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

Single-layer metal dichalcogenides are two-dimensional semiconductors that present strong potential for electronic and sensing applications complementary to that of graphene.

/pdf/electronics-and-optoelectronics-of-two-dimensional-2jbqr1unvw.pdf

Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

We present a method for calculating the stability of reaction intermediates of electrochemical processes on the basis of electronic structure calculations. We used that method in combination with detailed density functional calculations to develop a detailed description of the free-energy landscape of the electrochemical oxygen reduction reaction over Pt(111) as a function of applied bias. This allowed us to identify the origin of the overpotential found for this reaction. Adsorbed oxygen and hydroxyl are found to be very stable intermediates at potentials close to equilibrium, and the calculated rate constant for the activated proton/electron transfer to adsorbed oxygen or hydroxyl can account quantitatively for the observed kinetics. On the basis of a database of calculated oxygen and hydroxyl adsorption energies, the trends in the oxygen reduction rate for a large number of different transition and noble metals can be accounted for. Alternative reaction mechanisms involving proton/electron transfer to ...

/pdf/origin-of-the-overpotential-for-oxygen-reduction-at-a-fuel-jdt5gxiyj8.pdf

Origin of the Overpotential for Oxygen Reduction at a Fuel-Cell Cathode

TiO2 photocatalysis and related surface phenomena

Platinum-based heterogeneous catalysts are critical to many important commercial chemical processes, but their efficiency is extremely low on a per metal atom basis, because only the surface active-site atoms are used. Catalysts with single-atom dispersions are thus highly desirable to maximize atom efficiency, but making them is challenging. Here we report the synthesis of a single-atom catalyst that consists of only isolated single Pt atoms anchored to the surfaces of iron oxide nanocrystallites. This single-atom catalyst has extremely high atom efficiency and shows excellent stability and high activity for both CO oxidation and preferential oxidation of CO in H-2. Density functional theory calculations show that the high catalytic activity correlates with the partially vacant 5d orbitals of the positively charged, high-valent Pt atoms, which help to reduce both the CO adsorption energy and the activation barriers for CO oxidation.

Single-atom catalysis of CO oxidation using Pt1/FeOx

The Car-Parrinello ab-initio molecular dynamics method is heavily used in studies of the properties of materials, molecules etc. Our Car-Parrinello code, which is being continuously developed at CAMP, runs on several computer architectures. A parallel version of the program has been developed at CAMP based on message passing, currently using the PVM library. The parallel algorithm is based upon dividing the “special k-points” among processors. The number of processors used is typically 6-10. The code was run at the UNI•C 40-node SP2 with the IBM PVMe enhanced PVM message passing library. Satisfactory speedup of the parallel code as a function of the number of processors is achieved, the speedup being bound by the SP2 communications bandwidth.

https://link.springer.com/content/pdf/10.1007%2F3-540-60902-4_32.pdf

Parallel Ab-initio Molecular Dynamics

Catalysis by sub-nanometer size gold clusters

The use of machine learning (ML) in chemical physics has enabled the construction of interatomic potentials having the accuracy of ab initio methods and a computational cost comparable to that of classical force fields. Training an ML model requires an efficient method for the generation of training data. Here, we apply an accurate and efficient protocol to collect training data for constructing a neural network-based ML interatomic potential for nanosilicate clusters. Initial training data are taken from normal modes and farthest point sampling. Later on, the set of training data is extended via an active learning strategy in which new data are identified by the disagreement between an ensemble of ML models. The whole process is further accelerated by parallel sampling over structures. We use the ML model to run molecular dynamics simulations of nanosilicate clusters with various sizes, from which infrared spectra with anharmonicity included can be extracted. Such spectroscopic data are needed for understanding the properties of silicate dust grains in the interstellar medium and in circumstellar environments.

https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0150379/17979772/224108_1_5.0150379.pdf

A machine learning potential for simulating infrared spectra of nanosilicate clusters.

Powered by TCPDF (www.tcpdf.org) This material is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. Enevoldsen, Georg H.; Pinto, Henry P.; Foster, Adam S.; Jensen, Mona C.R.; Hofer, Werner A.; Hammer, Bjørk; Lauritsen, Jeppe V.; Besenbacher, Flemming Reply to comment on Imaging of the hydrogen subsurface site in rutile TiO2

/pdf/reply-to-comment-on-imaging-of-the-hydrogen-subsurface-site-i77a12v04l.pdf

Reply to comment on Imaging of the hydrogen subsurface site in rutile TiO2

Context. Fragmentation is an important decay mechanism for polycyclic aromatic hydrocarbons (PAHs) under harsh interstellar conditions and represents a possible formation pathway for small molecules such as H 2 , C 2 H 2 , and C 2 H 4 . Aims. Our aim is to investigate the dissociation mechanism of superhydrogenated PAHs that undergo energetic processing and the formation pathway of small hydrocarbons. Methods. We obtain, experimentally, the mass distribution of protonated tetrahydropyrene (C 16 H + 15 , [ p y + 5 H ] + ) and protonated hexahydropyrene (C 16 H + 17 , [ p y + 7 H ] + ) upon collision-induced dissociation (CID). The infrared (IR) spectra of their main fragments are recorded by infrared multiple-photon dissociation (IRMPD). Extended tight-binding (GFN2-xTB) based molecular dynamics (MD) simulations were performed in order to provide the missing structure information for this experiment and to identify fragmentation pathways. The pathways for fragmentation were further investigated at a hybrid density functional theory (DFT) and dispersion- corrected level. Results. A strong signal for loss of 28 mass units of [ p y + 7 H ] + is observed both in the CID experiment and the MD simulation, while [ p y + 5 H ] + shows a negligible signal for the product corresponding to a mass loss of 28. The 28 mass loss from [ p y + 7 H ] + is assigned to the loss of ethylene (C 2 H 4 ) and a good ﬁt between the calculated and experimental IR spectrum of the resulting fragment species is obtained. Further DFT calculations show favorable kinetic pathways for loss of C 2 H 4 from hydrogenated PAH conﬁgurations involving three consecutive CH 2 molecular entities. Conclusions. This joint experimental and theoretical investigation proposes a chemical pathway of ethylene formation from fragmentation of superhydrogenated PAHs. This pathway is sensitive to hydrogenated edges (e.g., the degree of hydrogenation and the hydrogenated positions). The inclusion of this pathway in astrochemical models may improve the estimated abundance of ethylene.

/pdf/top-down-formation-of-ethylene-from-fragmentation-of-29ufmbua.pdf

Bjørk Hammer

Papers

Parallel Ab-initio Molecular Dynamics

Catalysis by sub-nanometer size gold clusters

A machine learning potential for simulating infrared spectra of nanosilicate clusters.

Reply to comment on Imaging of the hydrogen subsurface site in rutile TiO2

Top-down formation of ethylene from fragmentation of superhydrogenated polycyclic aromatic hydrocarbons