https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Mattias+Slabanja+%28C3SE%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T06:09:01ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=Glenn&diff=4286Glenn2012-07-31T13:00:27Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=GROMACS, NumPy, R, VMD, Efield, Abaqus, Ansys, ASE, BioPerl, Comsol, Edge, Gaussian, GPAW, Matlab, MSC Nastran, OpenFOAM, Jaguar, SciPy, VMD<br />
}}<br />
<!-- Example text you may like to include/modify if you set quiet=true in the "resource info" template. Otherwise just delete this. <br />
{{PAGENAME}} is a {{#show: {{PAGENAME}}|?description}}, and is located at {{#show: {{PAGENAME}}|?centre}}.<br />
--><br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Glenn Glenn documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=MSC_Nastran&diff=4285MSC Nastran2012-07-31T12:59:05Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=Finite Element Analysis (FEA) solver |license=requires license |fields=Solid mechanics }} [http://www.mscsoftware.com/Products/CAE-Tools/MSC-Nastran...."</p>
<hr />
<div>{{software info<br />
|description=Finite Element Analysis (FEA) solver<br />
|license=requires license<br />
|fields=Solid mechanics<br />
}}<br />
[http://www.mscsoftware.com/Products/CAE-Tools/MSC-Nastran.aspx {{PAGENAME}}] is a software package for {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
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== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.mscsoftware.com/Products/CAE-Tools/MSC-Nastran.aspx Official website]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Glenn&diff=4284Glenn2012-07-31T12:53:18Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=GROMACS, NumPy, R, VMD, Efield, Abaqus, Ansys, ASE, BioPerl, Comsol, Edge, Gaussian, GPAW, Matlab, MSC Nastran, OpenFOAM, Paraview, Jaguar, SciPy, VMD<br />
}}<br />
<!-- Example text you may like to include/modify if you set quiet=true in the "resource info" template. Otherwise just delete this. <br />
{{PAGENAME}} is a {{#show: {{PAGENAME}}|?description}}, and is located at {{#show: {{PAGENAME}}|?centre}}.<br />
--><br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Glenn Glenn documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Glenn&diff=4283Glenn2012-07-31T12:46:53Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=GROMACS, NumPy, R, VMD, Efield, Abaqus, Ansys, ASE, BioPerl, Comsol, Edge, Gaussian, GPAW, Matlab, Nastran, OpenFOAM, Paraview, Jaguar, SciPy, VMD<br />
}}<br />
<!-- Example text you may like to include/modify if you set quiet=true in the "resource info" template. Otherwise just delete this. <br />
{{PAGENAME}} is a {{#show: {{PAGENAME}}|?description}}, and is located at {{#show: {{PAGENAME}}|?centre}}.<br />
--><br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Glenn Glenn documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Glenn&diff=4282Glenn2012-07-31T12:44:52Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=GROMACS, NumPy, R, VMD, Efield, Abaqus, Ansys, ASE, Bioperl, Comsol, Edge, Gaussian, GPAW, Matlab, Nastran, OpenFOAM, Paraview, Schrodinger, SciPy, VMD<br />
}}<br />
<!-- Example text you may like to include/modify if you set quiet=true in the "resource info" template. Otherwise just delete this. <br />
{{PAGENAME}} is a {{#show: {{PAGENAME}}|?description}}, and is located at {{#show: {{PAGENAME}}|?centre}}.<br />
--><br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Glenn Glenn documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Glenn&diff=3615Glenn2012-03-06T09:25:41Z<p>Mattias Slabanja (C3SE): Created page with "{{resource info |description=throughput cluster resource |centre=C3SE |software=GROMACS, NumPy, R, VMD }} <!-- Example text you may like to include/modify if you set quiet=true i..."</p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=GROMACS, NumPy, R, VMD<br />
}}<br />
<!-- Example text you may like to include/modify if you set quiet=true in the "resource info" template. Otherwise just delete this. <br />
{{PAGENAME}} is a {{#show: {{PAGENAME}}|?description}}, and is located at {{#show: {{PAGENAME}}|?centre}}.<br />
--><br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Glenn Glenn documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mattias_Slabanja_(C3SE)&diff=3142User:Mattias Slabanja (C3SE)2011-11-23T07:51:38Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{application expert info<br />
|first name=Mattias<br />
|last name=Slabanja<br />
|centre=C3SE<br />
|fields=Computational materials science<br />
|fte=50<br />
|financing=SNIC<br />
|general activities=Various modification and analysis tool development; Getting started support<br />
|other activities=<!--Semicolon separated list of things you do outside of your work as an application expert.; Like other part time duties.; Use minimal *but complete* sentences.--><br />
<!--|image=name of an uploaded image file--><br />
|office=<!--Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
|phone=<!--Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly. --><br />
