Author: mbanck
Date: Tue Feb 7 20:15:21 2012
New Revision: 3133
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3133
Log:
* 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 (ITP'd).
* tasks/visualisation: Moved gcrystal to ...
* tasks/crystallography: ... this.
Added:
projects/debichem/trunk/debichem/tasks/crystallography
projects/debichem/trunk/debichem/tasks/molecular-abinitio
projects/debichem/trunk/debichem/tasks/molecular-dynamics
projects/debichem/trunk/debichem/tasks/periodic-abinitio
Removed:
projects/debichem/trunk/debichem/tasks/abinitio
projects/debichem/trunk/debichem/tasks/molmech
Modified:
projects/debichem/trunk/debichem/tasks/modelling
projects/debichem/trunk/debichem/tasks/visualisation
Added: projects/debichem/trunk/debichem/tasks/crystallography
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/crystallography?rev=3133&op=file
==============================================================================
--- projects/debichem/trunk/debichem/tasks/crystallography (added)
+++ projects/debichem/trunk/debichem/tasks/crystallography Tue Feb 7 20:15:21
2012
@@ -1,0 +1,24 @@
+Task: Crystallography
+Description: DebiChem crystallography
+ This metapackage will install packages for crystallography which might be
+ useful for chemists.
+
+Depends: gcrystal
+
+Depends: shelxle
+Published-Title: ShelXle: a Qt graphical user interface for SHELXL
+Published-Authors: C. B. Hübschle, G. M. Sheldrick and B. Dittrich
+Published-In: J. Appl. Cryst. 44:1281-1284
+Published-Year: 2011
+Published-URL: http://journals.iucr.org/j/issues/2011/06/00/kk5092/
+Published-DOI: 10.1107/S0021889811043202
+
+Depends: xcrysden
+Homepage: http://www.xcrysden.org
+License: GPL
+Language: C, Fortran, Tcl/Tk
+WNPP: 486545
+Responsible: Michael Banck <[email protected]>
+Pkg-Description: Visualization tool for crystalline structures
+ XCrySDen is a package for visualizing crystalline structures and
+ densities.
Modified: projects/debichem/trunk/debichem/tasks/modelling
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/modelling?rev=3133&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/modelling (original)
+++ projects/debichem/trunk/debichem/tasks/modelling Tue Feb 7 20:15:21 2012
@@ -23,9 +23,3 @@
(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/molecular-abinitio
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/molecular-abinitio?rev=3133&op=file
==============================================================================
--- projects/debichem/trunk/debichem/tasks/molecular-abinitio (added)
+++ projects/debichem/trunk/debichem/tasks/molecular-abinitio Tue Feb 7
20:15:21 2012
@@ -1,0 +1,34 @@
+Task: Molecular Ab Initio Calculations
+Description: DebiChem Molecular Ab Initio Calculations
+ This metapackage will install packages doing molecular 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: 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
Added: projects/debichem/trunk/debichem/tasks/molecular-dynamics
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/molecular-dynamics?rev=3133&op=file
==============================================================================
--- projects/debichem/trunk/debichem/tasks/molecular-dynamics (added)
+++ projects/debichem/trunk/debichem/tasks/molecular-dynamics Tue Feb 7
20:15:21 2012
@@ -1,0 +1,58 @@
+Task: Molecular Dynamics
+Description: DebiChem Molecular Dynamics
+ This metapackage will install packages for running or analyzing both
+ classical and ab initio molecular dynamics simulations 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: 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: cp2k
+
+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 <[email protected]>, Steffen Moeller
<[email protected]>
+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..
+
+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/periodic-abinitio
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/periodic-abinitio?rev=3133&op=file
==============================================================================
--- projects/debichem/trunk/debichem/tasks/periodic-abinitio (added)
+++ projects/debichem/trunk/debichem/tasks/periodic-abinitio Tue Feb 7
20:15:21 2012
@@ -1,0 +1,32 @@
+Task: Periodic Ab Initio Calculations
+Description: DebiChem Periodic ab Initio Calculations
+ This metapackage will install packages doing periodic ab initio calculations
+ which might be useful for chemists.
+
+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: 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/visualisation
URL:
http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/visualisation?rev=3133&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/visualisation (original)
+++ projects/debichem/trunk/debichem/tasks/visualisation Tue Feb 7 20:15:21
2012
@@ -13,6 +13,14 @@
Depends: avogadro
+Depends: cclib
+Published-Title: cclib: a library for package-independent computational
chemistry algorithms
+Published-Authors: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner
+Published-In: J. Comput. Chem. 29(5):839-845
+Published-Year: 2008
+Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20823/abstract
+Published-DOI: 10.1002/jcc.20823
+
Depends: gabedit
Published-Title: Gabedit - A graphical user interface for computational
chemistry softwares
Published-Authors: A.-R. Allouche
@@ -24,8 +32,6 @@
Depends: garlic
Depends: gausssum
-
-Depends: gcrystal
Depends: gdis
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