Commits January 2011

commits@lists.einsteintoolkit.org

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 17)
by knarf＠cct.lsu.edu 24 Jan '11

24 Jan '11

User: knarf Date: 2011/01/24 11:50 AM Modified: / ET.tex Log: break paragraph into lines File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +15 -1 =================================================================== --- ET.tex 2011-01-24 17:41:21 UTC (rev 16) +++ ET.tex 2011-01-24 17:50:29 UTC (rev 17) @@ -242,7 +242,21 @@ \todo{Overall design, strategy.} -The mechanisms for the development and support of the Einstein Toolkit are designed to be open, transparent and community driven. All the source code, documentation and tools included in the Einstein Toolkit are distributed under open source licenses. The Einstein Toolkit maintains an SVN repository ({\tt svn.einsteintoolkit.org}) with open access which contains software supported by the Einstein Toolkit Maintainers, the toolkit web pages and documentation. An open wiki for documentation ({\tt docs.einsteintoollkit.org}) has been established where the community can contribute either through anonymous or personal authentication. All discussion about the toolkit takes place on an open mail list ({\tt users(a)einsteintoolkit.org}). The regular weekly meetings for the Einstein Toolkit Maintainers are open and the community are invited to participate, and minutes are recorded on the wiki. The Einstein Toolkit blog requires users to first request a login, but then can be freely posted to. Any user can post comments to entries already on the blog. +The mechanisms for the development and support of the Einstein Toolkit are +designed to be open, transparent and community driven. All the source code, +documentation and tools included in the Einstein Toolkit are distributed +under open source licenses. The Einstein Toolkit maintains an SVN repository +({\tt svn.einsteintoolkit.org}) with open access which contains software +supported by the Einstein Toolkit Maintainers, the toolkit web pages and +documentation. An open wiki for documentation +({\tt docs.einsteintoollkit.org}) has been established where the community +can contribute either through anonymous or personal authentication. All +discussion about the toolkit takes place on an open mail list +({\tt users(a)einsteintoolkit.org}). The regular weekly meetings for the +Einstein Toolkit Maintainers are open and the community are invited to +participate, and minutes are recorded on the wiki. The Einstein Toolkit +blog requires users to first request a login, but then can be freely +posted to. Any user can post comments to entries already on the blog. \section{Core Technologies}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 16)
by diener＠cct.lsu.edu 24 Jan '11

24 Jan '11

User: diener Date: 2011/01/24 11:41 AM Modified: / ET.tex Log: Some text about Object tracking. File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +17 -0 =================================================================== --- ET.tex 2011-01-24 17:40:13 UTC (rev 15) +++ ET.tex 2011-01-24 17:41:21 UTC (rev 16) @@ -494,7 +494,24 @@ \paragraph{Vacuum-Matter Coupling} \paragraph{Object tracking} +We provide a module (\codename{PunctureTracker}) for tracking black hole +positions when evolved with the moving puncture technique. This can be used +with (\codename{CarpetTracker}) to have the mesh refinement regions follow the +black holes as they move across the grid. The black hole position is +stored as the centroid of a spherical surface (even though there is no surface) +provided by \codename{SphericalSurface}. +Since the punctures only move due to the shift advection terms in +the BSSN equations, the puncture location is evolved very simply as +\begin{equation} + \frac{d x^i}{d t} = -\beta^i, \label{eq:puncturetracking} +\end{equation} +where $x^i$ is the puncture location and $\beta^i$ is the shift. Since the +puncture location usually does not coincide with gridpoints, the shift is +interpolated to the location of the puncture. +Equation~(\ref{eq:puncturetracking}) is implemented with a simple first order +Euler scheme, which seems to be accurate enough for controlling the mesh +refinement grids. \subsection{Infrastructure and Numerical Methods} \todo{1/2 page Erik}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 15)
by bcmsma＠astro.rit.edu 24 Jan '11