}}<br />
<br />
<br />
== Quick facts ==<br />
* Email: [mailto:slabanja@chalmers.se slabanja@chalmers.se]<br />
* Work at C3SE<br />
* Computational physics background (e.g. [[VASP]] user)<br />
* AE related activities includes<br />
** contributions to the [[ASE]] framework ([[SIESTA]] and [[LAMMPS]] calculators) <br />
** development of MD data analysis tools<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::VASP]]<br />
* [[expertise::ASE]]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2976Beda2011-10-17T10:54:31Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ANSYS, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, DIANA, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem, NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy, Quantum Espresso, R, SIESTA, VASP, VMD<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=DIANA&diff=2903DIANA2011-10-05T14:45:47Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=commercial FEM package<br />
|license=Requires license<br />
|fields=Solid mechanics<br />
}}<br />
[http://tnodiana.com/ {{PAGENAME}}] (DIsplacement ANAlyzer) is a {{#show: {{PAGENAME}} |?description}}, which is mainly aimed at problems in Civil engineering, such as structural, geotechnical, tunnelling and earthquake disciplines.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://tnodiana.com/content/DIANA Official website]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=DIANA&diff=2902DIANA2011-10-05T14:44:45Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=commercial FEM package<br />
|license=Requires license<br />
|fields=Solid mechanics<br />
}}<br />
[http://tnodiana.com/ {{PAGENAME}}] (DIsplacement ANAlyzer) is a {{#show: {{PAGENAME}} |?description}}, which is mainly aimed at problems in Civil engineering.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://tnodiana.com/content/DIANA Official website]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=DIANA&diff=2901DIANA2011-10-05T14:43:53Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=commercial FEM solver |license=Requires license |fields=Solid mechanics }} [http://tnodiana.com/ {{PAGENAME}}] (DIsplacement ANAlyzer) is a {{#show: ..."</p>
<hr />
<div>{{software info<br />
|description=commercial FEM solver<br />
|license=Requires license<br />
|fields=Solid mechanics<br />
}}<br />
[http://tnodiana.com/ {{PAGENAME}}] (DIsplacement ANAlyzer) is a {{#show: {{PAGENAME}} |?description}}, which is mainly aimed at problems in Civil engineering.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://tnodiana.com/content/DIANA Official website]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2900Beda2011-10-05T14:38:06Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ANSYS, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, DIANA, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem, NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy, Quantum Espresso, R, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2899Beda2011-10-05T14:35:53Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ANSYS, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem, NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy, Quantum Espresso, R, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Category:Solid_mechanics&diff=2898Category:Solid mechanics2011-10-05T14:34:04Z<p>Mattias Slabanja (C3SE): Created page with "{{research area info |description=application of computer science methods to solve continuum solid mechanics problems }} {{PAGENAME}} is the {{#show: Category:{{PAGENAME}}|?desc..."</p>
<hr />
<div>{{research area info<br />
|description=application of computer science methods to solve continuum solid mechanics problems <br />
}}<br />
{{PAGENAME}} is the {{#show: Category:{{PAGENAME}}|?description}}.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Software ==<br />
{{list software for category}}</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Abaqus&diff=2897Abaqus2011-10-05T14:31:56Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=finite-element package<br />
|license=Requires license<br />
|fields=Solid mechanics<br />
}}<br />
<br />
[http://www.simulia.com {{PAGENAME}}] is a commercial finite-element package mainly used in solid mechanics applications.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://en.wikipedia.org/wiki/Abaqus Wikipedia article]<br />
* [http://www.simula.com Product vendor]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Category:Computational_electromagnetics&diff=2896Category:Computational electromagnetics2011-10-05T14:26:58Z<p>Mattias Slabanja (C3SE): Created page with "{{research area info |description=application of computer science methods to solve and model electromagnetic fields }} {{PAGENAME}} is the {{#show: Category:{{PAGENAME}}|?descrip..."</p>
<hr />
<div>{{research area info<br />
|description=application of computer science methods to solve and model electromagnetic fields<br />
}}<br />
{{PAGENAME}} is the {{#show: Category:{{PAGENAME}}|?description}}.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Software ==<br />
