Free dynamics software for linux

JSBSim Flight Dynamics Model is an open source flight dynamics model (FDM) that compiles and runs under many operating systems, including Linux, Apple Macintosh, Microsoft Windows, Linux, IRIX, Cygwin (Unix on Windows), etc.
The FDM is essentially the physics/math model that defines the movement of an aircraft under the forces and moments applied to it using the various control mechanisms and from the forces of nature.
JSBSim has no native graphics. It can be run by itself as a standalone program, taking input from a script file and various aircraft configuration files; or, it can be run as an integrated part of a larger flight simulator implementation that includes a visual system.
The most notable example of the use of JSBSim is currently seen in the open source FlightGear simulator. JSBSim models the aerodynamic forces and moments by the classic coefficient buildup method.
JSBSim has seen the growth of a fairly large user base, with some of the more notable projects (of which I am aware) described on the Users page.
Main features:
- Fully configurable flight control system, aerodynamics, propulsion, landing gear arrangement, etc. through XML-based text file format.
- Rotational earth effects on the equations of motion (coriolis and centrifugal acceleration modeled).
- Configurable data output formats to screen, file, socket, or any combination of those.
Enhancements:
- This release includes new options for the standalone JSBSim executable, including improved real-time capability.
- This release also includes experimental (but tested) logic to reduce ground reactions jitter while on the ground.

Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++.
Ghemical project has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models [1] is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.
Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the source distribution.
The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.
The MPQC code is not included in the source distribution. In order to use the MPQC-based ab initio methods in Ghemical, you must first compile and install the MPQC program for your system, and then compile Ghemical using some specific settings that link the programs together; see the INSTALL file for more information. Ghemical also contains the OpenBabel package for import and export of many different file formats (as well as other tasks).
Installation
Once you have downloaded the latest release, you should extract all files from your archive file using "tar -zxvvf ghemical-1.00.tgz" or equivalently "gunzip ghemical-1.00.tgz; tar -xvvf ghemical-1.00.tar". After that please read the "INSTALL"-file you just extracted to get additional information.
Enhancements:
- bug fixes

GNU Archimedes is the GNU package for the design and simulation of submicron semiconductor devices. Archimedes is a 2D Fast Monte Carlo simulator which can take into account all the relevant quantum effects, thank to the implementation of the Bohm effective potential method.

The physics and geometry of a general device is introduced by typing a simple script, which makes, in this sense, GNU Archimedes a powerfull tool for the simulation of quite general semiconductor devices.

In the present release, GNU Archimedes is able to simulate electrons and heavy holes in Silicon and GaAs (Gamma and L-valleys) devices (holes are simulated by means of a simplified MEP model), and in the next release, which is in preparation, it will be able to make simulations in 1D, 2D and 3D (this release will be delivered as soon as possible).

The Scientifical and Industrial Motivations
In today semiconductor technology, the miniaturization of devices is more and more progressing. In this context, it is easy to see that numerical simulations play an important role at every level of device manufacture. In fact, the cost of designing and physically constructing prototypes for VLSI semiconductor devices is very high and without the availability of advanced simulators the efforts for devices miniaturization would, likely, be brought to a halt. From assessing the performance of individual transistors, to circuits and systems, and, consequently, with the promise of improved device performance, industries are encouraged to keep on miniaturizing with lower manufacture costs.

But, unfortunately, such simulations are not whithout their challenges... A first consequence of device miniaturization is that simulations of submicron semicondutor devices requires advanced transport models. Because of the presence of very high and rapidly varying electric field, phenomena occur which cannot be described by means of the well-known drift-diffusion models, which do not incorporate energy as a dynamical variable.

That is why some generalization has been sought in order to obtain more physically accurate models, like energy-transport and hydrodynamical models. The energy-transport models which are implemented in commercial simulators are based on phenomenological constitutive equations for the particle flux and energy flux depending on a set of parameters which are fitted to homogeneous bulk material Monte Carlo simulations. So, this is not, certainly, a satisfactory physical description of the internal electronic dynamics in a semiconductor device.

As current device technologies quickly approach the scales whereby quantum effects due to strong confinement of carriers and direct source-drain tunneling will begin to dominate, new simulation techniques are required in order to fully understand and acurately simulate the physics behind the technology operation.

Of all the simulation methods currently employed, ensemble Monte Carlo has always been, both in the accademic and industrial community, the most vigorous and trusted method for device simulation, as it is proven to be reliable and predictive, as one can easily see from the vast bibliography on this subject.

However, as Monte Carlo relies on the particle nature of the electron (in fact we consider an electron like a biliard ball), quantum effects associated with the wave-like nature of electrons cannot fully incorporated into the actual simulators, i.e. the ensemble Monte Carlo have to be lightly (or strongly, it depends on the point of view and on the methods implemented...) modified to take into account the quantum effects, at least at a first order of approximation, which is certainly enough to take into account correctly all the relevant quantum effects present in the present-day semiconductor devices (till 2015 probably...). In order to take into account the wave-like nature of electrons we use a recently introduced quantum theory, the so-called Bohm effective potential theory.

