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! Software !! Short description !! Loading environment
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! Software !! Short description !! License issues !! Loading environment
 
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|-
 
| Abaqus FEA
 
| Abaqus FEA
 
| SIMULIA Abaqus FEA (formerly ABAQUS) is a suite of software applications for finite element analysis and computer-aided engineering. WCSS has 25 license tokens shared by modules: Standard, Explicit, Foundation, Aqua, Design, CFD, AMS, Euler Lagrange, Multiphysics, CSE, Cosim Acusolve, Cosim Direct.
 
| SIMULIA Abaqus FEA (formerly ABAQUS) is a suite of software applications for finite element analysis and computer-aided engineering. WCSS has 25 license tokens shared by modules: Standard, Explicit, Foundation, Aqua, Design, CFD, AMS, Euler Lagrange, Multiphysics, CSE, Cosim Acusolve, Cosim Direct.
 +
| limited number of tokens
 
| module load abaqus
 
| module load abaqus
 
|-
 
|-
 
| ABINIT
 
| ABINIT
 
| An open-source suite of programs for materials science (GNU GPL). ABINIT implements density functional theory, using a plane wave basis set and pseudopotentials, to compute the electronic density and derived properties of materials ranging from molecules to surfaces to solids.
 
| An open-source suite of programs for materials science (GNU GPL). ABINIT implements density functional theory, using a plane wave basis set and pseudopotentials, to compute the electronic density and derived properties of materials ranging from molecules to surfaces to solids.
 +
| -
 
| module load abinit
 
| module load abinit
 
|-
 
|-
 
| Accelrys MS, DS  
 
| Accelrys MS, DS  
 
| Materials Studio is a suite of modeling and simulation programs for material science.<br/>Discovery Studio is a suite of modeling and simulation programs for life sciences.
 
| Materials Studio is a suite of modeling and simulation programs for material science.<br/>Discovery Studio is a suite of modeling and simulation programs for life sciences.
 +
| limited number of tokens
 
|
 
|
 
|-
 
|-
 
| ADF
 
| ADF
| ADF is a program for first-principles electronic structure calculations that make use of density functional theory (DFT).
+
| ADF is a program for first-principles electronic structure calculations that make use of density functional theory (DFT). WCSS license includes Natural Bond Orbital (NBO).
 +
| limited number of licenses (64 cores)
 
| module load adf
 
| module load adf
 
|-
 
|-
 
| Amber
 
| Amber
 
| Amber is a molecular dynamics software package that simulates force fields for molecular dynamics of biomolecules.
 
| Amber is a molecular dynamics software package that simulates force fields for molecular dynamics of biomolecules.
 +
| site license
 
| module load amber
 
| module load amber
 
|-
 
|-
 
| ANSYS Mechanical
 
| ANSYS Mechanical
 
| The software offers a solution for structural linear or nonlinear and dynamics analysis, provides a set of elements behavior, material models and equation solvers for a wide range of engineering problems.
 
| The software offers a solution for structural linear or nonlinear and dynamics analysis, provides a set of elements behavior, material models and equation solvers for a wide range of engineering problems.
 +
| limited number of tokens
 
| module load ansys_mechanical
 
| module load ansys_mechanical
 
|-
 
|-
 
| ANSYS CFX  
 
| ANSYS CFX  
 
| The software is a general purpose fluid dynamics program with parallelized solver.
 
| The software is a general purpose fluid dynamics program with parallelized solver.
 +
| limited number of tokens
 
| module load cfx
 
| module load cfx
 
|-  
 
|-  
 
| ANSYS Fluent
 
| ANSYS Fluent
 
| The software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions.
 
| The software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions.
 +
| limited number of tokens
 
| module load fluent
 
| module load fluent
 
|-
 
|-
 
| APBS
 
| APBS
 
| Software for evaluating the electrostatic properties of nanoscale biomolecular systems.
 
| Software for evaluating the electrostatic properties of nanoscale biomolecular systems.
 +
| -
 
| module load apbs
 
| module load apbs
 
|-
 
|-
 
| AutoDock
 
| AutoDock
 
| A suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
 
| A suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
 +
| -
 
| module load autodock
 
| module load autodock
 
|-
 
|-
 
| AutoDock Vina
 
| AutoDock Vina
 
| A program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy.
 
| A program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy.
 +
| -
 
| module load autodock_vina
 
| module load autodock_vina
 
|-
 
|-
 
| Cfour
 
| Cfour
 
| A package for performing high-level quantum chemical calculations on atoms and molecules, equipped with high-level ab initio methods for the calculation of atomic and molecular properties.
 
| A package for performing high-level quantum chemical calculations on atoms and molecules, equipped with high-level ab initio methods for the calculation of atomic and molecular properties.
 +
| site license
 
| module load cfour
 
| module load cfour
 
|-
 
|-
 
| CPMD
 
| CPMD
 
| The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
 
| The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
 +
| site license
 
| module load cpmd
 
| module load cpmd
 
|-
 
|-
 
| CRYSTAL09
 
| CRYSTAL09
 
| A general-purpose program for the ab-initio study of crystalline solids.
 
