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2008 Software Available for Licensing

Please direct general inquiries concerning the LANL software program to: software@lanl.gov. If you are a Laboratory software developer, please see Developer Resources under Related Links.

LA-CC Number Title Description

LA-CC 08-113 FUI v 2.0 alpha FUI is a program to fit functions to data. It is an extension written in C by Bernhard Sulzer (Lion bioscience AG Germany) of an f2c-ed Fortran program written by Ronald Beatty and Byron Goldstein (LANL, USA), calling the Slatec Fortran library (www.netlib.org/slatec). 12/18/08
LA-CC 08-112 PetANNet (aka PANN), v2.0 C++/Python re-implementation of neural network algorithm modeling brain visual cortex regions V1, V2, V4 and IT, based on code publicly available as MATLAB source code from MIT Center for Biological and Computational Learning (CBCL). PetANNet (aka PANN) is intended as a research grade test bed code for evaluating neural computational algorithms of human vision, running on individual workstations (Mac, Linux, Windows). PANN is funded by LDRD-DR Petscale Models of Synthetic Visual Cognition (PI Luis Bettencourt, T-7). 12/8/08
LA-CC 08-111 UncleMcFlux v2.0 UncleMcFlux is a Monte-Carlo un-collided flux estimator using ray-tracing techniques on uniform, logically rectangular grids. It uses libraries which are part of the Draco and ClubIMC projects. There are also used in the code Milagro, designated LA-CC-06-053 12/12/08
LA-CC 08-110 stfa2phs.v4d.f Version 4d This code carries out a stochastic homogenization analysis of a 2 phase composite system giving both bulk and local stress-strain responses for various type of inelastic processes at the microstructural level. 12/4/08
LA-CC 08-109 SORDS_IMAGING 0.1 This software is in development for use on the Domestic Nuclear Detection Office sponsored program called SORDS. This software will take data from the future detector system and perform gamma-ray imaging using Compton imaging and coded aperture imaging techniques. All of the algorithms used are based on published techniques. 11/20/08
LA-CC 08-108 LANL * v1.0 The presented code is a surrogate model based on a neural network technique to replace complex magnetic field model calculations. The code is limited to geosynchronous regions and can be made publicly available as a source code. The code and technique are described in detail in the attached draft intended for publication in Geoscientific Model Development Journal. 11/18/08
LA-CC 08-106 ChemCam Flight Software, v5.21 This is the flight software for NASA sponsored ChemCaminstrument, which is to be flown to the surface of Mars as a part of the NASA Mars Science Laboratory (MSL) mission. This software is responsible for all command and data communications between the MSL Rover and the ChemCam Instrument, all command and data communication between the Body Unit and Mast Unit (separate subsystems of the ChemCam instrument) and command and control of Body Unit subsystems. 11/13/08
LA-CC 08-105 Ring Current-Atmosphere Model (RAM) v1.0 The model calculates the evolution of ring current/ radiation belt distribution functions solving the bounce average kinetic equation considering convection, radical diffusion, collisional losses, and wave particle interactions. The code uses a Lax-Wendroff scheme and a first order upwind scheme with a superbee flux limiter method to solve numerically the conservative terms of kinetic equation. A Crank-Nicolson numerical scheme is used for the diffusive terms. 10/22/08
LA-CC 08-104 LANL Checkpointing Research Tool v0.0 An example tool to enable high performance computing researchers to study the performance issues with the checkpoint dump mechanisms used by many high performance computing sites. Converts data checkpoint dump writes one form to other forms (N processes to 1 file, N processes to N files, etc). This is an example code which enables researchers to simulate, analyze, and test performance of various data checkpointing mechanisms used by high performance computer codes at LANL and other sites. 11/7/08
LA-CC 08-103 YAP v4.6.8 YAP is a software library for computing finite-element solutions of electrostatic and magnetostatic problems, and for tracking charged particle trajectories. The library operates a multiblock structured and unstructured meshes, in both two dimensions and three dimensions. The YAP library includes an interface for the MICHELLE finite-element gun code, which uses the YAP libraries to model electron guns and collectors for microwave vacuum electron devices (MVEDs, a.k.a microwave tubes). 10/4/08
