[cig-commits] r16920 - in seismo/3D/SPECFEM3D/trunk/USER_MANUAL: . figures

dkomati1 at geodynamics.org dkomati1 at geodynamics.org
Mon Jun 7 15:40:17 PDT 2010


Author: dkomati1
Date: 2010-06-07 15:40:16 -0700 (Mon, 07 Jun 2010)
New Revision: 16920

Modified:
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/bibliography.bib
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/gauss_vs_triangle_mod.pdf
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/source_timing.pdf
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/specfem_3d-cover.pdf
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/specfem_3d-cover.psd
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.pdf
   seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex
Log:
converted the manual from SPECFEM3D_SESAME back to SPECFEM3D.


Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/bibliography.bib
===================================================================
--- seismo/3D/SPECFEM3D/trunk/USER_MANUAL/bibliography.bib	2010-06-07 22:24:09 UTC (rev 16919)
+++ seismo/3D/SPECFEM3D/trunk/USER_MANUAL/bibliography.bib	2010-06-07 22:40:16 UTC (rev 16920)
@@ -147,15 +147,16 @@
   address = {Amsterdam, The Netherlands}
 }
 
- at ARTICLE{AdPaBo07,
+ at INPROCEEDINGS{AdPaBo07,
   author = {S. Adams and J. Payne and R. Boppana},
   title = {Finite Difference Time Domain ({FDTD}) Simulations Using Graphics
 	Processors},
-  journal = {Proceedings of the Department of Defense High Performance Computing
+  booktitle = {Proceedings of the Department of Defense High Performance Computing
 	Modernization Program Users Group Conference},
   year = {2007},
   pages = {334-338},
   address = {Pittsburgh, Pennsylvania, USA},
+  publisher = {IEEE Computer Society, Washington, DC, USA},
   doi = {10.1109/HPCMP-UGC.2007.34}
 }
 
@@ -805,18 +806,22 @@
 	and Information Technology},
   year = {2008},
   pages = {291-294},
+  address = {Sydney, Australia},
+  publisher = {IEEE Computer Society, Washington, DC, USA},
   doi = {10.1109/CIT.2008.4594689}
 }
 
- at ARTICLE{BaRoTaPaGoSi08,
+ at INPROCEEDINGS{BaRoTaPaGoSi08,
   author = {A. Balevic and L. Rockstroh and A. Tausendfreund and S. Patzelt and
 	G. Goch and S. Simon},
   title = {Accelerating Simulations of Light Scattering Based on a Finite-Difference
 	Time-Domain Method with General Purpose {GPU}s},
-  journal = {Proceedings of the 11th IEEE International Conference on Computational
+  booktitle = {Proceedings of the 11th IEEE International Conference on Computational
 	Science and Engineering},
   year = {2008},
-  pages = {327-334}
+  pages = {327-334},
+  address = {Sao Paulo, Brazil},
+  publisher = {IEEE Computer Society, Washington, DC, USA}
 }
 
 @ARTICLE{BaEnHaJo88,
@@ -989,16 +994,18 @@
   pages = {1083-1096}
 }
 
- at ARTICLE{BaSaFiRo05,
+ at INPROCEEDINGS{BaSaFiRo05,
   author = {Baron, G. S. and Sarris, C. D. and Fiume, E. and Rogers Sr., Edward
 	S.},
   title = {Fast and accurate time-domain simulations with commodity graphics
 	hardware},
-  journal = {Proceedings of the 2005 IEEE Antennas and Propagation Society International
+  booktitle = {Proceedings of the 2005 IEEE Antennas and Propagation Society International
 	Symposium},
   year = {2005},
   volume = {4A},
   pages = {193-196},
+  address = {Seoul, Korea},
+  publisher = {IEEE Computer Society, Washington, DC, USA},
   doi = {10.1109/APS.2005.1552619}
 }
 
