[cig-commits] r14433 - in seismo/3D/ADJOINT_TOMO/flexwin: . USER_MANUAL USER_MANUAL/manual_figures
carltape at geodynamics.org
carltape at geodynamics.org
Tue Mar 24 14:21:32 PDT 2009
Author: carltape
Date: 2009-03-24 14:21:31 -0700 (Tue, 24 Mar 2009)
New Revision: 14433
Added:
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/AM-allcitations.bib
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/def_base.tex
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/flexwin_manual.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/flexwin_manual.tex
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/ABKT.eps
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/ABKT.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/ABKT_II_LHZ_seis.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/window_composite.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/window_overlap.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_figures/window_rejection_separation.pdf
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_introduction.tex
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_other.tex
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_technical.tex
seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_tuning.tex
Log:
Moved manual text and figures into FLEXWIN directory.
Added: seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/AM-allcitations.bib
===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/AM-allcitations.bib (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/AM-allcitations.bib 2009-03-24 21:21:31 UTC (rev 14433)
@@ -0,0 +1,7147 @@
+
+%% Created for alessia at 2008-12-10 10:38:17 +0100
+
+
+%% Saved with string encoding Unicode (UTF-8)
+
+
+ at string{ag = {Ann. Geophys.}}
+
+ at string{bgsa = {B. Geol. Soc. Am.}}
+
+ at string{bssa = {B. Seismol. Soc. Am.}}
+
+ at string{cs = {Curr. Sci. India}}
+
+ at string{eos = {EOS Trans. AGU}}
+
+ at string{epsl = {Earth Planet. Sc. Lett.}}
+
+ at string{g3 = {Geochem. Geophys. Geosyst.}}
+
+ at string{geol = {Geology}}
+
+ at string{geolmag = {Geol. Mag.}}
+
+ at string{geophys = {Geophysics}}
+
+ at string{gg = {Geol. Geofiz}}
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+ at string{gj = {Geophys. J.}}
+
+ at string{gji = {Geophys. J. Int.}}
+
+ at string{gjras = {Geophys. J. R. Astr. Soc.}}
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+ at string{grl = {Geophy. Res. Lett.}}
+
+ at string{gsatoday = {GSA Today}}
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+ at string{igr = {International Geology Review}}
+
+ at string{jg = {J. Geodyn.}}
+
+ at string{jgeo = {J. Geophys.}}
+
+ at string{jgr = {J. Geophys. Res.}}
+
+ at string{jgsi = {J. Geol. Soc. India}}
+
+ at string{js = {J. Seismol.}}
+
+ at string{jsee = {J. Seismology and Earthquake Engineering}}
+
+ at string{jsg = {J. Struct. Geol.}}
+
+ at string{jvgr = {J. Volcanol. Geotherm. Res.}}
+
+ at string{lithos = {Lithos}}
+
+ at string{mgr = {Marine Geophys. Res.}}
+
+ at string{mnras = {Mon. Not. R. Astron. Soc.}}
+
+ at string{nat = {Nature}}
+
+ at string{natlet = {Lett. Nature}}
+
+ at string{nature = {Nature}}
+
+ at string{pag = {Pure App. Geophys.}}
+
+ at string{pageoph = {Pure App. Geophys.}}
+
+ at string{pepi = {Phys. Earth Planet. Interiors}}
+
+ at string{procussr = {Proc. Acad. Sci. USSR}}
+
+ at string{ptrsla = {Philos. T. Roy. Soc. A}}
+
+ at string{qtrmets = {Q. J. R. Meteorol. Soc.}}
+
+ at string{rog = {Rev. Geophys.}}
+
+ at string{sci = {Science}}
+
+ at string{science = {Science}}
+
+ at string{sciexp = {Sciencexpress}}
+
+ at string{srl = {Seismol. Res. Lett.}}
+
+ at string{tect = {Tectonics}}
+
+ at string{tectphys = {Tectonophysics}}
+
+
+ at article{LiuTromp2008,
