Protomol

ProtoMol is a high-performance framework in c++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol’s sequential performance is excellent when compared to a leading MD program, and that it scales well for a moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.
Find Protomol at: http://sourceforge.net/projects/protomol/

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Posted in Theoretical and Computational | Leave a comment

LP_Solve

What is lp_solve and what is it not? The simple answer is, lp_solve is a Mixed Integer Linear Programming (MILP) solver. It is a free (see LGPL for the GNU lesser general public license) linear (integer) programming solver based on the revised simplex method and the Branch-and-bound method for the integers. It contains full source, examples and manuals. lp_solve solves pure linear, (mixed) integer/binary, semi-continuous and special ordered sets (SOS) models. Note the word linear. This means that equations must be of the first order. 5 * x – 3 * y is an example. However x * y is not linear and cannot be handled by lp_solve. Both the objective function and the constraints have this restriction. Also see Ratios. Via the Branch-and-bound algorithm, it can handle integer variables (see integer variables), semi-continuous variables (see semi-continuous variables) and Special Ordered Sets (see Special Ordered Sets (SOS)). lp_solve has no limit on model size and accepts standard both lp or mps input files, but even that can be extended. Note however that some models could give lp_solve a hard time and will even fail to solve. The larger the model the likely the chance for that. But even commercial solvers have problems with that. It can also be called as a library from different languages like C, VB, .NET, Delphi, Excel, Java, … It can also be called from AMPL via the lpsolve driver program. It can also be called from MATLAB, O-Matrix and Scilab via the a driver program. lp_solve is written in ANSI C and can be compiled on many different platforms like linux and WINDOWS.
Find LP_Solve at: http://lpsolve.sourceforge.net/

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Posted in Optimization | Leave a comment

C++ BigInt class

C++ BigInt class enables the user to work with arbitrary precision integers
Find C++ BigInt class at: https://sourceforge.net/projects/cpp-bigint/

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Posted in Number Theory | Leave a comment

Generating combinatorial objects in C++

Generating combinatorial objects: exponents, all exponents, permutations, color permutations, arrangements, combinations for any numbers and words
Find Generating combinatorial objects in C++ at: https://sourceforge.net/projects/comb-objects/

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Posted in Combinatorics | Leave a comment

LabPlot

Data analysis and visualisation. A new KDE-based graphing / plotting package that looks very powerful.
Find LabPlot at: http://labplot.sourceforge.net/

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LabPlot

A new plotting package just crossed our radar screens. LabPlot looks like a great new tool for generating scientific plots and graphs.

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Multidimensional Quadrature, Graphing, and Plotting

Ed is asking about Multidimensional Quadrature and we’ve got an active discussion about graphing / plotting software over in the OpenScience forums. Drop by and contribute!

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Turing Machines, Performance monitoring, and PDE/ODE solvers

Lots of new entries today. First is XPPAut, a tool for solving all sorts of PDEs and ODEs. We’ve also added a link to the C/C++ program performeter which looks like an interesting way to evaluate the performance of scientific codes.

Today also sees a new link to C++ Simulators of Turing and Post Machines for those of you who want to simulate the most fundamental computers.

Although it is not strictly scientific software, we’ve also included a link to the FCCU GNU/Linux Forensic Boot CD in our Forensics section.

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C++ Simulators of Turing and Post Machines

These C++ programs simulate nondeterministic / deterministic multitape Turing & Post machines, universal Turing machines, and Turing machines with faults, failures and recovery.
Find C++ Simulators of Turing and Post Machines at: http://sourceforge.net/projects/turing-machine/

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Posted in Artificial Intelligence | Leave a comment

C/C++ Program Perfometer

The C/C++ Program Perfometer is an open source tool which enables the programmer to measure the comparative performance of a C/C++ program or of separated pieces of code by one of several desired metrics: e.g., time, memory, or metrics defined by the programmer.
Find C/C++ Program Perfometer at: http://sourceforge.net/projects/cpp-perfometer/

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Posted in Measurement and Evaluation | Leave a comment