@@ -1871,16 +1878,6 @@
   number = {2}
 }
 
- at ARTICLE{DaEkDz08,
-  author = {C. A. Dalton and G. Ekstr\"{o}m and A. M. Dziewo\'nski},
-  title = {The global attenuation structure of the upper mantle},
-  journal = jgr,
-  year = {2008},
-  volume = {113},
-  pages = {B05317},
-  doi = {10.1029/2006JB004394}
-}
-
 @BOOK{Cag39,
   title = {R\'eflexion et R\'efraction des Ondes Sismiques Progressives},
   publisher = {Gauthiers-Villars},
@@ -2309,6 +2306,18 @@
   address = {Cambridge, UK}
 }
 
+ at ARTICLE{CeNuMa10,
+  author = {Ali Cevahir and Akira Nukada and Satoshi Matsuoka},
+  title = {High performance conjugate gradient solver on multi-{GPU} clusters
+	using hypergraph partitioning},
+  journal = {Computer Science Research and Development},
+  year = {2010},
+  volume = {25},
+  pages = {83-91},
+  number = {1-2},
+  doi = {10.1007/s00450-010-0112-6}
+}
+
 @ARTICLE{ChSaHa96,
   author = {F. J. Ch\'avez-Garc\'{\i}a and L. S\'anchez and D. Hatzfeld},
   title = {Topographic site effects and HVSR. A comparison between observation
@@ -2452,7 +2461,7 @@
 	Yann Capdeville and Bernard Valette and Gaetano Festa},
   title = {Spectral Element Analysis in Seismology},
   booktitle = {Advances in wave propagation in heterogeneous media},
-  publisher = {Elsevier - Academic Press},
+  publisher = {Elsevier - Academic Press, London, UK},
   year = {2007},
   editor = {Ru-Shan Wu and Val\'erie Maupin},
   volume = {48},
@@ -2719,10 +2728,11 @@
 }
 
 @BOOK{CoKaSh00,
-  title = {Discontinuous {G}alerkin Methods: Theory, Compuration and Applications},
+  title = {Discontinuous {G}alerkin Methods: Theory, Computation and Applications},
   publisher = {Springer},
   year = {2000},
-  author = {Bernardo Cockburn and George E. Karniadakis and Chi-Wang Shu}
+  author = {Bernardo Cockburn and George E. Karniadakis and Chi-Wang Shu},
+  address = {Heidelberg, Germany}
 }
 
 @BOOK{Aco92,
@@ -3094,6 +3104,16 @@
   pages = {327-340}
 }
 
+ at ARTICLE{DaEkDz08,
+  author = {C. A. Dalton and G. Ekstr\"{o}m and A. M. Dziewo\'nski},
+  title = {The global attenuation structure of the upper mantle},
+  journal = jgr,
+  year = {2008},
+  volume = {113},
+  pages = {B05317},
+  doi = {10.1029/2006JB004394}
+}
+
 @ARTICLE{ED99,
   author = {E. Danicki},
   title = {Resonant phenomena in bulk-wave scattering by in-plane periodic cracks},
@@ -3257,11 +3277,14 @@
 
 @ARTICLE{DeSe10,
   author = {Jon{\'a}s D. {De Basabe} and Mrinal K. Sen},
-  title = {Stability of the High-Order Finite Elements for Acoustic or Elastic
-	Wave Propagation with High-Order Time Stepping},
+  title = {Stability of the high-order finite elements for acoustic or elastic
+	wave propagation with high-order time stepping},
   journal = gji,
   year = {2010},
-  note = {, in press.}
+  volume = {181},
+  pages = {577-590},
+  number = {1},
+  doi = {10.1111/j.1365-246X.2010.04536.x}
 }
 
 @ARTICLE{DeSe07,
@@ -3545,6 +3568,17 @@
   doi = {10.1016/j.wavemoti.2007.03.003}
 }
 
+ at ARTICLE{Dro93,
+  author = {Jean-Jacques Droux},
+  title = {An algorithm to optimally color a mesh},
+  journal = cmame,
+  year = {1993},
+  volume = {104},
+  pages = {249-260},
+  number = {2},
+  doi = {10.1016/0045-7825(93)90199-8}
+}
+
 @ARTICLE{Dub93,
   author = {M. Dubiner},
   title = {Spectral methods on triangles and other domains},
@@ -3624,14 +3658,29 @@
   pages = {880-891}
 }
 