+ Author = {Liu, Q. and Tromp, J.},
+ Date-Added = {2008-12-10 10:36:51 +0100},
+ Date-Modified = {2008-12-10 10:38:11 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {265--286},
+ Title = {Finite-frequency sensitivity kernels for global seismic wave propagation based upon adjoint methods},
+ Volume = {174},
+ Year = {2008}}
+
+ at article{PanningRomanowicz2006,
+ Author = {Panning, M. and Romanowicz, B.},
+ Date-Added = {2008-11-12 13:24:58 +0100},
+ Date-Modified = {2008-11-12 13:25:58 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {361--379},
+ Title = {A three-dimensional radially anisotropic model of shear velocity in the whole mantle},
+ Volume = {167},
+ Year = {2006}}
+
+
+ at article{LawrenceShearer2008,
+ AUTHOR = {J. F. Lawrence and P. M. Shearer},
+ JOURNAL = gji,
+ PAGES = {143--158},
+ TITLE = {{Imaging mantle transition zone thickness with $SdS$-$SS$ finite-frequency sensitivity kernels}},
+ VOLUME = {174},
+ YEAR = {2008}
+}
+
+ at article{SiglochNolet2006,
+ Author = {Sigloch, K. and Nolet, G.},
+ Date-Added = {2008-11-10 18:15:44 +0100},
+ Date-Modified = {2008-11-10 18:17:27 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {271--287},
+ Title = {Measuring finite-frequency body-wave amplitudes and traveltimes},
+ Volume = {167},
+ Year = {2006}}
+
+ at article{HouserEtal2008,
+ Author = {Houser, C. and Masters, G. and Laske, G.},
+ Date-Added = {2008-11-10 18:14:20 +0100},
+ Date-Modified = {2008-11-10 18:15:24 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {195--212},
+ Title = {Shear and compressional velocity models of the mantle from cluster analysis of long-period waveforms},
+ Volume = {174},
+ Year = {2008}}
+
+ at article{vanDecarCrosson1990,
+ Author = {VanDecar, J.C. and Crosson, R.S.},
+ Date-Added = {2008-11-10 18:12:39 +0100},
+ Date-Modified = {2008-11-10 18:14:04 +0100},
+ Journal = bssa,
+ Pages = {150--169},
+ Title = {Determination of teleseismic relative phase arrival times using multi-channel cross-correlation and least squares},
+ Volume = {80},
+ Year = {1990}}
+
+ at article{LawrenceEtal2006,
+ AUTHOR = {J. F. Lawrence and P. M. Shearer and G. Masters},
+ JOURNAL = grl,
+ TITLE = {{Mapping attenuation beneath North America using waveform cross-correlation and cluster analysis}},
+ VOLUME = {33},
+ EID = {L07315},
+ DOI = {10.1029/2006GL025813},
+ YEAR = {2006}
+}
+
+ at article{vanHeijstWoodhouse1997,
+ Author = {Van Heijst, H.J. and Woodhouse, J.H.},
+ Date-Added = {2008-11-10 18:08:11 +0100},
+ Date-Modified = {2008-11-10 18:09:27 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {209--220},
+ Title = {Measuring surface-wave overtone phase velocities using a mode-branch stripping technique},
+ Volume = {131},
+ Year = {1997}}
+
+ at article{LebedevEtal2005,
+ AUTHOR = {S. Lebedev and G. Nolet and T. Meier and R. D. {van der Hilst}},
+ JOURNAL = gji,
+ PAGES = {951--964},
+ TITLE = {{Automated multimode inversion of surface and $S$ waveforms}},
+ VOLUME = {162},
+ YEAR = {2005}
+}
+
+ at article{VisserEtal2007,
+ AUTHOR = {K. Visser and S. Lebedev and J. Trampert and B. L. N. Kennett},
+ JOURNAL = grl,
+ TITLE = {{Global Love wave overtone measurements}},
+ VOLUME = {34},
+ EID = {L03302},
+ DOI = {10.1029/2006GL028671},
+ YEAR = {2007}
+}
+
+ at article{WithersEtal1998,
+ Author = {Withers, M. and Aster, R. and Young, C. and Beiriger, J. and Harris, M. and Moore, S. and Trujillo, J.},
+ Date-Added = {2008-11-07 13:24:26 +0100},
+ Date-Modified = {2008-11-07 13:25:59 +0100},
+ Journal = bssa,
+ Pages = {96--106},
+ Title = {A comparison of select trigger algorithms for automated global seismic phase and event detection},
+ Volume = {88},
+ Year = {1998}}
+