LA-CC 08-102 Method Automation Automated high-throughput for sample processing method for protein solubility prediction. Manuscript (submitted): Automated high-throughput platform for protein solubility screening using a split GFP system. Authors: Pawel Listwan, Thomas C. Terwilliger, Geoffrey S. Waldo. 10/31/08
LA-CC 08-101 Lavaredo v 0.6 The Laveredo Code simulates two-phase flow in highly heterogeneous porous media. The Multilevel Multiscale Mimetic method is implemented to discretize coupled system of PDEs. Using the multilevel hierarchy of discrete models the code allows one to upscale both pressure and saturation fields. The methodology is published in [1]. 1. D. Moulton, K. Lipnikov, and D. Svyatskiy "Multilevel Multiscale Mimetric method for two phase flows in porous media." Journal of Computational Physics, vol. 227(14), pp. 6727-6753, 08 10/3/08
LA-CC 08-100 EALink, v1.0 EALink is an application consisting of a customized xml editor integrated with Commercial Off-the-Shelf (COTS) Product Lifecycle Management (PLM )system. EALink was developed at LANL using a programming language called Arbortext command language, which is owned by Parametric Technology Corp (PTC). EALink stands for engineering Authorization Link and this application was developed to support LANL employees in authorizing work at Production Agencies. This tool was designed to meet NWC Technical Business Requirements captured in TBP-404 and IBP-404. 10/27/08
LA-CC 08-098 cmdVista v0.73.rc1 cmdVista is a code for generalized object extraction and agglomeration from raster images. It first converts the raster images to a vector image using the VISTA procedure (LAUR-06-2726, RaveGrid). It then progressively agglomerates polygons to extract higher order features in a hierarchical manner (Submitted to IDEAS as Image SHAPES, LAUR-07-8210). 10/21/08
LA-CC 08-097 ANGIO v14 ANGIO is a multi-scale cell-based simulation tool for investigating tumor-induced angiogenesis. ANGIO integrates a continuum model for nutrient transport, a stochastic lattice model for cellular dynamics, and a Boolean network model for biochemical signaling to deterministically link signaling molecules to vascular and tissue morphology. ANGIO translates and synthesizes a large body of compartmentalized research on angiogenesis and is a novel research tool that provides us with the ability to test system-level strategies for eradicating tumors or at least preventing continued tumor growth and metastasis. 10/7/08
LA-CC 08-096 CLEAR model v0.8 CLEAR model is a system dynamics model with a graphical user-interface. This model, custom developed for the Sonoma County region tracks the C02 emissions. Two CO2 sources were modeled; transportation and electricity generation. Emissions from these sources are modeled in several sectors, including residential and commercial (industrial) transportation and electricity demand and electricity demand for water supply and treatment. Economic and population growth drive changes in demand, and policies for renewable energy (wind, solar) and low-emissions transportation (hybrid cars, mass transportation) provide mitigation choices. Climate change in the form of increases in average daily temperature drives electricity and water demand. The interface allows users to insert emission reduction energy policies, such as the photovoltaic system and wind, and transportation policies. 10/9/08
LA-CC 08-095 SRFYDO v1.2 Version 1.0 of this software was previously submitted to SAFE-1 and assigned LA-CC-08-002. Substantial capability has been added, suggesting another review. Previously SRFYDO merely extracted data from spreadsheets for unspecified future statistical analysis. Version 1.2 performs reliability calculations per LANL's "Information Integration Technology (IIT)" approach, a Bayesian methodology used to combine expert judgment, results from automatic testing equipment, and flight result across multiple variants. Please see "Calculating System Reliability with SRFYDO: A User Guide" LA-UR-08-06161 10/8/08
