Extending And Modifying Lammps Writing Your Own Source Code

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Extending and Modifying LAMMPS Writing Your Own Source Code

Author : Dr. Shafat Mubin
Publisher : Packt Publishing Ltd
ISBN 13 : 1800567235
Total Pages : 394 pages
Book Rating : 4.8/5 (5 download)

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Book Synopsis Extending and Modifying LAMMPS Writing Your Own Source Code by : Dr. Shafat Mubin

Download or read book Extending and Modifying LAMMPS Writing Your Own Source Code written by Dr. Shafat Mubin and published by Packt Publishing Ltd. This book was released on 2021-02-19 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understand the LAMMPS source code and modify it to meet your research needs, and run simulations for bespoke applications involving forces, thermostats, pair potentials and more with ease Key FeaturesUnderstand the structure of the LAMMPS source codeImplement custom features in the LAMMPS source code to meet your research needsRun example simulations involving forces, thermostats, and pair potentials based on implemented featuresBook Description LAMMPS is one of the most widely used tools for running simulations for research in molecular dynamics. While the tool itself is fairly easy to use, more often than not you'll need to customize it to meet your specific simulation requirements. Extending and Modifying LAMMPS bridges this learning gap and helps you achieve this by writing custom code to add new features to LAMMPS source code. Written by ardent supporters of LAMMPS, this practical guide will enable you to extend the capabilities of LAMMPS with the help of step-by-step explanations of essential concepts, practical examples, and self-assessment questions. This LAMMPS book provides a hands-on approach to implementing associated methodologies that will get you up and running and productive in no time. You'll begin with a short introduction to the internal mechanisms of LAMMPS, and gradually transition to an overview of the source code along with a tutorial on modifying it. As you advance, you'll understand the structure, syntax, and organization of LAMMPS source code, and be able to write your own source code extensions to LAMMPS that implement features beyond the ones available in standard downloadable versions. By the end of this book, you'll have learned how to add your own extensions and modifications to the LAMMPS source code that can implement features that suit your simulation requirements. What you will learnIdentify how LAMMPS input script commands are parsed within the source codeUnderstand the architecture of the source codeRelate source code elements to simulated quantitiesLearn how stored quantities are accessed within the source codeExplore the mechanisms controlling pair styles, computes, and fixesModify the source code to implement custom features in LAMMPSWho this book is for This book is for students, faculty members, and researchers who are currently using LAMMPS or considering switching to LAMMPS, have a basic knowledge of how to use LAMMPS, and are looking to extend LAMMPS source code for research purposes. This book is not a tutorial on using LAMMPS or writing LAMMPS scripts, and it is assumed that the reader is comfortable with the basic LAMMPS syntax. The book is geared toward users with little to no experience in source code editing. Familiarity with C++ programming is helpful but not necessary.

Numerical Simulation in Molecular Dynamics

Author : Michael Griebel
Publisher : Springer Science & Business Media
ISBN 13 : 3540680950
Total Pages : 472 pages
Book Rating : 4.5/5 (46 download)

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Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel

Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer Science & Business Media. This book was released on 2007-08-16 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

Understanding Molecular Simulation

Author : Daan Frenkel
Publisher : Elsevier
ISBN 13 : 0080519989
Total Pages : 661 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Understanding Molecular Simulation by : Daan Frenkel

Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Molecular Simulation: From Algorithms to Applications 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. 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: - Transition path sampling and diffusive barrier crossing to simulaterare events - Dissipative particle dynamic as a course-grained simulation technique - Novel schemes to compute the long-ranged forces - Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations - Multiple-time step algorithms as an alternative for constraints - Defects in solids - The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules - Parallel tempering for glassy Hamiltonians 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.

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

Author : Sumit Sharma
Publisher : Elsevier
ISBN 13 : 0128169559
Total Pages : 368 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs by : Sumit Sharma

Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. - Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs - Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites - Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems

Molecular Dynamics

Author : Ben Leimkuhler
Publisher : Springer
ISBN 13 : 3319163752
Total Pages : 461 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Molecular Dynamics by : Ben Leimkuhler

Download or read book Molecular Dynamics written by Ben Leimkuhler and published by Springer. This book was released on 2015-05-18 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.

