SimulationTools for Mathematica

15th August 2013

We present “SimulationTools for Mathematica” (http://simulationtools.org/), available as free software under the GNU General Public License. SimulationTools is a Mathematica application for analysing data from numerical simulations. It has a modular design applicable to general grid-based numerical simulations, and contains specific support for the Cactus code, with a focus on the field of Numerical Relativity and the Einstein Toolkit.

SimulationTools provides a functional, programmable interface to simulation data. A highly-optimised HDF5 module can be used for reading HDF5 data from production simulations, including 1D, 2D and 3D grid data produced by the Carpet code. Simulation details such as filenames, file formats, and details of parallel I/O are hidden from the user.

Numeric data with attached coordinate information is manipulated using new data types. Many useful new functions are defined on these types, and most built-in numerical Mathematica functions such as +, -, *, /, Abs, Sin, Log and Max can be used transparently. There is also support for testing numerical convergence, with automatic resampling onto a common grid if desired.

SimulationTools has generic functionality useful for analysis of many types of data, as well as explicit support for codes including Cactus, Carpet, Llama, SimFactory and many other components of the Einstein Toolkit. It provides an overview of the state of a simulation, including speed, memory usage, and physics (e.g. trajectories and waveforms from a binary system). The design is modular, and support for output from other codes can be added.

Specific functionality for Numerical Relativity is available. Gravitational waveforms can be read from simulations using natural function semantics, and the waveforms can be manipulated, for example converting between Psi4 and strain and extrapolation to infinity. An abstraction for “binary systems” provides a convenient interface to the trajectories of members of a binary system tracked with codes from the Einstein Toolkit. Support for reading black hole masses and spins is also included. Data in the Numerical Relativity Data Format (as used in the NINJA and NR-AR projects) can be read using the same functions that are used for normal simulation data.

More details are available on the SimulationTools website (http://simulationtools.org), including an extensive feature summary, a list of capabilities and online documentation (http://simulationtools.org/Documentation/English/Tutorials/SimulationTools.html). Tutorials and reference documentation are also available within the standard Mathematica documentation system. Code quality is maintained to a high standard with ~400 unit tests.

SimulationTools has been in production use for over 5 years and has been used at several research institutions worldwide. We invite you to try out the code (http://simulationtools.org/download), join the mailing list (http://simulationtools.org/mailman/listinfo/users) and freely use SimulationTools for your research.


Ian Hinder and Barry Wardell

http://numrel.aei.mpg.de/people/hinder

http://barrywardell.net/

SimulationTools for Mathematica

15th August 2013

We present “SimulationTools for Mathematica” <http://simulationtools.org/>, available as free software under the GNU General Public License. SimulationTools is a Mathematica application for analysing data from numerical simulations. It has a modular design applicable to general grid-based numerical simulations, and contains specific support for the Cactus code, with a focus on the field of Numerical Relativity and the Einstein Toolkit.

SimulationTools provides a functional, programmable interface to simulation data. A highly-optimised HDF5 module can be used for reading HDF5 data from production simulations, including 1D, 2D and 3D grid data produced by the Carpet code. Simulation details such as filenames, file formats, and details of parallel I/O are hidden from the user.

Numeric data with attached coordinate information is manipulated using new data types. Many useful new functions are defined on these types, and most built-in numerical Mathematica functions such as +, -, *, /, Abs, Sin, Log and Max can be used transparently. There is also support for testing numerical convergence, with automatic resampling onto a common grid if desired.

SimulationTools has generic functionality useful for analysis of many types of data, as well as explicit support for codes including Cactus, Carpet, Llama, SimFactory and many other components of the Einstein Toolkit. It provides an overview of the state of a simulation, including speed, memory usage, and physics (e.g. trajectories and waveforms from a binary system). The design is modular, and support for output from other codes can be added.

Specific functionality for Numerical Relativity is available. Gravitational waveforms can be read from simulations using natural function semantics, and the waveforms can be manipulated, for example converting between Psi4 and strain and extrapolation to infinity. An abstraction for “binary systems” provides a convenient interface to the trajectories of members of a binary system tracked with codes from the Einstein Toolkit. Support for reading black hole masses and spins is also included. Data in the Numerical Relativity Data Format (as used in the NINJA and NR-AR projects) can be read using the same functions that are used for normal simulation data.

