Software: Różnice pomiędzy wersjami
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− | <small>< [[ | + | {{Prace-user-guide}} |
+ | <small>< [[Bem User Guide]] < Software </small> | ||
− | '' | + | '''Scientific software''' installed and available to users on [[Supernova overview|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). |
− | + | {|class="wikitable" | |
− | + | ! Software !! Short description !! License issues !! Loading environment | |
− | {| | + | |
− | ! Software !! Short description | + | |
|- | |- | ||
| 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 (~25) | ||
+ | | 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 | ||
|- | |- | ||
− | | 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. |
+ | | limited number of tokens (~30) | ||
+ | | | ||
|- | |- | ||
| ADF | | 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 |
+ | | 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 (1) | ||
+ | | module load ansys_mechanical | ||
|- | |- | ||
− | + | | ANSYS CFX | |
+ | | The software is a general purpose fluid dynamics program with parallelized solver. | ||
+ | | limited number of tokens (3x4) | ||
+ | | 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 (3x4) | ||
+ | | 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 | ||
|- | |- | ||
− | || | + | | CP2K |
+ | | CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials. | ||
+ | | - | ||
+ | | module load cp2k | ||
|- | |- | ||
− | || | + | | 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/2.0<br/>module load dalton/2011 | ||
|- | |- | ||
− | || | + | | 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 <br/> |
− | | | + | module load mode |
|- | |- | ||
− | || | + | | Mathematica |
+ | | | ||
+ | | limited number of tokens (only for WUT) | ||
+ | | module load mathematica | ||
|- | |- | ||
− | || Meep | + | | 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 avail 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. | ||
+ | | site license | ||
+ | | module load molden | ||
|- | |- | ||
− | || Molpro | + | | Molpro |
+ | | Molpro is a complete system of ''ab initio'' programs for molecular electronic structure calculations. | ||
+ | | site license | ||
+ | | module load molpro | ||
|- | |- | ||
− | || MOPAC | + | | 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 |
+ | | MIT Photonic Bands package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures. | ||
+ | | - | ||
+ | | module load mpb | ||
|- | |- | ||
− | || | + | | NAMD |
+ | | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | ||
+ | | - | ||
+ | | module load namd | ||
|- | |- | ||
− | || | + | | NWChem |
+ | | NWChem is a set of computational chemistry tools and can handle: Biomolecules, nanostructures, and solid-state; From quantum to classical, and all combinations, Gaussian basis functions or plane-waves; Scaling from one to thousands of processors; Properties and relativity. | ||
+ | | - | ||
+ | | module load nwchem | ||
|- | |- | ||
− | || | + | | OpenFOAM |
+ | | OpenFOAM (Open Field Operation and Manipulation) is a package for CFD simulations. | ||
+ | | - | ||
+ | | module load openfoam | ||
|- | |- | ||
− | || | + | | Orca |
+ | | Orca is an ''ab initio'', Density Functional and Semiempirical program package. | ||
+ | | - | ||
+ | | module load orca | ||
|- | |- | ||
− | || | + | | R |
+ | | R is a free software environment for statistical computing and graphics. | ||
+ | | - | ||
+ | | module load r | ||
|- | |- | ||
− | || | + | | Rosetta |
+ | | Rosetta is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. | ||
+ | | site license | ||
+ | | module load rosetta | ||
|- | |- | ||
− | || VMD | + | | Siesta |
+ | | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ''ab initio'' molecular dynamics simulations of molecules and solids. | ||
+ | | site license (user personal license required) | ||
+ | | module load siesta<br/> module load transiesta | ||
+ | |- | ||
+ | | TURBOMOLE | ||
+ | | TURBOMOLE is a package for ''ab initio'' electronic structure calculations. | ||
+ | | - | ||
+ | | module load turbomole | ||
+ | |- | ||
+ | | VASP | ||
+ | | VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. | ||
+ | | users must bring own license | ||
+ | | module load vasp <br/>(5.4.1-intel15.0 default) | ||
+ | |- | ||
+ | | VMD | ||
+ | | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | ||
+ | | | ||
+ | | module load vmd | ||
|- | |- | ||
− | || | + | | WIEN2k |
+ | | WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. | ||
+ | | users must bring own license | ||
+ | | module load wien2k | ||
|- | |- | ||
|} | |} | ||
− | <small>< [[ | + | <small>< [[Bem User Guide]] < Software </small> |
[[Category:User Guide]] | [[Category:User Guide]] |
Aktualna wersja na dzień 11:00, 15 lis 2019
PRACE User Guide | This page is a part of the PRACE User Guide dedicated for DECI Users with granted access to WCSS resources |
< Bem 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 (~25) | 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 (~30) | |
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 (1) | module load ansys_mechanical |
ANSYS CFX | The software is a general purpose fluid dynamics program with parallelized solver. | limited number of tokens (3x4) | 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 (3x4) | 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 |
CP2K | CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials. | - | module load cp2k |
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/2.0 module load dalton/2011 |
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 |
Mathematica | limited number of tokens (only for WUT) | module load mathematica | |
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 avail 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 | MIT Photonic Bands package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures. | - | module load mpb |
NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | - | module load namd |
NWChem | NWChem is a set of computational chemistry tools and can handle: Biomolecules, nanostructures, and solid-state; From quantum to classical, and all combinations, Gaussian basis functions or plane-waves; Scaling from one to thousands of processors; Properties and relativity. | - | module load nwchem |
OpenFOAM | OpenFOAM (Open Field Operation and Manipulation) is a package for CFD simulations. | - | module load openfoam |
Orca | Orca is an ab initio, Density Functional and Semiempirical program package. | - | module load orca |
R | R is a free software environment for statistical computing and graphics. | - | module load r |
Rosetta | Rosetta is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. | site license | module load rosetta |
Siesta | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | site license (user personal license required) | module load siesta module load transiesta |
TURBOMOLE | TURBOMOLE is a package for ab initio electronic structure calculations. | - | module load turbomole |
VASP | VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. | users must bring own license | module load vasp (5.4.1-intel15.0 default) |
VMD | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | module load vmd | |
WIEN2k | WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. | users must bring own license | module load wien2k |
< Bem User Guide < Software