Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The fact that a new text book introducing the essentials of computational chemistry contains more than 500 pages shows impressively the grown and still growing size and importance of this field of chemistry. The author’s objectives of the book, using his own words, are “to provide a survey of computational chemistry its underpinnings, its jargon, its strengths and weaknesses that will be accessible to both the experimental and theoretical communities”. This design as a general introduction into computational chemistry makes it an alternative to Andrew R. Leach’s well-established “Molecular Modeling” (Prentice Hall) and Frank Jensen’s “Introduction to Computational Chemistry” (Wiley), although the latter focuses on the theory of electronic structure methods. Cramer’s “Essentials” covers force field and molecular orbital theory, Monte Carlo and Molecular Dynamics simulations, thermodynamic and electronic (spectroscopic) property calculation, condensed phase treatment and a few more topics. Moreover, the book contains thirteen selected case studies sexamples taken from the literature sto illustrate the application of the just presented theoretical and computational models. This especially makes the text book well suited for both classroom discussion and self-study. Each chapter of “Essentials” covers a main topic of computational chemistry and will be briefly described here; all chapters are ended by a bibliography and suggested additional readings as well as the literature references cited in the text. In chapter 1 the author defines basic terms such as “theory”, “model”, and “computation”, introduces the concept of the potential energy surface and provides some general considerations about hardware and software. Interestingly, the first equation occurring in the text is not Schro ̈dinger’s equation, as is the case for most computational chemistry introductions, but the famous Einstein relation. The second chapter deals with molecular mechanics. It explains the different potential energy contributions, introduces the field of structure optimization, and provides an overview of the variety of modern force fields. Chapter 3 covers the simulation of molecular ensembles. It defines phase space and trajectories and shows the formalism of, and problems and difference between, Monte Carlo and molecular dynamics. In chapter 4 the author introduces the foundations of molecular orbital theory. Basic concepts such as Hamilton operator, LCAO basis set approach, many-electron wave functions, etc. are explained. To illuminate the LCAO variational process, the Hu ̈ckel theory is presented with an example. Chapter 5 deals with semiempirical molecular orbital (MO) theory. Besides the classical approaches (extended Hu ̈ckel, CNDO, INDO, NDDO) and methods (e.g., MNDO, AM1, PM3) and their performance, examples are provided from the ongoing development in that still fascinating area. Ab initio MO theory is presented in chapter 6; the basis set concept is discussed in detail, and, after some considerations from an user’s point of view, the general performance of ab initio methods is explicated. The next chapter covers the problem of electron correlation and gives the most prominent solutions for its treatment: configuration interaction, theory of the multiconfiguration self-consistent field, perturbation, and coupled cluster. Practical issues are also discussed. Chapter 8’s topic is density functional theory (DFT). Its theoretical foundation, methodology, and some functionals as well as its pros and cons compared to MO theory are presented together with a general performance overview. The next two chapters deal with charge distribution, derived and spectroscopic properties (e.g., atomic charges, polarizability, rotational, vibrational, and NMR spectra), and thermodynamic properties (e.g., zero-point vibrational energy, free energy of formation, and reaction). The modeling of condensed phases is addressed in chapters 11 (implicit models) and 12 (explicit models), which closes with a comparison between the two approaches. Chapter 13 familiarizes the reader with hybrid quantum mechanical/molecular mechanical (QM/MM) models. Polarization as well as the problematic implications of unsaturated QM and MM components are discussed, and empirical valence bond methods are also presented. The treatment of excited states is the topic of chapter 14; besides CI and MCSCF as computational methods, transition probabilities and solvatochromism are discussed. The last chapter deals with reaction dynamics, mostly adiabaticskinetics, rate constants, reaction paths, and transition state theory are section topics here sbut also nonadiabatic, introducing curve crossing and Marcus theory in brief. The appendix is divided into four parts: an acronym glossary (which is very helpful), an overview of symmetry and group theory, an introduction to spin algebra, and finally a section about orbital localization. A rather detailed index ends the book. The “Essentials” writing style fits the fascinating topic: one reads on and on andssurprise! sanother chapter has been absorbed. The text is complemented by a large number of black and white figures and clear tables, mostly self-explanatory with descriptive captions. The use of equations and mathematical formulas in general is well-balanced, and the level of math should be understandable for every natural scientist with some basic knowledge of physics. There are only a few minor shortcomings: for example, a literature reference cited in the text (“Beck et al.”, p 142) is missing in the bibliography; “Kronecker” is mistyped with o ̈; and the author completely forgot to reference Leach’s text book when referring to other computational chemistry introductions. However, the author has established a specific errata web page (http://pollux.chem.umn.edu/ ∼cramer/Errors.html) with all known errors. These will be corrected in the next printing or next revised edition, respectively. With its emphasis, on one hand, on the basic concepts and applications rather than pure theory and mathematics, and on the other hand, coverage of quantum mechanical and classical mechanical models including examples from inorganic, organic, and biological chemistry, “Essentials” is a useful tool not only for teaching and learning but also as a quick reference, and thus will most probably become one of the standard text books for computational chemistry.