So it is challenging and very interesting to develop such a code for 2D quantum submicron semiconductor devices. This is why I have decided to implement this code, but these are not the only motivations...

The Ethical Motivations
The very sad situation you quickly observe working in a semiconductor industry, but also in all places in which researches about semiconductor devices are made, the only codes for simulation you can find are not free and are proprietary codes.

That is a very bad situation because, at the present time, if you need to develop your own code for the purpose of simulating a device it is IMPOSSIBLE to obtain an advanced one in a short time, and, trust me, this is EXTREMELY BAD for scientific research... (Immagine if you had to re-discover the Newtonian laws every time you need them...) So, you can find a huge amount of papers describing a lot of numerical methods for simulating, in a very advanced way, semiconductor devices (even in the quantum case), but nobody will give you a code on which you can construct your own method (with the unlikely exception that at least one of the programmers is a friend of yours :) ).

Even worst, if you are a semiconductor device designer and you want to simulate "realistically" a new device, you have to pay (trust me, at very high costs!) a BINARY (just a binary and not the code!) from some well-known software industry. This binary will certainly have some bugs (because it is coded by humans which are not perfect...) and you will never have the possibility of fix them on your own. Of course, you can write to the software house and tell them that there is a bug, but, how many time do you will wait for a new release without those bugs? I dont think it will be a short time...

My impression is that, after a long research on the Web for a Free Software dealing with advanced 2D semiconductor device simulation, there was not a free code for the purpose of semiconductor devices simulation (i mean under GPL license). To be sure about it, I asked to the great Richard Stallman (by mail) if it will be worth to do a code like this and he encouraged me to code it, because there wasnt a code like this as free. So I decided to write this code..

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems.

What we are trying to do is to create a framework for testing, and a core set of tests that all may download and use to probe specific elements of systems performance.

Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org and Scalable Informatics LLC The idea is to enable end users, consumers, systems developers, and others to easily build and use meaningful tests for measurement and tuning reasons.

Joe Landman from Scalable Informatics LLC conceived the idea and wrote the original codes. We are looking for additional benchmark code suggestions, tests, data sets, etc.

Current baseline tests are several NCBI BLAST runs, several HMMer runs, and a variety of others. We plan to include ClustalW, X!Tandem, various chemistry, dynamics, and related tests, as well as several others.

Tests such as LINPACK or HPL simply do not provide meaningful performance indicators or predictive models for high performance informatics. Unfortunately, nor do a number of more recent and focused tests.

This is a problem as LINPACK and HPL specifically test the performance on various matrix operations, where you have effectively regular memory access patterns, and specific mathematical operations.

These codes are most useful for comparison to codes with heavy floating point operations, and interleaved memory traffic. These codes were not designed for comprehensive systems benchmarking, where disk I/O, memory latency, and other factors all contribute to the performance issues.

The best tests are the ones that are most similar to the codes you will run on the machine. The tests themselves should be reasonable approximations to a real execution of your code, using real data. You may need to pare it back in order to get realistic run times.

You should have a reasonable subset of data sizes. A single test does not tell you how your system scales, and one of the reasons for the existance of this test is specifically to allow you to test the performance while you increase various aspects of the workload.

You rarely get a quiescent system in a cluster, so we would recommend that you try to run in as realistic an operating environment as possible. A baseline in a quiescent system is fine, but it may set your expectations unreasonably.
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LAMMPS project is a Molecular Dynamics Simulator.
LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale or continuum levels.
LAMMPS runs on single-processor machines or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
LAMMPS is distributed as an open source code under the terms of the GPL license.
Enhancements:
- Changed to using NIST values for constants.
- A potential problem with alloy interactions has been fixed.
- Improved flexibility of user customization of output.
- The ability to add new styles of atom has been improved.
- A new atom method library, non-orthogonal lattice support, and support for semiconductors have been added.
- There are code speedups and bugfixes.

Decade is a tool for simulating rigid body dynamics. Decade can work as a standalone program.

Decade can also also work from the analysis of a SolidWorks assembly or a CATIA V5 product. Results are availables as text, graphs, and animation in SW and CATIA V5.

adevs is a C++ library for developing discrete event simulations based on the Parallel DEVS and DSDEVS formalisms.
DEVS has been applied to the study of social systems, ecological systems, computer networks and computer architecture, military systems at the tactical and theater levels, and in many other areas.
Recent advances in quantized approximations of continuous systems suggest promising computational techniques for high performance scientific computing (e.g. in the field of computational fluid dynamics).
Enhancements:
- This version corrects an error in the dynamic structure feature (this error only affected models that use component migration).
- A limited adevs-1.x backwards compatibility module is available.

MyPaint is a painting application with brush dynamics.

MyPaint is a fast painting/scribbling program. It is like the GIMP with only the airbrush tool, but with more dynamics.

For example you can noisify the brush radius depending on the pointer speed. It supports pressure sensitive graphic tablets. MyPaint has an infinite canvas and an own color selector, but no layers and no undo function.