A ports freeze means that commits will be few and far between and only by approval.

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liboglappth is a support library packages for science/ghemical
This is for the OpenGL stuff.
See also:
http://www.bioinformatics.org/pipermail/ghemical-devel/2007-September/000688.html

WWW: http://www.uku.fi/~thassine/projects/ghemical/

- New port silo-4.6.1

A mesh and field I/O library and scientific database

Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files. The files Silo produces and the data within
them can be easily shared and exchanged between wholly independently
developed applications running on disparate computing platforms.

Consequently, Silo facilitates the development of general purpose tools
for processing scientific data. One of the more popular tools that process
Silo data files is the VisIt visualization tool.

Silo supports gridless (point) meshes, structured meshes, unstructured-zoo
and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes,

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This port installs python bindings for openbabel.

WWW:    http://openbabel.sourceforge.net

PR:             ports/125768
Submitted by:   Max Brazhnikov <makc at issp.ac.ru>

Pycdf is a python interface to the Unidata netCDF library. It provides an
almost complete coverage of the netCDF C API, wrapping it inside easy to
use python classes.

WWW:  http://pysclint.sourceforge.net/pycdf/

PR:             ports/123303
Submitted by:   wenheping at gmail.com

[NEW PORT] graphics/2d-rewriter: Fractals generator based on pattern matching
and rewriting

        2d-rewriter is fractals generator based on pattern matching
        and rewriting. The program takes input containing initial
        object placement and rewriting rules and keeps applying
        rules to the data field until it reaches an arrangement
        where no rules can be applied.

PR:             ports/118906
Submitted by:   Igor Serikov <bt@turtle.freedns.us>

Jmol is a Java molecular viewer for
three-dimensional chemical structures.
Features include reading a variety
of file types and output from quantum
chemistry programs, and animation of
multi-frame files and computed normal
modes from quantum programs.

WWW:  http://sourceforge.net/projects/jmol/

PR:             ports/123631
Submitted by:   Wen heping <wenheping at gmail.com>

Colt is a package for scalable scientific and technical computing in Java. It
consists of several free Java libraries, for user convenience bundled under one
single uniform umbrella. Namely the Colt library, the Jet library, the CoreJava
library, and the Concurrent library.

The Colt library provides fundamental general-purpose data structures optimized
for numerical data, such as resizable arrays, dense and sparse matrices
(multi-dimensional arrays), linear algebra, associative containers and buffer
management.

WWW: http://dsd.lbl.gov/~hoschek/colt/

PR:             122913
Submitted by:   Wen heping <wenheping@gmail.com>

DTI visualization software from Stanford.

WWW: http://graphics.stanford.edu/projects/dti/

PR:             ports/120129
Submitted by:   Jason W. Bacon <jwbacon at tds.net>

Move speedcrunch from science to math.
No repo is requiered since there's no history to preserve.

Requsted by:    danfe@

SpeedCrunch is a multiplatform desktop calculator for power users.
It is designed to be enjoyed using keyboard. Result is shown in
scrollable display, history of expressions is available with up
and down arrow.

Some other features:
optional keypad, syntax highlight, matched parenthesis indicator,
just-in-time calculation (show result even before you finish typing)
and autocomplete for variables.

WWW: http://speedcrunch.digitalfanatics.org/

PR:             ports/114969
Submitted by:   Yinghong.Liu <relaxbsd at gmail.com>

- science/liblr is moved to science/liblinear (project renamed)

Code_Saturne is EDF's general purpose computational fluid dynamics
software. Developed since 1997 at EDF R&D, it is based on a co-located
Finite Volume approach that accepts meshes with any type of
cell (tetrahedral, hexahedral, prismatic, pyramidal, polyhedral, ...)
and any type of grid structure (unstructured, blockstructured, hybrid,
conforming or with hanging nodes, ...).
Its basic capabilities enable the handling of either incompressible or
expandable flows with or without heat transfer and turbulence (mixing
length, 2-equation models, v2f, Reynolds stress models, Large Eddy
Simulations, ...).