{{list software for category}}</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Efield&diff=2895Efield2011-10-05T14:24:51Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=simulation environment for electromagnetic simulations<br />
|license=Requires license<br />
|fields=Computational electromagnetics<br />
}}<br />
<br />
[http://www.efieldsolutions.com/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.efieldsolutions.com Official webpage]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Efield&diff=2894Efield2011-10-05T14:23:32Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=simulation environment for electromagnetic simulations |license= Requires license |fields= }} [http://www.efieldsolutions.com/ {{PAGENAME}}] is a {{..."</p>
<hr />
<div>{{software info<br />
|description=simulation environment for electromagnetic simulations<br />
|license= Requires license<br />
|fields=<br />
}}<br />
<br />
[http://www.efieldsolutions.com/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.efieldsolutions.com Official webpage]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Abaqus&diff=2893Abaqus2011-10-05T14:16:00Z<p>Mattias Slabanja (C3SE): /* Links */</p>
<hr />
<div>{{software info<br />
|description=finite-element package<br />
|license= Requires license<br />
|fields=<br />
}}<br />
<br />
[http://www.simulia.com {{PAGENAME}}] is a commercial finite-element package mainly used in solid mechanics applications.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://en.wikipedia.org/wiki/Abaqus Wikipedia article]<br />
* [http://www.simula.com Product vendor]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Abaqus&diff=2892Abaqus2011-10-05T14:14:25Z<p>Mattias Slabanja (C3SE): /* Links */</p>
<hr />
<div>{{software info<br />
|description=finite-element package<br />
|license= Requires license<br />
|fields=<br />
}}<br />
<br />
[http://www.simulia.com {{PAGENAME}}] is a commercial finite-element package mainly used in solid mechanics applications.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.simula.com Official website]<br />
* [http://en.wikipedia.org/wiki/Abaqus wikipedia article]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Abaqus&diff=2891Abaqus2011-10-05T14:14:01Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=finite-element package |license= Requires license |fields= }} [http://www.simulia.com {{PAGENAME}}] is a commercial finite-element package mainly us..."</p>
<hr />
<div>{{software info<br />
|description=finite-element package<br />
|license= Requires license<br />
|fields=<br />
}}<br />
<br />
[http://www.simulia.com {{PAGENAME}}] is a commercial finite-element package mainly used in solid mechanics applications.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
<!--<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
--><br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http:://www.simula.com Official website]<br />
* [http://en.wikipedia.org/wiki/Abaqus wikipedia article]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2890Beda2011-10-05T12:35:12Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem, NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy, Quantum Espresso, R, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2889Beda2011-10-05T12:34:37Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem, NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy Quantum Espresso, R, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2888Beda2011-10-05T12:34:08Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=Abaqus, ABINIT, ASE, BioPerl, BioPython, BLAST, CP2K, Comsol, Dacapo, Edge, Efield, Fire, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Intel compiler suite, Jaguar, LAMMPS, NWChem NumPy, Octopus, Octave, OpenFOAM, PowerFLOW, Schrodinger, Scipy Quantum Espresso, R, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mattias_Slabanja_(C3SE)&diff=2564User:Mattias Slabanja (C3SE)2011-09-21T11:36:25Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{application expert info<br />
|first name=Mattias<br />
|last name=Slabanja<br />
|centre=C3SE<br />
|fields=Computational materials science<br />
|fte=50<br />
|financing=SNIC<br />
|general activities=<!--Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=<!--Semicolon separated list of things you do outside of your work as an application expert.; Like other part time duties.; Use minimal *but complete* sentences.--><br />
<!--|image=name of an uploaded image file--><br />
|office=<!--Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
|phone=<!--Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly. --><br />
}}<br />
<br />
<br />
== Quick facts ==<br />
* Email: [mailto:slabanja@chalmers.se slabanja@chalmers.se]<br />
* Work at C3SE<br />
* Computational physics background (e.g. [[VASP]] user)<br />
* AE related activities includes<br />
** contributions to the [[ASE]] framework ([[SIESTA]] and [[LAMMPS]] calculators) <br />
** development of MD data analysis tools<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::VASP]]<br />
* [[expertise::ASE]]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mattias_Slabanja_(C3SE)&diff=2563User:Mattias Slabanja (C3SE)2011-09-21T07:59:02Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{application expert info<br />
