Sat, 26 Jul 2008 04:33:24 BST CiteULike: OndrejMarsalek's library [67 articles] http://www.citeulike.org/user/OndrejMarsalek CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/OndrejMarsalek/article/2516182 <i>Computer Physics Communications, Vol. 167, No. 3. (1 May 2005), pp. 151-164.</i><br /><br />A linear-scaling algorithm has been developed to perform large-scale molecular-dynamics (MD) simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory. A divide-and-conquer algorithm is used to compute the electronic structure, where non-additive contribution to the kinetic energy is included with an embedded cluster scheme. Electronic wave functions are represented on a real-space grid, which is augmented with coarse multigrids to accelerate the convergence of iterative solutions and adaptive fine grids around atoms to accurately calculate ionic pseudopotentials. Spatial decomposition is employed to implement the hierarchical-grid algorithm on massively parallel computers. A converged solution to the electronic-structure problem is obtained for a 32,768-atom amorphous CdSe system on 512 IBM POWER4 processors. The total energy is well conserved during MD simulations of liquid Rb, showing the applicability of this algorithm to first principles MD simulations. The parallel efficiency is 0.985 on 128 Intel Xeon processors for a 65,536-atom CdSe system. Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory Fuyuki Shimojo Rajiv Kalia Aiichiro Nakano Priya Vashishta doi:10.1016/j.cpc.2005.01.005 Computer Physics Communications, Vol. 167, No. 3. (1 May 2005), pp. 151-164. 2008-03-11T18:51:34-00:00 2005 Computer Physics Communications 167 3 151 164 check http://www.citeulike.org/user/OndrejMarsalek/article/2676041 <i></i> \urlhttp://www.scons.org/ 2008-04-16T04:41:09-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2632479 <i>(18 Jan 1999)</i><br /><br />A new algorithm is introduced to integrate the equations of rotational motion. The algorithm is derived within a leapfrog framework and the quantities involved into the integration are mid-step angular momenta and on-step orientational positions. Contrary to the standard implicit method by Fincham [Mol. Simul., 8, 165 (1992)], the revised angular momentum approach presented corresponds completely to the leapfrog idea on interpolation of dynamical variables without using any extrapolations. The proposed scheme intrinsically preserves rigid molecular structures and considerably improves stability properties and energy conservation. As is demonstrated on the basis of simulations for water, it allows to reproduce correct results with extra large step sizes of order 5 fs and 10 fs in the cases of energy- and temperature-conserving dynamics, respectively. We show also that iterative solutions can be avoided within our implicit scheme shifting from quaternions to the entire rotation-matrix representation. A new leapfrog integrator of rotational motion. The revised angular-momentum approach Igor Omelyan (18 Jan 1999) 2008-04-05T12:04:54-00:00 1999 check http://www.citeulike.org/user/OndrejMarsalek/article/2629676 <i>International Journal of Modern Physics C, Vol. 4 (1993), pp. 385-392.</i><br /><br />We consider symplectic methods for the numerical integration of Hamiltonian problems, i.e. methods that preserve the Poincaré integral invariants. Examples of symplectic methods are given and numerical experiments are reported. Symplectic Numerical Methods for Hamiltonian Problems JM Sanz-Serna MP Calvo doi:10.1142/S0129183193000410 International Journal of Modern Physics C, Vol. 4 (1993), pp. 385-392. 2008-04-04T13:48:30-00:00 1993 International Journal of Modern Physics C 4 385 392 algorithms masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/1886058 <i>Physical Review A, Vol. 31, No. 3. (March 1985), 1695.</i><br /><br />Nosé has modified Newtonian dynamics so as to reproduce both the canonical and the isothermal-isobaric probability densities in the phase space of an N -body system. He did this by scaling time (with s) and distance (with V 1/ D in D dimensions) through Lagrangian equations of motion. The dynamical equations describe the evolution of these two scaling variables and their two conjugate momenta p s and p v . Here we develop a slightly different set of equations; free of time scaling. We find the dynamical steady-state probability density in an extended phase space with variables x ; p x ; V ; ε̇ ; and ζ ; where the x are reduced distances and the two variables ε̇ and ζ act as thermodynamic friction coefficients. We find that these friction coefficients have Gaussian distributions. From the distributions the extent of small-system non-Newtonian behavior can be estimated. We illustrate the dynamical equations by considering their application to the simplest possible case; a one-dimensional classical harmonic oscillator. Canonical dynamics: Equilibrium phase-space distributions William Hoover doi:10.1103/PhysRevA.31.1695 Physical Review A, Vol. 31, No. 3. (March 1985), 1695. 