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At least 667 records · Page 37

Massively parallel implementation of the multi-reference Brillouin-Wigner CCSD method

This paper reports the parallel implementation of the Brillouin Wigner MultiReference Coupled Cluster method with Single and Double excitations (BW-MRCCSD). Preliminary tests for systems composed of 304 and 440 correlated obritals demonstrate the performance of our implementation across 1000 cores and clearly indicate the advantages of using improved task scheduling. Possible ways for further improvements of the parallel performance are also delineated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Greece's reformed EIA system: Evaluating its implementation and potential

Highlights: • Greek nationwide multidimensional EIA System effectiveness evaluation study • Innovation of reform: a central Electronic Environmental Registry (e-ER) • e-ER manages and publish results of the EIA, EMS and Inspection processes. • There is a chasm between new legal provisions and implementation in practice. • Results indicate persistent poor-quality EIA, bureaucracy, lack of transparency. - Abstract: The Memorandum of Understanding (MoU) signed by the Greek government and the troika in 2010 contained numerous austerity policies and requirements for administrative reforms, among which is that of the national Environmental Impact Assessment (EIA) system. Complying with this requirement, Law4014/2011 was passed, aiming at reducing bureaucracy and increasing the country's appeal to investors whilst ensuring environmental protection. The present paper provides the first systematic, multi-scale and multidimensional evaluation of the effectiveness of the new EIA system. The evaluation is based firstly on the results of a Pan-Hellenic survey, involving key EIA consultants and authorities; secondly, on additional, in-depth interviews with EIA specialists, National- Ministry and Regional EIA Authorities; and thirdly, on the content review of 105 Environmental Impact statements. The results highlight the persistence of serious problems despite the reform of the Hellenic EIA System. The data reveal a significant discrepancy between what is set out in law and the actual practice. Although Law 4014/2011 contains progressive and innovative elements (such as adopting a life cycle approach to the EIA process, and mandating the development and use of a central Electronic Environmental Registry (e-ER) to manage and publish results of the EIA process), the recorded failure to implement them in practice results in a non-transparent and ineffective EIA system. Recommendations for improvement are proposed as well as areas for further research.

54 ENVIRONMENTAL SCIENCES↗

A Multi-Institutional Study of Feasibility, Implementation, and Early Clinical Results With Noninvasive Breast Brachytherapy for Tumor Bed Boost

Purpose: To evaluate the feasibility, implementation, and early results of noninvasive breast brachytherapy (NIBB) for tumor bed boost with whole breast radiation therapy (WBRT). Methods and Materials: NIBB is a commercially available (AccuBoost, Billerica, MA) mammography-based, brachytherapy system in which the treatment applicators are centered on the planning target volume (PTV) to direct {sup 192}Ir emissions along orthogonal axes. A privacy-encrypted online data registry collected information from 8 independent academic and community-based institutions. Data were from 146 consecutive women with early-stage breast cancer after lumpectomy and WBRT receiving boost with NIBB between July 2007 and March 2010. Toxicity and cosmesis were graded according to the Common Toxicity Criteria (v. 3.0) and the Harvard scale. Median follow-up was 6 months (1-39 months). Results: Grade 1-2 skin toxicity was observed in 64%, 48%, and 21% during the acute (1-3 weeks), intermediate (4-26 weeks), and late-intermediate (>26 weeks) periods. There was no Grade 4 toxicity. At 6 months, for the entire cohort, cosmesis was excellent/good in 62%/38%. The subset receiving NIBB before WBRT had cosmetic scores of 32% and 63%, whereas during WBRT, 58% and 37% were rated as excellent and good, respectively. Breast compression was scored as 'uncomfortable' in 12%, 29%, and 59% when NIBB was delivered before, during, or after WBRT. For each patient, the fraction-to-fraction variability in PTV was low. Skin flash was associated with a higher proportion of excellent cosmesis (58% vs. 42%) relative to having the applicator all within breast tissue. Conclusions: These data indicate that NIBB is feasible and can be consistently implemented in a broad array of practice settings. Preliminary evaluation suggests that NIBB is associated with acceptably mild normal tissue toxicity and favorable early cosmesis. The application of NIBB before WBRT may be associated with better patient tolerance at the expense of less favorable cosmetic outcome.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Radiation Oncology Medical Student Clerkship: Implementation and Evaluation of a Bi-institutional Pilot Curriculum