|first name=Mattias<br />
|last name=Slabanja<br />
|centre=C3SE<br />
|fields=Computational materials science<br />
|fte=40<br />
|financing=SNIC<br />
|general activities=<!--Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=<!--Semicolon separated list of things you do outside of your work as an application expert.; Like other part time duties.; Use minimal *but complete* sentences.--><br />
<!--|image=name of an uploaded image file--><br />
|office=<!--Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
|phone=<!--Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly. --><br />
}}<br />
<br />
<br />
== Quick facts ==<br />
* Email: [mailto:slabanja@chalmers.se slabanja@chalmers.se]<br />
* Work at C3SE<br />
* Computational physics background (e.g. [[VASP]] user)<br />
* AE related activities includes<br />
** contributions to the [[ASE]] framework ([[SIESTA]] and [[LAMMPS]] calculators) <br />
** development of MD data analysis tools<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::VASP]]<br />
* [[expertise::ASE]]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Octopus&diff=2219Octopus2011-09-12T08:32:29Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=time dependet density-functional theory code |license=free |fields=Computational materials science; Computational chemistry }} [http://www.tddft.org/..."</p>
<hr />
<div>{{software info<br />
|description=time dependet density-functional theory code<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
}}<br />
[http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}. It can be used for both time dependent and non time dependent DFT calculations.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Octopus is released under GPL terms.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Beda&diff=2218Beda2011-09-12T08:26:53Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource<br />
|centre=C3SE<br />
|software=ABINIT, ASE, BLAST, CP2K, Comsol, Dacapo, Edge, Fluent, GPAW, GROMACS, Gaussian, Gnuplot, Jaguar, LAMMPS, NumPy, Octopus, OpenFOAM, Quantum Espresso, SIESTA, VASP<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.c3se.chalmers.se/index.php/Beda Beda documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Comsol&diff=2051Comsol2011-09-09T10:53:14Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=Commercial Mulitphysics Similation software<br />
|license=Requires license <br />
|fields=Computational materials science ; Computational fluid dynamics<br />
|resources=ferlin;<br />
beda<br />
}}<br />
[{{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}. <br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under a commercial license.<br />
<br />
<br />
== Links ==<br />
* [http://www.comsol.com/products/multiphysics/ Official website]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Jaguar&diff=2048Jaguar2011-09-09T10:51:13Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=ab initio quantum mechanics<br />
|license=Requires license<br />
|fields= Computational chemistry<br />
|resources=ferlin;<br />
beda<br />
}}<br />
Jaguar is a high-performance ab initio package for both gas and solution phase simulations.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The software is commercial software<br />
<br />
== LINKS ==<br />
* [http://www.schrodinger.com/products/14/7/ Official homepage]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Quantum_Espresso&diff=2005Quantum Espresso2011-09-09T08:46:39Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=DFT based electronic structure modeling codes<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[http://www.quantum-espresso.org {{PAGENAME}}] (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under GPL.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Quantum_Espresso&diff=2004Quantum Espresso2011-09-09T08:46:13Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=DFT based electronic structure modeling codes |license=free |fields=Computational materials science; Computational chemistry |resources=beda }} [www...."</p>
<hr />
<div>{{software info<br />
|description=DFT based electronic structure modeling codes<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[www.quantum-espresso.org {{PAGENAME}}] (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under GPL.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=GPAW&diff=2002GPAW2011-09-09T08:35:41Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=real-space DFT |license=free |fields=Computational materials science; Computational chemistry |resources=beda }} [https://wiki.fysik.dtu.dk/gpaw/inde..."</p>
<hr />
<div>{{software info<br />