2007-11-08T20:25:11-00:00 1985 Physical Review A 31 3 1695 American Physical Society algorithms masters md http://www.citeulike.org/user/OndrejMarsalek/article/2620636 <i>(1974)</i> Základy fysikálních měření (II)B (in Czech) Jaromír Brož (1974) 2008-04-01T17:24:47-00:00 1974 SPN masters http://www.citeulike.org/user/OndrejMarsalek/article/2616884 <i></i> \urlhttp://www.valgrind.org/ 2008-03-31T17:00:40-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2613738 <i>Vol. 1 (1963)</i> The Feynman Lectures on Physics Richard Feynman Robert Leighton Matthew Sands Vol. 1 (1963) 2008-03-30T19:23:39-00:00 1963 1 Addison-Wesley book masters http://www.citeulike.org/user/OndrejMarsalek/article/2613686 <i>Methods Comput. Phys. (1970)</i> Potential calculation and some applications RW Hockney Methods Comput. Phys. (1970) 2008-03-30T18:57:50-00:00 1970 Methods Comput. Phys. algorithms masters http://www.citeulike.org/user/OndrejMarsalek/article/2613645 <i>The Journal of Chemical Physics, Vol. 76, No. 1. (1982), pp. 637-649.</i> A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters William Swope Hans Andersen Peter Berens Kent Wilson The Journal of Chemical Physics, Vol. 76, No. 1. (1982), pp. 637-649. 2008-03-30T18:27:10-00:00 1982 The Journal of Chemical Physics 76 1 637 649 AIP algorithms masters md numerics http://www.citeulike.org/user/OndrejMarsalek/article/2613094 <i></i> \urlhttp://matplotlib.sourceforge.net/ 2008-03-30T14:13:07-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2613046 <i></i> \urlhttp://www.open-mpi.org/ 2008-03-30T13:50:33-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2613044 <i></i> \urlhttp://www.tacc.utexas.edu/resources/software/#blas 2008-03-30T13:47:14-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2613041 <i></i> \urlhttp://www.cise.ufl.edu/research/sparse/umfpack/ 2008-03-30T13:44:04-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2613031 <i></i> \urlhttp://www.gnu.org/software/gsl/ 2008-03-30T13:31:54-00:00 masters web http://www.citeulike.org/user/OndrejMarsalek/article/2610863 <i>The Journal of Chemical Physics, Vol. 100, No. 4. (1994), pp. 3068-3078.</i><br /><br />View this record in Web of Science Statistical thermodynamics in the classical molecular dynamics ensemble. III. Numerical results Rolf Lustig The Journal of Chemical Physics, Vol. 100, No. 4. (1994), pp. 3068-3078. 2008-03-29T14:53:35-00:00 1994 The Journal of Chemical Physics 100 4 3068 3078 AIP check http://www.citeulike.org/user/OndrejMarsalek/article/2608816 <i>(2006)</i> Rozvoj metod počítačové fyziky pro fyziku plazmatu a fyziku tenkých vrstev (in Czech) Jiří Šimek (2006) 2008-03-28T17:41:58-00:00 2006 masters http://www.citeulike.org/user/OndrejMarsalek/article/2606005 <i>J. Chem. Phys., Vol. 97 (August 1992), pp. 1990-2001.</i><br /><br />Not Available Reversible multiple time scale molecular dynamics M Tuckerman BJ Berne GJ Martyna J. Chem. Phys., Vol. 97 (August 1992), pp. 1990-2001. 2008-03-28T12:02:22-00:00 1992 J. Chem. Phys. 97 1990 2001 algorithms masters md numerics http://www.citeulike.org/user/OndrejMarsalek/article/2587483 <i></i> "Green's Identities." From MathWorld---A Wolfram Web Resource. \urlhttp://mathworld.wolfram.com/GreensIdentities.html Eric Weisstein 2008-03-25T19:15:23-00:00 masters math web http://www.citeulike.org/user/OndrejMarsalek/article/2587402 <i></i> Mathematics for Physicists III, lecture material available at \urlhttp://www.karlin.mff.cuni.cz/~soucek/ (in Czech) Vladimír Souček 2008-03-25T18:38:01-00:00 masters math http://www.citeulike.org/user/OndrejMarsalek/article/2580848 <i>(22 December 1994)</i> Partial Differential Equations DiBenedetto, Emmanuele (22 December 1994) 2008-03-24T14:40:56-00:00 1994 Birkhäuser Boston book masters math http://www.citeulike.org/user/OndrejMarsalek/article/1358464 <i>J. Phys.: Conf. Ser., Vol. 63, No. 1. (2007), 012009.</i> Improving performance of multi-dimensional Particle-In-Cell codes for modelling of medium pressure plasma Z Pekárek M Lahuta R Hrach doi:10.1088/1742-6596/63/1/012009 J. Phys.: Conf. Ser., Vol. 63, No. 1. (2007), 012009. 