24 Jan '11

User: bmundim Date: 2011/01/24 11:40 AM Modified: / ET.tex Log: thorn --> module File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +11 -11 =================================================================== --- ET.tex 2011-01-24 17:32:44 UTC (rev 14) +++ ET.tex 2011-01-24 17:40:13 UTC (rev 15) @@ -400,16 +400,16 @@ \subsection{Initial Data} \todo{1/2 page Josh, Bruno} -The Einstein Toolkit contains many thorns used to generate initial data for GR simulations, -including both vacuum and hydrodynamical configurations. These include thorns used primarily +The Einstein Toolkit contains many modules used to generate initial data for GR simulations, +including both vacuum and hydrodynamical configurations. These include modules used primarily for testing out various components of the evolution scheme as well as physically motivated -configurations that describe single of binary blacks and/or neutron stars. Many of the thorns +configurations that describe single of binary blacks and/or neutron stars. Many of the modules are self-contained, consisting of either all the code to generate exact initial solutions or the numerical tools required to construct solutions known semi-analytically. Others, though, require the installation of other numerical software packages that are included in the toolkit -as External libraries. The {\tt twopunctures} thorn \cite{Ansorg:2004ds}, commonly used in numerical +as External libraries. The {\tt twopunctures} module \cite{Ansorg:2004ds}, commonly used in numerical relativity to generate binary black hole data, invokes the GNU Scientific Library [GSL; \cite{Galassi:2009}]. -Several thorns have also been implemented to read in datafiles generated by the +Several modules have also been implemented to read in datafiles generated by the {\tt Lorene code} \cite{Loreneweb,GGTMB}, including the BHBH, BHNS, and NSNS data made publicly available through the Lorene website. @@ -420,10 +420,10 @@ in question represents vacuum or a hydrodynamical configuration. Finally, any necessary cleanup is typically performed at the end of the initial step, prior to the iterations forward in time. -For vacuum initial data configurations, an initial data thorn must supply $g_{ij}$, the spatial 3-metric, +For vacuum initial data configurations, an initial data module must supply $g_{ij}$, the spatial 3-metric, and $K_{ij}$, the extrinsic curvature. While the evolution scheme typically makes use of the BSSN formalism, the conversion between the physical and conformal metric and extrinsic curvature is handled solely within -evolution thorns, and is not referenced by initial data ones. Optionally, many initial data thorns also +evolution modules, and is not referenced by initial data ones. Optionally, many initial data modules also supply values for the lapse and shift vector, and in some cases time derivatives as well, though these may be supplied by other routines depending on the freedom to choose gauge conditions envisioned for a specific configuration. @@ -450,13 +450,13 @@ \end{enumerate} \item Black Hole configurations: \begin{enumerate} -\item {\tt IDAnalyticBH}: This thorn can generate Schwarzchild black holes, as well as the Misner solution +\item {\tt IDAnalyticBH}: This module can generate Schwarzchild black holes, as well as the Misner solution for multiple BHs and the brill-Lindquist binary BH solution. -\item {\tt IDAxibrillBH,~IDAxiOddBrillBH}: These thorns generate single black holes deformed by even and +\item {\tt IDAxibrillBH,~IDAxiOddBrillBH}: These modules generate single black holes deformed by even and odd parity axisymmetric perturbations, respectively. -\item {\tt DistortedBHIVP,~RotatingDBHIVP}: These thorns generate single black holes distorted by even +\item {\tt DistortedBHIVP,~RotatingDBHIVP}: These modules generate single black holes distorted by even and odd-parity non-axisymmetric perturbation, respectivey. -\item {\tt TwoPunctures}: This thorn generates accurate binary black-hole initial data. +\item {\tt TwoPunctures}: This module generates accurate binary black-hole initial data. \end{enumerate} \end{itemize}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 14)
by knarf＠cct.lsu.edu 24 Jan '11

24 Jan '11

User: knarf Date: 2011/01/24 11:32 AM Modified: / ET.tex Log: more on base modules Directory Changes: Directory: / ============ Property changes on: ___________________________________________________________________ Directory: /svn:ignore/ ======================= + *.aux *.bbl *.blg *.log *.out *.toc File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +28 -3 =================================================================== --- ET.tex 2011-01-24 17:20:25 UTC (rev 13) +++ ET.tex 2011-01-24 17:32:44 UTC (rev 14) @@ -367,11 +367,36 @@ detail, because general relativistic codes use different conventions in especially those areas. -\paragraph{Vacuum Spacetimes} +Spacetime evolution methods used within the Cactus framework use +different formulations, but all are based on the ADM +construction~\cite{Arnowitt:1962hi}. This makes this formulation the +natural choice of a common denominator to exchange data between +modules using different formulations. The following variables are +declared in the \codename{ADMBase} module: +the three-metric $\gamma_ij$, +the extrinsic curvature $K_ij$, +the lapse function $\alpha$ and shift function $\beta^i$, +both together with their first time derivatives. +This base module also defines common parameters to manage interaction +between different modules, like which type of initial data should +be setup or which evolution method should be used at run-time. -\paragraph{Relativistic Matter Spacetimes} +Similar to \codename{ADMBase}, a module called \codename{HydroBase} defines the common +basis for interactions between modules dealing with relativistic +hydrodynamics. It is using the conventions of the Valencia +formulation~\cite{Marti:1991wi,Banyuls:1997zz,Ibanez:2001:godunov}. +In particular, it defines the rest-mass density $\varrho$, the gas +pressure $p$, internal energy density $\epsilon$, the +contravariant gas three velocity defined as +$v^i = \frac{u^i}{\alpha u^0} + \frac{\beta^i}{\alpha}$, the electron +fraction $Y_e$, the temperature $T$, the specific entropy per +particle $s$ and the contravariant magnetic field vector $B^i$, defined +as $B^i = \frac{1}{\sqrt{4\pi}} n_{\nu} F^{*\nu i}$, in terms of the dual +$F^{*\mu\nu} = \frac{1}{2}\varepsilon^{\mu\nu\alpha\beta}F_{\alpha\beta}$ +to the Faraday tensor and the unit normal of the foliation of spacetime +$n^\mu$. \todo{FL: Is this too much information? Should we put some of the +formulas into a separate eq environment?} - \subsection{Initial Data} \todo{1/2 page Josh, Bruno}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 13)
by ian.hinder＠aei.mpg.de 24 Jan '11

24 Jan '11

User: hinder Date: 2011/01/24 11:20 AM Modified: / ET.tex Log: Add citations to Kranc section File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +2 -2 =================================================================== --- ET.tex 2011-01-24 17:13:56 UTC (rev 12) +++ ET.tex 2011-01-24 17:20:25 UTC (rev 13) @@ -308,7 +308,7 @@ \subsection{Kranc} \todo{1/3 page Ian} -Kranc is a Mathematica application which converts a high-level +Kranc\cite{Husa:2004ip,kranc04,krancweb} is a Mathematica application which converts a high-level continuum description of a PDE into a highly optimised module for Cactus, suitable for running on anything from a laptop to the world's largest HPC systems. Such codes contain a large amount of complexity, @@ -334,7 +334,7 @@ from the following features added to Kranc after the codes themselves were written: (i) OpenMP parallelisation support, necessary for efficient use of modern multi-core processors; (ii) support for -multipatch domains with the Llama code; (iii) automatic generation of +multipatch domains with the Llama\cite{Pollney:2009yz} code; (iii) automatic generation of vectorised code, where the equations are evaluated simultaneously by the processor for two grid points at the same time, (iv) common subexpression elimination, and various other optimisation strategies.

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 12)
by bcmsma＠astro.rit.edu 24 Jan '11