+ at incollection{SleemanVanEck2003,
+ Author = {Sleeman, R. and van Eck, T.},
+ Booktitle = {Methods and Applications of Signal Processing in Seismic Network Operations},
+ Date-Added = {2008-11-07 13:05:30 +0100},
+ Date-Modified = {2008-11-07 13:07:47 +0100},
+ Editor = {Takami, T. and Kitagawa, G.},
+ Pages = {173--194},
+ Publisher = {Springer},
+ Series = {Lecture Notes in Earth Sciences},
+ Title = {{Single station real-time P and S phase pickers for seismic observatories}},
+ Volume = {98},
+ Year = {2003}}
+
+ at article{EarleShearer1994,
+ Author = {Earle, P.S. and Shearer, P.M.},
+ Date-Added = {2008-11-07 13:03:47 +0100},
+ Date-Modified = {2008-11-07 13:04:48 +0100},
+ Journal = bssa,
+ Pages = {366--376},
+ Title = {Characterization of global seismograms using an automatic picking algorithm},
+ Volume = {84},
+ Year = {1994}}
+
+ at article{BaiKennett2000,
+ AUTHOR = {C. Bai and B. L. N. Kennett},
+ JOURNAL = bssa,
+ PAGES = {187--198},
+ TITLE = {{Automatic phase-detection and identification by full use of a single three-component broadband seismogram}},
+ VOLUME = {90},
+ YEAR = {2000}
+}
+
+ at incollection{AsterRowe2000,
+ AUTHOR = {R. Aster and C. Rowe},
+ TITLE = {{Automatic phase pick refinement and similar event association in large seismic datasets}},
+ BOOKTITLE = {Advances in Seismic Event Location},
+ PUBLISHER = {Kluwer},
+ ADDRESS = {Dordrecht, Netherlands},
+ EDITOR = {C. H. Thurber and N. Rabinowitz},
+ PAGES = {231--263},
+ YEAR = {2000}
+}
+
+ at article{Allen1982,
+ Author = {Allen, R.V.},
+ Date-Added = {2008-11-07 12:57:53 +0100},
+ Date-Modified = {2008-11-07 12:58:57 +0100},
+ Journal = bssa,
+ Pages = {S225--S242},
+ Title = {Automatic phase pickers: their present use and future prospects},
+ Volume = {72},
+ Year = {1982}}
+
+ at article{Allen1978,
+ Author = {Allen, R.V.},
+ Date-Added = {2008-11-07 12:56:07 +0100},
+ Date-Modified = {2008-11-07 12:57:37 +0100},
+ Journal = bssa,
+ Pages = {1521-1531},
+ Title = {Automatic earthquake recognition and timing from single traces},
+ Volume = {68},
+ Year = {1987}}
+
+ at article{LiTanimoto1993,
+ Author = {Li, X.D. and Tanimoto, T.},
+ Date-Added = {2008-04-07 12:36:02 +0200},
+ Date-Modified = {2008-04-07 12:38:19 +0200},
+ Journal = {Geophys. J. Int.},
+ Pages = {92--102},
+ Title = {Waveforms of long-period body waves in a slightly aspherical Earth model},
+ Volume = {112},
+ Year = {1993}}
+
+ at article{MegninRomanowicz1999,
+ Author = {M{\'e}gnin, C. and Romanowicz, B.},
+ Date-Added = {2008-03-25 17:00:27 +0100},
+ Date-Modified = {2008-03-25 17:02:28 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {366--380},
+ Title = {The effects of the theoretical formalism and data selection on mantle models derived from waveform tomography},
+ Volume = {138},
+ Year = {1999}}
+
+ at article{LiRomanowicz1996,
+ Author = {Li, X. and Romanowicz, B.},
+ Date-Added = {2008-03-25 16:56:34 +0100},
+ Date-Modified = {2008-03-25 16:58:49 +0100},
+ Journal = {J. Geophys. Res.},
+ Pages = {22,245--22,272},
+ Title = {Global mantle shear velocity model developed using nonlinear asymptotic coupling theory},
+ Volume = {101},
+ Year = {1996}}
+
+ at article{Romanowicz2008,
+ Author = {Romanowicz, B.},
+ Date-Added = {2008-03-25 15:28:40 +0100},
+ Date-Modified = {2008-03-25 15:56:24 +0100},
+ Journal = {Nature},
+ Pages = {266--268},
+ Title = {{Using seismic waves to image Earth's internal structure}},
+ Volume = {451},
+ Year = {2008}}
+
+ at article{BoschiEtal2007,
+ Author = {Boschi, L. and Ampuero, J.P. and Peter, D. and Mai, P.M. and Soldati, G. and Giardini, D.},
+ Date-Added = {2008-03-24 17:39:20 +0100},
+ Date-Modified = {2008-03-24 17:40:43 +0100},
+ Journal = {Phys. Earth Planet. Interiors},
+ Pages = {245--250},
+ Title = {Petascale computing and resolution in global seismic tomography},
+ Volume = {163},
+ Year = {2007}}
+
+ at article{TrampertSpetzler2006,
+ Author = {Trampert, J. and Spetzler, J.},
+ Date-Added = {2008-03-24 17:26:01 +0100},
+ Date-Modified = {2008-03-24 17:27:27 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {394--400},
+ Title = {Surface wave tomography: finite-frequency effects lost in the null space},
+ Volume = {164},
+ Year = {2006}}
+
+ at article{McLarenEtal2008,
+ AUTHOR = {M. K. McLaren and J. L. Hardebeck and N. van der Elst and J. Unruh and G. W. Bawden and J. L. Blai},
+ JOURNAL = {\bssa},
+ PAGES = {1659--1680},
+ TITLE = {{Complex faulting associated with the 22 December 2003 $M_{\rm W}$ 6.5 San Simeon, California, earthquake, aftershocks, and postseismic surface deformation}},
+ VOLUME = {98},
+ NUMBER = {4},
+ YEAR = {2008}}
+
+ at article{ThurberEtal2006,
+ Author = {Thurber, C. and Zhang, H. and Waldhauser, F. and Hardebeck, J. and Michael, A. and Eberhart-Phillips, D.},
+ Date-Added = {2008-03-22 19:53:11 +0100},
+ Date-Modified = {2008-03-22 19:59:50 +0100},
+ Journal = bssa,
+ Pages = {S38--S49},
+ Title = {{Three-dimensional compressional wavespeed model, earthquake relocations, and focal mechanisms for the Parkfield, California, region}},
+ Volume = {96},
+ Year = {2006}}
+
+ at article{LSHtomo,
+ AUTHOR = {G. Lin and P. M. Shearer and E. Hauksson and C. H. Thurber},
+ JOURNAL = jgr,
+ TITLE = {{A three-dimensional crustal seismic velocity model for southern California from a composite event method}},
+ VOLUME = {112},
+ NOTE = {{B11306, doi:10.1029/2007JB004977}},
+ YEAR = {2007}
+}
+
+ at article{LSHsource,
+ AUTHOR = {G. Lin and P. M. Shearer and E. Hauksson},
+ JOURNAL = jgr,
+ TITLE = {{Applying a three-dimensional velocity model, waveform cross correlation, and cluster analysis to locate southern California seismicity from 1981 to 2005}},
+ VOLUME = {112},
+ NOTE = {B12309, doi:10.1029/2007JB004986},
+ YEAR = {2007}}
+
+ at article{ClintonEtal2006,
+ Author = {Clinton, J.F. and Hauksson, E. and Solanki, K.},
+ Date-Added = {2008-03-22 19:49:00 +0100},
+ Date-Modified = {2008-03-22 19:49:55 +0100},
+ Journal = bssa,
+ Pages = {1689--1705},
+ Title = {{An evaluation of the SCSN moment tensor solutions: Robustness of the $M_{\rm w}$ magnitude scale, style of faulting, and automation of the method}},
+ Volume = {96},
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+
+ at article{LinEtal2007,
+ Author = {Lin, G. and Shearer, P.M. and Hauksson, E. and Thurber, C.H.},
+ Date-Added = {2008-03-22 19:46:43 +0100},
+ Date-Modified = {2008-03-22 19:48:01 +0100},
+ Doi = {10.1029/2007JB004977},
+ Journal = {J. Geophys. Res.},
+ Title = {{A three-dimensional crustal seismic velocity model for southern California from a composite event method}},
+ Volume = {112},
+ Year = {2007},
+ Bdsk-Url-1 = {http://dx.doi.org/10.1029/2007JB004977}}
+
+ at article{Hauksson2000,
+ Author = {Hauksson, E.},
+ Date-Added = {2008-03-22 19:44:35 +0100},
+ Date-Modified = {2008-03-22 19:46:03 +0100},
+ Journal = {J. Geophys. Res.},
+ Pages = {13875--13903},
+ Title = {{Crustal structure and seismicity distribution adjacent to the Pacific and North America plate boundary in southern California}},
+ Volume = {105},
+ Year = {2000}}
+
+ at article{LovelyEtal2006,
+ Author = {Lovely, P. and Shaw J.H. and Liu, Q. and Tromp, J.},
+ Date-Added = {2008-03-22 19:42:21 +0100},
+ Date-Modified = {2008-03-22 19:43:30 +0100},
+ Journal = bssa,
+ Pages = {1882--1896},
+ Title = {{A structural $V_{\rm P}$ model of the Salton Trough, California, and its implications for seismic hazard}},
+ Volume = {96},
