Erik Deumens | University of Florida (original) (raw)
Papers by Erik Deumens
Bulletin of the American …, 2005
In this presentation, I will introduce a theoretical scheme for studying the interaction of fast ... more In this presentation, I will introduce a theoretical scheme for studying the interaction of fast ions, electrons, and photons with molecules. Although the molecules under consideration are not, perhaps, of the size to make a biologist (or even a biochemist!) feel quite at home, ...
PUPIL, Program for User Package Interfacing and Linking, is a software environment – the program ... more PUPIL, Program for User Package Interfacing and Linking, is a software environment – the program – to allow developers to accomplish an increasingly important task, namely, systematic, efficient linking of several independent pieces of software or “user packages” – that have been and are actively being developed by researchers. PUPIL is general and can be used to link user packages from any scientific or engineering domain. However, it was originally developed with multi-scale simulation in materials physics and chemistry in mind, and several of the interfaces included in this release show that heritage.
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011
Skip to Main Content. Wiley Online Library will be disrupted 2 July from 10-12 BST for monthly ma... more Skip to Main Content. Wiley Online Library will be disrupted 2 July from 10-12 BST for monthly maintenance. ...
Pramana, 2007
Final results on a CMOS 0.18 µm front-end chip for silicon strips readout are summarized and prel... more Final results on a CMOS 0.18 µm front-end chip for silicon strips readout are summarized and preliminary results on time measurement are discussed. The status of the next version in 0.13 µm is briefly presented.
Nuclear Physics A, 1983
An analysis of generator coordinate method calculations on density vibrations in axially deformed... more An analysis of generator coordinate method calculations on density vibrations in axially deformed light nuclei, demonstrates that the normal modes are harmonic vibrations parallel and orthogonal to the symmetry axis.
![Research paper thumbnail of Erratum: Applications of the generator coordinate approximation to diatomic systems. I. The hydrogen molecular ion [J. Chem. Phys. 8 4, 3944 (1986)]](https://attachments.academia-assets.com/103876934/thumbnails/1.jpg)
](The Journal of Chemical Physics, 1986
The Journal of Chemical Physics, 2008
ACES III is a newly written program in which the computationally demanding components of the comp... more ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree–Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensiv...
International Journal of Quantum Chemistry, 2010
By using MPI-2 standard, we designed and implemented a new multiscale simulation architecture OPA... more By using MPI-2 standard, we designed and implemented a new multiscale simulation architecture OPAL. It requires minimum modification to existing simulation code as maintaining the execution efficiency. The new architecture is capable of dynamical region identification, dynamical process spawning, and is grid-computing friendly. We demonstrated its usage and power with a simple test case: NaCl dissociation in water. The code shows excellent linear scaling capability, and no obvious degradation is observed. The communication time used by OPAL is negligible compared with its execution time, proving its high efficiency.
A design pattern is considered in which a distributed memory, multi processor computer is viewed ... more A design pattern is considered in which a distributed memory, multi processor computer is viewed as an early generation processor. In such processors, each instruction operates on individual floating point numbers and consumes a variable yet significant number of cycles. In the design pattern, we consider the elementary data item for a modern parallel computer to be a block of many numbers. Each operation involves a significant amount of CPU work, since the operands and result are blocks. We also consider memory access operations to include the delays incurred sending blocks to remote nodes. By making all delays explicit and organizing the algorithm such as to provide sufficient work to make each operation take a measurable amount of time, a new paradigm for designing and optimizing data and floating point intensive algorithms emerges. The application of the design pattern to the construction of a parallel implementation of the Coupled Cluster Singles and Doubles energy and gradient calculation is discussed. The efficiency of developers and the performance of the created software are discussed.
Frontiers in Chemistry, 2020
Chemistry is considered as one of the more promising applications to science of near-term quantum... more Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only t...
Practice and Experience in Advanced Research Computing
Digital data is increasingly important and becoming more prevalent in research. As such, a signif... more Digital data is increasingly important and becoming more prevalent in research. As such, a significant and growing fraction of that data is subject to complex security and privacy standards for its storage and processing. With the introduction of contractual requirements for NIST Special Publication 800-171 and other compliance frameworks, universities are under expanded pressure to secure research infrastructure to ensure their researchers comply with laws, regulations, and contractual requirements. The University of Florida developed tiCrypt, a bundled security middleware product, and implemented their ResVault system to meet the growing need for secure research infrastructure. The University of Maryland and Princeton University, both seeking to meet compliance requirements for secure research, have also implemented systems using tiCrypt. As new institutions adopt tiCrypt, the Tera Insights development team continues to add functionality to meet the needs of a broad range of research workflows. CCS CONCEPTS • Security and privacy → Public key encryption; Security requirements; • General and reference → Design; • Computer systems organization → Special purpose systems.