24 Jan '11

User: bmundim Date: 2011/01/24 11:13 AM Modified: / ET.tex Log: First draft on the initial data section. File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +63 -2 =================================================================== --- ET.tex 2011-01-24 17:06:57 UTC (rev 11) +++ ET.tex 2011-01-24 17:13:56 UTC (rev 12) @@ -373,8 +373,69 @@ \subsection{Initial Data} -\todo{1/2 page Josh} +\todo{1/2 page Josh, Bruno} +The Einstein Toolkit contains many thorns used to generate initial data for GR simulations, +including both vacuum and hydrodynamical configurations. These include thorns used primarily +for testing out various components of the evolution scheme as well as physically motivated +configurations that describe single of binary blacks and/or neutron stars. Many of the thorns +are self-contained, consisting of either all the code to generate exact initial solutions or +the numerical tools required to construct solutions known semi-analytically. Others, though, +require the installation of other numerical software packages that are included in the toolkit +as External libraries. The {\tt twopunctures} thorn \cite{Ansorg:2004ds}, commonly used in numerical +relativity to generate binary black hole data, invokes the GNU Scientific Library [GSL; \cite{Galassi:2009}]. +Several thorns have also been implemented to read in datafiles generated by the +{\tt Lorene code} \cite{Loreneweb,GGTMB}, including the BHBH, BHNS, and NSNS data made publicly +available through the Lorene website. + +Scheduling of initial data routines generally follows a standard format. User-defined parameters +are run through a parameter check designed to catch obvious internal inconsistencies, in addition to +any known incompatibilities with other modules of the toolkit. Initial data is then generated +at the proper stage within the Cactus framework, determined primarily by whether the configuration +in question represents vacuum or a hydrodynamical configuration. Finally, any necessary cleanup +is typically performed at the end of the initial step, prior to the iterations forward in time. + +For vacuum initial data configurations, an initial data thorn must supply $g_{ij}$, the spatial 3-metric, +and $K_{ij}$, the extrinsic curvature. While the evolution scheme typically makes use of the BSSN formalism, +the conversion between the physical and conformal metric and extrinsic curvature is handled solely within +evolution thorns, and is not referenced by initial data ones. Optionally, many initial data thorns also +supply values for the lapse and shift vector, and in some cases time derivatives as well, though these +may be supplied by other routines depending on the freedom to choose gauge conditions envisioned for a +specific configuration. + +For hydrodynamic configurations, assuming that an equation of state has been specified, the user must also +supply the values of hydrodynamic variables at all grid locations, in particular the primitive variables +$\rho$, $v_i$ and the energy variable $\epsilon$ for all cases where we don't have a polytype EOS in the +form $P=P(\rho)$ (see Sec.~\ref{???} for a discussion of the use of EOS in the ET). For an MHD configuration, +one must supply all of these along with the initial magnetic field $B^i$ as well. + +The initial data routines currently implemented include the following: +\begin{itemize} +\item Vacuum spacetime tests: +\begin{enumerate} +\item {\tt IDConstraintViolate}: A vacuum spacetime in which the diagonal terms in the spatial metric are +modified by a spatial deformation to explicitly violate the Hamiltonian constraint. +\item {\tt Exact}: A set of exact spacetimes in various coordinates, along with tools to Lorentz boost +those configurations. +\end{enumerate} +\item Vacuum gravitational wave configurations: +\begin{enumerate} +\item {\tt IDBrillData}: A Brill wave spacetime \cite{Brill:1959}. +\item {\tt IDLinearWaves}: A spacetime containing a linear gravitational wave. +\end{enumerate} +\item Black Hole configurations: +\begin{enumerate} +\item {\tt IDAnalyticBH}: This thorn can generate Schwarzchild black holes, as well as the Misner solution +for multiple BHs and the brill-Lindquist binary BH solution. +\item {\tt IDAxibrillBH,~IDAxiOddBrillBH}: These thorns generate single black holes deformed by even and +odd parity axisymmetric perturbations, respectively. +\item {\tt DistortedBHIVP,~RotatingDBHIVP}: These thorns generate single black holes distorted by even +and odd-parity non-axisymmetric perturbation, respectivey. +\item {\tt TwoPunctures}: This thorn generates accurate binary black-hole initial data. +\end{enumerate} +\end{itemize} + + \paragraph{Gravitational Waves} \paragraph{Black Holes} @@ -424,7 +485,7 @@ \todo{2 pages in total, 1 plot per paragraph, Frank coordinates} \paragraph{Kerr-Schild} -\todo{1/2 page, who?} +\todo{1/2 page, Bruno} Show stable Kerr-evolution. What is commonly shown for this nowadays, the spectrum of the ringdown of a perturbation?

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[svn:einsteintoolkit] manifest/trunk/ (Rev. 67)
by bcmsma＠astro.rit.edu 24 Jan '11

24 Jan '11

User: bmundim Date: 2011/01/24 11:08 AM Modified: /trunk/ einsteintoolkit.bib Log: Add GSL reference. File Changes: Directory: /trunk/ ================== File [modified]: einsteintoolkit.bib Delta lines: +11 -0 =================================================================== --- trunk/einsteintoolkit.bib 2011-01-22 21:45:35 UTC (rev 66) +++ trunk/einsteintoolkit.bib 2011-01-24 17:08:52 UTC (rev 67) @@ -431,6 +431,17 @@ ##F ############################################################################ ##G ############################################################################ + +@Book{Galassi:2009, + author = {M. Galassi and J. Davies and J. Theiler and B. Gough + and G. Jungman and P. Alken and M. Booth and F. Rossi}, + title = {{GNU} Scientific Library Reference Manual}, + publisher = {Network Theory Ltd.}, + year = 2009, + edition = {3rd edition}, + isbn = {0-9546120-7-8}, +} + @Article{Giacomazzo:2007ti, suggested-for ="EinsteinEvolve/GRHydro", author = "Giacomazzo, Bruno and Rezzolla, Luciano",

