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60
Firstprinciples simulation: ideas, illustrations and the CASTEP code
 J
, 2002
"... Firstprinciples simulation, meaning densityfunctional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensedmatter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its imple ..."
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Firstprinciples simulation, meaning densityfunctional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensedmatter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its implementation, and illustrating some of the ways simulators approach problems through a small case study. I also discuss why and how modern software design methods have been used in writing a completely new modular version of the CASTEP code. 1. Overview The simulator builds a model of a real system and explores its behaviour. The model is a mathematical one and the exploration is done on a computer, and in many ways simulation studies share the same mentality as experimental ones. However, in a simulation there is absolute control and access to detail, the ability to compute almost any observable, and given enough computer muscle, exact answers for the model. These strengths have been exploited for
Quantum Monte Carlo simulations of fermions. A mathematical analysis of the fixednode approximation
 ESAIM: M2AN
, 2006
"... The Diffusion Monte Carlo (DMC) method is a powerful strategy to estimate the ground state energy E0 of a Nbody Schrödinger hamiltonian H = − 1 ∆ + V with 2 high accuracy. Briefly speaking, it consists in writing E0 as the longtime limit of the expectation value of a driftdiffusion process with ..."
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The Diffusion Monte Carlo (DMC) method is a powerful strategy to estimate the ground state energy E0 of a Nbody Schrödinger hamiltonian H = − 1 ∆ + V with 2 high accuracy. Briefly speaking, it consists in writing E0 as the longtime limit of the expectation value of a driftdiffusion process with source term, and in numerically simulating this process by means of a collection of random walkers. As for a number of stochastic methods, a DMC calculation makes use of an importance sampling function ψI which hopefully approximates some ground state ψ0 of H. In the fermionic case, it has been observed that the DMC method is biased, except in the special case when the nodal surfaces of ψI coincide with those of a ground state of H. The approximation arising from the fact that, in practice, the nodal surfaces of ψI differ from those of the ground states of H, is refered to as the Fixed Node Approximation (FNA). Our purpose in this article is to provide a mathematicial analysis of the FNA. We prove that, under some hypotheses, a DMC calculation performed with the importance sampling function ψI, provides an estimation of the infimum of the energy 〈ψ, Hψ〉 on the set of the fermionic test functions ψ that vanish on the nodal surfaces of ψI. 1
Longtimestep integrators for almostadiabatic quantum dynamics
 SIAM J. Sci. Comput
, 2004
"... Abstract. The highly oscillatory solution of a singularly perturbed Schrödinger equation with timedependent Hamiltonian is computed numerically. The new timesymmetric integrators presented here can be used efficiently with step sizes significantly larger than those required by traditional schemes. ..."
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Abstract. The highly oscillatory solution of a singularly perturbed Schrödinger equation with timedependent Hamiltonian is computed numerically. The new timesymmetric integrators presented here can be used efficiently with step sizes significantly larger than those required by traditional schemes. This is achieved by a transformation of the problem and an expansion technique for integrals over the oscillating components. The error behavior in the adiabatic case is thoroughly analyzed, and the performance of the methods is illustrated both in an almostadiabatic setup and in an avoided energy level crossing, where nonadiabatic state transitions occur.
Supporting CarParrinello Molecular Dynamics Application with UNICORE
 UNICORE Proceedings ICCS 2001, S an Franscico, CA, pp 580567 UNICORE 14/14 30.07.01
, 2001
"... Abstract. This paper presents the integration of application specific interfaces in the UNICORE Grid infrastructure. UNICORE provides a seamless and secure mechanism to access distributed supercomputer resources. The widely used CarParrinello Molecular Dynamics (CPMD) application was selected as a ..."
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Abstract. This paper presents the integration of application specific interfaces in the UNICORE Grid infrastructure. UNICORE provides a seamless and secure mechanism to access distributed supercomputer resources. The widely used CarParrinello Molecular Dynamics (CPMD) application was selected as a first example to demonstrate the capabilities of UNICORE to scientists. Through the graphical interface, developed at Research Centre Jülich, the user can prepare a CPMD job and run it on a variety of systems at different locations. In addition, the ”CPMD Wizard ” makes it easy to configure the full set of the control parameters, cell properties, pseudopotentials and atom positions for the CPMD simulation. 1
Analyzing checkpointing trends for applications on the IBM Blue Gene/P system
 In Parallel Processing Workshops, 2009. ICPPW’09. International Conference on
, 1998
"... Current petascale systems have tens of thousands of hardware components and complex system software stacks, which increase the probability of faults occurring during the lifetime of a process. Checkpointing has been a popular method of providing fault tolerance in highend systems. While considera ..."
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Current petascale systems have tens of thousands of hardware components and complex system software stacks, which increase the probability of faults occurring during the lifetime of a process. Checkpointing has been a popular method of providing fault tolerance in highend systems. While considerable research has been done to optimize checkpointing, in practice the method still involves a highcost overhead for users. In this paper, we study the checkpointing overhead seen by applications running on leadershipclass machines such as the IBM Blue Gene/P at Argonne National Laboratory. We study various applications and design a methodology to assist users in understanding and choosing checkpointing frequency and reducing the overhead incurred. In particular, we study three popular applications—the GridBased ProjectorAugmented Wave application, the CarrParrinello Molecular Dynamics application, and a Nek5000 computational fluid dynamics application—and analyze their memory usage and possible checkpointing trends on 32,768 processors of the Blue Gene/P system.
Langevin molecular dynamics derived from Ehrenfest dynamics
"... Abstract. Stochastic Langevin molecular dynamics for nuclei is derived from the Ehrenfest Hamiltonian system (also called quantum classical molecular dynamics) in a KacZwanzig setting, with the initial data for the electrons stochastically perturbed from the ground state and the ratio, M , of nucl ..."
