Search Results for "evolution simulation"
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Showing 44 open source projects for "evolution simulation"
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Error to trace to log to deploy. One click. No SSH.AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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Quantum++
Modern C++ quantum computing library
...Quantum++ is not restricted to qubit systems or specific quantum information processing tasks, being capable of simulating arbitrary quantum processes. The main design factors taken in consideration were ease of use, high portability, and high performance. The library's simulation capabilities are only restricted by the amount of available physical memory. On a typical machine (Intel i5 8Gb RAM) Quantum++ can successfully simulate the evolution of 25 qubits in a pure state or of 12 qubits in a mixed state reasonably fast. -
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GenX
X-Ray and Neutron Reflectivity Modeling
GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. -
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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Biogenesis Color Mod
Mod for evolution simulation and artificial life program Biogenesis
You can download the Color Mod at the Biogenesis main site too (included in the main download now). You also find the sourcecode there. If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Original project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ Includes Tyler Colemans "Features Mod": https://sourceforge.net/projects/biogenesisfeatu/ Biogenesis discussion... -
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Fosite - advection problem solver
numerical simulation code for solving transport equations in 1D/2D/3D
Fosite is a generic framework for the numerical solution of hyperbolic conservation laws in generalized orthogonal coordinates. Its main purpose is the simulation of compressible flows in accretion disks. The underlying numerical solution method belongs to the family of unsplit conservative finite volume TVD schemes. The method is 2nd order accurate in space and uses high order Runge-Kutta and multistep schemes for time evolution. In addition to the pure advection code several source terms have been implemented including viscous diffusion and gravitational acceleration. ... -
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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.... -
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C++QED
A framework for simulating open quantum dynamics
C++QED is an application-programming framework for simulating open quantum dynamics in general. It has demonstrated the ability to simulate full Master equation of up to several thousand, and quantum trajectories of up to several hundred thousand dimensions. The basic idea is to allow users to build arbitrarily complex interacting quantum systems out of free subsystems and interactions (elements), and simulate their time evolution with a number of available time-evolution... -
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CASUP
Cellular Automata library for SUPercomputers (CASUP)
CASUP is a Cellular Automata (CA) library for HPC and supercomputers. It can be used in materials science (microstructure evolution, grain coarsening, fracture etc.), physics (Ising magnetisation) and for many other CA. If you use the library, please reference it as: A. Shterenlikht, L. Margetts, Three-dimensional cellular automata modelling of cleavage propagation across crystal boundaries in polycrystalline microstructures, Proc. Roy. Soc. A 471:20150039, DOI:... -
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The goal of the Elle Project is to provide a general purpose modelling environment for the simulation of rock microstructure evolution. The code is based around a unified description of 2D microstructure.
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. By default, the class "GeneticCode" generates... -
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Opt4J
Modular Java framework for meta-heuristic optimization
Opt4J is an open source Java-based framework for evolutionary computation. It contains a set of (multi-objective) optimization algorithms such as evolutionary algorithms (including SPEA2 and NSGA2), differential evolution, particle swarm optimization, and simulated annealing. The benchmarks that are included comprise ZDT, DTLZ, WFG, and the knapsack problem. The goal of Opt4J is to simplify the evolutionary optimization of user-defined problems as well as the implementation of arbitrary... -
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Krowface (Krowdix 3.0) is a simulation and implementation tool of social networks. To visualize and analyze the evolution of different social networks in real time. And the creation of a social network, configuring the parameters that define it. All this through a simple web interface and user friendly.
