Gramm-software package for molecular dynamics on graphical processing units

© 2010, Pleiades Publishing, Ltd. This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru

Structural stability of clean, passivated, and partially dehydrogenated cuboid and octahedral nanodiamonds up to 2 nanometers in size

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. The next major experimental milestone may be the mechanosynthetic fabrication of atomically precise 3D structures, creating readily accessible diamond-based nanomechanical components engineered to form desired architectures possessing superlative mechanical strength, stiffness, and strength-to-weight ratio. To help motivate this future experimental work, the present paper addresses the basic stability of the simplest nanoscale diamond structures-cubes and octahedra-possessing clean, hydrogenated, or partially hydrogenated surfaces. Computational studies using Density Functional Theory (DFT) with the Car-Parrinello Molecular Dynamics (CPMD) code, consuming ~1,466,852.53 CPU-hours of runtime on the IBM Blue Gene/P supercomputer (23 TFlops), confirmed that fully hydrogenated nanodiamonds up to 2 nm (~900-1800 atoms) in size having only C(111) faces (octahedrons) or only C(110) and C(100) faces (cuboids) maintain stable sp 3 hybridization. Fully dehydrogenated cuboid nanodiamonds above 1 nm retain the diamond lattice pattern, but smaller dehydrogenated cuboids and dehydrogenated octahedron nanodiamonds up to 2 nm reconstruct to bucky-diamond or onion-like carbon (OLC). At least three adjacent passivating H atoms may be removed, even from the most graphitization-prone C(111) face, without reconstruction of the underlying diamond lattice. Copyright © 2011 American Scientific Publishers

Optimal approach trajectories for a hydrogen donation tool in positionally controlled diamond mechanosynthesis

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. A key step in diamond mechanosynthesis (DMS) may employ a Ge-substituted adamantane-based hydrogen donation tool (HDon) for the site-specific mechanical hydrogenation of depassivated diamond surfaces. This paper presents the first theoretical study of DMS tool-workpiece operating envelopes and optimal tool approach trajectories for a positionally controlled hydrogen donation tool during scanning-probe based UHV diamond mechanosynthesis. Trajectories were analyzed using Density Functional Theory (DFT) in PC-GAMESS at the B3LYP/6- 311G(d, p)//B3LYP/3-21G(2d, p) level of theory. The results of this study help to define equipment and tooltip motion requirements that may be needed to execute the proposed reaction sequence experimentally and provide support for early developmental targets as part of a comprehensive near-term DMS implementation program. © 2013 American Scientific Publishers. All rights reserved

Structural stability of clean and passivated nanodiamonds having ledge, step, or corner features

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. The next major experimental milestone may be the mechanosynthetic fabrication of atomically precise 3D structures, creating readily accessible diamond-based nanomechanical components engineered to form desired architectures possessing superlative mechanical strength, stiffness, and strength-to-weight ratio. To help motivate this future experimental work, the present paper addresses the basic stability of nanoscale diamond structures with clean or hydrogenated surfaces that possess certain simple features including ledges, steps, and corners. Computational studies using Density Functional Theory (DFT) with the Car-Parrinello Molecular Dynamics (CPMD) code, consuming~2,284,108.97 CPU-hours of runtime on the IBM Blue Gene/P supercomputer (23 TFlops), confirm that fully hydrogenated nanodiamonds 1-2 nm in size possessing ledges with various combinations of convex or concave edgelines where any two of the three principal diamond faces meet will maintain stable sp 3 hybridization. © 2012 American Scientific Publishers. All rights reserved

Gramm-software package for molecular dynamics on graphical processing units

© 2010, Pleiades Publishing, Ltd. This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru

Gramm-software package for molecular dynamics on graphical processing units

© 2010, Pleiades Publishing, Ltd. This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru

Optimal approach trajectories for a hydrogen donation tool in positionally controlled diamond mechanosynthesis

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. A key step in diamond mechanosynthesis (DMS) may employ a Ge-substituted adamantane-based hydrogen donation tool (HDon) for the site-specific mechanical hydrogenation of depassivated diamond surfaces. This paper presents the first theoretical study of DMS tool-workpiece operating envelopes and optimal tool approach trajectories for a positionally controlled hydrogen donation tool during scanning-probe based UHV diamond mechanosynthesis. Trajectories were analyzed using Density Functional Theory (DFT) in PC-GAMESS at the B3LYP/6- 311G(d, p)//B3LYP/3-21G(2d, p) level of theory. The results of this study help to define equipment and tooltip motion requirements that may be needed to execute the proposed reaction sequence experimentally and provide support for early developmental targets as part of a comprehensive near-term DMS implementation program. © 2013 American Scientific Publishers. All rights reserved

Gramm-software package for molecular dynamics on graphical processing units

© 2010, Pleiades Publishing, Ltd. This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru

Structural stability of clean, passivated, and partially dehydrogenated cuboid and octahedral nanodiamonds up to 2 nanometers in size

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. The next major experimental milestone may be the mechanosynthetic fabrication of atomically precise 3D structures, creating readily accessible diamond-based nanomechanical components engineered to form desired architectures possessing superlative mechanical strength, stiffness, and strength-to-weight ratio. To help motivate this future experimental work, the present paper addresses the basic stability of the simplest nanoscale diamond structures-cubes and octahedra-possessing clean, hydrogenated, or partially hydrogenated surfaces. Computational studies using Density Functional Theory (DFT) with the Car-Parrinello Molecular Dynamics (CPMD) code, consuming ~1,466,852.53 CPU-hours of runtime on the IBM Blue Gene/P supercomputer (23 TFlops), confirmed that fully hydrogenated nanodiamonds up to 2 nm (~900-1800 atoms) in size having only C(111) faces (octahedrons) or only C(110) and C(100) faces (cuboids) maintain stable sp 3 hybridization. Fully dehydrogenated cuboid nanodiamonds above 1 nm retain the diamond lattice pattern, but smaller dehydrogenated cuboids and dehydrogenated octahedron nanodiamonds up to 2 nm reconstruct to bucky-diamond or onion-like carbon (OLC). At least three adjacent passivating H atoms may be removed, even from the most graphitization-prone C(111) face, without reconstruction of the underlying diamond lattice. Copyright © 2011 American Scientific Publishers

Structural stability of clean and passivated nanodiamonds having ledge, step, or corner features

The use of precisely applied mechanical forces to induce site-specific chemical transformations is called positional mechanosynthesis, and diamond is an important early target for achieving mechanosynthesis experimentally. The next major experimental milestone may be the mechanosynthetic fabrication of atomically precise 3D structures, creating readily accessible diamond-based nanomechanical components engineered to form desired architectures possessing superlative mechanical strength, stiffness, and strength-to-weight ratio. To help motivate this future experimental work, the present paper addresses the basic stability of nanoscale diamond structures with clean or hydrogenated surfaces that possess certain simple features including ledges, steps, and corners. Computational studies using Density Functional Theory (DFT) with the Car-Parrinello Molecular Dynamics (CPMD) code, consuming~2,284,108.97 CPU-hours of runtime on the IBM Blue Gene/P supercomputer (23 TFlops), confirm that fully hydrogenated nanodiamonds 1-2 nm in size possessing ledges with various combinations of convex or concave edgelines where any two of the three principal diamond faces meet will maintain stable sp 3 hybridization. © 2012 American Scientific Publishers. All rights reserved