| A general-purpose program for the ab-initio study of crystalline solids.
 +
| site license
 
| module load crystal09
 
| module load crystal09
 
|-
 
|-
 
| Dalton
 
| Dalton
 
| The Dalton2.0 and Dalton2011 are available. Dalton2011 consists of two molecular electronic structure programs, DALTON and LSDALTON. Together, the two programs provide a functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are ONLY available in the Dalton2011 suite.  
 
| The Dalton2.0 and Dalton2011 are available. Dalton2011 consists of two molecular electronic structure programs, DALTON and LSDALTON. Together, the two programs provide a functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are ONLY available in the Dalton2011 suite.  
 +
| site license
 
| module load dalton
 
| module load dalton
 
|-
 
|-
 
| FDS-SMV
 
| FDS-SMV
 
| Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program that is used to display the output of FDS and CFAST simulations.
 
| Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program that is used to display the output of FDS and CFAST simulations.
 +
| -
 
| module load fds-smv
 
| module load fds-smv
 
|-
 
|-
 
| GAMESS
 
| GAMESS
 
| GAMESS is a program for ''ab initio'' molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF.  
 
| GAMESS is a program for ''ab initio'' molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF.  
 +
| site license
 
| module load gamess
 
| module load gamess
 
|-
 
|-
 
| Gaussian
 
| Gaussian
 
| Gaussian is the electronic structure program, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).
 
| Gaussian is the electronic structure program, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).
 +
| site license
 
| module load gaussian
 
| module load gaussian
 
|-  
 
|-  
 
| Gromacs
 
| Gromacs
 
| GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but is also used for research on non-biological systems, e.g. polymers.
 
| GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but is also used for research on non-biological systems, e.g. polymers.
 +
| -
 
| module load gromacs
 
| module load gromacs
 
|-
 
|-
 
| Lumerical FDTD, MODE
 
| Lumerical FDTD, MODE
 
| Lumerical FDTD is a high performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. Lumerical MODE is a versatile waveguide mode solver and propagation simulators for the design, analysis and optimization of waveguide devices, components and subsystems
 
| Lumerical FDTD is a high performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. Lumerical MODE is a versatile waveguide mode solver and propagation simulators for the design, analysis and optimization of waveguide devices, components and subsystems
 +
| limited number of licenses (MODE: 12, FDTD: 12)
 
| module load fdtd <br/>
 
| module load fdtd <br/>
 
module load mode
 
module load mode
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| Matlab
 
| Matlab
 
| MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation.
 
| MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation.
 +
| limited number of tokens
 
| module load matlab
 
| module load matlab
 
|-  
 
|-  
 
| Meep
 
| Meep
 
| Meep is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.  
 
| Meep is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.  
 +
| -
 
| module load meep
 
| module load meep
 
|-  
 
|-  
 
| MOLCAS
 
| MOLCAS
 
| is an ''ab initio'' computational chemistry software with focus placed on methods for calculating general electronic structures in molecular systems in both ground and excited states.
 
| is an ''ab initio'' computational chemistry software with focus placed on methods for calculating general electronic structures in molecular systems in both ground and excited states.
 +
| site license
 
| module load molcas
 
| module load molcas
 
|-  
 
|-  
 
| Molden
 
| Molden
 
| Molden is a package for displaying Molecular Density from the ''ab initio'' packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.  
 
| Molden is a package for displaying Molecular Density from the ''ab initio'' packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.  
 +
| site license
 
| module load molden
 
| module load molden
 
|-
 
|-
 
| Molpro  
 
| Molpro  
 
| Molpro is a complete system of ''ab initio'' programs for molecular electronic structure calculations.
 
| Molpro is a complete system of ''ab initio'' programs for molecular electronic structure calculations.
 +
| site license
 
| module load molpro
 
| module load molpro
 
|-
 
|-
 
| MOPAC
 
| MOPAC
 
| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.  
 
| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.  
 +
| license limited to 1 CPU (all available cores)
 
