freebsd-ports/science/Makefile

# $FreeBSD$
#

    COMMENT = Scientific ports

    SUBDIR += 2dhf
    SUBDIR += abinit
    SUBDIR += afni
    SUBDIR += at
    SUBDIR += bblimage
    SUBDIR += buddy
    SUBDIR += cdcl
    SUBDIR += cdf
    SUBDIR += chemtool
    SUBDIR += chemtool-devel
    SUBDIR += clhep
    SUBDIR += dcl
    SUBDIR += devisor
    SUBDIR += dft++
    SUBDIR += euler
    SUBDIR += felt
    SUBDIR += flounder
    SUBDIR += gave
    SUBDIR += gchempaint
    SUBDIR += gchemutils
    SUBDIR += gdis
    SUBDIR += gerris
    SUBDIR += getdp
    SUBDIR += ghemical
    SUBDIR += gnudatalanguage
    SUBDIR += gramps
    SUBDIR += gromacs
    SUBDIR += gsystem
    SUBDIR += hdf
    SUBDIR += hdf5
    SUBDIR += isaac-cfd
    SUBDIR += kmovisto
    SUBDIR += kst
    SUBDIR += lamprop
    SUBDIR += libctl
    SUBDIR += libsvm
    SUBDIR += libsvm-python
    SUBDIR += mayavi
    SUBDIR += mbdyn
    SUBDIR += mcstas
    SUBDIR += minc
    SUBDIR += mmtk
    SUBDIR += mpb
    SUBDIR += mpqc
    SUBDIR += mpqc-mpich
    SUBDIR += netcdf
    SUBDIR += oases
    SUBDIR += omnetpp
    SUBDIR += openbabel
    SUBDIR += openfoam
    SUBDIR += ovt
    SUBDIR += p5-Chemistry-Elements
    SUBDIR += paraview
    SUBDIR += psi3
    SUBDIR += py-paida
    SUBDIR += py-scipy
    SUBDIR += qcl
    SUBDIR += ruby-dcl
    SUBDIR += ruby-gphys
    SUBDIR += simlib
    SUBDIR += szip
    SUBDIR += udunits
    SUBDIR += v_sim
    SUBDIR += vis5d+
    SUBDIR += vmd
    SUBDIR += x11iraf
    SUBDIR += xloops-ginac
    SUBDIR += xmakemol

.include <bsd.port.subdir.mk>
Add new categories science and ukrainian. 2001-03-24 21:40:17 +00:00			`# $FreeBSD$`
			`#`
Sort entries. 2001-09-21 05:59:19 +00:00
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 2004-04-02 07:29:48 +00:00			`COMMENT = Scientific ports`

