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

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method.

https://biblio.ugent.be/publication/8514189/file/8514192.pdf

The ReaxFF reactive force-field: development, applications and future directions

We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

https://iopscience.iop.org/article/10.1088/0965-0393/20/4/045021/pdf

Structure identification methods for atomistic simulations of crystalline materials

Structural characterization of deformed crystals by analysis of common atomic neighborhood

Molecular-dynamics simulations were employed to study deformations on nickel nanowires subjected to uniaxial strain at 300 K using a recently reported embedded-atom (many body) model potential. This embedded-atom model can reproduce exactly the experimental second-order and third-order elastic moduli as well as the phase stability, equation of state and phonon frequency spectra are also in good agreement with experiments. Strong influence was observed in the Young modulus and force constant due to surface effects when considering nanowires with different cross sections. Applying strain rates, from 0.05 to $15%{\mathrm{ps}}^{\ensuremath{-}1},$ we found elastic behavior up to 11.5% strain with corresponding stress of 9.4 GPa. At low strain rates $(l0.05%{\mathrm{ps}}^{\ensuremath{-}1})$ the system passes through plastic deformations although keeping the crystalline structure. This ductile process is showed by several snapshots. At this low strain rate regime we observed that the nanowires shows superplasticity. For high strain rates $(g~7%{\mathrm{ps}}^{\ensuremath{-}1})$ the system changes continuously from crystalline to amorphous phase. Although this amorphization occurs with no use of liquid quenching or introduction of chemical or physical disorder, so being a different and interesting process, the amorphous resulted is unstable. We studied this instability monitoring the recrystallization process.

Large deformation and amorphization of Ni nanowires under uniaxial strain: A molecular dynamics study

A promising remedy to the failure of metallic glasses (MGs) by shear banding is the use of a dense network of glass-glass interfaces, i.e., a nanoglass (NG). Here we investigate the effect of grain size (d) on the failure of NG by performing molecular dynamics simulations of tensile-loading on Cu50Zr50 NG with d = 5 to 15 nm. Our results reveal a drastic change in deformation mode from a single shear band (d ∼ 15 to 10 nm), to cooperative shear failure (d ∼ 10 to 5 nm), to homogeneous superplastic flow (d ≤ 5 nm). Our results suggest that grain size can be an effective design parameter to tune the mechanical properties of MGs.

A transition from localized shear banding to homogeneous superplastic flow in nanoglass

Brittle fracture dynamics for three low-index crack surfaces, i.e., (110), (111), and (100), in crystalline cubic silicon carbide (3C-SiC) is studied using molecular dynamics simulation. The results exhibit significant orientation dependence: (110) fracture propagates in a cleavage manner; (111) fracture involves slip in the {111¯} planes; and crack branching is observed in (001) fracture. Calculated critical energy release rates, which characterize fracture toughness, are compared with available experimental and ab initio calculation data.

Paulo S. Branicio

Papers

Structural characterization of deformed crystals by analysis of common atomic neighborhood

Large deformation and amorphization of Ni nanowires under uniaxial strain: A molecular dynamics study

A transition from localized shear banding to homogeneous superplastic flow in nanoglass

Brittle dynamic fracture of crystalline cubic silicon carbide "3C-SiC… via molecular dynamics simulation

Strong and ductile nanolaminate composites combining metallic glasses and nanoglasses