Debian Science Project
Summary
Physics-dev
Debian Science Physics-dev packages

This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics.

You might also be interested in the science-physics metapackage.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Physics-dev packages

Official Debian packages with high relevance

fenics
Automated Solution of Differential Equations
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FEniCS is a collection of free software for automated, efficient solution of differential equations.

FEniCS has an extensive list of features, including automated solution of variational problems, automated error control and adaptivity, a comprehensive library of finite elements, high performance linear algebra and many more.

FEniCS is organized as a collection of interoperable components, including the problem-solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

This is a metapackage which depends on all FEniCS components.

This is the legacy version of FEniCS. You may want to consider installing the next-generation FEniCS-X (fenicx package).

fftw-dev
library for computing Fast Fourier Transforms
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This library computes FFTs in one or more dimensions. It is extremely fast. This package contains the statically linked library and the header files.

libasl-dev
development files for ASL
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The Advanced Simulation Library (ASL) is a free and open source hardware accelerated multiphysics simulation platform (and an extensible general purpose tool for solving Partial Differential Equations).

Its computational engine is written in OpenCL and utilizes matrix-free solution techniques which enable extraordinarily high performance, memory efficiency and deployability on a variety of massively parallel architectures, ranging from inexpensive FPGAs, DSPs and GPUs up to heterogeneous clusters and supercomputers. The engine is hidden entirely behind simple C++ classes, so that no OpenCL knowledge is required from application programmers. Mesh-free, immersed boundary approach allows one to move from CAD directly to simulation drastically reducing pre-processing efforts and amount of potential errors.

ASL can be used to model various coupled physical and chemical phenomena and employed in a multitude of fields: computational fluid dynamics, virtual sensing, industrial process data validation and reconciliation, image-guided surgery, computer-aided engineering, design space exploration, crystallography, etc...

This package contains the development files.

Please cite: Avtech Scientific <contact@avtechscientific.com>:
libbasix-dev
Finite Element Basis Function Definition Runtime Library (development headers)
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Computes FE basis functions and derivatives for the following elements:

  • Lagrange (interval, triangle, tetrahedron, prism, pyramid, quadrilateral, hexahedron)
  • Nédélec (triangle, tetrahedron)
  • Nédélec Second Kind (triangle, tetrahedron)
  • Raviart-Thomas (triangle, tetrahedron)
  • Regge (triangle, tetrahedron)
  • Crouzeix-Raviart (triangle, tetrahedron)

Computes quadrature rules on different cell types

Provides reference topology and geometry for reference cells of each type.

Python wrapper provided with pybind11.

This package installs the development files for the shared library.

libdeal.ii-dev
Differential Equations Analysis Library - development files
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deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. It uses state-of-the-art programming techniques to offer you a modern interface to the complex data structures and algorithms required.

This package contains the development files.

libdolfinx-dev
Shared links and header files for DOLFIN
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DOLFIN is the Python and C++ interface of the FEniCS project for the automated solution of differential equations, providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms; automatic and efficient assembly of linear systems; and support for general families of finite elements.

This package contains the common development files and depends on the real or complex development package.

This is the next-generation version of libdolfinx-dev (DOLFIN-X). The legacy version of DOLFIN is provided by libdolfin-dev.

libfclib-dev
read and write problems from the Friction Contact Library (headers)
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fclib is an open source collection of Frictional Contact (FC) problems stored in a specific HDF5 format, and an open source light implementation of Input/Output functions in C Language to read and write problems.

The goal of this work is to set up a collection of 2D and 3D Frictional Contact (FC) problems in order to set up a list of benchmarks; provide a standard framework for testing available and new algorithms; and share common formulations of problems in order to exchange data.

Fclib is an open-source scientific software primarily targeted at modeling and simulating nonsmooth dynamical systems

This package includes the libfclib development headers.

libfeel++-dev
A library for the finite element method
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Provides the header files and static libraries.

Feel++ is a versatile finite element library to solve partial differential equations.

Support 1D, 2D, 3D

Support the following basic entities: simplices (segment, triangle, tetrahedron) and product of simplices (quadrangle, hexahedron)

Support various point sets on these basic entities: equispaced points, quadrature points, interpolation points (Gauss-Lobatto, Fekete, WarpBlend?)

