22:34 pav 

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>

07:29 clsung 

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>

15:07 clsung 

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>

03:38 clsung 

Add crf++ 0.42, yet Another CRF toolkit.

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

03:36 clsung 

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

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

03:34 clsung 

Add pcp 2.2, machine learning program for pattern classification.

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

19:58 rafan 

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

PR:             ports/100419
Submitted by:   EelVex

07:30 maho 

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.

18:58 itetcu 

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

08:41 pav 

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, ...)
* Time range statistic (timavg, yearavg, monavg, dayavg, ...)
* Ensemble statistic (enssum, ensavg, ensstd, ensmin, ...)
* Regression (detrend)
* Field interpolation (remapbil, remapcon, remapdis, ...)
* Vertical interpolation (ml2pl, ml2hl)
* Time interpolation (inttime, intyear)

WWW: http://www.mpimet.mpg.de/fileadmin/software/cdo/

PR:             ports/98099
Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet@sunpoet.net>

12:05 thierry 

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

19:55 thierry 

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>

19:54 thierry 

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>

19:54 thierry 

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>

19:53 thierry 

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>

19:50 thierry 

MATC language library used by Elmer FEM package.

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

19:49 thierry 

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>

19:48 thierry 

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>

19:46 thierry 

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>

20:51 thierry 

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

10:38 garga 

Add fasthenry , a multipole-accelerated inductance analysis program.

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

10:36 garga 

Add fastcap , a three-dimensional capacitance extraction program.

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

15:30 thierry 

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>

11:55 vd 

Remove expired port science/glens

Approved by:    garga (mentor)

22:19 thierry 

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

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

20:40 thierry 

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>.

17:34 vd 

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)

10:13 thierry 

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

21:45 thierry 

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

18:48 thierry 

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/

12:45 thierry 

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>

16:22 pav 

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>

05:41 anholt 

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

15:50 pav 

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>

21:44 thierry 

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>

03:20 kris 

Remove mxp

Forgotten by:   maho
Approved by:    portmgr (self)

10:54 maho 

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/

19:30 glewis 

. 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/"

20:26 sem 

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>

20:15 sem 

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

14:17 pav 

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>

08:44 pav 

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

Repocopy by:    marcus

15:01 thierry 

Add buddy 2.4, a Binary Decision Diagram library.

PR:             71221
Submitted by:   Leland Wang

19:03 hq 

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>

21:52 glewis 

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)

20:46 thierry 

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

PR:             75529
Submitted by:   Pedro F. Giffuni

23:30 pav 

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>

23:08 thierry 

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

PR:             70816
Submitted by:   David Syphers.

04:52 sem 

Slave port to science/libsvm

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

21:38 pav 

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

22:53 pav 

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>

22:18 thierry 

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

Suggested by:   Pedro F. Giffuni.

01:36 maho 

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>

08:37 ijliao 

add py-scipy 0.3
Scientific tools for Python

16:34 pav 

Add vmd, a molecular visualization program for displaying, animating, and
analyzing large biomolecular systems using 3-D graphics and built-in scripting.

PR:             ports/70509
Submitted by:   Stephen Montgomery-Smith <stephen@math.missouri.edu>

08:45 maho 

Add abinit, calculates total energy, charge density
and electronic structure of systems.

15:44 markus 

Add kst 0.97.

kst is a program for looking at data streams. It can plot:

   - x-y plots
   - power spectra
   - histograms
   - equations (including equations of data streams).
   - data in files which are being updated as data is being logged,
     in which case it can act as a plotter for a chart recorder.
   - much more

You can use the mouse to rapidly zoom into interesting parts of the plots.

In addition to a complete GUI, kst has a convenient command line interface
for rapid access to plotting data in files. kst can read data from stdin.
It provides a DCOP interface for remote manipulation, and supports several
file formats in use in scientific projects around the world.

WWW: http://omega.astro.utoronto.ca/kst/
WWW: http://extragear.kde.org/apps/kst.php

07:29 kris 

Remove category pkg/COMMENT files in favour of a COMMENT variable in the
category makefile.

Submitted by:   Matthew Seaman <m.seaman@infracaninophile.co.uk>
PR:             59651

23:34 thierry 

Add ovt 2.3, the Orbit Visualization Tool.

PR:             57860
Submitted by:   Mykola Khotyaintsev <ko@nest.irfu.se>

04:50 maho 

A Density functional software. This software has a unique design
based upon the DFT++ algebraic framework introduced in Computer
Physics Communications 128, 1-45 (June 2000).
This framework allows us to transparently separate the computational
guts (cache optimization, parallelization, etc.) from the introduction
of new representations (plane waves, wavelets) and new
physics (new density functionals, linear response theory,
dielectric solutions).
The software is fully cache and register optimized,
and runs in serial, threaded, MPI and mixed threaded-MPI
parallel environments.

