Open Source Linux Simulation Software - Page 11
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Simulation Software for Linux
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iqr is a simulation software to graphically design and control large-scale neuronal models. Simulations in iqr can control real-world devices in real-time. iqr can be extended by new neuron, and synapse types, and custom interfaces to hardware.
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wavefront
2D Finite Element Analysis for Acoustics
Wavefront is a programme for simulating 2D acoustic systems, with a particular emphasis on determining wavefront shapes at the mouths of horns. It accepts CAD drawings in DXF format and produces animated displays of wave propagation as well as exporting various data as text files. It is GPL software and runns on Linux and Windows. -
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Zgoubi is a raytracing code. Since 1972 it pushes charged particles through accelerators and beam lines, by stepwise solution of Lorentz force equation - and their spins via Thomas-BMT differential equation. Zgoubi simulates beam dynamics and polarization in a variety of accelerators (storage ring, synchrotron, cyclotron, betatron, microtron, FFAG, multi-pass ERL, etc) and optical systems (beam lines, magnetic and electrostatic optical components, time-of-flight and mass spectrometers, etc). The code includes built-in fitting procedures with a wide variety of constraints; stochastic SR energy loss; the tracking of synchrotron radiation (SR) Poynting vector; space charge models; various Monte Carlo procedures, etc. Contact: francoisgmeot@gmail.com Documentation (History of accelerators that zgoubi deals with, theory, tutorials): https://link.springer.com/book/10.1007/978-3-031-59979-8 https://link.springer.com/book/10.1007/978-3-031-16715-7, Chap. 14.
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Combines Blender's graphical interface and rendering capabilities with MBDyn's multi-body dynamics, aerodynamics, and aeroelastics simulation and analysis, for rapid modeling and realistic rendering of physics based multi-body simulations.
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Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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CAMFR (CAvity Modelling FRamework) is a fast, flexible, friendly full-vectorial Maxwell solver. Although it can tackle general electromagnetic problems, its main focus is on applications in the field of photonics.
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DeepSee
Visualize deep ocean biogeochemical sediment samples in 2D and 3D!
DeepSee is an interactive workspace for deep ocean scientists to upload sediment core data and map images and see their sampling history displayed across multiple connected views at once! 🦑🦀🐚 🚀 For a live demo, visit: https://www.its.caltech.edu/~datavis/deepsee/ 🌱 To get started, visit our Wiki: https://sourceforge.net/p/deepsee/wiki/Home/ 🧑💻 To modify DeepSee for your own project, visit our GitHub repository: https://github.com/orphanlab/DeepSee/ --- Created by Adam Coscia, Haley M. Sapers, Noah Deutsch, Malika Khurana, John S. Magyar, Sergio A. Parra, Daniel R. Utter, Rebecca L. Wipfler, David W. Caress, Eric J. Martin, Jennifer B. Paduan, Maggie Hendrie, Santiago Lombeyda, Hillary Mushkin, Alex Endert, Scott Davidoff, and Victoria J. Orphan. Copyright (c) 2022-23 California Institute of Technology ("Caltech"). U.S. Government sponsorship acknowledged. All rights reserved. Open Source License Approved by Caltech/JPL APACHE LICENSE, VERSION 2.0 --- -
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EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.
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KEMP
A FDTD solver for electromagnetic wave simulations on a GPU cluster
KEMP is a fast FDTD solver on a GPU-based cluster. The FDTD (Finite-Difference Time-Domain) method is a popular numerical method for electromagnetic field simulations. KEMP enables hardware accelerations suitable for multi-GPU, multi-core CPU and GPU cluster. KEMP also provide easy configuration by using Python scripting language. -
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Kinetic Model Builder
GUI for building, simulating and optimizing kinetic models.