Purpose: To develop and evaluate a structured didactic curriculum to complement clinical experiences during radiation oncology clerkships at 2 academic medical centers. Methods and Materials: A structured didactic curriculum was developed to teach fundamentals of radiation oncology and improve confidence in clinical competence. Curriculum lectures included: (1) an overview of radiation oncology (history, types of treatments, and basic clinic flow); (2) fundamentals of radiation biology and physics; and (3) practical aspects of radiation treatment simulation and planning. In addition, a hands-on dosimetry session taught students fundamentals of treatment planning. The curriculum was implemented at 2 academic departments in 2012. Students completed anonymous evaluations using a Likert scale to rate the usefulness of curriculum components (1 = not at all, 5 = extremely). Likert scores are reported as (median [interquartile range]). Results: Eighteen students completed the curriculum during their 4-week rotation (University of Chicago n=13, Harvard Longwood Campus n=5). All curriculum components were rated as extremely useful: introduction to radiation oncology (5 [4-5]); radiation biology and physics (5 [5-5]); practical aspects of radiation oncology (5 [4-5]); and the treatment planning session (5 [5-5]). Students rated the curriculum as “quite useful” to “extremely useful” (1) to help students understand radiation oncology as a specialty; (2) to increase student comfort with their specialty decision; and (3) to help students with their future transition to a radiation oncology residency. Conclusions: A standardized curriculum for medical students completing a 4-week radiation oncology clerkship was successfully implemented at 2 institutions. The curriculum was favorably reviewed. As a result of completing the curriculum, medical students felt more comfortable with their specialty decision and better prepared to begin radiation oncology residency.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Finite difference numerical method for the superlattice Boltzmann transport equation and case comparison of CPU(C) and GPU(CUDA) implementations

We present a finite difference numerical algorithm for solving two dimensional spatially homogeneous Boltzmann transport equation which describes electron transport in a semiconductor superlattice subject to crossed time dependent electric and constant magnetic fields. The algorithm is implemented both in C language targeted to CPU and in CUDA C language targeted to commodity NVidia GPU. We compare performances and merits of one implementation versus another and discuss various software optimisation techniques.

97 MATHEMATICS AND COMPUTING↗

Cloud-based implementation of white-box model predictive control for a GEOTABS office building: A field test demonstration

Model predictive control (MPC) has been proven in simulations and pilot case studies to be a superior control strategy for large buildings. MPC can utilize the weather and occupancy schedule forecasts, together with the system model, to predict the future thermal behavior of the building and minimize the overall energy use and maximize thermal comfort. However, these advantages come with the cost of increased modeling effort, computational demands, communication infrastructure, and commissioning efforts. Thus a typical approach is to, often rapidly, simplify the building modeling and MPC optimization problem while paying a price of not reaching the full performance potential. It has been shown that by employing accurate physics-based models, MPC performance can be notably increased closer to its theoretical performance bound. However, implementation of such high-fidelity MPC in real buildings remains a challenge, resulting in a lack of successful field test studies. This work presents the methodology and field test demonstration of a computationally efficient implementation of the white-box MPC in an office building in Belgium. The detailed model of the building is based on first-principle physical equations. The deployment and supervision of MPC operation in a practical setting are supported by an automated cloud-based communication infrastructure. The motivating factor behind the cloud-based architecture is its compatibility with a commercially appealing control as a service concept. The building is equipped with a ground source heat pump (GSHP) and thermally activated building structures (TABS), where the combination of both is also known as GEOTABS. From a control perspective, GEOTABS buildings are particularly challenging systems due to large scale, complex heating, ventilation and air conditioning (HVAC) system, and slow dynamics with time delays. On the other hand, there is an increased potential for energy savings due to the high thermal mass, which acts as thermal storage. The MPC operation is demonstrated during the challenging transient seasons (switching between heating and cooling), and its performance is compared to a traditional rule-based controller (RBC). We provide a proof of concept of real MPC operation for the most difficult seasons with notable GSHP energy use savings equal to 53.5% and thermal comfort improvement by 36.9%. Other MPC applications found in the literature describe tests for only cooling or only heating, and up to now only for a black-box or a grey-box approach.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

