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

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes “velocity map imaging” possible, i.e., all particles with the same initial velocity vector are mapped onto the same point on the detector. Whereas the more common application of grid electrodes leads to transmission reduction, severe trajectory deflections and blurring due to the non-point source geometry, these problems are avoided with open lens electrodes. A three-plate assembly with aperture electrodes has been tested and its properties are compared with those of grid electrodes. The photodissociation processes occurring in molecular oxygen following the two-photon 3dπ(3Σ1g −)(v=2, N=2)←X(3Σg −) Rydberg excitation around 225 nm are presented here to show the improvement in spatial resolution in the ion and electron images. Simulated trajectory calculations show good agreement with experiment and ...

Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen

Physical Review B

Generations Yi Ma,† Xiuli Wang,† Yushuai Jia,† Xiaobo Chen,‡ Hongxian Han,*,† and Can Li*,† †State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences and Dalian National Laboratory for Clean Energy, 457 Zhongshan Road, Dalian 116023, China ‡Department of Chemistry, College of Arts and Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110, United States

Titanium dioxide-based nanomaterials for photocatalytic fuel generations.

The dynamics of the F+H/sub 2/ reaction have been investigated in a high resolution crossed molecular beam study. Differential cross sections and kinetic energy distributions were obtained for each HF vibrational state. The v = 1 and v = 2 states were predominantly backward scattered, but substantial forward scattering was observed for HF (v = 3) over the range of collision energies accessible in our apparatus, from 0.7 to 3.4 kcal/mol. The results strongly suggest that dynamical resonances play a significant role in the reaction dynamics of F+H/sub 2/ and that resonance effects are most prominent in the v = 3 product channel. Quantal reactive scattering calculations on F+H/sub 2/ predict that the v = 2 channel should be most strongly affected by resonances. This discrepancy is attributed to inadequacies in the potential energy surface used in the calculations, and several modifications to the surface are proposed based on the experimental results. Other features of the reaction are also discussed, including the integrated partial cross sections, the effect of H/sub 2/ rotation, and the reactivity of F(/sup 2/P/sub 1/2/).

/pdf/molecular-beam-studies-of-the-f-h2-reaction-4vzlr3bwj4.pdf

Molecular beam studies of the F+H2 reaction

By using laser methods to prepare specific quantum states of gas-phase nitric oxide molecules, we examined the role of vibrational motion in electron transfer to a molecule from a metal surface free from the complicating influence of solvation effects. The signature of the electron transfer process is a highly efficient multiquantum vibrational relaxation event, where the nitrogen oxide loses hundreds of kilojoules per mole of energy on a subpicosecond time scale. These results cannot be explained simply on the basis of Franck-Condon factors. The large-amplitude vibrational motion associated with molecules in high vibrational states strongly modulates the energetic driving force of the electron transfer reaction. These results show the importance of molecular vibration in promoting electron transfer reactions, a class of chemistry important to molecular electronics devices, solar energy conversion, and many biological processes.

https://science.sciencemag.org/content/sci/290/5489/111.full.pdf

Vibrational Promotion of Electron Transfer

The authors have measured the translational energy release for processes C2H2 193 nm/ C2H + H (I) and C2H 193 nm/ C2 + H (II) using the molecular time-of-flight method. By measuring the maximum release of translational energy for process I it has been determined that the C-H bond energy in acetylene, D0(C2H-H), is 132 +/- 2 kcal/mol. Since the translational energy distribution peaks well away from zero, it is quite unlikely that internal conversion of the electronically excited C2H2 is an important channel for dissociation in channel I. Because of the relatively small amount of energy appearing as product rotation, it is possible to get information on the vibrational structure of C2H radical from the translational energy distribution and it is found that the bending frequency in C2H is 550 +/- 100 cm . This experiment is consistent with earlier work which observed C2( /sub u/) in fluorescence. 21 references, 20 figures, 3 tables.

Photodissociation of acetylene at 193.3 nm

Many aspects of the collision dynamics of vibrational energy transfer are presented. Special emphasis is placed on three broad areas within this field:  (1) vibrational energy transfer in large molecules (>10 modes) at low excitation, (2) vibrational energy transfer in large molecules at high vibrational excitation, and (3) vibrational energy transfer of highly excited small molecules. Advances in laser methods have revolutionized experimental investigations of all of these areas. Recent results are presented, and directions for the future are discussed.

Vibrational energy transfer

The F+D2 and F+HD reactions were investigated in a high resolution crossed molecular beams experiment at several collision energies. The DF product from both reactions was predominantly backward scattered although some forward scattered DF(v=4) was observed at the highest energy studied. The HF angular distributions from F+HD were quite different, showing considerable forward scattered (v=3) and no other identifiable structure. These results disagree with classical trajectory studies, which predict only small variations in the product angular distributions among F+H2 and its isotopic variants. They agree, however, with the predicted dependence of dynamical resonance effects on isotopic substitution. The results therefore support the conclusions drawn in the previous paper regarding the role of dynamical resonances in the F+H2 reaction.

/pdf/molecular-beam-studies-of-the-f-d2-and-f-hd-reactions-ltepdeym7r.pdf

Alec M. Wodtke

Papers

Molecular beam studies of the F+H2 reaction

Vibrational Promotion of Electron Transfer

Photodissociation of acetylene at 193.3 nm

Vibrational energy transfer

Molecular beam studies of the F+D2 and F+HD reactions