A 3D graphical interface for building, simulating and optimizing Markov kinetic models in response to user defined time dependent stimuli. Models can be represented as either states and connecting transitions or interacting allosteric elements (see http://dx.doi.org/10.1085/jgp.201411183). Model parameters can be optimized by fitting model responses to user data. Optional user defined constraint equations for model parameters are parsed with EigenLab (https://github.com/marcel-goldschen-ohm/EigenLab). Convenient simulation and summarization across 2-dimensional sets of stimulus conditions makes constructing stimulus-response curves incredibly simple. For ion channels, this is useful for simulating dose-response or current-voltage curves both with and without a secondary stimulus (e.g. some drug). A series of video tutorials are available at https://www.youtube.com/watch?v=7I2XPkdOvCg&list=PL-J_lULjiFsCPL2pkz8_tFe_aJ4Fc8a8k&index=1. -
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MIST
A MATLAB toolbox to simulate optical systems
Modal Interferometer Simulation Tool (MIST) is a MATLAB toolbox that can simulate arbitrary resonant optical systems in the paraxial beam approximation. It allows the user to define any optical setup (composed typically of laser sources, mirrors, lenses, electro-optical modulators and detectors) and to compute the static laser field at any point. It uses a Hermite-Gauss modal decomposition to simulate diffraction limited optics. This tool is being developed mainly for simulation of large scale interferometers with resonant cavities used for the detection of gravitational waves. Subscribe to the mailing list for updates and news. If you use MIST in your own simulation work, please cite is as G. Vajente, "Fast modal simulation of paraxial optical systems: the MIST open source toolbox" Classical and Quantum Gravity 30, 075014 (2013) -
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Matrix Product State (MPS) Simulations
Numerical routines for variational matrix product state simulations.
Open Source MPS (OSMPS) is a collection of numerical routines for performing tensor network algorithms to simulate entangled, 1D many-body quantum systems. Our applications reach from ground state and excited states for statics to the dynamics of time-dependent Hamiltonians. We offer various time evolution methods with an emphasis on the support of long-range interactions through the matrix product state formalism. For more algorithms, see the list of features below. Please cite "M. L. Wall and L. D. Carr, New J. Phys. 14, 125015 (2012)" and "D. Jaschke, M. L. Wall, and L. D. Carr, Computer Physics Communications 225, 59–91 (2018)" if your publication involves OSMPS. -
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A Matlab/Octave toolbox to design, simulate, and analyze optical communication systems. Open-source, fast, user-friendly, and customizable, it includes cutting-edge solutions for modulation formats generation, performance estimation, optical fiber propagation. See more at https://optilux.sourceforge.io.
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PlaTec
Plate Tectonics simulator
PlaTec is a 2D terrain generator that uses a simplified model of plate tectonics to produce realistic heightmaps in real time. The simulator starts with a flat fractal map and splits it randomly into plates. Plates are moved around the map. If continents of two plates collide, they fold creating mountain belts. If oceanic crust of one plate collides with another plate, subduction occurs resulting in coastal mountain ranges or island chains. This project is part of my Bachelor of Engineering thesis in Metropolia University of Applied Sciences, Helsinki, Finland. The thesis is freely downloadable from http://urn.fi/URN:NBN:fi:amk-201204023993 . A Youtube video showing the simulator in action is available at http://www.youtube.com/watch?v=bi4b45tMEPE . -
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SystemC Network Simulation Library (SCNSL) is an extension of SystemC to allow modelling packet-based networks such as wireless networks, ethernet, fieldbus, etc. As done by basic SystemC for signals on the bus, SCNSL provides primitives to model packet trasmission, reception, contention on the channel and wireless path loss. The use of SCNSL allows the easy and complete modelling of distributed applications of networked embedded systems such as wireless sensor networks, routers, and distributed plant controllers. SCNSL has migrated: please go to GitLab for the latest version: https://gitlab.com/open-kappa/scnsl
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igafem
Open source 3D Matlab Isogeometric Analysis Code
Isogeometric analysis (IGA) is a fundamental step forward in computational mechanics that offers the possibility of integrating methods for analysis into Computer Aided Design (CAD) tools and vice versa. The benefits of such an approach are evident, since the time taken from design to analysis is greatly reduced leading to large savings in cost and time for industry. The tight coupling of CAD and analysis within IGA requires knowledge from both fields and it is one of the goals of the MIGFEM is to provide a simple-to-understand IGA FEM code. The work is funded under the FP7 Initial Training Network Funding under grant number 289361 'Integrating Numerical Simulation and Geometric Design Technology.' If you use this code or inspired by it please cite the following reference in your work: VP Nguyen, C Anitescu, S Bordas, T Rabczuk. "Isogeometric analysis: an overview and computer implementation aspects". Mathematics and Computers in Simulation, (2015), pp. 89-116, Vol 117. -
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That project aims at providing a clean API, and the corresponding C++ implementation, able to generate demand for travel solutions (e.g., from JFK to PEK on 25-05-2009) according to characteristics (e.g., Willingness-To-Pay, preferred airline, etc).