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Abstract. Stochastic Langevin molecular dynamics for nuclei is derived from the Ehrenfest Hamiltonian system (also called quantum classical molecular dynamics) in a KacZwanzig setting, with the initial data for the electrons stochastically perturbed from the ground state and the ratio, M , of nuclei and electron mass tending to infinity. The Ehrenfest nuclei dynamics is approximated by the Langevin dynamics with accuracy o(M −1/2 ) on bounded time intervals and by o(1) on unbounded time intervals, which makes the small O(M −1/2 ) friction and o(M −1/2 ) diffusion terms visible. The initial electron probability distribution is a Gibbs density at low temperture, derived by a stability and consistency argument: starting with any equilibrium measure of the Ehrenfest Hamiltonian system, the initial electron distribution is sampled from the equilibrium measure conditioned on the nuclei positions, which after long time leads to the nuclei positions in a Gibbs distribution (i.e. asymptotic stability); by consistency the original equilibrium measure is then a Gibbs measure. The diffusion and friction coefficients in the Langevin equation satisfy the Einstein's fluctuationdissipation relation.
Hydroxide and proton migration in aquaporins
 Biophys. J
, 2005
"... ABSTRACT Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio CarParrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contigu ..."
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ABSTRACT Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio CarParrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contiguous set of waterwater hydrogen bonds in which polarization of the water molecules vary with position along the channel axis. Deprotonation of the water chain promotes the reorientation of water molecules while the hydroxide ion rapidly migrates by sequentially accepting protons from the neighboring water molecules. The hydroxide ion is not attracted by a conserved, channellining arginine residue, but is immobilized at two centrally located, conserved AsparagineProlineAlanine motifs where fourfold coordination stabilizes the ion. Hydroxide transition from the channel vestibules into the channel lumen is strongly influenced by electrostatic coupling to two conserved oppositely aligned macrodipoles. This suggests that the macrodipole’s negative poles play a role in preventing hydroxide ions from entering into the channel’s inner vestibules. Water protonation within the lumen facilitates water reorientation and subsequent proton expelling occurs. In the periplasmic halfchannel, expelling occurs via the Grotthuss mechanism. Protonation within the cytoplasmic halfchannel implies wirebreakage at the AsnProAla motifs. The proton is here diffusively rejected as (H5O2) 1.
Ab Initio Molecular Dynamics Study of Nanoscale Thermal Energy Transport
 Journal of Heat Transfer
, 2008
"... ABSTRACT Abinitio molecular dynamics (MD) which employs density functional theory (DFT) is used to study thermal energy transport phenomena in nanoscale structures. Thermal equilibration in multiple thin layer structures with thicknesses less than 1 nanometer per layer is simulated. Different typ ..."
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ABSTRACT Abinitio molecular dynamics (MD) which employs density functional theory (DFT) is used to study thermal energy transport phenomena in nanoscale structures. Thermal equilibration in multiple thin layer structures with thicknesses less than 1 nanometer per layer is simulated. Different types of layer combinations are investigated. Periodic boundary conditions in all directions are used in all cases. Two neighboring layers are first set to different temperatures using NoseHoover thermostats, and then the process of energy equilibration is simulated with a "free run" (without any thermostat controlling the temperatures). The temperature evolutions in the two neighboring layers are computed. The atomic vibration power spectra are calculated and used to explain the phenomena observed in the simulation.
Bamboo Translating MPI applications to a latencytolerant, datadriven form
"... Abstract — We present Bamboo, a custom sourcetosource translator that transforms MPI C source into a datadriven form that automatically overlaps communication with available computation. Running on up to 98304 processors of NERSC’s Hopper system, we observe that Bamboo’s overlap capability speeds ..."
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Abstract — We present Bamboo, a custom sourcetosource translator that transforms MPI C source into a datadriven form that automatically overlaps communication with available computation. Running on up to 98304 processors of NERSC’s Hopper system, we observe that Bamboo’s overlap capability speeds up MPI implementations of a 3D Jacobi iterative solver and Cannon’s matrix multiplication. Bamboo’s generated code meets or exceeds the performance of hand optimized MPI, which includes splitphase coding, the method classically employed to hide communication. We achieved our results with only modest amounts of programmer annotation and no intrusive reprogramming of the original application source. I.
2001b. Proton transfer dynamics in acetylacetone. Journal of Physical Chemistry A 105(10):20452051. 20050324 33 Ras QM/MM, final version
 J. Chem. Phys
, 2003
"... Proton dynamics in the mediumstrong intramolecular hydrogen bond of acetylacetone (Pentane2,4dione) was studied using the mixed quantumclassical method density matrix evolution (DME). The proton involved in the hydrogen bond was treated as a quantum particle, involving several vibrational levels ..."
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Proton dynamics in the mediumstrong intramolecular hydrogen bond of acetylacetone (Pentane2,4dione) was studied using the mixed quantumclassical method density matrix evolution (DME). The proton involved in the hydrogen bond was treated as a quantum particle, involving several vibrational levels, while the rest of the system was treated using classical mechanics. Molecular simulations were performed in the gas phase and in a chloroform solution. The effects of deuteration were also considered. The vibrational spectrum was calculated by Fourier transform of the timedependent expectation value for the OH bond length. In the present case, we demonstrate by calculations and experimentally that coupling of the proton to the OO and both CO bonds, which are attached to the hydrogen bond (indirect relaxation mechanism) is more important than coupling to the solvent degrees of freedom in determining spectral shape. 1.