Statistical Mechanics: Theory and Molecular Simulation

Author : Mark Tuckerman
Publisher : OUP Oxford
ISBN 13 : 0191523461
Total Pages : 719 pages
Book Rating : 4.1/5 (915 download)

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Book Synopsis Statistical Mechanics: Theory and Molecular Simulation by : Mark Tuckerman

Download or read book Statistical Mechanics: Theory and Molecular Simulation written by Mark Tuckerman and published by OUP Oxford. This book was released on 2010-02-11 with total page 719 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.

Modern Fortran

Author : Milan Curcic
Publisher : Simon and Schuster
ISBN 13 : 1638350051
Total Pages : 414 pages
Book Rating : 4.6/5 (383 download)

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Book Synopsis Modern Fortran by : Milan Curcic

Download or read book Modern Fortran written by Milan Curcic and published by Simon and Schuster. This book was released on 2020-10-07 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern Fortran teaches you to develop fast, efficient parallel applications using twenty-first-century Fortran. In this guide, you’ll dive into Fortran by creating fun apps, including a tsunami simulator and a stock price analyzer. Filled with real-world use cases, insightful illustrations, and hands-on exercises, Modern Fortran helps you see this classic language in a whole new light. Summary Using Fortran, early and accurate forecasts for hurricanes and other major storms have saved thousands of lives. Better designs for ships, planes, and automobiles have made travel safer, more efficient, and less expensive than ever before. Using Fortran, low-level machine learning and deep learning libraries provide incredibly easy, fast, and insightful analysis of massive data. Fortran is an amazingly powerful and flexible programming language that forms the foundation of high performance computing for research, science, and industry. And it's come a long, long way since starting life on IBM mainframes in 1956. Modern Fortran is natively parallel, so it's uniquely suited for efficiently handling problems like complex simulations, long-range predictions, and ultra-precise designs. If you're working on tasks where speed, accuracy, and efficiency matter, it's time to discover—or re-discover—Fortran.. About the technology For over 60 years Fortran has been powering mission-critical scientific applications, and it isn't slowing down yet! Rock-solid reliability and new support for parallel programming make Fortran an essential language for next-generation high-performance computing. Simply put, the future is in parallel, and Fortran is already there. Purchase of the print book includes a free eBook in PDF, Kindle, and ePub formats from Manning Publications. About the book Modern Fortran teaches you to develop fast, efficient parallel applications using twenty-first-century Fortran. In this guide, you'll dive into Fortran by creating fun apps, including a tsunami simulator and a stock price analyzer. Filled with real-world use cases, insightful illustrations, and hands-on exercises, Modern Fortran helps you see this classic language in a whole new light. What's inside Fortran's place in the modern world Working with variables, arrays, and functions Module development Parallelism with coarrays, teams, and events Interoperating Fortran with C About the reader For developers and computational scientists. No experience with Fortran required. About the author Milan Curcic is a meteorologist, oceanographer, and author of several general-purpose Fortran libraries and applications. Table of Contents PART 1 - GETTING STARTED WITH MODERN FORTRAN 1 Introducing Fortran 2 Getting started: Minimal working app PART 2 - CORE ELEMENTS OF FORTRAN 3 Writing reusable code with functions and subroutines 4 Organizing your Fortran code using modules 5 Analyzing time series data with arrays 6 Reading, writing, and formatting your data PART 3 - ADVANCED FORTRAN USE 7 Going parallel with Fortan coarrays 8 Working with abstract data using derived types 9 Generic procedures and operators for any data type 10 User-defined operators for derived types PART 4 - THE FINAL STRETCH 11 Interoperability with C: Exposing your app to the web 12 Advanced parallelism with teams, events, and collectives

Computational Biophysics

Author : Klaus Schulten
Publisher : Newnes
ISBN 13 : 9780123870100
Total Pages : 0 pages
Book Rating : 4.8/5 (71 download)

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Book Synopsis Computational Biophysics by : Klaus Schulten

Download or read book Computational Biophysics written by Klaus Schulten and published by Newnes. This book was released on 2018-02-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Biophysics

Polymer Engineering Science and Viscoelasticity

Author : Hal F. Brinson
Publisher : Springer
ISBN 13 : 1489974857
Total Pages : 488 pages
Book Rating : 4.4/5 (899 download)

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Book Synopsis Polymer Engineering Science and Viscoelasticity by : Hal F. Brinson