- at ARTICLE{DuJoGuKeKo09,
+ at ARTICLE{DuDeFoKoRo10,
+  author = {Fabrice Dupros and de Martin, Florent and Evelyne Foerster and Dimitri
+	Komatitsch and Jean Roman},
+  title = {High-performance finite-element simulations of seismic wave propagation
+	in three-dimensional non linear inelastic geological media},
+  journal = {Parallel Computing},
+  year = {2010},
+  volume = {36},
+  pages = {308-325},
+  number = {5-6},
+  doi = {10.1016/j.parco.2009.12.011}
+}
+
+ at ARTICLE{DuJoGuKeKo10,
   author = {Guilhem Dupuy and Bruno Jobard and Sebastien Guillon and Noomane
 	Keskes and Dimitri Komatitsch},
   title = {Parallel extraction and simplification of large isosurfaces using
 	an extended tandem algorithm},
   journal = {Computer-Aided Design},
-  year = {2009},
-  volume = {In Press, Corrected Proof},
+  year = {2010},
+  volume = {42},
+  pages = {129-138},
+  number = {2},
   doi = {10.1016/j.cad.2009.04.016}
 }
 
@@ -3752,7 +3801,7 @@
 @ARTICLE{ElLeDa08,
   author = {Erich Elsen and Patrick LeGresley and Eric Darve},
   title = {Large calculation of the flow over a hypersonic vehicle using a {GPU}},
-  journal = {Journal of Computational Physics},
+  journal = jcp,
   year = {2008},
   volume = {227},
   pages = {10148--10161},
@@ -3824,16 +3873,6 @@
   address = {Amsterdam}
 }
 
- at ARTICLE{EUCrust07,
-  author = {M. Tesauro and M. K. Kaban and S. A. P. L. Cloetingh},
-  title = {EuCrust-07: A new reference model for the {European} crust},
-  journal = grl,
-  year = {2008},
-  volume = {35},
-  pages = {L05313},
-  doi = {10.1029/2007GL032244}
-}
-
 @BOOK{Euv94,
   title = {R\'esolution num\'erique des \'equations aux d\'eriv\'ees partielles
 	- Diff\'erences finies, \'el\'ements finis, probl\`emes en domaine
@@ -3936,6 +3975,17 @@
   number = {4}
 }
 
+ at ARTICLE{FaRi99,
+  author = {Falk, Richard S. and Richter, Gerard R.},
+  title = {Explicit Finite Element Methods for Symmetric Hyperbolic Equations},
+  journal = {SIAM J. Numer. Anal.},
+  year = {1999},
+  volume = {36},
+  pages = {935-952},
+  number = {3},
+  doi = {10.1137/S0036142997329463}
+}
+
 @ARTICLE{FaLiHe02,
   author = {G. X. Fan and Q. H. Liu and J. S. Hesthaven},
   title = {Multidomain pseudospectral time-domain simulations of scattering
@@ -4714,7 +4764,9 @@
   journal = {IEEE Transactions on Antennas and Propagation},
   year = {2010},
   volume = {58},
-  number = {2}
+  pages = {838-847},
+  number = {3},
+  doi = {10.1109/TAP.2009.2037765}
 }
 
 @ARTICLE{GeOh94,
@@ -5103,6 +5155,18 @@
   pages = {283-300}
 }
 
+ at ARTICLE{GrZa10,
+  author = {Michael Griebel and Peter Zaspel},
+  title = {A multi-{GPU} accelerated solver for the three-dimensional two-phase
+	incompressible {N}avier-{S}tokes equations},
+  journal = {Computer Science Research and Development},
+  year = {2010},
+  volume = {25},
+  pages = {65-73},
+  number = {1-2},
+  doi = {10.1007/s00450-010-0111-7}
+}
+
 @ARTICLE{GrBo79,
   author = {D. W. Griffiths and G. A. Bollinger},
   title = {The effect of {A}ppalachian mountain topography on seismic waves},
@@ -5141,6 +5205,17 @@
   pages = {331-353}
 }
 