LA-CC 08-094 ACS File System and I/O Tests, v1.0 A suite of tests that create and access files in distributions and patterns that are relevant to the Advanced Computing Systems (ACS) program customers. These tests are intended to be used by people working for or on behalf of the ACS program as well as the organizations that win contracts with the ACS programs to research file system and I/O solutions that are important to the ACS program customers.` 10/3/08
LA-CC 08-093 Next-Generation Attribute System Control Code This code runs on the data acquisition (DAQ) computer and data barrier (DB) microcontroller in Next Generation Attribute Measurement System (NG-AMS). The NG-AMS is a system to measure gamma and neutron emissions from sealed containers of plutonium in order to determine attributes of the enclosed plutonium. The measurement system operates behind an information barrier (IB) which controls the information that passes into and out of the NG-AMS. The IB prevents potentially sensitive information about the plutonium for being visible to the system operators, while still allowing them to verify the contents of the containers. The code on the DAQ computer is written in PERL. 10/6/08
LA-CC 08-092 Oralgen—oral pathogen sequence database Oral Pathogen Genome Sequence Database (ORALGEN), funded by NIH-NIDCR, is a specialized sequence database managed at Los Alamos National Laboratory supporting oral pathogen research. The database currently encompasses primary and derived molecular sequence data. In addition to tracking molecular sequences and the relevant literature, Oralgen performs basic analyses to facilitate research; interacts with the research community through attendance at major meetings; assists individual researchers; and publishes a Web site consisting of a MySQL relational database for users, tables of basic information, and mini- reviews, and serves as a training center in bioformatics. 10/3/08
LA-CC 08-091 BioNetGen-LANL, v2.0.46 BioNetGen (Biological) is a multicomponent software framework for modeling biochemical networks inside cells. Using either graphical or text based interface, a user can construct, simulate, and analyze network dynamics at the level of interactions among protein components. 10/2/08
LA-CC 08-090 Pigs v0.4 Pigs is a tool for learning object detectors for detecting objects in panchromatic imagery. Web site for Pigs 9/17/08
LA-CC 08-089 WVT_IDL, v1.0 This is a simple IDL code to set up initial conditions for Smooth Particle Hydrodynamics (SPH) simulations, which are mainly used in the astronomical community. The code is entirely self-contained and not based on any other LANL software or license. The code will be provided as a convenience for astronomy users, and accompany a paper detailing the algorithm (LA-UR-08-05763, "Generating optimal initial conditions for smooth particle hydrodynamics (SPH) simulations"). 9/11/08
LA-CC 08-088 LANL Plot Library v1.0 A Java package defining interfaces to facilitate plotting of data using the JFreeChart package. "User guide for Los Alamos National Laboratory Plotting Software for the Nuclear Weapon Analysis Tools, Version 1.0 "LA-UR-08-04273 in the user guide for the plotting package, was used within LANL Nuclear Weapons Tools Version 5.4 LA-CC-08-075 9/11/08
LA-CC 08-087 Needs-Based Act Gen, v1.0 The Matlab toolbox generates daily activity schedules based on agent and "needs-based" approach. Each need (e.g., hunger, sleep) is modeled as a numeric value that decreases with a function over time and increases by doing activities that fulfill each need. Using genetic algorithms, we optimize the parameters of each "need function" for a specified simulation period. With the addition of temporal constraints on the activities, we obtain daily schedules. Both the code and manual are available at: Julia Progress Journal. 8/13/08
LA-CC 08-086 RBNC, v1.0 The C++ code simulates Random Boolean Networks (RBNs), which are simple, discrete, dynamical systems composed of binary-state nodes that are interconnected by directed links. We used the code to study the damage spreading in such networks as a function of that network topology and parameters. The code generates statistics on how the damage spreads. The code has also been used for the following publication: LA-UR-07-0653. The code is available at the Random Boolean Networks. 8/20/08