|description=real-space DFT<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[https://wiki.fysik.dtu.dk/gpaw/index.html {{PAGENAME}}] a {{#show: {{PAGENAME}} |?description}} code using the projector-augmentet wave (PAW) method. Calculations with {{PAGENAME}} is done using the [[ASE]] environment. <br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under LGPL.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Dacapo&diff=2000Dacapo2011-09-09T08:29:53Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=plane-wave DFT |license=free |fields=Computational materials science; Computational chemistry |resources=beda }} [https://wiki.fysik.dtu.dk/dacapo/da..."</p>
<hr />
<div>{{software info<br />
|description=plane-wave DFT<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[https://wiki.fysik.dtu.dk/dacapo/dacapo {{PAGENAME}}] a {{#show: {{PAGENAME}} |?description}} code using ultra-soft pseudo-potentials. Calculations with {{PAGENAME}} is done using the [[ASE]] environment. <br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under GPL.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=CP2K&diff=1999CP2K2011-09-09T08:22:35Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=atomistic and molecular simulations code |license=free |fields=Computational materials science; Computational chemistry |resources=beda }} [http://cp..."</p>
<hr />
<div>{{software info<br />
|description=atomistic and molecular simulations code<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[http://cp2k.berlios.de/ {{PAGENAME}}] a {{#show: {{PAGENAME}} |?description}} with force calculation from, DFT using a mixed plane-wave and gaussian basis, or classical two or many-body potentials.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under GPL.<br />
<br />
<!--<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Manual]<br />
--></div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=ABINIT&diff=1998ABINIT2011-09-09T08:14:47Z<p>Mattias Slabanja (C3SE): Created page with "{{software info |description=density-functional theory code |license=free |fields=Computational materials science; Computational chemistry |resources=beda }} [www.abinit.org {{PA..."</p>
<hr />
<div>{{software info<br />
|description=density-functional theory code<br />
|license=free<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=beda<br />
}}<br />
[www.abinit.org {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}. It uses plane wave basis and pseudo-potentials, and has quite a lot of features for calculation various properties.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The {{PAGENAME}} code is distributed under GPL.<br />
<br />
<!--<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Manual]<br />
--></div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=NumPy&diff=1961NumPy2011-09-07T16:41:34Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=is the fundamental package needed for scientific computing with Python.<br />
|license=free<br />
|fields=Scientific Computing<br />
|resources=platon;<br />
beda<br />
}}<br />
[http://numpy.scipy.org {{PAGENAME}}] (abbreviation explained) is a software package for {{#show: {{PAGENAME}} |?description}}.<br />
== Experts ==<br />
<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Links ==<br />
* [http://numpy.scipy.org Official website]<br />
* [http://docs.scipy.org/doc/ Documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=NumPy&diff=1960NumPy2011-09-07T16:41:19Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=is the fundamental package needed for scientific computing with Python.<br />
|license=free<br />
|fields=Scientific Computing<br />
|resources=platon<br />
beda<br />
}}<br />
[http://numpy.scipy.org {{PAGENAME}}] (abbreviation explained) is a software package for {{#show: {{PAGENAME}} |?description}}.<br />
== Experts ==<br />
<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Links ==<br />
* [http://numpy.scipy.org Official website]<br />
* [http://docs.scipy.org/doc/ Documentation]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=BLAST&diff=1950BLAST2011-09-07T15:15:06Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=package for aligning nucleotide or amino acid sequences<br />
|license=free<br />
|fields=bioinformatics<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
[http://blast.ncbi.nlm.nih.gov/ BLAST] (basic alignment search tool) is a software {{#show: {{PAGENAME}} |?description}}, and its primary use is to search databases for sequences that are similar to a given candidate sequence.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Versions ==<br />
<br />
There are two BLAST versions that are in current widespread use; the legacy NCBI BLAST and the new rewrite BLAST+. <br />
<br />
BLAST+ was written to improve performance and maintainability, and to facilitate introduction of new features. It is similiar in most respects and has been made almost completely backwards compatible, by way of a wrapper script called <code>./legacy_blast.pl</code>. New projects are encouraged to use BLAST+ if at all possible.<br />
<br />
<br />
== Computational considerations ==<br />
<br />
=== Work locally ===<br />
<br />