GPU-based implementations of the noniterative regularized-CCSD(T) corrections: applications to strongly correlated systems

The details of the Graphical Processing Unit (GPU) implementation of the most compu- tationally intensive (T)-part of the recently introduced regularized CCSD(T) (Reg-CCSD(T)) method [K. Kowalski, M.Valiev 131, 234107 (2010)] for calculating electronic energies of strongly interacting systems are discussed. Parallel tests performed for several molecular systems show very good scalability of the triples part of the Reg-CCSD(T) approach. We also discuss the performance of the Reg-CCSD(T) GPU implementation as a function of the parameters defining the partitioning of the spinorbital domain (tiling structure). The accuracy of the Reg-CCSD(T) method is illustrated on two examples: the NiO2 molecule and open-shell Spiro cation (5,5’(4H,4H’)-spirobi[cyclopenta[c]pyrrole]2,2’,6,6’-tetrahydro cation), which is a frequently used model to study electron transfer processes. It is demonstrated that a simple regularization of the cluster amplitudes used in the non-iterative corrections accounting for the effect of triply excited configurations significantly improves the accuracies of groundstate energies in the presence of strong quasidegeneracy effects. For NiO2 we compare the Reg-CCSD(T) results with the CCSDT energies, whereas for Spiro cation we compare Reg-CCSD(T) results with the energies obtained with completely renormalized CCSD(T) method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Parallel implementation of multireference coupled-cluster theories based on the reference-level parallelism

A novel algorithm for implementing general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski-Monkhorst exponential Ansatz [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] is introduced. The proposed algorithm utilizes processor groups to calculate the equations for the MRCC amplitudes. In the basic formulation each processor group constructs the equations related to a specific subset of references. By flexible choice of processor groups and subset of reference-specific sufficiency conditions designated to a given group one can assure optimum utilization of available computing resources. The performance of this algorithm is illustrated on the examples of the Brillouin-Wigner and Mukherjee MRCC methods with singles and doubles (BW-MRCCSD and Mk-MRCCSD). A significant improvement in scalability and in reduction of time to solution is reported with respect to recently reported parallel implementation of the BW-MRCCSD formalism [J.Brabec, H.J.J. van Dam, K. Kowalski, J. Pittner, Chem. Phys. Lett. 514, 347 (2011)].

99 GENERAL AND MISCELLANEOUS↗

Two-photon absorption cross sections within equation-of-motion coupled-cluster formalism using resolution-of-the-identity and Cholesky decomposition representations: Theory, implementation, and benchmarks

The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Implementation multi representation and oral communication skills in Department of Physics Education on Elementary Physics II

The ability of multi representation has been widely studied, but there has been no implementation through a model of learning. This study aimed to determine the ability of the students multi representation, relationships multi representation capabilities and oral communication skills, as well as the application of the relations between the two capabilities through learning model Presentatif Based on Multi representation (PBM) in solving optical geometric (Elementary Physics II). A concurrent mixed methods research methods with qualitative–quantitative weights. Means of collecting data in the form of the pre-test and post-test with essay form, observation sheets oral communication skills, and assessment of learning by observation sheet PBM–learning models all have a high degree of respectively validity category is 3.91; 4.22; 4.13; 3.88. Test reliability with Alpha Cronbach technique, reliability coefficient of 0.494. The students are department of Physics Education Unnes as a research subject. Sequence multi representation tendency of students from high to low in sequence, representation of M, D, G, V; whereas the order of accuracy, the group representation V, D, G, M. Relationship multi representation ability and oral communication skills, comparable/proportional. Implementation conjunction generate grounded theory. This study should be applied to the physics of matter, or any other university for comparison.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Design and implementation of wireless dose logger network for radiological emergency decision support system