Essentials Of Computational Chemistry Theories And Models

Nanoscale liquid hydrocarbon adsorption on clay minerals: A molecular dynamics simulation of shale oils

Expansion of clay minerals in expansive soil, such as montmorillonite (MMT), is critical to a broad class of problems in science and engineering. Cement is one of the most widely used materials in ...

Revealing Expansion Mechanism of Cement-Stabilized Expansive Soil with Different Interlayer Cations through Molecular Dynamics Simulations

Swelling of montmorillonite (MMT) is a nonnegligible factor in many industrial processes owing to its great ability to absorb water in interlayer space. It is not easy to determine whether the exchangeable cations or the MMT layers interacts much stronger with water molecules to provide the dominant driving force for the swelling of MMT. In this work, driving force for the swelling of montmorillonite as affected by surface charge and exchangeable cations has been investigated through molecular dynamics simulations (MDs). The adsorption energy between water molecules and MMT layers and between interlayer cations and water molecules was calculated to qualitatively characterize the driving force for the swelling of MMT, and higher negative adsorption energy means greater driving force. It is found that the adsorption energy between interlayer cations and water molecules are far higher than that between MMT layers and water molecules. Thus, it is the exchangeable cations that provide the dominant driving force for MMT to swell. Besides, it is observed that interlayer cations with stronger hydration ability (Mg > Ca > Na > K) have more negative adsorption energy to water molecules, which indicates that the stronger the hydration ability of exchangeable cations the greater contribution they make to the total driving force for the swelling of MMT.

Driving force for the swelling of montmorillonite as affected by surface charge and exchangeable cations: A molecular dynamic study

Over the last two decades, the swelling properties of montmorillonite (MMT) have been studied in many experimental and simulation works, but less attention has been given to MMT containing a mixture of monovalent/monovalent and monovalent/bivalent cations in the interlayer spaces. We carried out a molecular dynamics simulation of the swelling patterns of Na-, Mg-, Na/Cs-, Na/Mg-MMT in an isobaric isothermal ensemble (NPT) at T = 300 K and p = 1 atm. The simulation reproduced a swelling pattern of Na-, Mg-, Na/Cs-, Na/Mg-MMT and the swelling curves obtained showed the difference between the hydration mechanisms of the type of MMT used in this study. We also found out that the differences in size and hydration energy of Na, Cs and Na, Mg ions have strong implications on the structure of interlayer water. This has led to the difference in the swelling curves of the simulated Na-, Mg-, Na/Cs- and Na/Mg-MMT. For Na/Cs-MMT, the hydration energy of Na cations increased compared to that in Na-MMT, the hyd...

Molecular dynamics study of the swelling patterns of Na/Cs-, Na/Mg-montmorillonites and hydration of interlayer cations

Molecular Dynamics Study of the Thermosensitive Properties of Poly (N-vinyl caprolactam) in Water

In the present work, we performed a molecular dynamics (MD) simulation of Na-montmorillonite (Na-Mt) in nonambient environment under the crystalline swelling to evaluate the effect of temperature and inorganic salts addition on the interlayer structure and the swelling behavior of Na-Mt. The activities of inorganic salts (NH4Cl, AlCl3, MgCl2 and FeCl3) on the hydration process of Na-Mt at high temperatures (200, 300, 400, 500, and 600 K) and high pressure (HTHP) of P=6 GPa in an isobaric isothermal ensemble (NPT) were investigated. The results showed that addition of inorganic salts into Na-Mt enhanced mobility of the interlayer species, and shrunk the hydration shell of the interlayer ions with a rise in temperature. The salts inhibited swelling by reducing the mobility of the interlayer species and the basal spacing. The type of cations present between the layers, their hydration energies affected the structure and properties of Na-Mt. Chlorine played an important role in the inhibition process of inorganic salts by exerting strong attractive forces on interlayer H2O molecules. Compared with the other salts, the most stable state of Na-Mt at HTHP is achieved with NH4Cl. These results could help a better understanding of the inhibition effect of inorganic salts on Na-Mt and predict the hydration process of Na-Mt at HTHP for further improvement of its structure.
Highlights 

Cl anion hydration energy change is more evident with salt type than temperature
Inorganic salt and temperature increase shrink the hydration shell of interlayer ions
NH4Cl addition provides a good inhibition at high temperature and high pressure
Increasing temperature and hydration degree promote the cation exchange process

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Tingji Ding

Papers

Molecular dynamics study of the swelling patterns of Na/Cs-, Na/Mg-montmorillonites and hydration of interlayer cations

Molecular Dynamics Study of the Thermosensitive Properties of Poly (N-vinyl caprolactam) in Water

Effects of Inorganic Salts Addition on Na-montmorillonite Clay at High Temperature and High Pressure: Insights from Molecular Dynamics Simulation

Dissociation mechanism of methane hydrate by CaCl2: an experimental and molecular dynamics study

Inhibition Mechanism of Cationic Polyacrylamide on Montmorillonite Surface Hydration: A Molecular Dynamics Simulation Study