2007-06-02T19:48:06-00:00 2007 J. Phys.: Conf. Ser. 1742-6596 63 1 012009 Institute of Physics Publishing algorithms electrostatics masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2568159 <i>(2003)</i> Introduction to computer simulations: Monte-Carlo and molecular dynamics methods (in Czech) I Nezbeda J Kolafa M Kotrla (2003) 2008-03-20T22:17:12-00:00 2003 Karolinum book masters mc md http://www.citeulike.org/user/OndrejMarsalek/article/2553134 <i></i> personal communication D Pražák 2008-03-18T22:54:14-00:00 masters http://www.citeulike.org/user/OndrejMarsalek/article/2553131 <i></i> personal communication Z Pekárek 2008-03-18T22:52:55-00:00 masters http://www.citeulike.org/user/OndrejMarsalek/article/2551962 <i>Plasma Physics and Controlled Fusion, Vol. 47, No. 5A. (2005), pp. A231-A260.</i><br /><br />Particle simulation of plasmas, employed since the 1960s, provides a self-consistent, fully kinetic representation of general plasmas. Early incarnations looked for fundamental plasma effects in one-dimensional systems with [?]102-103 particles in periodic electrostatic systems on computers with [?]100 kB memory. Recent advances model boundary conditions, such as external circuits to wave launchers, collisions and effects of particle-surface impact, all in fully relativistic three-dimensional electromagnetic systems using [?]106-1010 particles on massively parallel computers. While particle codes still enjoy prominance in a number of basic physics areas, they are now often used for engineering devices as well. Particle simulation of plasmas: review and advances JP Verboncoeur doi:10.1088/0741-3335/47/5A/017 Plasma Physics and Controlled Fusion, Vol. 47, No. 5A. (2005), pp. A231-A260. 2008-03-18T16:09:21-00:00 2005 Plasma Physics and Controlled Fusion 47 5A A231 A260 masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2258191 <i>Annalen der Physik, Vol. 369, No. 3. (1921), pp. 253-287.</i><br /><br />No Abstract. Die Berechnung optischer und elektrostatischer Gitterpotentiale PP Ewald doi:10.1002/andp.19213690304 Annalen der Physik, Vol. 369, No. 3. (1921), pp. 253-287. 2008-01-19T21:19:27-00:00 1921 Annalen der Physik 369 3 253 287 algorithms electrostatics masters http://www.citeulike.org/user/OndrejMarsalek/article/1820925 <i>(29 June 1989)</i><br /><br />Computer simulation is an essential tool in studying the chemistry and physics of liquids. Simulations allow us to develop models and to test them against experimental data. They can be used to evaluate approximate theories of liquids, and to provide detailed information on the structure and dynamics of model liquids at the molecular level. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods. The first four chapters describe these methods in detail, and provide the essential background in intermolecular forces and statistical mechanics. Chapters 5 and 6 emphasize the practical aspects of writing efficient programs and analysing the simulation results. The remaining chapters cover advanced techniques, non-equilibrium methods, Brownian dynamics, quantum simulations, and some important applications. FORTRAN code is presented in the text. Computer Simulation of Liquids MP Allen DJ Tildesley (29 June 1989) 2007-10-25T12:46:28-00:00 1989 Oxford University Press, USA book masters md http://www.citeulike.org/user/OndrejMarsalek/article/1605654 <i>(15 October 2001)</i><br /><br /><b>Understanding Molecular Simulation: From Algorithms to Applications</b> explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.<br><br>Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on:<br><br>· Transition path sampling and diffusive barrier crossing to simulaterare events<br>· Dissipative particle dynamic as a course-grained simulation technique<br>· Novel schemes to compute the long-ranged forces<br>· Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations<br>· Multiple-time step algorithms as an alternative for constraints<br>· Defects in solids<br>· The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules<br>· Parallel tempering for glassy Hamiltonians<br><br>Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed. Understanding Molecular Simulation (Computational Science Series, Vol 1) Daan Frenkel B Smit (15 October 2001) 2007-08-29T15:54:18-00:00 2001 Academic Press book masters md http://www.citeulike.org/user/OndrejMarsalek/article/1081156 <i>Journal of Computational Physics, Vol. 73, No. 2. (December 1987), pp. 325-348.