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

We report on a comparison of methods based on XRD patterns for calculating crystal size In this case, XRD peaks were extracted from hydroxyapatite obtained from cow, pig, and chicken bones Hydroxyapatite was synthesized through the thermal treatment of natural bones at 950 °C XRD patterns were selected by adjustment of X-Pert software for each method and for calculating the size of the crystals Methods consisted of Scherrer (three models), Monshi-Scherrer, three models of Williamson-Hall (namely the Uniform Deformation Model (UDM), the Uniform Stress Deformation Model (USDM), and the Uniform Deformation Energy Density Model (UDEDM)), Halder-Wanger (H-W), and the Size Strain Plot Method (SSP) These methods have been used and compared together The sizes of crystallites obtained by the XRD patterns in each method for hydroxyapatite from cow, pig, and chicken were 1371, 457, and 196 nm in the Scherrer method when considering all of the available peaks together (straight line model) A new model (straight line passing the origin) gave 60, 60, and 53 nm, which shows much improvement The average model gave 56, 58, and 52 nm, for each of the three approaches, respectively, for cow, pig, and chicken The Monshi-Scherrer method gave 60, 60, and 57 nm Values of 56, 62, and 65 nm were given by the UDM method The values calculated by the USDM method were 60, 62, and 62 nm The values of 62, 62, and 65 nm were given by the UDEDM method for cow, pig, and chicken, respectively Furthermore, the crystal size value was 4 nm for all samples in the H-W method Values were also calculated as 43, 62, and 57 nm in the SSP method for cow, pig, and chicken tandemly According to the comparison of values in each method, the Scherrer method (straight line model) for considering all peaks led to unreasonable values Nevertheless, other values were in the acceptable range, similar to the reported values in the literature Experimental analyses, such as specific surface area by gas adsorption (Brunauer-Emmett-Teller (BET)) and Transmission Electron Microscopy (TEM), were utilized In the final comparison, parameters of accuracy, ease of calculations, having a check point for the researcher, and difference between the obtained values and experimental analysis by BET and TEM were considered The Monshi-Scherrer method provided ease of calculation and a decrease in errors by applying least squares to the linear plot There is a check point for this line that the slope must not be far from one Then, the intercept gives the most accurate crystal size In this study, the setup of values for BET (56, 52, and 49 nm) was also similar to the Monshi-Scherrer method and the use of it in research studies of nanotechnology is advised

https://www.mdpi.com/2079-4991/10/9/1627/pdf

Comparing Methods for Calculating Nano Crystal Size of Natural Hydroxyapatite Using X-Ray Diffraction.

Preparation, characterization, and investigation of the catalytic property of α-Fe2O3-ZnO nanoparticles in the photodegradation and mineralization of methylene blue

The approaches to stabilize the perovskite structure of formamidinium lead iodide (FAPI) commonly result in a blue shift of the band gap, which limits the maximum photoconversion efficiency. Here, ...

/pdf/chemi-structural-stabilization-of-formamidinium-lead-iodide-417gamgdke.pdf

Chemi-Structural Stabilization of Formamidinium Lead Iodide Perovskite by Using Embedded Quantum Dots

Fabrication of Ce3+ substituted nickel ferrite-reduced graphene oxide heterojunction with high photocatalytic activity under visible light irradiation.

X-ray diffraction analysis by Williamson-Hall, Halder-Wagner and size-strain plot methods of CdSe nanoparticles- a comparative study

Surface and displacement damage engineering on CdSe nanocrystalline thin film by swift heavy Ag ions: A theoretical investigation by SRIM/TRIM package

120 MeV Ni10+ swift heavy ions irradiation on CdSe nanocrystals induces cubic to hexagonal phase transformation - A study of microstructural modification

Phase transformation of CdSe nanocrystals at high fluence irradiation of 120 MeV swift Ni10+ and Ag7+ ions – X-ray diffraction and Raman spectral analysis

Debojyoti Nath

Papers

X-ray diffraction analysis by Williamson-Hall, Halder-Wagner and size-strain plot methods of CdSe nanoparticles- a comparative study

Surface and displacement damage engineering on CdSe nanocrystalline thin film by swift heavy Ag ions: A theoretical investigation by SRIM/TRIM package

120 MeV Ni10+ swift heavy ions irradiation on CdSe nanocrystals induces cubic to hexagonal phase transformation - A study of microstructural modification

Phase transformation of CdSe nanocrystals at high fluence irradiation of 120 MeV swift Ni10+ and Ag7+ ions – X-ray diffraction and Raman spectral analysis

Atomistic strain and structural analysis of 120 MeV Ni ions irradiated CdSe nanocrystals through molecular dynamics simulation method