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Biogenesis X Mod
Mod of the evolution simulation and artificial life program Biogenesis
This project is a modification of the original evolution simulation & artificial life project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ In both, the original project and this modification, 2-dimensional organisms consisting of line segments interact with each other, reproduce and evolve in time. Compared to the original project, this modification explores the following features: * alternative mutation mechanisms * an alternative stress-based aging mechanism It is based on the new_design branch of Biogenesis (https://sourceforge.net/p/biogenesis/git/ci/new_design/tree/), its source code can be obatained from http://sourceforge.net/p/biogenesisxmod/code/ci/xmod/tree/ If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. ... -
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ESTReMo
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds. -
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virtualbelgium
parallelized micro-simulation of large population
The VirtualBelgium project aims at developing understanding of the evolution of the Belgian population using simulation and considers various aspects of this evolution (demographics, residential choice, activity patterns, mobility, ...). It is based on a validated synthetic population for the country and is intrinsically multi-disciplinary. -
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XNDiff
X-ray and Neutron powder pattern simulation analysis
Keywords (XNDiff): -SAXS -SANS -absolute units -core (double)shell crystalline nanoparticles -with a parallelepidal shape -particle assemblies -powder and ensemble average -C/C++ -Unix -OpenMP -HPC Cluster Keywords (BatchMultiFit): -simultaneous fits for several SAXS and SANS curves with simulation data from XNDiff -SANS data can be smeared with dq values from experimental data sets or analytical functions -Mathematica console -local and global optimizers (simulated annealing, differential evolution, Nelder-Mead, ...) can be used -range for fit parameters and further constraints between fit parameters -parallelized (typ. 4-8 threads) TODO (BatchMultiFit): -read and use errorbars from experimental data sets -allow different q-ranges for different data sets in the fits -rewrite and test in Python using e.g. the lmfit module: https://pypi.python.org/pypi/lmfit/ to get rid of Mathematica and to run it on HPC clusters -
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A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
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Lagrange Rally 3D
3D vehicle simulator based on Lagrangian dynamics to simulate dynamics
3D vehicle simulator in which vechicle's configuration as a whole (articulated body) , is represented by a 'vector' of generalised coordinates. so concepts like usual position and orientation of main body and wheels is all defined by the generalised coordinates.Using Lagrangian dynamics, theese coordinates are evolving in time in a realistic manner according to F=ma but as if there were also all constraint forces concretasing the presence of joints: hinge, prismatic, rigid connection, etc.... -
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XCTruck3D _Truck
realistic truck simulator with 3D graphics done from zero
A truck/car simulator,with realistic physics and oldstyle graphics: it displays pixels through the SDL graphics routines, or the X11 if using that version (has some issues:so use the SDL ver).While the 3D graphics is done by the program itself without external libraries.The environment is a hilly terrain:total freedom to drive around.A remake of the classic "Terep 2". Written in the C programming language: although the code is 30 pages long, it's simple. Trailer can be detouched pressming... -
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This project has been moved to https://bitbucket.org/pbazant/evoversum/src/master/ . Evoversum is a fast Darwinian evolution simulator. The program simulates a 2D world populated with "animals" which struggle for food, reproduce and may also eat each other. The subject of evolution is their behavior, which may become quite complex. There is an updated video tutorial at http://www.youtube.com/watch?v=nPkZvyVDWJU !
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This utility, lingen, implements evolution of native machine code via linear genetic programming. The assembly level code uses a subset of assembly language which manipulates and performs calculations using the floating point unit (FPU) of the CPU.
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Penacho
Smokestack pollutant dispersion simulator
Penacho calculates and draws the gas dispersion of a smokestack in the atmosphere. The plume evolution and the pollutant concentration distribution over the surrounding area can be seen in an interactive 3D graph. -
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MIDA
Mitochondiral Infectious Damage Adaptation (MIDA) model of aging
This project provides the source code for the Mitochondiral Infectious Damage Adaptation (MIDA) model of aging. A probabilistic modeling approach is applied by solving the master equation in mitochondrial quality state space in the presence of fusion-fission events, decay of functional quality, mitophagy and mitochondrial biogenesis, as well as molecular damage originating from a random source or from infectious events during fusion and fission. The provided source code is written in... -
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The goal of this project is to provide a platform for simulating biological aging and evolution of the population. The simulation is done using Penna bit-string model. Its based on the mutation accumulation theory.
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Arena is a computer simulation in which programs compete for CPU time and access to main memory. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density dependent natural selection are amenable to investigation.