| module load mopac
 
| module load mopac
 
|-
 
|-
 
| MPB
 
| MPB
 
|  
 
|  
 +
|
 
| module load mpb
 
| module load mpb
 
|-
 
|-
 
| NAMD
 
| NAMD
 
|  
 
|  
 +
|
 
| module load namd
 
| module load namd
 
|-
 
|-
 
| NWChem
 
| NWChem
 
|  
 
|  
 +
|
 
| module load nwchem
 
| module load nwchem
 
|-
 
|-
 
| OpenFOAM
 
| OpenFOAM
 
|  
 
|  
 +
|
 
| module load openfoam
 
| module load openfoam
 
|-
 
|-
 
| Orca
 
| Orca
 
|  
 
|  
 +
|
 
| module load orca
 
| module load orca
 
|-
 
|-
 
| R
 
| R
 
|  
 
|  
 +
|
 
| module load r
 
| module load r
 
|-
 
|-
 
| Siesta
 
| Siesta
 
|  
 
|  
 +
|
 
| module load siesta<br/> module load transiesta
 
| module load siesta<br/> module load transiesta
 
|-
 
|-
 
| TURBOMOLE
 
| TURBOMOLE
 
|  
 
|  
 +
|
 
| module load turbomole
 
| module load turbomole
 
|-
 
|-
 
| VMD
 
| VMD
 
|  
 
|  
 +
|
 
| module load vmd
 
| module load vmd
 
|-
 
|-
 
| Wien2k
 
| Wien2k
 +
|
 
|
 
|
 
| module load wien2k
 
| module load wien2k
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| Xaim
 
| Xaim
 
|  
 
|  
 +
|
 
| module load xaim
 
| module load xaim
 
|-
 
|-

Wersja z 09:26, 1 cze 2012

< Supernova User Guide < Software

Scientific software installed and available to users on Supernova. Some of the applications may require additional steps from users before they are allowed to use the software, like registration or acquiring a user license. Some applications have limited licenses (e.g. tokens for N concurrent jobs, for M concurrent users).

Software Short description License issues Loading environment
Abaqus FEA SIMULIA Abaqus FEA (formerly ABAQUS) is a suite of software applications for finite element analysis and computer-aided engineering. WCSS has 25 license tokens shared by modules: Standard, Explicit, Foundation, Aqua, Design, CFD, AMS, Euler Lagrange, Multiphysics, CSE, Cosim Acusolve, Cosim Direct. limited number of tokens module load abaqus
ABINIT An open-source suite of programs for materials science (GNU GPL). ABINIT implements density functional theory, using a plane wave basis set and pseudopotentials, to compute the electronic density and derived properties of materials ranging from molecules to surfaces to solids. - module load abinit
Accelrys MS, DS Materials Studio is a suite of modeling and simulation programs for material science.
Discovery Studio is a suite of modeling and simulation programs for life sciences.
limited number of tokens
ADF ADF is a program for first-principles electronic structure calculations that make use of density functional theory (DFT). WCSS license includes Natural Bond Orbital (NBO). limited number of licenses (64 cores) module load adf
Amber Amber is a molecular dynamics software package that simulates force fields for molecular dynamics of biomolecules. site license module load amber
ANSYS Mechanical The software offers a solution for structural linear or nonlinear and dynamics analysis, provides a set of elements behavior, material models and equation solvers for a wide range of engineering problems. limited number of tokens module load ansys_mechanical
ANSYS CFX The software is a general purpose fluid dynamics program with parallelized solver. limited number of tokens module load cfx
ANSYS Fluent The software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions. limited number of tokens module load fluent
APBS Software for evaluating the electrostatic properties of nanoscale biomolecular systems. - module load apbs
AutoDock A suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. - module load autodock
AutoDock Vina A program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy. - module load autodock_vina
Cfour A package for performing high-level quantum chemical calculations on atoms and molecules, equipped with high-level ab initio methods for the calculation of atomic and molecular properties. site license module load cfour
CPMD The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. site license module load cpmd
CRYSTAL09 A general-purpose program for the ab-initio study of crystalline solids. site license module load crystal09
Dalton The Dalton2.0 and Dalton2011 are available. Dalton2011 consists of two molecular electronic structure programs, DALTON and LSDALTON. Together, the two programs provide a functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are ONLY available in the Dalton2011 suite. site license module load dalton
FDS-SMV Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program that is used to display the output of FDS and CFAST simulations. - module load fds-smv
GAMESS GAMESS is a program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. site license module load gamess
Gaussian Gaussian is the electronic structure program, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures). site license module load gaussian
Gromacs GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but is also used for research on non-biological systems, e.g. polymers. - module load gromacs
Lumerical FDTD, MODE Lumerical FDTD is a high performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. Lumerical MODE is a versatile waveguide mode solver and propagation simulators for the design, analysis and optimization of waveguide devices, components and subsystems limited number of licenses (MODE: 12, FDTD: 12) module load fdtd

module load mode

Matlab MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation. limited number of tokens module load matlab
Meep Meep is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. - module load meep
MOLCAS is an ab initio computational chemistry software with focus placed on methods for calculating general electronic structures in molecular systems in both ground and excited states. site license module load molcas
Molden Molden is a package for displaying Molecular Density from the ab initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. site license module load molden
Molpro Molpro is a complete system of ab initio programs for molecular electronic structure calculations. site license module load molpro
MOPAC MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation. license limited to 1 CPU (all available cores) module load mopac
MPB module load mpb
NAMD module load namd
NWChem module load nwchem
OpenFOAM module load openfoam
Orca module load orca
R module load r
Siesta module load siesta
module load transiesta
TURBOMOLE module load turbomole
VMD module load vmd
Wien2k module load wien2k
Xaim module load xaim


< Supernova User Guide < Software