</i><br /><br />An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles whose interactions are Coulombic or gravitational in nature. For a system of N particles, an amount of work of the order O(N2) has traditionally been required to evaluate all pairwise interactions, unless some approximation or truncation method is used. The algorithm of the present paper requires an amount of work proportional to N to evaluate all interactions to within roundoff error, making it considerably more practical for large-scale problems encountered in plasma physics, fluid dynamics, molecular dynamics, and celestial mechanics. A fast algorithm for particle simulations L Greengard V Rokhlin doi:10.1016/0021-9991(87)90140-9 Journal of Computational Physics, Vol. 73, No. 2. (December 1987), pp. 325-348. 2007-02-01T00:59:06-00:00 1987 Journal of Computational Physics 73 2 325 348 algorithms electrostatics masters plasma treecode http://www.citeulike.org/user/OndrejMarsalek/article/2538955 <i>(2007)</i> Condensed Matter Theory II, lecture at MFF UK, material available from the author (in Czech) P Lipavský (2007) 2008-03-16T13:29:33-00:00 2007 lecture masters sf http://www.citeulike.org/user/OndrejMarsalek/article/2537861 <i>General Electric Rev, Vol. 27 (1924)</i> Langmuir probe technique I Langmuir Mott Smith General Electric Rev, Vol. 27 (1924) 2008-03-15T21:28:58-00:00 1924 General Electric Rev 27 masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2472228 <i>(2005)</i> Plasma Theory, lecture at MFF UK, material available from the author L Krlín (2005) 2008-03-05T11:43:03-00:00 2005 lecture masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2453162 <i>(1974)</i> Introduction to Plasma Physics Francis Chen (1974) 2008-03-01T18:04:19-00:00 1974 Plenum Press, New York masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2453125 <i>SIAM Journal on Matrix Analysis and Applications, Vol. 18, No. 1. (1997), pp. 140-158.</i><br /><br />Pages 140-158, An Unsymmetric-Pattern Multifrontal Method for Sparse LU Factorization Timothy Davis Iain Duff SIAM Journal on Matrix Analysis and Applications, Vol. 18, No. 1. (1997), pp. 140-158. 2008-03-01T17:55:00-00:00 1997 SIAM Journal on Matrix Analysis and Applications 18 1 140 158 SIAM masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/2453122 <i>ACM Trans. Math. Softw., Vol. 25, No. 1. (March 1999), pp. 1-20.</i> A combined unifrontal/multifrontal method for unsymmetric sparse matrices Timothy Davis Iain Duff doi:10.1145/305658.287640 ACM Trans. Math. Softw., Vol. 25, No. 1. (March 1999), pp. 1-20. 2008-03-01T17:53:31-00:00 1999 ACM Trans. Math. Softw. 0098-3500 25 1 1 20 ACM masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/953087 <i>ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 196-199.</i> Algorithm 832: UMFPACK V4.3---an unsymmetric-pattern multifrontal method Timothy Davis doi:10.1145/992200.992206 ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 196-199. 2006-11-20T12:01:32-00:00 2004 ACM Trans. Math. Softw. 0098-3500 30 2 196 199 ACM Press masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/2453120 <i>ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 165-195.</i> A column pre-ordering strategy for the unsymmetric-pattern multifrontal method Timothy Davis doi:10.1145/992200.992205 ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 165-195. 2008-03-01T17:50:51-00:00 2004 ACM Trans. Math. Softw. 0098-3500 30 2 165 195 ACM masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/2453108 <i>(20 Sep 2007)</i><br /><br />We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPU's is compared to their main processor counterpart. We achieve speedups of up to 80, 40 and 150 fold, respectively. With newest generation of GPU's one can run standard MD simulations at 10^7 flops/$. Harvesting graphics power for MD simulations JA van Meel A Arnold D Frenkel Portegies Zwart RG Belleman (20 Sep 2007) 2008-03-01T17:40:42-00:00 2007 cuda md software http://www.citeulike.org/user/OndrejMarsalek/article/1705347 <i>J Comput Chem (25 September 2007)</i><br /><br />Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed. (c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2007. Accelerating molecular modeling applications with graphics processors. John E Stone James C Phillips Peter L Freddolino David J Hardy Leonardo G Trabuco Klaus Schulten doi:10.1002/jcc.20829 J Comput Chem (25 September 2007) 2007-09-28T15:56:32-00:00 2007 J Comput Chem 0192-8651 cuda electrostatics md software http://www.citeulike.org/user/OndrejMarsalek/article/2453098 <i>High Performance Computing – HiPC 2007 (2007), pp. 185-196.