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 11)
by ian.hinder＠aei.mpg.de 24 Jan '11

24 Jan '11

User: hinder Date: 2011/01/24 11:06 AM Modified: / ET.tex Log: Add initial draft of Kranc section; no citations yet File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +34 -0 =================================================================== --- ET.tex 2011-01-24 15:47:29 UTC (rev 10) +++ ET.tex 2011-01-24 17:06:57 UTC (rev 11) @@ -308,7 +308,41 @@ \subsection{Kranc} \todo{1/3 page Ian} +Kranc is a Mathematica application which converts a high-level +continuum description of a PDE into a highly optimised module for +Cactus, suitable for running on anything from a laptop to the world's +largest HPC systems. Such codes contain a large amount of complexity, +including expanded tensorial expressions, numerical methods, and the +large amount of ``glue'' code needed for interfacing a modern HPC +application with the underlying framework. Kranc absorbs this +complexity and allows a physicist to concentrate on writing only the +Kranc script which describes the continuum equations. +This approach brings with it many advantages. With these complicated +elements factored out, a physicist can write many different Kranc +codes, all taking advantage of the features of Kranc and avoid +unnecessary or trivial but painstaking duplication. The codes might +be variations on a theme, for example versions which use different +sets of variables or formulations of the equations, or they could +represent completely different physical systems. The use of a +symbolic algebra package, Mathematica, enables high-level +optimisations to be implemented in Kranc which are not performed by +the compiler. + +Any enhancements to Kranc can be automatically applied to all codes +which are generated using Kranc. Existing codes have easily benefited +from the following features added to Kranc after the codes themselves +were written: (i) OpenMP parallelisation support, necessary for +efficient use of modern multi-core processors; (ii) support for +multipatch domains with the Llama code; (iii) automatic generation of +vectorised code, where the equations are evaluated simultaneously by +the processor for two grid points at the same time, (iv) common +subexpression elimination, and various other optimisation strategies. + +Within the Einstein Toolkit, the Einstein evolution thorn McLachlan, +as well as the wave extraction thorn WeylScal4, are both generated +using Kranc, and hence support all the above features. + \section{Components} \subsection{Base Modules}

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[svn:einsteintoolkit] www/info/support/ (Rev. 456)
by knarf＠cct.lsu.edu 24 Jan '11

24 Jan '11

User: knarf Date: 2011/01/24 10:20 AM Modified: /info/support/ index.php Log: correct EVO meeting url File Changes: Directory: /info/support/ ========================= File [modified]: index.php Delta lines: +1 -1 =================================================================== --- info/support/index.php 2011-01-24 16:16:23 UTC (rev 455) +++ info/support/index.php 2011-01-24 16:20:33 UTC (rev 456) @@ -66,7 +66,7 @@ While the main sound channel will be the regular conference phone line, <a href="http://evo.caltech.edu/">EVO</a> might be used if it is useful to share additional material, e.g. slides/video/screen sharing during a presentation. -The title of the EVO meeting is <a href="http://evo.caltech.edu/evoNext/koala.jnlp?meeting=eneueMv8v2aia9a2In"><i>Einstein Toolkit weekly</i></a>. +The title of the EVO meeting is <a href="http://evo.caltech.edu/evoNext/koala.jnlp?meeting=eIe9esvvv8anaiatII"><i>Einstein Toolkit weekly</i></a>. </p> <h4>Phone call minutes</h4>

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[svn:einsteintoolkit] www/info/documentation/ (Rev. 455)
by schnetter＠cct.lsu.edu 24 Jan '11

24 Jan '11

User: eschnett Date: 2011/01/24 10:16 AM Modified: /info/documentation/ index.php Log: Correct pointer to wiki File Changes: Directory: /info/documentation/ =============================== File [modified]: index.php Delta lines: +1 -1 =================================================================== --- info/documentation/index.php 2010-12-16 19:01:40 UTC (rev 454) +++ info/documentation/index.php 2011-01-24 16:16:23 UTC (rev 455) @@ -26,7 +26,7 @@ </ul> </ul> -<p>Please see the <a href="http://docs.einsteintoolkit.org">Einstein Toolkit Wiki</a> for more documentation:</p> +<p>Please see the <a href="http://docs.einsteintoolkit.org/et-docs/">Einstein Toolkit Wiki</a> for more documentation:</p> <ul>

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Commits January 2011