[Blends-commit] r3013 - in /projects/debichem/trunk/debichem: debian/changelog tasks/abinitio tasks/molmech tasks/polymer tasks/visualisation
mbanck at users.alioth.debian.org
mbanck at users.alioth.debian.org
Tue Nov 1 21:09:37 UTC 2011
Author: mbanck
Date: Tue Nov 1 21:09:35 2011
New Revision: 3013
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3013
Log:
* Added and/or updated publication/registration info for adun.app, gromacs,
massxpert, mmass, gabedit, rasmol, psi3, abinit, nwchem, aces3 and
quantum-espresso.
Modified:
projects/debichem/trunk/debichem/debian/changelog
projects/debichem/trunk/debichem/tasks/abinitio
projects/debichem/trunk/debichem/tasks/molmech
projects/debichem/trunk/debichem/tasks/polymer
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=3013&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/debian/changelog (original)
+++ projects/debichem/trunk/debichem/debian/changelog Tue Nov 1 21:09:35 2011
@@ -7,6 +7,9 @@
[ Michael Banck ]
* tasks/abinitio: Added nwchem, aces3, cp2k and quantum-espresso.
+ * Added and/or updated publication/registration info for adun.app, gromacs,
+ massxpert, mmass, gabedit, rasmol, psi3, abinit, nwchem, aces3 and
+ quantum-espresso.
-- Michael Banck <mbanck at debian.org> Tue, 01 Nov 2011 19:38:48 +0100
Modified: projects/debichem/trunk/debichem/tasks/abinitio
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/abinitio?rev=3013&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/abinitio (original)
+++ projects/debichem/trunk/debichem/tasks/abinitio Tue Nov 1 21:09:35 2011
@@ -5,16 +5,48 @@
Depends: mpqc
+
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/molmech
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/molmech?rev=3013&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/molmech (original)
+++ projects/debichem/trunk/debichem/tasks/molmech Tue Nov 1 21:09:35 2011
@@ -4,9 +4,23 @@
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
Modified: projects/debichem/trunk/debichem/tasks/polymer
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/polymer?rev=3013&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/polymer (original)
+++ projects/debichem/trunk/debichem/tasks/polymer Tue Nov 1 21:09:35 2011
@@ -5,4 +5,20 @@
view mass spectra.
-Depends: massxpert, mmass, lutefisk
+Depends: massxpert
+Published-Title: massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
+Published-Authors: F. Rusconi
+Published-In: Bioinformatics 25(20):2741-2742
+Published-Year: 2009
+Published-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741
+Published-DOI: 10.1093/bioinformatics/btp504
+
+Depends: mmass
+Published-Title: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data
+Published-Authors: M. Strohalm, D. Kavan, P. Novak, M. Volny and V. Havlicek
+Published-In: Anal. Chem. 82(11):4648-4651
+Published-Year: 2010
+Published-URL: http://pubs.acs.org/doi/abs/10.1021/ac100818g
+Published-DOI: 10.1021/ac100818g
+
+Depends: lutefisk
Modified: projects/debichem/trunk/debichem/tasks/visualisation
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/visualisation?rev=3013&op=diff
==============================================================================
--- projects/debichem/trunk/debichem/tasks/visualisation (original)
+++ projects/debichem/trunk/debichem/tasks/visualisation Tue Nov 1 21:09:35 2011
@@ -4,8 +4,20 @@
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: gabedit
+Published-Title: Gabedit - A graphical user interface for computational chemistry softwares
+Published-Authors: A.-R. Allouche
+Published-In: J. Comput. Chem. 32(1):174-182
+Published-Year: 2011
+Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21600/abstract
+Published-DOI: 10.1002/jcc.21600
Depends: gausssum
@@ -24,9 +36,11 @@
Depends: rasmol
Registration: http://www.rasmol.org/register.shtml
Published-Title: RasMol: Biomolecular graphics for all
-Published-Authors: Roger Sayle and E. James Milner-White
-Published-In: Trends in Biochemical Sciences (TIBS)
+Published-Authors: R. A. Sayle and E.-J. Milner-White
+Published-In: Trends Biochem. Sci. 20(9):374
Published-Year: 1995
+Published-URL: http://www.sciencedirect.com/science/article/pii/S0968000400890805
+Published-DOI: 10.1016/S0968-0004(00)89080-5
Depends: v-sim
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