<http://rd.edf.com/code_saturne/>

Add liblr-1.0, a library for large regularized logistic regression.

The chemical-mime-data package is a collection of data files to add support for
various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME.

WWW: http://chemical-mime.sourceforge.net/

The Blue Obelisk Data Repository lists many important chemoinformatics data
such as element and isotope properties, atomic radii, etc. including references
to original literature. Developers can use this repository to make their
software interoperable.

WWW: http://wiki.cubic.uni-koeln.de/bowiki/index.php/DataRepository

Parallel-NetCDF is a library providing high-performance I/O while still
maintaining file-format compatibility with Unidata's NetCDF. NetCDF gives
scientific programmers a space-efficient and portable means for storing data.
However, it does so in a serial manner, making it difficult to achieve high
I/O performance. By making some small changes to the API specified by NetCDF,
we can use MPI-IO and its collective operations.

WWW: http://trac.mcs.anl.gov/projects/parallel-netcdf

PR:             ports/112265
Submitted by:   Chao Shin <quakelee at cn.FreeBSD.org>

NIfTI-1 is a new Analyze-style data format, proposed by the NIfTI DFWG
as a short-term measure to facilitate inter-operation of functional MRI
data analysis software packages.

WWW:    http://nifti.nimh.nih.gov/

PR:             ports/112183
Submitted by:   Jason W. Bacon

2007-03-27 emulators/kmamerun: Project was abandoned 4 years ago and expects an
old version of XMAME, please use other frontends instead (like gxmame)
2007-03-28 graphics/hobbes-icons-xpm: Archaic port
2007-04-10 japanese/firefox-ja: Incomplete pkg-plist
2007-04-10 japanese/lookup-xemacs: Does not install
2007-04-10 lang/linux-hla: Does not compile
2007-04-10 mail/vmailmgr: Incomplete pkg-plist
2007-04-10 multimedia/qvamps: Touches filesystem prior to 'make install'
2007-03-10 net-mgmt/sting: Broken on all supported versions of FreeBSD
2007-04-10 net-mgmt/tas: Incomplete pkg-plist
2007-04-10 net-p2p/verlihub-plugins: Does not configure, it needs at least
verlihub 1.0
2007-04-10 news/inn-stable: Fails to patch
2007-04-10 palm/malsync: Does not build with new pilot-link
2007-04-10 russian/elm.language: Leaves behind files on deinstall
2007-04-10 russian/pine.language: Leaves behind config file on deinstall
2007-04-01 science/py-scipy03: Replaced by py-scipy
2007-04-10 security/php4-cryptopp: Does not compile

The CFD General Notation System (CGNS) provides a standard for recording and
recovering computer data associated with the numerical solution of the equations
of fluid dynamics.

GAMESS is freely available ab-initio molecular orbital
calculation program calculates energy, molecular structure,
vibrational frequencies from the basic principle of quantum mechanics.

A site license for GAMESS is available at no cost to both academic
and industrial users. Please refer
http://wwwmsg.fi.ameslab.gov/GAMESS/dist.menu.html
for details.

We also included simple launcher called `gamess'
for your convenience. You don't set any environment variable
to run gamess. Just type
% gamess <somefile.inp>
is enough.

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2007-01-01 graphics/teddy: No new releases in the past 4 years
2007-01-01 net/arla: "does not compile"
2007-01-02 sysutils/lsmlib: distfile and homepage disappeared
2007-01-02 security/ifd-gpr400: distfile and homepage disappeared
2007-01-04 science/mmtk: distfile and homepage disappeared
2007-01-04 print/xtem: distfile and homepage disappeared
2007-01-04 net/mrt: distfile and homepage disappeared

Libint is a library for evaluating ERI (electron replusion integral)
over Cartesian Gaussian fuctions for modern atomic and molecular theory;
esp. for science/mpqc and science/psi3.

add linsmith 0.99.3
Smith charting program

- Reflect repocopy ofscience/py-scipy -> science/py-scipy03

Add g3data 1.5.0, utility for extracting data from graphs.

