Development of general-purpose particle and heavy ion transport monte carlo code

International Nuclear Information System (INIS)

Iwase, Hiroshi; Nakamura, Takashi; Niita, Koji

2002-01-01

The high-energy particle transport code NMTC/JAM, which has been developed at JAERI, was improved for the high-energy heavy ion transport calculation by incorporating the JQMD code, the SPAR code and the Shen formula. The new NMTC/JAM named PHITS (Particle and Heavy-Ion Transport code System) is the first general-purpose heavy ion transport Monte Carlo code over the incident energies from several MeV/nucleon to several GeV/nucleon. (author)

PHITS-a particle and heavy ion transport code system

International Nuclear Information System (INIS)

Niita, Koji; Sato, Tatsuhiko; Iwase, Hiroshi; Nose, Hiroyuki; Nakashima, Hiroshi; Sihver, Lembit

2006-01-01

The paper presents a summary of the recent development of the multi-purpose Monte Carlo Particle and Heavy Ion Transport code System, PHITS. In particular, we discuss in detail the development of two new models, JAM and JQMD, for high energy particle interactions, incorporated in PHITS, and show comparisons between model calculations and experiments for the validations of these models. The paper presents three applications of the code including spallation neutron source, heavy ion therapy and space radiation. The results and examples shown indicate PHITS has great ability of carrying out the radiation transport analysis of almost all particles including heavy ions within a wide energy range

The failure mechanisms of HTR coated particle fuel and computer code

International Nuclear Information System (INIS)

Yang Lin; Liu Bing; Shao Youlin; Liang Tongxiang; Tang Chunhe

2010-01-01

The basic constituent unit of fuel element in HTR is ceramic coated particle fuel. And the performance of coated particle fuel determines the safety of HTR. In addition to the traditional detection of radiation experiments, establishing computer code is of great significance to the research. This paper mainly introduces the structure and the failure mechanism of TRISO-coated particle fuel, as well as a few basic assumptions,principles and characteristics of some existed main overseas codes. Meanwhile, this paper has proposed direction of future research by comparing the advantages and disadvantages of several computer codes. (authors)

Optimization of Particle-in-Cell Codes on RISC Processors

Science.gov (United States)

Decyk, Viktor K.; Karmesin, Steve Roy; Boer, Aeint de; Liewer, Paulette C.

1996-01-01

General strategies are developed to optimize particle-cell-codes written in Fortran for RISC processors which are commonly used on massively parallel computers. These strategies include data reorganization to improve cache utilization and code reorganization to improve efficiency of arithmetic pipelines.

IFR code for secondary particle dynamics

International Nuclear Information System (INIS)

Teague, M.R.; Yu, S.S.

1985-01-01

A numerical simulation has been constructed to obtain a detailed, quantitative estimate of the electromagnetic fields and currents existing in the Advanced Test Accelerator under conditions of laser guiding. The code treats the secondary electrons by particle simulation and the beam dynamics by a time-dependent envelope model. The simulation gives a fully relativistic description of secondary electrons moving in self-consistent electromagnetic fields. The calculations are made using coordinates t, x, y, z for the electrons and t, ct-z, r for the axisymmetric electromagnetic fields and currents. Code results, showing in particular current enhancement effects, will be given

Adaptation of multidimensional group particle tracking and particle wall-boundary condition model to the FDNS code

Science.gov (United States)

Chen, Y. S.; Farmer, R. C.

1992-01-01

A particulate two-phase flow CFD model was developed based on the FDNS code which is a pressure based predictor plus multi-corrector Navier-Stokes flow solver. Turbulence models with compressibility correction and the wall function models were employed as submodels. A finite-rate chemistry model was used for reacting flow simulation. For particulate two-phase flow simulations, a Eulerian-Lagrangian solution method using an efficient implicit particle trajectory integration scheme was developed in this study. Effects of particle-gas reaction and particle size change to agglomeration or fragmentation were not considered in this investigation. At the onset of the present study, a two-dimensional version of FDNS which had been modified to treat Lagrangian tracking of particles (FDNS-2DEL) had already been written and was operational. The FDNS-2DEL code was too slow for practical use, mainly because it had not been written in a form amenable to vectorization on the Cray, nor was the full three-dimensional form of FDNS utilized. The specific objective of this study was to reorder to calculations into long single arrays for automatic vectorization on the Cray and to implement the full three-dimensional version of FDNS to produce the FDNS-3DEL code. Since the FDNS-2DEL code was slow, a very limited number of test cases had been run with it. This study was also intended to increase the number of cases simulated to verify and improve, as necessary, the particle tracking methodology coded in FDNS.

Particle In Cell Codes on Highly Parallel Architectures

Science.gov (United States)

Tableman, Adam

2014-10-01

We describe strategies and examples of Particle-In-Cell Codes running on Nvidia GPU and Intel Phi architectures. This includes basic implementations in skeletons codes and full-scale development versions (encompassing 1D, 2D, and 3D codes) in Osiris. Both the similarities and differences between Intel's and Nvidia's hardware will be examined. Work supported by grants NSF ACI 1339893, DOE DE SC 000849, DOE DE SC 0008316, DOE DE NA 0001833, and DOE DE FC02 04ER 54780.

StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

Science.gov (United States)

Gaburov, Evghenii; Lombardi, James C., Jr.; Portegies Zwart, Simon; Rasio, F. A.

2018-05-01

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.

The accurate particle tracer code

Science.gov (United States)

Wang, Yulei; Liu, Jian; Qin, Hong; Yu, Zhi; Yao, Yicun

2017-11-01

The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runaway electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world's fastest computer, the Sunway TaihuLight supercomputer, by supporting master-slave architecture of Sunway many-core processors. Based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.

BOA, Beam Optics Analyzer A Particle-In-Cell Code

International Nuclear Information System (INIS)

Bui, Thuc

2007-01-01

The program was tasked with implementing time dependent analysis of charges particles into an existing finite element code with adaptive meshing, called Beam Optics Analyzer (BOA). BOA was initially funded by a DOE Phase II program to use the finite element method with adaptive meshing to track particles in unstructured meshes. It uses modern programming techniques, state-of-the-art data structures, so that new methods, features and capabilities are easily added and maintained. This Phase II program was funded to implement plasma simulations in BOA and extend its capabilities to model thermal electrons, secondary emissions, self magnetic field and implement a more comprehensive post-processing and feature-rich GUI. The program was successful in implementing thermal electrons, secondary emissions, and self magnetic field calculations. The BOA GUI was also upgraded significantly, and CCR is receiving interest from the microwave tube and semiconductor equipment industry for the code. Implementation of PIC analysis was partially successful. Computational resource requirements for modeling more than 2000 particles begin to exceed the capability of most readily available computers. Modern plasma analysis typically requires modeling of approximately 2 million particles or more. The problem is that tracking many particles in an unstructured mesh that is adapting becomes inefficient. In particular memory requirements become excessive. This probably makes particle tracking in unstructured meshes currently unfeasible with commonly available computer resources. Consequently, Calabazas Creek Research, Inc. is exploring hybrid codes where the electromagnetic fields are solved on the unstructured, adaptive mesh while particles are tracked on a fixed mesh. Efficient interpolation routines should be able to transfer information between nodes of the two meshes. If successfully developed, this could provide high accuracy and reasonable computational efficiency.

ORBXYZ: a 3D single-particle orbit code for following charged-particle trajectories in equilibrium magnetic fields

International Nuclear Information System (INIS)

Anderson, D.V.; Cohen, R.H.; Ferguson, J.R.; Johnston, B.M.; Sharp, C.B.; Willmann, P.A.

1981-01-01

The single particle orbit code, TIBRO, has been modified extensively to improve the interpolation methods used and to allow use of vector potential fields in the simulation of charged particle orbits on a 3D domain. A 3D cubic B-spline algorithm is used to generate spline coefficients used in the interpolation. Smooth and accurate field representations are obtained. When vector potential fields are used, the 3D cubic spline interpolation formula analytically generates the magnetic field used to push the particles. This field has del.BETA = 0 to computer roundoff. When magnetic induction is used the interpolation allows del.BETA does not equal 0, which can lead to significant nonphysical results. Presently the code assumes quadrupole symmetry, but this is not an essential feature of the code and could be easily removed for other applications. Many details pertaining to this code are given on microfiche accompanying this report

Cold-Leg Small Break LOCA Analysis of APR1400 Plant Using a SPACE/sEM Code

International Nuclear Information System (INIS)

Lim, Sang Gyu; Lee, Suk Ho; Yu, Keuk Jong; Kim, Han Gon; Lee, Jae Yong

2013-01-01

The Small Break Loss-of-Coolant Accident (SBLOCA) evaluation methodology (EM) for APR1400, called sEM, is now being developed using SPACE code. SPACE/sEM is to set up a conservative evaluation methodology in accordance with appendix K of 10 CFR 50. Major required and acceptable features of the evaluation models are described as below. - Fission product decay : 1.2 times of ANS97 decay curve - Critical flow model : Henry-Fauske Moody two phase critical flow model - Metal-Water reaction model : Baker-Just equation - Critical Heat Flux (CHF) : B and W, Barnett and Modified Barnett correlation - Post-CHF : Groeneveld 5.7 film boiling correlation A series of test matrix is established to validate SPACE/sEM code in terms of major SBLOCA phenomena, e.g. core level swelling and boiling, core heat transfer, critical flow, loop seal clearance and their integrated effects. The separated effect tests (SETs) and integrated effect tests (IETs) are successfully performed and these results shows that SPACE/sEM code has a conservatism comparing with experimental data. Finally, plant calculations of SBLOCA for APR1400 are conducted as described below. - Break location sensitivity : DVI line, hot-leg, cold-leg, pump suction leg. - Break size spectrum : 0.4ft 2 ∼0.02ft 2 (DVI) 0.5ft 2 ∼0.02ft 2 (hot-leg, cold-leg, pump suction leg) This paper deals with break size spectrum analysis of cold-leg break accidents. Based on the calculation results, emergency core cooling system (ECCS) performances of APR1400 and typical SBLOCA phenomena can be evaluated. Cold-leg SBLOCA analysis for APR1400 is performed using SPACE/sEM code under harsh environment condition. SPACE/sEM code shows the typical SBLOCA behaviors and it is reasonably predicted. Although SPACE/sEM code has conservative models and correlations based on appendix K of 10 CFR 50, PCT does not exceed the requirement (1477 K). It is concluded that ECCS in APR1400 has a sufficient performance in cold-leg SBLOCA

Cold-Leg Small Break LOCA Analysis of APR1400 Plant Using a SPACE/sEM Code

Energy Technology Data Exchange (ETDEWEB)

Lim, Sang Gyu; Lee, Suk Ho; Yu, Keuk Jong; Kim, Han Gon; Lee, Jae Yong [Central Research Institute, KHNP, Ltd., Daejeon (Korea, Republic of)

2013-10-15

The Small Break Loss-of-Coolant Accident (SBLOCA) evaluation methodology (EM) for APR1400, called sEM, is now being developed using SPACE code. SPACE/sEM is to set up a conservative evaluation methodology in accordance with appendix K of 10 CFR 50. Major required and acceptable features of the evaluation models are described as below. - Fission product decay : 1.2 times of ANS97 decay curve - Critical flow model : Henry-Fauske Moody two phase critical flow model - Metal-Water reaction model : Baker-Just equation - Critical Heat Flux (CHF) : B and W, Barnett and Modified Barnett correlation - Post-CHF : Groeneveld 5.7 film boiling correlation A series of test matrix is established to validate SPACE/sEM code in terms of major SBLOCA phenomena, e.g. core level swelling and boiling, core heat transfer, critical flow, loop seal clearance and their integrated effects. The separated effect tests (SETs) and integrated effect tests (IETs) are successfully performed and these results shows that SPACE/sEM code has a conservatism comparing with experimental data. Finally, plant calculations of SBLOCA for APR1400 are conducted as described below. - Break location sensitivity : DVI line, hot-leg, cold-leg, pump suction leg. - Break size spectrum : 0.4ft{sup 2}∼0.02ft{sup 2}(DVI) 0.5ft{sup 2}∼0.02ft{sup 2}(hot-leg, cold-leg, pump suction leg) This paper deals with break size spectrum analysis of cold-leg break accidents. Based on the calculation results, emergency core cooling system (ECCS) performances of APR1400 and typical SBLOCA phenomena can be evaluated. Cold-leg SBLOCA analysis for APR1400 is performed using SPACE/sEM code under harsh environment condition. SPACE/sEM code shows the typical SBLOCA behaviors and it is reasonably predicted. Although SPACE/sEM code has conservative models and correlations based on appendix K of 10 CFR 50, PCT does not exceed the requirement (1477 K). It is concluded that ECCS in APR1400 has a sufficient performance in cold-leg SBLOCA.

Particle tracing code for multispecies gas

International Nuclear Information System (INIS)

Eaton, R.R.; Fox, R.L.; Vandevender, W.H.

1979-06-01

Details are presented for the development of a computer code designed to calculate the flow of a multispecies gas mixture using particle tracing techniques. The current technique eliminates the need for a full simulation by utilizing local time averaged velocity distribution functions to obtain the dynamic properties for probable collision partners. The development of this concept reduces statistical scatter experienced in conventional Monte Carlo simulations. The technique is applicable to flow problems involving gas mixtures with disparate masses and trace constituents in the Knudsen number, Kn, range from 1.0 to less than 0.01. The resulting code has previously been used to analyze several aerodynamic isotope enrichment devices

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

Science.gov (United States)

Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

2016-09-01

Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

Code-B-1 for stress/strain calculation for TRISO fuel particle (Contract research)

International Nuclear Information System (INIS)

Aihara, Jun; Ueta, Shohei; Shibata, Taiju; Sawa, Kazuhiro

2011-12-01

We have developed Code-B-1 for the prediction of the failure probabilities of the coated fuel particles for the high temperature gas-cooled reactors (HTGRs) under operation by modification of an existing code. A finite element method (FEM) is employed for the stress calculation part and Code-B-1 can treat the plastic deformation of the coating layer of the coated fuel particles which the existing code cannot treat. (author)

FLUKA: A Multi-Particle Transport Code

Energy Technology Data Exchange (ETDEWEB)

Ferrari, A.; Sala, P.R.; /CERN /INFN, Milan; Fasso, A.; /SLAC; Ranft, J.; /Siegen U.

2005-12-14

This report describes the 2005 version of the Fluka particle transport code. The first part introduces the basic notions, describes the modular structure of the system, and contains an installation and beginner's guide. The second part complements this initial information with details about the various components of Fluka and how to use them. It concludes with a detailed history and bibliography.

Papa, a Particle Tracing Code in Pascal

NARCIS (Netherlands)

Haselhoff, E.H.; Haselhoff, Eltjo H.; Ernst, G.J.

1990-01-01

During the design of a 10 ¿m high-gain FEL oscillator (TEUFEL Project) we developed a new particle-tracing code to perform simulations of thermionic- and photo-cathode electron injectors/accelerators. The program allows predictions of current, energy and beam emittance in a user-specified linac

Load-balancing techniques for a parallel electromagnetic particle-in-cell code

Energy Technology Data Exchange (ETDEWEB)

PLIMPTON,STEVEN J.; SEIDEL,DAVID B.; PASIK,MICHAEL F.; COATS,REBECCA S.

2000-01-01

QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER.

Load-balancing techniques for a parallel electromagnetic particle-in-cell code

International Nuclear Information System (INIS)

Plimpton, Steven J.; Seidel, David B.; Pasik, Michael F.; Coats, Rebecca S.

2000-01-01

QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER

High energy particle transport code NMTC/JAM

International Nuclear Information System (INIS)

Niita, Koji; Meigo, Shin-ichiro; Takada, Hiroshi; Ikeda, Yujiro

2001-03-01

We have developed a high energy particle transport code NMTC/JAM, which is an upgraded version of NMTC/JAERI97. The applicable energy range of NMTC/JAM is extended in principle up to 200 GeV for nucleons and mesons by introducing the high energy nuclear reaction code JAM for the intra-nuclear cascade part. For the evaporation and fission process, we have also implemented a new model, GEM, by which the light nucleus production from the excited residual nucleus can be described. According to the extension of the applicable energy, we have upgraded the nucleon-nucleus non-elastic, elastic and differential elastic cross section data by employing new systematics. In addition, the particle transport in a magnetic field has been implemented for the beam transport calculations. In this upgrade, some new tally functions are added and the format of input of data has been improved very much in a user friendly manner. Due to the implementation of these new calculation functions and utilities, consequently, NMTC/JAM enables us to carry out reliable neutronics study of a large scale target system with complex geometry more accurately and easily than before. This report serves as a user manual of the code. (author)

Beam-induced motion correction for sub-megadalton cryo-EM particles.

Science.gov (United States)

Scheres, Sjors Hw

2014-08-13

In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa. Copyright © 2014, Scheres.

The CNCSN: one, two- and three-dimensional coupled neutral and charged particle discrete ordinates code package

International Nuclear Information System (INIS)

Voloschenko, A.M.; Gukov, S.V.; Kryuchkov, V.P.; Dubinin, A.A.; Sumaneev, O.V.

2005-01-01

The CNCSN package is composed of the following codes: -) KATRIN-2.0: a three-dimensional neutral and charged particle transport code; -) KASKAD-S-2.5: a two-dimensional neutral and charged particle transport code; -) ROZ-6.6: a one-dimensional neutral and charged particle transport code; -) ARVES-2.5: a preprocessor for the working macroscopic cross-section format FMAC-M for transport calculations; -) MIXERM: a utility code for preparing mixtures on the base of multigroup cross-section libraries in ANISN format; -) CEPXS-BFP: a version of the Sandia National Lab. multigroup coupled electron-photon cross-section generating code CEPXS, adapted for solving the charged particles transport in the Boltzmann-Fokker-Planck formulation with the use of discrete ordinate method; -) SADCO-2.4: Institute for High-Energy Physics modular system for generating coupled nuclear data libraries to provide high-energy particles transport calculations by multigroup method; -) KATRIF: the post-processor for the KATRIN code; -) KASF: the post-processor for the KASKAD-S code; and ROZ6F: the post-processor for the ROZ-6 code. The coding language is Fortran-90

Optimization of the particle pusher in a diode simulation code

International Nuclear Information System (INIS)

Theimer, M.M.; Quintenz, J.P.

1979-09-01

The particle pusher in Sandia's particle-in-cell diode simulation code has been rewritten to reduce the required run time of a typical simulation. The resulting new version of the code has been found to run up to three times as fast as the original with comparable accuracy. The cost of this optimization was an increase in storage requirements of about 15%. The new version has also been written to run efficiently on a CRAY-1 computing system. Steps taken to affect this reduced run time are described. Various test cases are detailed

Parallelization of a Monte Carlo particle transport simulation code

Science.gov (United States)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

Antiproton annihilation physics annihilation physics in the Monte Carlo particle transport code particle transport code SHIELD-HIT12A

DEFF Research Database (Denmark)

Taasti, Vicki Trier; Knudsen, Helge; Holzscheiter, Michael

2015-01-01

The Monte Carlo particle transport code SHIELD-HIT12A is designed to simulate therapeutic beams for cancer radiotherapy with fast ions. SHIELD-HIT12A allows creation of antiproton beam kernels for the treatment planning system TRiP98, but first it must be benchmarked against experimental data. An...

Hot particle dose calculations using the computer code VARSKIN Mod 2

International Nuclear Information System (INIS)

Durham, J.S.

1991-01-01

The only calculational model recognised by the Nuclear Regulatory Commission (NRC) for hot particle dosimetry is VARSKIN Mod 1. Because the code was designed to calculate skin dose from distributed skin contamination and not hot particles, it is assumed that the particle has no thickness and, therefore, that no self-absorption occurs within the source material. For low energy beta particles such as those emitted from 60 Co, a significant amount of self-shielding occurs in hot particles and VARSKIN Mod 1 overestimates the skin dose. In addition, the presence of protective clothing, which will reduce the calculated skin dose for both high and low energy beta emitters, is not modelled in VARSKIN Mod 1. Finally, there is no provision in VARSKIN Mod 1 to calculate the gamma contribution to skin dose from radionuclides that emit both beta and gamma radiation. The computer code VARSKIN Mod 1 has been modified to model three-dimensional sources, insertion of layers of protective clothing between the source and skin, and gamma dose from appropriate radionuclides. The new code, VARSKIN Mod 2, is described and the sensitivity of the calculated dose to source geometry, diameter, thickness, density, and protective clothing thickness are discussed. Finally, doses calculated using VARSKIN Mod 2 are compared to doses measured from hot particles found in nuclear power plants. (author)

Parallel treatment of simulation particles in particle-in-cell codes on SUPRENUM

International Nuclear Information System (INIS)

Seldner, D.

1990-02-01

This report contains the program documentation and description of the program package 2D-PLAS, which has been developed at the Nuclear Research Center Karlsruhe in the Institute for Data Processing in Technology (IDT) under the auspices of the BMFT. 2D-PLAS is a parallel program version of the treatment of the simulation particles of the two-dimensional stationary particle-in-cell code BFCPIC which has been developed at the Nuclear Research Center Karlsruhe. This parallel version has been designed for the parallel computer SUPRENUM. (orig.) [de

The OpenMC Monte Carlo particle transport code

International Nuclear Information System (INIS)

Romano, Paul K.; Forget, Benoit

2013-01-01

Highlights: ► An open source Monte Carlo particle transport code, OpenMC, has been developed. ► Solid geometry and continuous-energy physics allow high-fidelity simulations. ► Development has focused on high performance and modern I/O techniques. ► OpenMC is capable of scaling up to hundreds of thousands of processors. ► Results on a variety of benchmark problems agree with MCNP5. -- Abstract: A new Monte Carlo code called OpenMC is currently under development at the Massachusetts Institute of Technology as a tool for simulation on high-performance computing platforms. Given that many legacy codes do not scale well on existing and future parallel computer architectures, OpenMC has been developed from scratch with a focus on high performance scalable algorithms as well as modern software design practices. The present work describes the methods used in the OpenMC code and demonstrates the performance and accuracy of the code on a variety of problems.

Survey of particle codes in the Magnetic Fusion Energy Program

International Nuclear Information System (INIS)

1977-12-01

In the spring of 1976, the Fusion Plasma Theory Branch of the Division of Magnetic Fusion Energy conducted a survey of all the physics computer codes being supported at that time. The purpose of that survey was to allow DMFE to prepare a description of the codes for distribution to the plasma physics community. This document is the first of several planned and covers those types of codes which treat the plasma as a group of particles

Implementing particle-in-cell plasma simulation code on the BBN TC2000

International Nuclear Information System (INIS)

Sturtevant, J.E.; Maccabe, A.B.

1990-01-01

The BBN TC2000 is a multiple instruction, multiple data (MIMD) machine that combines a physically distributed memory with a logically shared memory programming environment using the unique Butterfly switch. Particle-In-Cell (PIC) plasma simulations model the interaction of charged particles with electric and magnetic fields. This paper describes the implementation of both a 1-D electrostatic and a 2 1/2-D electromagnetic PIC (particle-in-cell) plasma simulation code on a BBN TC2000. Performance is compared to implementations of the same code on the shared memory Sequent Balance and distributed memory Intel iPSC hypercube

DART: A simulation code for charged particle beams

International Nuclear Information System (INIS)

White, R.C.; Barr, W.L.; Moir, R.W.

1989-01-01

This paper presents a recently modified version of the 2-D code, DART, which can simulate the behavior of a beam of charged particles whose trajectories are determined by electric and magnetic fields. This code was originally used to design laboratory-scale and full-scale beam direct converters. Since then, its utility has been expanded to allow more general applications. The simulation includes space charge, secondary electrons, and the ionization of neutral gas. A beam can contain up to nine superimposed beamlets of different energy and species. The calculation of energy conversion efficiency and the method of specifying the electrode geometry are described. Basic procedures for using the code are given, and sample input and output fields are shown. 7 refs., 18 figs

Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

Science.gov (United States)

Sandalski, Stou

Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

PEREGRINE: An all-particle Monte Carlo code for radiation therapy

International Nuclear Information System (INIS)

Hartmann Siantar, C.L.; Chandler, W.P.; Rathkopf, J.A.; Svatos, M.M.; White, R.M.

1994-09-01

The goal of radiation therapy is to deliver a lethal dose to the tumor while minimizing the dose to normal tissues. To carry out this task, it is critical to calculate correctly the distribution of dose delivered. Monte Carlo transport methods have the potential to provide more accurate prediction of dose distributions than currently-used methods. PEREGRINE is a new Monte Carlo transport code developed at Lawrence Livermore National Laboratory for the specific purpose of modeling the effects of radiation therapy. PEREGRINE transports neutrons, photons, electrons, positrons, and heavy charged-particles, including protons, deuterons, tritons, helium-3, and alpha particles. This paper describes the PEREGRINE transport code and some preliminary results for clinically relevant materials and radiation sources

Canonical momenta and numerical instabilities in particle codes

International Nuclear Information System (INIS)

Godfrey, B.B.

1975-01-01

A set of warm plasma dispersion relations appropriate to a large class of electromagnetic plasma simulation codes is derived. The numerical Cherenkov instability is shown by analytic and numerical analysis of these dispersion relations to be the most significant nonphysical effect involving transverse electromagnetic waves. The instability arises due to a spurious phase shift between resonant particles and light waves, caused by a basic incompatibility between the Lagrangian treatment of particle positions and the Eulerian treatment of particle velocities characteristic of most PIC--CIC algorithms. It is demonstrated that, through the use of canonical momentum, this mismatch is alleviated sufficiently to completely eliminate the Cherenkov instability. Collateral effects on simulation accuracy and on other numerical instabilities appear to be minor

DART: a simulation code for charged particle beams

International Nuclear Information System (INIS)

White, R.C.; Barr, W.L.; Moir, R.W.

1988-01-01

This paper presents a recently modified verion of the 2-D DART code designed to simulate the behavior of a beam of charged particles whose paths are affected by electric and magnetic fields. This code was originally used to design laboratory-scale and full-scale beam direct converters. Since then, its utility has been expanded to allow more general applications. The simulation technique includes space charge, secondary electron effects, and neutral gas ionization. Calculations of electrode placement and energy conversion efficiency are described. Basic operation procedures are given including sample input files and output. 7 refs., 18 figs

Load balancing in highly parallel processing of Monte Carlo code for particle transport

International Nuclear Information System (INIS)

Higuchi, Kenji; Takemiya, Hiroshi; Kawasaki, Takuji

1998-01-01

In parallel processing of Monte Carlo (MC) codes for neutron, photon and electron transport problems, particle histories are assigned to processors making use of independency of the calculation for each particle. Although we can easily parallelize main part of a MC code by this method, it is necessary and practically difficult to optimize the code concerning load balancing in order to attain high speedup ratio in highly parallel processing. In fact, the speedup ratio in the case of 128 processors remains in nearly one hundred times when using the test bed for the performance evaluation. Through the parallel processing of the MCNP code, which is widely used in the nuclear field, it is shown that it is difficult to attain high performance by static load balancing in especially neutron transport problems, and a load balancing method, which dynamically changes the number of assigned particles minimizing the sum of the computational and communication costs, overcomes the difficulty, resulting in nearly fifteen percentage of reduction for execution time. (author)

Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels.

Science.gov (United States)

Liu, Ruxiu; Wang, Ningquan; Kamili, Farhan; Sarioglu, A Fatih

2016-04-21

Numerous biophysical and biochemical assays rely on spatial manipulation of particles/cells as they are processed on lab-on-a-chip devices. Analysis of spatially distributed particles on these devices typically requires microscopy negating the cost and size advantages of microfluidic assays. In this paper, we introduce a scalable electronic sensor technology, called microfluidic CODES, that utilizes resistive pulse sensing to orthogonally detect particles in multiple microfluidic channels from a single electrical output. Combining the techniques from telecommunications and microfluidics, we route three coplanar electrodes on a glass substrate to create multiple Coulter counters producing distinct orthogonal digital codes when they detect particles. We specifically design a digital code set using the mathematical principles of Code Division Multiple Access (CDMA) telecommunication networks and can decode signals from different microfluidic channels with >90% accuracy through computation even if these signals overlap. As a proof of principle, we use this technology to detect human ovarian cancer cells in four different microfluidic channels fabricated using soft lithography. Microfluidic CODES offers a simple, all-electronic interface that is well suited to create integrated, low-cost lab-on-a-chip devices for cell- or particle-based assays in resource-limited settings.

Design of sampling tools for Monte Carlo particle transport code JMCT

International Nuclear Information System (INIS)

Shangguan Danhua; Li Gang; Zhang Baoyin; Deng Li

2012-01-01

A class of sampling tools for general Monte Carlo particle transport code JMCT is designed. Two ways are provided to sample from distributions. One is the utilization of special sampling methods for special distribution; the other is the utilization of general sampling methods for arbitrary discrete distribution and one-dimensional continuous distribution on a finite interval. Some open source codes are included in the general sampling method for the maximum convenience of users. The sampling results show sampling correctly from distribution which are popular in particle transport can be achieved with these tools, and the user's convenience can be assured. (authors)

Progress of laser-plasma interaction simulations with the particle-in-cell code

International Nuclear Information System (INIS)

Sakagami, Hitoshi; Kishimoto, Yasuaki; Sentoku, Yasuhiko; Taguchi, Toshihiro

2005-01-01

As the laser-plasma interaction is a non-equilibrium, non-linear and relativistic phenomenon, we must introduce a microscopic method, namely, the relativistic electromagnetic PIC (Particle-In-Cell) simulation code. The PIC code requires a huge number of particles to validate simulation results, and its task is very computation-intensive. Thus simulation researches by the PIC code have been progressing along with advances in computer technology. Recently, parallel computers with tremendous computational power have become available, and thus we can perform three-dimensional PIC simulations for the laser-plasma interaction to investigate laser fusion. Some simulation results are shown with figures. We discuss a recent trend of large-scale PIC simulations that enable direct comparison between experimental facts and computational results. We also discharge/lightning simulations by the extended PIC code, which include various atomic and relaxation processes. (author)

Modification V to the computer code, STRETCH, for predicting coated-particle behavior

International Nuclear Information System (INIS)

Valentine, K.H.

1975-04-01

Several modifications have been made to the stress analysis code, STRETCH, in an attempt to improve agreement between the calculated and observed behavior of pyrocarbon-coated fuel particles during irradiation in a reactor environment. Specific areas of the code that have been modified are the neutron-induced densification model and the neutron-induced creep calculation. Also, the capability for modeling surface temperature variations has been added. HFIR Target experiments HT-12 through HT-15 have been simulated with the modified code, and the neutron-fluence vs particle-failure predictions compare favorably with the experimental results. Listings of the modified FORTRAN IV main source program and additional FORTRAN IV functions are provided along with instructions for supplying the additional input data. (U.S.)

Streamlined Darwin methods for particle beam injectors

International Nuclear Information System (INIS)

Boyd, J.K.

1987-01-01

Physics issues that involve inductive effects, such as beam fluctuations, electromagnetic (EM) instability, or interactions with a cavity require a time-dependent simulation. The most elaborate time-dependent codes self-consistently solve Maxwell's equations and the force equation for a large number of macroparticles. Although these full EM particle-in-cell (PIC) codes have been used to study a broad range of phenomena, including beam injectors, they have several drawbacks. In an explicit solution of Maxwell's equations, the time step is restricted by a Courant condition. A second disadvantage is the production of anomalously large numerical fluctuations, caused by representing many real particles by a single computational macroparticle. Last, approximate models of internal boundaries can create nonphysical radiation in a full EM simulation. In this work, many of the problems of a fully electromagnetic simulation are avoided by using the Darwin field model. The Darwin field model is the magnetoinductive limit of Maxwell's equations, and it retains the first-order relativistic correction to the particle Lagrangian. It includes the part of the displacement current necessary to satisfy the charge-continuity equation. This feature is important for simulation of nonneutral beams. Because the Darwin model does not include the solenoidal vector component of the displacement current, it cannot be used to study high-frequency phenomena or effects caused by rapid current changes. However, because wave motion is not followed, the Courant condition of a fully electromagnetic code can be exceeded. In addition, inductive effects are modeled without creating nonphysical radiation

Neutron secondary-particle production cross sections and their incorporation into Monte-Carlo transport codes

International Nuclear Information System (INIS)

Brenner, D.J.; Prael, R.E.; Little, R.C.

1987-01-01

Realistic simulations of the passage of fast neutrons through tissue require a large quantity of cross-sectional data. What are needed are differential (in particle type, energy and angle) cross sections. A computer code is described which produces such spectra for neutrons above ∼14 MeV incident on light nuclei such as carbon and oxygen. Comparisons have been made with experimental measurements of double-differential secondary charged-particle production on carbon and oxygen at energies from 27 to 60 MeV; they indicate that the model is adequate in this energy range. In order to utilize fully the results of these calculations, they should be incorporated into a neutron transport code. This requires defining a generalized format for describing charged-particle production, putting the calculated results in this format, interfacing the neutron transport code with these data, and charged-particle transport. The design and development of such a program is described. 13 refs., 3 figs

ALFITeX. A new code for the deconvolution of complex alpha-particle spectra

International Nuclear Information System (INIS)

Caro Marroyo, B.; Martin Sanchez, A.; Jurado Vargas, M.

2013-01-01

A new code for the deconvolution of complex alpha-particle spectra has been developed. The ALFITeX code is written in Visual Basic for Microsoft Office Excel 2010 spreadsheets, incorporating several features aimed at making it a fast, robust and useful tool with a user-friendly interface. The deconvolution procedure is based on the Levenberg-Marquardt algorithm, with the curve fitting the experimental data being the mathematical function formed by the convolution of a Gaussian with two left-handed exponentials in the low-energy-tail region. The code also includes the capability of fitting a possible constant background contribution. The application of the singular value decomposition method for matrix inversion permits the fit of any kind of alpha-particle spectra, even those presenting singularities or an ill-conditioned curvature matrix. ALFITeX has been checked with its application to the deconvolution and the calculation of the alpha-particle emission probabilities of 239 Pu, 241 Am and 235 U. (author)

Randomly dispersed particle fuel model in the PSG Monte Carlo neutron transport code

International Nuclear Information System (INIS)

Leppaenen, J.

2007-01-01

High-temperature gas-cooled reactor fuels are composed of thousands of microscopic fuel particles, randomly dispersed in a graphite matrix. The modelling of such geometry is complicated, especially using continuous-energy Monte Carlo codes, which are unable to apply any deterministic corrections in the calculation. This paper presents the geometry routine developed for modelling randomly dispersed particle fuels using the PSG Monte Carlo reactor physics code. The model is based on the delta-tracking method, and it takes into account the spatial self-shielding effects and the random dispersion of the fuel particles. The calculation routine is validated by comparing the results to reference MCNP4C calculations using uranium and plutonium based fuels. (authors)

Introduction to the Latest Version of the Test-Particle Monte Carlo Code Molflow+

CERN Document Server

Ady, M

2014-01-01

The Test-Particle Monte Carlo code Molflow+ is getting more and more attention from the scientific community needing detailed 3D calculations of vacuum in the molecular flow regime mainly, but not limited to, the particle accelerator field. Substantial changes, bug fixes, geometry-editing and modelling features, and computational speed improvements have been made to the code in the last couple of years. This paper will outline some of these new features, and show examples of applications to the design and analysis of vacuum systems at CERN and elsewhere.

PHITS: Particle and heavy ion transport code system, version 2.23

International Nuclear Information System (INIS)

Niita, Koji; Matsuda, Norihiro; Iwamoto, Yosuke; Sato, Tatsuhiko; Nakashima, Hiroshi; Sakamoto, Yukio; Iwase, Hiroshi; Sihver, Lembit

2010-10-01

A Particle and Heavy-Ion Transport code System PHITS has been developed under the collaboration of JAEA (Japan Atomic Energy Agency), RIST (Research Organization for Information Science and Technology) and KEK (High Energy Accelerator Research Organization). PHITS can deal with the transport of all particles (nucleons, nuclei, mesons, photons, and electrons) over wide energy ranges, using several nuclear reaction models and nuclear data libraries. Geometrical configuration of the simulation can be set with GG (General Geometry) or CG (Combinatorial Geometry). Various quantities such as heat deposition, track length and production yields can be deduced from the simulation, using implemented estimator functions called 'tally'. The code also has a function to draw 2D and 3D figures of the calculated results as well as the setup geometries, using a code ANGEL. Because of these features, PHITS has been widely used for various purposes such as designs of accelerator shielding, radiation therapy and space exploration. Recently PHITS introduces an event generator for particle transport parts in the low energy region. Thus, PHITS was completely rewritten for the introduction of the event generator for neutron-induced reactions in energy region less than 20 MeV. Furthermore, several new tallis were incorporated for estimation of the relative biological effects. This document provides a manual of the new PHITS. (author)

Development of a relativistic Particle In Cell code PARTDYN for linear accelerator beam transport

Energy Technology Data Exchange (ETDEWEB)

Phadte, D., E-mail: deepraj@rrcat.gov.in [LPD, Raja Ramanna Centre for Advanced Technology, Indore 452013 (India); Patidar, C.B.; Pal, M.K. [MAASD, Raja Ramanna Centre for Advanced Technology, Indore (India)

2017-04-11

A relativistic Particle In Cell (PIC) code PARTDYN is developed for the beam dynamics simulation of z-continuous and bunched beams. The code is implemented in MATLAB using its MEX functionality which allows both ease of development as well higher performance similar to a compiled language like C. The beam dynamics calculations carried out by the code are compared with analytical results and with other well developed codes like PARMELA and BEAMPATH. The effect of finite number of simulation particles on the emittance growth of intense beams has been studied. Corrections to the RF cavity field expressions were incorporated in the code so that the fields could be calculated correctly. The deviations of the beam dynamics results between PARTDYN and BEAMPATH for a cavity driven in zero-mode have been discussed. The beam dynamics studies of the Low Energy Beam Transport (LEBT) using PARTDYN have been presented.

GRADSPH: A parallel smoothed particle hydrodynamics code for self-gravitating astrophysical fluid dynamics

NARCIS (Netherlands)

Vanaverbeke, S.; Keppens, R.; Poedts, S.; Boffin, H.

2009-01-01

We describe the algorithms implemented in the first version of GRADSPH, a parallel, tree-based, smoothed particle hydrodynamics code for simulating self-gravitating astrophysical systems written in FORTRAN 90. The paper presents details on the implementation of the Smoothed Particle Hydro (SPH)

The local skin dose conversion coefficients of electrons, protons and alpha particles calculated using the Geant4 code.

Science.gov (United States)

Zhang, Bintuan; Dang, Bingrong; Wang, Zhuanzi; Wei, Wei; Li, Wenjian

2013-10-01

The skin tissue-equivalent slab reported in the International Commission on Radiological Protection (ICRP) Publication 116 to calculate the localised skin dose conversion coefficients (LSDCCs) was adopted into the Monte Carlo transport code Geant4. The Geant4 code was then utilised for computation of LSDCCs due to a circular parallel beam of monoenergetic electrons, protons and alpha particles electrons and alpha particles are found to be in good agreement with the results using the MCNPX code of ICRP 116 data. The present work thus validates the LSDCC values for both electrons and alpha particles using the Geant4 code.

Numerical code to determine the particle trapping region in the LISA machine

International Nuclear Information System (INIS)

Azevedo, M.T. de; Raposo, C.C. de; Tomimura, A.

1984-01-01

A numerical code is constructed to determine the trapping region in machine like LISA. The variable magnetic field is two deimensional and is coupled to the Runge-Kutta through the Tchebichev polynomial. Various particle orbits including particle interactions were analysed. Beside this, a strong electric field is introduced to see the possible effects happening inside the plasma. (Author) [pt

Alignment of cryo-EM movies of individual particles by optimization of image translations.

Science.gov (United States)

Rubinstein, John L; Brubaker, Marcus A

2015-11-01

Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1 MDa protein particles. Another algorithm allows individual images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM. Copyright © 2015 Elsevier Inc. All rights reserved.

FLUKA A multi-particle transport code (program version 2005)

CERN Document Server

Ferrari, A; Fassò, A; Ranft, Johannes

2005-01-01

This report describes the 2005 version of the Fluka particle transport code. The first part introduces the basic notions, describes the modular structure of the system, and contains an installation and beginner’s guide. The second part complements this initial information with details about the various components of Fluka and how to use them. It concludes with a detailed history and bibliography.

THREEDANT: A code to perform three-dimensional, neutral particle transport calculations

International Nuclear Information System (INIS)

Alcouffe, R.E.

1994-01-01

The THREEDANT code solves the three-dimensional neutral particle transport equation in its first order, multigroup, discrate ordinate form. The code allows an unlimited number of groups (depending upon the cross section set), angular quadrature up to S-100, and unlimited Pn order again depending upon the cross section set. The code has three options for spatial differencing, diamond with set-to-zero fixup, adaptive weighted diamond, and linear modal. The geometry options are XYZ and RZΘ with a special XYZ option based upon a volume fraction method. This allows objects or bodies of any shape to be modelled as input which gives the code as much geometric description flexibility as the Monte Carlo code MCNP. The transport equation is solved by source iteration accelerated by the DSA method. Both inner and outer iterations are so accelerated. Some results are presented which demonstrate the effectiveness of these techniques. The code is available on several types of computing platforms

Auxiliary plasma heating and fueling models for use in particle simulation codes

International Nuclear Information System (INIS)

Procassini, R.J.; Cohen, B.I.

1989-01-01

Computational models of a radiofrequency (RF) heating system and neutral-beam injector are presented. These physics packages, when incorporated into a particle simulation code allow one to simulate the auxiliary heating and fueling of fusion plasmas. The RF-heating package is based upon a quasilinear diffusion equation which describes the slow evolution of the heated particle distribution. The neutral-beam injector package models the charge exchange and impact ionization processes which transfer energy and particles from the beam to the background plasma. Particle simulations of an RF-heated and a neutral-beam-heated simple-mirror plasma are presented. 8 refs., 5 figs

A 3d particle simulation code for heavy ion fusion accelerator studies

International Nuclear Information System (INIS)

Friedman, A.; Bangerter, R.O.; Callahan, D.A.; Grote, D.P.; Langdon, A.B.; Haber, I.

1990-01-01

We describe WARP, a new particle-in-cell code being developed and optimized for ion beam studies in true geometry. We seek to model transport around bends, axial compression with strong focusing, multiple beamlet interaction, and other inherently 3d processes that affect emittance growth. Constraints imposed by memory and running time are severe. Thus, we employ only two 3d field arrays (ρ and φ), and difference φ directly on each particle to get E, rather than interpolating E from three meshes; use of a single 3d array is feasible. A new method for PIC simulation of bent beams follows the beam particles in a family of rotated laboratory frames, thus ''straightening'' the bends. We are also incorporating an envelope calculation, an (r, z) model, and 1d (axial) model within WARP. The BASIS development and run-time system is used, providing a powerful interactive environment in which the user has access to all variables in the code database. 10 refs., 3 figs

Particle tracking code of simulating global RF feedback

International Nuclear Information System (INIS)

Mestha, L.K.

1991-09-01

It is well known in the ''control community'' that a good feedback controller design is deeply rooted in the physics of the system. For example, when accelerating the beam we must keep several parameters under control so that the beam travels within the confined space. Important parameters include the frequency and phase of the rf signal, the dipole field, and the cavity voltage. Because errors in these parameters will progressively mislead the beam from its projected path in the tube, feedback loops are used to correct the behavior. Since the feedback loop feeds energy to the system, it changes the overall behavior of the system and may drive it to instability. Various types of controllers are used to stabilize the feedback loop. Integrating the beam physics with the feedback controllers allows us to carefully analyze the beam behavior. This will not only guarantee optimal performance but will also significantly enhance the ability of the beam control engineer to deal effectively with the interaction of various feedback loops. Motivated by this theme, we developed a simple one-particle tracking code to simulate particle behavior with feedback controllers. In order to achieve our fundamental objective, we can ask some key questions: What are the input and output parameters? How can they be applied to the practical machine? How can one interface the rf system dynamics such as the transfer characteristics of the rf cavities and phasing between the cavities? Answers to these questions can be found by considering a simple case of a single cavity with one particle, tracking it turn-by-turn with appropriate initial conditions, then introducing constraints on crucial parameters. Critical parameters are rf frequency, phase, and amplitude once the dipole field has been given. These are arranged in the tracking code so that we can interface the feedback system controlling them

SoAx: A generic C++ Structure of Arrays for handling particles in HPC codes

Science.gov (United States)

Homann, Holger; Laenen, Francois

2018-03-01

The numerical study of physical problems often require integrating the dynamics of a large number of particles evolving according to a given set of equations. Particles are characterized by the information they are carrying such as an identity, a position other. There are generally speaking two different possibilities for handling particles in high performance computing (HPC) codes. The concept of an Array of Structures (AoS) is in the spirit of the object-oriented programming (OOP) paradigm in that the particle information is implemented as a structure. Here, an object (realization of the structure) represents one particle and a set of many particles is stored in an array. In contrast, using the concept of a Structure of Arrays (SoA), a single structure holds several arrays each representing one property (such as the identity) of the whole set of particles. The AoS approach is often implemented in HPC codes due to its handiness and flexibility. For a class of problems, however, it is known that the performance of SoA is much better than that of AoS. We confirm this observation for our particle problem. Using a benchmark we show that on modern Intel Xeon processors the SoA implementation is typically several times faster than the AoS one. On Intel's MIC co-processors the performance gap even attains a factor of ten. The same is true for GPU computing, using both computational and multi-purpose GPUs. Combining performance and handiness, we present the library SoAx that has optimal performance (on CPUs, MICs, and GPUs) while providing the same handiness as AoS. For this, SoAx uses modern C++ design techniques such template meta programming that allows to automatically generate code for user defined heterogeneous data structures.

Development of 2D particle-in-cell code to simulate high current, low ...

Indian Academy of Sciences (India)

Abstract. A code for 2D space-charge dominated beam dynamics study in beam trans- port lines is developed. The code is used for particle-in-cell (PIC) simulation of z-uniform beam in a channel containing solenoids and drift space. It can also simulate a transport line where quadrupoles are used for focusing the beam.

Syrlic: a Lagrangian code to handle industrial problems involving particles and droplets

International Nuclear Information System (INIS)

Peniguel, C.

1997-01-01

Numerous industrial applications require to solve droplets or solid particles trajectories and their effects on the flow. (fuel injection in combustion engine, agricultural spraying, spray drying, spray cooling, spray painting, particles separator, dispersion of pollutant, etc). SYRLIC is being developed to handle the dispersed phase while the continuous phase is tackled by classical Eulerian codes like N3S-EF, N3S-NATUR, ESTET. The trajectory of each droplet is calculated on unstructured grids or structured grids according the Eulerian code with SYRLIC is coupled. The forces applied to each particle are recalculated along each path. The Lagrangian approach treats the convection and the source terms exactly. It is particularly adapted to problems involving a wide range of particles characteristics (diameter, mass, etc). In the near future, wall interaction, heat transfer, evaporation more complex physics, etc, will be included. Turbulent effects will be accounted for by a Langevin equation. The illustration shows the trajectories followed by water droplets (diameter from 1 mm to 4 mm) in a cooling tower. the droplets are falling down due to gravity but are deflected towards the center of the tower because of a lateral wind. It is clear that particles are affected differently according their diameter. The Eulerian flow field used to compute the forces has been generated by N3S-AERO, on an unstructured mesh

Parallel processing of Monte Carlo code MCNP for particle transport problem

Energy Technology Data Exchange (ETDEWEB)

Higuchi, Kenji; Kawasaki, Takuji

1996-06-01

It is possible to vectorize or parallelize Monte Carlo codes (MC code) for photon and neutron transport problem, making use of independency of the calculation for each particle. Applicability of existing MC code to parallel processing is mentioned. As for parallel computer, we have used both vector-parallel processor and scalar-parallel processor in performance evaluation. We have made (i) vector-parallel processing of MCNP code on Monte Carlo machine Monte-4 with four vector processors, (ii) parallel processing on Paragon XP/S with 256 processors. In this report we describe the methodology and results for parallel processing on two types of parallel or distributed memory computers. In addition, we mention the evaluation of parallel programming environments for parallel computers used in the present work as a part of the work developing STA (Seamless Thinking Aid) Basic Software. (author)

CASINO, a code for simulation of charged particles in an axisymmetric Tokamak

International Nuclear Information System (INIS)

Dillner, Oe.

1992-01-01

The present report comprises a documentation of CASINO, a simulation code developed as a means for the study of high energy charged particles in an axisymmetric Tokamak. The background of the need for such a numerical tool is presented. In the description of the numerical model used for the orbit integration, the method using constants of motion, the Lao-Hirsman geometry for the flux surfaces and a method for reducing the necessary number of particles is elucidated. A brief outline of the calculational sequence is given as a flow chart. The essential routines and functions as well as the common blocks are briefly described. The input and output routines are shown. Finally the documentation is completed by a short discussion of possible extensions of the code and a test case. (au)

R-Matrix Codes for Charged-particle Induced Reactionsin the Resolved Resonance Region

Energy Technology Data Exchange (ETDEWEB)

Leeb, Helmut [Technical Univ. of Wien, Vienna (Austria); Dimitriou, Paraskevi [Intl Atomic Energy Agency (IAEA), Vienna (Austria); Thompson, Ian J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-01-01

A Consultant’s Meeting was held at the IAEA Headquarters, from 5 to 7 December 2016, to discuss the status of R-matrix codes currently used in calculations of charged-particle induced reaction cross sections at low energies. The meeting was a follow-up to the R-matrix Codes meeting held in December 2015, and served the purpose of monitoring progress in: the development of a translation code to enable exchange of input/output parameters between the various codes in different formats, fitting procedures and treatment of uncertainties, the evaluation methodology, and finally dissemination. The details of the presentations and technical discussions, as well as additional actions that were proposed to achieve all the goals of the meeting are summarized in this report.

Development of CAD-Based Geometry Processing Module for a Monte Carlo Particle Transport Analysis Code

International Nuclear Information System (INIS)

Choi, Sung Hoon; Kwark, Min Su; Shim, Hyung Jin

2012-01-01

As The Monte Carlo (MC) particle transport analysis for a complex system such as research reactor, accelerator, and fusion facility may require accurate modeling of the complicated geometry. Its manual modeling by using the text interface of a MC code to define the geometrical objects is tedious, lengthy and error-prone. This problem can be overcome by taking advantage of modeling capability of the computer aided design (CAD) system. There have been two kinds of approaches to develop MC code systems utilizing the CAD data: the external format conversion and the CAD kernel imbedded MC simulation. The first approach includes several interfacing programs such as McCAD, MCAM, GEOMIT etc. which were developed to automatically convert the CAD data into the MCNP geometry input data. This approach makes the most of the existing MC codes without any modifications, but implies latent data inconsistency due to the difference of the geometry modeling system. In the second approach, a MC code utilizes the CAD data for the direct particle tracking or the conversion to an internal data structure of the constructive solid geometry (CSG) and/or boundary representation (B-rep) modeling with help of a CAD kernel. MCNP-BRL and OiNC have demonstrated their capabilities of the CAD-based MC simulations. Recently we have developed a CAD-based geometry processing module for the MC particle simulation by using the OpenCASCADE (OCC) library. In the developed module, CAD data can be used for the particle tracking through primitive CAD surfaces (hereafter the CAD-based tracking) or the internal conversion to the CSG data structure. In this paper, the performances of the text-based model, the CAD-based tracking, and the internal CSG conversion are compared by using an in-house MC code, McSIM, equipped with the developed CAD-based geometry processing module

Los Alamos neutral particle transport codes: New and enhanced capabilities

International Nuclear Information System (INIS)

Alcouffe, R.E.; Baker, R.S.; Brinkley, F.W.; Clark, B.A.; Koch, K.R.; Marr, D.R.

1992-01-01

We present new developments in Los Alamos discrete-ordinates transport codes and introduce THREEDANT, the latest in the series of Los Alamos discrete ordinates transport codes. THREEDANT solves the multigroup, neutral-particle transport equation in X-Y-Z and R-Θ-Z geometries. THREEDANT uses computationally efficient algorithms: Diffusion Synthetic Acceleration (DSA) is used to accelerate the convergence of transport iterations, the DSA solution is accelerated using the multigrid technique. THREEDANT runs on a wide range of computers, from scientific workstations to CRAY supercomputers. The algorithms are highly vectorized on CRAY computers. Recently, the THREEDANT transport algorithm was implemented on the massively parallel CM-2 computer, with performance that is comparable to a single-processor CRAY-YMP We present the results of THREEDANT analysis of test problems

Verification and Validation of Monte Carlo n-Particle Code 6 (MCNP6) with Neutron Protection Factor Measurements of an Iron Box

Science.gov (United States)

2014-03-27

Vehicle Code System (VCS), the Monte Carlo Adjoint SHielding (MASH), and the Monte Carlo n- Particle ( MCNP ) code. Of the three, the oldest and still most...widely utilized radiation transport code is MCNP . First created at Los Alamos National Laboratory (LANL) in 1957, the code simulated neutral...particle types, and previous versions of MCNP were repeatedly validated using both simple and complex 10 geometries [12, 13]. Much greater discussion and

Monte Carlo method implemented in a finite element code with application to dynamic vacuum in particle accelerators

CERN Document Server

Garion, C

2009-01-01

Modern particle accelerators require UHV conditions during their operation. In the accelerating cavities, breakdowns can occur, releasing large amount of gas into the vacuum chamber. To determine the pressure profile along the cavity as a function of time, the time-dependent behaviour of the gas has to be simulated. To do that, it is useful to apply accurate three-dimensional method, such as Test Particles Monte Carlo. In this paper, a time-dependent Test Particles Monte Carlo is used. It has been implemented in a Finite Element code, CASTEM. The principle is to track a sample of molecules during time. The complex geometry of the cavities can be created either in the FE code or in a CAD software (CATIA in our case). The interface between the two softwares to export the geometry from CATIA to CASTEM is given. The algorithm of particle tracking for collisionless flow in the FE code is shown. Thermal outgassing, pumping surfaces and electron and/or ion stimulated desorption can all be generated as well as differ...

The use of electromagnetic particle-in-cell codes in accelerator applications

International Nuclear Information System (INIS)

Eppley, K.

1988-12-01

The techniques developed for the numerical simulation of plasmas have numerous applications relevant to accelerators. The operation of many accelerator components involves transients, interactions between beams and rf fields, and internal plasma oscillations. These effects produce non-linear behavior which can be represented accurately by particle in cell (PIC) simulations. We will give a very brief overview of the algorithms used in PIC Codes. We will examine the range of parameters over which they are useful. We will discuss the factors which determine whether a two or three dimensional simulation is most appropriate. PIC codes have been applied to a wide variety of diverse problems, spanning many of the systems in a linear accelerator. We will present a number of practical examples of the application of these codes to areas such as guns, bunchers, rf sources, beam transport, emittance growth and final focus. 8 refs., 8 figs., 2 tabs

Algorithm for Wave-Particle Resonances in Fluid Codes - Final Report

CERN Document Server

Mattor, N

2000-01-01

We review the work performed under LDRD ER grant 98-ERD-099. The goal of this work is to write a subroutine for a fluid turbulence code that allows it to incorporate wave-particle resonances (WPR). WPR historically have required a kinetic code, with extra dimensions needed to evolve the phase space distribution function, f(x, v, t). The main results accomplished under this grant have been: (1) Derivation of a nonlinear closure term for 1D electrostatic collisionless fluid; (2) Writing of a 1D electrostatic fluid code, ''es1f,'' with a subroutine to calculate the aforementioned closure term; (3) derivation of several methods to calculate the closure term, including Eulerian, Euler-local, fully local, linearized, and linearized zero-phase-velocity, and implementation of these in es1f; (4) Successful modeling of the Landau damping of an arbitrary Langmuir wave; (5) Successful description of a kinetic two-stream instability up to the point of the first bounce; and (6) a spin-off project which uses a mathematical ...

Two- and three-dimensional magnetoinductive particle codes with guiding center electron motion

International Nuclear Information System (INIS)

Geary, J.L.; Tajima, T.; Leboeuf, J.N.; Zaidman, E.G.; Han, J.H.

1986-07-01

A magnetoinductive (Darwin) particle simulation model developed for examining low frequency plasma behavior with large time steps is presented. Electron motion perpendicular to the magnetic field is treated as massless keeping only the guiding center motion. Electron motion parallel to the magnetic field retains full inertial effects as does the ion motion. This model has been implemented in two and three dimensions. Computational tests of the equilibrium properties of the code are compared with linear theory and the fluctuation dissipation theorem. This code has been applied to the problems of Alfven wave resonance heating and twist-kink modes

PRIAM: A self consistent finite element code for particle simulation in electromagnetic fields

International Nuclear Information System (INIS)

Le Meur, G.; Touze, F.

1990-06-01

A 2 1/2 dimensional, relativistic particle simulation code is described. A short review of the used mixed finite element method is given. The treatment of the driving terms (charge and current densities), initial, boundary conditions are exposed. Graphical results are shown

Particle-in-cell/accelerator code for space-charge dominated beam simulation

Energy Technology Data Exchange (ETDEWEB)

2012-05-08

Warp is a multidimensional discrete-particle beam simulation program designed to be applicable where the beam space-charge is non-negligible or dominant. It is being developed in a collaboration among LLNL, LBNL and the University of Maryland. It was originally designed and optimized for heave ion fusion accelerator physics studies, but has received use in a broader range of applications, including for example laser wakefield accelerators, e-cloud studies in high enery accelerators, particle traps and other areas. At present it incorporates 3-D, axisymmetric (r,z) planar (x-z) and transverse slice (x,y) descriptions, with both electrostatic and electro-magnetic fields, and a beam envelope model. The code is guilt atop the Python interpreter language.

Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators

International Nuclear Information System (INIS)

Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.

1999-01-01

In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design

Algorithm for Wave-Particle Resonances in Fluid Codes - Final Report

International Nuclear Information System (INIS)

Mattor, N.

2000-01-01

We review the work performed under LDRD ER grant 98-ERD-099. The goal of this work is to write a subroutine for a fluid turbulence code that allows it to incorporate wave-particle resonances (WPR). WPR historically have required a kinetic code, with extra dimensions needed to evolve the phase space distribution function, f(x, v, t). The main results accomplished under this grant have been: (1) Derivation of a nonlinear closure term for 1D electrostatic collisionless fluid; (2) Writing of a 1D electrostatic fluid code, ''es1f,'' with a subroutine to calculate the aforementioned closure term; (3) derivation of several methods to calculate the closure term, including Eulerian, Euler-local, fully local, linearized, and linearized zero-phase-velocity, and implementation of these in es1f; (4) Successful modeling of the Landau damping of an arbitrary Langmuir wave; (5) Successful description of a kinetic two-stream instability up to the point of the first bounce; and (6) a spin-off project which uses a mathematical technique developed for the closure, known as the Phase Velocity Transform (PVT) to decompose turbulent fluctuations

VINE-A NUMERICAL CODE FOR SIMULATING ASTROPHYSICAL SYSTEMS USING PARTICLES. II. IMPLEMENTATION AND PERFORMANCE CHARACTERISTICS

International Nuclear Information System (INIS)

Nelson, Andrew F.; Wetzstein, M.; Naab, T.

2009-01-01

We continue our presentation of VINE. In this paper, we begin with a description of relevant architectural properties of the serial and shared memory parallel computers on which VINE is intended to run, and describe their influences on the design of the code itself. We continue with a detailed description of a number of optimizations made to the layout of the particle data in memory and to our implementation of a binary tree used to access that data for use in gravitational force calculations and searches for smoothed particle hydrodynamics (SPH) neighbor particles. We describe the modifications to the code necessary to obtain forces efficiently from special purpose 'GRAPE' hardware, the interfaces required to allow transparent substitution of those forces in the code instead of those obtained from the tree, and the modifications necessary to use both tree and GRAPE together as a fused GRAPE/tree combination. We conclude with an extensive series of performance tests, which demonstrate that the code can be run efficiently and without modification in serial on small workstations or in parallel using the OpenMP compiler directives on large-scale, shared memory parallel machines. We analyze the effects of the code optimizations and estimate that they improve its overall performance by more than an order of magnitude over that obtained by many other tree codes. Scaled parallel performance of the gravity and SPH calculations, together the most costly components of most simulations, is nearly linear up to at least 120 processors on moderate sized test problems using the Origin 3000 architecture, and to the maximum machine sizes available to us on several other architectures. At similar accuracy, performance of VINE, used in GRAPE-tree mode, is approximately a factor 2 slower than that of VINE, used in host-only mode. Further optimizations of the GRAPE/host communications could improve the speed by as much as a factor of 3, but have not yet been implemented in VINE

Solutions to HYDROCOIN [Hydrologic Code Intercomparison] Level 1 problems using STOKES and PARTICLE (Cases 1,2,4,7)

International Nuclear Information System (INIS)

Gureghian, A.B.; Andrews, A.; Steidl, S.B.; Brandstetter, A.

1987-10-01

HYDROCOIN (Hydrologic Code Intercomparison) Level 1 benchmark problems are solved using the finite element ground-water flow code STOKES and the pathline generating code PARTICLE developed for the Office of Crystalline Repository Development (OCRD). The objective of the Level 1 benchmark problems is to verify the numerical accuracy of ground-water flow codes by intercomparison of their results with analytical solutions and other numerical computer codes. Seven test cases were proposed for Level 1 to the Swedish Nuclear Power Inspectorate, the managing participant of HYDROCOIN. Cases 1, 2, 4, and 7 were selected by OCRD because of their appropriateness to the nature of crystalline repository hydrologic performance. The background relevance, conceptual model, and assumptions of each case are presented. The governing equations, boundary conditions, input parameters, and the solution schemes applied to each case are discussed. The results are shown in graphic and tabular form with concluding remarks. The results demonstrate the two-dimensional verification of STOKES and PARTICLE. 5 refs., 61 figs., 30 tabs

Particle and heavy ion transport code system, PHITS, version 2.52

International Nuclear Information System (INIS)

Sato, Tatsuhiko; Matsuda, Norihiro; Hashimoto, Shintaro; Iwamoto, Yosuke; Noda, Shusaku; Ogawa, Tatsuhiko; Nakashima, Hiroshi; Fukahori, Tokio; Okumura, Keisuke; Kai, Tetsuya; Niita, Koji; Iwase, Hiroshi; Chiba, Satoshi; Furuta, Takuya; Sihver, Lembit

2013-01-01

An upgraded version of the Particle and Heavy Ion Transport code System, PHITS2.52, was developed and released to the public. The new version has been greatly improved from the previously released version, PHITS2.24, in terms of not only the code itself but also the contents of its package, such as the attached data libraries. In the new version, a higher accuracy of simulation was achieved by implementing several latest nuclear reaction models. The reliability of the simulation was improved by modifying both the algorithms for the electron-, positron-, and photon-transport simulations and the procedure for calculating the statistical uncertainties of the tally results. Estimation of the time evolution of radioactivity became feasible by incorporating the activation calculation program DCHAIN-SP into the new package. The efficiency of the simulation was also improved as a result of the implementation of shared-memory parallelization and the optimization of several time-consuming algorithms. Furthermore, a number of new user-support tools and functions that help users to intuitively and effectively perform PHITS simulations were developed and incorporated. Due to these improvements, PHITS is now a more powerful tool for particle transport simulation applicable to various research and development fields, such as nuclear technology, accelerator design, medical physics, and cosmic-ray research. (author)

SHARP: A Spatially Higher-order, Relativistic Particle-in-cell Code

Energy Technology Data Exchange (ETDEWEB)

Shalaby, Mohamad; Broderick, Avery E. [Department of Physics and Astronomy, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); Chang, Philip [Department of Physics, University of Wisconsin-Milwaukee, 1900 E. Kenwood Boulevard, Milwaukee, WI 53211 (United States); Pfrommer, Christoph [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany); Lamberts, Astrid [Theoretical Astrophysics, California Institute of Technology, Pasadena, CA 91125 (United States); Puchwein, Ewald, E-mail: mshalaby@live.ca [Institute of Astronomy and Kavli Institute for Cosmology, University of Cambridge, Madingley Road, Cambridge, CB3 0HA (United Kingdom)

2017-05-20

Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher-order accurate relativistic PIC algorithm in one spatial dimension, which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher-order interpolation functions to achieve a spatially higher-order accurate algorithm (up to the fifth order). We validate our algorithm against several test problems—thermal stability of stationary plasma, stability of linear plasma waves, and two-stream instability in the relativistic and non-relativistic regimes. Comparing our simulations to exact solutions of the dispersion relations, we demonstrate that SHARP can quantitatively reproduce important kinetic features of the linear regime. Our simulations have a superior ability to control energy non-conservation and avoid numerical heating in comparison to common second-order schemes. We provide a natural definition for convergence of a general PIC algorithm: the complement of physical modes captured by the simulation, i.e., those that lie above the Poisson noise, must grow commensurately with the resolution. This implies that it is necessary to simultaneously increase the number of particles per cell and decrease the cell size. We demonstrate that traditional ways for testing for convergence fail, leading to plateauing of the energy error. This new PIC code enables us to faithfully study the long-term evolution of plasma problems that require absolute control of the energy and momentum conservation.

Implementation of a 3D plasma particle-in-cell code on a MIMD parallel computer

International Nuclear Information System (INIS)

Liewer, P.C.; Lyster, P.; Wang, J.

1993-01-01

A three-dimensional plasma particle-in-cell (PIC) code has been implemented on the Intel Delta MIMD parallel supercomputer using the General Concurrent PIC algorithm. The GCPIC algorithm uses a domain decomposition to divide the computation among the processors: A processor is assigned a subdomain and all the particles in it. Particles must be exchanged between processors as they move. Results are presented comparing the efficiency for 1-, 2- and 3-dimensional partitions of the three dimensional domain. This algorithm has been found to be very efficient even when a large fraction (e.g. 30%) of the particles must be exchanged at every time step. On the 512-node Intel Delta, up to 125 million particles have been pushed with an electrostatic push time of under 500 nsec/particle/time step

Application of a Java-based, univel geometry, neutral particle Monte Carlo code to the searchlight problem

International Nuclear Information System (INIS)

Charles A. Wemple; Joshua J. Cogliati

2005-01-01

A univel geometry, neutral particle Monte Carlo transport code, written entirely in the Java programming language, is under development for medical radiotherapy applications. The code uses ENDF-VI based continuous energy cross section data in a flexible XML format. Full neutron-photon coupling, including detailed photon production and photonuclear reactions, is included. Charged particle equilibrium is assumed within the patient model so that detailed transport of electrons produced by photon interactions may be neglected. External beam and internal distributed source descriptions for mixed neutron-photon sources are allowed. Flux and dose tallies are performed on a univel basis. A four-tap, shift-register-sequence random number generator is used. Initial verification and validation testing of the basic neutron transport routines is underway. The searchlight problem was chosen as a suitable first application because of the simplicity of the physical model. Results show excellent agreement with analytic solutions. Computation times for similar numbers of histories are comparable to other neutron MC codes written in C and FORTRAN

The three-dimensional, discrete ordinates neutral particle transport code TORT: An overview

International Nuclear Information System (INIS)

Azmy, Y.Y.

1996-01-01

The centerpiece of the Discrete Ordinates Oak Ridge System (DOORS), the three-dimensional neutral particle transport code TORT is reviewed. Its most prominent features pertaining to large applications, such as adjustable problem parameters, memory management, and coarse mesh methods, are described. Advanced, state-of-the-art capabilities including acceleration and multiprocessing are summarized here. Future enhancement of existing graphics and visualization tools is briefly presented

Random geometry capability in RMC code for explicit analysis of polytype particle/pebble and applications to HTR-10 benchmark

International Nuclear Information System (INIS)

Liu, Shichang; Li, Zeguang; Wang, Kan; Cheng, Quan; She, Ding

2018-01-01

Highlights: •A new random geometry was developed in RMC for mixed and polytype particle/pebble. •This capability was applied to the full core calculations of HTR-10 benchmark. •Reactivity, temperature coefficient and control rod worth of HTR-10 were compared. •This method can explicitly model different packing fraction of different pebbles. •Monte Carlo code with this method can simulate polytype particle/pebble type reactor. -- Abstract: With the increasing demands of high fidelity neutronics analysis and the development of computer technology, Monte Carlo method is becoming more and more attractive in accurate simulation of pebble bed High Temperature gas-cooled Reactor (HTR), owing to its advantages of the flexible geometry modeling and the use of continuous-energy nuclear cross sections. For the double-heterogeneous geometry of pebble bed, traditional Monte Carlo codes can treat it by explicit geometry description. However, packing methods such as Random Sequential Addition (RSA) can only produce a sphere packing up to 38% volume packing fraction, while Discrete Element Method (DEM) is troublesome and also time consuming. Moreover, traditional Monte Carlo codes are difficult and inconvenient to simulate the mixed and polytype particles or pebbles. A new random geometry method was developed in Monte Carlo code RMC to simulate the particle transport in polytype particle/pebble in double heterogeneous geometry systems. This method was verified by some test cases, and applied to the full core calculations of HTR-10 benchmark. The reactivity, temperature coefficient and control rod worth of HTR-10 were compared for full core and initial core in helium and air atmosphere respectively, and the results agree well with the benchmark results and experimental results. This work would provide an efficient tool for the innovative design of pebble bed, prism HTRs and molten salt reactors with polytype particles or pebbles using Monte Carlo method.

PyMercury: Interactive Python for the Mercury Monte Carlo Particle Transport Code

International Nuclear Information System (INIS)

Iandola, F.N.; O'Brien, M.J.; Procassini, R.J.

2010-01-01

Monte Carlo particle transport applications are often written in low-level languages (C/C++) for optimal performance on clusters and supercomputers. However, this development approach often sacrifices straightforward usability and testing in the interest of fast application performance. To improve usability, some high-performance computing applications employ mixed-language programming with high-level and low-level languages. In this study, we consider the benefits of incorporating an interactive Python interface into a Monte Carlo application. With PyMercury, a new Python extension to the Mercury general-purpose Monte Carlo particle transport code, we improve application usability without diminishing performance. In two case studies, we illustrate how PyMercury improves usability and simplifies testing and validation in a Monte Carlo application. In short, PyMercury demonstrates the value of interactive Python for Monte Carlo particle transport applications. In the future, we expect interactive Python to play an increasingly significant role in Monte Carlo usage and testing.

Energetic particle physics with applications in fusion and space plasmas

International Nuclear Information System (INIS)

Cheng, C.Z.

1997-01-01

Energetic particle physics is the study of the effects of energetic particles on collective electromagnetic (EM) instabilities and energetic particle transport in plasmas. Anomalously large energetic particle transport is often caused by low frequency MHD instabilities, which are driven by these energetic particles in the presence of a much denser background of thermal particles. The theory of collective energetic particle phenomena studies complex wave-particle interactions in which particle kinetic physics involving small spatial and fast temporal scales can strongly affect the MHD structure and long-time behavior of plasmas. The difficulty of modeling kinetic-MHD multiscale coupling processes stems from the disparate scales which are traditionally analyzed separately: the macroscale MHD phenomena are studied using the fluid MHD framework, while microscale kinetic phenomena are best described by complicated kinetic theories. The authors have developed a kinetic-MHD model that properly incorporates major particle kinetic effects into the MHD fluid description. For tokamak plasmas a nonvariational kinetic-MHD stability code, the NOVA-K code, has been successfully developed and applied to study problems such as the excitation of fishbone and Toroidal Alfven Eigenmodes (TAE) and the sawtooth stabilization by energetic ions in tokamaks. In space plasmas the authors have employed the kinetic-MHD model to study the energetic particle effects on the ballooning-mirror instability which explains the multisatellite observation of the stability and field-aligned structure of compressional Pc 5 waves in the magnetospheric ring current plasma

DCHAIN-SP 2001: High energy particle induced radioactivity calculation code

Energy Technology Data Exchange (ETDEWEB)

Kai, Tetsuya; Maekawa, Fujio; Kasugai, Yoshimi; Takada, Hiroshi; Ikeda, Yujiro [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kosako, Kazuaki [Sumitomo Atomic Energy Industries, Ltd., Tokyo (Japan)

2001-03-01

For the purpose of contribution to safety design calculations for induced radioactivities in the JAERI/KEK high-intensity proton accelerator project facilities, the DCHAIN-SP which calculates the high energy particle induced radioactivity has been updated to DCHAIN-SP 2001. The following three items were improved: (1) Fission yield data are included to apply the code to experimental facility design for nuclear transmutation of long-lived radioactive waste where fissionable materials are treated. (2) Activation cross section data below 20 MeV are revised. In particular, attentions are paid to cross section data of materials which have close relation to the facilities, i.e., mercury, lead and bismuth, and to tritium production cross sections which are important in terms of safety of the facilities. (3) User-interface for input/output data is sophisticated to perform calculations more efficiently than that in the previous version. Information needed for use of the code is attached in Appendices; the DCHAIN-SP 2001 manual, the procedures of installation and execution of DCHAIN-SP, and sample problems. (author)

SPACE CHARGE SIMULATION METHODS INCORPORATED IN SOME MULTI - PARTICLE TRACKING CODES AND THEIR RESULTS COMPARISON

International Nuclear Information System (INIS)

BEEBE - WANG, J.; LUCCIO, A.U.; D IMPERIO, N.; MACHIDA, S.

2002-01-01

Space charge in high intensity beams is an important issue in accelerator physics. Due to the complicity of the problems, the most effective way of investigating its effect is by computer simulations. In the resent years, many space charge simulation methods have been developed and incorporated in various 2D or 3D multi-particle-tracking codes. It has becoming necessary to benchmark these methods against each other, and against experimental results. As a part of global effort, we present our initial comparison of the space charge methods incorporated in simulation codes ORBIT++, ORBIT and SIMPSONS. In this paper, the methods included in these codes are overviewed. The simulation results are presented and compared. Finally, from this study, the advantages and disadvantages of each method are discussed

SPACE CHARGE SIMULATION METHODS INCORPORATED IN SOME MULTI - PARTICLE TRACKING CODES AND THEIR RESULTS COMPARISON.

Energy Technology Data Exchange (ETDEWEB)

BEEBE - WANG,J.; LUCCIO,A.U.; D IMPERIO,N.; MACHIDA,S.

2002-06-03

Space charge in high intensity beams is an important issue in accelerator physics. Due to the complicity of the problems, the most effective way of investigating its effect is by computer simulations. In the resent years, many space charge simulation methods have been developed and incorporated in various 2D or 3D multi-particle-tracking codes. It has becoming necessary to benchmark these methods against each other, and against experimental results. As a part of global effort, we present our initial comparison of the space charge methods incorporated in simulation codes ORBIT++, ORBIT and SIMPSONS. In this paper, the methods included in these codes are overviewed. The simulation results are presented and compared. Finally, from this study, the advantages and disadvantages of each method are discussed.

The CNCSN-2: One, two-and three-dimensional coupled neutral and charged particle discrete ordinates code system

International Nuclear Information System (INIS)

Voloschenko, A. M.; Gukov, S. V.; Russkov, A. A.; Gurevich, M. I.; Shkarovsky, D. A.; Kryuchkov, V. P.; Sumaneev, O. V.; Dubinin, A. A.

2009-01-01

KATRIN, KASKAD-Sand ROZ-6 codes solve the multigroup transport equation for neutrons, photons and charged particles in 3D. BOT3P-5., ConDat can be used as preprocessor. ARVES-2.5, a cross-section preprocessor (the package of utilities for operating with the cross section file in FMAC-M format) is included. Auxiliary codes MIXERM, CEPXS-BFP, CEPXS-BFP, SADCO-2.4 and CNCSN-2 are used

GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM.

Science.gov (United States)

Hauer, Florian; Gerle, Christoph; Fischer, Niels; Oshima, Atsunori; Shinzawa-Itoh, Kyoko; Shimada, Satoru; Yokoyama, Ken; Fujiyoshi, Yoshinori; Stark, Holger

2015-09-01

We developed a method, named GraDeR, which substantially improves the preparation of membrane protein complexes for structure determination by single-particle cryo-electron microscopy (cryo-EM). In GraDeR, glycerol gradient centrifugation is used for the mild removal of free detergent monomers and micelles from lauryl maltose-neopentyl glycol detergent stabilized membrane complexes, resulting in monodisperse and stable complexes to which standard processes for water-soluble complexes can be applied. We demonstrate the applicability of the method on three different membrane complexes, including the mammalian FoF1 ATP synthase. For this highly dynamic and fragile rotary motor, we show that GraDeR allows visualizing the asymmetry of the F1 domain, which matches the ground state structure of the isolated domain. Therefore, the present cryo-EM structure of FoF1 ATP synthase provides direct structural evidence for Boyer's binding change mechanism in the context of the intact enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines

International Nuclear Information System (INIS)

Batygin, Y.

2004-01-01

A code library BEAMPATH for 2 - dimensional and 3 - dimensional space charge dominated beam dynamics study in linear particle accelerators and beam transport lines is developed. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids and bending magnets. The programming method includes hierarchical program design using program-independent modules and a flexible combination of modules to provide the most effective version of the structure for every specific case of simulation. Numerical techniques as well as the results of beam dynamics studies are presented

Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines

Energy Technology Data Exchange (ETDEWEB)

Batygin, Y.

2004-10-28

A code library BEAMPATH for 2 - dimensional and 3 - dimensional space charge dominated beam dynamics study in linear particle accelerators and beam transport lines is developed. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids and bending magnets. The programming method includes hierarchical program design using program-independent modules and a flexible combination of modules to provide the most effective version of the structure for every specific case of simulation. Numerical techniques as well as the results of beam dynamics studies are presented.

Coding in Muscle Disease.

Science.gov (United States)

Jones, Lyell K; Ney, John P

2016-12-01

Accurate coding is critically important for clinical practice and research. Ongoing changes to diagnostic and billing codes require the clinician to stay abreast of coding updates. Payment for health care services, data sets for health services research, and reporting for medical quality improvement all require accurate administrative coding. This article provides an overview of administrative coding for patients with muscle disease and includes a case-based review of diagnostic and Evaluation and Management (E/M) coding principles in patients with myopathy. Procedural coding for electrodiagnostic studies and neuromuscular ultrasound is also reviewed.

SSCTRK: A particle tracking code for the SSC

International Nuclear Information System (INIS)

Ritson, D.

1990-07-01

While many indirect methods are available to evaluate dynamic aperture there appears at this time to be no reliable substitute to tracking particles through realistic machine lattices for a number of turns determined by the storage times. Machine lattices are generated by ''Monte Carlo'' techniques from the expected rms fabrication and survey errors. Any given generated machine can potentially be a lucky or unlucky fluctuation from the average. Therefore simulation to serve as a predictor of future performance must be done for an ensemble of generated machines. Further, several amplitudes and momenta are necessary to predict machine performance. Thus to make Monte Carlo type simulations for the SSC requires very considerable computer resources. Hitherto, it has been assumed that this was not feasible, and alternative indirect methods have been proposed or tried to answer the problem. We reexamined the feasibility of using direct computation. Previous codes have represented lattices by a succession of thin elements separated by bend-drifts. With ''kick-drift'' configurations, tracking time is linear in the multipole order included, and the code is symplectic. Modern vector processors simultaneously handle a large number of cases in parallel. Combining the efficiencies of kick drift tracking with vector processing, in fact, makes realistic Monte Carlo simulation entirely feasible. SSCTRK uses the above features. It is structured to have a very friendly interface, a very wide latitude of choice for cases to be run in parallel, and, by using pure FORTRAN 77, to interchangeably run on a wide variety of computers. We describe in this paper the program structure operational checks and results achieved

Solution of charged particle transport equation by Monte-Carlo method in the BRANDZ code system

International Nuclear Information System (INIS)

Artamonov, S.N.; Androsenko, P.A.; Androsenko, A.A.

1992-01-01

Consideration is given to the issues of Monte-Carlo employment for the solution of charged particle transport equation and its implementation in the BRANDZ code system under the conditions of real 3D geometry and all the data available on radiation-to-matter interaction in multicomponent and multilayer targets. For the solution of implantation problem the results of BRANDZ data comparison with the experiments and calculations by other codes in complexes systems are presented. The results of direct nuclear pumping process simulation for laser-active media by a proton beam are also included. 4 refs.; 7 figs

TIERCE: A code system for particles and radiation transport in thick targets

Energy Technology Data Exchange (ETDEWEB)

Bersillon, O.; Bauge, E.; Borne, F.; Clergeau, J.F.; Collin, M.; Cotten, D.; Delaroche, J.P.; Duarte, H.; Flament, J.L.; Girod, M.; Gosselin, G.; Granier, T.; Hilaire, S.; Morel, P.; Perrier, R.; Romain, P.; Roux, L. [CEA, Bruyeres-le-Chatel (France). Service de Physique Nucleaire

1997-09-01

Over the last few years, a great effort at Bruyeres-le-Chatel has been the development of the TIERCE code system for the transport of particles and radiations in complex geometry. The comparison of calculated results with experimental data, either microscopic (double differential spectra, residual nuclide yield...) or macroscopic (energy deposition, neutron leakage...), shows the need to improve the nuclear reaction models used. We present some new developments concerning data required for the evaporation model in the framework of a microscopic approach. 22 refs., 6 figs.

Progress on the Development of the hPIC Particle-in-Cell Code

Science.gov (United States)

Dart, Cameron; Hayes, Alyssa; Khaziev, Rinat; Marcinko, Stephen; Curreli, Davide; Laboratory of Computational Plasma Physics Team

2017-10-01

Advancements were made in the development of the kinetic-kinetic electrostatic Particle-in-Cell code, hPIC, designed for large-scale simulation of the Plasma-Material Interface. hPIC achieved a weak scaling efficiency of 87% using the Algebraic Multigrid Solver BoomerAMG from the PETSc library on more than 64,000 cores of the Blue Waters supercomputer at the University of Illinois at Urbana-Champaign. The code successfully simulates two-stream instability and a volume of plasma over several square centimeters of surface extending out to the presheath in kinetic-kinetic mode. Results from a parametric study of the plasma sheath in strongly magnetized conditions will be presented, as well as a detailed analysis of the plasma sheath structure at grazing magnetic angles. The distribution function and its moments will be reported for plasma species in the simulation domain and at the material surface for plasma sheath simulations. Membership Pending.

Ordered particles versus ordered pointers in the hybrid ordered plasma simulation (HOPS) code

International Nuclear Information System (INIS)

Anderson, D.V.; Shumaker, D.E.

1993-01-01

From a computational standpoint, particle simulation calculations for plasmas have not adapted well to the transitions from scalar to vector processing nor from serial to parallel environments. They have suffered from inordinate and excessive accessing of computer memory and have been hobbled by relatively inefficient gather-scatter constructs resulting from the use of indirect indexing. Lastly, the many-to-one mapping characteristic of the deposition phase has made it difficult to perform this in parallel. The authors' code sorts and reorders the particles in a spatial order. This allows them to greatly reduce the memory references, to run in directly indexed vector mode, and to employ domain decomposition to achieve parallelization. The field model solves pre-maxwell equations by interatively implicit methods. The OSOP (Ordered Storage Ordered Processing) version of HOPS keeps the particle tables ordered by rebuilding them after each particle pushing phase. Alternatively, the RSOP (Random Storage Ordered Processing) version keeps a table of pointers ordered by rebuilding them. Although OSOP is somewhat faster than RSOP in tests on vector-parallel machines, it is not clear this advantage will carry over to massively parallel computers

Modelling of a general purpose irradiation chamber using a Monte Carlo particle transport code

International Nuclear Information System (INIS)

Dhiyauddin Ahmad Fauzi; Sheik, F.O.A.; Nurul Fadzlin Hasbullah

2013-01-01

Full-text: The aim of this research is to stimulate the effectiveness use of a general purpose irradiation chamber to contain pure neutron particles obtained from a research reactor. The secondary neutron and gamma particles dose discharge from the chamber layers will be used as a platform to estimate the safe dimension of the chamber. The chamber, made up of layers of lead (Pb), shielding, polyethylene (PE), moderator and commercial grade aluminium (Al) cladding is proposed for the use of interacting samples with pure neutron particles in a nuclear reactor environment. The estimation was accomplished through simulation based on general Monte Carlo N-Particle transport code using Los Alamos MCNPX software. Simulations were performed on the model of the chamber subjected to high neutron flux radiation and its gamma radiation product. The model of neutron particle used is based on the neutron source found in PUSPATI TRIGA MARK II research reactor which holds a maximum flux value of 1 x 10 12 neutron/ cm 2 s. The expected outcomes of this research are zero gamma dose in the core of the chamber and neutron dose rate of less than 10 μSv/ day discharge from the chamber system. (author)

Development and Verification of Smoothed Particle Hydrodynamics Code for Analysis of Tsunami near NPP

Energy Technology Data Exchange (ETDEWEB)

Jo, Young Beom; Kim, Eung Soo [Seoul National Univ., Seoul (Korea, Republic of)

2014-10-15

It becomes more complicated when considering the shape and phase of the ground below the seawater. Therefore, some different attempts are required to precisely analyze the behavior of tsunami. This paper introduces an on-going activities on code development in SNU based on an unconventional mesh-free fluid analysis method called Smoothed Particle Hydrodynamics (SPH) and its verification work with some practice simulations. This paper summarizes the on-going development and verification activities on Lagrangian mesh-free SPH code in SNU. The newly developed code can cover equation of motions and heat conduction equation so far, and verification of each models is completed. In addition, parallel computation using GPU is now possible, and GUI is also prepared. If users change input geometry or input values, they can simulate for various conditions geometries. A SPH method has large advantages and potential in modeling of free surface, highly deformable geometry and multi-phase problems that traditional grid-based code has difficulties in analysis. Therefore, by incorporating more complex physical models such as turbulent flow, phase change, two-phase flow, and even solid mechanics, application of the current SPH code is expected to be much more extended including molten fuel behaviors in the sever accident.

First experience with particle-in-cell plasma physics code on ARM-based HPC systems

Science.gov (United States)

Sáez, Xavier; Soba, Alejandro; Sánchez, Edilberto; Mantsinen, Mervi; Mateo, Sergi; Cela, José M.; Castejón, Francisco

2015-09-01

In this work, we will explore the feasibility of porting a Particle-in-cell code (EUTERPE) to an ARM multi-core platform from the Mont-Blanc project. The used prototype is based on a system-on-chip Samsung Exynos 5 with an integrated GPU. It is the first prototype that could be used for High-Performance Computing (HPC), since it supports double precision and parallel programming languages.

Novel methods in the Particle-In-Cell accelerator Code-Framework Warp

Energy Technology Data Exchange (ETDEWEB)

Vay, J-L [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Grote, D. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Cohen, R. H. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Friedman, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2012-12-26

The Particle-In-Cell (PIC) Code-Framework Warp is being developed by the Heavy Ion Fusion Science Virtual National Laboratory (HIFS-VNL) to guide the development of accelerators that can deliver beams suitable for high-energy density experiments and implosion of inertial fusion capsules. It is also applied in various areas outside the Heavy Ion Fusion program to the study and design of existing and next-generation high-energy accelerators, including the study of electron cloud effects and laser wakefield acceleration for example. This study presents an overview of Warp's capabilities, summarizing recent original numerical methods that were developed by the HIFS-VNL (including PIC with adaptive mesh refinement, a large-timestep 'drift-Lorentz' mover for arbitrarily magnetized species, a relativistic Lorentz invariant leapfrog particle pusher, simulations in Lorentz-boosted frames, an electromagnetic solver with tunable numerical dispersion and efficient stride-based digital filtering), with special emphasis on the description of the mesh refinement capability. In addition, selected examples of the applications of the methods to the abovementioned fields are given.

How <em>Varroa> Parasitism Affects the Immunological and Nutritional Status of the Honey Bee, <em>Apis melliferaem>

Directory of Open Access Journals (Sweden)

Katherine A. Aronstein

2012-06-01

Full Text Available We investigated the effect of the parasitic mite <em>Varroa destructorem> on the immunological and nutritional condition of honey bees, <em>Apis melliferaem>, from the perspective of the individual bee and the colony. Pupae, newly-emerged adults and foraging adults were sampled from honey bee colonies at one site in S. Texas, USA. <em>Varroa>‑infested bees displayed elevated titer of Deformed Wing Virus (DWV, suggestive of depressed capacity to limit viral replication. Expression of genes coding three anti-microbial peptides (<em>defensin1, abaecin, hymenoptaecinem> was either not significantly different between <em>Varroa>-infested and uninfested bees or was significantly elevated in <em>Varroa>-infested bees, varying with sampling date and bee developmental age. The effect of <em>Varroa> on nutritional indices of the bees was complex, with protein, triglyceride, glycogen and sugar levels strongly influenced by life-stage of the bee and individual colony. Protein content was depressed and free amino acid content elevated in <em>Varroa>-infested pupae, suggesting that protein synthesis, and consequently growth, may be limited in these insects. No simple relationship between the values of nutritional and immune-related indices was observed, and colony-scale effects were indicated by the reduced weight of pupae in colonies with high <em>Varroa> abundance, irrespective of whether the individual pupa bore <em>Varroa>.

'ACTIV' - a package of codes for charged particle and neutron activation analysis

International Nuclear Information System (INIS)

Cincu, Em.; Alexandreanu, B.; Manu, V.; Moisa, V.

1997-01-01

The 'ACTIV' Program is an advanced software package dedicated to applications of the thermal neutron and charged particle activation (NAA and CPA) induced reactions. The program is designed to run on personal computers compatible IBM PC-Models XT/AT, 286 or more advanced, operating under DOS version 5.0 or later, on systems with minimum 5 MB of hard disk memory. The package consists of 6 software modules and a Nuclear Data Base comprising physical, nuclear reaction and decay data for: thermal neutron, proton, deuteron and α-particle induced reactions on 15 selected metallic elements; the nuclear reaction data corresponds to the energy range (5-100) MeV. In the first version - ACTIV 1.0 - the set of input data concerns: the sample type, irradiation and measurement conditions, the γ-ray spectrum identification code, selected detection efficiency calibration curve, selected radionuclides, selected standardization method for elemental analysis, version of results. At present, the 'ACTIV' package comprises 6 soft modules for processing the experimental data, which ensure computation of the quantities: radionuclide activities, activation yield data (case of CPA) and elemental concentration by relative and absolute standardization methods. Recently, the software designed to processing complex γ-ray spectra was acquired and installed on our PC 486 (8 MB RAM, 100 MHz). The next step in developing the 'ACTIV' program envisages improving the existing computing codes, completing the data libraries, incorporating a new soft for the direct use of the 'Quantum TM MCA' data, developing modules dedicated to uncertainty computation and optimization of the activation experiments

REX-ISOLDE RFQ Beam Dynamics Studies using CST EM Studio

CERN Document Server

Fraser, M A

2014-01-01

The original CNC milling files used to machine the electrodes of the REX-ISOLDE RFQ were acquired in late 2012 and electrostatic simulations were carried out using CST EM Studio in order to attain a 3D field map of the electric fields in the region around the beam axis. The objective was to construct a beam dynamics simulation tool that frees us from the constraints of the PARMTEQM code, which was used to design the RFQ, and that will afford us more flexibility in the studies needed for pre-bunching into the RFQ with an external multi-harmonic buncher. This note details the geometry of the electrodes and their simulation in CST EM Studio, the implementation of particle tracking in the computed field map using TRACK and benchmarking studies with PARMTEQM v3.09.

Mathematical model and computer code for coated particles performance at normal operating conditions

International Nuclear Information System (INIS)

Golubev, I.; Kadarmetov, I.; Makarov, V.

2002-01-01

Computer modeling of thermo-mechanical behavior of coated particles during operating both at normal and off-normal conditions has a very significant role particularly on a stage of new reactors development. In Russia a big experience has been accumulated on fabrication and reactor tests of CP and fuel elements with UO 2 kernels. However, this experience cannot be using in full volume for development of a new reactor installation GT-MHR. This is due to very deep burn-up of the fuel based on plutonium oxide (up to 70% fima). Therefore the mathematical modeling of CP thermal-mechanical behavior and failure prediction becomes particularly important. The authors have a clean understanding that serviceability of fuel with high burn-ups are defined not only by thermo-mechanics, but also by structured changes in coating materials, thermodynamics of chemical processes, 'amoeba-effect', formation CO etc. In the report the first steps of development of integrate code for numerical modeling of coated particles behavior and some calculating results concerning the influence of various design parameters on fuel coated particles endurance for GT-MHR normal operating conditions are submitted. A failure model is developed to predict the fraction of TRISO-coated particles. In this model it is assumed that the failure of CP depends not only on probability of SiC-layer fracture but also on the PyC-layers damage. The coated particle is considered as a uniform design. (author)

A parallel 3D particle-in-cell code with dynamic load balancing

International Nuclear Information System (INIS)

Wolfheimer, Felix; Gjonaj, Erion; Weiland, Thomas

2006-01-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated

A parallel 3D particle-in-cell code with dynamic load balancing

Energy Technology Data Exchange (ETDEWEB)

Wolfheimer, Felix [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)]. E-mail: wolfheimer@temf.de; Gjonaj, Erion [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany); Weiland, Thomas [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)

2006-03-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated.

SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

Energy Technology Data Exchange (ETDEWEB)

Luo, Yun

2015-11-21

SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam–beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam–beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam–beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this paper, I will present the code architecture, physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.

PIConGPU - How to build one of the fastest GPU particle-in-cell codes in the world

Energy Technology Data Exchange (ETDEWEB)

Burau, Heiko; Debus, Alexander; Helm, Anton; Huebl, Axel; Kluge, Thomas; Widera, Rene; Bussmann, Michael; Schramm, Ulrich; Cowan, Thomas [HZDR, Dresden (Germany); Juckeland, Guido; Nagel, Wolfgang [TU Dresden (Germany); ZIH, Dresden (Germany); Schmitt, Felix [NVIDIA (United States)

2013-07-01

We present the algorithmic building blocks of PIConGPU, one of the fastest implementations of the particle-in-cell algortihm on GPU clusters. PIConGPU is a highly-scalable, 3D3V electromagnetic PIC code that is used in laser plasma and astrophysical plasma simulations.

Study of neutral particle behavior and particle confinement in JT-60U

International Nuclear Information System (INIS)

Takenaga, Hidenobu; Shimizu, Katsuhiro; Asakura, Nobuyuki; Shimada, Michiya; Kikuchi, Mitsuru; Tsuji-Iio, Shunji; Uchino, Kiichiro; Muraoka, Katsunori.

1995-07-01

In order to understand the particle confinement properties in JT-60U, the particle confinement time was estimated through analyses of the neutral particle behavior. First, the neutral particle transport simulation code DEGAS using a Monte-Carlo technique was combined with the simple divertor code for calculating the edge plasma parameters, and was developed to calculate under the experimental conditions in JT-60U. Then, the charged particle source in the main plasma due to the ionization of the neutral particles was evaluated from the analyses of the neutral particle penetration to the main plasma based on results of the simulation code and measurements of D α emission intensities. Finally, the particle confinement time was estimated from the analysis of particle balance. The analyses were performed systematically for the L-mode plasma and H-mode plasma of JT-60U, and a data base of the particle confinement time was obtained. The dependence of the particle confinement time on the plasma parameters and the relationship between the properties of the particle confinement and the energy confinement were examined. (author)

EM modeling for GPIR using 3D FDTD modeling codes

Energy Technology Data Exchange (ETDEWEB)

Nelson, S.D.

1994-10-01

An analysis of the one-, two-, and three-dimensional electrical characteristics of structural cement and concrete is presented. This work connects experimental efforts in characterizing cement and concrete in the frequency and time domains with the Finite Difference Time Domain (FDTD) modeling efforts of these substances. These efforts include Electromagnetic (EM) modeling of simple lossless homogeneous materials with aggregate and targets and the modeling dispersive and lossy materials with aggregate and complex target geometries for Ground Penetrating Imaging Radar (GPIR). Two- and three-dimensional FDTD codes (developed at LLNL) where used for the modeling efforts. Purpose of the experimental and modeling efforts is to gain knowledge about the electrical properties of concrete typically used in the construction industry for bridges and other load bearing structures. The goal is to optimize the performance of a high-sample-rate impulse radar and data acquisition system and to design an antenna system to match the characteristics of this material. Results show agreement to within 2 dB of the amplitudes of the experimental and modeled data while the frequency peaks correlate to within 10% the differences being due to the unknown exact nature of the aggregate placement.

Development Of A Parallel Performance Model For The THOR Neutral Particle Transport Code

Energy Technology Data Exchange (ETDEWEB)

Yessayan, Raffi; Azmy, Yousry; Schunert, Sebastian

2017-02-01

The THOR neutral particle transport code enables simulation of complex geometries for various problems from reactor simulations to nuclear non-proliferation. It is undergoing a thorough V&V requiring computational efficiency. This has motivated various improvements including angular parallelization, outer iteration acceleration, and development of peripheral tools. For guiding future improvements to the code’s efficiency, better characterization of its parallel performance is useful. A parallel performance model (PPM) can be used to evaluate the benefits of modifications and to identify performance bottlenecks. Using INL’s Falcon HPC, the PPM development incorporates an evaluation of network communication behavior over heterogeneous links and a functional characterization of the per-cell/angle/group runtime of each major code component. After evaluating several possible sources of variability, this resulted in a communication model and a parallel portion model. The former’s accuracy is bounded by the variability of communication on Falcon while the latter has an error on the order of 1%.

Beam Dynamics in an Electron Lens with the Warp Particle-in-cell Code

CERN Document Server

Stancari, Giulio; Redaelli, Stefano

2014-01-01

Electron lenses are a mature technique for beam manipulation in colliders and storage rings. In an electron lens, a pulsed, magnetically confined electron beam with a given current-density profile interacts with the circulating beam to obtain the desired effect. Electron lenses were used in the Fermilab Tevatron collider for beam-beam compensation, for abort-gap clearing, and for halo scraping. They will be used in RHIC at BNL for head-on beam-beam compensation, and their application to the Large Hadron Collider for halo control is under development. At Fermilab, electron lenses will be implemented as lattice elements for nonlinear integrable optics. The design of electron lenses requires tools to calculate the kicks and wakefields experienced by the circulating beam. We use the Warp particle-in-cell code to study generation, transport, and evolution of the electron beam. For the first time, a fully 3-dimensional code is used for this purpose.

Improving the Calibration of Image Sensors Based on IOFBs, Using Differential Gray-Code Space Encoding

Directory of Open Access Journals (Sweden)

Carlos Luna Vázquez

2012-07-01

Full Text Available This paper presents a fast calibration method to determine the transfer function for spatial correspondences in image transmission devices with <em>Incoherent> em>>Optical Fiberem>> em>Bundles> em>(IOFBs, by performing a scan of the input, using differential patterns generated from a Gray code (<em>Differential Gray-Code Space Encodingem>, DGSE. The results demonstrate that this technique provides a noticeable reduction in processing time and better quality of the reconstructed image compared to other, previously employed techniques, such as point or fringe scanning, or even other known space encoding techniques.

A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.

Science.gov (United States)

Zhu, Yanan; Ouyang, Qi; Mao, Youdong

2017-07-21

Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly "knowledgeable". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.

First experience with particle-in-cell plasma physics code on ARM-based HPC systems

OpenAIRE

Sáez, Xavier; Soba, Alejandro; Sánchez, Edilberto; Mantsinen, Mervi; Mateo, Sergio; Cela, José M.; Castejón, Francisco

2015-01-01

In this work, we will explore the feasibility of porting a Particle-in-cell code (EUTERPE) to an ARM multi-core platform from the Mont-Blanc project. The used prototype is based on a system-on-chip Samsung Exynos 5 with an integrated GPU. It is the first prototype that could be used for High-Performance Computing (HPC), since it supports double precision and parallel programming languages. The research leading to these results has received funding from the European Com- munity's Seventh...

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization.

Science.gov (United States)

Yang, Xinyu; Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead.

Apar-T: code, validation, and physical interpretation of particle-in-cell results

Science.gov (United States)

Melzani, Mickaël; Winisdoerffer, Christophe; Walder, Rolf; Folini, Doris; Favre, Jean M.; Krastanov, Stefan; Messmer, Peter

2013-10-01

We present the parallel particle-in-cell (PIC) code Apar-T and, more importantly, address the fundamental question of the relations between the PIC model, the Vlasov-Maxwell theory, and real plasmas. First, we present four validation tests: spectra from simulations of thermal plasmas, linear growth rates of the relativistic tearing instability and of the filamentation instability, and nonlinear filamentation merging phase. For the filamentation instability we show that the effective growth rates measured on the total energy can differ by more than 50% from the linear cold predictions and from the fastest modes of the simulation. We link these discrepancies to the superparticle number per cell and to the level of field fluctuations. Second, we detail a new method for initial loading of Maxwell-Jüttner particle distributions with relativistic bulk velocity and relativistic temperature, and explain why the traditional method with individual particle boosting fails. The formulation of the relativistic Harris equilibrium is generalized to arbitrary temperature and mass ratios. Both are required for the tearing instability setup. Third, we turn to the key point of this paper and scrutinize the question of what description of (weakly coupled) physical plasmas is obtained by PIC models. These models rely on two building blocks: coarse-graining, i.e., grouping of the order of p ~ 1010 real particles into a single computer superparticle, and field storage on a grid with its subsequent finite superparticle size. We introduce the notion of coarse-graining dependent quantities, i.e., quantities depending on p. They derive from the PIC plasma parameter ΛPIC, which we show to behave as ΛPIC ∝ 1/p. We explore two important implications. One is that PIC collision- and fluctuation-induced thermalization times are expected to scale with the number of superparticles per grid cell, and thus to be a factor p ~ 1010 smaller than in real plasmas, a fact that we confirm with

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

Energy Technology Data Exchange (ETDEWEB)

Liu, Peiyuan [Univ. of Colorado, Boulder, CO (United States); Brown, Timothy [Univ. of Colorado, Boulder, CO (United States); Fullmer, William D. [Univ. of Colorado, Boulder, CO (United States); Hauser, Thomas [Univ. of Colorado, Boulder, CO (United States); Hrenya, Christine [Univ. of Colorado, Boulder, CO (United States); Grout, Ray [National Renewable Energy Lab. (NREL), Golden, CO (United States); Sitaraman, Hariswaran [National Renewable Energy Lab. (NREL), Golden, CO (United States)

2016-01-29

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling of the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.

LPIC++. A parallel one-dimensional relativistic electromagnetic particle-in-cell code for simulating laser-plasma-interaction

International Nuclear Information System (INIS)

Lichters, R.; Pfund, R.E.W.; Meyer-ter-Vehn, J.

1997-08-01

The code LPIC++ presented here, is based on a one-dimensional, electromagnetic, relativistic PIC code that has originally been developed by one of the authors during a PhD thesis at the Max-Planck-Institut fuer Quantenoptik for kinetic simulations of high harmonic generation from overdense plasma surfaces. The code uses essentially the algorithm of Birdsall and Langdon and Villasenor and Bunemann. It is written in C++ in order to be easily extendable and has been parallelized to be able to grow in power linearly with the size of accessable hardware, e.g. massively parallel machines like Cray T3E. The parallel LPIC++ version uses PVM for communication between processors. PVM is public domain software, can be downloaded from the world wide web. A particular strength of LPIC++ lies in its clear program and data structure, which uses chained lists for the organization of grid cells and enables dynamic adjustment of spatial domain sizes in a very convenient way, and therefore easy balancing of processor loads. Also particles belonging to one cell are linked in a chained list and are immediately accessable from this cell. In addition to this convenient type of data organization in a PIC code, the code shows excellent performance in both its single processor and parallel version. (orig.)

Distribution Pattern of Fe, Sr, Zr and Ca Elements as Particle Size Function in the Code River Sediments from Upstream to Downstream

International Nuclear Information System (INIS)

Sri Murniasih; Muzakky

2007-01-01

The analysis of Fe, Sr, Zr and Ca elements concentration of granular sediment from upstream to downstream of Code river has been done. The aim of this research is to know the influence of particle size on the concentration of Fe, Sr, Zr and Ca elements in the Code river sediments from upstream to downstream and its distribution pattern. The instrument used was x-ray fluorescence with Si(Li) detector. Analysis results show that more Fe and Sr elements are very much found in 150 - 90 μm particle size, while Zr and Ca elements are very much found in < 90 μm particle size. Distribution pattern of Fe, Sr, Zr and Ca elements distribution in Code river sediments tends to increase relatively from upstream to downstream following its conductivity. The concentration of Fe, Sr, Zr and Ca elements are 1.49 ± 0.03 % - 5.93 ± 0.02 % ; 118.20 ± 10.73 ppm - 468.21 ± 20.36 ppm; 19.81 ppm ± 0.86 ppm - 76.36 ± 3.02 ppm and 3.22 ± 0.25 % - 11.40 ± 0.31 % successively. (author)

Vectorization, parallelization and porting of nuclear codes on the VPP500 system (parallelization). Progress report fiscal 1996

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Hideo; Kawai, Wataru; Nemoto, Toshiyuki [Fujitsu Ltd., Tokyo (Japan); and others

1997-12-01

Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. These results are reported in 3 parts, i.e., the vectorization part, the parallelization part and the porting part. In this report, we describe the parallelization. In this parallelization part, the parallelization of 2-Dimensional relativistic electromagnetic particle code EM2D, Cylindrical Direct Numerical Simulation code CYLDNS and molecular dynamics code for simulating radiation damages in diamond crystals DGR are described. In the vectorization part, the vectorization of two and three dimensional discrete ordinates simulation code DORT-TORT, gas dynamics analysis code FLOWGR and relativistic Boltzmann-Uehling-Uhlenbeck simulation code RBUU are described. And then, in the porting part, the porting of reactor safety analysis code RELAP5/MOD3.2 and RELAP5/MOD3.2.1.2, nuclear data processing system NJOY and 2-D multigroup discrete ordinate transport code TWOTRAN-II are described. And also, a survey for the porting of command-driven interactive data analysis plotting program IPLOT are described. (author)

Vectorization, parallelization and porting of nuclear codes on the VPP500 system (vectorization). Progress report fiscal 1996

Energy Technology Data Exchange (ETDEWEB)

Nemoto, Toshiyuki; Kawai, Wataru [Fujitsu Ltd., Tokyo (Japan); Kawasaki, Nobuo [and others

1997-12-01

Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. These results are reported in 3 parts, i.e., the vectorization part, the parallelization part and the porting part. In this report, we describe the vectorization. In this vectorization part, the vectorization of two and three dimensional discrete ordinates simulation code DORT-TORT, gas dynamics analysis code FLOWGR and relativistic Boltzmann-Uehling-Uhlenbeck simulation code RBUU are described. In the parallelization part, the parallelization of 2-Dimensional relativistic electromagnetic particle code EM2D, Cylindrical Direct Numerical Simulation code CYLDNS and molecular dynamics code for simulating radiation damages in diamond crystals DGR are described. And then, in the porting part, the porting of reactor safety analysis code RELAP5/MOD3.2 and RELAP5/MOD3.2.1.2, nuclear data processing system NJOY and 2-D multigroup discrete ordinate transport code TWOTRAN-II are described. And also, a survey for the porting of command-driven interactive data analysis plotting program IPLOT are described. (author)

Vectorization, parallelization and porting of nuclear codes on the VPP500 system (porting). Progress report fiscal 1996

Energy Technology Data Exchange (ETDEWEB)

Nemoto, Toshiyuki [Fujitsu Ltd., Tokyo (Japan); Kawasaki, Nobuo; Tanabe, Hidenobu [and others

1998-01-01

Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. These results are reported in 3 parts, i.e., the vectorization part, the parallelization part and the porting part. In this report, we describe the porting. In this porting part, the porting of reactor safety analysis code RELAP5/MOD3.2 and RELAP5/MOD3.2.1.2, nuclear data processing system NJOY and 2-D multigroup discrete ordinate transport code TWOTRAN-II are described. And also, a survey for the porting of command-driven interactive data analysis plotting program IPLOT are described. In the parallelization part, the parallelization of 2-Dimensional relativistic electromagnetic particle code EM2D, Cylindrical Direct Numerical Simulation code CYLDNS and molecular dynamics code for simulating radiation damages in diamond crystals DGR are described. And then, in the vectorization part, the vectorization of two and three dimensional discrete ordinates simulation code DORT-TORT, gas dynamics analysis code FLOWGR and relativistic Boltzmann-Uehling-Uhlenbeck simulation code RBUU are described. (author)

Update on comparison of the particle production using Mars simulation code

CERN Document Server

Prior, G; Kirk, H G; Souchlas, N; Ding, X

2011-01-01

In the International Design Study for the Neutrino Factory (IDS-NF), a 5-15 GeV (kinetic energy) proton beam impinges a Hg jet target, in order to produce pions that will decay into muons. The muons are captured and transformed into a beam, then passed to the downstream acceleration system. The target sits in a solenoid eld tapering from 20 T down to below 2 T, over several meters, permitting an optimized capture of the pions that will produce useful muons for the machine. The target and pion capture systems have been simulated using MARS. This paper presents an updated comparison of the particles production using the MARS code versions m1507 and m1510 on different machines located at the European Organization for Nuclear Research (CERN) and Brookhaven National Laboratory (BNL).

Biological dose estimation for charged-particle therapy using an improved PHITS code coupled with a microdosimetric kinetic model

International Nuclear Information System (INIS)

Sato, Tatsuhiko; Watanabe, Ritsuko; Kase, Yuki; Niita, Koji; Sihver, Lembit

2009-01-01

High-energy heavy ions (HZE particles) have become widely used for radiotherapy of tumors owing to their high biological effectiveness. In the treatment planning of such charged-particle therapy, it is necessary to estimate not only physical but also biological dose, which is the product of physical dose and relative biological effectiveness (RBE). In the Heavy-ion Medical Accelerator in Chiba (HIMAC), the biological dose is estimated by a method proposed by Kanai et al., which is based on the linear-quadratic (LQ) model with its parameters α and β determined by the dose distribution in terms of the unrestricted linear energy transfer (LET). Thus, RBE is simply expressed as a function of LET in their model. However, RBE of HZE particles cannot be uniquely determined from their LET because of their large cross sections for high-energy δ-ray production. Hence, development of a biological dose estimation model that can explicitly consider the track structure of δ-rays around the trajectory of HZE particles is urgently needed. Microdosimetric quantities such as lineal energy y are better indexes for representing RBE of HZE particles in comparison to LET, since they can express the decrease of ionization densities around their trajectories due to the production of δ-rays. The difference of the concept between LET and y is illustrated in Figure 1. However, the use of microdosimetric quantities in computational dosimetry was severely limited because of the difficulty in calculating their probability densities (PDs) in macroscopic matter. We therefore improved the 3-dimensional particle transport simulation code PHITS, providing it with the capability of estimating the microdosimetric PDs in a macroscopic framework by incorporating a mathematical function that can instantaneously calculate the PDs around the trajectory of HZE particles with precision equivalent to a microscopic track-structure simulation. A new method for estimating biological dose from charged-particle

Enhancements to the Combinatorial Geometry Particle Tracker in the Mercury Monte Carlo Transport Code: Embedded Meshes and Domain Decomposition

International Nuclear Information System (INIS)

Greenman, G.M.; O'Brien, M.J.; Procassini, R.J.; Joy, K.I.

2009-01-01

Two enhancements to the combinatorial geometry (CG) particle tracker in the Mercury Monte Carlo transport code are presented. The first enhancement is a hybrid particle tracker wherein a mesh region is embedded within a CG region. This method permits efficient calculations of problems with contain both large-scale heterogeneous and homogeneous regions. The second enhancement relates to the addition of parallelism within the CG tracker via spatial domain decomposition. This permits calculations of problems with a large degree of geometric complexity, which are not possible through particle parallelism alone. In this method, the cells are decomposed across processors and a particles is communicated to an adjacent processor when it tracks to an interprocessor boundary. Applications that demonstrate the efficacy of these new methods are presented

Computer codes used in particle accelerator design: First edition

International Nuclear Information System (INIS)

1987-01-01

This paper contains a listing of more than 150 programs that have been used in the design and analysis of accelerators. Given on each citation are person to contact, classification of the computer code, publications describing the code, computer and language runned on, and a short description of the code. Codes are indexed by subject, person to contact, and code acronym

Controlling Energy Radiations of Electromagnetic Waves via Frequency Coding Metamaterials.

Science.gov (United States)

Wu, Haotian; Liu, Shuo; Wan, Xiang; Zhang, Lei; Wang, Dan; Li, Lianlin; Cui, Tie Jun

2017-09-01

Metamaterials are artificial structures composed of subwavelength unit cells to control electromagnetic (EM) waves. The spatial coding representation of metamaterial has the ability to describe the material in a digital way. The spatial coding metamaterials are typically constructed by unit cells that have similar shapes with fixed functionality. Here, the concept of frequency coding metamaterial is proposed, which achieves different controls of EM energy radiations with a fixed spatial coding pattern when the frequency changes. In this case, not only different phase responses of the unit cells are considered, but also different phase sensitivities are also required. Due to different frequency sensitivities of unit cells, two units with the same phase response at the initial frequency may have different phase responses at higher frequency. To describe the frequency coding property of unit cell, digitalized frequency sensitivity is proposed, in which the units are encoded with digits "0" and "1" to represent the low and high phase sensitivities, respectively. By this merit, two degrees of freedom, spatial coding and frequency coding, are obtained to control the EM energy radiations by a new class of frequency-spatial coding metamaterials. The above concepts and physical phenomena are confirmed by numerical simulations and experiments.

The LIONS code (version 1.0)

International Nuclear Information System (INIS)

Bertrand, P.

1993-01-01

The new LIONS code (Lancement d'IONS or Ion Launching), a dynamical code implemented in the SPIRaL project for the CIME cyclotron studies, is presented. The various software involves a 3D magnetostatic code, 2D or 3D electrostatic codes for generation of realistic field maps, and several dynamical codes for studying the behaviour of the reference particle from the cyclotron center up to the ejection and for launching particles packets complying with given correlations. Its interactions with the other codes are described. The LIONS code, written in Fortran 90 is already used in studying the CIME cyclotron, from the center to the ejection. It is designed to be used, with minor modifications, in other contexts such as for the simulation of mass spectrometer facilities

Particle-in-cell plasma simulation codes on the connection machine

International Nuclear Information System (INIS)

Walker, D.W.

1991-01-01

Methods for implementing three-dimensional, electromagnetic, relativistic PIC plasma simulation codes on the Connection Machine (CM-2) are discussed. The gather and scatter phases of the PIC algorithm involve indirect indexing of data, which results in a large amount of communication on the CM-2. Different data decompositions are described that seek to reduce the amount of communication while maintaining good load balance. These methods require the particles to be spatially sorted at the start of each time step, which introduced another form of overhead. The different methods are implemented in CM Fortran on the CM-2 and compared. It was found that the general router is slow in performing the communication in the gather and scatter steps, which precludes an efficient CM Fortran implementation. An alternative method that uses PARIS calls and the NEWS communication network to pipeline data along the axes of the VP set is suggested as a more efficient algorithm

New features of the mercury Monte Carlo particle transport code

International Nuclear Information System (INIS)

Procassini, Richard; Brantley, Patrick; Dawson, Shawn

2010-01-01

Several new capabilities have been added to the Mercury Monte Carlo transport code over the past four years. The most important algorithmic enhancement is a general, extensible infrastructure to support source, tally and variance reduction actions. For each action, the user defines a phase space, as well as any number of responses that are applied to a specified event. Tallies are accumulated into a correlated, multi-dimensional. Cartesian-product result phase space. Our approach employs a common user interface to specify the data sets and distributions that define the phase, response and result for each action. Modifications to the particle trackers include the use of facet halos (instead of extrapolative fuzz) for robust tracking, and material interface reconstruction for use in shape overlaid meshes. Support for expected-value criticality eigenvalue calculations has also been implemented. Computer science enhancements include an in-line Python interface for user customization of problem setup and output. (author)

Research on Primary Shielding Calculation Source Generation Codes

Science.gov (United States)

Zheng, Zheng; Mei, Qiliang; Li, Hui; Shangguan, Danhua; Zhang, Guangchun

2017-09-01

Primary Shielding Calculation (PSC) plays an important role in reactor shielding design and analysis. In order to facilitate PSC, a source generation code is developed to generate cumulative distribution functions (CDF) for the source particle sample code of the J Monte Carlo Transport (JMCT) code, and a source particle sample code is deveoped to sample source particle directions, types, coordinates, energy and weights from the CDFs. A source generation code is developed to transform three dimensional (3D) power distributions in xyz geometry to source distributions in r θ z geometry for the J Discrete Ordinate Transport (JSNT) code. Validation on PSC model of Qinshan No.1 nuclear power plant (NPP), CAP1400 and CAP1700 reactors are performed. Numerical results show that the theoretical model and the codes are both correct.

Parallel Finite Element Particle-In-Cell Code for Simulations of Space-charge Dominated Beam-Cavity Interactions

International Nuclear Information System (INIS)

Candel, A.; Kabel, A.; Ko, K.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.

2007-01-01

Over the past years, SLAC's Advanced Computations Department (ACD) has developed the parallel finite element (FE) particle-in-cell code Pic3P (Pic2P) for simulations of beam-cavity interactions dominated by space-charge effects. As opposed to standard space-charge dominated beam transport codes, which are based on the electrostatic approximation, Pic3P (Pic2P) includes space-charge, retardation and boundary effects as it self-consistently solves the complete set of Maxwell-Lorentz equations using higher-order FE methods on conformal meshes. Use of efficient, large-scale parallel processing allows for the modeling of photoinjectors with unprecedented accuracy, aiding the design and operation of the next-generation of accelerator facilities. Applications to the Linac Coherent Light Source (LCLS) RF gun are presented

Test Particle Simulations of Electron Injection by the Bursty Bulk Flows (BBFs) using High Resolution Lyon-Feddor-Mobarry (LFM) Code

Science.gov (United States)

Eshetu, W. W.; Lyon, J.; Wiltberger, M. J.; Hudson, M. K.

2017-12-01

Test particle simulations of electron injection by the bursty bulk flows (BBFs) have been done using a test particle tracer code [1], and the output fields of the Lyon-Feddor-Mobarry global magnetohydro- dynamics (MHD) code[2]. The MHD code was run with high resolu- tion (oct resolution), and with specified solar wind conditions so as to reproduce the observed qualitative picture of the BBFs [3]. Test par- ticles were injected so that they interact with earthward propagating BBFs. The result of the simulation shows that electrons are pushed ahead of the BBFs and accelerated into the inner magnetosphere. Once electrons are in the inner magnetosphere they are further energized by drift resonance with the azimuthal electric field. In addition pitch angle scattering of electrons resulting in the violation conservation of the first adiabatic invariant has been observed. The violation of the first adiabatic invariant occurs as electrons cross a weak magnetic field region with a strong gradient of the field perturbed by the BBFs. References 1. Kress, B. T., Hudson,M. K., Looper, M. D. , Albert, J., Lyon, J. G., and Goodrich, C. C. (2007), Global MHD test particle simulations of ¿ 10 MeV radiation belt electrons during storm sudden commencement, J. Geophys. Res., 112, A09215, doi:10.1029/2006JA012218. Lyon,J. G., Fedder, J. A., and Mobarry, C.M., The Lyon- Fedder-Mobarry (LFM) Global MHD Magnetospheric Simulation Code (2004), J. Atm. And Solar-Terrestrial Phys., 66, Issue 15-16, 1333- 1350,doi:10.1016/j.jastp. Wiltberger, Merkin, M., Lyon, J. G., and Ohtani, S. (2015), High-resolution global magnetohydrodynamic simulation of bursty bulk flows, J. Geophys. Res. Space Physics, 120, 45554566, doi:10.1002/2015JA021080.

Tripoli-3: monte Carlo transport code for neutral particles - version 3.5 - users manual

International Nuclear Information System (INIS)

Vergnaud, Th.; Nimal, J.C.; Chiron, M.

2001-01-01

The TRIPOLI-3 code applies the Monte Carlo method to neutron, gamma-ray and coupled neutron and gamma-ray transport calculations in three-dimensional geometries, either in steady-state conditions or having a time dependence. It can be used to study problems where there is a high flux attenuation between the source zone and the result zone (studies of shielding configurations or source driven sub-critical systems, with fission being taken into account), as well as problems where there is a low flux attenuation (neutronic calculations -- in a fuel lattice cell, for example -- where fission is taken into account, usually with the calculation on the effective multiplication factor, fine structure studies, numerical experiments to investigate methods approximations, etc). TRIPOLI-3 has been operational since 1995 and is the version of the TRIPOLI code that follows on from TRIPOLI-2; it can be used on SUN, RISC600 and HP workstations and on PC using the Linux or Windows/NT operating systems. The code uses nuclear data libraries generated using the THEMIS/NJOY system. The current libraries were derived from ENDF/B6 and JEF2. There is also a response function library based on a number of evaluations, notably the dosimetry libraries IRDF/85, IRDF/90 and also evaluations from JEF2. The treatment of particle transport is the same in version 3.5 as in version 3.4 of the TRIPOLI code; but the version 3.5 is more convenient for preparing the input data and for reading the output. The french version of the user's manual exists. (authors)

Magnetic reconnection simulation using the 2.5D em [electromagnetic] direct implicit code AVANTI

International Nuclear Information System (INIS)

Hewett, D.W.; Francis, G.E.; Max, C.E.

1988-01-01

Collisionless reconnection of magnetic field lines depends upon electron inertia effects and details of the electron and ion distribution functions, thus requiring a kinetic description of both. Though traditional explicit PIC techniques provide this description in principle, they are severely limited in parameters by time step constraints. This parameter regime has been expanded by using the recently constructed 2.5 D electromagnetic code AVANTI in this work. The code runs stably with arbitrarily large Δt and is quite robust with respect to large fluctuations occurring due to small numbers of particles per cell. We have found several qualitatively new features. The reconnection process is found to occur in distinct stages: early spontaneous reconnection fed by the free energy of an initial anisotropy in the electron component, coalescence of the resulting small-scale filaments of electron current, accompanied by electron jetting, and oscillatory flow of electrons through the magnetic X-point, superposed on continuing nonlinear growth of ion-mediated reconnection. The time evolution of stage is strongly dependent on M i /m e . 12 refs., 6 figs

The Live Coding of <em>Slub> - Art Oriented Programming as Media Critique

DEFF Research Database (Denmark)

Andersen, Christian Ulrik

2007-01-01

Computer art is often associated with computer-generated expressions (digital audio/images in music, video, stage design, etc.). In recent computer art, however, the code-text itself – not the generated output – has become the artwork (Perl Poetry, ASCII Art, obfuscated code, etc.). This paper wi...

