Linear-Logic Based Analysis of Constraint Handling Rules with Disjunction

Constraint Handling Rules (CHR) is a declarative committed-choice programming language with a strong relationship to linear logic. Its generalization CHR with Disjunction (CHRv) is a multi-paradigm declarative programming language that allows the embedding of horn programs. We analyse the assets and the limitations of the classical declarative semantics of CHR before we motivate and develop a linear-logic declarative semantics for CHR and CHRv. We show how to apply the linear-logic semantics to decide program properties and to prove operational equivalence of CHRv programs across the boundaries of language paradigms

Minimising biases in Full Configuration Interaction Quantum Monte Carlo

We show that Full Configuration Interaction Quantum Monte Carlo (FCIQMC) is a Markov Chain in its present form. We construct the Markov matrix of FCIQMC for a two determinant system and hence compute the stationary distribution. These solutions are used to quantify the dependence of the population dynamics on the parameters defining the Markov chain. Despite the simplicity of a system with only two determinants, it still reveals a population control bias inherent to the FCIQMC algorithm. We investigate the effect of simulation parameters on the population control bias for the neon atom and suggest simulation setups to in general minimise the bias. We show a reweighting scheme to remove the bias caused by population control commonly used in Diffusion Monte Carlo [J. Chem. Phys. 99, 2865 (1993)] is effective and recommend its use as a post processing step.Comment: Supplementary material available as 'Ancillary Files

Hybrid XML Retrieval: Combining Information Retrieval and a Native XML Database

This paper investigates the impact of three approaches to XML retrieval: using Zettair, a full-text information retrieval system; using eXist, a native XML database; and using a hybrid system that takes full article answers from Zettair and uses eXist to extract elements from those articles. For the content-only topics, we undertake a preliminary analysis of the INEX 2003 relevance assessments in order to identify the types of highly relevant document components. Further analysis identifies two complementary sub-cases of relevance assessments ("General" and "Specific") and two categories of topics ("Broad" and "Narrow"). We develop a novel retrieval module that for a content-only topic utilises the information from the resulting answer list of a native XML database and dynamically determines the preferable units of retrieval, which we call "Coherent Retrieval Elements". The results of our experiments show that -- when each of the three systems is evaluated against different retrieval scenarios (such as different cases of relevance assessments, different topic categories and different choices of evaluation metrics) -- the XML retrieval systems exhibit varying behaviour and the best performance can be reached for different values of the retrieval parameters. In the case of INEX 2003 relevance assessments for the content-only topics, our newly developed hybrid XML retrieval system is substantially more effective than either Zettair or eXist, and yields a robust and a very effective XML retrieval.Comment: Postprint version. The editor version can be accessed through the DO

Breeding for improved responsiveness to arbuscular mycorrhizal fungi in onion

Arbuscular mycorrhizal fungi (AMF) play an important role in the uptake of nutrients and water from soil. Onions, Allium cepa L., are plants with a shallow root system. As a result, onion plants need a lot of fertiziler for their growth. Furthermore, onion plants are sensitive to drought. The aim of the current research project is to study the beneficial effect of mycorrhizal fungi on the growth and development of Allium species and to determine whether it is possible to improve onions for mycorrhizal responsiveness by means of breeding. Variation among Allium species and segregation observed in a interspecific tri-hybrid population indicate that selection and thus breeding for high responsiveness to AMF is possible

Diagrammatic Coupled Cluster Monte Carlo

We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker--Campbell--Hausdorff expansion of the similarity transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach -- diagCCMC -- allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, greatly reducing the memory cost associated with the stochastic solution of the coupled cluster equations. We show that for perfectly local, noninteracting systems, diagCCMC is able to represent the coupled cluster wavefunction with a memory cost that scales linearly with system size. The favorable memory cost is observed with the only assumption of fixed stochastic granularity and is valid for arbitrary levels of coupled cluster theory. Significant reduction in memory cost is also shown to smoothly appear with dissociation of a finite chain of helium atoms. This approach is also shown not to break down in the presence of strong correlation through the example of a stretched nitrogen molecule. Our novel methodology moves the theoretical basis of coupled cluster Monte Carlo closer to deterministic approaches.Comment: 31 pages, 6 figure

Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE