User: knarf Date: 2011/11/06 12:33 AM

Modified: / ET.tex

Log: make sure lines are not broken before citations

File Changes:

Directory: / ============

File [modified]: ET.tex Delta lines: +57 -58 =================================================================== --- ET.tex 2011-11-06 05:30:41 UTC (rev 162) +++ ET.tex 2011-11-06 05:33:06 UTC (rev 163) @@ -122,13 +122,13 @@ in the study of astrophysical systems containing black holes (BHs) and neutron stars (NSs). While the first fully general relativistic (GR) simulations of merging NS-NS binaries were reported in 1999, with further -advances for the next few years \cite{Shibata:1999wm,Shibata:2002jb, +advances for the next few years~\cite{Shibata:1999wm,Shibata:2002jb, Shibata:2003ga,Shibata:2005ss,Shibata:2006nm}, systems containing BHs proved much more numerically intractable until 2005. That year, computational breakthroughs were made in using a generalized harmonic gauge (GHG) \cite{Pretorius:2005gq} and then a ``moving puncture'' approach \cite{Campanelli:2005dd, Baker:2005vv} in the BSSN -(Baumgarte-Shapiro-Shibata-Nakamura) formalism \cite{Shibata:1995we,Baumgarte:1998te} +(Baumgarte-Shapiro-Shibata-Nakamura) formalism~\cite{Shibata:1995we,Baumgarte:1998te} that allowed for the first stable long-term evolutions of moving single and multiple BH systems. These results quickly transformed the field with the ability to effectively evolve the Einstein field equations @@ -147,7 +147,7 @@ Ajith:2007kx} and references therein), comparisons between numerical waveforms~\cite{Baker:2006yw,Baker:2007fb}, determination of the spin of -the remnant BH formed in BH-BH mergers~(e.g, \cite{Campanelli:2006uy, +the remnant BH formed in BH-BH mergers~(e.g,~\cite{Campanelli:2006uy, Campanelli:2006fg,Campanelli:2006fy, Herrmann:2007ex,Rezzolla:2007rz,Berti:2007nw} and references therein), and studies of eccentric BH-BH binaries @@ -159,25 +159,25 @@ settings since the mid-1990s, focusing on BH accretion processes and relativistic jet production and evolution (see, e.g.,~\cite{Font:2008aa} for a review of the numerical formalism, -and \cite{Hawley2009apss} for a review of work on disk and jet models). +and~\cite{Hawley2009apss} for a review of work on disk and jet models). GRMHD coupled with curvature evolution, on the other hand, which is crucial for modeling large-scale bulk dynamics in compact binary or single-star collapse scenarios, has started to produce astrophysically interesting results only in the past $\sim 3-5$ years, enabled primarily by the availability of the long-term stable curvature evolution systems discussed above as well as improved GRMHD -algorithms~(see \cite{Font:2008aa} for a review). +algorithms~(see~\cite{Font:2008aa} for a review). In addition to these developments, substantial progress has been made in using physically motivated equations of state (EOS), -including tabulated versions (e.g., \cite{Pandharipande:1989hn, +including tabulated versions (e.g.,~\cite{Pandharipande:1989hn, Douchin:2001sv,Akmal:1998cf}) and temperature-dependent models -(e.g., \cite{Shen:1998by,Shen:1998gq,Lattimer:1991nc}). Some codes also +(e.g.,~\cite{Shen:1998by,Shen:1998gq,Lattimer:1991nc}). Some codes also incorporate microphysical effects, such as neutrino cooling \cite{Sekiguchi:2011zd}.

Many of the successful techniques used to evolve BH-BH binaries have proven to be equally applicable to merging -NS-NS and BH-NS binaries (see, e.g., \cite{Faber:2009zz,Duez:2009yz} for reviews), allowing for further investigations into the former +NS-NS and BH-NS binaries (see, e.g.,~\cite{Faber:2009zz,Duez:2009yz} for reviews), allowing for further investigations into the former and the first full GR simulations of the latter. All recent results use either the GHG formalism (Caltech/Cornell, LSU/BYU/LIU, and Princeton) or BSSN ``moving puncture'' gauge (or variants thereof; AEI/Sissa, Illinois, @@ -185,27 +185,27 @@ refinement, since unigrid models cannot produce accurate long-term evolutions without requiring exorbitant computational resources. Many groups' codes now include GRMHD (used widely for NS-NS mergers, and for BH-NS mergers -in \cite{Chawla:2010sw}, and some include microphysical effects as well. +in~\cite{Chawla:2010sw}, and some include microphysical effects as well. The groups that have reported simulations of NS-NS or BH-NS mergers include: \begin{description} -\item[AEI/Sissa]: BH-NS mergers using GRHD \cite{Loffler:2006nu} and NS-NS -mergers using GRHD \cite{Baiotti:2008ra,Baiotti:2009gk,Baiotti:2010xh, -Baiotti:2011am,Rezzolla:2010fd} and GRMHD \cite{Giacomazzo:2009mp, +\item[AEI/Sissa]: BH-NS mergers using GRHD~\cite{Loffler:2006nu} and NS-NS +mergers using GRHD~\cite{Baiotti:2008ra,Baiotti:2009gk,Baiotti:2010xh, +Baiotti:2011am,Rezzolla:2010fd} and GRMHD~\cite{Giacomazzo:2009mp, Giacomazzo:2010bx,Rezzolla:2011da}. \item[Caltech/Cornell]: A {\em pseudospectral}, GRHD code has been used -to simulate BH-NS mergers \cite{Duez:2008rb,Duez:2009yy,Foucart:2010eq}. -\item[Illinois]: BH-NS mergers using GRHD \cite{Etienne:2007jg,Etienne:2008re} -and NS-NS mergers using GRMHD \cite{Liu:2008xy}. -\item[Jena]: NS-NS mergers using GRHD \cite{Thierfelder:2011yi}. -\item[LSU/BYU/LIU]: BH-NS mergers using GRMHD \cite{Chawla:2010sw} and -NS-NS mergers using GRHD \cite{Anderson:2007kz} -and GRMHD \cite{Anderson:2008zp}. -\item[Princeton]: BH-NS mergers using GRHD \cite{Stephens:2011as}. -\item[Tokyo/Kyoto]: BH-NS mergers using GRHD \cite{Shibata:2006bs, +to simulate BH-NS mergers~\cite{Duez:2008rb,Duez:2009yy,Foucart:2010eq}. +\item[Illinois]: BH-NS mergers using GRHD~\cite{Etienne:2007jg,Etienne:2008re} +and NS-NS mergers using GRMHD~\cite{Liu:2008xy}. +\item[Jena]: NS-NS mergers using GRHD~\cite{Thierfelder:2011yi}. +\item[LSU/BYU/LIU]: BH-NS mergers using GRMHD~\cite{Chawla:2010sw} and +NS-NS mergers using GRHD~\cite{Anderson:2007kz} +and GRMHD~\cite{Anderson:2008zp}. +\item[Princeton]: BH-NS mergers using GRHD~\cite{Stephens:2011as}. +\item[Tokyo/Kyoto]: BH-NS mergers using GRHD~\cite{Shibata:2006bs, Shibata:2006ks,Shibata:2007zm,Yamamoto:2008js,Shibata:2009cn, Kyutoku:2010zd,Shibata:2010zz} and NS-NS mergers using GRHD \cite{Yamamoto:2008js,Kiuchi:2009jt, Kiuchi:2010ze,Hotokezaka:2011dh}, -most recently with the inclusion of neutrino cooling \cite{Sekiguchi:2011zd}. +most recently with the inclusion of neutrino cooling~\cite{Sekiguchi:2011zd}. \todo{Check for updates to list before submission!} \end{description}

@@ -214,10 +214,10 @@ in NSs. GRHD has been used to study, among many other applications, massive stars collapsing to protoneutron stars \cite{Ott:2006eu,Ott:2006eh,Shibata:2004kb}, the collapse of rotating, -hypermassive NSs to BHs in 2D and 3D (see, e.g., \cite{Shibata:2006hr, +hypermassive NSs to BHs in 2D and 3D (see, e.g.,~\cite{Shibata:2006hr, Shibata:1999yx,Duez:2005sf,Duez:2005cj,Baiotti:2004wn,Baiotti:2005vi, Baiotti:2006wn}), and non-axisymmetric instabilities in -rapidly rotating polytropic NS models \cite{Shibata:1999yx,Baiotti:2006wn, +rapidly rotating polytropic NS models~\cite{Shibata:1999yx,Baiotti:2006wn, Manca:2007ca}.

In parallel to the advances in both our physical understanding of @@ -226,22 +226,22 @@ aim of providing a computational core that can enable the new science, broaden the community, facilitate interdisciplinary research and take advantage of emerging petascale computers and advanced cyberinfrastructure: -the {\tt Cactus} computational toolkit \cite{Cactuscode:web}. While it was +the {\tt Cactus} computational toolkit~\cite{Cactuscode:web}. While it was developed in large part by computer scientists, its development was driven by the direct input from other fields, especially numerical relativity, succeeding in applying expertise in computer science directly to problems in numerical relativity.