Support continuous and discontinuous Galerkin methods

Support various polynomial sets:

  • Lagrange(continuous,discontinuous,all dimensions,all interpolation point sets)

  • Dubiner(discontinuous), boundary adapted(continuous)

  • Legendre(discontinuous), boundary adapted(continuous)

Provide mathematical concept for higher order abstraction (Function spaces and associated elements, forms and operators)

Provide a language embedded in C++ for variational formulations, projection and numerical integration

libfftw3-dev
Library for computing Fast Fourier Transforms - development
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The FFTW library computes Fast Fourier Transforms (FFT) in one or more dimensions. It is extremely fast. This package contains the statically linked library, header files and test programs.

This package contains the header files and static libraries. For documentation, see libfftw3-doc.

Please cite: Matteo Frigo and Steven G. Johnson: The Design and Implementation of FFTW3. (eprint) 93(2):216–231 (2005)
Registry entries: SciCrunch 
libnfft3-dev
development files for the NFFT library
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NFFT3 is a software library written in C for computing nonequispaced fast Fourier and related transformations. In detail, NFFT3 implements:

1) The nonequispaced fast Fourier transform (NFFT)

  • the forward transform (NFFT)
  • the adjoint transform (adjoint NFFT)

2) Generalisations of the NFFT

  • to arbitrary knots in time and frequency domain (NNFFT)
  • to the sphere S^2 (NFSFT)
  • to the hyperbolic cross (NSFFT)
  • to real-valued data, i.e. (co)sine transforms, (NFCT, NFST)
  • to the rotation group (NFSOFT)

3) Generalised inverses based on iterative methods, e.g. CGNR, CGNE

4) Applications in

  • medical imaging (i) magnetic resonance imaging (ii) computerised tomography
  • summation schemes (i) fast Gauss transform (FGT) (ii) singular kernels (iii) zonal kernels
  • polar FFT, discrete Radon transform, ridgelet transform

This package provides the development files for the NFFT library.

Please cite: J. Keiner, S. Kunis and D. Potts: Using NFFT 3 - a software library for various nonequispaced fast Fourier transforms. (eprint) ACM Trans. Math. Softw. 36(4):19-1-19-30 (2009)
libopenctm-dev
Library headers for compression of 3D triangle meshes
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OpenCTM — the Open Compressed Triangle Mesh file format — is a file format, a software library and a tool set for compression of 3D triangle meshes. The geometry is compressed to a fraction of comparable file formats, and the format is easily accessible through a simple, portable API.

This package contains the development files needed for compiling programs using OpenCTM.

libp4est-dev
Algorithms for Parallel Adaptive Mesh Refinement - development files
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The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scale to hundreds of thousands of processor cores.

This package contains the development files.

libplb-dev
CFD solver based on the lattice Boltzmann method. Development files
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A software tool for classical CFD, particle-based models and complex physical interaction, Palabos offers a powerful environment for your fluid flow simulations.

Through the innovative matrix-based interface, setting up a massively parallel simulation or developing a new physical model has become simpler than ever. The package contains development files.

libspfft-dev
Sparse 3D FFT library with MPI, OpenMP, CUDA / ROCm support (development files)
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SpFFT was originally intended for transforms of data with spherical cutoff in frequency domain, as required by some computational material science codes. For distributed computations, SpFFT uses a slab decomposition in space domain and pencil decomposition in frequency domain (all sparse data within a pencil must be on one rank). If desired, the library can be compiled without any parallelization (MPI, OpenMP, CUDA / ROCm).

This package contains development files.

libxray-absorption-perl
x-ray absorption data for the elements
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Xray::Absorption supports access to X-ray absorption data. It is designed to be a transparent interface to absorption data from a variety of sources. Currently, the only sources of data are the 1969 McMaster tables, the 1999 Elam tables, the 1993 Henke tables, and the 1995 Chantler tables. The Brennan-Cowen implementation of the Cromer-Liberman tables is available as a drop-on-top addition to this package. More resources can be added easily.