09:32 maho 

The PSI3 suite of quantum chemical programs is designed for efficient,
high-accuracy calculations of properties of small to medium-sized molecules.
The package's current capabilities include a variety of Hartree-Fock,
coupled cluster, complete-active-space self-consistent-field,
and multi-reference configuration interaction models.
Molecular point-group symmetry is utilized throughout to maximize efficiency.

16:52 pav 

Add gave, a gtk+ based grid data analyser and viewer written in Ruby.

PR:             ports/64249
Submitted by:   Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>

16:34 pav 

Add ruby-gphys, a multi-purpose class to handle gridded physical
quantities for Ruby.

PR:             ports/64248
Submitted by:   Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>

23:54 pav 

Add ruby-dcl, a ruby interface to DCL, a scienific graphical library.
Add ruby-dcl-gtk, a slave port for ruby-dcl with gtk patches.

PR:             ports/62873, ports/62874
Submitted by:   <murashin@edamame.summing.com>

22:44 pav 

Add cdcl-gtk, a slave port for science/cdcl with enabled Gtk support.

PR:             ports/62872
Submitted by:   Shin'ya Murakami <murashin@edamame.summing.com>

22:35 pav 

Add cdcl, a scientific graphic library for geoscience

PR:             ports/62871
Submitted by:   Shin'ya Murakami <murashin@edamame.summing.com>

22:55 pav 

Unhook hdf* ports in graphics, hook them in science.

03:09 pav 

Gramps (Genealogical Research and Analysis Management Programming System)
is an open source genealogy program. It is written in Python, using the
GTK/GNOME interface.

WWW: http://gramps.sourceforge.net

PR:             ports/62171
Submitted by:   Andreas Fehlner <fehlner@gmx.de>

09:08 glewis 

. Welcome felt to the science category.

PR:             58178
Submitted by:   Pedro F. Giffuni <giffunip@yahoo.com>

04:19 ijliao 

add kmovisto 0.5.1
A real 3-D molecule viewer

02:30 maho 

Remove #
chemtool-devel is now real developer version of chemtool.

12:45 edwin 

New port: science/at Acoustic ToolBox

        The Acoustic ToolBox includes four acoustic models:

           BELLHOP: A beam/ray trace code
           KRAKEN:  A normal mode code
           SCOOTER: A finite element FFP code
           SPARC:   A time domain FFP code

        A common input structure has been used throughout so that
        only minor modifications are needed to switch from one
        program to another.

        All the models produce shade files which can be processed
        using a common set of plotting routines to plot transmission
        loss vs. range or vs. range and depth.  These plotting
        routines are contained in the GLOBAL directory.

PR:             ports/42378
Submitted by:   Heiner Strauss <heiner@bilch.com>

09:50 maho 

Added a Numerical Hartree-Fock Program for Diatomic Molecules.
This program package calcluates virtually exact solution of the
Hartree-Fock and Hartree-Fock-Salter equations for diatomic
molecules (distributed under GPL).

21:34 kris 

Comment out chemtool-devel, which provides a duplicate chemtool-1.6 version
since the upgrade of chemtool.

Pointy hat to:  maho

01:29 maho 

Added new port chemtool-devel.
Chemtool is a nice drawing tool for chemist, however,
it has not been released almost 1 year. So I added
developer version as -devel.

Have fun!

02:33 maho 

Add new port science/ghemical
a computational chemistry software package

00:09 marcus 

Add gchempaint, a 2D chemical structure editor for GNOME 2.

PR:             50539
Submitted by:   Pav Lucistnik <pav@oook.cz>

00:04 marcus 

Add gchemutils a set of C++ class and GTK+-2 widgets related to chemistry.

PR:             50538
Submitted by:   Pav Lucistnik <pav@oook.cz>

10:22 ijliao 

add mpb 1.4.2
MIT Photonic-Bands

07:28 ijliao 

add libctl 2.2
Control Language Library

17:04 ijliao 

add openbabel 1.100.0
Chemistry file translation program

10:02 ijliao 

add xloops-ginac 0.1.3
A program calculating Feynman diagrams

20:11 ijliao 

add flounder 0.32a
A quick way to visualize regularly spaced 4D data

09:26 ijliao 

add mmtk 2.2
An Open Source program library for molecular simulation applications

PR:             42332
Submitted by:   Glenn Johnson <glennpj@charter.net>

08:39 ijliao 

add glens 0.3
OpenGL gravitational lens simulator

06:52 ijliao 

add bblimage 0.66
A set of software tools for medical image processing

06:53 ijliao 

add mpqc-mpich

PR:             40631
Submitted by:   Nakata Maho <chat95@mbox.kyoto-inet.or.jp>

03:31 ijliao 

add oases 2.2
Ocean Acoustics and Seismic Exploration Synthesis

PR:             38548
Submitted by:   Heiner Strau? <heiner@bilch.com>

03:59 ijliao 

add euler 1.60.4
A program computes with real and complex numbers and matrices