PR:             ports/103397
Submitted by:   trasz <trasz at pin.if.uz.zgora.pl>

Paje is a graphical tool that displays traces produced during the
execution of multithreaded programs. Other programs can also generate
traces for this tool.
PR:             103677
Submitted by:   Gürkan Sengün

GTAMS Analyzer is a complete coding and analysis package. It is a "port" of
TAMS Analyzer for Macintosh OS X. Note, at some point the two projects will
have identical file formats, at which point  the initial G (for GNUstep)
will be dropped. GTAMS stands for GNUstep Text Analysis Markup System, it
is a convention for identifying themes in text. The software offers a wide
range of tools for applying themes to texts and identifying patterns of
themes within and between texts.
PR:             103680
Submitted by:   Gürkan Sengün

Medit is an interactive mesh visualization software, developed by the Gamma
project at INRIA-Rocquencourt.

It is intended to display computation results (in mechanics of the solids or
fluids, thermics, electromagnetism, etc.) on grids 2d (triangles and
quadrangles), 3d (tetrahedrons or hexahedrons) or surfaces (triangles and
quandrangles).

ITK is an open-source software toolkit for performing registration and
segmentation. Segmentation is the process of identifying and classifying
data found in a digitally sampled representation. Typically the sampled
representation is an image acquired from such medical instrumentation as
CT or MRI scanners. Registration is the task of aligning or developing
correspondences between data. For example, in the medical environment,
a CT scan may be aligned with a MRI scan in order to combine the
information contained in both.

WWW: http://www.itk.org

Port maintainer: Jason W. Bacon
                 bacon@smithers.neuro.mcw.edu

PR:             ports/95166
Submitted by:   bacon at smithers.neuro.mcw.edu

Gwyddion is a modular SPM (Scanning Probe Microsopy) data visualization and
analysis tool written with Gtk+.

It can be used for all most frequently used data processing operations
including: leveling, false color plotting, shading, filtering, denoising, data
editing, integral transforms, grain analysis, profile extraction, fractal
analysis, and many more.  The program is primarily focused on SPM data analysis
(e.g. data obtained from AFM, STM, NSOM, and similar microscopes).  However, it
can also be used for analysis of SEM (Scanning Electron Microscopy) data or any
other 2D data.

WWW: http://gwyddion.net/

PR:             ports/101773
Submitted by:   David Necas <yeti@gwyddion.net>

Add p5-Algorithm-SVMLight 0.05, perl interface to SVMLight
Machine-Learning Package.

PR:             ports/101297
Submitted by:   Gea-Suan Lin <gslin at gslin.org>

Add svmlight 6.01, an implementation of Support Vector Machines (SVMs)
in C.

PR:             ports/100944
Submitted by:   Gea-Suan Lin <gslin at gslin.org>

Add crf++ 0.42, yet Another CRF toolkit.

PR:             ports/100909
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

Add ghmm 0.7.0a, general Hidden Markov Model Library in C.

PR:             ports/100886
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

Add pcp 2.2, machine learning program for pattern classification.

PR:             ports/100798
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

Add xmds , XMDS is a code generator that integrates equations;.

PR:             ports/100419
Submitted by:   EelVex

Libghemical port. This port installs support libraries of
science/ghemical port. From version 2.0, science/ghemical becomes
large, splitted into two parts. Update of ghemical port will
follow soon.

Objecto Oriented Finite Element Analysis of Real Material Microstructures
__________________

OOF is designed to help materials scientists calculate macroscopic
properties from images of real or simulated microstructures. It is
composed of two cooperating parts: ppm2oof and oof. ppm2oof reads images
in the ppm (Portable Pixel Map) format and assigns material properties to
features in the image. oof conducts virtual experiments on the data
structures created by ppm2oof to determine the macroscopic properties of
the microstructure. Currently, the programs calculate stresses and
strains, but someday we hope to include thermal, electric, and magnetic
field calculations.

