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

Previous attempts to combine Hartree–Fock theory with local density‐functional theory have been unsuccessful in applications to molecular bonding. We derive a new coupling of these two theories that maintains their simplicity and computational efficiency, and yet greatly improves their predictive power. Very encouraging results of tests on atomization energies, ionization potentials, and proton affinities are reported, and the potential for future development is discussed.

A New Mixing of Hartree-Fock and Local Density-Functional Theories

We present an analysis of the performances of a parameter free density functional model (PBE0) obtained combining the so called PBE generalized gradient functional with a predefined amount of exact exchange. The results obtained for structural, thermodynamic, kinetic and spectroscopic (magnetic, infrared and electronic) properties are satisfactory and not far from those delivered by the most reliable functionals including heavy parameterization. The way in which the functional is derived and the lack of empirical parameters fitted to specific properties make the PBE0 model a widely applicable method for both quantum chemistry and condensed matter physics.

Toward reliable density functional methods without adjustable parameters: The PBE0 model

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

Recent extensions of the DMol3 local orbital density functional method for band structure calculations of insulating and metallic solids are described. Furthermore the method for calculating semilocal pseudopotential matrix elements and basis functions are detailed together with other unpublished parts of the methodology pertaining to gradient functionals and local orbital basis sets. The method is applied to calculations of the enthalpy of formation of a set of molecules and solids. We find that the present numerical localized basis sets yield improved results as compared to previous results for the same functionals. Enthalpies for the formation of H, N, O, F, Cl, and C, Si, S atoms from the thermodynamic reference states are calculated at the same level of theory. It is found that the performance in predicting molecular enthalpies of formation is markedly improved for the Perdew–Burke–Ernzerhof [Phys. Rev. Lett. 77, 3865 (1996)] functional.

From molecules to solids with the DMol3 approach

Gaussian-type orbital and auxiliary basis sets have been optimized for local spin density functional calculations This first paper deals with the atoms boron through neon Subsequent papers will provide a list through xenon The basis sets have been tested for their ability to give equilibrium geometries, bond dissociation energies, hydrogenation energies, and dipole moments These results indicate that the present optimization technique yields reliable basis sets for molecular calculations Keywords: Gaussian basis sets, density functional theory, boron–neon, geometries, energies of reactions

Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation

Density Functional Methods in Chemistry

https://isiarticles.com/bundles/Article/pre/pdf/22294.pdf

A generalized synchronous transit method for transition state location

We present the theory, computational implementation, and applications of a density functional Gaussian‐type‐orbital approach called DGauss. For a range of typical organic and small inorganic molecules, it is found that this approach results in equilibrium geometries, vibrational frequencies, bond dissociation energies, and reaction energies that are in many cases significantly closer to experiment than those obtained with Hartree–Fock theory. On the local spin density functional level, DGauss predicts equilibrium bond lengths within about 0.02 A or better compared with experiment, bond angles, and dihedral angles to within 1–2°, and vibrational frequencies within about 3%–5%. While Hartree–Fock optimized basis sets such as the 6‐31 G** set can be used in DGauss calculations to give good geometries, the accurate prediction of reaction energies requires the use of density functional optimized Gaussian‐type basis sets. Nonlocal corrections as proposed by Becke and Perdew for the exchange and correlation ener...

Density functional Gaussian‐type‐orbital approach to molecular geometries, vibrations, and reaction energies

In this paper, we present the implementation of the ‘‘conductorlike screening model’’ (COSMO) into the density functional program DMol. The electronic structure and geometry of the solute are described by a density functional method (DFT). The solute is placed into a cavity which has the shape of the solute molecule. Outside of the cavity, the solvent is represented by a homogeneous dielectric medium. The electrostatic interaction between solute and solvent is modeled through cavity surface charges induced by the solvent. The COSMO theory, based on the screening in conductors, allows for the direct determination of the surface charges within the SCF procedure using only the electrostatic potentials. This represents the major computational advantage over many of other reaction field methods. Since the DMol/COSMO energy is fully variational, accurate gradients with respect to the solute coordinates can be calculated for the first time, without any restriction on the shape of the cavity. The solvation energies and optimized molecular structures are calculated for several polar solutes. In addition, the trends in basicity of amines and the relative stabilities of molecular conformers are studied. Our results suggest that for neutral solutes, agreement between calculated and experimental solvation energies of better than about 2 kcal/mol can be achieved.

Jan Andzelm

Papers

Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation

Density Functional Methods in Chemistry

A generalized synchronous transit method for transition state location

Density functional Gaussian‐type‐orbital approach to molecular geometries, vibrations, and reaction energies

Incorporation of solvent effects into density functional calculations of molecular energies and geometries