Download or read book Polymer Engineering Science and Viscoelasticity written by Hal F. Brinson and published by Springer. This book was released on 2015-01-24 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a unified mechanics and materials perspective on polymers: both the mathematics of viscoelasticity theory as well as the physical mechanisms behind polymer deformation processes. Introductory material on fundamental mechanics is included to provide a continuous baseline for readers from all disciplines. Introductory material on the chemical and molecular basis of polymers is also included, which is essential to the understanding of the thermomechanical response. This self-contained text covers the viscoelastic characterization of polymers including constitutive modeling, experimental methods, thermal response, and stress and failure analysis. Example problems are provided within the text as well as at the end of each chapter. New to this edition: · One new chapter on the use of nano-material inclusions for structural polymer applications and applications such as fiber-reinforced polymers and adhesively bonded structures · Brings up-to-date polymer production and sales data and equipment and procedures for evaluating polymer characterization and classification · The work serves as a comprehensive reference for advanced seniors seeking graduate level courses, first and second year graduate students, and practicing engineers

Computer Simulation of Liquids

Author : M. P. Allen
Publisher : Oxford University Press
ISBN 13 : 9780198556459
Total Pages : 412 pages
Book Rating : 4.5/5 (564 download)

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Book Synopsis Computer Simulation of Liquids by : M. P. Allen

Download or read book Computer Simulation of Liquids written by M. P. Allen and published by Oxford University Press. This book was released on 1989 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods.

Simulation of Complex Systems

Author : Aykut Argun
Publisher :
ISBN 13 : 9780750338431
Total Pages : 0 pages
Book Rating : 4.3/5 (384 download)

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Book Synopsis Simulation of Complex Systems by : Aykut Argun

Download or read book Simulation of Complex Systems written by Aykut Argun and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book deals with the most fundamental and essential techniques to simulate complex systems, from the dynamics of molecules to the spreading of diseases, from optimization using ant colonies to the simulation of the Game of Life.

Crystal Plasticity Finite Element Methods

Author : Franz Roters
Publisher : John Wiley & Sons
ISBN 13 : 3527642099
Total Pages : 188 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Crystal Plasticity Finite Element Methods by : Franz Roters

Download or read book Crystal Plasticity Finite Element Methods written by Franz Roters and published by John Wiley & Sons. This book was released on 2011-08-04 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the leading experts in computational materials science, this handy reference concisely reviews the most important aspects of plasticity modeling: constitutive laws, phase transformations, texture methods, continuum approaches and damage mechanisms. As a result, it provides the knowledge needed to avoid failures in critical systems udner mechanical load. With its various application examples to micro- and macrostructure mechanics, this is an invaluable resource for mechanical engineers as well as for researchers wanting to improve on this method and extend its outreach.

Programming and Performance Visualization Tools

Author : Abhinav Bhatele
Publisher : Springer
ISBN 13 : 3030178722
Total Pages : 292 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Programming and Performance Visualization Tools by : Abhinav Bhatele

Download or read book Programming and Performance Visualization Tools written by Abhinav Bhatele and published by Springer. This book was released on 2019-04-24 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains the revised selected papers of 4 workshops held in conjunction with the International Conference on High Performance Computing, Networking, Storage and Analysis (SC) in November 2017 in Denver, CO, USA, and in November 2018 in Dallas, TX, USA: the 6th and 7th International Workshop on Extreme-Scale Programming Tools, ESPT 2017 and ESPT 2018, and the 4th and 5th International Workshop on Visual Performance Analysis, VPA 2017 and VPA 2018. The 11 full papers of ESPT 2017 and ESPT 2018 and the 6 full papers of VPA 2017 and VPA 2018 were carefully reviewed and selected for inclusion in this book. The papers discuss the requirements for exascale-enabled tools as well as new approaches of applying visualization and visual analytic techniques to large-scale applications. Topics of interest include: programming tools; methodologies for performance engineering; tool technologies for extreme-scale challenges (e.g., scalability, resilience, power); tool support for accelerated architectures and large-scale multi-cores; tool infrastructures and environments; evolving/future application requirements for programming tools and technologies; application developer experiences with programming and performance tools; scalable displays of performance data; case studies demonstrating the use of performance visualization in practice; data models to enable scalable visualization; graph representation of unstructured performance data; presentation of high-dimensional data; visual correlations between multiple data sources; human-computer interfaces for exploring performance data; and multi-scale representations of performance data for visual exploration.

