Search Results for "command line tools" - Page 3
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Showing 349 open source projects for "command line tools"
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MEMBPLUGIN
MEMBPLUGIN: studying membrane complexity in VMD
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. -
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abumpack
Fortran library with the Abaqus user material subroutines UMAT/VUMAT
This library contains several of user material subroutines for implicit quasi-static (UMAT) and explicit dynamic (VUMAT) versions of the Abaqus solver. The project web site: http://abumpack.sf.net. The Abaqus is a proprietary finite element (FE) code ( http://www.3ds.com/products-services/simulia/products/abaqus/). Users can write subroutines for use with the Abaqus. Linear elastic, isotropic hardening plasticity, Gurson-Tvergaard-Needleman (GTN), Rousselier constitutive models are... -
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KMC-KaiC
Kinetic Monte Carlo simulation of the in-vitro Kai Circadian clock
This code is a dedicated Kinetic Monte Carlo (KMC) algorithm which simulates a model of the post-translational Kai circadian clock. The code allows you to simulate the Kai system at the level of individual KaiC hexamers and monomers and explicitly tracks the turnover of every ATP nucleotide. Apart from ATP hydrolysis, all reactions obey detailed balance. The application of the code is described in our article titled "A Thermodynamically consistent model of the post-translational Kai... -
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RElt
calculates overlap, kinetic integrals for numerical atomic orbitals.
The efficient algorithm calculating the overlap and the kinetic integrals for the numerical atomic orbitals is implemented. The described algorithm exploits the properties of the prolate spheroidal coordinates. The overlap and the kinetic integrals in R^3 are reduced to the integrals over the rectangular domain in R^2, what substantially reduces the complexity of the problem. We prove that the integrand over the rectangular domain is continuous and does not have any slope singularities. For... -
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Scripted Roulette
Simulation tool for the casino game Roulette
Scripted Roulette is an original application which helps you to develop and analyze new betting strategies for the casino game Roulette. Learn and understand more about the chances you really have to win. -
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RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
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A star
it is an implementation of A* algorithm with examples of its usage.
A start (A*) is the algorithm for searching the shortest path in the weighted graphs. My implementation is provided with various interesting applications, i.e. 15 puzzle. This project is related to my other projects located at sourceforge as well: https://sourceforge.net/projects/path-finder-qt/ https://sourceforge.net/projects/shortest-path-graph-a-star/ For detail of A* algorithm see wiki page: https://en.wikipedia.org/wiki/A*_search_algorithm -
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optpack
FE simulation based automatic global optimisation in modern Fortran
A collection of Fortran 2003, 90 and 77 routines, modules and programs for automatic simulation based global constrained optimisation. The initial application is for FE simulation of elasto-plastic buckling of steel rods aimed at tuning the hardening model. Unix shell scripts are used extensively. High concurrency is achieved with parallel multi-start global search and with parallel MPI FE. Powell's BOBYQA or LINCOA are used (not included in this package). Automatic mesh generation of 3D... -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
RAtom solves nonlinear Kohn-Sham equation for the neutral atom. The adaptive algorithm based on finite element method (FEM) is implemented. Discretization of the differential eigenvalue problem is done by finite element method with Lobatto polynomials as a basis functions. High order Gauss quadratures are applied in order to obtain the total energy of atom with absolut accuracy of 1E-6 hartree. Disctretization leads to generalized eigenvalue problem, which is solved by procedures from... -
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Gene-Environment iNteraction Simulator 2
A tool able to simulate gene-environment and gene-gene interactions.
...GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface. -
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experix laboratory control system
instrument control, data acquisition display and analysis
Experix is a command-line driven environment for laboratory data acquisition and device control and graphical presentation and analysis of data. Written in C for GNU-Linux . Tested on PC and Raspberry Pi. The core is written very generally in order to support applications by means of script files. Device interfaces: PCMCIA daq (2 devices tested) via kernel module with interrupt handler and memory-mapped data; USB daq (1 device tested) using libusbx; running an equipment servicing program via pipes. ... -
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RSchr-5
Solves one-electron Schrödinger equation, with SLEPc and PETSc
RSchr-5 calculates the smallest eigenvalues of the one-electron Schrödinger equation. The solved problem is defined on the finite domain, which is a box. The problem is solved with the zero Dirichlet boundary conditions. The implemented algorithm uses Finite Element Method with B-splines as basis functions. Disctretization leads to generalized eigenvalue problem. Program RSchr-5 solves the generalized eigenvalue problem by algorithms implemented in SLEPc amd PETSc libraries. It uses... -
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A neuronal network simulator using NeuroML (as generated by neuroConstruct) for network description. Conductance- and rate-based Hodgkin-Huxley neuron models, and a number of other neurons & synapses. A 5-6-order RK method is used for integration.
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AirTSP
Simulated Airline Travel Solution Provider Library
AirTSP is also named AirTSP (TSP standing for Travel Service Provider). That project aims at providing a clean API and a simple implementation, as a C++ library, of an Airline Schedule Management System. It is intended to be used in simulated environments only: it is not designed to work in the real-world of Airline IT operations. AirTSP/AirTSP makes an extensive use of existing open-source libraries for increased functionality, speed and accuracy. In particular the Boost (C++... -
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...ETFOMM can be used as a DLL as a substitute for CORSIM in the TSIS package. It is compatible with TRAFED and TRAFVU. ETFOMM can also be used as a separate executable from a Windows or Linux command line. ETFOMM may also be linked into another application using the provided Application Programming Interface (API). TRAFVU and TRAFED are trademarks of ITT Industries, Inc., Systems Division.
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Calculation of radiation view factors by adaptive integration. A cross-platform port of the public-domain code by George Walton.
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COTSon scalable simulation infrastructure
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Advanced Simulation Library
Free multiphysics simulation software package
Advanced Simulation Library (ASL) is a free and open source multiphysics simulation software package. Its computational engine is based, among others, on the Lattice Boltzmann Methods (http://en.wikipedia.org/wiki/Lattice_Boltzmann_methods) and is written in OpenCL (http://en.wikipedia.org/wiki/OpenCL) which enable extraordinarily efficient deployment (http://asl.org.il/benchmarks) on a variety of massively parallel architectures, ranging from inexpensive FPGAs, DSPs and GPUs up to... -
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SystemC-WMS (Wave Mixed Signal Simulator) is a class library that extends the standard SystemC kernel to allow modeling and simulation of complex systems comprising analog parts from heterogeneous domain (electrical, mechanical, thermal, ...).
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Volterra2.0
Volterra series Identification Tool
Orthogonal method for the Identification of Volterra series. It is an extension of Lee-Schetzen method with two major improvments: 1. Reduced identification uncertainty in diagonal kernel points. 2. Possibility to identify each Volterra kernel with an input with different variance. This feature reduces the identification noise on lower order kernels and improve the "resolution" on higher order kernels. For reference see: Simone Orcioni. Improving the approximation ability of... -
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Quantum Wells, Wires and Dots
A set of tools for simulating semiconductor nanostructures.
This software accompanies the textbook "Quantum Wells, Wires and Dots" (4th Edition), Paul Harrison and Alex Valavanis, Wiley, Chichester (2015). It is adapted (by the same authors) from code that was originally supplied on a CD with the first edition of the book [1] and is now made available under the GPL3 license. In brief, we encourage everyone to use the software in your studies and research, to study and modify the source-code and to share it widely. However, you are not permitted to... -
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CFD2D
The incompressible Navier-Stokes equations solver in 2D domains
CFD2D is open source software for Linux for solving the non-dimensionalized incompressible Navier-Stokes equations (NSE) inside an arbitrary two-dimensional domain inscribed in a unit square with Dirichlet and "do-nothing" boundary conditions. The space discretization is based on Finite Element Method (FEM) using an approximately uniform triangular mesh. The two choices of FE spaces are offered, these are of the so called MINI-element and of the Taylor-Hood element. The first element... -
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments -
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LBM3fm
LBM3fm - Lattice Boltzmann method for film flow modelling
This program provides the moment method boundary condition treatment for multi-phase flow modelling with lattice Boltzmann methods. For feedback, leave a review, leave a comment on the discussion page or send me a private mail.