+ at ARTICLE{GrScSc06,
+  author = {Marcus J. Grote and Anna Schneebeli and Dominik Sch\"{o}tzau},
+  title = {Discontinuous {G}alerkin Finite Element Method for the Wave Equation},
+  journal = {SIAM Journal on Numerical Analysis},
+  year = {2006},
+  volume = {44},
+  pages = {2408-2431},
+  number = {6},
+  doi = {10.1137/05063194X}
+}
+
 @ARTICLE{GuLi06,
   author = {Murthy N. Guddati and Keng Wit Lim},
   title = {Continued fraction absorbing boundary conditions for convex polygonal
@@ -5751,6 +5826,18 @@
   doi = {10.1006/jcph.2001.6887}
 }
 
+ at ARTICLE{HuHuRa99,
+  author = {Hu, Fang Q. and Hussaini, M. Y. and Rasetarinera, Patrick},
+  title = {An analysis of the discontinuous {G}alerkin method for wave propagation
+	problems},
+  journal = jcp,
+  year = {1999},
+  volume = {151},
+  pages = {921-946},
+  number = {2},
+  doi = {10.1006/jcph.1999.6227}
+}
+
 @ARTICLE{Huang95,
   author = {J. Y. Huang},
   title = {Interaction of {$SH$} waves with a finite crack in half space},
@@ -6633,6 +6720,14 @@
   month = aug
 }
 
+ at BOOK{KiHw10,
+  title = {Programming Massively Parallel Processors: A Hands-on Approach},
+  publisher = {Morgan Kaufmann},
+  year = {2010},
+  author = {Kirk, David B. and Hwu, Wen-mei W.},
+  address = {Boston, Massachusetts, USA}
+}
+
 @INPROCEEDINGS{kiyashchenkoplessix2005,
   author = {D. A. Kiyashchenko and R. E. Plessix},
   title = {True amplitude multi-one-way migration: comparison of different imaging
@@ -6707,7 +6802,7 @@
   publisher = {North-Holland},
   year = {1987},
   author = {S. Kobayashi},
-  address = {Amsterdam}
+  address = {Amsterdam, The Netherlands}
 }
 
 @ARTICLE{KohnNir,
@@ -6809,9 +6904,22 @@
 	{MPI} on a large-scale {GPU} cluster},
   journal = jcp,
   year = {2010},
-  note = {Submitted.}
+  note = {In press.}
 }
 
+ at ARTICLE{KoGoErMi10,
+  author = {Dimitri Komatitsch and Dominik G\"oddeke and Gordon Erlebacher and
+	David Mich\'ea},
+  title = {Modeling the propagation of elastic waves using spectral elements
+	on a cluster of 192 {GPU}s},
+  journal = {Computer Science Research and Development},
+  year = {2010},
+  volume = {25},
+  pages = {75-82},
+  number = {1-2},
+  doi = {10.1007/s00450-010-0109-1}
+}
+
 @ARTICLE{KoLaMi08a,
   author = {Dimitri Komatitsch and Jes\'us Labarta and David Mich\'ea},
   title = {A simulation of seismic wave propagation at high resolution in the
@@ -8233,7 +8341,7 @@
 @ARTICLE{MaOl03,
   author = {Carey Marcinkovich and Kim Bak Olsen},
   title = {On the implementation of perfectly matched layers in a three-dimensional
-	fourth-order velocity-stress finite difference scheme},
+	fourth-order velocity-stress finite-difference scheme},
   journal = jgr,
   year = {2003},
   volume = {108},
@@ -8326,16 +8434,6 @@
   doi = {10.1190/1.2939484}
 }
 
- at ARTICLE{MaKoGeBr10,
-  author = {Roland Martin and Dimitri Komatitsch and Stephen Gedney and Emilien
-	Bruthiaux},
-  title = {A high-order time and space formulation of the unsplit perfectly
-	matched layer for the seismic wave equation},
-  journal = cmes,
-  year = {2010},
-  note = {Submitted.}
-}
-
 @ARTICLE{MaKoGe08,
   author = {Roland Martin and Dimitri Komatitsch and Stephen D. Gedney},
   title = {A variational formulation of a stabilized unsplit convolutional perfectly
@@ -8347,6 +8445,19 @@
   number = {3}
 }
 