This success prompted usage of the {\tt Cactus} computational toolkit in other -areas, such as ocean forecast models \cite{Djikstra2005} and chemical reaction -simulations \cite{Camarda2001}. At the same time, the growing +areas, such as ocean forecast models~\cite{Djikstra2005} and chemical reaction +simulations~\cite{Camarda2001}. At the same time, the growing number of results in numerical relativity increased the need for commonly available utilities such as comparison and analysis tools, typically those specifically designed for astrophysical problems. Including them within the {\tt Cactus} computational toolkit was not felt to fit within its rapidly expanding scope. This triggered -the creation of the Einstein Toolkit \cite{EinsteinToolkit:web}. While large +the creation of the Einstein Toolkit~\cite{EinsteinToolkit:web}. While large parts of the Einstein toolkit presently do make use of the {\tt Cactus} toolkit, this is not an requirement at all, and other contributions are welcome and have been accepted. @@ -281,9 +281,8 @@

\item {\bf Equation of state (EOS), microphysics, and radiation transport}. Most presently published 3D GR(M)HD simulations, with the - exceptions of recent work on massive star collapse - \cite{???}\todo{Citation?} and binary mergers - (see, e.g., \cite{Sekiguchi:2011zd}), + exceptions of recent work on massive star collapse~\cite{???}\todo{Citation?} and binary mergers + (see, e.g.,~\cite{Sekiguchi:2011zd}), relied on a simple zero-temperature descriptions of NS stellar structure, with many assuming simple polytropic forms. Such EOSs are computationally @@ -299,7 +298,7 @@ the cooling of NS-NS merger remnants and must not be left out when attempting to accurately model such events. Only few studies have incorporated neutrino and/or photon transport and interactions in - approximate ways (see, e.g., \cite{Ott:2006eu,Farris:2008fe,Sekiguchi:2011zd}) \todo{Cite more}. + approximate ways (see, e.g.,~\cite{Ott:2006eu,Farris:2008fe,Sekiguchi:2011zd}) \todo{Cite more}.

\item {\bf High-order schemes and AMR@}. Numerical accuracy is a central issue in long-term GR(M)HD simulations and must be addressed @@ -307,7 +306,7 @@ grid points on regions where finer resolution is needed, and (2) high-order numerical techniques.

-Several AMR codes, including the {\tt Carpet} driver \cite{CarpetCode:web} +Several AMR codes, including the {\tt Carpet} driver~\cite{CarpetCode:web} included in the Einstein Toolkit, are publicly available. An important task going forward is to facilitate the coupling of existing and future GRMHD codes @@ -462,8 +461,8 @@ The Einstein Toolkit offers two drivers, \codename{PUGH} and {\tt Carpet}. \codename{PUGH} provides domains consisting of a uniform grid with Cartesian topology, and is highly scalable (up to more than -130,000 cores on a Blue Gene/P \cite{Cactuscode:BlueGene:web}.) -{\tt Carpet} \cite{Schnetter:2003rb, Schnetter:2006pg, +130,000 cores on a Blue Gene/P~\cite{Cactuscode:BlueGene:web}.) +{\tt Carpet}~\cite{Schnetter:2003rb, Schnetter:2006pg, CarpetCode:web} provides multi-block methods and adaptive mesh refinement (AMR@). Multi-block methods cover the domain with a set of (possibly distorted) blocks that exchange boundary information via techniques such as @@ -471,7 +470,7 @@ methods are supported by {\tt Carpet}, the Einstein Toolkit itself does not yet contain any multi-block coordinate systems.} The AMR capabilities -employ the standard Berger-Oliger algorithm \cite{Berger:1984zza} with +employ the standard Berger-Oliger algorithm~\cite{Berger:1984zza} with subcycling in time.

AMR implies that resolution in the simulation @@ -497,7 +496,7 @@ interpolation operations are implemented efficiently in {\tt Carpet}, and are applied automatically as specified in the execution schedule, i.e.\ without requiring function calls in user code. -Figure \ref{fig:carpet-details} describes some details of the +Figure~\ref{fig:carpet-details} describes some details of the Berger-Oliger time stepping algorithm. More details are described in \cite{Schnetter:2003rb}.

@@ -540,7 +539,7 @@ simulations lies in menial tasks that require no physical or numerical insight.

