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LCLS-II New Instruments Workshops Report

The LCLS-II New Instruments workshops chaired by Phil Heimann and Jerry Hastings were held on March 19-22, 2012 at the SLAC National Accelerator Laboratory. The goal of the workshops was to identify the most exciting science and corresponding parameters which will help define the LCLS-II instrumentation. This report gives a synopsis of the proposed investigations and an account of the workshop. Scientists from around the world have provided short descriptions of the scientific opportunities they envision at LCLS-II. The workshops focused on four broadly defined science areas: biology, materials sciences, chemistry and atomic, molecular and optical physics (AMO). Below we summarize the identified science opportunities in the four areas. The frontiers of structural biology lie in solving the structures of large macromolecular biological systems. Most large protein assemblies are inherently difficult to crystallize due to their numerous degrees of freedom. Serial femtosecond protein nanocrystallography, using the 'diffraction-before-destruction' approach to outrun radiation damage has been very successfully pioneered at LCLS and diffraction patterns were obtained from some of the smallest protein crystals ever. The combination of femtosecond x-ray pulses of high intensity and nanosized protein crystals avoids the radiation damage encountered by conventional x-ray crystallography with focused beams and opens the door for atomic structure determinations of the previously largely inaccessible class of membrane proteins that are notoriously difficult to crystallize. The obtained structures will allow the identification of key protein functions and help in understanding the origin and control of diseases. Three dimensional coherent x-ray imaging at somewhat lower resolution may be used for larger objects such as viruses. The chemistry research areas of primary focus are the predictive understanding of catalytic mechanisms, with particular emphasis on photo- and heterogeneous catalysis. Of particular interest is the efficient conversion of light to electrical or chemical energy, which requires understanding the non-adiabatic dynamics of electronic excited states. Ultrafast x-ray scattering presents an excellent opportunity to investigate structural dynamics of molecular systems with atomic resolution, and x-ray scattering and spectroscopy present an excellent opportunity to investigating the dynamics of the electronic charge distribution. Harnessing solar energy to generate fuels, either indirectly with photovoltaics and electrochemical catalysis or directly with photocatalysts, presents a critical technological challenge that will require the use of forefront scientific tools such as ultrafast x-rays. At the center of this technical challenge is the rational design of efficient and cost effective catalysts. Important materials science opportunities relate to information technology applications, in particular the transport and storage of information on increasingly smaller length- and faster time-scales. Of interest are the understanding of the intrinsic size limits associated with the storage of information bits and the speed limits of information or bit processing. Key questions revolve about how electronic charges and spins of materials can be manipulated by electric and magnetic fields. This requires the exploration of speed limits subject to the fundamental conservation laws of energy and linear and angular momentum and the different coupling of polar electric and axial magnetic fields to charge and spin. Of interest are novel composite materials, including molecular systems combining multi electric and magnetic functionality. Ultrafast x-rays offer the required probing speed, can probe either the charge or spin properties through polarization control and through scattering and spectroscopy cover the entire energy-time-momentum-distance phase space. In the field of atomic and molecular science, LCLS II promises to elucidate the fundamental interactions among electrons and between electrons and nuclei, and to explore the frontiers of light-matter interactions. The high x-ray intensities unique to LCLS II will allow for highly localized electron excitation and probing at different positions inside a molecule, thereby interrogating the fundamental electron correlations. At the ultimate intensities, a breakdown of our established model of x-ray - matter interaction is predicted, leading to possibly new regimes of plasma physics.