+ at ARTICLE{MaKoGeBr10,
+  author = {Roland Martin and Dimitri Komatitsch and Stephen D. Gedney and Emilien
+	Bruthiaux},
+  title = {A high-order time and space formulation of the unsplit perfectly
+	matched layer for the seismic wave equation using {Auxiliary Differential
+	Equations (ADE-PML)}},
+  journal = cmes,
+  year = {2010},
+  volume = {56},
+  pages = {17-42},
+  number = {1}
+}
+
 @ARTICLE{MaPr07,
   author = {Y. J. Masson and S. R. Pride},
   title = {Poroelastic finite-difference modeling of seismic attenuation and
@@ -8601,21 +8712,24 @@
 @ARTICLE{MePa08,
   author = {Kristel C. Meza-Fajardo and Apostolos S. Papageorgiou},
   title = {A nonconvolutional, split-field, perfectly matched layer for wave
-	propagation in isotropic and anisotropic elastic media; stability
+	propagation in isotropic and anisotropic elastic media: Stability
 	analysis},
   journal = bssa,
   year = {2008},
   volume = {98},
   pages = {1811-1836},
-  number = {4}
+  number = {4},
+  doi = {10.1785/0120070223}
 }
 
 @ARTICLE{MiKo10,
   author = {David Mich\'{e}a and Dimitri Komatitsch},
-  title = {Accelerating a 3{D} finite-difference wave propagation code using graphics cards},
+  title = {Accelerating a 3{D} finite-difference wave propagation code using
+	graphics cards},
   journal = gji,
   year = {2010},
-  note = {in press.}
+  note = {in press.},
+  doi = {10.1111/j.1365-246X.2010.04616.x}
 }
 
 @INPROCEEDINGS{Mic09,
@@ -8699,7 +8813,8 @@
   journal = grl,
   year = {2005},
   volume = {32},
-  pages = {L01306}
+  pages = {L01306},
+  doi = {10.1029/2004GL021598}
 }
 
 @ARTICLE{MoKrBy01,
@@ -8730,7 +8845,7 @@
   title = {The Finite-difference Time-domain method for Modeling of Seismic
 	Wave Propagation},
   booktitle = {Advances in wave propagation in heterogeneous media},
-  publisher = {Elsevier - Academic Press},
+  publisher = {Elsevier - Academic Press, London, UK},
   year = {2007},
   editor = {Ru-Shan Wu and Val\'erie Maupin},
   volume = {48},
@@ -9161,7 +9276,7 @@
   author = {Lars Nyland and Mark Harris and Jan Prins},
   title = {Fast {N}-body simulation with {CUDA}},
   booktitle = {GPU Gems 3},
-  publisher = {Addison-Wesley Professional},
+  publisher = {Addison-Wesley Professional, Boston, MA, USA},
   year = {2007},
   chapter = {31},
   pages = {677--695},
@@ -9300,15 +9415,6 @@
   pages = {12-49}
 }
 
- at ARTICLE{OsGeDeMe10,
-  author = {Matthieu Ospici and Luigi Genovese and Thierry Deutsch and Jean-Fran\c{c}ois
-	M\'ehaut},
-  title = {The impact of {GPU}s on performance and energy consumption},
-  journal = {IEEE Transactions on Parallel and Distributed Systems},
-  year = {2009},
-  note = {, Submitted.}
-}
-
 @ARTICLE{Ott71,
   author = {M. Ottaviani},
   title = {Elastic wave propagation in two evenly-welded quarter-spaces},
@@ -9957,6 +10063,18 @@
   pages = {2005-2008}
 }
 
+ at ARTICLE{RaNaLi09,
+  author = {Nikunj Raghuvanshi and Rahul Narain and Ming C. Lin},
+  title = {Efficient and Accurate Sound Propagation Using Adaptive Rectangular
+	Decomposition},
+  journal = {IEEE Transactions on Visualization and Computer Graphics},
+  year = {2009},
+  volume = {15},
+  pages = {789-801},
+  number = {5},
+  doi = {10.1109/TVCG.2009.28}
+}
+
 @ARTICLE{Rah04,
   author = {A. N. Rahmouni},
   title = {Un mod\`ele {PML} bien pos\'e pour l'\'elastodynamique anisotrope
@@ -10150,6 +10268,16 @@
   pages = {1-66}
 }
 
