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

Atmospheric degradation of volatile organic compounds

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

A detailed chemical kinetic mechanism has been developed to describe the oxidation of small hydrocarbon and oxygenated hydrocarbon species. The reactivity of these small fuels and intermediates is of critical importance in understanding and accurately describing the combustion characteristics, such as ignition delay time, flame speed, and emissions of practical fuels. The chosen rate expressions have been assembled through critical evaluation of the literature, with minimum optimization performed. The mechanism has been validated over a wide range of initial conditions and experimental devices, including flow reactor, shock tube, jet-stirred reactor, and flame studies. The current mechanism contains accurate kinetic descriptions for saturated and unsaturated hydrocarbons, namely methane, ethane, ethylene, and acetylene, and oxygenated species; formaldehyde, methanol, acetaldehyde, and ethanol.

A Hierarchical and Comparative Kinetic Modeling Study of C1 − C2 Hydrocarbon and Oxygenated Fuels

A detailed chemical kinetic model for ethanol oxidation has been developed and validated against a variety of experimental data sets. Laminar flame speed data (obtained from a constant volume bomb and counterflow twin-flame), ignition delay data behind a reflected shock wave, and ethanol oxidation product profiles from a jet-stirred and turbulent flow reactor were used in this computational study. Good agreement was found in modeling of the data sets obtained from the five different experimental systems. The computational results show that high temperature ethanol oxidation exhibits strong sensitivity to the fall-off kinetics of ethanol decomposition, branching ratio selection for C2H5OH + OH Products, and reactions involving the hydroperoxyl (HO2) radical.



The multichanneled ethanol decomposition process is analyzed by RRKM/Master Equation theory, and the results are compared with those obtained from earlier studies. The ten-parameter Troe form is used to define the C2H5OH(+M) CH3 + CH2OH(+M) rate expression as 


k∞ = 5.94E23 T−1.68 exp(−45880 K/T) (s−1)




ko = 2.88E85 T−18.9 exp(−55317 K/T) (cm3/mol/sec)




Fcent = 0.5 exp(−T/200 K) + 0.5 exp(−T/890 K) + exp(−4600 K/T)



and the C2H5OH(+M) C2H4 + H2O(+M) rate expression as 


k∞ = 2.79E13 T0.09 exp(−33284 K/T) (s−1)




ko = 2.57E83 T−18.85 exp(−43509 K/T) (cm3/mol/sec)




F cent = 0.3 exp(−T/350 K) + 0.7 exp(−T/800 K) + exp(−3800 K/T)



with an applied energy transfer per collision value of = 500 cm−1.



An empirical branching ratio estimation procedure is presented which determines the temperature dependent branching ratios of the three distinct sites of hydrogen abstraction from ethanol. The calculated branching ratios for C2H5OH + OH, C2H5OH + O, C2H5OH + H, and C2H5OH + CH3 are compared to experimental data. © 1999 John Wiley & Sons, Inc. Int J Chem Kinet 31: 183–220, 1999

A detailed chemical kinetic model for high temperature ethanol oxidation

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338–7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

COMPASS II: extended coverage for polymer and drug-like molecule databases.

The most commonly used theoretical models for describing chemical kinetics are accurate in two limits. When relaxation is fast with respect to reaction time scales, thermal transition state theory (TST) is the theoretical tool of choice. In the limit of slow relaxation, an energy resolved description like RRKM theory is more appropriate. For intermediate relaxation regimes, where much of the chemistry in nature occurs, theoretical approaches are somewhat less well established. However, in recent years master equation approaches have been successfully used to analyze and predict nonequilibrium chemical kinetics across a range of intermediate relaxation regimes spanning atmospheric, combustion, and (very recently) solution phase organic chemistry. In this article, we describe a Master Equation Solver for Multi-Energy Well Reactions (MESMER), a user-friendly, object-oriented, open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where energy transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user options specified via keywords and also includes some unique statistical mechanics approaches like contracted basis set methods and nonadiabatic RRKM theory for modeling spin-hopping. It is our hope that the design principles implemented in MESMER will facilitate its development and usage by workers across a range of fields concerned with chemical kinetics. As accurate thermodynamics data become more widely available, electronic structure theory is increasingly reliable, and as our fundamental understanding of energy transfer improves, we envision that tools like MESMER will eventually enable routine and reliable prediction of nonequilibrium kinetics in arbitrary systems.

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MESMER: an open-source master equation solver for multi-energy well reactions.

We survey the use of the Monte Carlo method within the Materials Studio application, which integrates a large number of modules for molecular simulation. Several of these modules work by generating...

Monte Carlo methods in Materials Studio

▪ Abstract The master equation provides a quantitative description of the interaction between collisional energy transfer and chemical reaction for dissociation, isomerization, and association processes. The approach is outlined for both irreversible and reversible dissociation, isomerization, and association reactions. There is increasing interest, especially in combustion, in association reactions that involve several linked potential wells, with the possibility of isomerization, collisional stabilization, and dissociation along several product channels. A major aim of the application of the master equation to such systems is the linking of the eigenvalues obtained by its solution to the rate coefficients for the phenomenological chemical reactions that describe the system and that are used in combustion models. The approach is illustrated by reference to the reactions C2H5 + O2, H + SO2, and the dissociation and isomerization of alkyl radicals.

Master equation models for chemical reactions of importance in combustion

Laser flash photolysis measurements on the kinetics of the title system in a He bath gas are reported for the temperatures 290, 473, and 700 K and a pressure range of 7.6−678 Torr. CH3 and OH radicals were generated simultaneously by 193 nm photolysis of acetone containing traces of water, with CH3 in large excess. The course of reaction was followed by monitoring the concentration of OH using laser-induced fluorescence (LIF), while CH3 was monitored by absorption at 216.4 nm. The experimental data were analyzed in the first instance by a simple model based on the decay of OH and CH3, which was verified by more comprehensive numerical simulations. Further analysis of the data, using a combined master equation/inverse Laplace transform/RRKM procedure, yielded estimates of the association rate coefficient of CH3 and OH ( = (8.0 ± 0.3) × 10-11 (T/300 K-0.79±0.09 cm3 molecule-1 s-1) and for the enthalpy change for the CH3 + OH → 1CH2 + H2O channel (Δ = 1.6 ± 2.0 kJ mol-1). Pressure-dependent rate coefficients...

Struan H. Robertson

Papers

COMPASS II: extended coverage for polymer and drug-like molecule databases.

MESMER: an open-source master equation solver for multi-energy well reactions.

Monte Carlo methods in Materials Studio

Master equation models for chemical reactions of importance in combustion

Temperature and Pressure Dependence of the Multichannel Rate Coefficients for the CH3 + OH System