+ Year = {2006}}
+
+ at article{KennettEngdahl1991,
+ Author = {B. L. N. {Kennett} and E. R. {Engdahl}},
+ Date-Added = {2008-04-30 01:46:39 +0100},
+ Date-Modified = {2008-04-30 01:47:12 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {429--465},
+ Title = {{Traveltimes for global earthquake location and phase identification}},
+ Volume = {105},
+ Year = {1991}}
+
+ at article{KomatitschEtal2004,
+ Author = {Komatitsch, D. and Liu, Q. and Tromp, J. and S\"uss, P. and Stidham, C. and Shaw J.H.},
+ Date-Added = {2008-03-22 19:38:39 +0100},
+ Date-Modified = {2008-03-22 19:41:12 +0100},
+ Journal = bssa,
+ Pages = {187--206},
+ Title = {{Simulations of ground motion in the Los Angeles basin based upon the spectral-element method}},
+ Volume = {94},
+ Year = {2004}}
+
+ at article{ChenEtal2007,
+ AUTHOR = {M. Chen and J. Tromp and D. Helmberger and H. Kanamori},
+ TITLE = {{Waveform modeling of the slab beneath Japan}},
+ JOURNAL = jgr,
+ VOLUME = {112},
+ YEAR = {2007},
+ EID = {B02305},
+ DOI = {10.1029/2006JB004394}
+}
+
+ at article{ZhaoEtal1992,
+ Author = {Zhao, D. and Horiuchi, S. and Hasegawa, A.},
+ Date-Added = {2008-03-22 19:29:02 +0100},
+ Date-Modified = {2008-03-22 19:30:21 +0100},
+ Journal = {Tectonophysics},
+ Pages = {289--301},
+ Title = {{Seismic velocity structure of the crust beneath the Japan Islands}},
+ Volume = {212},
+ Year = {1992}}
+
+
+ at article{ZhaoEtal1994,
+ AUTHOR = {D. Zhao and A. Hasegawa and H. Kanamori},
+ TITLE = {{Deep structure of Japan subduction zone as derived from local, regional, and teleseismic events}},
+ JOURNAL = jgr,
+ PAGES = {22,313--22,329},
+ VOLUME = {99},
+ NUMBER = {B11},
+ YEAR = {1994}
+}
+
+ at article{ChenEtal2007b,
+ AUTHOR = {P. Chen and L. Zhao and T. H. Jordan},
+ JOURNAL = bssa,
+ PAGES = {1094--1120},
+ TITLE = {{Full 3D tomography for the crustal structure of the Los Angeles region}},
+ VOLUME = {97},
+ YEAR = {2007}
+}
+
+ at article{Takeuchi2007,
+ Author = {Takeuchi, N.},
+ Date-Added = {2008-03-22 16:08:37 +0100},
+ Date-Modified = {2008-03-22 16:09:31 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {1153--1163},
+ Title = {Whole mantle SH velocity model constrained by waveform inversion based on three-dimensional Born kernels},
+ Volume = {169},
+ Year = {2007}}
+
+ at article{ChenEtal2007a,
+ Author = {Chen, P. and Jordan, T.H. and Zhao, L.},
+ Date-Added = {2008-03-22 16:05:30 +0100},
+ Date-Modified = {2008-03-22 16:11:31 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {175--181},
+ Title = {{Full three-dimensional tomography: a comparison between the scattering-integral and adjoint-wavefield methods}},
+ Volume = {170},
+ Year = {2007}}
+
+ at article{PeterEtal2007,
+ Author = {Peter, D. and Tape, C. and Boschi, L. and Woodhouse, J.H.},
+ Date-Added = {2008-03-22 16:03:11 +0100},
+ Date-Modified = {2008-03-22 16:04:31 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {1098--1117},
+ Title = {{Surface wave tomography: global membrane waves and adjoint methods}},
+ Volume = {171},
+ Year = {2007}}
+
+ at article{MaroneEtal2007,
+ Author = {Marone, F. and Gung, Y. and Romanowicz, B.},
+ Date-Added = {2008-03-22 15:59:27 +0100},
+ Date-Modified = {2008-03-22 16:00:33 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {206--222},
+ Title = {Three-dimensional radial anisotropic structure of the North American upper mantle from inversion of surface waveform data},
+ Volume = {171},
+ Year = {2007}}
+
+ at article{Pollitz2007,
+ Author = {Pollitz, F.F.},
+ Date-Added = {2008-03-22 15:57:15 +0100},
+ Date-Modified = {2008-03-22 15:58:20 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {630--656},
+ Title = {Finite-frequency traveltime tomography of San Francisco Bay region crustal velocity structure},
+ Volume = {171},
+ Year = {2007}}
+
+ at article{TianEtal2007,
+ Author = {Tian, Y. and Montelli, R. and Nolet, G. and Dahlen, F.A.},
+ Date-Added = {2008-03-22 15:54:55 +0100},
+ Date-Modified = {2008-03-22 15:56:17 +0100},
+ Journal = {J. Comput. Phys.},
+ Pages = {2271--2288},
+ Title = {Computing traveltime and amplitude sensitivity kernels in finite-frequency tomography},
+ Volume = {226},
+ Year = {2007}}
+
+ at article{MontelliEtal2006,
+ Author = {Montelli, R. and Nolet, G. and Dahlen, F.A. and Masters, G.},
+ Date-Added = {2008-03-22 15:52:02 +0100},
+ Date-Modified = {2008-03-22 15:53:45 +0100},
+ Doi = {10.1029/2006GC001248},
+ Journal = {Geochem. Geophys. Geosyst.},
+ Title = {{A catalogue of deep mantle plumes: New results from finite-frequency tomography}},
+ Volume = {7},
+ Year = {2006},
+ Bdsk-Url-1 = {http://dx.doi.org/10.1029/2006GC001248}}
+
+ at article{ZhouEtal2006,
+ AUTHOR = {Y. Zhou and G. Nolet and F. A. Dahlen and G. Laske},
+ JOURNAL = jgr,
+ TITLE = {{Global upper-mantle structure from finite-frequency surface-wave tomography}},
+ VOLUME = {111},
+ EID = {B04304},
+ DOI = {10.1029/2005JB003677},
+ YEAR = {2006}
+}
+
+ at article{ZhouEtal2005,
+ Author = {Zhou, Y. and Dahlen, F.A. and Nolet, G. and Laske, G.},
+ Date-Added = {2008-03-22 15:43:40 +0100},
+ Date-Modified = {2008-03-22 15:45:27 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {1087--1111},
+ Title = {{Finite-frequency effects in global surface-wave tomography}},
+ Volume = {163},
+ Year = {2005}}
+
+ at article{SieminskiEtal2007b,
+ Author = {Sieminski, A. and Liu, Q. and Trampert, J. and Tromp, J.},
+ Date-Added = {2008-03-22 15:38:06 +0100},
+ Date-Modified = {2008-03-22 15:40:04 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {368--389},
+ Title = {Finite-frequency sensitivity of body waves to anisotropy based on adjoint methods},
+ Volume = {171},
+ Year = {2007}}
+
+ at article{SieminskiEtal2007a,
+ Author = {Sieminski, A. and Liu, Q. and Trampert, J. and Tromp, J.},
+ Date-Added = {2008-03-22 15:34:20 +0100},
+ Date-Modified = {2008-03-22 15:36:55 +0100},
+ Journal = {Geophys. J. Int.},
+ Pages = {1153--1174},
+ Title = {{Finite-frequency sensitivity of surface waves to anisotropy based upon adjoint methods}},
+ Volume = {168},
+ Year = {2007}}
+
+ at article{Abers1998,
+ Author = {Abers, G.A.},
+ Journal = bssa,
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+ Title = {Array measurements of phases used in receiver-function calculations: {I}mportance of scattering},
+ Volume = 88,
+ Year = 1998}
+
+ at article{AcharyyaEtal1998,
+ Author = {Acharyya, S.K. and Kayal, J.R. and Roy, A. and Chaturvedi, R.K.},
+ Date-Modified = {2008-03-24 18:43:33 +0100},
+ Journal = jgsi,
+ Pages = {295--304},
+ Title = {Jabalpur earthquake of {M}ay 22, 1997: {C}onstraint from aftershock study},
+ Volume = 51,
+ Year = 1998}
+
+ at article{AkiKaminuma1963,
+ Author = {Aki, K. and Kaminuma, K.},
+ Date-Modified = {2008-03-24 18:43:25 +0100},
+ Journal = {Bull. Earthq. Res. Inst.},
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+ at article{Al-AmriGharib2000,
+ Author = {Al-Amri, A.M. and Gharib, A.A.},
+ Date-Modified = {2008-03-24 18:43:14 +0100},
+ Journal = js,
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+ Title = {Lithospheric seismic structure of the eastern region of the {A}rabian {P}eninsula},
+ Volume = 29,
+ Year = 2000}
+
+ at article{Al-Amri1999,
+ Author = {Al-Amri, A.M.S.},
+ Journal = gji,
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+ Volume = 136,
+ Year = 1999}
+
+ at article{AlbersChristensen1996,
+ Author = {Albers, M. and Christensen, U.R.},
+ Journal = grl,