Modeling an emittance-dominated elliptical sheet beam with a 212-dimensional particle-in-cell code

International Nuclear Information System (INIS)

Carlsten, Bruce E.

2005-01-01

Modeling a 3-dimensional (3-D) elliptical beam with a 212-D particle-in-cell (PIC) code requires a reduction in the beam parameters. The 212-D PIC code can only model the center slice of the sheet beam, but that can still provide useful information about the beam transport and distribution evolution, even if the beam is emittance dominated. The reduction of beam parameters and resulting interpretation of the simulation is straightforward, but not trivial. In this paper, we describe the beam parameter reduction and emittance issues related to the initial beam distribution. As a numerical example, we use the case of a sheet beam designed for use with a planar traveling-wave amplifier for high power generator for RF ranging from 95 to 300GHz [Carlsten et al., IEEE Trans. Plasma Sci. 33 (2005) 85]. These numerical techniques also apply to modeling high-energy elliptical bunches in RF accelerators

Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

International Nuclear Information System (INIS)

Vay, J.-L.; Furman, M.A.; Azevedo, A.W.; Cohen, R.H.; Friedman, A.; Grote, D.P.; Stoltz, P.H.

2004-01-01

We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE

Tristan code and its application

Science.gov (United States)

Nishikawa, K.-I.

Since TRISTAN: The 3-D Electromagnetic Particle Code was introduced in 1990, it has been used for many applications including the simulations of global solar windmagnetosphere interaction. The most essential ingridients of this code have been published in the ISSS-4 book. In this abstract we describe some of issues and an application of this code for the study of global solar wind-magnetosphere interaction including a substorm study. The basic code (tristan.f) for the global simulation and a local simulation of reconnection with a Harris model (issrec2.f) are available at http:/www.physics.rutger.edu/˜kenichi. For beginners the code (isssrc2.f) with simpler boundary conditions is suitable to start to run simulations. The future of global particle simulations for a global geospace general circulation (GGCM) model with predictive capability (for Space Weather Program) is discussed.

FRESCO: fusion reactor simulation code for tokamaks

International Nuclear Information System (INIS)

Mantsinen, M.J.

1995-03-01

The study of the dynamics of tokamak fusion reactors, a zero-dimensional particle and power balance code FRESCO (Fusion Reactor Simulation Code) has been developed at the Department of Technical Physics of Helsinki University of Technology. The FRESCO code is based on zero-dimensional particle and power balance equations averaged over prescribed plasma profiles. In the report the data structure of the FRESCO code is described, including the description of the COMMON statements, program input, and program output. The general structure of the code is described, including the description of subprograms and functions. The physical model used and examples of the code performance are also included in the report. (121 tabs.) (author)

Recent Improvements in the SHIELD-HIT Code

DEFF Research Database (Denmark)

Hansen, David Christoffer; Lühr, Armin Christian; Herrmann, Rochus

2012-01-01

Purpose: The SHIELD-HIT Monte Carlo particle transport code has previously been used to study a wide range of problems for heavy-ion treatment and has been benchmarked extensively against other Monte Carlo codes and experimental data. Here, an improved version of SHIELD-HIT is developed concentra......Purpose: The SHIELD-HIT Monte Carlo particle transport code has previously been used to study a wide range of problems for heavy-ion treatment and has been benchmarked extensively against other Monte Carlo codes and experimental data. Here, an improved version of SHIELD-HIT is developed...

Towards the optimization of a gyrokinetic Particle-In-Cell (PIC) code on large-scale hybrid architectures

International Nuclear Information System (INIS)

Ohana, N; Lanti, E; Tran, T M; Brunner, S; Hariri, F; Villard, L; Jocksch, A; Gheller, C

2016-01-01

With the aim of enabling state-of-the-art gyrokinetic PIC codes to benefit from the performance of recent multithreaded devices, we developed an application from a platform called the “PIC-engine” [1, 2, 3] embedding simplified basic features of the PIC method. The application solves the gyrokinetic equations in a sheared plasma slab using B-spline finite elements up to fourth order to represent the self-consistent electrostatic field. Preliminary studies of the so-called Particle-In-Fourier (PIF) approach, which uses Fourier modes as basis functions in the periodic dimensions of the system instead of the real-space grid, show that this method can be faster than PIC for simulations with a small number of Fourier modes. Similarly to the PIC-engine, multiple levels of parallelism have been implemented using MPI+OpenMP [2] and MPI+OpenACC [1], the latter exploiting the computational power of GPUs without requiring complete code rewriting. It is shown that sorting particles [3] can lead to performance improvement by increasing data locality and vectorizing grid memory access. Weak scalability tests have been successfully run on the GPU-equipped Cray XC30 Piz Daint (at CSCS) up to 4,096 nodes. The reduced time-to-solution will enable more realistic and thus more computationally intensive simulations of turbulent transport in magnetic fusion devices. (paper)

Current status of high energy nucleon-meson transport code

Energy Technology Data Exchange (ETDEWEB)

Takada, Hiroshi; Sasa, Toshinobu [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

1998-03-01

Current status of design code of accelerator (NMTC/JAERI code), outline of physical model and evaluation of accuracy of code were reported. To evaluate the nuclear performance of accelerator and strong spallation neutron origin, the nuclear reaction between high energy proton and target nuclide and behaviors of various produced particles are necessary. The nuclear design of spallation neutron system used a calculation code system connected the high energy nucleon{center_dot}meson transport code and the neutron{center_dot}photon transport code. NMTC/JAERI is described by the particle evaporation process under consideration of competition reaction of intranuclear cascade and fission process. Particle transport calculation was carried out for proton, neutron, {pi}- and {mu}-meson. To verify and improve accuracy of high energy nucleon-meson transport code, data of spallation and spallation neutron fragment by the integral experiment were collected. (S.Y.)

Language Recognition via Sparse Coding

Science.gov (United States)

2016-09-08

explanation is that sparse coding can achieve a near-optimal approximation of much complicated nonlinear relationship through local and piecewise linear...training examples, where x(i) ∈ RN is the ith example in the batch. Optionally, X can be normalized and whitened before sparse coding for better result...normalized input vectors are then ZCA- whitened [20]. Em- pirically, we choose ZCA- whitening over PCA- whitening , and there is no dimensionality reduction

VDE/disruption EM analysis for ITER in-vessel components

International Nuclear Information System (INIS)

Miki, N.; Ioki, K.; Ilio, F.; Kodama, T.; Chiocchio, S.; Williamson, D.; Roccella, M.; Barabaschi, P.; Sayer, R.S.

1998-01-01

This paper summarises the results of EM analyses for ITER in-vessel components, such as blanket modules, backplate and divertor modules. In the ITER design the following two disruption scenarios are taken into account: centered or radial disruption, and vertical displacement event (VDE). Eddy currents and forces due to plasma disruption were calculated using the 3D shell element code EDDYCUFF and the 3D solid element code EMAS. The plasma motion and current decay used in the EM analysis was supplied by 2-D axisymmetric plasma equilibrium codes, TSC and MAXFEA. (authors)

Porting the 3D Gyrokinetic Particle-in-cell Code GTC to the CRAY/NEC SX-6 Vector Architecture: Perspectives and Challenges

International Nuclear Information System (INIS)

Ethier, S.; Lin, Z.

2003-01-01

Several years of optimization on the super-scalar architecture has made it more difficult to port the current version of the 3D particle-in-cell code GTC to the CRAY/NEC SX-6 vector architecture. This paper explains the initial work that has been done to port this code to the SX-6 computer and to optimize the most time consuming parts. Early performance results are shown and compared to the same test done on the IBM SP Power 3 and Power 4 machines

Plasma simulation by macroscale, electromagnetic particle code and its application to current-drive by relativistic electron beam injection

International Nuclear Information System (INIS)

Tanaka, M.; Sato, T.

1985-01-01

A new implicit macroscale electromagnetic particle simulation code (MARC) which allows a large scale length and a time step in multi-dimensions is described. Finite mass electrons and ions are used with relativistic version of the equation of motion. The electromagnetic fields are solved by using a complete set of Maxwell equations. For time integration of the field equations, a decentered (backward) finite differencing scheme is employed with the predictor - corrector method for small noise and super-stability. It is shown both in analytical and numerical ways that the present scheme efficiently suppresses high frequency electrostatic and electromagnetic waves in a plasma, and that it accurately reproduces low frequency waves such as ion acoustic waves, Alfven waves and fast magnetosonic waves. The present numerical scheme has currently been coded in three dimensions for application to a new tokamak current-drive method by means of relativistic electron beam injection. Some remarks of the proper macroscale code application is presented in this paper

Discrete particle noise in particle-in-cell simulations of plasma microturbulence

International Nuclear Information System (INIS)

Nevins, W.M.; Hammett, G.W.; Dimits, A.M.; Dorland, W.; Shumaker, D.E.

2005-01-01

Recent gyrokinetic simulations of electron temperature gradient (ETG) turbulence with the global particle-in-cell (PIC) code GTC [Z. Lin et al., Proceedings of the 20th Fusion Energy Conference, Vilamoura, Portugal, 2004 (IAEA, Vienna, 2005)] yielded different results from earlier flux-tube continuum code simulations [F. Jenko and W. Dorland, Phys. Rev. Lett. 89, 225001 (2002)] despite similar plasma parameters. Differences between the simulation results were attributed to insufficient phase-space resolution and novel physics associated with global simulation models. The results of the global PIC code are reproduced here using the flux-tube PIC code PG3EQ [A. M. Dimits et al., Phys. Rev. Lett. 77, 71 (1996)], thereby eliminating global effects as the cause of the discrepancy. The late-time decay of the ETG turbulence and the steady-state heat transport observed in these PIC simulations are shown to result from discrete particle noise. Discrete particle noise is a numerical artifact, so both these PG3EQ simulations and, by inference, the GTC simulations that they reproduced have little to say about steady-state ETG turbulence and the associated anomalous heat transport. In the course of this work several diagnostics are developed to retrospectively test whether a particular PIC simulation is dominated by discrete particle noise

Simulation of thermal-neutron-induced single-event upset using particle and heavy-ion transport code system

International Nuclear Information System (INIS)

Arita, Yutaka; Kihara, Yuji; Mitsuhasi, Junichi; Niita, Koji; Takai, Mikio; Ogawa, Izumi; Kishimoto, Tadafumi; Yoshihara, Tsutomu

2007-01-01

The simulation of a thermal-neutron-induced single-event upset (SEU) was performed on a 0.4-μm-design-rule 4 Mbit static random access memory (SRAM) using particle and heavy-ion transport code system (PHITS): The SEU rates obtained by the simulation were in very good agreement with the result of experiments. PHITS is a useful tool for simulating SEUs in semiconductor devices. To further improve the accuracy of the simulation, additional methods for tallying the energy deposition are required for PHITS. (author)

Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules.

Science.gov (United States)

Miyaguchi, Katsuyuki

2014-10-01

Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo. © 2014 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

Energy Technology Data Exchange (ETDEWEB)

Vay, J.-L.; Furman, M.A.; Azevedo, A.W.; Cohen, R.H.; Friedman, A.; Grote, D.P.; Stoltz, P.H.

2004-04-19

We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE.

ZENO: N-body and SPH Simulation Codes

Science.gov (United States)

Barnes, Joshua E.

2011-02-01

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere. Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include: Structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems.Snapshot generation routines create particle distributions with various properties. Systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium.Snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.Simulation codes include both pure N-body and combined N-body/SPH programs: Pure N-body codes are available in both uniprocessor and parallel versions.SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions.Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

Beam-dynamics codes used at DARHT

Energy Technology Data Exchange (ETDEWEB)

Ekdahl, Jr., Carl August [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-02-01

Several beam simulation codes are used to help gain a better understanding of beam dynamics in the DARHT LIAs. The most notable of these fall into the following categories: for beam production – Tricomp Trak orbit tracking code, LSP Particle in cell (PIC) code, for beam transport and acceleration – XTR static envelope and centroid code, LAMDA time-resolved envelope and centroid code, LSP-Slice PIC code, for coasting-beam transport to target – LAMDA time-resolved envelope code, LSP-Slice PIC code. These codes are also being used to inform the design of Scorpius.

ACT-XN: Revised version of an activation calculation code for fusion reactor analysis. Supplement of the function for the sequential reaction activation by charged particles

International Nuclear Information System (INIS)

Yamauchi, Michinori; Sato, Satoshi; Nishitani, Takeo; Konno, Chikara; Hori, Jun-ichi; Kawasaki, Hiromitsu

2007-09-01

The ACT-XN is a revised version of the ACT4 code, which was developed in the Japan Atomic Energy Research Institute (JAERI) to calculate the transmutation, induced activity, decay heat, delayed gamma-ray source etc. for fusion devices. The ACT4 code cannot deal with the sequential reactions of charged particles generated by primary neutron reactions. In the design of present experimental reactors, the activation due to sequential reactions may not be of great concern as it is usually buried under the activity by primary neutron reactions. However, low activation material is one of the important factors for constructing high power fusion reactors in future, and unexpected activation may be produced through sequential reactions. Therefore, in the present work, the ACT4 code was newly supplemented with the calculation functions for the sequential reactions and renamed the ACT-XN. The ACT-XN code is equipped with functions to calculate effective cross sections for sequential reactions and input them in transmutation matrix. The FISPACT data were adopted for (x,n) reaction cross sections, charged particles emission spectra and stopping powers. The nuclear reaction chain data library were revised to cope with the (x,n) reactions. The charged particles are specified as p, d, t, 3 He(h) and α. The code was applied to the analysis of FNS experiment for LiF and Demo-reactor design with FLiBe, and confirmed that it reproduce the experimental values within 15-30% discrepancies. In addition, a notice was presented that the dose rate due to sequential reaction cannot always be neglected after a certain period cooling for some of the low activation material. (author)

Charged-particle calculations using Boltzmann transport methods

International Nuclear Information System (INIS)

Hoffman, T.J.; Dodds, H.L. Jr.; Robinson, M.T.; Holmes, D.K.

1981-01-01

Several aspects of radiation damage effects in fusion reactor neutron and ion irradiation environments are amenable to treatment by transport theory methods. In this paper, multigroup transport techniques are developed for the calculation of charged particle range distributions, reflection coefficients, and sputtering yields. The Boltzmann transport approach can be implemented, with minor changes, in standard neutral particle computer codes. With the multigroup discrete ordinates code, ANISN, determination of ion and target atom distributions as functions of position, energy, and direction can be obtained without the stochastic error associated with atomistic computer codes such as MARLOWE and TRIM. With the multigroup Monte Carlo code, MORSE, charged particle effects can be obtained for problems associated with very complex geometries. Results are presented for several charged particle problems. Good agreement is obtained between quantities calculated with the multigroup approach and those obtained experimentally or by atomistic computer codes

EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing.

Science.gov (United States)

Berndsen, Zachary; Bowman, Charles; Jang, Haerin; Ward, Andrew B

2017-12-01

The Electron Microscopy Hole Punch (EMHP) is a streamlined suite of tools for quick assessment, sorting and hole masking of electron micrographs. With recent advances in single-particle electron cryo-microscopy (cryo-EM) data processing allowing for the rapid determination of protein structures using a smaller computational footprint, we saw the need for a fast and simple tool for data pre-processing that could run independent of existing high-performance computing (HPC) infrastructures. EMHP provides a data preprocessing platform in a small package that requires minimal python dependencies to function. https://www.bitbucket.org/chazbot/emhp Apache 2.0 License. bowman@scripps.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Particle beam dynamics simulations using the POOMA framework

International Nuclear Information System (INIS)

Humphrey, W.; Ryne, R.; Cleland, T.; Cummings, J.; Habib, S.; Mark, G.; Ji Qiang

1998-01-01

A program for simulation of the dynamics of high intensity charged particle beams in linear particle accelerators has been developed in C++ using the POOMA Framework, for use on serial and parallel architectures. The code models the trajectories of charged particles through a sequence of different accelerator beamline elements such as drift chambers, quadrupole magnets, or RF cavities. An FFT-based particle-in-cell algorithm is used to solve the Poisson equation that models the Coulomb interactions of the particles. The code employs an object-oriented design with software abstractions for the particle beam, accelerator beamline, and beamline elements, using C++ templates to efficiently support both 2D and 3D capabilities in the same code base. The POOMA Framework, which encapsulates much of the effort required for parallel execution, provides particle and field classes, particle-field interaction capabilities, and parallel FFT algorithms. The performance of this application running serially and in parallel is compared to an existing HPF implementation, with the POOMA version seen to run four times faster than the HPF code

Vectorization, parallelization and porting of nuclear codes. 2001

International Nuclear Information System (INIS)

Akiyama, Mitsunaga; Katakura, Fumishige; Kume, Etsuo; Nemoto, Toshiyuki; Tsuruoka, Takuya; Adachi, Masaaki

2003-07-01

Several computer codes in the nuclear field have been vectorized, parallelized and transported on the super computer system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 10 codes in fiscal 2001. In this report, the parallelization of Neutron Radiography for 3 Dimensional CT code NR3DCT, the vectorization of unsteady-state heat conduction code THERMO3D, the porting of initial program of MHD simulation, the tuning of Heat And Mass Balance Analysis Code HAMBAC, the porting and parallelization of Monte Carlo N-Particle transport code MCNP4C3, the porting and parallelization of Monte Carlo N-Particle transport code system MCNPX2.1.5, the porting of induced activity calculation code CINAC-V4, the use of VisLink library in multidimensional two-fluid model code ACD3D and the porting of experiment data processing code from GS8500 to SR8000 are described. (author)

Synthetic radiation diagnostics in PIConGPU. Integrating spectral detectors into particle-in-cell codes

Energy Technology Data Exchange (ETDEWEB)

Pausch, Richard; Burau, Heiko; Huebl, Axel; Steiniger, Klaus [Helmholtz-Zentrum Dresden-Rossendorf (Germany); Technische Universitaet Dresden (Germany); Debus, Alexander; Widera, Rene; Bussmann, Michael [Helmholtz-Zentrum Dresden-Rossendorf (Germany)

2016-07-01

We present the in-situ far field radiation diagnostics in the particle-in-cell code PIConGPU. It was developed to close the gap between simulated plasma dynamics and radiation observed in laser plasma experiments. Its predictive capabilities, both qualitative and quantitative, have been tested against analytical models. Now, we apply this synthetic spectral diagnostics to investigate plasma dynamics in laser wakefield acceleration, laser foil irradiation and plasma instabilities. Our method is based on the far field approximation of the Lienard-Wiechert potential and allows predicting both coherent and incoherent radiation spectrally from infrared to X-rays. Its capability to resolve the radiation polarization and to determine the temporal and spatial origin of the radiation enables us to correlate specific spectral signatures with characteristic dynamics in the plasma. Furthermore, its direct integration into the highly-scalable GPU framework of PIConGPU allows computing radiation spectra for thousands of frequencies, hundreds of detector positions and billions of particles efficiently. In this talk we will demonstrate these capabilities on resent simulations of laser wakefield acceleration (LWFA) and high harmonics generation during target normal sheath acceleration (TNSA).

Automated data collection in single particle electron microscopy

Science.gov (United States)

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

(Nearly) portable PIC code for parallel computers

International Nuclear Information System (INIS)

Decyk, V.K.

1993-01-01

As part of the Numerical Tokamak Project, the author has developed a (nearly) portable, one dimensional version of the GCPIC algorithm for particle-in-cell codes on parallel computers. This algorithm uses a spatial domain decomposition for the fields, and passes particles from one domain to another as the particles move spatially. With only minor changes, the code has been run in parallel on the Intel Delta, the Cray C-90, the IBM ES/9000 and a cluster of workstations. After a line by line translation into cmfortran, the code was also run on the CM-200. Impressive speeds have been achieved, both on the Intel Delta and the Cray C-90, around 30 nanoseconds per particle per time step. In addition, the author was able to isolate the data management modules, so that the physics modules were not changed much from their sequential version, and the data management modules can be used as open-quotes black boxes.close quotes

N-body simulations for f(R) gravity using a self-adaptive particle-mesh code

International Nuclear Information System (INIS)

Zhao Gongbo; Koyama, Kazuya; Li Baojiu

2011-01-01

We perform high-resolution N-body simulations for f(R) gravity based on a self-adaptive particle-mesh code MLAPM. The chameleon mechanism that recovers general relativity on small scales is fully taken into account by self-consistently solving the nonlinear equation for the scalar field. We independently confirm the previous simulation results, including the matter power spectrum, halo mass function, and density profiles, obtained by Oyaizu et al.[Phys. Rev. D 78, 123524 (2008)] and Schmidt et al.[Phys. Rev. D 79, 083518 (2009)], and extend the resolution up to k∼20 h/Mpc for the measurement of the matter power spectrum. Based on our simulation results, we discuss how the chameleon mechanism affects the clustering of dark matter and halos on full nonlinear scales.

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines

Directory of Open Access Journals (Sweden)

Jingjing Xu

2015-08-01

Full Text Available In this paper, a wireless sensor network (WSN technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD algorithm with particle swarm optimization (PSO, namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization.

Multi-Sensor Detection with Particle Swarm Optimization for Time-Frequency Coded Cooperative WSNs Based on MC-CDMA for Underground Coal Mines.

Science.gov (United States)

Xu, Jingjing; Yang, Wei; Zhang, Linyuan; Han, Ruisong; Shao, Xiaotao

2015-08-27

In this paper, a wireless sensor network (WSN) technology adapted to underground channel conditions is developed, which has important theoretical and practical value for safety monitoring in underground coal mines. According to the characteristics that the space, time and frequency resources of underground tunnel are open, it is proposed to constitute wireless sensor nodes based on multicarrier code division multiple access (MC-CDMA) to make full use of these resources. To improve the wireless transmission performance of source sensor nodes, it is also proposed to utilize cooperative sensors with good channel conditions from the sink node to assist source sensors with poor channel conditions. Moreover, the total power of the source sensor and its cooperative sensors is allocated on the basis of their channel conditions to increase the energy efficiency of the WSN. To solve the problem that multiple access interference (MAI) arises when multiple source sensors transmit monitoring information simultaneously, a kind of multi-sensor detection (MSD) algorithm with particle swarm optimization (PSO), namely D-PSO, is proposed for the time-frequency coded cooperative MC-CDMA WSN. Simulation results show that the average bit error rate (BER) performance of the proposed WSN in an underground coal mine is improved significantly by using wireless sensor nodes based on MC-CDMA, adopting time-frequency coded cooperative transmission and D-PSO algorithm with particle swarm optimization.

Experimental transport analysis code system in JT-60

International Nuclear Information System (INIS)

Hirayama, Toshio; Shimizu, Katsuhiro; Tani, Keiji; Shirai, Hiroshi; Kikuchi, Mitsuru

1988-03-01

Transport analysis codes have been developed in order to study confinement properties related to particle and energy balance in ohmically and neutral beam heated plasmas of JT-60. The analysis procedure is divided into three steps as follows: 1) LOOK ; The shape of the plasma boundary is identified with a fast boundary identification code of FBI by using magnetic data, and flux surfaces are calculated with a MHD equilibrium code of SELENE. The diagnostic data are mapped to flux surfaces for neutral beam heating calculation and/or for radial transport analysis. 2) OFMC ; On the basis of transformed data, an orbit following Monte Carlo code of OFMC calculates both profiles of power deposition and particle source of neutral beam injected into a plasma. 3) SCOOP ; In the last stage, a one dimensional transport code of SCOOP solves particle and energy balance for electron and ion, in order to evaluate transport coefficients as well as global parameters such as energy confinement time and the stored energy. The analysis results are provided to a data bank of DARTS that is used to find an overview of important consideration on confinement with a regression analysis code of RAC. (author)

The OpenMOC method of characteristics neutral particle transport code

International Nuclear Information System (INIS)

Boyd, William; Shaner, Samuel; Li, Lulu; Forget, Benoit; Smith, Kord

2014-01-01

Highlights: • An open source method of characteristics neutron transport code has been developed. • OpenMOC shows nearly perfect scaling on CPUs and 30× speedup on GPUs. • Nonlinear acceleration techniques demonstrate a 40× reduction in source iterations. • OpenMOC uses modern software design principles within a C++ and Python framework. • Validation with respect to the C5G7 and LRA benchmarks is presented. - Abstract: The method of characteristics (MOC) is a numerical integration technique for partial differential equations, and has seen widespread use for reactor physics lattice calculations. The exponential growth in computing power has finally brought the possibility for high-fidelity full core MOC calculations within reach. The OpenMOC code is being developed at the Massachusetts Institute of Technology to investigate algorithmic acceleration techniques and parallel algorithms for MOC. OpenMOC is a free, open source code written using modern software languages such as C/C++ and CUDA with an emphasis on extensible design principles for code developers and an easy to use Python interface for code users. The present work describes the OpenMOC code and illustrates its ability to model large problems accurately and efficiently

Coding and Billing in Surgical Education: A Systems-Based Practice Education Program.

Science.gov (United States)

Ghaderi, Kimeya F; Schmidt, Scott T; Drolet, Brian C

Despite increased emphasis on systems-based practice through the Accreditation Council for Graduate Medical Education core competencies, few studies have examined what surgical residents know about coding and billing. We sought to create and measure the effectiveness of a multifaceted approach to improving resident knowledge and performance of documenting and coding outpatient encounters. We identified knowledge gaps and barriers to documentation and coding in the outpatient setting. We implemented a series of educational and workflow interventions with a group of 12 residents in a surgical clinic at a tertiary care center. To measure the effect of this program, we compared billing codes for 1 year before intervention (FY2012) to prospectively collected data from the postintervention period (FY2013). All related documentation and coding were verified by study-blinded auditors. Interventions took place at the outpatient surgical clinic at Rhode Island Hospital, a tertiary-care center. A cohort of 12 plastic surgery residents ranging from postgraduate year 2 through postgraduate year 6 participated in the interventional sequence. A total of 1285 patient encounters in the preintervention group were compared with 1170 encounters in the postintervention group. Using evaluation and management codes (E&M) as a measure of documentation and coding, we demonstrated a significant and durable increase in billing with supporting clinical documentation after the intervention. For established patient visits, the monthly average E&M code level increased from 2.14 to 3.05 (p coding and billing of outpatient clinic encounters. Using externally audited coding data, we demonstrate significantly increased rates of higher complexity E&M coding in a stable patient population based on improved documentation and billing awareness by the residents. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Use of a hybrid code for global-scale plasma simulation

International Nuclear Information System (INIS)

Swift, D.W.

1996-01-01

This paper presents a demonstration of the use of a hybrid code to model the Earth's magnetosphere on a global scale. The typical hybrid code calculates the interaction of fully kinetic ions and a massless electron fluid with the magnetic field. This code also includes a fluid ion component to approximate the cold ionospheric plasma that spatially overlaps with the discrete particle component. Other innovative features of the code include a numerically generated curvilinear coordinate system and subcycling of the magnetic field update to the particle push. These innovations allow the code to accommodate disparate time and distance scales. The demonstration is a simulation of the noon meridian plane of the magnetosphere. The code exhibits the formation of fast and slow-mode shocks and tearing reconnection at the magnetopause. New results include particle acceleration in the cusp and nearly field aligned currents linking the cusp and polar ionosphere. The paper also describes a density depletion instability and measures to avoid it. 27 refs., 4 figs

A fully-implicit Particle-In-Cell Monte Carlo Collision code for the simulation of inductively coupled plasmas

Science.gov (United States)

Mattei, S.; Nishida, K.; Onai, M.; Lettry, J.; Tran, M. Q.; Hatayama, A.

2017-12-01

We present a fully-implicit electromagnetic Particle-In-Cell Monte Carlo collision code, called NINJA, written for the simulation of inductively coupled plasmas. NINJA employs a kinetic enslaved Jacobian-Free Newton Krylov method to solve self-consistently the interaction between the electromagnetic field generated by the radio-frequency coil and the plasma response. The simulated plasma includes a kinetic description of charged and neutral species as well as the collision processes between them. The algorithm allows simulations with cell sizes much larger than the Debye length and time steps in excess of the Courant-Friedrichs-Lewy condition whilst preserving the conservation of the total energy. The code is applied to the simulation of the plasma discharge of the Linac4 H- ion source at CERN. Simulation results of plasma density, temperature and EEDF are discussed and compared with optical emission spectroscopy measurements. A systematic study of the energy conservation as a function of the numerical parameters is presented.

Multiple sample, radioactive particle counting apparatus

International Nuclear Information System (INIS)

Reddy, R.R.V.; Kelso, D.M.

1978-01-01

An apparatus is described for determining the respective radioactive particle sample count being emitted from radioactive particle containing samples. It includes means for modulating the information on the radioactive particles being emitted from the samples, coded detecting means for sequentially detecting different respective coded combinations of the radioactive particles emitted from more than one but less than all of the samples, and processing the modulated information to derive the sample count for each sample. It includes a single light emitting crystal next to a number of samples, an encoder belt sequentially movable between the crystal and the samples. The encoder belt has a coded array of apertures to provide corresponding modulated light pulses from the crystal, and a photomultiplier tube to convert the modulated light pulses to decodable electrical signals for deriving the respective sample count

High-fidelity plasma codes for burn physics

Energy Technology Data Exchange (ETDEWEB)

Cooley, James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Graziani, Frank [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Marinak, Marty [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Murillo, Michael [Michigan State Univ., East Lansing, MI (United States)

2016-10-19

Accurate predictions of equation of state (EOS), ionic and electronic transport properties are of critical importance for high-energy-density plasma science. Transport coefficients inform radiation-hydrodynamic codes and impact diagnostic interpretation, which in turn impacts our understanding of the development of instabilities, the overall energy balance of burning plasmas, and the efficacy of self-heating from charged-particle stopping. Important processes include thermal and electrical conduction, electron-ion coupling, inter-diffusion, ion viscosity, and charged particle stopping. However, uncertainties in these coefficients are not well established. Fundamental plasma science codes, also called high-fidelity plasma codes, are a relatively recent computational tool that augments both experimental data and theoretical foundations of transport coefficients. This paper addresses the current status of HFPC codes and their future development, and the potential impact they play in improving the predictive capability of the multi-physics hydrodynamic codes used in HED design.

Interaction of free charged particles with a chirped electromagnetic pulse

NARCIS (Netherlands)

Khachatryan, A.G.; van Goor, F.A.; Boller, Klaus J.

2004-01-01

We study the effect of chirp on electromagnetic (EM) pulse interaction with a charged particle. Both the one-dimensional (1D) and 3D cases are considered. It is found that, in contrast to the case of a nonchirped pulse, the charged particle energy can be changed after the interaction with a 1D EM

The dynamics of low-β plasma clouds as simulated by a three-dimensional, electromagnetic particle code

International Nuclear Information System (INIS)

Neubert, T.; Miller, R.H.; Buneman, O.; Nishikawa, K.I.