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Knitter produces a 3-dimensional model of a knitting pattern. It supports KnitML, as well as a native language similar to that of traditional knitting patterns.
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Simple 8085 assembler and disassembler for educational use. The 8085asm generates the map file and intel hex file. It support the directives EQU, ORG, DB, DS and END.
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The ACTIVE-IST project is a set of libraries (e.g. JAUS SDK) for rapid development of cross-platform applications with Unmanned Systems using the JAUS Standard (AS5710, AS6009), Simulations, Human-Interface Devices, and more.
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ADiGator
A MATLAB Automatic Differentiation Tool
ADiGator is a source transformation via operator overloading tool for the automatic differentiation of mathematical functions written in MATLAB. Given a user written file, together with information on the inputs of said file, ADiGator uses forward mode automatic differentiation to generate a new file which contains the calculations required to compute the numeric derivatives of the original user function. Furthermore, these calculations are written entirely in the native MATLAB language, and thus the process may be repeated to obtain nth order derivative files. The package is particularly appealing for applications where the same derivative must be found at multiple different points, i.e. non-linear root finding/optimization, stiff ode integration, etc. -
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Acoustic Research Tool (ART)
Acoustic Simulation Library for Frequency and Time Domain Simulations.
ART is a flexible simulation framework for wind instruments. It includes a growing library of modelling elements. So far bore discontinuities, branches, tone holes, cylindrical and conical tubes, Bessel horns and bent tubes are available for frequency domain modelling. In the time domain generic bidirectional propagation elements, scattering elements, fractional delays, convolution with reflection functions and general z-domain networks are available and can be described using MuParserX expressions. Cylindrical and conical ducts can also be defined based on their geometry. Available models and their parameters can be enumerated and combined to form simulators for complex acoustical structures. Parameters can be specified symbolically by expressions containing other parameter values or global variables. Dependencies between parameters are resolved at run time. However, MuParserX expressions are compiled at design time. Zero-delay loops are detected and reported. -
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BRAHMS is a Modular Execution Framework for dynamical systems. It knits together independently-authored software modules implementing dynamical processes into an integrated system, and supervises the deployment and execution of that system.
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BlueSky Open Air Traffic Simulator
BlueSky Open Air Traffic sim, (Windows/Linux/Mac, Python 2.x based)
BlueSky is an Open Air Traffic Simulation for research purposes. It includes only open, license free data for navigation and aircraft performance but is also compatible with BADA 3. Can be used for ATC research or any other aviation or air transport related simulation studies. Is also able to visualize ADS-B traffic. BlueSky commands, and thus the scenario files, are compatible with the TMX simulator in use by NLR and NASA. BlueSky is originally developed, and still moderated, by prof. Jacco M. Hoekstra and staff and students of the TU Delft. More documentation can be found at the website and inside the doc folder.