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+ Title = {The excess temperature of plumes rising from the core-mantle boundary},
+ Volume = 23,
+ Year = 1996}
+
+ at unpublished{AlexanderEtal,
+ Author = {Alexander, S.S. and Hsu, R.C. and Gupta, I.N. and Salzberg, D.H},
+ Note = {Grant No. F49620-94-1-0179},
+ Title = {Development of discriminants and improved locations for regional events in Iran}}
+
+ at phdthesis{Allen2001,
+ Author = {Allen, R.M.},
+ School = {Princeton University},
+ Title = {The mantle plume beneath {I}celand and its interaction with the {N}orth {A}tlantic {R}idge: a seismological investigation},
+ Year = 2001}
+
+ at article{AllenEtal2002,
+ Author = {Allen, R.M. and Nolet, G. and Jason Morgan, W. and Vogfy\"ord, K. and Nettles, M. and Ekstr\"om, G. and Gergsson, B.H. and Erlendsson, P. and Foulger, G.R. and Jakobst\'ottir, S. and Julian, B.R. and Pritchard. M. and Ragnarsson, S. and Stef\'ansson, R.},
+ Journal = gji,
+ Note = {In review},
+ Title = {Plume driven plumbing and crustal formation in {I}celand},
+ Year = 2002}
+
+ at unpublished{AllenEtal,
+ Author = {Allen, M.B. and Jackson, J.A. and Walker, R.},
+ Note = {submitted to Tectonics, April 2003},
+ Title = {Pliocene-{Q}uaternary re-organization of the {A}rabia-{E}urasia collision: matching short-term and long-term deformation rates}}
+
+ at article{AlptekinEtal1986,
+ Author = {Alptekin, O. and Nabelek, J.L. and Toksoz, M.N.},
+ Date-Modified = {2008-03-24 18:42:56 +0100},
+ Journal = tectphys,
+ Pages = {73--88},
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+ at article{AlsinaSM1993,
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+ Volume = 20,
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+ at article{AlsinaEtal1996,
+ Author = {Alsina, D. and Woodward, R.L. and Snieder, R.K.},
+ Date-Modified = {2008-03-24 18:42:28 +0100},
+ Journal = jgr,
+ Number = {B7},
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+ Volume = 101,
+ Year = 1996}
+
+ at article{AlsinaSnieder1996,
+ Author = {Alsina, D. and Snieder, R.},
+ Date-Modified = {2008-03-24 18:42:39 +0100},
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+ at article{AmatoEtal1998,
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+ Date-Modified = {2008-03-24 18:42:19 +0100},
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+ at article{Ambraseys2001,
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+ Volume = 145,
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+ at unpublished{Ammon,
+ Author = {Ammon, C.J.},
+ Note = {submitted to GJI (fast-track)},
+ Title = {Seismic source inversion as a multiple-objective optimization problem}}
+
+ at article{AmmonRZ1990,
+ Author = {Ammon, C.J. and Randall, G.E. and Zandt, G.},
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+ at article{AndersonH1976,
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+ Volume = 82,
+ Year = 2001}
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+ at article{AntolikEtal2003,
+ Author = {Antolik, M. and Gu, Y.J. and Ekstr\"om, G. and Dziewonski, A.M.},
+ Journal = gji,
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+ at article{ArtemievaEtal2004,
+ Author = {Artemieva, I.M. and Billien, M. and L\'ev\^eque, J.J. and Mooney, W.},
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+ at article{ArtyushkovMT2000,
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+ at article{ArvidssonBE+1998,
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+ at article{AshalathaSS1994,
+ Author = {Ashalatha, B. and Subrahmanyam, C. and Singh, R.N.},
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+ at article{AssumpcaoS1988,
+ Author = {Assump{\c c\~a}o, M. and Su{\'a}rez, G.},