14 SOLAR ENERGY↗

Bayesian Analysis of Savings from Retrofit Projects

Estimates of savings from retrofit projects depend on statistical models, but because of the complicated analysis required to determine the uncertainty of the estimates, savings uncertainty is not often considered. Numerous simplified methods have been proposed to determine savings uncertainty, but in all but the simplest cases, these methods provide approximate results only. The objective of this paper is to show that Bayesian inference provides a consistent framework for estimating savings and savings uncertainty in retrofit projects. We review the mathematical background of Bayesian inference and Bayesian regression, and present two examples of estimating savings and savings uncertainty in retrofit projects. The first is a simple case where both baseline and post-retrofit monthly natural gas use can be modeled as a linear function of monthly heating degree days. The Efficiency Valuation Organization (EVO 2007) defines two methods of determining savings in such cases: reporting period savings, which is an estimate of the savings during the post-retrofit period; and normalized savings, which is an estimate of the savings that would be obtained during a typical year at the project site. For reporting period savings, classical statistical analysis provides exact analytic results for both savings and savings uncertainty in this case. We use Bayesian analysis to calculate reporting period savings and savings uncertainty and show that the results are identical to the analytical results. For normalized savings, the literature contains no exact expression for the uncertainty of normalized savings; we use Bayesian inference to calculate this quantity for the first time, and compare it with the result of an approximate formula that has been proposed. The second example concerns a problem where the baseline data exhibit nonlinearity and serial autocorrelation, both of which are common in real-world retrofit projects. No analytical solutions exist to determine savings or savings uncertainty in this situation, but several simplified formulas have been proposed. We model the data using a 5-parameter model with first-order autoregressive errors, and use Bayesian inference to develop distributions for the model parameters and for the reporting period savings, which allows us to determine the savings uncertainty. We find the energy savings to be about 5% lower than the result obtained by ignoring the autocorrelation. In addition, the Bayesian analysis finds the savings uncertainty to be narrower than the approximate uncertainty calculated using the simplified formula. These results show that Bayesian inference can be used to determine savings and savings uncertainty for a wide variety of real-world problems.

Im, Piljae↗

Communication Simulations for Power System Applications

New smart grid technologies and concepts, such as dynamic pricing, demand response, dynamic state estimation, and wide area monitoring, protection, and control, are expected to require considerable communication resources. As the cost of retrofit can be high, future power grids will require the integration of high-speed, secure connections with legacy communication systems, while still providing adequate system control and security. While considerable work has been performed to create co-simulators for the power domain with load models and market operations, limited work has been performed in integrating communications directly into a power domain solver. The simulation of communication and power systems will become more important as the two systems become more inter-related. This paper will discuss ongoing work at Pacific Northwest National Laboratory to create a flexible, high-speed power and communication system co-simulator for smart grid applications. The framework for the software will be described, including architecture considerations for modular, high performance computing and large-scale scalability (serialization, load balancing, partitioning, cross-platform support, etc.). The current simulator supports the ns-3 (telecommunications) and GridLAB-D (distribution systems) simulators. Ongoing and future work will be described, including planned future expansions for a traditional transmission solver. A test case using the co-simulator, utilizing a transactive demand response system created for the Olympic Peninsula and AEP gridSMART demonstrations, requiring two-way communication between distributed and centralized market devices, will be used to demonstrate the value and intended purpose of the co-simulation environment.

co-simulation↗

Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared memory programming interface to manipulate distributed defense arrays. Using a combination of GA and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Scalability studies will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Global Arrays↗

Fast Mix Table Construction for Material Discretization

An effective hybrid Monte Carlo--deterministic implementation typically requires the approximation of a continuous geometry description with a discretized piecewise-constant material field. The inherent geometry discretization error can be reduced somewhat by using material mixing, where multiple materials inside a discrete mesh voxel are homogenized. Material mixing requires the construction of a ``mix table,'' which stores the volume fractions in every mixture so that multiple voxels with similar compositions can reference the same mixture. Mix table construction is a potentially expensive serial operation for large problems with many materials and voxels. We formulate an efficient algorithm to construct a sparse mix table in $O(\text{number of voxels}\times \log \text{number of mixtures})$ time. The new algorithm is implemented in ADVANTG and used to discretize continuous geometries onto a structured Cartesian grid. When applied to an end-of-life MCNP model of the High Flux Isotope Reactor with 270 distinct materials, the new method improves the material mixing time by a factor of 100 compared to a naive mix table implementation.

Johnson, Seth R↗

Local intelligent electronic device (IED) rendering templates over limited bandwidth communication link to manage remote IED

The present disclosure provides systems and methods for remote device management. According to various embodiments, a local intelligent electronic device (IED) may be in communication with a remote IED via a limited bandwidth communication link, such as a serial link. The limited bandwidth communication link may not support traditional remote management interfaces. According to one embodiment, a local IED may present an operator with a management interface for a remote IED by rendering locally stored templates. The local IED may render the locally stored templates using sparse data obtained from the remote IED. According to various embodiments, the management interface may be a web client interface and/or an HTML interface. The bandwidth required to present a remote management interface may be significantly reduced by rendering locally stored templates rather than requesting an entire management interface from the remote IED. According to various embodiments, an IED may comprise an encryption transceiver.