</i><br /><br />Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) to design and implement a new parallel algorithm. This results in an implementation with significant runtime savings on an off-the-shelf computer graphics card. Molecular Dynamics Simulations on Commodity GPUs with CUDA Weiguo Liu Bertil Schmidt Gerrit Voss Wolfgang Müller-Wittig doi:10.1007/978-3-540-77220-0_20 High Performance Computing – HiPC 2007 (2007), pp. 185-196. 2008-03-01T17:35:17-00:00 2007 High Performance Computing – HiPC 2007 185 196 cuda md software http://www.citeulike.org/user/OndrejMarsalek/article/2453095 <i>Journal of Computational Physics, Vol. In Press, Accepted Manuscript</i> General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units Joshua Anderson Chris Lorenz A Travesset doi:10.1016/j.jcp.2008.01.047 Journal of Computational Physics, Vol. In Press, Accepted Manuscript 2008-03-01T17:34:01-00:00 Journal of Computational Physics In Press, Accepted Manuscript cuda md software http://www.citeulike.org/user/OndrejMarsalek/article/2444154 <i>Journal of Computational Physics, Vol. 87 (March 1990), 161.</i><br /><br />Not Available A Modified Tree Code Don't Laugh: It Runs JE Barnes Journal of Computational Physics, Vol. 87 (March 1990), 161. 2008-02-28T16:36:46-00:00 1990 Journal of Computational Physics 87 161 algorithms masters treecode http://www.citeulike.org/user/OndrejMarsalek/article/2444110 <i>SIAM Journal on Scientific and Statistical Computing, Vol. 6, No. 1. (1985), pp. 85-103.</i> An Efficient Program for Many-Body Simulation Andrew Appel SIAM Journal on Scientific and Statistical Computing, Vol. 6, No. 1. (1985), pp. 85-103. 2008-02-28T16:23:15-00:00 1985 SIAM Journal on Scientific and Statistical Computing 6 1 85 103 SIAM algorithms electrostatics masters plasma treecode http://www.citeulike.org/user/OndrejMarsalek/article/2444075 <i>Computer Physics Communications, Vol. 19 (April 1980), pp. 215-261.</i><br /><br /><A HREF="/cgi-bin/nph-data_query?link_type=EJOURNAL&bibcode=1980CoPhC..19..215E">Electronic Article Available</A> from <A HREF="http://www.elsevier.com">Elsevier Science.</A> P3M3DP-The three-dimensional periodic particle-particle/ particle-mesh program JW Eastwood RW Hockney DN Lawrence doi:10.1016/0010-4655(80)90052-1 Computer Physics Communications, Vol. 19 (April 1980), pp. 215-261. 2008-02-28T16:08:32-00:00 1980 Computer Physics Communications 19 215 261 algorithms electrostatics masters plasma http://www.citeulike.org/user/OndrejMarsalek/article/2444043 <i>Computer Physics Communications, Vol. 164, No. 1-3., pp. 306-310.</i><br /><br />A treecode algorithm is presented for computing the electrostatic potential and electric field in a system of charged particles. The algorithm is grid-free and with N particles it reduces the operation count to O(NlogN), as opposed to O(N2) which is required for direct summation of pairwise interactions. The key idea is to replace the particle-particle interactions by particle-cluster interactions which are evaluated using a Taylor approximation in Cartesian coordinates. The treecode is combined here with a boundary integral method to simulate electron dynamics in a Penning-Malmberg trap. A treecode algorithm for simulating electron dynamics in a Penning-Malmberg trap AJ Christlieb R Krasny JP Verboncoeur doi:10.1016/j.cpc.2004.06.076 Computer Physics Communications, Vol. 164, No. 1-3., pp. 306-310. 2008-02-28T15:57:40-00:00 Computer Physics Communications 164 1-3 306 310 algorithms electrostatics masters plasma treecode http://www.citeulike.org/user/OndrejMarsalek/article/1872417 <i>Physical Review, Vol. 159, No. 1. (5 July 1967), 98.</i><br /><br />The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential has been integrated for various values of the temperature and density; relative; generally; to a fluid state. The equilibrium properties have been calculated and are shown to agree very well with the corresponding properties of argon. It is concluded that; to a good approximation; the equilibrium state of argon can be described through a two-body potential. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules Loup Verlet doi:10.1103/PhysRev.159.98 Physical Review, Vol. 159, No. 1. (5 July 1967), 98. 