1992-01-01

The dynamics of low-β plasma clouds moving perpendicular to an ambient magnetic field in vacuum and in a background plasma is simulated by means of a three-dimensional, electromagnetic, and relativistic particle simulation code. The simulations show the formation of the space charge sheaths at the sides of the cloud with the associated polarization electric field which facilitate the cross-field propagation, as well as the sheaths at the front and rear end of the cloud caused by the larger ion Larmor radius, which allows ions to move ahead and lag behind the electrons as they gyrate. Results on the cloud dynamics and electromagnetic radiation include the following: (1) In a background plasma, electron and ion sheaths expand along the magnetic field at the same rate, whereas in vacuum the electron sheath expands much faster than the ion sheath. (2) Sheath electrons are accelerated up to relativistic energies. This result indicates that artificial plasma clouds released in the ionosphere or magnetosphere may generate optical emissions (aurora) as energetic sheath electrons scatter in the upper atmosphere. (3) The expansion of the electron sheaths is analogous to the ejection of high-intensity electron beams from spacecraft. (4) Second-order and higher-order sheaths are formed which extend out into the ambient plasma. (5) Formation of the sheaths and the polarization field reduces the forward momentum of the cloud. (6) The coherent component of the particle gyromotion is damped in time as the particles establish a forward directed drift velocity. (7) The coherent particle gyrations generate electromagnetic radiation

Agile deployment and code coverage testing metrics of the boot software on-board Solar Orbiter's Energetic Particle Detector

Science.gov (United States)

Parra, Pablo; da Silva, Antonio; Polo, Óscar R.; Sánchez, Sebastián

2018-02-01

In this day and age, successful embedded critical software needs agile and continuous development and testing procedures. This paper presents the overall testing and code coverage metrics obtained during the unit testing procedure carried out to verify the correctness of the boot software that will run in the Instrument Control Unit (ICU) of the Energetic Particle Detector (EPD) on-board Solar Orbiter. The ICU boot software is a critical part of the project so its verification should be addressed at an early development stage, so any test case missed in this process may affect the quality of the overall on-board software. According to the European Cooperation for Space Standardization ESA standards, testing this kind of critical software must cover 100% of the source code statement and decision paths. This leads to the complete testing of fault tolerance and recovery mechanisms that have to resolve every possible memory corruption or communication error brought about by the space environment. The introduced procedure enables fault injection from the beginning of the development process and enables to fulfill the exigent code coverage demands on the boot software.

Parallelization of quantum molecular dynamics simulation code

International Nuclear Information System (INIS)

Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

1998-02-01

A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

Simulation of halo particles with Simpsons

International Nuclear Information System (INIS)

Machida, Shinji

2003-01-01

Recent code improvements and some simulation results of halo particles with Simpsons will be presented. We tried to identify resonance behavior of halo particles by looking at tune evolution of individual macro particle

Simulation of halo particles with Simpsons

Science.gov (United States)

Machida, Shinji

2003-12-01

Recent code improvements and some simulation results of halo particles with Simpsons will be presented. We tried to identify resonance behavior of halo particles by looking at tune evolution of individual macro particle.

Ripple enhanced transport of suprathermal alpha particles

International Nuclear Information System (INIS)

Tani, K.; Takizuka, T.; Azumi, M.

1986-01-01

The ripple enhanced transport of suprathermal alpha particles has been studied by the newly developed Monte-Carlo code in which the motion of banana orbit in a toroidal field ripple is described by a mapping method. The existence of ripple-resonance diffusion has been confirmed numerically. We have developed another new code in which the radial displacement of banana orbit is given by the diffusion coefficients from the mapping code or the orbit following Monte-Carlo code. The ripple loss of α particles during slowing down has been estimated by the mapping model code as well as the diffusion model code. From the comparison of the results with those from the orbit-following Monte-Carlo code, it has been found that all of them agree very well. (author)

The All Particle Method: 1991 status report

International Nuclear Information System (INIS)

Cullen, D.E.; Ballinger, C.T.; Perkins, S.T.

1991-07-01

At the present time a Monte Carlo transport computer code is being designed and implemented at Lawrence Livermore National Laboratory to include the transport of: neutrons, photons, electrons and light charged particles as well as the coupling between all species of particles, e.g. photon induced electron emission. Since this code is being designed to handle all particles, this approach is called the ''All Particle Method.'' This paper describes the current design philosophy and status of the Monte Carlo transport code and its supporting data bases. The treatment of neutrons and photons used by the All Particle Method code is conventional and as such this topic will not be discussed in this paper. Here emphasis is on discussion of our recent work to extend our ability to perform electron transport, as well as photon transport, as it is effected by coupling to electron transport, and atomic relaxation. First we discuss our new extended photon and electron interaction and atomic relaxation data bases. Next we illustrate the extended capabilities that these new data bases provide by presenting the results of several Monte Carlo transport calculations

Steam condensation modelling in aerosol codes

International Nuclear Information System (INIS)

Dunbar, I.H.

1986-01-01

The principal subject of this study is the modelling of the condensation of steam into and evaporation of water from aerosol particles. These processes introduce a new type of term into the equation for the development of the aerosol particle size distribution. This new term faces the code developer with three major problems: the physical modelling of the condensation/evaporation process, the discretisation of the new term and the separate accounting for the masses of the water and of the other components. This study has considered four codes which model the condensation of steam into and its evaporation from aerosol particles: AEROSYM-M (UK), AEROSOLS/B1 (France), NAUA (Federal Republic of Germany) and CONTAIN (USA). The modelling in the codes has been addressed under three headings. These are the physical modelling of condensation, the mathematics of the discretisation of the equations, and the methods for modelling the separate behaviour of different chemical components of the aerosol. The codes are least advanced in area of solute effect modelling. At present only AEROSOLS/B1 includes the effect. The effect is greater for more concentrated solutions. Codes without the effect will be more in error (underestimating the total airborne mass) the less condensation they predict. Data are needed on the water vapour pressure above concentrated solutions of the substances of interest (especially CsOH and CsI) if the extent to which aerosols retain water under superheated conditions is to be modelled. 15 refs

Implementation of collisions on GPU architecture in the Vorpal code

Science.gov (United States)

Leddy, Jarrod; Averkin, Sergey; Cowan, Ben; Sides, Scott; Werner, Greg; Cary, John

2017-10-01

The Vorpal code contains a variety of collision operators allowing for the simulation of plasmas containing multiple charge species interacting with neutrals, background gas, and EM fields. These existing algorithms have been improved and reimplemented to take advantage of the massive parallelization allowed by GPU architecture. The use of GPUs is most effective when algorithms are single-instruction multiple-data, so particle collisions are an ideal candidate for this parallelization technique due to their nature as a series of independent processes with the same underlying operation. This refactoring required data memory reorganization and careful consideration of device/host data allocation to minimize memory access and data communication per operation. Successful implementation has resulted in an order of magnitude increase in simulation speed for a test-case involving multiple binary collisions using the null collision method. Work supported by DARPA under contract W31P4Q-16-C-0009.

N-body simulations for f(R) gravity using a self-adaptive particle-mesh code

Science.gov (United States)

Zhao, Gong-Bo; Li, Baojiu; Koyama, Kazuya

2011-02-01

We perform high-resolution N-body simulations for f(R) gravity based on a self-adaptive particle-mesh code MLAPM. The chameleon mechanism that recovers general relativity on small scales is fully taken into account by self-consistently solving the nonlinear equation for the scalar field. We independently confirm the previous simulation results, including the matter power spectrum, halo mass function, and density profiles, obtained by Oyaizu [Phys. Rev. DPRVDAQ1550-7998 78, 123524 (2008)10.1103/PhysRevD.78.123524] and Schmidt [Phys. Rev. DPRVDAQ1550-7998 79, 083518 (2009)10.1103/PhysRevD.79.083518], and extend the resolution up to k˜20h/Mpc for the measurement of the matter power spectrum. Based on our simulation results, we discuss how the chameleon mechanism affects the clustering of dark matter and halos on full nonlinear scales.

Translation of ARAC computer codes

International Nuclear Information System (INIS)

Takahashi, Kunio; Chino, Masamichi; Honma, Toshimitsu; Ishikawa, Hirohiko; Kai, Michiaki; Imai, Kazuhiko; Asai, Kiyoshi

1982-05-01

In 1981 we have translated the famous MATHEW, ADPIC and their auxiliary computer codes for CDC 7600 computer version to FACOM M-200's. The codes consist of a part of the Atmospheric Release Advisory Capability (ARAC) system of Lawrence Livermore National Laboratory (LLNL). The MATHEW is a code for three-dimensional wind field analysis. Using observed data, it calculates the mass-consistent wind field of grid cells by a variational method. The ADPIC is a code for three-dimensional concentration prediction of gases and particulates released to the atmosphere. It calculates concentrations in grid cells by the particle-in-cell method. They are written in LLLTRAN, i.e., LLNL Fortran language and are implemented on the CDC 7600 computers of LLNL. In this report, i) the computational methods of the MATHEW/ADPIC and their auxiliary codes, ii) comparisons of the calculated results with our JAERI particle-in-cell, and gaussian plume models, iii) translation procedures from the CDC version to FACOM M-200's, are described. Under the permission of LLNL G-Division, this report is published to keep the track of the translation procedures and to serve our JAERI researchers for comparisons and references of their works. (author)

Monte Carlo codes use in neutron therapy; Application de codes Monte Carlo en neutrontherapie

Energy Technology Data Exchange (ETDEWEB)

Paquis, P.; Mokhtari, F.; Karamanoukian, D. [Hopital Pasteur, 06 - Nice (France); Pignol, J.P. [Hopital du Hasenrain, 68 - Mulhouse (France); Cuendet, P. [CEA Centre d' Etudes de Saclay, 91 - Gif-sur-Yvette (France). Direction des Reacteurs Nucleaires; Fares, G.; Hachem, A. [Faculte des Sciences, 06 - Nice (France); Iborra, N. [Centre Antoine-Lacassagne, 06 - Nice (France)

1998-04-01

Monte Carlo calculation codes allow to study accurately all the parameters relevant to radiation effects, like the dose deposition or the type of microscopic interactions, through one by one particle transport simulation. These features are very useful for neutron irradiations, from device development up to dosimetry. This paper illustrates some applications of these codes in Neutron Capture Therapy and Neutron Capture Enhancement of fast neutrons irradiations. (authors)

Spot: a new Monte Carlo solver for fast alpha particles

International Nuclear Information System (INIS)

Schneider, M.; Eriksson, L.G.; Basiuk, V.; Imbeaux, F.

2004-01-01

The predictive transport code CRONOS has been augmented by an orbit following Monte Carlo code, SPOT (Simulation of Particle Orbits in a Tokamak). The SPOT code simulates the dynamics of nonthermal particles, and takes into account effects of finite orbit width and collisional transport of fast ions. Recent developments indicate that it might be difficult to avoid, at least transiently, current holes in a reactor. They occur already on existing tokamaks during advanced tokamak scenarios. The SPOT code has been used to study the alpha particle behaviour in the presence of current holes for both JET and ITER relevant parameters. (authors)

Parallel pic plasma simulation through particle decomposition techniques

International Nuclear Information System (INIS)

Briguglio, S.; Vlad, G.; Di Martino, B.; Naples, Univ. 'Federico II'

1998-02-01

Particle-in-cell (PIC) codes are among the major candidates to yield a satisfactory description of the detail of kinetic effects, such as the resonant wave-particle interaction, relevant in determining the transport mechanism in magnetically confined plasmas. A significant improvement of the simulation performance of such codes con be expected from parallelization, e.g., by distributing the particle population among several parallel processors. Parallelization of a hybrid magnetohydrodynamic-gyrokinetic code has been accomplished within the High Performance Fortran (HPF) framework, and tested on the IBM SP2 parallel system, using a 'particle decomposition' technique. The adopted technique requires a moderate effort in porting the code in parallel form and results in intrinsic load balancing and modest inter processor communication. The performance tests obtained confirm the hypothesis of high effectiveness of the strategy, if targeted towards moderately parallel architectures. Optimal use of resources is also discussed with reference to a specific physics problem [it

Radiation protection studies for medical particle accelerators using FLUKA Monte Carlo code

International Nuclear Information System (INIS)

Infantino, Angelo; Mostacci, Domiziano; Cicoria, Gianfranco; Lucconi, Giulia; Pancaldi, Davide; Vichi, Sara; Zagni, Federico; Marengo, Mario

2017-01-01

Radiation protection (RP) in the use of medical cyclotrons involves many aspects both in the routine use and for the decommissioning of a site. Guidelines for site planning and installation, as well as for RP assessment, are given in international documents; however, the latter typically offer analytic methods of calculation of shielding and materials activation, in approximate or idealised geometry set-ups. The availability of Monte Carlo (MC) codes with accurate up-to-date libraries for transport and interaction of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of modern computers, makes the systematic use of simulations with realistic geometries possible, yielding equipment and site-specific evaluation of the source terms, shielding requirements and all quantities relevant to RP at the same time. In this work, the well-known FLUKA MC code was used to simulate different aspects of RP in the use of biomedical accelerators, particularly for the production of medical radioisotopes. In the context of the Young Professionals Award, held at the IRPA 14 conference, only a part of the complete work is presented. In particular, the simulation of the GE PETtrace cyclotron (16.5 MeV) installed at S. Orsola-Malpighi University Hospital evaluated the effective dose distribution around the equipment; the effective number of neutrons produced per incident proton and their spectral distribution; the activation of the structure of the cyclotron and the vault walls; the activation of the ambient air, in particular the production of "4"1Ar. The simulations were validated, in terms of physical and transport parameters to be used at the energy range of interest, through an extensive measurement campaign of the neutron environmental dose equivalent using a rem-counter and TLD dosemeters. The validated model was then used in the design and the licensing request of a new Positron Emission Tomography facility. (authors)

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

Science.gov (United States)

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

Comparison of a 3D multi‐group SN particle transport code with Monte Carlo for intercavitary brachytherapy of the cervix uteri

Science.gov (United States)

Wareing, Todd A.; Failla, Gregory; Horton, John L.; Eifel, Patricia J.; Mourtada, Firas

2009-01-01

A patient dose distribution was calculated by a 3D multi‐group SN particle transport code for intracavitary brachytherapy of the cervix uteri and compared to previously published Monte Carlo results. A Cs‐137 LDR intracavitary brachytherapy CT data set was chosen from our clinical database. MCNPX version 2.5.c, was used to calculate the dose distribution. A 3D multi‐group SN particle transport code, Attila version 6.1.1 was used to simulate the same patient. Each patient applicator was built in SolidWorks, a mechanical design package, and then assembled with a coordinate transformation and rotation for the patient. The SolidWorks exported applicator geometry was imported into Attila for calculation. Dose matrices were overlaid on the patient CT data set. Dose volume histograms and point doses were compared. The MCNPX calculation required 14.8 hours, whereas the Attila calculation required 22.2 minutes on a 1.8 GHz AMD Opteron CPU. Agreement between Attila and MCNPX dose calculations at the ICRU 38 points was within ±3%. Calculated doses to the 2 cc and 5 cc volumes of highest dose differed by not more than ±1.1% between the two codes. Dose and DVH overlays agreed well qualitatively. Attila can calculate dose accurately and efficiently for this Cs‐137 CT‐based patient geometry. Our data showed that a three‐group cross‐section set is adequate for Cs‐137 computations. Future work is aimed at implementing an optimized version of Attila for radiotherapy calculations. PACS number: 87.53.Jw

Recent Progress on the Marylie/Impact Beam Dynamics Code

International Nuclear Information System (INIS)

Ryne, R.D.; Qiang, J.; Bethel, E.W.; Pogorelov, I.; Shalf, J.; Siegerist, C.; Venturini, M.; Dragt, A.J.; Adelmann, A.; Abell, D.; Amundson, J.; Spentzouris, P.; Neri, F.; Walstrom, P.; Mottershead, C.T.; Samulyak, R.

2006-01-01

MARYLIE/IMPACT (ML/I) is a hybrid code that combines the beam optics capabilities of MARYLIE with the parallel Particle-In-Cell capabilities of IMPACT. In addition to combining the capabilities of these codes, ML/I has a number of powerful features, including a choice of Poisson solvers, a fifth-order rf cavity model, multiple reference particles for rf cavities, a library of soft-edge magnet models, representation of magnet systems in terms of coil stacks with possibly overlapping fields, and wakefield effects. The code allows for map production, map analysis, particle tracking, and 3D envelope tracking, all within a single, coherent user environment. ML/I has a front end that can read both MARYLIE input and MAD lattice descriptions. The code can model beams with or without acceleration, and with or without space charge. Developed under a US DOE Scientific Discovery through Advanced Computing (SciDAC) project, ML/I is well suited to large-scale modeling, simulations having been performed with up to 100M macroparticles. The code inherits the powerful fitting and optimizing capabilities of MARYLIE augmented for the new features of ML/I. The combination of soft-edge magnet models, high-order capability, space charge effects, and fitting/optimization capabilities, make ML/I a powerful code for a wide range of beam optics design problems. This paper provides a description of the code and its unique capabilities

Study on EM-parameters and EM-wave absorption properties of materials with bio-flaky particles added

Energy Technology Data Exchange (ETDEWEB)

Zhang, Wenqiang, E-mail: zwqcau@gmail.com [College of Engineering, China Agricultural University, Beijing 100083 (China); Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, Beihang University, Beijing 100191 (China); Zhang, Deyuan; Xu, Yonggang [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, Beihang University, Beijing 100191 (China); McNaughton, Ryan [Department of Biomedical Engineering, Boston University, Boston 02215 (United States)

2016-01-01

Bio-flaky particles, fabricated through deposition of carbonyl iron on the surface of disk shaped diatomite, demonstrated beneficial performance on electromagnetic parameters. This paper will detail the improvements to the electromagnetic parameters and absorbing properties of traditional absorbing material generated by the addition of bio-flaky particles. Composites' electromagnetic parameters were measured using the transmission method. Calculated test results confirmed with bio-flaky particles were added, composites' permittivity increased due to the high permeability of bio-flaky particles. Secondly, the permeability of composites increased as a result of the increased volume content of iron particles. Composites with bio-flaky particles added exhibited superlative absorption properties at 0.5 mm thickness, with a maximum reflection loss of approximately −5.1 dB at 14.4 GHz. - Highlights: • Light weight absorbing composites were fabricated with bio-flaky particles added. • SEM results show bio-flaky particles could help the arrangement of FCIPs. • Composites' RL could be improved with bio-flaky particles added. • The RL peak move to lower frequency with bio-flaky particles added.

Study on EM-parameters and EM-wave absorption properties of materials with bio-flaky particles added

International Nuclear Information System (INIS)

Zhang, Wenqiang; Zhang, Deyuan; Xu, Yonggang; McNaughton, Ryan

2016-01-01

Bio-flaky particles, fabricated through deposition of carbonyl iron on the surface of disk shaped diatomite, demonstrated beneficial performance on electromagnetic parameters. This paper will detail the improvements to the electromagnetic parameters and absorbing properties of traditional absorbing material generated by the addition of bio-flaky particles. Composites' electromagnetic parameters were measured using the transmission method. Calculated test results confirmed with bio-flaky particles were added, composites' permittivity increased due to the high permeability of bio-flaky particles. Secondly, the permeability of composites increased as a result of the increased volume content of iron particles. Composites with bio-flaky particles added exhibited superlative absorption properties at 0.5 mm thickness, with a maximum reflection loss of approximately −5.1 dB at 14.4 GHz. - Highlights: • Light weight absorbing composites were fabricated with bio-flaky particles added. • SEM results show bio-flaky particles could help the arrangement of FCIPs. • Composites' RL could be improved with bio-flaky particles added. • The RL peak move to lower frequency with bio-flaky particles added.

TRANGE: computer code to calculate the energy beam degradation in target stack; TRANGE: programa para calcular a degradacao de energia de particulas carregadas em alvos

Energy Technology Data Exchange (ETDEWEB)

Bellido, Luis F.

1995-07-01

A computer code to calculate the projectile energy degradation along a target stack was developed for an IBM or compatible personal microcomputer. A comparison of protons and deuterons bombarding uranium and aluminium targets was made. The results showed that the data obtained with TRANGE were in agreement with other computers code such as TRIM, EDP and also using Williamsom and Janni range and stopping power tables. TRANGE can be used for any charged particle ion, for energies between 1 to 100 MeV, in metal foils and solid compounds targets. (author). 8 refs., 2 tabs.

Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

Science.gov (United States)

de Wit, C; Fautz, C; Xu, Y

2000-09-01

Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell

Relating quantum discord with the quantum dense coding capacity

Energy Technology Data Exchange (ETDEWEB)

Wang, Xin; Qiu, Liang, E-mail: lqiu@cumt.edu.cn; Li, Song; Zhang, Chi [China University of Mining and Technology, School of Sciences (China); Ye, Bin [China University of Mining and Technology, School of Information and Electrical Engineering (China)

2015-01-15

We establish the relations between quantum discord and the quantum dense coding capacity in (n + 1)-particle quantum states. A necessary condition for the vanishing discord monogamy score is given. We also find that the loss of quantum dense coding capacity due to decoherence is bounded below by the sum of quantum discord. When these results are restricted to three-particle quantum states, some complementarity relations are obtained.

Relating quantum discord with the quantum dense coding capacity

International Nuclear Information System (INIS)

Wang, Xin; Qiu, Liang; Li, Song; Zhang, Chi; Ye, Bin

2015-01-01

We establish the relations between quantum discord and the quantum dense coding capacity in (n + 1)-particle quantum states. A necessary condition for the vanishing discord monogamy score is given. We also find that the loss of quantum dense coding capacity due to decoherence is bounded below by the sum of quantum discord. When these results are restricted to three-particle quantum states, some complementarity relations are obtained

Recent Improvements to the IMPACT-T Parallel Particle Tracking Code

International Nuclear Information System (INIS)

Qiang, J.; Pogorelov, I.V.; Ryne, R.

2006-01-01

The IMPACT-T code is a parallel three-dimensional quasi-static beam dynamics code for modeling high brightness beams in photoinjectors and RF linacs. Developed under the US DOE Scientific Discovery through Advanced Computing (SciDAC) program, it includes several key features including a self-consistent calculation of 3D space-charge forces using a shifted and integrated Green function method, multiple energy bins for beams with large energy spread, and models for treating RF standing wave and traveling wave structures. In this paper, we report on recent improvements to the IMPACT-T code including modeling traveling wave structures, short-range transverse and longitudinal wakefields, and longitudinal coherent synchrotron radiation through bending magnets

Implementing displacement damage calculations for electrons and gamma rays in the Particle and Heavy-Ion Transport code System

Science.gov (United States)

Iwamoto, Yosuke

2018-03-01

In this study, the Monte Carlo displacement damage calculation method in the Particle and Heavy-Ion Transport code System (PHITS) was improved to calculate displacements per atom (DPA) values due to irradiation by electrons (or positrons) and gamma rays. For the damage due to electrons and gamma rays, PHITS simulates electromagnetic cascades using the Electron Gamma Shower version 5 (EGS5) algorithm and calculates DPA values using the recoil energies and the McKinley-Feshbach cross section. A comparison of DPA values calculated by PHITS and the Monte Carlo assisted Classical Method (MCCM) reveals that they were in good agreement for gamma-ray irradiations of silicon and iron at energies that were less than 10 MeV. Above 10 MeV, PHITS can calculate DPA values not only for electrons but also for charged particles produced by photonuclear reactions. In DPA depth distributions under electron and gamma-ray irradiations, build-up effects can be observed near the target's surface. For irradiation of 90-cm-thick carbon by protons with energies of more than 30 GeV, the ratio of the secondary electron DPA values to the total DPA values is more than 10% and increases with an increase in incident energy. In summary, PHITS can calculate DPA values for all particles and materials over a wide energy range between 1 keV and 1 TeV for electrons, gamma rays, and charged particles and between 10-5 eV and 1 TeV for neutrons.

MC21 v.6.0 - A continuous-energy Monte Carlo particle transport code with integrated reactor feedback capabilities

International Nuclear Information System (INIS)

Grieshemer, D.P.; Gill, D.F.; Nease, B.R.; Carpenter, D.C.; Joo, H.; Millman, D.L.; Sutton, T.M.; Stedry, M.H.; Dobreff, P.S.; Trumbull, T.H.; Caro, E.

2013-01-01

MC21 is a continuous-energy Monte Carlo radiation transport code for the calculation of the steady-state spatial distributions of reaction rates in three-dimensional models. The code supports neutron and photon transport in fixed source problems, as well as iterated-fission-source (eigenvalue) neutron transport problems. MC21 has been designed and optimized to support large-scale problems in reactor physics, shielding, and criticality analysis applications. The code also supports many in-line reactor feedback effects, including depletion, thermal feedback, xenon feedback, eigenvalue search, and neutron and photon heating. MC21 uses continuous-energy neutron/nucleus interaction physics over the range from 10 -5 eV to 20 MeV. The code treats all common neutron scattering mechanisms, including fast-range elastic and non-elastic scattering, and thermal- and epithermal-range scattering from molecules and crystalline materials. For photon transport, MC21 uses continuous-energy interaction physics over the energy range from 1 keV to 100 GeV. The code treats all common photon interaction mechanisms, including Compton scattering, pair production, and photoelectric interactions. All of the nuclear data required by MC21 is provided by the NDEX system of codes, which extracts and processes data from EPDL-, ENDF-, and ACE-formatted source files. For geometry representation, MC21 employs a flexible constructive solid geometry system that allows users to create spatial cells from first- and second-order surfaces. The system also allows models to be built up as hierarchical collections of previously defined spatial cells, with interior detail provided by grids and template overlays. Results are collected by a generalized tally capability which allows users to edit integral flux and reaction rate information. Results can be collected over the entire problem or within specific regions of interest through the use of phase filters that control which particles are allowed to score each

Dynamic load balancing in a concurrent plasma PIC code on the JPL/Caltech Mark III hypercube

International Nuclear Information System (INIS)

Liewer, P.C.; Leaver, E.W.; Decyk, V.K.; Dawson, J.M.

1990-01-01

Dynamic load balancing has been implemented in a concurrent one-dimensional electromagnetic plasma particle-in-cell (PIC) simulation code using a method which adds very little overhead to the parallel code. In PIC codes, the orbits of many interacting plasma electrons and ions are followed as an initial value problem as the particles move in electromagnetic fields calculated self-consistently from the particle motions. The code was implemented using the GCPIC algorithm in which the particles are divided among processors by partitioning the spatial domain of the simulation. The problem is load-balanced by partitioning the spatial domain so that each partition has approximately the same number of particles. During the simulation, the partitions are dynamically recreated as the spatial distribution of the particles changes in order to maintain processor load balance

Charged particles in external electromagnetic fields

International Nuclear Information System (INIS)

Giovannini, N.P.D.

1976-01-01

The present study contains a general theoretical group analysis of the problem of a charged massive particle moving in an (arbitrary) classical external electromagnetic field. This analysis is essentially based on the space-time symmetry properties of e.m. fields and e.m. field equations, as well as the fact that the considered equations of motion depend on the field via a potential

3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer

International Nuclear Information System (INIS)

Wang, J.; Liewer, P.C.

1994-01-01

A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed

A PIC-MCC code for simulation of streamer propagation in air

DEFF Research Database (Denmark)

Chanrion, Olivier Arnaud; Neubert, Torsten

2008-01-01

A particle code has been developed to study the distribution and acceleration of electrons in electric discharges in air. The code can follow the evolution of a discharge from the initial stage of a single free electron in a background electric field to the formation of an electron avalanche...... and its transition into a streamer. The code is in 2D axi-symmetric coordinates, allowing quasi 3D simulations during the initial stages of streamer formation. This is important for realistic simulations of problems where space charge fields are essential such as in streamer formation. The charged...... particles are followed in a Cartesian mesh and the electric field is updated with Poisson's equation from the charged particle densities. Collisional processes between electrons and air molecules are simulated with a Monte Carlo technique, according to cross section probabilities. The code also includes...

Nyx: Adaptive mesh, massively-parallel, cosmological simulation code

Science.gov (United States)

Almgren, Ann; Beckner, Vince; Friesen, Brian; Lukic, Zarija; Zhang, Weiqun

2017-12-01

Nyx code solves equations of compressible hydrodynamics on an adaptive grid hierarchy coupled with an N-body treatment of dark matter. The gas dynamics in Nyx use a finite volume methodology on an adaptive set of 3-D Eulerian grids; dark matter is represented as discrete particles moving under the influence of gravity. Particles are evolved via a particle-mesh method, using Cloud-in-Cell deposition/interpolation scheme. Both baryonic and dark matter contribute to the gravitational field. In addition, Nyx includes physics for accurately modeling the intergalactic medium; in optically thin limits and assuming ionization equilibrium, the code calculates heating and cooling processes of the primordial-composition gas in an ionizing ultraviolet background radiation field.

VOA: a 2-d plasma physics code

International Nuclear Information System (INIS)

Eltgroth, P.G.

1975-12-01

A 2-dimensional relativistic plasma physics code was written and tested. The non-thermal components of the particle distribution functions are represented by expansion into moments in momentum space. These moments are computed directly from numerical equations. Currently three species are included - electrons, ions and ''beam electrons''. The computer code runs on either the 7600 or STAR machines at LLL. Both the physics and the operation of the code are discussed

Recent progress in 3D EM/EM-PIC simulation with ARGUS and parallel ARGUS

International Nuclear Information System (INIS)

Mankofsky, A.; Petillo, J.; Krueger, W.; Mondelli, A.; McNamara, B.; Philp, R.

1994-01-01

ARGUS is an integrated, 3-D, volumetric simulation model for systems involving electric and magnetic fields and charged particles, including materials embedded in the simulation region. The code offers the capability to carry out time domain and frequency domain electromagnetic simulations of complex physical systems. ARGUS offers a boolean solid model structure input capability that can include essentially arbitrary structures on the computational domain, and a modular architecture that allows multiple physics packages to access the same data structure and to share common code utilities. Physics modules are in place to compute electrostatic and electromagnetic fields, the normal modes of RF structures, and self-consistent particle-in-cell (PIC) simulation in either a time dependent mode or a steady state mode. The PIC modules include multiple particle species, the Lorentz equations of motion, and algorithms for the creation of particles by emission from material surfaces, injection onto the grid, and ionization. In this paper, we present an updated overview of ARGUS, with particular emphasis given in recent algorithmic and computational advances. These include a completely rewritten frequency domain solver which efficiently treats lossy materials and periodic structures, a parallel version of ARGUS with support for both shared memory parallel vector (i.e. CRAY) machines and distributed memory massively parallel MIMD systems, and numerous new applications of the code

Coding considerations for standalone molecular dynamics simulations of atomistic structures

Science.gov (United States)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Use of the Coding Causes of Death in HIV in the classification of deaths in Northeastern Brazil.

