[Debichem-devel] Redundant citations in tasks files (Was: r3692 - in /projects/debichem/trunk/debichem: debian/changelog tasks/abinitio tasks/modelling tasks/molmech tasks/visualisation)

Fri Feb 15 22:54:37 UTC 2013

Hi Michael,

I think I have said it previousely, but to be sure I will repeat:  If
there is a debian/upstream file the citation information in the task is
totally ignored.

On Fri, Feb 15, 2013 at 06:59:34PM -0000, mbanck at users.alioth.debian.org wrote:
> Added: projects/debichem/trunk/debichem/tasks/abinitio
> URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/abinitio?rev=3692&op=file
> ==============================================================================
> --- projects/debichem/trunk/debichem/tasks/abinitio (added)
> +++ projects/debichem/trunk/debichem/tasks/abinitio Fri Feb 15 18:59:34 2013
> @@ -1,0 +1,54 @@
> +Depends: mpqc
> +Published-Title: http://www.mpqc.org
> +Published-Authors: The Massively Parallel Quantum Chemistry Program (MPQC), Version 3.0.0 Prerelease, C. L. Janssen, I. B. Nielsen, M. L. Leininger, E. F. Valeev, J. P. Kenny, E. T. Seidl
> +Published-URL: http://www.mpqc.org

OK, because debian/upstream does not have these fields (even if it is
hackish and needs enhancements in the blends code.)

> +Depends: psi3
> +Published-Title: PSI3: an open-source Ab Initio electronic structure package
> +Published-Authors: T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann, Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen, Edward T. Seidl, Joseph P. Kenny and Wesley D. Allen
> +Published-In: J. Comput. Chem. 28(9):1610-1616
> +Published-Year: 2007
> +Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20573/abstract
> +Published-DOI: 10.1002/jcc.20573

Redundant (ignored)

> +Depends: abinit
> +Published-Title: ABINIT: First-principles approach to material and nanosystem properties
> +Published-Authors: X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Côté, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D.R. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. J. T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. J. Verstraete, G. Zerah and J. W. Zwanziger
> +Published-In: Comput. Phys. Commun. 180(12):2582-2615
> +Published-Year: 2009
> +Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465509002276
> +Published-DOI: 10.1016/j.cpc.2009.07.007

Uhmm, this package seems to be not in VCS but definitely should.

> +Depends: nwchem
> +Published-Title: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations
> +Published-Authors: M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus and W.A. de Jong
> +Published-In: Comput. Phys. Commun. 181(9):1477-1489
> +Published-Year: 2010
> +Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465510001438
> +Published-DOI: 10.1016/j.cpc.2010.04.018

Just commited debian/upstream file containing this information so it
will be redundant soon.

> +Depends: aces3
> +Published-Title: Parallel Implementation of Electronic Structure Energy, Gradient and Hessian Calculations
> +Published-Authors: V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens and R. J. Bartlett
> +Published-In: J. Chem. Phys. 128:194104
> +Published-Year: 2008
> +Published-URL: http://jcp.aip.org/resource/1/jcpsa6/v128/i19/p194104_s1
> +Published-DOI: 10.1063/1.2920482 
> +Registration: http://www.qtp.ufl.edu/ACES/register.html

Just commited debian/upstream file containing this information so it
will be redundant soon (the Registration field should remain in the
tasks file because it is not yet(!) regarded from debian/upstream.)

> +Depends: quantum-espresso
> +Published-Title: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials
> +Published-Authors: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch
> +Published-In: J. Phys. Condens. Matter 21:395502
> +Published-Year: 2009
> +Published-URL: http://iopscience.iop.org/0953-8984/21/39/395502
> +Published-DOI: 10.1088/0953-8984/21/39/395502

Just commited debian/upstream file containing this information so it
will be redundant soon.

> +Depends: adun.app
> +Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator
> +Published-Authors: M.A. Johnston, I.F. GalvÃ¡n and J. VillÃ| -Freixa
> +Published-In: J. Comput. Chem. 26(15):1647-1659
> +Published-Year: 2005
> +Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT
> +Published-DOI: 10.1002/jcc.20312

This publication is not mentioned in adun.app packages debian/upstream.
If you consider this publication more relevant than

 Author: Michael A. Johnston and Ignacio Fdez. Galván and Jordi Villà-Freixa
 Title: >
  Framework-based design of a new all-purpose molecular simulation application: The Adun simulator

you should add it there *before* this reference.

> +Depends: gromacs
> +Published-Title: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
> +Published-Authors: B. Hess, C. Kutzner, D. van der Spoel and E. Lindahl
> +Published-In: J. Chem. Theory Comput. 4(3):435-447
> +Published-Year: 2008
> +Published-URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q
> +Published-DOI: 10.1021/ct700301q
> +X-Published-Other: Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis. J. Mol. Model. 2001;7(8):306.17
> +X-Published-Other: Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, Flexible, and Free. J Comput. Chem. 2005;26(16):1701.18

Ignored because overriden by debian/upstream information.

> +Depends: vmd
> +License: non-free
> +Homepage: http://www.ks.uiuc.edu/Research/vmd/
> +Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/
> +Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/
> +Responsible: Michael Banck <mbanck at debian.org>, Steffen Moeller <moeller at debian.org>
> +Pkg-Description: presentation of traces of molecular dynamics runs
> + VMD stands for Visual Molecular Dynamics. While text books
> + and even structure databases because of technical problems only
> + present static pictures of proteins or DNA, for the understanding
> + of the properties of those molecules their vibration or their
> + movement in general is important.
> + .
> + The movements itself are calculated by molecular dynamics programs,
> + such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
> + latter two are already in the distribution. VMD has a series of
> + nice features, from displaying through animation to analysing.
> + It can be scripted, clustered, and runs on all common OS..

You do not need *any* of this information except the Depends line -
all is drained from VCS as you can see here:

  http://blends.alioth.debian.org/debichem/tasks/molecular-dynamics#vmd

Hope this information helps to simplify your work

    Andreas.

-- 
http://fam-tille.de