A decision support system (DSS) is implemented in Radiological Safety Division, Indira Gandhi Centre for Atomic Research for providing guidance for emergency decision making in case of an inadvertent nuclear accident. Real time gamma dose rate measurement around the stack is used for estimating the radioactive release rate (source term) by using inverse calculation. Wireless gamma dose logging network is designed, implemented, and installed around the Madras Atomic Power Station reactor stack to continuously acquire the environmental gamma dose rate and the details are presented in the paper. The network uses XBee–Pro wireless modules and PSoC controller for wireless interfacing, and the data are logged at the base station. A LabView based program is developed to receive the data, display it on the Google Map, plot the data over the time scale, and register the data in a file to share with DSS software. The DSS at the base station evaluates the real time source term to assess radiation impact.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification

A MapReduce-based implementation called MR- MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs.

59 BASIC BIOLOGICAL SCIENCES↗

Deterministic implementation of weak quantum cubic nonlinearity

We propose a deterministic implementation of weak cubic nonlinearity, which is a basic building block of a full-scale continuous-variable quantum computation. Our proposal relies on preparation of a specific ancillary state and transferring its nonlinear properties onto the desired target by means of deterministic Gaussian operations and feed forward. We show that, despite the imperfections arising from the deterministic nature of the operation, the weak quantum nonlinearity can be implemented and verified with the current level of technology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementing an X-ray validation pipeline for the Protein Data Bank

The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described. There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Implementing High Performance Remote Method Invocation in CCA

We report our effort in engineering a high performance remote method invocation (RMI) mechanism for the Common Component Architecture (CCA). This mechanism provides a highly efficient and easy-to-use mechanism for distributed computing in CCA, enabling CCA applications to effectively leverage parallel systems to accelerate computations. This work is built on the previous work of Babel RMI. Babel is a high performance language interoperability tool that is used in CCA for scientific application writers to share, reuse, and compose applications from software components written in different programming languages. Babel provides a transparent and flexible RMI framework for distributed computing. However, the existing Babel RMI implementation is built on top of TCP and does not provide the level of performance required to distribute fine-grained tasks. We observed that the main reason the TCP based RMI does not perform well is because it does not utilize the high performance interconnect hardware on a cluster efficiently. We have implemented a high performance RMI protocol, HPCRMI. HPCRMI achieves low latency by building on top of a low-level portable communication library, Aggregated Remote Message Copy Interface (ARMCI), and minimizing communication for each RMI call. Our design allows a RMI operation to be completed by only two RDMA operations. We also aggressively optimize our system to reduce copying. In this paper, we discuss the design and our experimental evaluation of this protocol. Our experimental results show that our protocol can improve RMI performance by an order of magnitude.

99 GENERAL AND MISCELLANEOUS↗

TH-A-16A-01: Image Quality for the Radiation Oncology Physicist: Review of the Fundamentals and Implementation

The expansion and integration of diagnostic imaging technologies such as On Board Imaging (OBI) and Cone Beam Computed Tomography (CBCT) into radiation oncology has required radiation oncology physicists to be responsible for and become familiar with assessing image quality. Unfortunately many radiation oncology physicists have had little or no training or experience in measuring and assessing image quality. Many physicists have turned to automated QA analysis software without having a fundamental understanding of image quality measures. This session will review the basic image quality measures of imaging technologies used in the radiation oncology clinic, such as low contrast resolution, high contrast resolution, uniformity, noise, and contrast scale, and how to measure and assess them in a meaningful way. Additionally a discussion of the implementation of an image quality assurance program in compliance with Task Group recommendations will be presented along with the advantages and disadvantages of automated analysis methods. Learning Objectives: Review and understanding of the fundamentals of image quality. Review and understanding of the basic image quality measures of imaging modalities used in the radiation oncology clinic. Understand how to implement an image quality assurance program and to assess basic image quality measures in a meaningful way.

07 ISOTOPE AND RADIATION SOURCES↗