Science.gov (United States)

Alves, Diana Neves; Bresani-Salvi, Cristiane Campello; Batista, Joanna d'Arc Lyra; Ximenes, Ricardo Arraes de Alencar; Miranda-Filho, Demócrito de Barros; Melo, Heloísa Ramos Lacerda de; Albuquerque, Maria de Fátima Pessoa Militão de

2017-01-01

Describe the coding process of death causes for people living with HIV/AIDS, and classify deaths as related or unrelated to immunodeficiency by applying the Coding Causes of Death in HIV (CoDe) system. A cross-sectional study that codifies and classifies the causes of deaths occurring in a cohort of 2,372 people living with HIV/AIDS, monitored between 2007 and 2012, in two specialized HIV care services in Pernambuco. The causes of death already codified according to the International Classification of Diseases were recoded and classified as deaths related and unrelated to immunodeficiency by the CoDe system. We calculated the frequencies of the CoDe codes for the causes of death in each classification category. There were 315 (13%) deaths during the study period; 93 (30%) were caused by an AIDS-defining illness on the Centers for Disease Control and Prevention list. A total of 232 deaths (74%) were related to immunodeficiency after application of the CoDe. Infections were the most common cause, both related (76%) and unrelated (47%) to immunodeficiency, followed by malignancies (5%) in the first group and external causes (16%), malignancies (12 %) and cardiovascular diseases (11%) in the second group. Tuberculosis comprised 70% of the immunodeficiency-defining infections. Opportunistic infections and aging diseases were the most frequent causes of death, adding multiple disease burdens on health services. The CoDe system increases the probability of classifying deaths more accurately in people living with HIV/AIDS. Descrever o processo de codificação das causas de morte em pessoas vivendo com HIV/Aids, e classificar os óbitos como relacionados ou não relacionados à imunodeficiência aplicando o sistema Coding Causes of Death in HIV (CoDe). Estudo transversal, que codifica e classifica as causas dos óbitos ocorridos em uma coorte de 2.372 pessoas vivendo com HIV/Aids acompanhadas entre 2007 e 2012 em dois serviços de atendimento especializado em HIV em

Development of M3C code for Monte Carlo reactor physics criticality calculations

International Nuclear Information System (INIS)

Kumar, Anek; Kannan, Umasankari; Krishanani, P.D.

2015-06-01

The development of Monte Carlo code (M3C) for reactor design entails use of continuous energy nuclear data and Monte Carlo simulations for each of the neutron interaction processes. BARC has started a concentrated effort for developing a new general geometry continuous energy Monte Carlo code for reactor physics calculation indigenously. The code development required a comprehensive understanding of the basic continuous energy cross section sets. The important features of this code are treatment of heterogeneous lattices by general geometry, use of point cross sections along with unionized energy grid approach, thermal scattering model for low energy treatment, capability of handling the microscopic fuel particles dispersed randomly. The capability of handling the randomly dispersed microscopic fuel particles which is very useful for the modeling of High-Temperature Gas-Cooled reactor fuels which are composed of thousands of microscopic fuel particle (TRISO fuel particle), randomly dispersed in a graphite matrix. The Monte Carlo code for criticality calculation is a pioneering effort and has been used to study several types of lattices including cluster geometries. The code has been verified for its accuracy against more than 60 sample problems covering a wide range from simple (like spherical) to complex geometry (like PHWR lattice). Benchmark results show that the code performs quite well for the criticality calculation of the system. In this report, the current status of the code, features of the code, some of the benchmark results for the testing of the code and input preparation etc. are discussed. (author)

Aersol particle losses in sampling systems

International Nuclear Information System (INIS)

Fan, B.J.; Wong, F.S.; Ortiz, C.A.; Anand, N.K.; McFarland, A.R.

1993-01-01

When aerosols are sampled from stacks and ducts, it is usually necessary to transport them from the point of sampling to a location of collection or analysis. Losses of aerosol particles can occur in the inlet region of the probe, in straight horizontal and vertical tubes and in elbows. For probes in laminary flow, the Saffman lift force can cause substantial losses of particles in a short inlet region. An empirical model has been developed to predict probe inlet losses, which are often on the order of 40% for 10 μm AED particles. A user-friendly PC computer code, DEPOSITION, has been setup to model losses in transport systems. Experiments have been conducted to compare the actual aerosol particle losses in transport systems with those predicted by the DEPOSITION code

Nonlinear effects of energetic particle driven instabilities in tokamaks

Energy Technology Data Exchange (ETDEWEB)

Bruedgam, Michael

2010-03-25

In a tokamak plasma, a population of superthermal particles generated by heating methods can lead to a destabilization of various MHD modes. Due to nonlinear wave-particle interactions, a consequential fast particle redistribution reduces the plasma heating and can cause severe damages to the wall of the fusion device. In order to describe the wave-particle interaction, the drift-kinetic perturbative HAGIS code is applied which evolves the particle trajectories and the waves nonlinearly. For a simulation speed-up, the 6-d particle phase-space is reduced by the guiding centre approach to a 5-d description. The eigenfunction of the wave is assumed to be invariant, but its amplitude and phase is altered in time. A sophisticated {delta}/f-method is employed to model the change in the fast particle distribution so that numerical noise and the excessive number of simulated Monte-Carlo points are reduced significantly. The original code can only calculate the particle redistribution inside the plasma region. Therefore, a code extension has been developed during this thesis which enlarges the simulation region up to the vessel wall. By means of numerical simulations, this thesis addresses the problem of nonlinear waveparticle interactions in the presence of multiple MHD modes with significantly different eigenfrequencies and the corresponding fast particle transport inside the plasma. In this context, a new coupling mechanism between resonant particles and waves has been identified that leads to enhanced mode amplitudes and fast particle losses. The extension of the code provides for the first time the possibility of a quantitative and qualitative comparison between simulation results and recent measurements in the experiment. The findings of the comparison serve as a validation of both the theoretical model and the interpretation of the experimental results. Thus, a powerful interface tool has been developed for a deeper insight of nonlinear wave-particle interaction

Nonlinear effects of energetic particle driven instabilities in tokamaks

International Nuclear Information System (INIS)

Bruedgam, Michael

2010-01-01

In a tokamak plasma, a population of superthermal particles generated by heating methods can lead to a destabilization of various MHD modes. Due to nonlinear wave-particle interactions, a consequential fast particle redistribution reduces the plasma heating and can cause severe damages to the wall of the fusion device. In order to describe the wave-particle interaction, the drift-kinetic perturbative HAGIS code is applied which evolves the particle trajectories and the waves nonlinearly. For a simulation speed-up, the 6-d particle phase-space is reduced by the guiding centre approach to a 5-d description. The eigenfunction of the wave is assumed to be invariant, but its amplitude and phase is altered in time. A sophisticated δ/f-method is employed to model the change in the fast particle distribution so that numerical noise and the excessive number of simulated Monte-Carlo points are reduced significantly. The original code can only calculate the particle redistribution inside the plasma region. Therefore, a code extension has been developed during this thesis which enlarges the simulation region up to the vessel wall. By means of numerical simulations, this thesis addresses the problem of nonlinear waveparticle interactions in the presence of multiple MHD modes with significantly different eigenfrequencies and the corresponding fast particle transport inside the plasma. In this context, a new coupling mechanism between resonant particles and waves has been identified that leads to enhanced mode amplitudes and fast particle losses. The extension of the code provides for the first time the possibility of a quantitative and qualitative comparison between simulation results and recent measurements in the experiment. The findings of the comparison serve as a validation of both the theoretical model and the interpretation of the experimental results. Thus, a powerful interface tool has been developed for a deeper insight of nonlinear wave-particle interaction. (orig.)

Role of anti-competitor toxins in the origin and maintenance of diversity in Saccharomyces yeast microbial populations

NARCIS (Netherlands)

Pieczynska, M.D.

2015-01-01

<em>Abstract>

<em>Saccharomyces em>cells occasionally carry cytoplasmic ds-RNA “killer” viruses coding for low-mass proteins, which upon secretion to the environment can kill related cells that do not carry the viral particles. Such killer viruses are not infectious,

Importance biasing scheme implemented in the PRIZMA code

International Nuclear Information System (INIS)

Kandiev, I.Z.; Malyshkin, G.N.

1997-01-01

PRIZMA code is intended for Monte Carlo calculations of linear radiation transport problems. The code has wide capabilities to describe geometry, sources, material composition, and to obtain parameters specified by user. There is a capability to calculate path of particle cascade (including neutrons, photons, electrons, positrons and heavy charged particles) taking into account possible transmutations. Importance biasing scheme was implemented to solve the problems which require calculation of functionals related to small probabilities (for example, problems of protection against radiation, problems of detection, etc.). The scheme enables to adapt trajectory building algorithm to problem peculiarities

DANTSYS: A diffusion accelerated neutral particle transport code system

Energy Technology Data Exchange (ETDEWEB)

Alcouffe, R.E.; Baker, R.S.; Brinkley, F.W.; Marr, D.R.; O`Dell, R.D.; Walters, W.F.

1995-06-01

The DANTSYS code package includes the following transport codes: ONEDANT, TWODANT, TWODANT/GQ, TWOHEX, and THREEDANT. The DANTSYS code package is a modular computer program package designed to solve the time-independent, multigroup discrete ordinates form of the boltzmann transport equation in several different geometries. The modular construction of the package separates the input processing, the transport equation solving, and the post processing (or edit) functions into distinct code modules: the Input Module, one or more Solver Modules, and the Edit Module, respectively. The Input and Edit Modules are very general in nature and are common to all the Solver Modules. The ONEDANT Solver Module contains a one-dimensional (slab, cylinder, and sphere), time-independent transport equation solver using the standard diamond-differencing method for space/angle discretization. Also included in the package are solver Modules named TWODANT, TWODANT/GQ, THREEDANT, and TWOHEX. The TWODANT Solver Module solves the time-independent two-dimensional transport equation using the diamond-differencing method for space/angle discretization. The authors have also introduced an adaptive weighted diamond differencing (AWDD) method for the spatial and angular discretization into TWODANT as an option. The TWOHEX Solver Module solves the time-independent two-dimensional transport equation on an equilateral triangle spatial mesh. The THREEDANT Solver Module solves the time independent, three-dimensional transport equation for XYZ and RZ{Theta} symmetries using both diamond differencing with set-to-zero fixup and the AWDD method. The TWODANT/GQ Solver Module solves the 2-D transport equation in XY and RZ symmetries using a spatial mesh of arbitrary quadrilaterals. The spatial differencing method is based upon the diamond differencing method with set-to-zero fixup with changes to accommodate the generalized spatial meshing.

DANTSYS: A diffusion accelerated neutral particle transport code system

International Nuclear Information System (INIS)

Alcouffe, R.E.; Baker, R.S.; Brinkley, F.W.; Marr, D.R.; O'Dell, R.D.; Walters, W.F.

1995-06-01

The DANTSYS code package includes the following transport codes: ONEDANT, TWODANT, TWODANT/GQ, TWOHEX, and THREEDANT. The DANTSYS code package is a modular computer program package designed to solve the time-independent, multigroup discrete ordinates form of the boltzmann transport equation in several different geometries. The modular construction of the package separates the input processing, the transport equation solving, and the post processing (or edit) functions into distinct code modules: the Input Module, one or more Solver Modules, and the Edit Module, respectively. The Input and Edit Modules are very general in nature and are common to all the Solver Modules. The ONEDANT Solver Module contains a one-dimensional (slab, cylinder, and sphere), time-independent transport equation solver using the standard diamond-differencing method for space/angle discretization. Also included in the package are solver Modules named TWODANT, TWODANT/GQ, THREEDANT, and TWOHEX. The TWODANT Solver Module solves the time-independent two-dimensional transport equation using the diamond-differencing method for space/angle discretization. The authors have also introduced an adaptive weighted diamond differencing (AWDD) method for the spatial and angular discretization into TWODANT as an option. The TWOHEX Solver Module solves the time-independent two-dimensional transport equation on an equilateral triangle spatial mesh. The THREEDANT Solver Module solves the time independent, three-dimensional transport equation for XYZ and RZΘ symmetries using both diamond differencing with set-to-zero fixup and the AWDD method. The TWODANT/GQ Solver Module solves the 2-D transport equation in XY and RZ symmetries using a spatial mesh of arbitrary quadrilaterals. The spatial differencing method is based upon the diamond differencing method with set-to-zero fixup with changes to accommodate the generalized spatial meshing

Positron emission zone plate holography for particle tracking

Energy Technology Data Exchange (ETDEWEB)

Gundogdu, O. [University of Birmingham, School of Physics and Astronomy, Birmingham B15 2TT (United Kingdom)]. E-mail: o.gundogdu@surrey.ac.uk

2006-01-15

Positron Emission Particle Tracking (PEPT) is a powerful non-invasive technique that has been used extensively for tracking a single particle. In this paper, we present a study of zone plate holography method in order to track multiple particles, mainly two particles. The main aim is to use as small number of events as possible in the order to make it possible to track particles in fast moving industrial systems. A zone plate with 100% focal efficiency is simulated and applied to the Positron Emission Tomography (PET) data for multiple particle tracking. A simple trajectory code was employed to explore the effects of the nature of the experimental trajectories. A computer holographic reconstruction code that simulates optical reconstruction was developed. The different aspects of the particle location, particle activity ratios for enabling tagging of particles and zone plate and hologram locations are investigated. The effect of the shot noise is investigated and the limitations of the zone plate holography are reported.

Positron emission zone plate holography for particle tracking

International Nuclear Information System (INIS)

Gundogdu, O.

2006-01-01

Positron Emission Particle Tracking (PEPT) is a powerful non-invasive technique that has been used extensively for tracking a single particle. In this paper, we present a study of zone plate holography method in order to track multiple particles, mainly two particles. The main aim is to use as small number of events as possible in the order to make it possible to track particles in fast moving industrial systems. A zone plate with 100% focal efficiency is simulated and applied to the Positron Emission Tomography (PET) data for multiple particle tracking. A simple trajectory code was employed to explore the effects of the nature of the experimental trajectories. A computer holographic reconstruction code that simulates optical reconstruction was developed. The different aspects of the particle location, particle activity ratios for enabling tagging of particles and zone plate and hologram locations are investigated. The effect of the shot noise is investigated and the limitations of the zone plate holography are reported

2D arc-PIC code description: methods and documentation

CERN Document Server

Timko, Helga

2011-01-01

Vacuum discharges are one of the main limiting factors for future linear collider designs such as that of the Compact LInear Collider. To optimize machine efficiency, maintaining the highest feasible accelerating gradient below a certain breakdown rate is desirable; understanding breakdowns can therefore help us to achieve this goal. As a part of ongoing theoretical research on vacuum discharges at the Helsinki Institute of Physics, the build-up of plasma can be investigated through the particle-in-cell method. For this purpose, we have developed the 2D Arc-PIC code introduced here. We present an exhaustive description of the 2D Arc-PIC code in two parts. In the first part, we introduce the particle-in-cell method in general and detail the techniques used in the code. In the second part, we provide a documentation and derivation of the key equations occurring in the code. The code is original work of the author, written in 2010, and is therefore under the copyright of the author. The development of the code h...

Interaction of free charged particles with a chirped electromagnetic pulse

International Nuclear Information System (INIS)

Khachatryan, A.G.; Goor, F.A. van; Boller, K.-J.

2004-01-01

We study the effect of chirp on electromagnetic (EM) pulse interaction with a charged particle. Both the one-dimensional (1D) and 3D cases are considered. It is found that, in contrast to the case of a nonchirped pulse, the charged particle energy can be changed after the interaction with a 1D EM chirped pulse. Different types of chirp and pulse envelopes are considered. In the case of small chirp, an analytical expression is found for arbitrary temporal profiles of the chirp and the pulse envelope. In the 3D case, the interaction with a chirped pulse results in a polarization-dependent scattering of charged particles

Single-particle electron microscopy in the study of membrane protein structure.

Science.gov (United States)

De Zorzi, Rita; Mi, Wei; Liao, Maofu; Walz, Thomas

2016-02-01

Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Implementation of Japanese male and female tomographic phantoms to multi-particle Monte Carlo code for ionizing radiation dosimetry

International Nuclear Information System (INIS)

Lee, Choonsik; Nagaoka, Tomoaki; Lee, Jai-Ki

2006-01-01

Japanese male and female tomographic phantoms, which have been developed for radio-frequency electromagnetic-field dosimetry, were implemented into multi-particle Monte Carlo transport code to evaluate realistic dose distribution in human body exposed to radiation field. Japanese tomographic phantoms, which were developed from the whole body magnetic resonance images of Japanese average adult male and female, were processed as follows to be implemented into general purpose multi-particle Monte Carlo code, MCNPX2.5. Original array size of Japanese male and female phantoms, 320 x 160 x 866 voxels and 320 x 160 x 804 voxels, respectively, were reduced into 320 x 160 x 433 voxels and 320 x 160 x 402 voxels due to the limitation of memory use in MCNPX2.5. The 3D voxel array of the phantoms were processed by using the built-in repeated structure algorithm, where the human anatomy was described by the repeated lattice of tiny cube containing the information of material composition and organ index number. Original phantom data were converted into ASCII file, which can be directly ported into the lattice card of MCNPX2.5 input deck by using in-house code. A total of 30 material compositions obtained from International Commission on Radiation Units and Measurement (ICRU) report 46 were assigned to 54 and 55 organs and tissues in the male and female phantoms, respectively, and imported into the material card of MCNPX2.5 along with the corresponding cross section data. Illustrative calculation of absorbed doses for 26 internal organs and effective dose were performed for idealized broad parallel photon and neutron beams in anterior-posterior irradiation geometry, which is typical for workers at nuclear power plant. The results were compared with the data from other Japanese and Caucasian tomographic phantom, and International Commission on Radiological Protection (ICRP) report 74. The further investigation of the difference in organ dose and effective dose among tomographic

The FLUKA code: An accurate simulation tool for particle therapy

CERN Document Server

Battistoni, Giuseppe; Böhlen, Till T; Cerutti, Francesco; Chin, Mary Pik Wai; Dos Santos Augusto, Ricardo M; Ferrari, Alfredo; Garcia Ortega, Pablo; Kozlowska, Wioletta S; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis

2016-01-01

Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically-based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in-vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with bot...

Load management strategy for Particle-In-Cell simulations in high energy particle acceleration

Energy Technology Data Exchange (ETDEWEB)

Beck, A., E-mail: beck@llr.in2p3.fr [Laboratoire Leprince-Ringuet, École polytechnique, CNRS-IN2P3, Palaiseau 91128 (France); Frederiksen, J.T. [Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø (Denmark); Dérouillat, J. [CEA, Maison de La Simulation, 91400 Saclay (France)

2016-09-01

In the wake of the intense effort made for the experimental CILEX project, numerical simulation campaigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic limitations both in terms of physical accuracy and computational performances. These limitations are illustrated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-performance PIC code for high energy particle acceleration.

Electron microscopy of atmospheric particles

Science.gov (United States)

Huang, Po-Fu

Electron microscopy coupled with energy dispersive spectrometry (EM/EDS) is a powerful tool for single particle analysis. However, the accuracy with which atmospheric particle compositions can be quantitatively determined by EDS is often hampered by substrate-particle interactions, volatilization losses in the low pressure microscope chamber, electron beam irradiation and use of inaccurate quantitation factors. A pseudo-analytical solution was derived to calculate the temperature rise due to the dissipation of the electron energy on a particle-substrate system. Evaporative mass loss for a spherical cap-shaped sulfuric acid particle resting on a thin film supported by a TEM grid during electron beam impingement has been studied. Measured volatilization rates were found to be in very good agreement with theoretical predictions. The method proposed can also be used to estimate the vapor pressure of a species by measuring the decay of X-ray intensities. Several types of substrates were studied. We found that silver-coated silicon monoxide substrates give carbon detection limits comparable to commercially available substrates. An advantage of these substrates is that the high thermal conductivity of the silver reduces heating due to electron beam impingement. In addition, exposure of sulfuric acid samples to ammonia overnight substantially reduces sulfur loss in the electron beam. Use of size-dependent k-factors determined from particles of known compositions shows promise for improving the accuracy of atmospheric particle compositions measured by EM/EDS. Knowledge accumulated during the course of this thesis has been used to analyze atmospheric particles (Minneapolis, MN) selected by the TDMA and collected by an aerodynamic focusing impactor. 'Less' hygroscopic particles, which do not grow to any measurable extent when humidified to ~90% relative humidity, included chain agglomerates, spheres, flakes, and irregular shapes. Carbon was the predominant element detected in

Electro-magnetic cascade calculation using EGS4 code

International Nuclear Information System (INIS)

Namito, Yoshihito; Hirayama, Hideo

2001-01-01

The outline of the general-purpose electron-photon transport code EGS4 (Electron-Gamma-Shower Version 4) is described. In section 1, the history of the electron photon Monte Carlo transport code toward EGS4 is described. In section 2, the features of the EGS4 and the physical processes treated, cross section preparation and language is explained. The upper energy limit of EGS4 is a few thousand GeV. The lower energy limit of EGS4 is 1 keV and 10 keV for photon and electron, respectively. In section 3, particle transport method in EGS4 code is discussed. The points are; condensed history method, continuous slowing down approximation and multiple scattering approximation. Order of the particle transport calculation is also mentioned. The switches to control scoring routine AUSGAB is listed. In section 4, the output from the code is described. In section 5, several benchmark calculations are described. (author)

Study of the radioactive particle tracking technique using gamma-ray attenuation and MCNP-X code to evaluate industrial agitators

Energy Technology Data Exchange (ETDEWEB)

Dam, Roos Sophia de F.; Salgado, César M., E-mail: rsophia.dam@gmail.com, E-mail: otero@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

2017-07-01

Agitators or mixers are highly used in the chemical, food, pharmaceutical and cosmetic industries. During the fabrication process, the equipment may fail and compromise the appropriate stirring or mixing procedure. Besides that, it is also important to determine the right point of homogeneity of the mixture. Thus, it is very important to have a diagnosis tool for these industrial units to assure the quality of the product and to keep the market competitiveness. The radioactive particle tracking (RPT) technique is widely used in the nuclear field. In this paper, a method based on the principles of the RPT technique is presented. Counts obtained by an array of detectors properly positioned around the unit will be correlated to predict the instantaneous positions occupied by the radioactive particle by means of an appropriate mathematical search location algorithm. Detection geometry developed employs eight NaI(Tl) scintillator detectors and a Cs-137 (662 keV) source with isotropic emission of gamma-rays. The modeling of the detection system is performed using the Monte Carlo Method, by means of the MCNP-X code. In this work a methodology is presented to predict the position of a radioactive particle to evaluate the performance of agitators in industrial units by means of an Artificial Neural Network (ANN). (author)

Comparative study of Monte Carlo particle transport code PHITS and nuclear data processing code NJOY for recoil cross section spectra under neutron irradiation

Energy Technology Data Exchange (ETDEWEB)

Iwamoto, Yosuke, E-mail: iwamoto.yosuke@jaea.go.jp; Ogawa, Tatsuhiko

2017-04-01

Because primary knock-on atoms (PKAs) create point defects and clusters in materials that are irradiated with neutrons, it is important to validate the calculations of recoil cross section spectra that are used to estimate radiation damage in materials. Here, the recoil cross section spectra of fission- and fusion-relevant materials were calculated using the Event Generator Mode (EGM) of the Particle and Heavy Ion Transport code System (PHITS) and also using the data processing code NJOY2012 with the nuclear data libraries TENDL2015, ENDF/BVII.1, and JEFF3.2. The heating number, which is the integral of the recoil cross section spectra, was also calculated using PHITS-EGM and compared with data extracted from the ACE files of TENDL2015, ENDF/BVII.1, and JENDL4.0. In general, only a small difference was found between the PKA spectra of PHITS + TENDL2015 and NJOY + TENDL2015. From analyzing the recoil cross section spectra extracted from the nuclear data libraries using NJOY2012, we found that the recoil cross section spectra were incorrect for {sup 72}Ge, {sup 75}As, {sup 89}Y, and {sup 109}Ag in the ENDF/B-VII.1 library, and for {sup 90}Zr and {sup 55}Mn in the JEFF3.2 library. From analyzing the heating number, we found that the data extracted from the ACE file of TENDL2015 for all nuclides were problematic in the neutron capture region because of incorrect data regarding the emitted gamma energy. However, PHITS + TENDL2015 can calculate PKA spectra and heating numbers correctly.

Tracking studies in PEP and description of the computer code PATRICIA

International Nuclear Information System (INIS)

Kheifets, S.

1982-05-01

The code PATRICIA (particle tracking in circular accelerators) is designed mainly for tracking particles in an electron storage ring. A modification of this program is a part of a system of codes PAQUASEX which is designated for configuration survey over a grid of points in the space of main configuration parameters nu/sub x/, nu/sub y/, ν/sub x/, ν/sub y/, and eta/sub x/

TreePM: A Code for Cosmological N-Body Simulations

Indian Academy of Sciences (India)

R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

particle summation of the short range force takes a lot of time in highly clustered ... Our approach is to divide force into long and short range components ..... code, the memory requirement is obviously greater than that for either one code. We.

Studies of Particle Wake Potentials in Plasmas

Science.gov (United States)

Ellis, Ian; Graziani, Frank; Glosli, James; Strozzi, David; Surh, Michael; Richards, David; Decyk, Viktor; Mori, Warren

2011-10-01

Fast Ignition studies require a detailed understanding of electron scattering, stopping, and energy deposition in plasmas with variable values for the number of particles within a Debye sphere. Presently there is disagreement in the literature concerning the proper description of these processes. Developing and validating proper descriptions requires studying the processes using first-principle electrostatic simulations and possibly including magnetic fields. We are using the particle-particle particle-mesh (PPPM) code ddcMD and the particle-in-cell (PIC) code BEPS to perform these simulations. As a starting point in our study, we examine the wake of a particle passing through a plasma in 3D electrostatic simulations performed with ddcMD and with BEPS using various cell sizes. In this poster, we compare the wakes we observe in these simulations with each other and predictions from Vlasov theory. Prepared by LLNL under Contract DE-AC52-07NA27344 and by UCLA under Grant DE-FG52-09NA29552.

Coded aperture imaging of alpha source spatial distribution

International Nuclear Information System (INIS)

Talebitaher, Alireza; Shutler, Paul M.E.; Springham, Stuart V.; Rawat, Rajdeep S.; Lee, Paul

2012-01-01

The Coded Aperture Imaging (CAI) technique has been applied with CR-39 nuclear track detectors to image alpha particle source spatial distributions. The experimental setup comprised: a 226 Ra source of alpha particles, a laser-machined CAI mask, and CR-39 detectors, arranged inside a vacuum enclosure. Three different alpha particle source shapes were synthesized by using a linear translator to move the 226 Ra source within the vacuum enclosure. The coded mask pattern used is based on a Singer Cyclic Difference Set, with 400 pixels and 57 open square holes (representing ρ = 1/7 = 14.3% open fraction). After etching of the CR-39 detectors, the area, circularity, mean optical density and positions of all candidate tracks were measured by an automated scanning system. Appropriate criteria were used to select alpha particle tracks, and a decoding algorithm applied to the (x, y) data produced the de-coded image of the source. Signal to Noise Ratio (SNR) values obtained for alpha particle CAI images were found to be substantially better than those for corresponding pinhole images, although the CAI-SNR values were below the predictions of theoretical formulae. Monte Carlo simulations of CAI and pinhole imaging were performed in order to validate the theoretical SNR formulae and also our CAI decoding algorithm. There was found to be good agreement between the theoretical formulae and SNR values obtained from simulations. Possible reasons for the lower SNR obtained for the experimental CAI study are discussed.

SU-E-T-590: Optimizing Magnetic Field Strengths with Matlab for An Ion-Optic System in Particle Therapy Consisting of Two Quadrupole Magnets for Subsequent Simulations with the Monte-Carlo Code FLUKA

International Nuclear Information System (INIS)

Baumann, K; Weber, U; Simeonov, Y; Zink, K

2015-01-01

Purpose: Aim of this study was to optimize the magnetic field strengths of two quadrupole magnets in a particle therapy facility in order to obtain a beam quality suitable for spot beam scanning. Methods: The particle transport through an ion-optic system of a particle therapy facility consisting of the beam tube, two quadrupole magnets and a beam monitor system was calculated with the help of Matlab by using matrices that solve the equation of motion of a charged particle in a magnetic field and field-free region, respectively. The magnetic field strengths were optimized in order to obtain a circular and thin beam spot at the iso-center of the therapy facility. These optimized field strengths were subsequently transferred to the Monte-Carlo code FLUKA and the transport of 80 MeV/u C12-ions through this ion-optic system was calculated by using a user-routine to implement magnetic fields. The fluence along the beam-axis and at the iso-center was evaluated. Results: The magnetic field strengths could be optimized by using Matlab and transferred to the Monte-Carlo code FLUKA. The implementation via a user-routine was successful. Analyzing the fluence-pattern along the beam-axis the characteristic focusing and de-focusing effects of the quadrupole magnets could be reproduced. Furthermore the beam spot at the iso-center was circular and significantly thinner compared to an unfocused beam. Conclusion: In this study a Matlab tool was developed to optimize magnetic field strengths for an ion-optic system consisting of two quadrupole magnets as part of a particle therapy facility. These magnetic field strengths could subsequently be transferred to and implemented in the Monte-Carlo code FLUKA to simulate the particle transport through this optimized ion-optic system

Physics of codes

International Nuclear Information System (INIS)

Cooper, R.K.; Jones, M.E.

1989-01-01

The title given this paper is a bit presumptuous, since one can hardly expect to cover the physics incorporated into all the codes already written and currently being written. The authors focus on those codes which have been found to be particularly useful in the analysis and design of linacs. At that the authors will be a bit parochial and discuss primarily those codes used for the design of radio-frequency (rf) linacs, although the discussions of TRANSPORT and MARYLIE have little to do with the time structures of the beams being analyzed. The plan of this paper is first to describe rather simply the concepts of emittance and brightness, then to describe rather briefly each of the codes TRANSPORT, PARMTEQ, TBCI, MARYLIE, and ISIS, indicating what physics is and is not included in each of them. It is expected that the vast majority of what is covered will apply equally well to protons and electrons (and other particles). This material is intended to be tutorial in nature and can in no way be expected to be exhaustive. 31 references, 4 figures

The Los Alamos accelerator code group

International Nuclear Information System (INIS)

Krawczyk, F.L.; Billen, J.H.; Ryne, R.D.; Takeda, Harunori; Young, L.M.

1995-01-01

The Los Alamos Accelerator Code Group (LAACG) is a national resource for members of the accelerator community who use and/or develop software for the design and analysis of particle accelerators, beam transport systems, light sources, storage rings, and components of these systems. Below the authors describe the LAACG's activities in high performance computing, maintenance and enhancement of POISSON/SUPERFISH and related codes and the dissemination of information on the INTERNET

MUXS: a code to generate multigroup cross sections for sputtering calculations

International Nuclear Information System (INIS)

Hoffman, T.J.; Robinson, M.T.; Dodds, H.L. Jr.