Quantum Studies: Mathematics and Foundations, 2019
The recent rigorous derivation of the Born rule from the dynamical law of quantum mechanics [Phys... more The recent rigorous derivation of the Born rule from the dynamical law of quantum mechanics [Phys. Rep. 525(2013) 1-166] is taken as incentive to reexamine whether quantum mechanics has to be an inherently probabilistic theory.
The European Physical Journal D, 2016
Abstract Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at... more Abstract Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at projectile energies 0.1 < E < 10 keV/amu, using electron nuclear dynamics (END) − a semi-classical approximation which not only includes electron translation factors for avoiding spurious couplings but also employs full dynamical trajectories to treat nuclear motions. Both the total and partial cross sections are reported for the collision of C6+ ions with atomic and molecular hydrogen. A comparison with other theoretical and experimental results shows, in general good agreement except at very low energy, considered here. For H2, the one- and two-electron charge exchange cross sections are calculated and compared with other theoretical and experimental results. Small but non-negligible isotope effects are found at the lowest energy studied in the charge transfer of C6+ with H. In low energy region, it is observed that H2 has larger isotope effects than H atom due to the polarizability effect which is larger than the mass effect. Graphical abstract
AIP Conference Proceedings, 2007
Probabilities and cross sections for charge transfer by He2+ impact on atomic hydrogen (H), deute... more Probabilities and cross sections for charge transfer by He2+ impact on atomic hydrogen (H), deuterium (D), and tritium (T) at low collision energies are calculated using the END approach. Differences by orders of magnitude are observed between the cross sections for H, D, and T. A method is introduced to separate the contributions of charge transfer mechanisms due to radial
Lecture Notes in Physics
ABSTRACT A time-dependent approach to molecular dynamics involving both nuclei and electrons is p... more ABSTRACT A time-dependent approach to molecular dynamics involving both nuclei and electrons is presented. Some of our findings from an application of the theory to a two-level model, with the nuclei treated classically, are discussed in some detail as an illustration of the importance of choice of appropriate basis states and of how nuclear-electron coupling is accounted for. The need for an appropriate time-averaging scheme for the fast electron and nuclear modes is demonstrated and such a procedure is outlined.
Bulletin of the American …, 2005
In this presentation, I will introduce a theoretical scheme for studying the interaction of fast ... more In this presentation, I will introduce a theoretical scheme for studying the interaction of fast ions, electrons, and photons with molecules. Although the molecules under consideration are not, perhaps, of the size to make a biologist (or even a biochemist!) feel quite at home, ...
PUPIL, Program for User Package Interfacing and Linking, is a software environment – the program ... more PUPIL, Program for User Package Interfacing and Linking, is a software environment – the program – to allow developers to accomplish an increasingly important task, namely, systematic, efficient linking of several independent pieces of software or “user packages” – that have been and are actively being developed by researchers. PUPIL is general and can be used to link user packages from any scientific or engineering domain. However, it was originally developed with multi-scale simulation in materials physics and chemistry in mind, and several of the interfaces included in this release show that heritage.
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011
Skip to Main Content. Wiley Online Library will be disrupted 2 July from 10-12 BST for monthly ma... more Skip to Main Content. Wiley Online Library will be disrupted 2 July from 10-12 BST for monthly maintenance. ...
Pramana, 2007
Final results on a CMOS 0.18 µm front-end chip for silicon strips readout are summarized and prel... more Final results on a CMOS 0.18 µm front-end chip for silicon strips readout are summarized and preliminary results on time measurement are discussed. The status of the next version in 0.13 µm is briefly presented.
Nuclear Physics A, 1983
An analysis of generator coordinate method calculations on density vibrations in axially deformed... more An analysis of generator coordinate method calculations on density vibrations in axially deformed light nuclei, demonstrates that the normal modes are harmonic vibrations parallel and orthogonal to the symmetry axis.
The Journal of Chemical Physics, 1986
The Journal of Chemical Physics, 2008
ACES III is a newly written program in which the computationally demanding components of the comp... more ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree–Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensiv...