-The Simulation Factory \cite{Thomas:2010aa, SimFactory:web} offers a +The Simulation Factory~\cite{Thomas:2010aa, SimFactory:web} offers a set of abstractions for the tasks necessary to set up and successfully finish numerical simulations based on the {\tt Cactus} framework. These abstractions hide tedious low-level management operations, they @@ -551,7 +550,7 @@ supercomputers to be used in a uniform manner.

Using the Simulation Factory, we are able to offer a -tutorial for the Einstein Toolkit \cite{EinsteinToolkit:web} that lets +tutorial for the Einstein Toolkit~\cite{EinsteinToolkit:web} that lets new users download, configure, build, and run full simulations of the coupled Einstein/relativistic hydrodynamics equations on a supercomputer with a few simple commands. Users need no prior @@ -932,10 +931,10 @@ A substantial fraction of the published work on the components of the Einstein toolkit involves the evolution of BH-BH binary systems. The most widely used routine to generate initial data for these is the -\codename{TwoPunctures} code, described originally in \cite{Ansorg:2004ds}, which solves -the binary puncture equations for a pair of BHs \cite{Brandt:1997tf}. +\codename{TwoPunctures} code, described originally in~\cite{Ansorg:2004ds}, which solves +the binary puncture equations for a pair of BHs~\cite{Brandt:1997tf}. To do so, one assumes the extrinsic curvature for each BH corresponds to -the Bowen-York form \cite{Bowen:1980yu}, +the Bowen-York form~\cite{Bowen:1980yu}, \begin{eqnarray} K_{(n)}^{ij}&=&\frac{3}{2r^2}(P^in^j+P^jn^i-(\gamma^{ij}-n^in^jP^kn_k))\nonumber\ &&+\frac{3}{r^3}(\varepsilon^{ikl}S_kn_ln^j+\varepsilon^{jkl}S_kn_ln^i) @@ -989,7 +988,7 @@ \subsubsection{Lorene-based binary data}

The ET contains three routines that can read in publicly available data generated -by the {\tt Lorene} code \cite{Lorene:web,Gourgoulhon:2000nn}, though it does not +by the {\tt Lorene} code~\cite{Lorene:web,Gourgoulhon:2000nn}, though it does not currently include the capability of generating such data from scratch. For a number of reasons, such functionality is not truly required; in particular, {\tt Lorene} is a serial code and there is no time-savings at all to call it as @@ -1027,9 +1026,9 @@ \end{figure}

\codename{Meudon_Bin_BH} can read in BH-BH binary initial data described -in \cite{Grandclement:2001ed}, while \codename{Meudon_Bin_NS} -handles binary NS data from \cite{Gourgoulhon:2000nn}. \codename{Meudon_Mag_NS} -may be used to read in magnetized isolated NS data \cite{Lorene:web}. +in~\cite{Grandclement:2001ed}, while \codename{Meudon_Bin_NS} +handles binary NS data from~\cite{Gourgoulhon:2000nn}. \codename{Meudon_Mag_NS} +may be used to read in magnetized isolated NS data~\cite{Lorene:web}.

\subsubsection{TOVSolver} \label{sec:TOVSolver} @@ -1197,7 +1196,7 @@ \ K_0(x^\mu) & := & 0 \end{eqnarray} -and $\Gamma$-driver shift condition \cite{Alcubierre:2002kk}: +and $\Gamma$-driver shift condition~\cite{Alcubierre:2002kk}: \begin{eqnarray} G(\alpha,\phi,x^\mu) & := & (3/4), \alpha^{-2} \ @@ -1217,7 +1216,7 @@ $\beta^i$ and thus that of the spatial coordinates $x^i$ will be exponentially damped. This damping time scale is set by the gauge parameter $\eta$ (see Eq.~\ref{eq:eta}) which has dimension $1/T$ (inverse time). -As described, e.g., in \cite{Muller:2009jx, Schnetter:2010cz}, this +As described, e.g., in~\cite{Muller:2009jx, Schnetter:2010cz}, this time scale may need to be adapted in different regions of the domain to avoid spurious high-frequency behavior in regions that otherwise evolve only very slowly, e.g., far away from the source. @@ -1270,7 +1269,7 @@