More details are available on the SimulationTools website <http://simulationtools.org>, including an extensive feature summary, a list of capabilities and online documentation <http://simulationtools.org/Documentation/English/Tutorials/SimulationTools.html>. Tutorials and reference documentation are also available within the standard Mathematica documentation system. Code quality is maintained to a high standard with ~400 unit tests.

SimulationTools has been in production use for over 5 years and has been used at several research institutions worldwide. We invite you to try out the code  <http://simulationtools.org/download>, join the mailing list <http://simulationtools.org/mailman/listinfo/users> and freely use SimulationTools for your research.


Ian Hinder and Barry Wardell

http://numrel.aei.mpg.de/people/hinder

http://barrywardell.net/

Llama Multi-Block Infrastructure publicly available

http://llamacode.org/

The Llama Multi-Block Infrastructure for Cactus is now publicly available under the GNU General Public License. Llama provides three-dimensional multi-block capability for Cactus-based simulations that can be combined with Carpet’s adaptive mesh refinement functionality. Llama decomposes the domain into multiple (potentially overlapping) blocks with different local coordinate systems. This allows e.g. spherical domains, spherical excision, adaptive radial/angular resolution, etc., without incurring coordinate singularities.

Llama provides several patch systems suitable for single and binary objects in relativistic astrophysics, and is well integrated with the Einstein Toolkit . Llama was already used for several publications , and we believe the code is ready to be used in other projects. We are seeking volunteers to help us add tutorials and documentation, improve error messages, and generally shake down and brush up the code for a future inclusion in the Einstein Toolkit.

To aid others in getting started using Llama, we will be hosting a virtual workshop where we provide an overview of the code and answer questions. Details will be announced shortly.

Llama constitutes the fruit of a significant effort of several people over several years. We make Llama public to help modernize the computational tools used in our community, and in the hope to boost Llama itself by inviting contributions from everybody. We ask you to acknowledge our effort by following the citation guidelines described on .

The Llama groomers:

R. Haas, I. Hinder, D. Pollney, C. Reisswig, E. Schnetter, B. Wardell

New book: "3+1 Formalism in General Relativity" by Eric Gourgoulhon

3+1 Formalism in General Relativity: Bases of Numerical Relativity

Eric Gourgoulhon
Springer, 2012
294 pages

Contents:
1. Introduction
2. Basic Differential Geometry
3. Geometry of Hypersurfaces
4. Geometry of Foliations
5. 3+1 Decomposition of Einstein Equation
6. 3+1 Equations for Matter and Electromagnetic Field
7. Conformal Decomposition
8. Asymptotic Flatness and Global Quantities
9. The Initial Data Problem
10. Choice of Foliation and Spatial Coordinates
11. Evolution Schemes
A. Conformal Killing Operator and Conformal Vector Laplacian
B. Sage Codes

More details at http://relativite.obspm.fr/3p1

Einstein Toolkit Release

We are pleased to announce the second release (code name “Chandrasekhar”) of the Einstein Toolkit, an open, community developed software infrastructure for relativistic astrophysics. This release is mainly a maintenance release incorporating fixes accumulated since the previous release in June 2010, as well as additional test suites.

The Einstein Toolkit is a collection of software components and tools for simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community including CactusEinstein, the Carpet AMR infrastructure and on the public version of the Whisky hydrodynamics code (now modified and called GRHydro). The Cactus Framework is used as the underlying computational infrastructure providing large-scale parallelization, general computational components, and a model for collaborative, portable code development. The toolkit includes modules to build complete codes for simulating black hole spacetimes as well as systems governed by relativistic hydrodynamics. Current development in the consortium is targeted at providing additional infrastructure for general relativistic magnetohydrodynamics.

The Einstein Toolkit uses a distributed software model and its different modules are developed, distributed, and supported either by the core team of Einstein Toolkit Maintainers, or by individual groups. Where modules are provided by external groups, the Einstein Toolkit Maintainers provide quality control for modules for inclusion in the toolkit and help coordinate support. The Einstein Toolkit Maintainers currently involve postdocs and faculty from five different institutions, and host weekly meetings that are open for anyone to join in.

Guiding principles for the design and implementation of the toolkit include: open, community-driven software development; well thought out and stable interfaces; separation of physics software from computational science infrastructure; provision of complete working production code; training and education for a new generation of researchers.

