20   Generalized Verlet algorithm for efficient molecular dynamic.. (context) - Grubmuller, Heller et al. - 1991
18   Molecular Modelling: Principles and Applications (context) - Leach - 1996
17   object-oriented molecular dynamics program (context) - Nelson, Humphrey et al. - 1996
17   Longer Time Steps for Molecular Dynamics (context) - Izaguirre - 1999  ACM
17   Longer time steps for molecular dynamics (context) - Izaguirre, Reich et al. - 1999  ACM
16   Reversible multiple time scale molecular dynamics (context) - Tuckerman, Berne et al. - 1990
15   Quantum Mechanics (context) - Merzbacher - 1998  ACM
14   AMBER: Assisted model building with energy refinement (context) - Weiner, Kollman - 1981
13   Accelerated molecular dynamics simulation 61 with the parall.. (context) - Board, Causey et al. - 1992
13   the convergence of a relaxation method with natural constrai.. (context) - Bakhvalov - 1966
13   A portable distributed implementation of the parallel multip.. (context) - Rankin, Board - 1995  ACM   DBLP
11   Parallelization strategies for a molecular dynamics program - Clark, van Hanxleden et al. - 1992
10   A new parallel method for molecular dynamics simulation of m.. - Plimpton, Hendrickson - 1996  DBLP
10   A smooth particle mesh Ewald method (context) - Essmann, Perera et al. - 1995
10   Hyper-systolic parallel computing - Lippert, Seyfried et al. - 1998  ACM   DBLP
10   Die Berechnung optischer und elektrostatischer Gitterpotenti.. (context) - Ewald - 1921
9   Springer Verlag (context) - Coulange - 1998
9   method for Ewald sums in large systems (context) - Darden, York et al. - 1993
9   A domain decomposition parallel processing algorithm for mol.. - Brown, Minoux et al. - 1997
9   Performance of fast multipole methods for calculating electr.. (context) - Shimada, Kaneko et al. - 1994  ACM   DBLP
9   Multiple grid methods for classical molecular dynamics (context) - Skeel, Tezcan et al. - 2002  DBLP
9   Langevin stabilization of molecular dynamics (context) - Izaguirre, Catarello et al. - 2090
9   Difficulties with multiple timestepping and the fast multipo.. (context) - Bishop, Skeel et al. - 1997
8   How to mesh up Ewald sums (context) - Deserno, Holm - 1998
8   A multipole-based algorithm for efficient calculation of for.. - Lambert, Darden et al. - 1996  ACM
8   A new molecular dynamics method combining the reference syst.. - Zhou, Berne - 1995
8   Advanced algorithms for molecular dynamics simulation: The p.. (context) - Windemuth - 1995
8   An algorithm for the simulation of condensed matter which gr.. (context) - Perram, Petersen et al. - 1988
7   PROTOMOL: An object oriented framework for molecular dynamic.. (context) - Izaguirre, Willcock et al. - 2000
7   Ewald summation techniques in perspective: A survey (context) - Toukmaji, Jr - 1996
7   Practical construction of modified Hamiltonians - Skeel, Hardy - 2001
7   The Matrix Template Library: A unifying framework for numeri.. - Siek, Lumsdaine - 1998  DBLP
7   Error analysis of symplectic multiple time stepping (context) - Littell, Skeel et al. - 1997  ACM
6   Optimized particle mesh Ewaldmultiple time step integration .. (context) - Case, particle et al. - 2001
6   Symplectic integrators and the conservation of angular momen.. (context) - Zhang, Skeel - 1995  DBLP
6   On multiple time-step algorithms and the Ewald sum (context) - Forester, Smith - 1994
6   Long-time-step methods for oscillatory differential equation.. (context) - Garca-Archilla, Sanz-Serna et al. - 1998  ACM
5   Multigrid methods for classical molecular dynamics simulatio.. (context) - Sagui, Darden - 2001
5   The library that thinks it is a compiler (context) - Veldhuizen - 1998
5   Optimisation of the Ewald sum for large systems (context) - Fincham - 1994
4   Structure and Mandelung energy of spherical Coulomb crystals (context) - Hasse, Avilov - 1991
4   Steered molecular dynamics and mechanical functions of prote.. (context) - Isralewitz, Gao et al. - 2001
4   New splitting formulations for lattice summations (context) - Batcho, Schlick - 2001
4   Generalized mollified multiple time stepping methods for mol.. (context) - Izaguirre - 2001
4   Simulation of electrostatic systems in periodic boundary con.. (context) - De Leeuw, Perram et al. - 1980
4   Multiscale Computational Methods in Chemistry and Physics (context) - Brandt, Bernholc et al. - 2001  ACM
4   The mollified impulse method for oscillatory differential eq.. (context) - Garca-Archilla, Sanz-Serna et al. - 1997
4   The fast Fourier--Poisson method for calculating Ewald sums (context) - York, Yang - 1994
4   BOOGA -- A component-oriented framework for computer grahics (context) - Amann, Streit et al. - 1997
3   Performance Programming Techniques (context) - Bulka, Mayhew - 1999