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). 2003-07-24 09:50:24 +00:00			`SUBDIR += 2dhf`
Add abinit, calculates total energy, charge density and electronic structure of systems. 2004-08-14 08:45:42 +00:00			`SUBDIR += abinit`
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) 2006-01-25 17:34:35 +00:00			`SUBDIR += afni`
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> 2003-09-08 12:45:59 +00:00			`SUBDIR += at`
add bblimage 0.66 A set of software tools for medical image processing 2002-07-22 06:52:25 +00:00			`SUBDIR += bblimage`
Add buddy 2.4, a Binary Decision Diagram library. PR: 71221 Submitted by: Leland Wang 2005-01-22 15:01:02 +00:00			`SUBDIR += buddy`
Add cdcl, a scientific graphic library for geoscience PR: ports/62871 Submitted by: Shin'ya Murakami <murashin@edamame.summing.com> 2004-02-27 22:35:23 +00:00			`SUBDIR += cdcl`
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>. 2006-01-28 20:40:56 +00:00			`SUBDIR += cdf`
add chemtool Chemtool is a program for drawing organic molecules easily and store them as an Postscript, X-Bitmap, LaTeX and XFig file ps. first science ports ? 2001-03-30 19:23:00 +00:00			`SUBDIR += chemtool`
Remove # chemtool-devel is now real developer version of chemtool. 2003-10-04 02:30:06 +00:00			`SUBDIR += chemtool-devel`
Fix broken ordering and remove sample directory. 2001-05-08 00:03:05 +00:00			`SUBDIR += clhep`
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> 2005-02-24 20:26:31 +00:00			`SUBDIR += dcl`
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> 2005-01-21 19:03:52 +00:00			`SUBDIR += devisor`
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. 2004-03-20 04:50:45 +00:00			`SUBDIR += dft++`
add euler 1.60.4 A program computes with real and complex numbers and matrices 2002-05-14 03:59:02 +00:00			`SUBDIR += euler`
. Welcome felt to the science category. PR: 58178 Submitted by: Pedro F. Giffuni <giffunip@yahoo.com> 2003-11-08 09:08:52 +00:00			`SUBDIR += felt`
add flounder 0.32a A quick way to visualize regularly spaced 4D data 2002-10-14 20:11:17 +00:00			`SUBDIR += flounder`
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> 2004-03-14 16:52:34 +00:00			`SUBDIR += gave`
Add gchempaint, a 2D chemical structure editor for GNOME 2. PR: 50539 Submitted by: Pav Lucistnik <pav@oook.cz> 2003-04-08 00:09:55 +00:00			`SUBDIR += gchempaint`
Add gchemutils a set of C++ class and GTK+-2 widgets related to chemistry. PR: 50538 Submitted by: Pav Lucistnik <pav@oook.cz> 2003-04-08 00:04:57 +00:00			`SUBDIR += gchemutils`
add gdis 0.73.3 Display and manipulation of isolated molecules and periodic systems 2002-03-05 03:36:20 +00:00			`SUBDIR += gdis`
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> 2005-09-25 12:45:46 +00:00			`SUBDIR += gerris`
Add getdp 1.0.0, a rather general finite element solver using mixed finite elements. Suggested by: Pedro F. Giffuni. 2004-11-15 22:18:09 +00:00			`SUBDIR += getdp`
Add new port science/ghemical a computational chemistry software package 2003-05-04 02:33:52 +00:00			`SUBDIR += ghemical`
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/ 2005-10-31 18:48:23 +00:00			`SUBDIR += gnudatalanguage`
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> 2004-02-01 03:09:52 +00:00			`SUBDIR += gramps`
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> 2004-10-19 01:36:11 +00:00			`SUBDIR += gromacs`
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> 2004-12-28 23:30:00 +00:00			`SUBDIR += gsystem`
Unhook hdf* ports in graphics, hook them in science. 2004-02-25 22:55:01 +00:00			`SUBDIR += hdf`
			`SUBDIR += hdf5`
Add isaac-cfd 4.2, Integrated Solution Algorithm for Arbitrary Configuration. PR: 75529 Submitted by: Pedro F. Giffuni 2004-12-29 20:46:47 +00:00			`SUBDIR += isaac-cfd`
add kmovisto 0.5.1 A real 3-D molecule viewer 2003-10-24 04:19:28 +00:00			`SUBDIR += kmovisto`
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 2004-04-30 15:44:32 +00:00			`SUBDIR += kst`
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> 2005-05-15 21:44:02 +00:00			`SUBDIR += lamprop`
add libctl 2.2 Control Language Library 2003-04-04 07:28:22 +00:00			`SUBDIR += libctl`
Add libsvm 2.33, a library for Support Vector Machines. PR: 32997 Submitted by: Chia-Hsing Yu <davidyu@oio.cx> 2001-12-19 03:44:59 +00:00			`SUBDIR += libsvm`