Coarse-Graining of Condensed Phase and Biomolecular Systems

Author : Gregory A. Voth
Publisher : CRC Press
ISBN 13 : 1420059564
Total Pages : 492 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Coarse-Graining of Condensed Phase and Biomolecular Systems by : Gregory A. Voth

Download or read book Coarse-Graining of Condensed Phase and Biomolecular Systems written by Gregory A. Voth and published by CRC Press. This book was released on 2008-09-22 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.

High-Performance Computing Using FPGAs

Author : Wim Vanderbauwhede
Publisher : Springer Science & Business Media
ISBN 13 : 1461417910
Total Pages : 798 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis High-Performance Computing Using FPGAs by : Wim Vanderbauwhede

Download or read book High-Performance Computing Using FPGAs written by Wim Vanderbauwhede and published by Springer Science & Business Media. This book was released on 2013-08-23 with total page 798 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-Performance Computing using FPGA covers the area of high performance reconfigurable computing (HPRC). This book provides an overview of architectures, tools and applications for High-Performance Reconfigurable Computing (HPRC). FPGAs offer very high I/O bandwidth and fine-grained, custom and flexible parallelism and with the ever-increasing computational needs coupled with the frequency/power wall, the increasing maturity and capabilities of FPGAs, and the advent of multicore processors which has caused the acceptance of parallel computational models. The Part on architectures will introduce different FPGA-based HPC platforms: attached co-processor HPRC architectures such as the CHREC’s Novo-G and EPCC’s Maxwell systems; tightly coupled HRPC architectures, e.g. the Convey hybrid-core computer; reconfigurably networked HPRC architectures, e.g. the QPACE system, and standalone HPRC architectures such as EPFL’s CONFETTI system. The Part on Tools will focus on high-level programming approaches for HPRC, with chapters on C-to-Gate tools (such as Impulse-C, AutoESL, Handel-C, MORA-C++); Graphical tools (MATLAB-Simulink, NI LabVIEW); Domain-specific languages, languages for heterogeneous computing(for example OpenCL, Microsoft’s Kiwi and Alchemy projects). The part on Applications will present case from several application domains where HPRC has been used successfully, such as Bioinformatics and Computational Biology; Financial Computing; Stencil computations; Information retrieval; Lattice QCD; Astrophysics simulations; Weather and climate modeling.

Nonequilibrium Molecular Dynamics

Author : Billy D. Todd
Publisher : Cambridge University Press
ISBN 13 : 0521190096
Total Pages : 371 pages
Book Rating : 4.5/5 (211 download)

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Book Synopsis Nonequilibrium Molecular Dynamics by : Billy D. Todd

Download or read book Nonequilibrium Molecular Dynamics written by Billy D. Todd and published by Cambridge University Press. This book was released on 2017-03-10 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt: This coherent collection of theory, algorithms, and illustrative results presents the field of nonequilibrium molecular dynamics in detail.

Impactful Times

Author : James R. Asay
Publisher : Springer
ISBN 13 : 331933347X
Total Pages : 676 pages
Book Rating : 4.3/5 (193 download)

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Book Synopsis Impactful Times by : James R. Asay

Download or read book Impactful Times written by James R. Asay and published by Springer. This book was released on 2017-05-02 with total page 676 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a history of shock compression science, including development of experimental, material modeling, and hydrodynamics code technologies over the past six decades at Sandia National Laboratories. The book is organized into a discussion of major accomplishments by decade with over 900 references, followed by a unique collection of 45 personal recollections detailing the trials, tribulations, and successes of building a world-class organization in the field. It explains some of the challenges researchers faced and the gratification they experienced when a discovery was made. Several visionary researchers made pioneering advances that integrated these three technologies into a cohesive capability to solve complex scientific and engineering problems. What approaches worked, which ones did not, and the applications of the research are described. Notable applications include the turret explosion aboard the USS Iowa and the Shoemaker-Levy comet impact on Jupiter. The personal anecdotes and recollections make for a fascinating account of building a world-renowned capability from meager beginnings. This book will be inspiring to the expert, the non expert, and the early-career scientist. Undergraduate and graduate students in science and engineering who are contemplating different fields of study should find it especially compelling.