Check the Homepage for online manuals and new versions

WWW:     http://www.ctcms.nist.gov/oof/

PR:             ports/98601
Submitted by:   Pedro F. Giffuni

CDO is a collection of command line Operators to manipulate and analyse Climate
model Data. Supported file formats are GRIB, netCDF, SERVICE, EXTRA and IEG.
There are more than 250 operators available. The following table gives a short
overview about the main categories.

* File information (info, sinfo, diff, ...)
* File operations (copy, cat, merge, split*, ...)
* Selection (selcode, selvar, sellevel, seltimestep, ...)
* Missing values (setctomiss, setmisstoc, setrtomiss)
* Arithmetic (add, sub, mul, div, ...)
* Mathematical functions (sqrt, exp, log, sin, cos, ...)
* Comparision (eq, ne, le, lt, ge, gt, ...)
* Conditions (ifthen, ifnotthen, ifthenc, ifnotthenc)
* Field statistic (fldsum, fldavg, fldstd, fldmin, fldmax, ...)
* Vertical statistic (vertsum, vertavg, vertstd, vertmin, ...)

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Add science/minc2.

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:             ports/93495
Submitted by:   Jason Bacon <bacon (at) smithers.neuro.mcw.edu>
Repocopied by:  marcus

ElmerPost - the Visualization of Numerical Results.

The function of ElmerPost is to visualize the numerical results produced
by ElmerSolver and other finite element programs. ElmerPost operates with
the data specific to the unknown variables (temperature, velocity,
pressure, displacement etc.) defined in the mathematical model. ElmerPost
plots e.g. contours and vector fields, and can manipulate computed data
into another form using the built-in MATC-language (for instance heat
fluxes from temperature distributions).

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

ElmerFront - the Graphical User Interface.

ElmerFront is a tool for initializing the computational process in Elmer.
It communicates with external software producing geometrical data, i.e.,
CAD files and computational meshes. ElmerFront generates its own finite
element meshes, allows the user to build mathematical models graphically,
and finally produces input data for ElmerSolver.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

ElmerSolver - the Solution of Partial Differential Equations.

ElmerSolver is thus an independent module that processes the computational
mesh and the model input file containing references to the selected
equations and model parameters. ElmerSolver makes the equations into a
discrete form, handles coupled systems, non-linearities and
time-dependences, and provides output data for visualization.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

HUTIter library for use in the Elmer FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM).

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

MATC language library used by Elmer FEM package.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

Input/Output Data base interface for use in the ELMER FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM)

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

ElmerGrid is a utility program for fast creation of structured 2D and
extruded and rotated 3D geometries. ElmerGrid is independent but fully
supports ElmerSolver and ElmerPost. It may be used to create linear,
quadratic and cubic triangles and rectangles. It has also versatile
capabilities in mesh manipulation.

ElmerGrid may also be used in grid manipulation. ElmerGrid may, for
example, be used to transfer different mesh formats to that understood by
ElmerSolver or ElmerPost. ElmerGrid also includes mesh partitioning
routines that have been optimized for ElmerSolver. The partitioning may be
done by METIS or by a simple geometric division.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

A Mesh Generation Utility for use with the ELMER FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM)

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

A program for doing calculation on Smith Chart, similar in functionality to
xsmc but with a simpler user interface; written with GNU/GTK library and
released under GNU/GPL. Written by Lapo Pieri IK5NAX

WWW: http://www.qsl.net/ik5nax

PR:             ports/93224
Submitted by:   Diane Bruce <db (at) db.net> - VA3DB

Add fasthenry , a multipole-accelerated inductance analysis program.

PR:             ports/93969
Submitted by:   Pedro Giffuni <giffunip@asme.org>

Add fastcap , a three-dimensional capacitance extraction program.

PR:             ports/93968
Submitted by:   Pedro Giffuni <giffunip@asme.org>

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:             ports/91918
Submitted by:   Jason W. Bacon <bacon (at) smithers.neuro.mcw.edu>

Remove expired port science/glens

Approved by:    garga (mentor)

Repocopy math/netcdf to science/netcdf, along with cdf, hdf and hdf5.