1982-10-01

This report documents MUXS, a computer code to generate multigroup cross sections for charged particle transport problems. Cross sections generated by MUXS can be used in many multigroup transport codes, with minor modifications to these codes, to calculate sputtering yields, reflection coefficients, penetration distances, etc

Fusion PIC code performance analysis on the Cori KNL system

Energy Technology Data Exchange (ETDEWEB)

Koskela, Tuomas S. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Deslippe, Jack [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Friesen, Brian [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Raman, Karthic [INTEL Corp. (United States)

2017-05-25

We study the attainable performance of Particle-In-Cell codes on the Cori KNL system by analyzing a miniature particle push application based on the fusion PIC code XGC1. We start from the most basic building blocks of a PIC code and build up the complexity to identify the kernels that cost the most in performance and focus optimization efforts there. Particle push kernels operate at high AI and are not likely to be memory bandwidth or even cache bandwidth bound on KNL. Therefore, we see only minor benefits from the high bandwidth memory available on KNL, and achieving good vectorization is shown to be the most beneficial optimization path with theoretical yield of up to 8x speedup on KNL. In practice we are able to obtain up to a 4x gain from vectorization due to limitations set by the data layout and memory latency.

Radiation transport phenomena and modeling - part A: Codes

International Nuclear Information System (INIS)

Lorence, L.J.

1997-01-01

The need to understand how particle radiation (high-energy photons and electrons) from a variety of sources affects materials and electronics has motivated the development of sophisticated computer codes that describe how radiation with energies from 1.0 keV to 100.0 GeV propagates through matter. Predicting radiation transport is the necessary first step in predicting radiation effects. The radiation transport codes that are described here are general-purpose codes capable of analyzing a variety of radiation environments including those produced by nuclear weapons (x-rays, gamma rays, and neutrons), by sources in space (electrons and ions) and by accelerators (x-rays, gamma rays, and electrons). Applications of these codes include the study of radiation effects on electronics, nuclear medicine (imaging and cancer treatment), and industrial processes (food disinfestation, waste sterilization, manufacturing.) The primary focus will be on coupled electron-photon transport codes, with some brief discussion of proton transport. These codes model a radiation cascade in which electrons produce photons and vice versa. This coupling between particles of different types is important for radiation effects. For instance, in an x-ray environment, electrons are produced that drive the response in electronics. In an electron environment, dose due to bremsstrahlung photons can be significant once the source electrons have been stopped

LFSC - Linac Feedback Simulation Code

Energy Technology Data Exchange (ETDEWEB)

Ivanov, Valentin; /Fermilab

2008-05-01

The computer program LFSC (Code>) is a numerical tool for simulation beam based feedback in high performance linacs. The code LFSC is based on the earlier version developed by a collective of authors at SLAC (L.Hendrickson, R. McEwen, T. Himel, H. Shoaee, S. Shah, P. Emma, P. Schultz) during 1990-2005. That code was successively used in simulation of SLC, TESLA, CLIC and NLC projects. It can simulate as pulse-to-pulse feedback on timescale corresponding to 5-100 Hz, as slower feedbacks, operating in the 0.1-1 Hz range in the Main Linac and Beam Delivery System. The code LFSC is running under Matlab for MS Windows operating system. It contains about 30,000 lines of source code in more than 260 subroutines. The code uses the LIAR ('Linear Accelerator Research code') for particle tracking under ground motion and technical noise perturbations. It uses the Guinea Pig code to simulate the luminosity performance. A set of input files includes the lattice description (XSIF format), and plane text files with numerical parameters, wake fields, ground motion data etc. The Matlab environment provides a flexible system for graphical output.

Energetic Particle Loss Estimates in W7-X

Science.gov (United States)

Lazerson, Samuel; Akaslompolo, Simppa; Drevlak, Micheal; Wolf, Robert; Darrow, Douglass; Gates, David; W7-X Team

2017-10-01

The collisionless loss of high energy H+ and D+ ions in the W7-X device are examined using the BEAMS3D code. Simulations of collisionless losses are performed for a large ensemble of particles distributed over various flux surfaces. A clear loss cone of particles is present in the distribution for all particles. These simulations are compared against slowing down simulations in which electron impact, ion impact, and pitch angle scattering are considered. Full device simulations allow tracing of particle trajectories to the first wall components. These simulations provide estimates for placement of a novel set of energetic particle detectors. Recent performance upgrades to the code are allowing simulations with > 1000 processors providing high fidelity simulations. Speedup and future works are discussed. DE-AC02-09CH11466.

Enhanced stopping of macro-particles in particle-in-cell simulations

International Nuclear Information System (INIS)

May, J.; Tonge, J.; Ellis, I.; Mori, W. B.; Fiuza, F.; Fonseca, R. A.; Silva, L. O.; Ren, C.

2014-01-01

We derive an equation for energy transfer from relativistic charged particles to a cold background plasma appropriate for finite-size particles that are used in particle-in-cell simulation codes. Expressions for one-, two-, and three-dimensional particles are presented, with special attention given to the two-dimensional case. This energy transfer is due to the electric field of the wake set up in the background plasma by the relativistic particle. The enhanced stopping is dependent on the q 2 /m, where q is the charge and m is the mass of the relativistic particle, and therefore simulation macro-particles with large charge but identical q/m will stop more rapidly. The stopping power also depends on the effective particle shape of the macro-particle. These conclusions are verified in particle-in-cell simulations. We present 2D simulations of test particles, relaxation of high-energy tails, and integrated fast ignition simulations showing that the enhanced drag on macro-particles may adversely affect the results of these simulations in a wide range of high-energy density plasma scenarios. We also describe a particle splitting algorithm which can potentially overcome this problem and show its effect in controlling the stopping of macro-particles

The Complete Mitochondrial Genome of the Pink Stem Borer, <em>Sesamia inferensem>, in Comparison with Four Other Noctuid Moths

Directory of Open Access Journals (Sweden)

Yu-Zhou Du

2012-08-01

Full Text Available The complete 15,413-bp mitochondrial genome (mitogenome of <em>Sesamia inferensem> (Walker (Lepidoptera: Noctuidae was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs utilized the standard ATN, but the <em>cox1 em>gene used CGA as the initiation codon; <em>cox1em>, <em>cox2em>, and <em>nad4em> genes had the truncated termination codon T in the <em>S. inferens em>mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for <em>trnS1(AGNem>, in which the dihydrouridine (DHU arm did not form a stable stem-loop structure. Both the secondary structures of <em>rrnL> and <em>rrnS> genes inferred from the <em>S. inferens em>mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif “ATAGA” followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the <em>S. inferens em>mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite “(AT₇”, without a poly-A element upstream of the<em> trnM em>in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

MCNPX{trademark} -- The LAHET{trademark}/MCNP{trademark} code merger

Energy Technology Data Exchange (ETDEWEB)

Hughes, H.G.; Adams, K.J.; Chadwick, M.B. [and others

1997-08-01

The MCNP code is written and maintained by Group X-TM at Los Alamos National Laboratory. In response to the demands of the accelerator community, the authors have undertaken a major effort to expand the capabilities of MCNP to increase the set of transportable particles; to make use of newly evaluated high-energy nuclear data tables for neutrons, protons, and potentially other particles; and to incorporate physics models for use where tabular data are unavailable. A preliminary version of the expanded code, called MCNPX, has now been issued for testing. The new code includes all existing LAHET physics modules, and has the ability to utilize the 150-MeV data libraries that have recently been released by LANL Group T-2.

Best practices for managing large CryoEM facilities.

Science.gov (United States)

Alewijnse, Bart; Ashton, Alun W; Chambers, Melissa G; Chen, Songye; Cheng, Anchi; Ebrahim, Mark; Eng, Edward T; Hagen, Wim J H; Koster, Abraham J; López, Claudia S; Lukoyanova, Natalya; Ortega, Joaquin; Renault, Ludovic; Reyntjens, Steve; Rice, William J; Scapin, Giovanna; Schrijver, Raymond; Siebert, Alistair; Stagg, Scott M; Grum-Tokars, Valerie; Wright, Elizabeth R; Wu, Shenping; Yu, Zhiheng; Zhou, Z Hong; Carragher, Bridget; Potter, Clinton S

2017-09-01

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Vectorization, parallelization and porting of nuclear codes (vectorization and parallelization). Progress report fiscal 1998

International Nuclear Information System (INIS)

Ishizuki, Shigeru; Kawai, Wataru; Nemoto, Toshiyuki; Ogasawara, Shinobu; Kume, Etsuo; Adachi, Masaaki; Kawasaki, Nobuo; Yatake, Yo-ichi

2000-03-01

Several computer codes in the nuclear field have been vectorized, parallelized and transported on the FUJITSU VPP500 system, the AP3000 system and the Paragon system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 12 codes in fiscal 1998. These results are reported in 3 parts, i.e., the vectorization and parallelization on vector processors part, the parallelization on scalar processors part and the porting part. In this report, we describe the vectorization and parallelization on vector processors. In this vectorization and parallelization on vector processors part, the vectorization of General Tokamak Circuit Simulation Program code GTCSP, the vectorization and parallelization of Molecular Dynamics NTV (n-particle, Temperature and Velocity) Simulation code MSP2, Eddy Current Analysis code EDDYCAL, Thermal Analysis Code for Test of Passive Cooling System by HENDEL T2 code THANPACST2 and MHD Equilibrium code SELENEJ on the VPP500 are described. In the parallelization on scalar processors part, the parallelization of Monte Carlo N-Particle Transport code MCNP4B2, Plasma Hydrodynamics code using Cubic Interpolated Propagation Method PHCIP and Vectorized Monte Carlo code (continuous energy model / multi-group model) MVP/GMVP on the Paragon are described. In the porting part, the porting of Monte Carlo N-Particle Transport code MCNP4B2 and Reactor Safety Analysis code RELAP5 on the AP3000 are described. (author)

Scaling relations between structure and rheology of ageing casein particle gels

NARCIS (Netherlands)

Mellema, M.

2000-01-01

Mellema, M. (Michel), <em>Scaling relations between structure and rheology of ageing casein particle gelsem> , PhD Thesis, Wageningen University, 150 + 10 pages, references by chapter, English and Dutch summaries (2000).

The relation between (colloidal)

The vector and parallel processing of MORSE code on Monte Carlo Machine

International Nuclear Information System (INIS)

Hasegawa, Yukihiro; Higuchi, Kenji.

1995-11-01

Multi-group Monte Carlo Code for particle transport, MORSE is modified for high performance computing on Monte Carlo Machine Monte-4. The method and the results are described. Monte-4 was specially developed to realize high performance computing of Monte Carlo codes for particle transport, which have been difficult to obtain high performance in vector processing on conventional vector processors. Monte-4 has four vector processor units with the special hardware called Monte Carlo pipelines. The vectorization and parallelization of MORSE code and the performance evaluation on Monte-4 are described. (author)

The Los Alamos accelerator code group

Energy Technology Data Exchange (ETDEWEB)

Krawczyk, F.L.; Billen, J.H.; Ryne, R.D.; Takeda, Harunori; Young, L.M.

1995-05-01

The Los Alamos Accelerator Code Group (LAACG) is a national resource for members of the accelerator community who use and/or develop software for the design and analysis of particle accelerators, beam transport systems, light sources, storage rings, and components of these systems. Below the authors describe the LAACG`s activities in high performance computing, maintenance and enhancement of POISSON/SUPERFISH and related codes and the dissemination of information on the INTERNET.

High-Fidelity RF Gun Simulations with the Parallel 3D Finite Element Particle-In-Cell Code Pic3P

Energy Technology Data Exchange (ETDEWEB)

Candel, A; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Schussman, G.; Ko, K.; /SLAC

2009-06-19

SLAC's Advanced Computations Department (ACD) has developed the first parallel Finite Element 3D Particle-In-Cell (PIC) code, Pic3P, for simulations of RF guns and other space-charge dominated beam-cavity interactions. Pic3P solves the complete set of Maxwell-Lorentz equations and thus includes space charge, retardation and wakefield effects from first principles. Pic3P uses higher-order Finite Elementmethods on unstructured conformal meshes. A novel scheme for causal adaptive refinement and dynamic load balancing enable unprecedented simulation accuracy, aiding the design and operation of the next generation of accelerator facilities. Application to the Linac Coherent Light Source (LCLS) RF gun is presented.

Development of code PRETOR for stellarator simulation

International Nuclear Information System (INIS)

Dies, J.; Fontanet, J.; Fontdecaba, J.M.; Castejon, F.; Alejandre, C.

1998-01-01

The Department de Fisica i Enginyeria Nuclear (DFEN) of the UPC has some experience in the development of the transport code PRETOR. This code has been validated with shots of DIII-D, JET and TFTR, it has also been used in the simulation of operational scenarios of ITER fast burnt termination. Recently, the association EURATOM-CIEMAT has started the operation of the TJ-II stellarator. Due to the need of validating the results given by others transport codes applied to stellarators and because all of them made some approximations, as a averaging magnitudes in each magnetic surface, it was thought suitable to adapt the PRETOR code to devices without axial symmetry, like stellarators, which is very suitable for the specific needs of the study of TJ-II. Several modifications are required in PRETOR; the main concerns to the models of: magnetic equilibrium, geometry and transport of energy and particles. In order to solve the complex magnetic equilibrium geometry the powerful numerical code VMEC has been used. This code gives the magnetic surface shape as a Fourier series in terms of the harmonics (m,n). Most of the geometric magnitudes are also obtained from the VMEC results file. The energy and particle transport models will be replaced by other phenomenological models that are better adapted to stellarator simulation. Using the proposed models, it is pretended to reproduce experimental data available from present stellarators, given especial attention to the TJ-II of the association EURATOM-CIEMAT. (Author)

The intercomparison of aerosol codes

International Nuclear Information System (INIS)

Dunbar, I.H.; Fermandjian, J.; Gauvain, J.

1988-01-01

The behavior of aerosols in a reactor containment vessel following a severe accident could be an important determinant of the accident source term to the environment. Various processes result in the deposition of the aerosol onto surfaces within the containment, from where they are much less likely to be released. Some of these processes are very sensitive to particle size, so it is important to model the aerosol growth processes: agglomeration and condensation. A number of computer codes have been written to model growth and deposition processes. They have been tested against each other in a series of code comparison exercises. These exercises have investigated sensitivities to physical and numerical assumptions and have also proved a useful means of quality control for the codes. Various exercises in which code predictions are compared with experimental results are now under way

Code Modernization of VPIC

Science.gov (United States)

Bird, Robert; Nystrom, David; Albright, Brian

2017-10-01

The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

A parallel code named NEPTUNE for 3D fully electromagnetic and pic simulations

International Nuclear Information System (INIS)

Dong Ye; Yang Wenyuan; Chen Jun; Zhao Qiang; Xia Fang; Ma Yan; Xiao Li; Sun Huifang; Chen Hong; Zhou Haijing; Mao Zeyao; Dong Zhiwei

2010-01-01

A parallel code named NEPTUNE for 3D fully electromagnetic and particle-in-cell (PIC) simulations is introduced, which could run on the Linux system with hundreds to thousand CPUs. NEPTUNE is suitable to simulate entire 3D HPM devices; many HPM devices are simulated and designed by using it. In NEPTUNE code, the electromagnetic fields are updated by using the finite-difference in time domain (FDTD) method of solving Maxwell equations and the particles are moved by using Buneman-Boris advance method of solving relativistic Newton-Lorentz equation. Electromagnetic fields and particles are coupled by using liner weighing interpolation PIC method, and the electric filed components are corrected by using Boris method of solve Poisson equation in order to ensure charge-conservation. NEPTUNE code could construct many complicated geometric structures, such as arbitrary axial-symmetric structures, plane transforming structures, slow-wave-structures, coupling holes, foils, and so on. The boundary conditions used in NEPTUNE code are introduced in brief, including perfectly electric conductor boundary, external wave boundary, and particle boundary. Finally, some typical HPM devices are simulated and test by using NEPTUNE code, including MILO, RBWO, VCO, and RKA. The simulation results are with correct and credible physical images, and the parallel efficiencies are also given. (authors)

Potential of the MCNP computer code

International Nuclear Information System (INIS)

Kyncl, J.

1995-01-01

The MCNP code is designed for numerical solution of neutron, photon, and electron transport problems by the Monte Carlo method. The code is based on the linear transport theory of behavior of the differential flux of the particles. The code directly uses data from the cross section point data library for input. Experience is outlined, gained in the application of the code to the calculation of the effective parameters of fuel assemblies and of the entire reactor core, to the determination of the effective parameters of the elementary fuel cell, and to the numerical solution of neutron diffusion and/or transport problems of the fuel assembly. The agreement between the calculated and observed data gives evidence that the MCNP code can be used with advantage for calculations involving WWER type fuel assemblies. (J.B.). 4 figs., 6 refs

LFSC - Linac Feedback Simulation Code

International Nuclear Information System (INIS)

Ivanov, Valentin; Fermilab

2008-01-01

The computer program LFSC ( ) is a numerical tool for simulation beam based feedback in high performance linacs. The code LFSC is based on the earlier version developed by a collective of authors at SLAC (L.Hendrickson, R. McEwen, T. Himel, H. Shoaee, S. Shah, P. Emma, P. Schultz) during 1990-2005. That code was successively used in simulation of SLC, TESLA, CLIC and NLC projects. It can simulate as pulse-to-pulse feedback on timescale corresponding to 5-100 Hz, as slower feedbacks, operating in the 0.1-1 Hz range in the Main Linac and Beam Delivery System. The code LFSC is running under Matlab for MS Windows operating system. It contains about 30,000 lines of source code in more than 260 subroutines. The code uses the LIAR ('Linear Accelerator Research code') for particle tracking under ground motion and technical noise perturbations. It uses the Guinea Pig code to simulate the luminosity performance. A set of input files includes the lattice description (XSIF format), and plane text files with numerical parameters, wake fields, ground motion data etc. The Matlab environment provides a flexible system for graphical output

Monte Carlo codes use in neutron therapy

International Nuclear Information System (INIS)

Paquis, P.; Mokhtari, F.; Karamanoukian, D.; Pignol, J.P.; Cuendet, P.; Iborra, N.

1998-01-01

Monte Carlo calculation codes allow to study accurately all the parameters relevant to radiation effects, like the dose deposition or the type of microscopic interactions, through one by one particle transport simulation. These features are very useful for neutron irradiations, from device development up to dosimetry. This paper illustrates some applications of these codes in Neutron Capture Therapy and Neutron Capture Enhancement of fast neutrons irradiations. (authors)

Particle-in-Cell Laser-Plasma Simulation on Xeon Phi Coprocessors

OpenAIRE

Surmin, I. A.; Bastrakov, S. I.; Efimenko, E. S.; Gonoskov, A. A.; Korzhimanov, A. V.; Meyerov, I. B.

2015-01-01

This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our experience of porting and optimization of the existing parallel Particle-in-Cell code PICADOR. Direct porting with no code modification gives performance on Xeon Phi close to 8-core CPU on a benchmark problem with 50 particles per cell. We demonstrate step-by-step...

GANDALF - Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids

Science.gov (United States)

Hubber, D. A.; Rosotti, G. P.; Booth, R. A.

2018-01-01

GANDALF is a new hydrodynamics and N-body dynamics code designed for investigating planet formation, star formation and star cluster problems. GANDALF is written in C++, parallelized with both OPENMP and MPI and contains a PYTHON library for analysis and visualization. The code has been written with a fully object-oriented approach to easily allow user-defined implementations of physics modules or other algorithms. The code currently contains implementations of smoothed particle hydrodynamics, meshless finite-volume and collisional N-body schemes, but can easily be adapted to include additional particle schemes. We present in this paper the details of its implementation, results from the test suite, serial and parallel performance results and discuss the planned future development. The code is freely available as an open source project on the code-hosting website github at https://github.com/gandalfcode/gandalf and is available under the GPLv2 license.

Installation of aerosol behavior model into multi-dimensional thermal hydraulic analysis code AQUA

International Nuclear Information System (INIS)

Kisohara, Naoyuki; Yamaguchi, Akira

1997-12-01

The safety analysis of FBR plant system for sodium leak phenomena needs to evaluate the deposition of the aerosol particle to the components in the plant, the chemical reaction of aerosol to humidity in the air and the effect of the combustion heat through aerosol to the structural component. For this purpose, ABC-INTG (Aerosol Behavior in Containment-INTeGrated Version) code has been developed and used until now. This code calculates aerosol behavior in the gas area of uniform temperature and pressure by 1 cell-model. Later, however, more detailed calculation of aerosol behavior requires the installation of aerosol model into multi-cell thermal hydraulic analysis code AQUA. AQUA can calculate the carrier gas flow, temperature and the distribution of the aerosol spatial concentration. On the other hand, ABC-INTG can calculate the generation, deposition to the wall and flower, agglomeration of aerosol particle and figure out the distribution of the aerosol particle size. Thus, the combination of these two codes enables to deal with aerosol model coupling the distribution of the aerosol spatial concentration and that of the aerosol particle size. This report describes aerosol behavior model, how to install the aerosol model to AQUA and new subroutine equipped to the code. Furthermore, the test calculations of the simple structural model were executed by this code, appropriate results were obtained. Thus, this code has prospect to predict aerosol behavior by the introduction of coupling analysis with multi-dimensional gas thermo-dynamics for sodium combustion evaluation. (J.P.N.)

Peripheral Codes in ASTRA for the TJ-II

International Nuclear Information System (INIS)

Lopez-Bruna, D.; Reynolds, J. M.; Cappa, A.; Martinell, J.; Garcia, J.; Gutierrez-Tapia, C.

2010-01-01

The study of data from the TJ-II device is often done with transport calculations based on the ASTRA transport system. However, complicated independent codes are used to obtain fundamental ingredients in these calculations, such as the particle and/or energy sources. These codes are accessible from ASTRA through the procedures explained in this report. (Author) 37 refs.

Particle simulation algorithms with short-range forces in MHD and fluid flow

International Nuclear Information System (INIS)

Cable, S.; Tajima, T.; Umegaki, K.

1992-07-01

Attempts are made to develop numerical algorithms for handling fluid flows involving liquids and liquid-gas mixtures. In these types of systems, the short-range intermolecular interactions are important enough to significantly alter behavior predicted on the basis of standard fluid mechanics and magnetohydrodynamics alone. We have constructed a particle-in-cell (PIC) code for the purpose of studying the effects of these interactions. Of the algorithms considered, the one which has been successfully implemented is based on a MHD particle code developed by Brunel et al. In the version presented here, short range forces are included in particle motion by, first, calculating the forces between individual particles and then, to prevent aliasing, interpolating these forces to the computational grid points, then interpolating the forces back to the particles. The code has been used to model a simple two-fluid Rayleigh-Taylor instability. Limitations to the accuracy of the code exist at short wavelengths, where the effects of the short-range forces would be expected to be most pronounced

A Comprehensive Comparison of Relativistic Particle Integrators

Science.gov (United States)

Ripperda, B.; Bacchini, F.; Teunissen, J.; Xia, C.; Porth, O.; Sironi, L.; Lapenta, G.; Keppens, R.

2018-03-01

We compare relativistic particle integrators commonly used in plasma physics, showing several test cases relevant for astrophysics. Three explicit particle pushers are considered, namely, the Boris, Vay, and Higuera–Cary schemes. We also present a new relativistic fully implicit particle integrator that is energy conserving. Furthermore, a method based on the relativistic guiding center approximation is included. The algorithms are described such that they can be readily implemented in magnetohydrodynamics codes or Particle-in-Cell codes. Our comparison focuses on the strengths and key features of the particle integrators. We test the conservation of invariants of motion and the accuracy of particle drift dynamics in highly relativistic, mildly relativistic, and non-relativistic settings. The methods are compared in idealized test cases, i.e., without considering feedback onto the electrodynamic fields, collisions, pair creation, or radiation. The test cases include uniform electric and magnetic fields, {\\boldsymbol{E}}× {\\boldsymbol{B}} fields, force-free fields, and setups relevant for high-energy astrophysics, e.g., a magnetic mirror, a magnetic dipole, and a magnetic null. These tests have direct relevance for particle acceleration in shocks and in magnetic reconnection.

An information theoretic approach to use high-fidelity codes to calibrate low-fidelity codes

Energy Technology Data Exchange (ETDEWEB)

Lewis, Allison, E-mail: lewis.allison10@gmail.com [Department of Mathematics, North Carolina State University, Raleigh, NC 27695 (United States); Smith, Ralph [Department of Mathematics, North Carolina State University, Raleigh, NC 27695 (United States); Williams, Brian [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Figueroa, Victor [Sandia National Laboratories, Albuquerque, NM 87185 (United States)

2016-11-01

For many simulation models, it can be prohibitively expensive or physically infeasible to obtain a complete set of experimental data to calibrate model parameters. In such cases, one can alternatively employ validated higher-fidelity codes to generate simulated data, which can be used to calibrate the lower-fidelity code. In this paper, we employ an information-theoretic framework to determine the reduction in parameter uncertainty that is obtained by evaluating the high-fidelity code at a specific set of design conditions. These conditions are chosen sequentially, based on the amount of information that they contribute to the low-fidelity model parameters. The goal is to employ Bayesian experimental design techniques to minimize the number of high-fidelity code evaluations required to accurately calibrate the low-fidelity model. We illustrate the performance of this framework using heat and diffusion examples, a 1-D kinetic neutron diffusion equation, and a particle transport model, and include initial results from the integration of the high-fidelity thermal-hydraulics code Hydra-TH with a low-fidelity exponential model for the friction correlation factor.

Miniaturizing EM Sample Preparation: Opportunities, Challenges, and "Visual Proteomics".

Science.gov (United States)

Arnold, Stefan A; Müller, Shirley A; Schmidli, Claudio; Syntychaki, Anastasia; Rima, Luca; Chami, Mohamed; Stahlberg, Henning; Goldie, Kenneth N; Braun, Thomas

2018-03-01

This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (TEM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Particle Control in Phase Space by Global K-Means Clustering

DEFF Research Database (Denmark)

Frederiksen, Jacob Trier; Lapenta, G.; Pessah, M. E.

2015-01-01

We devise and explore an iterative optimization procedure for controlling particle populations in particle-in-cell (PIC) codes via merging and splitting of computational macro-particles. Our approach, is to compute an optimal representation of the global particle phase space structure while decre...

Code-code comparisons of DIVIMP's 'onion-skin model' and the EDGE2D fluid code

International Nuclear Information System (INIS)

Stangeby, P.C.; Elder, J.D.; Horton, L.D.; Simonini, R.; Taroni, A.; Matthews, O.F.; Monk, R.D.

1997-01-01

In onion-skin modelling, O-SM, of the edge plasma, the cross-field power and particle flows are treated very simply e.g. as spatially uniform. The validity of O-S modelling requires demonstration that such approximations can still result in reasonable solutions for the edge plasma. This is demonstrated here by comparison of O-SM with full 2D fluid edge solutions generated by the EDGE2D code. The target boundary conditions for the O-SM are taken from the EDGE2D output and the complete O-SM solutions are then compared with the EDGE2D ones. Agreement is generally within 20% for n e , T e , T i and parallel particle flux density Γ for the medium and high recycling JET cases examined and somewhat less good for a strongly detached CMOD example. (orig.)

Criticality benchmarks for COG: A new point-wise Monte Carlo code

International Nuclear Information System (INIS)

Alesso, H.P.; Pearson, J.; Choi, J.S.

1989-01-01

COG is a new point-wise Monte Carlo code being developed and tested at LLNL for the Cray computer. It solves the Boltzmann equation for the transport of neutrons, photons, and (in future versions) charged particles. Techniques included in the code for modifying the random walk of particles make COG most suitable for solving deep-penetration (shielding) problems. However, its point-wise cross-sections also make it effective for a wide variety of criticality problems. COG has some similarities to a number of other computer codes used in the shielding and criticality community. These include the Lawrence Livermore National Laboratory (LLNL) codes TART and ALICE, the Los Alamos National Laboratory code MCNP, the Oak Ridge National Laboratory codes 05R, 06R, KENO, and MORSE, the SACLAY code TRIPOLI, and the MAGI code SAM. Each code is a little different in its geometry input and its random-walk modification options. Validating COG consists in part of running benchmark calculations against critical experiments as well as other codes. The objective of this paper is to present calculational results of a variety of critical benchmark experiments using COG, and to present the resulting code bias. Numerous benchmark calculations have been completed for a wide variety of critical experiments which generally involve both simple and complex physical problems. The COG results, which they report in this paper, have been excellent

Evaluation of <em>HER2em> Gene Amplification in Breast Cancer Using Nuclei Microarray <em>in em>S>itu em>Hybridization

Directory of Open Access Journals (Sweden)

Xuefeng Zhang

2012-05-01

Full Text Available Fluorescence<em> em>>in situ em>hybridization (FISH assay is considered the “gold standard” in evaluating <em>HER2/neu (HER2em> gene status. However, FISH detection is costly and time consuming. Thus, we established nuclei microarray with extracted intact nuclei from paraffin embedded breast cancer tissues for FISH detection. The nuclei microarray FISH (NMFISH technology serves as a useful platform for analyzing <em>HER2em> gene/chromosome 17 centromere ratio. We examined <em>HER2em> gene status in 152 cases of invasive ductal carcinomas of the breast that were resected surgically with FISH and NMFISH. <em>HER2em> gene amplification status was classified according to the guidelines of the American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP. Comparison of the cut-off values for <em>HER2em>/chromosome 17 centromere copy number ratio obtained by NMFISH and FISH showed that there was almost perfect agreement between the two methods (κ coefficient 0.920. The results of the two methods were almost consistent for the evaluation of <em>HER2em> gene counts. The present study proved that NMFISH is comparable with FISH for evaluating <em>HER2em> gene status. The use of nuclei microarray technology is highly efficient, time and reagent conserving and inexpensive.

Sensitivity analysis using the FRAPCON-1/EM: development of a calculation model for licensing

International Nuclear Information System (INIS)

Chapot, J.L.C.

1985-01-01

The FRAPCON-1/EM is version of the FRAPCON-1 code which analyses fuel rods performance under normal operation conditions. This version yields conservative results and is used by the NRC in its licensing activities. A sensitivity analysis was made, to determine the combination of models from the FRAPCON-1/EM which yields the most conservative results for a typical Angra-1 reactor fuel rod. The present analysis showed that this code can be used as a calculation tool for the licensing of the Angra-1 reload. (F.E.) [pt

Neonatal Phosphate Nutrition Alters <em>in em>Vivo> and <em>in em>Vitro> Satellite Cell Activity in Pigs