International Journal of Quantum Chemistry, 2010
By using MPI-2 standard, we designed and implemented a new multiscale simulation architecture OPA... more By using MPI-2 standard, we designed and implemented a new multiscale simulation architecture OPAL. It requires minimum modification to existing simulation code as maintaining the execution efficiency. The new architecture is capable of dynamical region identification, dynamical process spawning, and is grid-computing friendly. We demonstrated its usage and power with a simple test case: NaCl dissociation in water. The code shows excellent linear scaling capability, and no obvious degradation is observed. The communication time used by OPAL is negligible compared with its execution time, proving its high efficiency.
A design pattern is considered in which a distributed memory, multi processor computer is viewed ... more A design pattern is considered in which a distributed memory, multi processor computer is viewed as an early generation processor. In such processors, each instruction operates on individual floating point numbers and consumes a variable yet significant number of cycles. In the design pattern, we consider the elementary data item for a modern parallel computer to be a block of many numbers. Each operation involves a significant amount of CPU work, since the operands and result are blocks. We also consider memory access operations to include the delays incurred sending blocks to remote nodes. By making all delays explicit and organizing the algorithm such as to provide sufficient work to make each operation take a measurable amount of time, a new paradigm for designing and optimizing data and floating point intensive algorithms emerges. The application of the design pattern to the construction of a parallel implementation of the Coupled Cluster Singles and Doubles energy and gradient calculation is discussed. The efficiency of developers and the performance of the created software are discussed.
Frontiers in Chemistry, 2020
Chemistry is considered as one of the more promising applications to science of near-term quantum... more Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only t...
Practice and Experience in Advanced Research Computing
Digital data is increasingly important and becoming more prevalent in research. As such, a signif... more Digital data is increasingly important and becoming more prevalent in research. As such, a significant and growing fraction of that data is subject to complex security and privacy standards for its storage and processing. With the introduction of contractual requirements for NIST Special Publication 800-171 and other compliance frameworks, universities are under expanded pressure to secure research infrastructure to ensure their researchers comply with laws, regulations, and contractual requirements. The University of Florida developed tiCrypt, a bundled security middleware product, and implemented their ResVault system to meet the growing need for secure research infrastructure. The University of Maryland and Princeton University, both seeking to meet compliance requirements for secure research, have also implemented systems using tiCrypt. As new institutions adopt tiCrypt, the Tera Insights development team continues to add functionality to meet the needs of a broad range of research workflows. CCS CONCEPTS • Security and privacy → Public key encryption; Security requirements; • General and reference → Design; • Computer systems organization → Special purpose systems.
Quantum Studies: Mathematics and Foundations, 2019
The recent rigorous derivation of the Born rule from the dynamical law of quantum mechanics [Phys... more The recent rigorous derivation of the Born rule from the dynamical law of quantum mechanics [Phys. Rep. 525(2013) 1-166] is taken as incentive to reexamine whether quantum mechanics has to be an inherently probabilistic theory.
The European Physical Journal D, 2016
Abstract Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at... more Abstract Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at projectile energies 0.1 < E < 10 keV/amu, using electron nuclear dynamics (END) − a semi-classical approximation which not only includes electron translation factors for avoiding spurious couplings but also employs full dynamical trajectories to treat nuclear motions. Both the total and partial cross sections are reported for the collision of C6+ ions with atomic and molecular hydrogen. A comparison with other theoretical and experimental results shows, in general good agreement except at very low energy, considered here. For H2, the one- and two-electron charge exchange cross sections are calculated and compared with other theoretical and experimental results. Small but non-negligible isotope effects are found at the lowest energy studied in the charge transfer of C6+ with H. In low energy region, it is observed that H2 has larger isotope effects than H atom due to the polarizability effect which is larger than the mass effect. Graphical abstract
AIP Conference Proceedings, 2007
Probabilities and cross sections for charge transfer by He2+ impact on atomic hydrogen (H), deute... more Probabilities and cross sections for charge transfer by He2+ impact on atomic hydrogen (H), deuterium (D), and tritium (T) at low collision energies are calculated using the END approach. Differences by orders of magnitude are observed between the cross sections for H, D, and T. A method is introduced to separate the contributions of charge transfer mechanisms due to radial
Lecture Notes in Physics
ABSTRACT A time-dependent approach to molecular dynamics involving both nuclei and electrons is p... more ABSTRACT A time-dependent approach to molecular dynamics involving both nuclei and electrons is presented. Some of our findings from an application of the theory to a two-level model, with the nuclei treated classically, are discussed in some detail as an illustration of the importance of choice of appropriate basis states and of how nuclear-electron coupling is accounted for. The need for an appropriate time-averaging scheme for the fast electron and nuclear modes is demonstrated and such a procedure is outlined.