Search Results for "monte carlo pde" - Page 4
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Showing 191 open source projects for "monte carlo pde"
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PolySim
Polymer simulation utilites
Polymer simulation utilites for bead coarse-grained models of polymers. Includes 1) lattice monte carlo. Many kinds of lattices are supported. It shouldn't be a problem to implement any new specific one (discrete models) 2) off-lattice monte carlo and molecular dynamics (continuous models) Latter one is rebuild of earlier version of simpatico (http://gemini.cems.umn.edu/research/morse/code/simpatico/home.php) project. Input and output are based on PDB file format which is better... -
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We consider a problem of finding maximum weight subgraphs (MWS) that satisfy hard constraints in a weighted graph. The constraints specify the graph nodes that must belong to the solution as well as mutual exclusions of graph nodes, i.e., pairs of nodes that cannot belong to the same solution. Our main contribution is a novel inference approach for solving this problem in a sequential monte carlo (SMC) sampling framework. Usually in an SMC framework there is a natural ordering of the states...
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MoccaCPU
Java based CPU stress testing tool
MoccaCPU is a CPU stress testing tool written in Java. It uses the Monte-Carlo-Algorithm to calculate approximate values of π (Pi) during the test. Mutiple threads can be started to use the full capacity of all given CPU cores. -
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endo-MCML
MC model of Endoscopic Optical Spectroscopy for tubular organ
We present a Monte Carlo static light migration model (Endo-MCML) to simulate endoscopic optical spectroscopy for tubular organs such as esophagus and colon or organs lying behind tubular organs like prostate. Differ from the well-known multi-layered slab tissue model (MCML), our model employs multi-layered hollow cylinder which emitting and receiving light both from the inner boundary to meet the conditions of endoscopy. Inhomogeneous sphere can also be added in tissue layers to model cancer... -
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jaMCp3
just another Monte Carlo for polarized photon propagation
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FamSeq
Variant calling on the basis of pedigree information
... implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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ASEP
Monte Carlo Simulations of Asymmetric Exclusion Processes
Monte Carlo simulations of various classes of asymmetric exclusion processes (ASEP) with open and periodic boundaries. ASEP is a paradigmatic model of non equilibrium statistical mechanics. It can be utilized to model various non-equilibrium phenomena in Biology such as molecular motor transport and protein synthesis. The code's comments will be gradually expanded upon; if there are mistaken or unclear comments they will be corrected. We cannot give an estimation as to when because... -
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FiberMC
Light scattering simulation tool for fibrous media
This Monte Carlo simulation tool calculates multiple scattering down at particle level by small spherical objects and infinitely long cylinders. -
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Hrothgar Parallel LM/MCMC Minimizer
A versatile MCMC and downhill optimization engine
Hrothgar is a parallel minimizer and Markov Chain Monte Carlo generator by Andisheh Mahdavi of San Francisco State University. It has been used to solve optimization problems in astrophysics (galaxy cluster mass profiles) as well as in experimental particle physics (hadronic tau decays). It is probably adaptable enough to be applied to your merit function if you can write it in C. -
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Photonics is a photon tracking Monte Carlo package, which calculates photon flux and time distributions in a heterogeneous medium surrounding a light source. The propagation medium and detector and light sources are highly customizable.
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all... -
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Free C++ toolkit to facilitate Monte-Carlo simulation. This is a library covered under the LGPL. "MCS-libre" stands for "Monte Carlo Simulation - libre". Documentation and examples are provided.
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Chaoskop2
Calculation and Presentation of Fractal Graphics, Chaos Theory
Calculation and Visualization of Fractals and other Elements of the Chaos Theory. VB.NET Project containing more than 80 Routines; the User can determine general Parameters like Order and Iterations; some Routines allow change of special Parameters. -
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RaTrav
mean first passage times and node occupancies calculations
RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single or multiple final states in network-like systems are used. The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. References: M... -
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HYDRA is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use and to extend while allowing integration with other software to
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MCPerm: Monte Carlo SNP permutation
Monte Carlo permutation method for SNP multiple test correlation
MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association study Traditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple testing corrections in case-control association study. However, it relies on the original single nucleotide polymorphism (SNP) genotypes and phenotypes data to perform a large number of random shuffles, and thus it is computationally intensive... -
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GridMD is the C++ class library intended to help the developers to quickly build the molecular dynamics or Monte-Carlo simulation programs and to run it in the distributed environment.
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vonMises
Package for dealing with the von Mises periodogram
This is the package of C++ programs facilitating the practical use of the von Mises periodogram. The von Mises periodogram is a data-analysis period-search tool that models the periodic signal with the so-called von Mises function, K exp(nu cos x). The package can be used to compute the periodogram itself, as well as its detection significance levels. It can also perform some Monte Carlo simulations of the periodogram. The details of the theory are given in the following refereed paper... -
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Jointly optimized BF Assisted AEC
Jointly optimized BF Assisted AEC
.... The convergence analysis provides a stability bound for the adaptation step-size. Monte Carlo simulations can be performed to illustrate the accuracy of the model, which can then used to provide design guidelines. Application of the new model confirms previous experimental findings that the same cancellation performance of a single-microphone AEC can be achieved with a shorter AEC when the possibility of spatial filtering is available. -
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=== This project has moved to github === https://github.com/APTG/libdedx libdEdx is a physics library for stopping power calculations. Stopping power is the energy loss of a particle per unit length (dE/dx). libdedx is supposed to be both fast and easy to use, and features multiple standard dE/dx lists (ICRU, MSTAR...)
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PyKMC is a work in progress on-the-fly kinetic Monte Carlo package. It currently allows for automatic defect-decomposition, lattice minimisation, NEB and String saddle point calculations and RAT transition searches - using LAMMPS or LBOMD.
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Low latency trading platform
The documents for my achievements of the low latency technology
.... Altera OpenCL (on going, just for academic research) OpenCL/Perl/Bat/C++/DDR2/Ethernet/UcOS/Nios II/ Make modification of the Alter OpenCL SDK except the OpecCL C to HDL synthesis to use Ethernet to communicate between Host and Kernel. Rewrite the perl command lines to meet special aims. Monte Carlo Black Schole simulation and QuantLib based on OpenCL standard.