[Blends-commit] r3692 - in /projects/debichem/trunk/debichem: debian/changelog tasks/abinitio tasks/modelling tasks/molmech tasks/visualisation

mbanck at users.alioth.debian.org mbanck at users.alioth.debian.org
Fri Feb 15 18:59:34 UTC 2013 

Author: mbanck
Date: Fri Feb 15 18:59:34 2013
New Revision: 3692

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3692
Log:
Revert revision 3133 and parts of revision 3419, add new packages from those revisions to old tasks

Added:
    projects/debichem/trunk/debichem/tasks/abinitio
    projects/debichem/trunk/debichem/tasks/molmech
Modified:
    projects/debichem/trunk/debichem/debian/changelog
    projects/debichem/trunk/debichem/tasks/modelling
    projects/debichem/trunk/debichem/tasks/visualisation

Modified: projects/debichem/trunk/debichem/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/debian/changelog?rev=3692&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/debian/changelog (original)
+++ projects/debichem/trunk/debichem/debian/changelog Fri Feb 15 18:59:34 2013
@@ -2,24 +2,12 @@
 
   [ Michael Banck ]
   * tasks/visualisation: Added jmol and qutemol.
-  * tasks/abinitio: Split up to ...
-  * tasks/molecular-abinitio: ... this and ...
-  * tasks/periodic-abinitio: ... this.
-  * tasks/molmech: Renamed to ...
-  * tasks/molecular-dynamics: ... this.
-  * tasks/molecular-dynamics: Removed ghemical and avogadro, added cp2k and
-    nwchem.
-  * tasks/modelling: Moved nmoldyn to ...
-  * tasks/molecular-dynamics: ... this.
   * tasks/visualisation: Added cclib.
-  * tasks/crystallography: New task, including shelxle and xcrysden.
-  * tasks/visualisation: Moved gcrystal to ...
-  * tasks/crystallography: ... this.
   * tasks/semiempirical: Added cp2k.
   * tasks/cheminformatics: Added python-indigo.
+  * tasks/visualization: Added shelxle, xcrysden and drawxtl.
 
   [ Daniel Leidert ]
-  * tasks/crystallography: Added drawxtl.
   * debian/control.stub (Standards-Version): Bumped to 3.9.3.
     (Vcs-Browser): Adjusted.
 

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 @@
+Task: Ab Initio Calculations
+Description: DebiChem Ab Initio Calculations
+ This metapackage will install packages doing ab initio calculations which
+ might be useful for chemists.
+
+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
+
+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
+
+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
+
+Depends: openmx
+
+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
+
+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
+
+Depends: cp2k
+
+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

Modified: projects/debichem/trunk/debichem/tasks/modelling
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/modelling?rev=3692&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/modelling (original)
+++ projects/debichem/trunk/debichem/tasks/modelling Fri Feb 15 18:59:34 2013
@@ -23,3 +23,9 @@
  (Amber 94, Amber 99, several elastic network models). MMTK also
  serves as a code basis that can be easily extended and modified to
  deal with non-standard situations in molecular simulations.
+
+Depends: nmoldyn
+Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/
+Pkg-Description: interactive analysis program for Molecular Dynamics simulations
+ nMOLDYN is especially designed for the computation and decomposition of neutron
+ scattering spectra, but also computes other quantities.

Added: projects/debichem/trunk/debichem/tasks/molmech
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/molmech?rev=3692&op=file
==============================================================================
--- projects/debichem/trunk/debichem/tasks/molmech (added)
+++ projects/debichem/trunk/debichem/tasks/molmech Fri Feb 15 18:59:34 2013
@@ -1,0 +1,46 @@
+Task: Molecular Mechanics
+Description: DebiChem Molecular Mechanics
+ This metapackage will install Molecular Mechanics
+ which might be useful for chemists.
+
+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. Galván 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
+
+Depends: avogadro
+
+Depends: ghemical
+
+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
+
+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..
+

Modified: projects/debichem/trunk/debichem/tasks/visualisation
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/visualisation?rev=3692&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/visualisation (original)
+++ projects/debichem/trunk/debichem/tasks/visualisation Fri Feb 15 18:59:34 2013
@@ -22,6 +22,8 @@
 
 Depends: gausssum
 
+Depends: gcrystal
+
 Depends: gdis
 
 Depends: gdpc
@@ -40,3 +42,9 @@
 Depends: xbs
 
 Depends: xmakemol
+
+Depends: shelxle
+
+Depends: xcrysden
+
+Depends: drawxtl

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