[Blends-commit] [SCM] science branch, master, updated. ce031e91bdf74e242d2814beb733f47ddf60be5d
Yann Pouillon
yann.pouillon at gmail.com
Fri May 22 11:49:31 UTC 2015
The following commit has been merged in the master branch:
commit ce031e91bdf74e242d2814beb733f47ddf60be5d
Author: Yann Pouillon <yann.pouillon at gmail.com>
Date: Fri May 22 13:48:50 2015 +0200
Updated the nanoscale-physics metapackages descriptions to reflect the most current situation
diff --git a/tasks/nanoscale-physics b/tasks/nanoscale-physics
index cba68cd..07760f4 100644
--- a/tasks/nanoscale-physics
+++ b/tasks/nanoscale-physics
@@ -22,7 +22,7 @@ Depends: abinit, mpqc, openmx, psi3, quantum-espresso
Depends: drawxtl
-Depends: etsf-io
+Depends: etsf-io, libxc
Depends: feynmf
@@ -38,11 +38,15 @@ Depends: libfftw3-3
Depends: libgsl0ldbl, gsl-bin
-Depends: netcdf-bin, netcdf-doc, nco, ncview
+Depends: netcdf-bin
+
+Recommends: nco, ncview
+
+Suggests: hdf5-helpers, hdf5-tools, netcdf-doc
Depends: openmpi-bin|mpich
-Suggests: openmpi-doc|mpich-doc|lam-mpidoc
+Suggests: openmpi-doc|mpich-doc
Depends: science-numericalcomputation
Why: Numerical programming environments similar to Matlab/IDL
@@ -51,7 +55,7 @@ Depends: avogadro, garlic, gdis, ghemical, v-sim
Depends: gwyddion
-Recommends: axiom, maxima
+Suggests: axiom, maxima
Why: Symbolic maths
Recommends: cadabra
@@ -64,6 +68,8 @@ Why: Periodic table data
Recommends: graphviz
+Suggests: libgraphviz-perl, python-pygraphviz
+
Recommends: libblacs-mpi1
Recommends: libscalapack-mpi1
@@ -74,30 +80,29 @@ Why: ODE solvers, optimization algorithms, symbolic maths
Recommends: pyxplot
Why: publication-quality figures
-Depends: crystfel
-
-Suggests: dx, dx-doc
-
-Suggests: gmsh
-Why: Support ongoing finite-element projects
+Suggests: dx, dxsamples, dx-doc
Suggests: gpiv, gpivtools
+Why: molecular dynamics
Suggests: feel++-apps
Why: Partial differential equation library, FEA, CFD
-Suggests: qtiplot, scidavis
+Suggests: pymca, qtiplot, scidavis
Why: Handle file formats used by experimentalists
-Suggests: science-statistics, science-mathematics
+Depends: qtoctave, scilab, scilab-sivp
+
+Depends: cbflib-bin
-Suggests: scilab-sivp
+Depends: python-lmfit | python3-lmfit
+
+Suggests: science-statistics, science-mathematics
Depends: ape
Homepage: http://www.tddft.org/programs/APE/
Responsible: Yann Pouillon <yann.pouillon at gmail.com>
License: GPL
-WNPP: 602092
Published-Title: Generating relativistic pseudo-potentials with explicit incorporation of semi-core states using APE, the Atomic Pseudo-potentials Engine
Published-Authors: M. J. T. Oliveira, F. Nogueira
Published-Year: 2008
@@ -114,7 +119,6 @@ Depends: atompaw
Homepage: http://www.wfu.edu/~natalie/papers/pwpaw/man.html
Responsible: Yann Pouillon <yann.pouillon at gmail.com>
License: GPL
-WNPP: 602093
Published-Title: A Projector Augmented Wave (PAW) code for electronic structure calculations, Part I: atompaw for generating atom-centered functions
Published-Authors: N. A. W. Holzwarth, A. R. Tackett, G. E. Matthews
Published-Year: 2001
@@ -135,7 +139,6 @@ Depends: bigdft
Homepage: http://inac.cea.fr/L_Sim/BigDFT/
Responsible: Damien Caliste <damien.caliste at cea.fr>
License: GPL
-WNPP: 602096
Published-Title: Daubechies wavelets as a basis set for density functional pseudopotential calculations
Published-Authors: L. Genovese, A. Neelov, S. Goedecker, T. Deutsch, S. A. Ghasemi, A. Willand, D. Caliste, O. Zilberberg, M. Rayson, A. Bergman, R. Schneider
Published-Year: 2008
@@ -157,15 +160,6 @@ Pkg-Description: Wavelet-based electronic-structure calculations
Depends: cp2k
-Depends: espresso++
-Homepage: http://espresso.scai.fraunhofer.de/
-License: Not yet known (hopefully free)
-Pkg-Description: Extensible Simulation Package for Research on Soft matter
- ESPResSo is a highly versatile software package for the scientific
- simulation and analysis of coarse-grained atomistic or bead-spring
- models as they are used in soft matter research, with emphasis on
- charged systems.