97 MATHEMATICS AND COMPUTING↗

A High Performance Computing Platform for Performing High-Volume Studies With Windows-based Power Grid Tools

Serial Windows-based programs are widely used in power utilities. For applications that require high volume simulations, the single CPU runtime can be on the order of days or weeks. The lengthy runtime, along with the availability of low cost hardware, is leading utilities to seriously consider High Performance Computing (HPC) techniques. However, the vast majority of the HPC computers are still Linux-based and many HPC applications have been custom developed external to the core simulation engine without consideration for ease of use. This has created a technical gap for applying HPC-based tools to today’s power grid studies. To fill this gap and accelerate the acceptance and adoption of HPC for power grid applications, this paper presents a prototype of generic HPC platform for running Windows-based power grid programs on Linux-based HPC environment. The preliminary results show that the runtime can be reduced from weeks to hours to improve work efficiency.

High-performance computing, power grid, power syst↗

Distributed Merge Trees

Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions. As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization. We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.

97 MATHEMATICS AND COMPUTING↗

User interface for a tele-operated robotic hand system

Disclosed here is a user interface for a robotic hand. The user interface anchors a user's palm in a relatively stationary position and determines various angles of interest necessary for a user's finger to achieve a specific fingertip location. The user interface additionally conducts a calibration procedure to determine the user's applicable physiological dimensions. The user interface uses the applicable physiological dimensions and the specific fingertip location, and treats the user's finger as a two link three degree-of-freedom serial linkage in order to determine the angles of interest. The user interface communicates the angles of interest to a gripping-type end effector which closely mimics the range of motion and proportions of a human hand. The user interface requires minimal contact with the operator and provides distinct advantages in terms of available dexterity, work space flexibility, and adaptability to different users.

42 ENGINEERING↗

Replica-exchange Wang Landau sampling: pushing the limits of Monte Carlo simulations in materials sciences

We describe the study of thermodynamics of materials using replica-exchange Wang Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang Landau Monte Carlo method. To evaluate the performance and scalability of the method, we investigate the magnetic phase transition in body-centered cubic (bcc) iron using the classical Heisenberg model parameterized with first principles calculations. We demonstrate that our framework leads to a significant speedup without compromising the accuracy and precision and facilitates the study of much larger systems than is possible with its serial counterpart.

Perera, Meewanage Dilina N↗

Analysis of New High-Q0 SRF Cavity Tests by Nitrogen Gas Doping at Jefferson Lab

In order to refine systematic understanding and establish confident process control, Jefferson Lab has joined with partners to investigate and thoroughly characterize the dramatically higher Q0 of 1.3 GHz niobium cavities first reported by FNAL in 2013[1]. With partial support from the LCLS-II project, JLab has undertaken a parametric study of nitrogen doping in vacuum furnace at 800 °C followed by variable depth surface removal in the 5 - 20 μm range. Q0 above 3×1010 are typical at 2.0 K and 16 MV/m accelerating field. We report observations from the single cell study and current interpretations. In addition to the parametric single cell study, we also report on the ongoing serial testing of six nitrogen-doped 9-cell cavities as baseline prototypes for LCLS-II.

Palczewski, Ari D.↗

Iodine Standard Materials: Preparation and Inter-Laboratory Comparisons

The Idaho National Laboratory is preparing to enter the community of AMS practioners who analyze for 129Iodine. We expect to take delivery of a 0.5 MV compact accelerator mass spectrometry system, built by NEC, in the early summer of 2014. The primary mission for this instrument is iodine; it is designed to analyze iodine in the +3 charge state. As part of the acceptance testing for this instrument, both at NEC and on-site in our laboratory, some sort of standard or reference material is needed to verify performance. Appropriate standard materials are not readily available in the commercial marketplace. Small quantities can sometimes be acquired from other laboratories already engaged in iodine analyses. In the longer-term, meaningful quantities of standard materials are needed for routine use in analyses, and for quality control functions1. We have prepared some standard materials, starting with elemental Woodward iodine and NIST SRM 3231 [Iodine-129 Isotopic Standard (high level)] 10-6 solution. The goal was to make mixtures at the 5x10-10, 5x10-11, 5x10-12 ratio levels, along with some unmodified Woodward, in the chemical form of silver iodide. Approximately twenty grams of each of these mixtures were prepared. The elemental Woodward iodine was dissolved in chloroform, then reduced to iodide using sodium bisulfite in water. At this point the NIST spike material was added, in the form of sodium iodide. The mixed iodides were oxidized back to iodine in chloroform using hydrogen peroxide. This oxidation step was essential for isotopic equilibration of the 127 and 129 atoms. The iodine was reduced to iodide using sodium bisulfite as before. Excess sulfites and sulfates were precipitated with barium nitrate. After decanting, silver nitrate was used to precipitate the desired silver iodide. Once the silver iodide was produced, the material was kept in darkness as much as possible to minimize photo-oxidation. The various mixtures were synthesized independently of each other; there were no serial dilutions involved. Aliquots of these four materials have been submitted to five established AMS laboratories where iodine analyses are routinely performed: ETH (Zurich), CNA (Seville), PRIME (Purdue), LLNL (California), and Isotrace (Toronto.) Results from four of these laboratories have been received; in general they indicate that the desired 129/127 ratios have been achieved. We will discuss the results of this informal round-robin exercise. If the installation of the instrument in Idaho goes well, we may have some very preliminary results from the new system. An integral part of data reporting is the approach to data reduction. Accordingly, there will also be some discussion of various philosophies of data handling in regard to the use of standards to adjust data, and background subtraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Voltage Regulation Using a Permanent Magnet Synchronous Generator with a Series Compensator: Preprint