PR:             92497
Submitted by:   /me
Repocopied by:  marcus

Common Data Format (CDF) is a conceptual data abstraction for storing
multi-dimensional data sets. The basic component of CDF is a software
programming interface that is a device independent view of the CDF data
model. The application developer is insulated from the actual physical
file format for reasons of conceptual simplicity, device independence,
and future expandability. CDF files created on any given platform can
be transported to any other platform on to which CDF is ported and used
with any CDF tools or layered applications.

A comparison between CDF, netCDF, HDF and HDF5 is available at
<http://cdf.gsfc.nasa.gov/html/FAQ.html>.

Add new port science/afni

AFNI (Advanced Functional Neuro Imaging) is a tool for analyzing
3 dimensional images, especially functional MRI images used in
brain mapping research.

WWW: http://afni.nimh.nih.gov/

PR:             ports/90752
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu>
Reviewed by:    garga (mentor)
Approved by:    garga (mentor)

The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate
anything from complex fluid flows involving chemical reactions, turbulence and
heat transfer, to solid dynamics, electromagnetics and the pricing of financial
options.

WWW: http://www.opencfd.co.uk/openfoam/index.html

PR:             ports/91886
Submitted by:   thierry

Add V_Sim, a program to visualize atomic structures such as crystals, grain
boundaries and so on.

GDL - GNU Data Language - is a free IDL (Interactive Data Language)
compatible incremental compiler (i.e.  runs IDL programs).

IDL is a registered trademark of Research Systems Inc.
(see: <http://www.rsinc.com/>)

Remark: slave port for Python module intentionnally not yet committed.

WWW: http://gnudatalanguage.sourceforge.net/

Add gerris 0.6.0, a scientific CFD simulator.

Gerris is an Open Source Free Software library for the solution of partial
differential equations describing fluid flow. Gerris is supported by NIWA
(National Institute of Water and Atmospheric research) and by the
Marsden Fund of the Royal Society of New Zealand. The code is written
entirely in C and uses both the GLib Library and the GTS Library for
geometrical functions and object-oriented programming.

PR:             86297
Submitted by:   Oliver Dunkl <odunkl (at) gmx.net>

PAIDA is pure Python scientific analysis package and implements AIDA (Abstract
Interfaces for Data Analysis).

PR:             ports/83599
Submitted by:   Vsevolod Stakhov <vsevolod@highsecure.ru>

New port: ParaView is a powerful scientific visualization application, designed
with the need to visualize large data sets in mind.

New port for mbdyn, which is a MultiBody Dynamics simulation software. It comes
with lots of libraries etc.  There are two knobs which are in development at
the moment so I disabled them with an IGNORE message.  They need some work and
maybe some testing.

PR:             ports/81136
Submitted by:   Kay Lehmann <kay_lehmann@web.de>

Add lamprop 1.3.1.

Lamprop takes in input file describing the lay-up and constituent materials
of a fiber-reinforced composite laminate, and calculates some mechanical
and other properties. The submitter is the original author of the software,
and will maintain the port.

PR:             81066
Submitted by:   Roland Smith <rsmith (at) xs4all.nl>

Remove mxp

Forgotten by:   maho
Approved by:    portmgr (self)

Add mxp (Mandelbrot explorer). Mxp is an X application for computing and
exploring
Mandelbrot sets.  Features of mxp include:
        - zoom and un-zoom
        - dynamic resizing of drawing window
        - setup save/load
        - asynchronous image generation (buttons always work)
        - GIF output
        - animation
        - nine color schemes
        - color rotation
        - color change options
        - detailed statistics

WWW:  http://www.ibiblio.org/pub/Linux/apps/math/fractals/

. Add a port of the Szip scientific compression library, used by current
  versions of HDF:

  "Szip is an implementation of the extended-Rice lossless compression
   algorithm.

   WWW: http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/"

DCL is scientific graphic library for geoscience, written in Fortran.