-
Depends: exciting
Homepage: http://exciting-code.org/
Responsible: Yann Pouillon <yann.pouillon at gmail.com>
@@ -186,7 +180,7 @@ Pkg-Description: All-electron full-potential electronic-structure code
Depends: gpaw
Homepage: https://wiki.fysik.dtu.dk/gpaw/
-Responsible: Ask Hjorth Larsen <askhl at fysik.dtu.dk>
+Responsible: Marcin Dulak <marcin.dulak at gmail.com>
License: GPL
WNPP: 602748
Published-Title: Real-space grid implementation of the projector augmented wave method
@@ -195,6 +189,7 @@ Published-Year: 2005
Published-In: Physical Review B, 71:035109
Published-URL: http://prb.aps.org/abstract/PRB/v71/i3/e035109
Published-DOI: 10.1103/PhysRevB.71.035109
+Pkg-URL: https://build.opensuse.org/package/show/home:dtufys/gpaw-0.10.0
Pkg-Description: Real-space PAW-based electronic structure code
GPAW is a density-functional theory (DFT) Python code based on the
projector-augmented wave (PAW) method. It uses real-space uniform grids
@@ -204,7 +199,6 @@ Depends: octopus
Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
Responsible: Miguel Marques <miguel.marques at tddft.org>
License: LGPL
-WNPP: 602111
Published-Title: octopus: a tool for the application of time-dependent density functional theory
Published-Authors: A. Castro, H. Appel, M. Oliveira, C.A. Rozzi, X. Andrade, F. Lorenzen, M. A. L. Marques, E. K. U. Gross, A. Rubio
Published-Year: 2006
@@ -220,8 +214,6 @@ Pkg-Description: Real-space TDDFT-based electronic-structure code
Electron-nucleus interaction is described within the pseudopotential
approximation.
-Depends: pymca
-
Depends: python-ase
Published-Title: An object-oriented scripting interface to a legacy electronic structure code
Published-Author: S. R. Bahn and K. W. Jacobsen
@@ -230,23 +222,41 @@ Published-In: Computing in Science and Engineering, 4:56-66
Published-URL: http://dx.doi.org/10.1109/5992.998641
Published-DOI: 10.1109/5992.998641
-Depends: wannier90
-Homepage: http://www.wannier.org/
-Responsible: Yann Pouillon <yann.pouillon at gmail.com>
+Depends: wannier90-1
+Why: several projects still depend on this version
+Homepage: http://wannier.org/code/wannier90-1.2.tar.gz
+Responsible: Arash Mostofi <a.mostofi at imperial.ac.uk>
License: GPL
-WNPP: 578829
Published-Title: A Tool for Obtaining Maximally-Localised Wannier Functions
Published-Authors: A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari
Published-Year: 2008
Published-In: Computer Physics Communications, 178:685-699
Published-URL: http://dx.doi.org/10.1016/j.cpc.2007.11.016
Published-DOI: 10.1016/j.cpc.2007.11.016
+Remark: packaging efforts can be found at https://launchpad.net/wannier90
Pkg-Description: Maximally Localized Wannier Functions
Wannier90 is an electronic-structure software computing
maximally-localized Wannier functions (MLWF). It works on top of other
electronic-structure software, such as Abinit, FLEUR, and PwSCF.