+ at ARTICLE{RiWh03,
+  author = {B. Rivi\`ere and M. F. Wheeler},
+  title = {Discontinuous Finite Element Methods for Acoustic and Elastic Wave
+	Problems},
+  journal = {Contemporary Mathematics},
+  year = {2003},
+  volume = {329},
+  pages = {271-282}
+}
+
 @ARTICLE{Rob96,
   author = {J. O. A. Robertsson},
   title = {A numerical free-surface condition for elastic/viscoelastic finite-difference
@@ -10351,6 +10479,19 @@
   doi = {10.1029/2003GL018304}
 }
 
+ at ARTICLE{RoBeCoKo10,
+  author = {Diego Rossinelli and Michael Bergdorf and Georges-Henri Cottet and
+	Petros Koumoutsakos},
+  title = {{GPU} accelerated simulations of bluff body flows using vortex particle
+	methods},
+  journal = jcp,
+  year = {2010},
+  volume = {229},
+  pages = {3316-3333},
+  number = {9},
+  doi = {10.1016/j.jcp.2010.01.004}
+}
+
 @ARTICLE{Roy08,
   author = {D. Royer},
   title = {Stresses and displacements for some Rayleigh-type surface acoustic
@@ -10657,6 +10798,17 @@
   pages = {365-380}
 }
 
+ at ARTICLE{SaKoTr10,
+  author = {Brian Savage and Dimitri Komatitsch and Jeroen Tromp},
+  title = {Effects of {3D} attenuation on seismic wave amplitude and phase measurements},
+  journal = bssa,
+  year = {2010},
+  volume = {100},
+  pages = {1241-1251},
+  number = {3},
+  doi = {10.1785/0120090263}
+}
+
 @INPROCEEDINGS{SavWiTr05,
   author = {Savage, B. and D. A. Wiens and J. Tromp},
   title = {Effects of 3{D} Velocity and Attenuation in the {T}onga-{F}iji Subduction
@@ -11368,6 +11520,18 @@
   doi = {10.1109/75.594858}
 }
 
+ at ARTICLE{SuTsCh10,
+  author = {Alfeus Sunarso and Tomohiro Tsuji and Shigeomi Chono},
+  title = {{GPU}-accelerated molecular dynamics simulation for study of liquid
+	crystalline flows},
+  journal = jcp,
+  year = {2010},
+  volume = {229},
+  pages = {5486-5497},
+  number = {15},
+  doi = {10.1016/j.jcp.2010.03.047}
+}
+
 @ARTICLE{Syn57,
   author = {J. L. Synge},
   title = {Elastic waves in anisotropic media},
@@ -11597,6 +11761,16 @@
   number = {6}
 }
 
+ at ARTICLE{EUCrust07,
+  author = {M. Tesauro and M. K. Kaban and S. A. P. L. Cloetingh},
+  title = {EuCrust-07: A new reference model for the {European} crust},
+  journal = grl,
+  year = {2008},
+  volume = {35},
+  pages = {L05313},
+  doi = {10.1029/2007GL032244}
+}
+
 @ARTICLE{Tes00,
   author = {Ekkehart Tessmer},
   title = {Seismic finite-difference modeling with spatially varying time steps},
@@ -11963,16 +12137,6 @@
   pages = {847-855}
 }
 
- at ARTICLE{trompetal2005,
-  author = {J. Tromp and C. Tape and Q. Liu},
-  title = {Seismic Tomography, Adjoint Methods, Time Reversal, and Banana-Doughnut
-	Kernels},
-  journal = gji,
-  year = {2005},
-  volume = {160},
-  pages = {195-216}
-}
-
 @ARTICLE{TrTaLi05,
   author = {Jeroen Tromp and Carl Tape and Qinya Liu},
   title = {Seismic tomography, adjoint methods, time reversal and banana-doughnut
@@ -12253,6 +12417,18 @@
   doi = {10.1145/1413370.1413402}
 }
 