Slave port to science/libsvm PR: ports/73981 Submitted by: Rong-En Fan <rafan(at)infor.org> 2004-12-11 04:52:40 +00:00			`SUBDIR += libsvm-python`
add mayavi 1.1 The MayaVi Data Visualizer 2002-03-09 10:58:55 +00:00			`SUBDIR += mayavi`
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> 2005-05-22 15:50:06 +00:00			`SUBDIR += mbdyn`
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> 2005-02-18 14:17:20 +00:00			`SUBDIR += mcstas`
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> 2006-02-12 15:30:03 +00:00			`SUBDIR += minc`
add mmtk 2.2 An Open Source program library for molecular simulation applications PR: 42332 Submitted by: Glenn Johnson <glennpj@charter.net> 2002-09-16 09:26:20 +00:00			`SUBDIR += mmtk`
add mpb 1.4.2 MIT Photonic-Bands 2003-04-04 10:22:55 +00:00			`SUBDIR += mpb`
New port: xmakemol - a motif molecule viewer program PR: ports/27981 Submitted by: Chi Zhang <chizhang@midway.uchicago.edu> 2001-09-12 16:36:24 +00:00			`SUBDIR += mpqc`
add mpqc-mpich PR: 40631 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> 2002-07-16 06:53:52 +00:00			`SUBDIR += mpqc-mpich`
Repocopy math/netcdf to science/netcdf, along with cdf, hdf and hdf5. PR: 92497 Submitted by: /me Repocopied by: marcus 2006-01-30 22:19:24 +00:00			`SUBDIR += netcdf`
add oases 2.2 Ocean Acoustics and Seismic Exploration Synthesis PR: 38548 Submitted by: Heiner Strau? <heiner@bilch.com> 2002-05-28 03:31:29 +00:00			`SUBDIR += oases`
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> 2004-11-15 22:53:44 +00:00			`SUBDIR += omnetpp`
add openbabel 1.100.0 Chemistry file translation program 2003-01-05 17:04:59 +00:00			`SUBDIR += openbabel`
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 2006-01-22 10:13:06 +00:00			`SUBDIR += openfoam`
Add ovt 2.3, the Orbit Visualization Tool. PR: 57860 Submitted by: Mykola Khotyaintsev <ko@nest.irfu.se> 2004-03-23 23:34:29 +00:00			`SUBDIR += ovt`
Add p5-Chemistry-Elements 0.91, perl extension for working with Chemical Elements. PR: 33412 Submitted by: Seamus Venasse <svenasse@polaris.ca> 2002-02-08 06:15:14 +00:00			`SUBDIR += p5-Chemistry-Elements`
New port: ParaView is a powerful scientific visualization application, designed with the need to visualize large data sets in mind. 2005-06-14 05:41:20 +00:00			`SUBDIR += paraview`
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. 2004-03-19 09:32:49 +00:00			`SUBDIR += psi3`
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> 2005-07-18 16:22:48 +00:00			`SUBDIR += py-paida`
add py-scipy 0.3 Scientific tools for Python 2004-08-26 08:37:09 +00:00			`SUBDIR += py-scipy`
- Move emulators/qcl -> science/qcl on maintainer's request. Repocopy by: marcus 2005-02-10 08:44:55 +00:00			`SUBDIR += qcl`
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> 2004-02-27 23:54:14 +00:00			`SUBDIR += ruby-dcl`
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> 2004-03-14 16:34:51 +00:00			`SUBDIR += ruby-gphys`
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 2004-11-27 21:38:03 +00:00			`SUBDIR += simlib`
. 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/" 2005-03-17 19:30:00 +00:00			`SUBDIR += szip`
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) 2005-01-14 21:52:08 +00:00			`SUBDIR += udunits`
Add V_Sim, a program to visualize atomic structures such as crystals, grain boundaries and so on. 2005-12-10 21:45:28 +00:00			`SUBDIR += v_sim`
add vis5d+ 1.2.1 An OpenGL-based volumetric visualization program for scientific datasets 2002-01-09 14:51:38 +00:00			`SUBDIR += vis5d+`
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> 2004-08-21 16:34:57 +00:00			`SUBDIR += vmd`
Add x11iraf 1.3.1, which provides graphical tools to work with IRAF. PR: 70816 Submitted by: David Syphers. 2004-12-26 23:08:06 +00:00			`SUBDIR += x11iraf`
add xloops-ginac 0.1.3 A program calculating Feynman diagrams 2002-10-15 10:02:15 +00:00			`SUBDIR += xloops-ginac`
New port: xmakemol - a motif molecule viewer program PR: ports/27981 Submitted by: Chi Zhang <chizhang@midway.uchicago.edu> 2001-09-12 16:36:24 +00:00			`SUBDIR += xmakemol`
Add new categories science and ukrainian. 2001-03-24 21:40:17 +00:00
			`.include <bsd.port.subdir.mk>`