+ .
+ This is an old version still used by several packages. A patched version
+ compatible with the ETSF Software Suite is available from
+ https://launchpad.net/wannier90.
-Depends: qtoctave
+Depends: wannier90-2
+Homepage: http://www.wannier.org/
+Responsible: Arash Mostofi <a.mostofi at imperial.ac.uk>
+License: GPL
+Published-Title: A Tool for Obtaining Maximally-Localised Wannier Functions
+Published-Authors: A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari
+Published-Year: 2008
+Published-In: Computer Physics Communications, 178:685-699
+Published-URL: http://dx.doi.org/10.1016/j.cpc.2007.11.016
+Published-DOI: 10.1016/j.cpc.2007.11.016
+Pkg-Description: Maximally Localized Wannier Functions
+ Wannier90 is an electronic-structure software computing
+ maximally-localized Wannier functions (MLWF). It works on top of other
+ electronic-structure software, such as Abinit, FLEUR, and PwSCF.
Depends: octaviz
Pkg-URL: http://snapshot.debian.org/package/octaviz/
@@ -265,8 +275,23 @@ Remark: Removed from Debian
Reasons are given here: http://bugs.debian.org/535537
Depends: fdmnes
+Why: X-ray spectroscopy
Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/
-Depends: cbflib-bin
+Depends: liblevmar-2-6
+Homepage: http://users.ics.forth.gr/~lourakis/levmar/
+Responsible: Yann Pouillon <yann.pouillon at gmail.com>
+License: GPL
+Remark: packaging efforts can be found at https://launchpad.net/levmar
+Pkg-Description: Levenberg-Marquardt nonlinear least squares algorithms
+ The Levenberg-Marquardt (LM) algorithm is an iterative technique that finds
+ a local minimum of a function that is expressed as the sum of squares of
+ nonlinear functions. It has become a standard technique for nonlinear
+ least-squares problems and can be thought of as a combination of steepest
+ descent and the Gauss-Newton method.
+ .
+ This library provides native ANSI C implementations of the Levenberg-Marquardt
+ optimization algorithm, usable also from C++, Matlab, Perl, Python, Haskell
+ and Tcl. Both unconstrained and constrained (under linear equations,
+ inequality and box constraints) Levenberg-Marquardt variants are included.
-Depends: python-lmfit | python3-lmfit
diff --git a/tasks/nanoscale-physics-dev b/tasks/nanoscale-physics-dev
index 071ba72..37d1496 100644
--- a/tasks/nanoscale-physics-dev
+++ b/tasks/nanoscale-physics-dev
@@ -16,22 +16,20 @@ Depends: libetsf-io-dev, libetsf-io-doc
Suggests: libfftw3-doc
-Depends: libfftw3-dev, fftw-dev, sfftw-dev
+Depends: libfftw3-dev
Depends: libgsl0-dev, gsl-bin, gsl-doc-info, gsl-ref-html|gsl-ref-psdoc
Depends: libnetcdf-dev, netcdf-doc, r-cran-rnetcdf
-Depends: libtrilinos-dev, libtrilinos-doc
-Why: High-performance computing
+Recommends: libhdf5-dev
Depends: libxc-dev
Depends: libopenmpi-dev | libmpich-dev
-Depends: wannier90-dev
-WNPP: 578829
-Responsible: Yann Pouillon <yann.pouillon at gmail.com>
+Depends: wannier90-1-dev
+Responsible: Arash Mostofi <a.mostofi at imperial.ac.uk>
Homepage: http://www.wannier.org/
License: GPL
Language: Fortran 90
@@ -58,78 +56,21 @@ Suggests: oce-draw
Depends: liboce-visualization-dev, liboce-ocaf-dev
-Suggests: python-netcdf
-
+Suggests: python-netcdf, python-h5py
-Depends: libfox95
-Homepage: http://www1.gly.bris.ac.uk/~walker/FoX/
-Responsible: Yann Pouillon <yann.pouillon at gmail.com>
-License: BSD-like
-WNPP: 602100
-Pkg-Description: A Fortran library for XML
- FoX is an XML library written in Fortran 95. It allows software
- developers to read, write and modify XML documents from Fortran
- applications without the complications of dealing with multi-language
- development.