For more information about using or contributing to the Einstein Toolkit, or to join the Einstein Toolkit Consortium, please visit our web pages http://einsteintoolkit.org.

The Einstein Toolkit is primarily supported by NSF 0903973/0903782/0904015 (CIGR), and also by NSF 0701566/0855892 (XiRel), 0721915 (Alpaca), 0905046/0941653 (PetaCactus) and 0710874 (LONI Grid).

The “Chandrasekhar” Release Team on behalf of the Einstein Toolkit Consortium (2010-11-23)

Numerical Relativity: Solving Einstein's Equations on the Computer (New Book)

Numerical Relativity: Solving Einstein’s Equations on the Computer

T. W. Baumgarte and S. L. Shapiro
Cambridge University Press, 2010

Aimed at students and researchers entering the field, this pedagogical introduction to numerical relativity will also interest scientists seeking a broad survey of its challenges and achievements. Assuming only a basic knowledge of classical general relativity, this textbook develops the mathematical formalism from first principles, then highlights some of the pioneering simulations involving black holes and neutron stars, gravitational collapse and gravitational waves. Applications include calculations of coalescing binary black holes and binary neutron stars, rotating stars, colliding star clusters, gravitational and magnetorotational collapse, critical phenomena, the generation of gravitational waves, and many more.

Features of the book include:

- 300 exercises help readers master new material as it is presented.

- Numerous illustrations, many in color, assist in visualizing new geometric concepts and highlighting the results of computer simulations.

- Summary boxes encapsulate some of the most important results for quick reference.

- Applications cover topics of current physical and astrophysical significance.

For details, see http://www.cambridge.org/us/knowledge/isbn/item2707919/?site_locale=en_US

Einstein Toolkit Release

We are pleased to announce the first release (code name “Bohr”) of the Einstein Toolkit, an open, community developed software infrastructure for relativistic astrophysics. The Einstein Toolkit is a collection of over 130 software components and tools for simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community including CactusEinstein, the Whisky hydrodynamics code, and the Carpet AMR infrastructure. The Cactus Framework is used as the underlying computational infrastructure providing large-scale parallelization, general computational components, and a model for collaborative, portable code development. The toolkit includes modules to build complete codes for simulating black hole spacetimes as well as systems governed by relativistic hydrodynamics. Current development in the consortium is targeted at providing additional infrastructure for general relativistic magnetohydrodynamics.

The Einstein Toolkit uses a distributed software model and its different modules are developed, distributed, and supported either by the core team of Einstein Toolkit Maintainers, or by individual groups. Where modules are provided by external groups, the Einstein Toolkit Maintainers provide quality control for modules for inclusion in the toolkit and help coordinate support. The Einstein Toolkit Maintainers currently involve postdocs and faculty from five different institutions, and hold weekly meetings that are open for anyone to join in.

Guiding principles for the design and implementation of the toolkit include:

1: Open, community-driven software development that encourages the sharing of code across the community, prevents code duplication, and leads to sustainable support and development of essential code.

2: Well thought out and stable interfaces between components that enable multiple implementations of physics capabilities, and allow groups or individuals to concentrate on their areas of interest.

3: Separation of physics software from computational science infrastructure so that new technologies for large scale computing, processor accelerators, or parallel I/O can be easily integrated with science codes.

4: The provision of complete working production codes to provide: prototypes, standard benchmarks, and testcases; codes that are available for and usable by the general astrophysics community; tools for new researchers and groups to enter this field; training and education for a new generation of researchers.

For more information about using or contributing to the Einstein Toolkit, or to join the Einstein Toolkit Consortium, please visit our web pages at <http://einsteintoolkit.org>.

We thank the numerous people who contributed to this software over the past many years; there are too many to be listed here. We also gratefully acknowledge those who helped in the past months to make this release happen. The Einstein Toolkit is primarily supported by NSF 0903973/0903782/0904015 (CIGR), and also by NSF 0701566/0855892 (XiRel), 0721915 (Alpaca), 0725070 (Blue Waters), and 0905046/0941653 (PetaCactus).