libxray-scattering-perl
x-ray scattering data for the elements
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Xray::Scattering supports access to X-ray scattering data for atoms and ions. It is designed to be a transparent interface to scattering data from a variety of sources. Currently, the only sources of data are the Cromer-Mann tables from the International Tables of Crystallography and the 1995 Waasmaier-Kirfel tables. More resources can be added easily.

libxray-spacegroup-perl
symmetry operations for the crystal space groups
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Xray::SpaceGroup provides an object-oriented interface to a database of space group symmetries transcribed from volume A of the International Tables of Crystallography.

pyfai
Fast Azimuthal Integration scripts
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PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

python3-basix
Finite Element Basis Function Definition Runtime Library (Python 3)
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Computes FE basis functions and derivatives for the following elements:

  • Lagrange (interval, triangle, tetrahedron, prism, pyramid, quadrilateral, hexahedron)
  • Nédélec (triangle, tetrahedron)
  • Nédélec Second Kind (triangle, tetrahedron)
  • Raviart-Thomas (triangle, tetrahedron)
  • Regge (triangle, tetrahedron)
  • Crouzeix-Raviart (triangle, tetrahedron)

Computes quadrature rules on different cell types

Provides reference topology and geometry for reference cells of each type.

Python wrapper provided with pybind11.

This package installs the library for Python 3.

python3-dmsh
High-quality 2D mesh generator based on distmesh
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dmsh: "The worst mesh generator you'll ever use."

Inspired by distmesh, dmsh is slow, requires a lot of memory, and isn't terribly robust either.

On the plus side, it's got a usable interface, is pure Python (and hence easily installable on any system), and if it works, it produces pretty high-quality meshes.

Combined with optimesh, dmsh produces the highest-quality 2D meshes in the west.

Example capabilities:

  • Primitives
  • circle, rectangle, polygon
  • halfspace
  • Combinations
  • difference
  • nonconstant edge length
  • union
  • intersection
  • Transformations
  • rotation, translation, scaling
  • Local refinement
python3-dolfin
Base Python interface for DOLFIN (Python 3)
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DOLFIN is the Python and C++ interface of the FEniCS project for the automated solution of differential equations, providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms; automatic and efficient assembly of linear systems; and support for general families of finite elements.

This is the base package depending on specific dolfin builds. By default the version built against the preferred version of PETSc in /usr/lib/petsc is selected (with 32-bit indexing, but the alternative version (64-bit PETSc) can be selected by setting the environment variable PETSC_DIR.

This is the legacy version of DOLFIN, you may want to install the next-generation python3-dolfinx (DOLFIN-X) instead.

python3-dolfinx
Python interface for DOLFIN (Python 3)
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DOLFIN is the Python and C++ interface of the FEniCS project for the automated solution of differential equations, providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms; automatic and efficient assembly of linear systems; and support for general families of finite elements.

This is the next-generation version of libdolfinx-dev (DOLFIN-X). The legacy version of DOLFIN is provided by python3-dolfin.

This is a base package depending on the dolfinx packages with real or complex number support. By default the version built against the preferred version of PETSc in /usr/lib/petsc is selected, but the alternative version can be selected by setting the environment variable PETSC_DIR.

python3-ffcx
next-gen compiler for finite element variational forms (Python 3)
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The FEniCS Form Compiler FFC provides state-of-the-art automatic and efficient evaluation of general multilinear forms (variational formulations) for FEniCS. FFC functions as the form evaluation system for DOLFIN but can also be used to compile forms for other systems.

FFC works as a compiler for multilinear forms by generating code (C or C++) for the evaluation of a multilinear form given in mathematical notation. This new approach to form evaluation makes it possible to combine generality with efficiency; the form can be given in mathematical notation and the generated code is as efficient as hand-optimized code.

This package installs the next-generation FFC-X library for Python 3.

python3-gpyfft
Wrapper for the OpenCL FFT library clFFT (Python 3)
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This python wrapper is designed to tightly integrate with PyOpenCL. It consists of a low-level Cython based wrapper with an interface similar to the underlying C library. On top of that it offers a high-level interface designed to work on data contained in instances of pyopencl.array.Array, a numpy work-alike array class for GPU computations. The high-level interface takes some inspiration from pyFFTW. For details of the high-level interface see fft.py.