PR:             ports/76856
Submitted by:   Shin'ya Murakami <murakami (at) ahs.scitec.kobe-u.ac.jp>

science/cdcl         -> update to 5.3 and use gtk by default
science/cdcl-gtk     -> delete
science/ruby-dcl     -> update to 1.5 and use gtk by default
science/ruby-dcl-gtk -> delete
science/ruby-gphys   -> update to 0.3.5 and fix dependency
science/gave         -> update to 1.1.3 and fix dependency

PR:             ports/76853
Submitted by:   maintainer

McStas - Monte Carlo simulation of neutron instruments

McStas is an ongoing project to create a general tool for simulating neutron
scattering instruments. The project is conducted at Risoe National Laboratory
in cooperation with the ILL.

McStas is based on a compiler that reads a high-level specification language
defining the instrument to be simulated and produces C code that performs the
Monte Carlo Simulation.

WWW: http://neutron.risoe.dk/

PR:             ports/66031
Submitted by:   Joerg Pulz <Joerg.Pulz@frm2.tum.de>

- Move emulators/qcl -> science/qcl on maintainer's request.

Repocopy by:    marcus

Add buddy 2.4, a Binary Decision Diagram library.

PR:             71221
Submitted by:   Leland Wang

DeViSoR is abbreviated for "Design and Visualization of Software Resource". The
DeViSoRGrid application is part of that software family and is primarily used
for the following tasks, so far in 2D only:

  * Geometry generation
  * Manual coarse mesh generation
  * Grid visualisation at all levels

All of this can be done in a very confortable manner using a simple point and
click interface like in common vector-based image processing software. Both the
reliable FEAT file format and the new FEAST format with integrated parallelism
are supported.

WWW:    http://www.featflow.de/

PR:             75973
Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

Add a port of udunits:

 The Unidata units library, udunits, supports conversion of unit
 specifications between formatted and binary forms, arithmetic
 manipulation of unit specifications, and conversion of values
 between compatible scales of measurement.

 WWW: http://www.unidata.ucar.edu/packages/udunits/

Obtained from:  Gentoo (partially)

Add isaac-cfd 4.2, Integrated Solution Algorithm for Arbitrary
Configuration.

PR:             75529
Submitted by:   Pedro F. Giffuni

Add gsystem, a virtual reality simulation framework, specialised on life and
evolution simulation. I'm a main developer of this framework and I will also
keep the FreeBSD port up-to-date, as I'm using FreeBSD as my primary platform.
See http://www.g-system.at for details.

PR:             ports/75466
Submitted by:   Raphael Langerhorst <raphael-langerhorst@gmx.at>

Add x11iraf 1.3.1, which provides graphical tools to work with IRAF.

PR:             70816
Submitted by:   David Syphers.

Slave port to science/libsvm

PR:             ports/73981
Submitted by:   Rong-En Fan <rafan(at)infor.org>

SIMLIB/C++ is the SIMulation LIBrary for C++ programming language. You can
create models directly in C++ language with the use of predefined simulation
tools from the library. SIMLIB allows object-oriented description of models
based on simulation abstractions. Current version allows a description of
continuous, discrete, combined, 2D/3D vector, and fuzzy models.

Requested by:   Roman Divacky

Add omnetpp, a public-source, component-based, modular and open-architecture
simulation environment with strong GUI support and an embeddable simulation
kernel.  Its primary application area is the simulation of communication
networks and because of its generic and flexible architecture, it has been
successfully used in other areas like the simulation of IT systems, queueing
networks, hardware architectures and business processes as well.

PR:             ports/73920
Submitted by:   Bjoern Koenig <bkoenig@cs.tu-berlin.de>

Add getdp 1.0.0, a rather general finite element solver using mixed
finite elements.

Suggested by:   Pedro F. Giffuni.

New port science/gromacs
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems
with hundreds to millions of particles, and also the World's
fastest Molecular Dynamics under GPL.

PR:             71211
Submitted by:   Stephen Montgomery-Smith <stephen@math.missouri.edu>
Reviewed by:    Bruno Afonso <brunomiguel@dequim.ist.utl.pt>

add py-scipy 0.3
Scientific tools for Python