Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/
MOPAC7 is a semi-empirical quantum-mechanics code written by James J. P. Stewart and co-workers. The purpose of this project is to maintain MOPAC7 as a stand-alone program as well as a library that provides the functionality of MOPAC7 to other programs.
Framework for blockstructured adaptive finite volume methods. Provides MPI-parallelized variant of the Berger-Oliger AMR algorithm for Beowulf-clusters. Uses Clawpack. Visualization and conversion tools for HDF4 files included.
BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.
SIGPROC - a collection of signal processing programs developed for pulsar data reduction has been developed and maintained since 1999. The package is used to search for and visualize the presence of pulsed signals in noisy radio astronomy data.
Simulation, analysis, and management of the movement of water
Please see the “Files” link above to download different versions. The One-Water Hydrologic Flow Model (MODFLOW-OWHM, One-Water) is an integrated hydrologic flow (IHM) model that is an enhanced fusion of multiple MODFLOW (MF) versions. While maintaining compatibility with existing MF versions, MF-OWHM includes: linkages for coupled heads, flows, and deformation; facilitation of self-updating models, additional observation and parameter options for higher-order calibrations; and redesigned code for faster simulations. MF-OWHM represents a complete IHM that fully links the movement and use of groundwater, surface water, and imported water for consumption by agriculture and natural vegetation on the landscape, and for potable and other uses. This provides the foundation needed to address integrated hydrologic problems such as evaluation of conjunctive-use alternatives, sustainability analysis, including potential adaptation and mitigation strategies, and best management practices
Package for using CERN's MINUIT with C main program and fcn().
record MIDI files from the PC keyboard
Record a melody as a MIDI file, right from the computer keyboard with no special hardware required. Current work on the project is aimed at music analysis. Rhythm and harmony have completed subroutines. A future version of the program will analyze MIDI files, rate their musical value, and recombine them to produce new tunes.
Virtual Box VDI of SliTaz Linux with Savuka installed and configured
Savuka global analysis software (www.osmanbilsel.net) is installed and configured in a light version of SliTaz linux (www.SliTaz.org). root name: root root password: root username: tux password: root Instructions: -Download and install 7zip (www.7-zip.org) -Extract files to HDD -Install included VirtualBox (not tested on other versions, but shouldn't matter) -Within VirtualBox make a new machine ----Machine/New --------Name: Savuka / Type: Linux / Version: Other Linux (32-bit) --------1024MB RAM -------- Use Existing virtual drive (point to extracted Savuka.vdi) ---- Machine/Settigns/Display: set video memory to 50 MB, enable 2D and 3D acceleration ---- Machine/Settings/Shared Folders: Create new machine folder. Point to any data directory, folder name: DATA, select Auto-mount. Note: "Folder name" must be 'DATA' in all caps to link on boot Thats it! More Info: www.osmanbilsel.net www.paulnobrega.net
CENAT in Costa Rica is enforcing the use of clustering techniques to aid scientific development. beowulf-cenat is the first step towards the implementation of cluster tools, documentation and standards for CR, including Grid on a later stage.
F.EN.I.A. is a Fortran 95 library providing rich graphical output of 2D and 3D scientific data in the SVG and VTK (.vtp) formats. The output can be viewed with cross-platform, open-source viewers like Inkscape, Firefox and Paraview.
An integrated atmospheric model for weather and climate prediction and simulation. It includes portable versions of global spectral model, regional spectral model, and non-hydrostatic mesoscale spectral model.
A group of statistical tools used in the development and structuring of clinical trials by the American Cancer Society. Sample size calculators.
Calculation of normal depth in open channel based on Manning equation.
Solver for Manning's equation used for determination of normal depth in open channels. This is pre-alfa version for further development. The main executable file is bash script "mansol.sh", which should be run with the name of data file as argument. Some examples are given. During the execution, the main codes located in "sources" directory are compiled with gfortran.
PSRPOP - a package to simulate radio pulsar populations has been undergoing development and use since 2003. The package is used to infer the underlying properties of pulsars and help make predictions for future surveys.
SPICE is a 2D in space, 3D in velocity Particle-In-Cell code intended to simulate plasma-wall interaction.
open source analogue of IBM OS/2 operating system
RAMSES is a general purpose simulation code for self-gravitating fluid dynamics with adaptive mesh refinement.