This package installs the library for Python 3.

python3-ltfatpy
Large Time-Frequency Toolbox (LTFAT) in Python
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The ltfatpy package is a partial Python port of the Large Time/Frequency Analysis Toolbox (LTFAT), a MATLAB®/Octave toolbox for working with time-frequency analysis and synthesis.

It is intended both as an educational and a computational tool.

The package provides a large number of linear transforms including Gabor transforms along with routines for constructing windows (filter prototypes) and routines for manipulating coefficients.

This package provides the modules for Python 3.

python3-meshplex
fast tools for simplex meshes (Python 3)
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Compute all sorts of interesting points, areas, and volumes in triangular and tetrahedral meshes, with a focus on efficiency. Useful in many contexts, e.g., finite-element and finite-volume computations.

This package installs the library for Python 3.

python3-meshzoo
simple geometric meshes (Python 3)
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When generating meshes for FEM/FVM computations, sometimes your geometry is so simple that you don't need a complex mesh generator (like pygmsh, MeshPy, mshr, pygalmesh, dmsh), but something simple and fast that makes use of the structure of the domain. Enter meshzoo.

Examples: Triangle, Rectangle, Regular polygon, Disk, Möbius strip, Sphere (surface), Ball (solid), Tube, Cube.

This package installs the module for Python 3.

python3-multipletau
??? missing short description for package python3-multipletau :-(
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python3-pyfftw
Pythonic wrapper around FFTW - Python 3
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Pythonic wrapper around FFTW, the speedy FFT library. The ultimate aim is to present a unified interface for all the possible transforms that FFTW can perform.

Both the complex DFT and the real DFT are supported, as well as arbitrary axes of abitrary shaped and strided arrays, which makes it almost feature equivalent to standard and real FFT functions of numpy.fft (indeed, it supports the clongdouble dtype which numpy.fft does not).

pyFFTW is BSD-licensed and should not be confused with python-fftw, a GPL-licensed python module with the same aim of providing python bindings to FFTW3. Or python3-gpyfft, which provides bindings to the OpenCL FFT library clFFT.

This package provides the Python 3 bindings.

python3-pygalmesh
Python 3 frontend to CGAL's 3D mesh generators
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pygalmesh makes it easy to create high-quality 3D volume and surface meshes.

CGAL offers two different approaches for mesh generation:

  • Meshes defined implicitly by level sets of functions.
  • Meshes defined by a set of bounding planes.

pygalmesh provides a front-end to the first approach, which has the following advantages and disadvantages:

  • All boundary points are guaranteed to be in the level set within any specified residual. This results in smooth curved surfaces.
  • Sharp intersections of subdomains (e.g., in unions or differences of sets) need to be specified manually (via feature edges, see below), which can be tedious.

On the other hand, the bounding-plane approach (realized by mshr), has the following properties:

  • Smooth, curved domains are approximated by a set of bounding planes, resulting in more of less visible edges.
  • Intersections of domains can be computed automatically, so domain unions etc. have sharp edges where they belong.

pygalmesh and mshr are therefore complementary.

pygalmesh also interfaces CGAL's 3D periodic mesh generation.

This package installs the pygalmesh module for Python 3.

It also provides the utility scripts pygalmesh-from-inr and pygalmesh-volume-from-surface for generating volume meshes from INR or surface meshes.

python3-pynfft
Python bindings for the NFFT3 library - Python 3
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This package provides Python bindings to the NFFT library, useful for performing Fourier transforms on non-uniformly sampled data with efficient speed. The bindings were generated using Cython and abstract the creation and execution of NFFT plans out using classes.

This package provides the Python 3 version of the bindings.

python3-pyode
Python bindings for The Open Dynamics Engine
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PyODE is a set of open-source Python bindings for The Open Dynamics Engine, an open-source physics engine. PyODE also includes an XODE parser.

This package provides PyODE for supported versions of Python.

python3-quantities
Library for computation of physical quantities with units, based on numpy
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Quantities is designed to handle arithmetic and conversions of physical quantities, which have a magnitude, dimensionality specified by various units, and possibly an uncertainty. Quantities builds on the popular numpy library and is designed to work with numpy ufuncs, many of which are already supported.

sfftw-dev
library for computing Fast Fourier Transforms
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This library computes FFTs in one or more dimensions. It is extremely fast. This package contains the statically linked library and the header files.

trilinos-all-dev
object-oriented framework for large-scale problems - development files (ALL)
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The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

This package depends on all Trilinos development packages.