The “Bohr” Release Team on behalf of the Einstein Toolkit Consortium
(2010-06-17)

NRDA09/MICRA09 Double special issue published in Classical and Quantum Gravity

I am delighted to announce the publication of the following double special issue in Classical and Quantum Gravity:

Invited papers from Numerical Relativity and Data Analysis (NRDA) 2009,
Albert Einstein Institute, Potsdam, 6 – 9 July, 2009
Guest Editors: S Husa and B Krishnan

Invited papers from Microphysics In Computational Relativistic Astrophysics (MICRA) 2009,
Niels Bohr International Academy, Copenhagen, 24 – 28 August 2009
Guest Editors: C D Ott, C Pethick and L Rezzolla

The NRDA meeting was aimed at fostering closer interactions between simulations of gravitational wave sources and the ongoing searches for gravitational wave signals.

The MICRA meeting brought together researchers in numerical modeling and physics of matter at high densities, where general relativity plays a central role.

I take this opportunity to thank all of the authors, referees and guest editors who gave their time and expertise to create this excellent issue.

The special issue will be free for 6 months from date of publication. I invite you to read the articles on the new IOPscience service!

Yours sincerely,

Adam Day
Publisher
Classical and Quantum Gravity
iopscience.org/cqg

Workshop on Unstructured Meshes in Dynamical Spacetimes

We are pleased to announce the Workshop on Unstructured Meshes in Dynamical Spacetimes in Jena, Germany on 25-27 August 2010.

This workshop on the use of unstructured meshes in numerical relativity has been devised as a means to bring together experts in numerical relativity, finite elements, finite volumes, discrete differential forms, and Regge calculus to encourage discussion between the communities and identify areas in which new progress can be made.

Topics for talks and discussions will be aimed at
-Finite element methods in numerical relativity
-Dynamical space-time meshing
-Applications for finite-volume methods
-Higher order geometric discretizations of Einstein’s equations
-Numerical methods based on Regge calculus
-Advances in discrete differential forms.

Registration is currently open, and we are accepting contributed talks. The deadline for submission of abstracts is 31 July 2010.

http://cse.mathe.uni-jena.de/wumds/

Sincerely,
Snorre H. Christiansen (University of Oslo)
Jonathan R. McDonald (Friedrich Schiller University, Jena)
Warner A. Miller (Florida Atlantic University, Boca Raton)
Gerhard Zumbusch (Friedrich Schiller University, Jena)

Lecture Notes in Physics, Vol. 783 – New Volume

We are pleased to deliver your requested table of contents alert for a new volume of “Lecture Notes in Physics”.

Volume 783: Elements of Numerical Relativity and Relativistic Hydrodynamics by Carles Bona, Carlos Palenzuela-Luque, Carles Bona-Casas is now available on the SpringerLink web site at

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zc.3D7U.bW89MQ%5f%5fDBTAFPd0

By clicking on the URLs below you can access the abstracts for each article. If your browser does not support direct URL access, please copy and paste the selected URL to your web browser.

====================================================

TABLE OF CONTENTS:

The 4D Spacetime

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 1 – 24
DOI: 10.1007/978-3-642-01164-1_1
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zi.3D7U.bW89MQ%5f%5fDCGcFQD0

- – - – - – - – - – - – - – - – - – - – - – - – -

The Evolution Formalism

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 25 – 48
DOI: 10.1007/978-3-642-01164-1_2
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zk.3D7U.bW89MQ%5f%5fDCNQFQF0

- – - – - – - – - – - – - – - – - – - – - – - – -

Free Evolution

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 49 – 77
DOI: 10.1007/978-3-642-01164-1_3
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zm.3D7U.bW89MQ%5f%5fDCUEFQH0

- – - – - – - – - – - – - – - – - – - – - – - – -

First-Order Hyperbolic Systems

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 79 – 108
DOI: 10.1007/978-3-642-01164-1_4
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zo.3D7U.bW89MQ%5f%5fDCaYFQJ0

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Numerical Methods

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 109 – 142
DOI: 10.1007/978-3-642-01164-1_5
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zq.3D7U.bW89MQ%5f%5fDDBMFQL0

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Black Hole Simulations

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 143 – 170
DOI: 10.1007/978-3-642-01164-1_6
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zs.3D7U.bW89MQ%5f%5fDDIAFQN0

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Matter Spacetimes

Author(s): Carles Bona, Carles Bona-Casas, Carlos Palenzuela-Luque
Page: 171 – 209
DOI: 10.1007/978-3-642-01164-1_7
URL:

http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1hCe3z.BySyHW..N.I8Zu.3D7U.bW89MQ%5f%5fDDOUFQP0