Many of the features in BLAST require access to database flatfiles, and standard practice when running a compute cluster is to copy all necessary files to a node local directory before any work is done with them. This behaviour is highly encouraged on most resources, since multiple simultaneous accesses to the same large files on a shared disk is likely to cause problems for all computations currently running on the resource, and not only for the owner of the badly behaving jobs. For this reason, most SNIC resources have amenities in place to aid you in running your BLAST jobs in an optimal manner (for example <code>prepare_db</code> and <code>$BLASTDB</code>, described for example [https://extras.csc.fi/mgrid/blast_re/ here]).<br />
<br />
=== Use all your processors ===<br />
<br />
BLAST uses only one processor core by default, but you increase this number using the <code>-a</code> command line option (<code>-num_threads</code> for BLAST+), which can often provide a significant increase in speed. If you are using a preinstalled BLAST version on a SNIC resource, the recommended number of cores to use is given by the <code>$BLAST_NUM_CPUS</code> environment variable (e.g. used like <code> blastall -a $BLAST_NUM_CPUS ... </code>). However, in some situations you may want to consider decreasing this number, particularly if your searches generate a large enough number of hits to deplete RAM, causing the OS to start swapping data and results to disk, which will near slow your job to a stop (see below).<br />
<br />
=== Do not run out of memory ===<br />
<br />
If possible, you should ensure that you have enough RAM to hold the database as well as the results and still have some headroom. This ensures that BLAST will not need to read data from disk unnecessarily, which otherwise would cause significant slowdown. This can be done for example by:<br />
<br />
* '''Choose a system with enough RAM''' <br/> Multiprocessor systems generally have more memory than single processor systems, and the database will also require proportionally less memory, since only one copy is needed in the OS file cache regardless of the number of processors using it.<br />
* '''Partition the search space''' <br/> For huge databases or very restricted amounts available memory it may be required to split the database into manageable chunks and process them as separate jobs.<br />
<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Links ==<br />
* [http://blast.ncbi.nlm.nih.gov/ Official website]<br />
* [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs Manual]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=User:Mattias_Slabanja_(C3SE)&diff=1949User:Mattias Slabanja (C3SE)2011-09-07T15:12:40Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{application expert info<br />
|first name=Mattias<br />
|last name=Slabanja<br />
|centre=C3SE<br />
|fields=Computational materials science<br />
|other activities=<br />
<!--|image=name of an uploaded image file--><br />
|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored<br />
}}<br />
<br />
== Quick facts ==<br />
* Email: [mailto:slabanja@chalmers.se slabanja@chalmers.se]<br />
* Work at C3SE<br />
* Computational physics background (e.g. [[VASP]] user)<br />
* Recent AE related activities includes<br />
** contributions to the [[LAMMPS]] interface in the [[ASE]] framework<br />
** contributions to the [[SIESTA]] interface in the [[ASE]] framework<br />
<br />
== Expertise ==<br />
* [[expertise::VASP]]<br />
* [[expertise::ASE]]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=VASP&diff=1946VASP2011-09-07T14:53:32Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=electronic structure calculation<br />
|license=requires license<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
The Vienna Ab initio Simulation Package ({{PAGENAME}}) is a program for performing {{#show: {{PAGENAME}} |?description}}. It is commonly used in the physics and materials science communities.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
{{PAGENAME}} is not a "free" software. A valid {{PAGENAME}} license is required to be allowed to use it, even for centre provided installations.<br />
<br />
== Links ==<br />
* [http://cms.mpi.univie.ac.at/marsweb Main web page]. News about bug fixes and general information about VASP.<br />
* [http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html VASP online manual]. Find out what all those INCAR keyword means, what their default values are, etc.<br />
* [http://cms.mpi.univie.ac.at/vasp-forum/forum.php The VASP forum]. For discussing "tricks of the VASP-trade", which knobs to turn, why results look strange, etc. To be able to post questions, you have to be registered and you need a VASP license.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=OpenFOAM&diff=1944OpenFOAM2011-09-07T14:53:07Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=free, open source CFD software package by OpenCFD Ltd<br />
|resources=beda<br />
|license=free<br />
|fields=Computational fluid dynamics<br />
}}<br />
The {{PAGENAME}} (Open Field Operation and Manipulation) CFD Toolbox is a {{#show: {{PAGENAME}} |?description}}. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.<br />