- .
- The developer is offered three principle APIs which are accessed as
- Fortran modules. FoX_wxml is an XML writer used to sequentially create
- arbitrary XML documents quickly with minimal memory requirements.
- FoX_sax is a streaming, validating parser based on java's Simple API
- for XML. The third module, FoX_dom, offers a full implementation of the
- W3C Document Object Model (DOM).
-
-Depends: libnbc
-Homepage: http://www.unixer.de/research/nbcoll/libnbc/
-Responsible: Yann Pouillon <yann.pouillon at gmail.com>
-License: BSD
-WNPP: 602104
-Published-Title: Implementation and Performance Analysis of Non-Blocking Collective Operations for MPI
-Published-Authors: T. Hoefler, A. Lumsdaine, W. Rehm
-Published-Year: 2007
-Published-In: Proceedings of the 2007 International Conference on High Performance Computing, Networking, Storage and Analysis, SC07
-Published-URL: http://www.unixer.de/publications/?pub=46
-Published-DOI: 10.1145/1362622.1362692
-Pkg-Description: Non-Blocking MPI Collective Operations
- LibNBC is a prototypic implementation of a nonblocking interface for MPI
- collective operations. Based on ANSI C and MPI-1, it supports all MPI-1
- collective operations in a nonblocking manner.
-
-Depends: libpspio
-Homepage: http://www.tddft.org/trac/libpspio/
+Depends: libpspio-dev
+Homepage: https://launchpad.net/libpspio
Responsible: Yann Pouillon <yann.pouillon at gmail.com>
License: LGPL
-WNPP: 640664
Pkg-Description: Library to read and write pseudopotentials
Pseudopotentials consist in atomic data used for atomic-scale electronic
structure calculations. Libpspio is a library to read and write
pseudopotentials in various formats, allowing as well for conversion in
some cases.
-Depends: libxc
-Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
-Responsible: Damien Caliste <damien.caliste at cea.fr>
-License: LGPL
-WNPP: 602110
-Pkg-Description: Library of DFT exchange-correlation functionals
- Libxc is a library of exchange-correlation functionals. The aim is to
- provide a portable, well tested and reliable set of exchange and
- correlation functionals that can be used by all the ETSF codes and also
- other codes.
- .
- In libxc you can find different types of functionals: LDA, GGA,
- hybrids, mGGA (experimental) and LCA (not working). This functionals
- depend on local information, in the sense that the value of the
- potential at a given point depends only on the values of the density -
- and the gradient of the density and the kinetic energy density, for the
- GGA and mGGA cases, or the vorticity for LCA - at a given point.
- .
- As of today, more than 100 functionals are available for various kinds
- of electronic-structure calculations.
-
Depends: spglib
Homepage: http://sourceforge.net/projects/spglib/
-Responsible: Yann Pouillon <yann.pouillon at gmail.com>
+Responsible: DebiChem Project <debichem-devel at lists.alioth.debian.org>
License: BSD
WNPP: 602113
Pkg-Description: Crystal symmetry finder library
--
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