2007-11-06T07:38:21-00:00 1967 Physical Review 159 1 98 American Physical Society algorithms masters md numerics http://www.citeulike.org/user/OndrejMarsalek/article/2444014 <i>Journal of Computational Physics, Vol. 20 (February 1976), 130.</i><br /><br />Not Available Some Multistep Methods for Use in Molecular Dynamics Calculations D Beeman Journal of Computational Physics, Vol. 20 (February 1976), 130. 2008-02-28T15:47:14-00:00 1976 Journal of Computational Physics 20 130 algorithms masters md numerics http://www.citeulike.org/user/OndrejMarsalek/article/1386464 <i>(01 August 2007)</i><br /><br />Co-authored by four leading scientists from academia and industry, Numerical Recipes Third Edition starts with basic mathematics and computer science and proceeds to complete, working routines. Widely recognized as the most comprehensive, accessible and practical basis for scientific computing, this new edition incorporates more than 400 Numerical Recipes routines, many of them new or upgraded. The executable C++ code, now printed in color for easy reading, adopts an object-oriented style particularly suited to scientific applications. The whole book is presented in the informal, easy-to-read style that made earlier editions so popular. Find more information at <a href = "http://www.nr.com">www.nr.com or <a href = "http://www.cambridge.org/numericalrecipes">www.cambridge.org/numericalrecipes. New key features: <ul> <li>2 new chapters, 25 new sections, 25% longer than Second Edition</li> <li>Thorough upgrades throughout the text</li> <li>Over 100 completely new routines and upgrades of many more.</li> <li>New Classification and Inference chapter, including Gaussian mixture models, HMMs, hierarchical clustering, Support Vector Machines</li><li>New Computational Geometry chapter covers KD trees, quad- and octrees, Delaunay triangulation, and algorithms for lines, polygons, triangles, and spheres</li> <li>New sections include interior point methods for linear programming, Monte Carlo Markov Chains, spectral and pseudospectral methods for PDEs, and many new statistical distributions</li> <li>An expanded treatment of ODEs with completely new routines</li> </ul> Plus comprehensive coverage of <ul> <li>linear algebra, interpolation, special functions, random numbers, nonlinear sets of equations, optimization, eigensystems, Fourier methods and wavelets, statistical tests, ODEs and PDEs, integral equations, and inverse theory</li> </ul> And much, much more! For more information, or to buy the book, visit <a href = "http://www.cambridge.org/numericalrecipes">www.cambridge.org/numericalrecipes. For support, or to subscribe to an online version, please visit <a href = "http://www.nr.com">www.nr.com. Numerical Recipes: The Art of Scientific Computing William Press Saul Teukolsky William Vetterling Brian Flannery (01 August 2007) 2007-06-13T05:09:04-00:00 2007 Cambridge University Press algorithms book masters numerics http://www.citeulike.org/user/OndrejMarsalek/article/487581 <i>The Journal of Chemical Physics, Vol. 72, No. 4. (1980), pp. 2384-2393.</i><br /><br />In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a particular simulation, and it is assumed that time averages of properties of the simulated fluid are equal to microcanonical ensemble averages of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temperature and/or pressure or under conditions in which the energy and volume of the fluid can fluctuate. This paper proposes and discusses three methods for performing molecular dynamics simulations under conditions of constant temperature and/or pressure, rather than constant energy and volume. For these three methods, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic–isobaric, canonical, and isothermal–isobaric ensembles. Each method is a way of describing the dynamics of a certain number of particles in a volume element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or density of the simulated volume element. The influence of the surroundings is taken into account without introducing unwanted surface effects. Examples of situations where these methods may be useful are discussed. The Journal of Chemical Physics is copyrighted by The American Institute of Physics. doi:10.1063/1.439486 PACS: 61.20.Ja Additional Information Full Text: [ PDF (944 kB) GZipped PS Molecular dynamics simulations at constant pressure and/or temperature Hans Andersen doi:10.1063/1.439486 The Journal of Chemical Physics, Vol. 72, No. 4. (1980), pp. 2384-2393. 2006-01-31T18:12:44-00:00 1980 The Journal of Chemical Physics 72 4 2384 2393 AIP algorithms masters md