3   Fast Ewald sums for general van der Waals potentials (context) - Chen, Cagin et al. - 1997  DBLP
3   A tutorial on the prototyping of multiple time stepping inte.. - Izaguirre, Matthey et al. - 2001
3   Accuracy and efficiency of the particle mesh Ewald method (context) - Petersen - 1995
3   and the Ewald method for large periodic Coulombic systems (context) - Pollock, Glosli et al. - 1996
3   An Ewald summation based multipole method (context) - Duan, Krasny - 2000
3   Acceleration of convergence for lattice sums (context) - Karawasa, Goddard - 1989
3   Acceleration of the canonical molecular dynamics simulation .. - Kawata, Mikami - 1999
3   FAMUSAMM: An algorithm for rapid evaluation of electrostatic.. - Eichinger, Grubmuller et al. - 1997
3   Phase transitions in anisotropically confined ionic crystals (context) - Schiffer - 1993
2   Large Scale Molecular Simulations with Application to Polyme.. (context) - Gao - 1998
2   A system for interactive molecular dynamics (context) - Stone, Gullingsrud et al. - 2001
2   The reduced cell multipole method for coulomb interactions i.. (context) - Ding, Karasawa - 1992
2   A molecular dynamics run with (context) - Roth, Gahler et al. - 2000
2   Flops molecular dynamics on the Connection Machine (context) - Lomdahl, Tamayo et al. - 1993
2   Ewald summation and multiple time step methods for molecular.. (context) - Komeiji - 2000
2   Programming Problems (context) - Sutter, Engineering - 2000  ACM
2   Rapid calculation of two-dimensional Ewald summation (context) - Kawata, Mikami - 2001
2   Particle mesh Ewald method for threedimensional systems with.. (context) - Kawata, Nagashima - 2001
2   Cutoff errors in the Ewald summation formulae for point char.. (context) - Kolafa, Perram - 1992
2   Theoretical Biophysics Group (context) - Hardy, API - 1999
2   Targeted mollified impulse method for molecular dynamics (context) - Ma, Izaguirre - 2002
2   A highly portable parallel implementation of AMBER using the.. (context) - Vincent, Merz - 1995
1   Institute of Computer Science and Applied Mathematics (context) - Matthey, Master's - 1997
1   CompuCell home page (context) - Computational, Sciences et al. - 2002
1   Ewald summation technique for one-dimensional charge distrib.. (context) - Langridge, Hart et al. - 2001
1   Ball: Biochemical algorithms library (context) - Boghossian, Kohlbacher et al. - 1999  DBLP
1   DMMD -- A modular molecular dynamics program for MPP-systems - Attig, Lewerenz et al. - 1999
1   Extensions and Applications of the Graphics Framework BOOGA (context) - Buhlmann - 1998
1   A general-purpose parallel molecular dynamics simulation pac.. (context) - Smith, Forester - 1996
1   Computer simulation of molecular dynamics: Methodology (context) - van Gunsteren, Berendsen - 1990
1   Competition between two forms of ordering in finite Coulomb .. (context) - Tosuji, Kishimoto et al. - 2002
1   Edinburgh Parallel Computing Center (context) - Smith, modelling - 1997
1   Accurate modeling of the intramolecular electrostatic energy.. (context) - Dudek, Ponder - 1995
1   Lucretius: A molecular dynamics simulation program (context) - Smith, Ayyagari et al. - 1999
1   Zuhlke Informatik (context) - Johnson, Seminar - 1996
1   MDynaMix -- a scalable portable parallel MD simulation packa.. (context) - Lyubartsev, Laaksonen - 2000
1   Single- and Multi-Species Coulomb Ion Crystals: Structures (context) - Hornekr - 2000
1   Classical dynamics (context) - Sutmann - 2000
1   Efficient Parallel Implementations of Multipole Based NBody .. - Rankin - 1997
1   Institute of Computer Science and Applied Mathematics (context) - Streit, ein et al. - 1997
1   Estimate of the cutoff errors in the Ewald summation for dip.. (context) - Wang, Holm - 2001
1   Moldy: A portable molecular dynamics simulation program for .. (context) - Refson - 2000
1   Large scale molecular dynamics simulations with fast multipo.. (context) - Wang, Lupo et al. - 1999  ACM
1   EGO -- an efficient molecular dynamics program and its appli.. (context) - Esser, Grassberger et al. - 2000
1   Parallel molecular dynamics using force decomposition (context) - Okunbor, Murty - 1998
1   A relaxation method for solving elliptic differential equati.. (context) - Fedorenko - 1961
1   Comparison between PROTOMOL and NEMD for a simple Lennard-Jo.. (context) - Hafskjold, Rekvig - 2002
1   A package for molecular simulation and trajectory (context) - Lindahl, Hess et al. - 2001
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An Object-Oriented Approach to Model Scenes of Buildings - Matthey, Bieri   (Correct)
ProtoMol: A Molecular Dynamics Framework with Incremental.. - Matthey, Izaguirre (2000)   (Correct)
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