During time evolution, a Sommerfeld-type radiative boundary condition is applied to all components of the evolved BSSN variables as -described in \cite{Alcubierre:2000xu}. The main feature of this boundary +described in~\cite{Alcubierre:2000xu}. The main feature of this boundary condition is that it assumes approximate spherical symmetry of the solution, while applying the actual boundary condition on the boundary of a cubic grid where the face normals are not aligned with the radial @@ -1328,7 +1327,7 @@ this boundary condition leads to stable evolutions if applied sufficiently far from the source. Errors introduced at the boundary (both errors in the geometry and constraint violations) propagate -inwards with the speed of light \cite{Brown:2008sb}. Gauge changes +inwards with the speed of light~\cite{Brown:2008sb}. Gauge changes introduced by the boundary condition, which are physically not observable, propagate faster, with a speed up to $\sqrt{2}$ for the gauge conditions used in \codename{McLachlan}. @@ -1348,7 +1347,7 @@

The primary hydrodynamics evolution routine in the Einstein Toolkit is \codename{GRHydro}, a code derived from the public \codename{Whisky} -code \cite{Baiotti:2004wn,Hawke:2005zw,Baiotti:2010zf,Whisky:web} +code~\cite{Baiotti:2004wn,Hawke:2005zw,Baiotti:2010zf,Whisky:web} designed primarily by researchers at AEI and their collaborators. It includes a high resolution shock capturing (HRSC) scheme to evolve hydrodynamic quantities, with several different reconstruction methods @@ -1400,7 +1399,7 @@

We choose a definition of the 3-velocity that corresponds to the velocity seen by an Eulerian observer at rest in the current spatial -3-hypersurface \cite{}, +3-hypersurface~\cite{}, \begin{equation} v^i = \frac{u^i}{W} + \frac{\beta^i}{\alpha},,, \label{eq:vel} @@ -1480,7 +1479,7 @@ different forms of the slope limiter available. In practice, all try to accomplish the same task of preserving monotonicity and removing the possibility of spuriously creating local extrema. Implemented methods -include minmod, superbee \cite{Roe:1986cb}, and monotonized central \cite{vanLeer:1977aa}. +include minmod, superbee~\cite{Roe:1986cb}, and monotonized central~\cite{vanLeer:1977aa}.

The piecewise parabolic method (PPM) is a multi-step method based around a quadratic fit to nearby points interpolated to cell faces @@ -1513,7 +1512,7 @@ in question in space and time.

The simplest method implemented is the Harten-Lax-van Leer-Einfeldt -solver \cite{Harten:1983on,Einfeldt:1988og} (HLL or HLLE, depending on the reference), +solver~\cite{Harten:1983on,Einfeldt:1988og} (HLL or HLLE, depending on the reference), which uses a two wave approximation to calculate the evolution along the shock front. With $\xi_-$ and $\xi_+$ the most negative and most positive wave speeds present on either side of the interface, @@ -1546,7 +1545,7 @@ \end{equation} It is these flux terms that are then used to evolve the hydrodynamic quantities.

-The Roe solver \cite{Roe:1981ar} involves linearizing the evolution system +The Roe solver~\cite{Roe:1981ar} involves linearizing the evolution system for the hydrodynamic evolution. Eq.~\ref{eq:Riemann}, defining the Jacobian matrix $A\equiv \frac{\partial f}{\partial q}$, and working out the eigenvalues $\lambda^i$ and left and right eigenvectors, @@ -1572,7 +1571,7 @@

\subsubsection{Conservative to primitive conversion}

-In order to invert Eqs.~\ref{eq:p2c1} -- \ref{eq:p2c3}, solving for +In order to invert Eqs.~\ref{eq:p2c1}~--~\ref{eq:p2c3}, solving for the primitive variables based on the values of the conservative ones, \codename{GRHydro} uses a 1-dimensional Newton-Raphson approach that solves for a consistent value of the pressure. Defining the (known) @@ -1656,7 +1655,7 @@ is encapsulated in the constant adiabatic index $\Gamma$. This EOS has been used extensively in simulations of NS-NS and BH-NS mergers.

-The hybrid EOS, first introduced by \cite{Janka:1993da}, is a 2-piece +The hybrid EOS, first introduced by~\cite{Janka:1993da}, is a 2-piece piecewise polytropic with a thermal component designed for the application in simple models of stellar collapse. At densities below nuclear, a polytropic EOS with $\Gamma = \Gamma_1 \approx 4/3$ is @@ -1878,7 +1877,7 @@ years~\cite{Szabados:2004ql}. Even though only a few rigorous proofs exist that establish the properties of these latter quantities, they have been demonstrated to be surprisingly helpful in numerical simulations -(see, e.g., \cite{Lovelace:2009dg}), and are therefore +(see, e.g.,~\cite{Lovelace:2009dg}), and are therefore an indispensable tool in numerical relativity. \codename{QuasiLocalMeasures} takes as input a horizon surface, or any other surface that the user specifies, like a large coordinate