+ at ARTICLE{VoShKi10,
+  author = {Peter E. J. Vos and Spencer J. Sherwin and Robert M. Kirby},
+  title = {From $h$ to $p$ efficiently: Implementing finite and spectral/$hp$
+	element methods to achieve optimal performance for low- and high-order
+	discretisations},
+  journal = jcp,
+  year = {2010},
+  volume = {229},
+  pages = {5161-5181},
+  doi = {10.1016/j.jcp.2010.03.031}
+}
+
 @ARTICLE{VaRoCh02,
   author = {van Vossen, Robbert and Johan O. A. Robertsson and Chris H. Chapman},
   title = {Finite-difference modeling of wave propagation in a fluid-solid configuration},
@@ -12726,16 +12902,6 @@
   address = {Washington D.C., USA}
 }
 
- at ARTICLE{zhang2003,
-  author = {Y. Zhang, G. Zhang and N. Bleistein},
-  title = {True amplitude wave equation migration arising from true amplitude
-	one-way wave equations},
-  journal = {Inverse Problems},
-  year = {2003},
-  volume = {19},
-  pages = {1113-1138}
-}
-
 @ARTICLE{YaWaCh07,
   author = {Juekuan Yang and Yujuan Wang and Yunfei Chen},
   title = {{GPU} accelerated molecular dynamics simulation of thermal conductivities},
@@ -12892,6 +13058,16 @@
   pages = {911-926}
 }
 
+ at ARTICLE{zhang2003,
+  author = {Y. Zhang and G. Zhang and N. Bleistein},
+  title = {True amplitude wave equation migration arising from true amplitude
+	one-way wave equations},
+  journal = {Inverse Problems},
+  year = {2003},
+  volume = {19},
+  pages = {1113-1138}
+}
+
 @ARTICLE{ZhCa96,
   author = {L. Zhao and A. C. Cangellaris},
   title = {{GT-PML}: generalized theory of {P}erfectly {M}atched {L}ayers and

Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/gauss_vs_triangle_mod.pdf
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Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/source_timing.pdf
===================================================================
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Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/specfem_3d-cover.pdf
===================================================================
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Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/figures/specfem_3d-cover.psd
===================================================================
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Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.pdf
===================================================================
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Modified: seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex
===================================================================
--- seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex	2010-06-07 22:24:09 UTC (rev 16919)
+++ seismo/3D/SPECFEM3D/trunk/USER_MANUAL/manual_SPECFEM3D.tex	2010-06-07 22:40:16 UTC (rev 16920)
@@ -136,7 +136,7 @@
 for details. It was a finalist again in 2008 for a run at 0.16 petaflops (sustained) on 149,784 processors of the `Jaguar' Cray XT5 system at Oak Ridge National Laboratories (USA) \citep{CaKoLaTiMiLeSnTr08}.
 
 Future improvements will include support for GPU graphics card acceleration \citep{KoMiEr09,KoErGoMi10,MiKo10}
-as well as Convolutional-Perfectly Matched absorbing Layers (C-PML) \citep{KoMa07,MaKoEz08,MaKo09,MaKoGeBr10}.
+as well as Convolutional or Auxiliary Differential Equation Perfectly Matched absorbing Layers (C-PML or ADE-PML) \citep{KoMa07,MaKoEz08,MaKo09,MaKoGeBr10}.
 
 \section{Citation}
 
@@ -810,7 +810,7 @@
 earthquakes with large ruptures such as the Lander's earthquake \citep{WaHe94}.
 Second, they can be used to generate finite-frequency sensitivity
 kernels that are a critical part of tomographic inversions based upon
-3D reference models \citep{trompetal2005,LiTr06,TrKoLi08,LiTr08}. In either
+3D reference models \citep{TrTaLi05,LiTr06,TrKoLi08,LiTr08}. In either
 case, source parameter or velocity structure updates are sought to
 minimize a specific misfit function (e.g., waveform or traveltime
 differences), and the adjoint simulation provides a means of computing



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