A wind power plant (WPP) is often operated at unity power factor, and the utility host where the WPP connects prefers to regulate the voltage. Although this may not be an issue in a stiff grid, the connection to a weak grid can be a problematic. This paper explores the advantages of having voltage regulation capability via reactive power control. Another issue in wind power generation is that not all turbines are able to control their reactive power due to technical reasons or contractual obligations. A synchronous condenser (SC) using a permanent magnet synchronous generator (PMSG) is proposed to provide necessary reactive power for regulating voltage at a weak grid connection. A PMSG has the advantage of higher efficiency and reliability. Because of its lack of a field winding, a PMSG is typically controlled by a full-power converter, which can be costly. In the proposed system, the reactive power of the SC is controlled by a serially connected compensator operating in a closed-loop configuration. The compensator also damps the PMSG’s tendency to oscillate. The compensator’s VA rating is only a fraction of the rating of the SC and the PMSG. In this initial investigation, the proposed scheme is shown to be effective by computer simulations.

17 WIND ENERGY↗

Integrated Network Decompositions and Dynamic Programming for Graph Optimization (INDDGO)

The INDDGO software package offers a set of tools for finding exact solutions to graph optimization problems via tree decompositions and dynamic programming algorithms. Currently the framework offers serial and parallel (distributed memory) algorithms for finding tree decompositions and solving the maximum weighted independent set problem. The parallel dynamic programming algorithm is implemented on top of the MADNESS task-based runtime.

Source record↗

Public Key FPGA Software

The Public Key (PK) FPGA software performs asymmetric authentication using the 163-bit Elliptic Curve Digital Signature Algorithm (ECDSA) on an embedded FPGA platform. A digital signature is created on user-supplied data, and communication with a host system is performed via a Serial Peripheral Interface (SPI) bus. Software includes all components necessary for signing, including custom random number generator for key creation and SHA-256 for data hashing.

Hymel, Ross↗

spammpack, Version 2013-06-18

This library is an implementation of the Sparse Approximate Matrix Multiplication (SpAMM) algorithm introduced. It provides a matrix data type, and an approximate matrix product, which exhibits linear scaling computational complexity for matrices with decay. The product error and the performance of the multiply can be tuned by choosing an appropriate tolerance. The library can be compiled for serial execution or parallel execution on shared memory systems with an OpenMP capable compiler

Source record↗

Polytope

Polytope is a library that wraps several algorithms for generating the Voronoi diagram in both serial and distributed parallel.

Source record↗

Aleph

Aleph is a PIC/DSMC (particle-in-cell/direct simulation Monte Carlo) software package for the simulation of low temperature plasmas. Aleph is intended to be a production quality code capable of handling complex 3D geometries. Unstructured triangular (2D) or tetrahedral (3D) meshes are used to represent simulation domains. Aleph runs either in serial on a single processor or desktop machine, or can be run in parallel using the MPI message-passing library, to enable faster performance on large problems. Aleph employs dynamic load balancing to efficiently harness thousands of processors on high performance computers and enable simulations of up to millions of mesh elements and billions of particles. Multiple decompositions of the same mesh are used: one for the particles, and one for the field solves. Electrostatic fields are computed using an unstructured mesh finite element method (FEM), and the resulting linear systems are solved using solvers from the Trilinos package (http://trilinos.org/).

Source record↗