LA-CC 08-085 acdrsi v75 adrsi software consists of approximately 60 matlab scripts, collectively containing 2000 lines of Matlab code. The code implements algorithms for anomalous change detection in multi-band imagery, which are described in a journal publication: J. Theiler. "Quantitative comparison of quadratic covariance-based anomalous change detectors." Applied Optics 47 (08) F12-F26. 8/21/08
LA-CC 08-084 mc3 v1.0 mc3 is a web application prototype for the next generation of LDRD's business management system. Mc3 is built using ICEfaces software components and is being released to vendor ICESoft Technologies for its review and testing. No proprietary LANL code or data will be included in the mc3 release. 8/22/08
LA-CC 08-078 IEISS Version 3.x This code provides modeling and simulation support for infrastructure analysis. Infrastructure includes electric power, natural gas, POL, oil, water, telecommunications, Internet, and SCADA. Additional reference material available. 8/4/09
LA-CC 08-077 LogiSims Version 1.x This code provides optimization support for logistics problems such as resource allocation, resource planning and resource distribution. These problems include applications such as infrastructure restoration, relief supply distribution, disaster planning and migration, etc. Additional reference material is attached. 8/4/09
LA-CC 08-076 CBECG 1.0 A conjugate gradient solver for banded matrix on the Cell Broadband Engine, with problem setup code for Poisson equation on 2D Cartesian grids. 8/27/09
LA-CC 08-075 CO2-PENS, Version 1.0 CO2-PENS is a coupled system-process level model aimed at analysis of long-term performance of an integrated geologic CO2 sequestion operation. CO2-PENS can be used to track movement of CO2 from sources, such as coal-fired power plants, into geologic storage reservoirs. It can be used to understand the impact of long-term storage of CO2 on the reservoir including potential release to any failure. CO2-PENS is modular, with DLLs linked into main system code. The linked DLLs are used to calculate physical processes using either analytical expressions or numerical solutions. The main system model is written within the Gold Sim modeling framework, and the current suite of DLLs are FORTRAN codes. 8/3/09
LA-CC 08-074 Scout 1.X Scout is a programming language for data analysis and visualization that leverages the power of traditional CPUs and graphics processors for computations. The work is described in two publications: Scout: A Data Parallel Programming Environment for Graphic Processors (LA-UR-07-2094 ) and Scout: A Hardware-Accelerated Systems for Quantitatively Driven Visualization and Analysis (LA-UR-04-6226 ). Note: the 0.X of Scout Version was granted LA-CC-09-069-- the 1.0 Version adds support for program execution on cluster-based supercomputers. 8/12/09
LA-CC 08-073 ExtendSim7 Auditor and Separator Blocks These custom blocks work with the data analysis tool ExtendSim, which is a product of the company ImagineThat. It assists the laboratory with large engineering projects. 8/4/09
LA-CC 08-072 Sparse graph generator and decoder, Version 1.0 This randomly generates low-density parity-check error correction codes with user-defined properties and then tests their performance under varying error probabilities, using belief propagation for the decoding algorithm. 7/29/09
LA-CC 08-071 Codeword-stabilized code finder, Version1.0 This code searches for a general class of quantum error-correcting codes known as codeword-stabilized (CWS) codes. We ran instances of this code for a few weeks, but we did not find anything interesting that hadn't already been posted on arXiv.org, so its has not led to any publications. 7/28/09
LA-CC 08-070 Tone code simulator, Version 1.0 This code was initially developed while I was a grad student at Caltech and later brought to Los Alamos where it has undergone minor modifications. The code performs numerical simulations of topological quantum error-correcting codes under various error models. The results of these simulations have led to the papers posted at quant-ph/051013, .quan-ph/0610082, and quan-ph/ 0703143 on arXiv.org. (LA-UR-05-5617) (LA-UR-06-7153) (LA-UR-07-2576) 7/28/09
LA-CC 08-069 General Mesh Viewer, Version 4.5 GMV reads data from an easy to produce input file and interactively displays selected information on the screen. Simple pull down menus, windows and mouse controls enable the user to maximize the value of the information to be visualized. 9/14/09

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