OpenFOAM is supplied with numerous pre-configured solvers, utilities and libraries and so can be used like any typical simulation package. However, it is open, not only in terms of source code, but also in its structure and hierarchical design, so that its solvers, utilities and libraries are fully extensible.<br />
OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells. The fluid flow solvers are developed within a robust, implicit, pressure-velocity, iterative solution framework, although alternative techniques are applied to other continuum mechanics solvers. Domain decomposition parallelism is fundamental to the design of OpenFOAM and integrated at a low level so that solvers can generally be developed without the need for any ’parallel-specific’ coding.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Links ==<br />
* [http://www.openfoam.com/ OpenFOAM homepage]<br />
* [http://www.openfoam.com/docs/user/ User guide (html)]<br />
* [http://foam.sourceforge.net/docs/Guides-a4/UserGuide.pdf User guide (pdf)]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=SIESTA&diff=1943SIESTA2011-09-07T14:53:00Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=density-functional theory code for very large systems<br />
|license=requires license<br />
|fields=Computational materials science; Computational chemistry<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
[http://www.nanotec.es/products/siesta.php {{PAGENAME}}] (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a {{#show: {{PAGENAME}} |?description}} based on atomic orbital basis sets.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
The SIESTA code is distributed under a "free for academic use"-license.<br />
<br />
<!--<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Manual]<br />
--></div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=LAMMPS&diff=1941LAMMPS2011-09-07T14:51:49Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=classical molecular dynamics code<br />
|license=free<br />
|fields=Molecular dynamics; Computational materials science<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
[http://lammps.sandia.gov/ {{PAGENAME}}] (Large-scale Atomic/Molecular Massively Parallel Simulator) is a {{#show: {{PAGENAME}} |?description}} developed at Sandia.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
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== License ==<br />
{{show license}}<br />
<br />
LAMMPS is distributed under the GPL terms.<br />
<!--<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Manual]<br />
--></div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Gnuplot&diff=1940Gnuplot2011-09-07T14:51:32Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=portable command-line driven graphing utility<br />
|fields=plotting utility<br />
|license=free<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
{{PAGENAME}} is a {{#show: {{PAGENAME}} |?description}}.<br />
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== Experts ==<br />
{{list experts}}<br />
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== Availability ==<br />
{{list resources for software}}<br />
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== License ==<br />
{{show license}}<br />
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== Links ==<br />
* [http://www.gnuplot.info/ Official website]<br />
* [http://www.gnuplot.info/documentation.html Documentation index]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Gaussian&diff=1939Gaussian2011-09-07T14:51:16Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=widely used quantum chemistry software<br />
|license=site license<br />
|fields=Computational chemistry<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
{{PAGENAME}} is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
==Tips and Tricks==<br />
*Converting checkpoint files from G03 format to G09 format:<Br><br />
G09 cannot read G03 checkpoint files, so if you wish to use a G03 checkpoint file as the starting point for a G09 calculation, you first need to convert the file to the G09 checkpoint file format. Fortunately, Gaussian provides a utility for this called [http://www.gaussian.com/g_tech/g_ur/u_c8609.htm c8609]. To use it you simply write<Br><br />
$ c8609 g03_checkpoint_file.chk<Br><br />
NOTE that this utility overwrites the original file, so if you want to keep the original file then you need to make a copy first!<br />
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==Post-processing scripts and utilities==<br />
* Openbabel<br />
* cclib<br />
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== Availability ==<br />
{{list resources for software}}<br />
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== License ==<br />
{{show license}}<br />
<br />
[[NSC]] has a site license that allows SNIC users to run {{PAGENAME}} without restrictions.<br />
<br />
== Links ==<br />
* [http://www.gaussian.com Official website]<br />
* [http://www.gaussian.com/g_tech/g_ur/g09help.htm Online manual]<br />
<br />
== Experts ==<br />
{{list experts}}</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Fluent&diff=1938Fluent2011-09-07T14:50:56Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=commercial computational fluid dynamics package<br />