Please cite: Michael Heroux, Roscoe Bartlett, Vicki Howle Robert Hoekstra, Jonathan Hu, Tamara Kolda, Richard Lehoucq, Kevin Long, Roger Pawlowski, Eric Phipps, Andrew Salinger, Heidi Thornquist, Ray Tuminaro, James Willenbring and Alan Williams: An Overview of Trilinos (SAND2003-2927) (2003)

Official Debian packages with lower relevance

libopm-common-dev
Tools for Eclipse reservoir simulation files -- development files
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

This package contains the shared buildsystem of all OPM modules, the headers for input, parsing, and output of files in Eclipse format, a format widely used in the reservoir simulation community, and generic utilities used in other OPM modules.

libopm-grid-dev
DUNE grid implementations for reservoir simulation -- development files
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-grid provides implementations of grids for reservoir simulation, corner point or more general pillar grids, following the DUNE grid interface: CpGrid, a parallel corner point grid, and PolyhedralGrid a more general serial grid implementation of an unstructured, legacy, grid.

A standard grid type in the petroleum industry, corner-point grids fills the domain with a relatively low number of cells while still providing sufficient flexibility to model faults, fractures and erosion. The grid format was originally designed with an eye towards geological modeling rather than numerical simulation, but is still suitable for e.g. low order finite volume discretizations.

This package provides the development files for the grid implementations, i.e. the headers and shared library links.

libopm-material-dev
transitional package
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This is a transitional package. It can safely be removed.

libopm-models-dev
C++ simulation framework for porous media flow -- development files
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-models is a header-only simulation framework which is primary focused on fully implicit models for flow and transport in porous media. It uses finite volume schemes for discretization and automatic differentiation for calculating the Jacobians. Its main objectives is to provide an easily usable, well maintainable, high performance framework which is capable of capturing all macro-scale scenarios relevant for academic research and industrial applications involving flow and transport processes in porous media.

This package provides the development files (headers) needed to build applications based on opm-models.

libopm-simulators-dev
Parallel porous media / reservoir simulators -- development files
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-simulators provides a research (ebos) and a production (flow) fully implicit black-oil simulators, supporting one to three phases and supporting solvent and polymer options. It uses cell centered finite volume schemes with two point flux approximation and automatic differentiation for the discretization and uses state of the art linear and nonlinear solvers. It supports standard and multi segment well models and reading and writing file in Eclipse format, a very common format used in the oil reservoir simulation community.

Package provides the development files (headers and shared library links).

libopm-upscaling-dev
Porous media upscaling tools -- development files
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-upscaling provides tools for single phase and relative permeability upscaling. During upscaling effective parameters (like porosity, permeability, and capillary pressure) for a simulation on a coarser scale are computed from properties of a simulation on a fine scale.

Package provides the development files (headers and shared library links).

python3-opm-common
Tools for Eclipse reservoir simulation files -- Python wrappers
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

This package contains the Python wrappers for reading, parsing, and writing files in Eclipse format, a format widely used in the reservoir simulation community.

python3-opm-simulators
Python wrappers for the Open porous media / reservoir simulators
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The Open Porous Media (OPM) software suite provides libraries and tools for modeling and simulation of porous media processes, especially for simulating CO2 sequestration and improved and enhanced oil recovery.

opm-simulators provides a research (ebos) and a production (flow) fully implicit black-oil simulators, supporting one to three phases and supporting solvent and polymer options. It uses cell centered finite volume schemes with two point flux approximation and automatic differentiation for the discretization and uses state of the art linear and nonlinear solvers. It supports standard and multi segment well models and reading and writing file in Eclipse format, a very common format used in the oil reservoir simulation community.

Package provides Python wrappers for the simulators.

Debian packages in contrib or non-free

libtriangle-dev
High-quality 2-D mesh generator -- development files
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Triangle is a library/program for meshing 2-D surfaces and manifolds.

This package contains its static library, headers, and shared library symbolic link, which are needed to compile programs using the triangle library.

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