|fields=Computational fluid dynamics<br />
|resources=kappa;matter;neolith;beda<br />
}}<br />
{{PAGENAME}} is a popular {{#show: {{PAGENAME}} |?description}} which is developed by ANSYS Inc. It contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions. It can cover most CFD applications ranging from the compressible air flow over an aircraft wing to combustion in a furnace, from multi-phase bubble columns to oil platforms, from low Reynolds number blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.<br />
Advanced solver technology provides fast, accurate CFD results, flexible moving and deforming meshes, and superior parallel scalability. User-defined functions allow the implementation of new user models and the extensive customization of existing ones. The interactive solver setup, solution and post-processing capabilities of FLUENT make it easy to pause a calculation, examine results with integrated post-processing, change any setting, and then continue the calculation within a single application.<br />
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== Experts ==<br />
{{list experts}}<br />
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== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Links ==<br />
* [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT FLUENT homepage]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Edge&diff=1936Edge2011-09-07T14:50:40Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=unstructured CFD solver<br />
|fields=Computational fluid dynamics<br />
|resources=kappa;matter;beda<br />
}}<br />
{{PAGENAME}} is an {{#show: {{PAGENAME}} |?description}} developed at the Swedish Defence Research Agency (Totalförsvarets forskningsinstitut) (FOI) since 1997. The code is fully RANS capable, and features several turbulence models from algebraic to state-of-the-art two-equation models. Furthermore the code also includes LES and DES models and the ability to run in "Euler" and laminar mode. Time-accurate and aeroelastic simulations are also possible.<br />
<br />
The Edge flow solver is based on a node-centered finite volume scheme. For steady flows, the equations are integrated towards steady state with an explicit multi-stage Runge-Kutta scheme. To accelerate convergence, residual smoothing and a multi-grid technique can be employed. Low Mach-number preconditioning is also available. Time-accurate computations are implemented using dual time-stepping: implicit time marching with explicit sub-iterations.<br />
<br />
The copyright holder is FOI. All rights to Edge are reserved by FOI. An idividual user-based written agreement with FOI is required to get access to the code. Edge or parts of Edge may not be sold, distributed or in any other way made available to third parties without a written permission from FOI.<br />
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== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== License ==<br />
{{show license}}<br />
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== Links ==<br />
* [http://www.foi.se/edge Edge homepage]<br />
* [http://www.foi.se/upload/projects/edge/documentation-latest/edge-user.pdf User manual]</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=ASE&diff=1935ASE2011-09-07T14:49:07Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=framework for setting up and analyzing atomistic simulations<br />
|license=free<br />
|fields=Computational materials science<br />
|resources=beda<br />
}}<br />
[https://wiki.fysik.dtu.dk/ase/ {{PAGENAME}}] (Atomic Simulation Environment) is a {{#show: {{PAGENAME}} |?description}}.<br />
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== Experts ==<br />
{{list experts}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<!--<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Manual]<br />
--><br />
== License ==<br />
{{show license}}<br />
<br />
ASE is released under the LGPL license.</div>Mattias Slabanja (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=GROMACS&diff=1934GROMACS2011-09-07T14:48:25Z<p>Mattias Slabanja (C3SE): </p>
<hr />
<div>{{software info<br />
|description=versatile package for molecular dynamics<br />
|fields=Molecular dynamics; Computational chemistry; Bioinformatics<br />
|resources=kappa;matter;neolith;beda<br />
|license=free<br />
}}<br />
{{PAGENAME}} is a {{#show: {{PAGENAME}} |?description}} ([http://en.wikipedia.org/wiki/Molecular_dynamics MD], Newtonian motion simulation in systems with hundreds to millions of particles).<br />
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== Experts ==<br />
{{list experts}}<br />
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== Availability ==<br />
{{list resources for software}}<br />
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== License ==<br />
{{show license}}<br />
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== Links ==<br />
<br />
* [http://www.gromacs.org/ Official website]<br />
* [http://manual.gromacs.org/current/ Manual]</div>Mattias Slabanja (C3SE)