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+ at article{Asudeh1982a,
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+ at article{Asudeh1982b,
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+ at article{Asudeh1983,
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+ at article{AsudehMcKenzie1981,
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+ at article{AtwaterStock1998,
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+ at article{AxenEtal2001,
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+ Title = {Exhumation of the west-central {A}lborz {M}ountains, {I}ran, {C}aspian subsidence, and collision-related tectonics},
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+ at book{BabuskaCara1991,
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+ Year = 1991}
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+ at article{BabuskaEtal1998,
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+ Year = 1993}
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+ at article{BakerEtal1993,
+ Author = {Baker, C. and Jackson, J. and Priestley, K.},
+ Journal = gji,
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+ at article{BakerEtal1997,
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+ at techreport{BapatEtal1983,
+ Author = {Bapat, A. and Kulkarni, R.C. and Gutha, S.K.},
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+ at article{BaranowskiEtal1984,
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+ Volume = 104,
+ Year = 1999}
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+ at article{BarruolEtal2002,
+ Author = {Barruol, G. and others},
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+ at article{BhattacharyaEtal1997,
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+ at article{BeckerEtal2003,
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+ Title = {The 14 {M}arch, 1998 {F}andoqa earthquake ($M_w$~6.6) in {K}erman province, southeast~Iran: re--reupture of the 1981 {S}irch earthquake fault, triggering of slip on adjacent thrusts, and the active tectonics of the {G}owk fault zone},
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+ Title = {The $M_s=6.2$, {J}une 15, 1995 {A}igion earthquake ({G}reece): evidence for low angle normal faulting in the {C}orinth rift},
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+ Author = {Bilham, R. and Blume, F. and Bendick, R. and Gaur, V.K.},
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+ Author = {Bilham, R.},
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+ Publisher = {Geological Society, London, Special Publications},
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+ Year = 2002}
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+ at article{BlackmanKendall2002,
+ Author = {Blackman, D.K. and Kendall, J.-M.},
+ Journal = g3,
+ Note = {2001GC000247},
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+ at article{Bokelmann1995,
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+ at article{BoschiEkstrom2002,
+ Author = {Boschi, L. and Ekstr\"om, G.},
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+ Volume = 107,
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+ at article{BoschiEtal2004,
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+ School = {Oregon State University},
+ Title = {Seismotectonics of the explorer region and of the {B}lanco {T}ransform {F}ault {Z}one},
+ Year = 1999}
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+ at article{BraunmillerNabelek1990,
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+ Author = {Garetsky, R.G. and Karatayev, G.I. and Zlotski, G. and Astapenko, V.N. and Belinsky, A.A. and Terletsky, V.V. and Thybo, H. and Sand, R. and Yliniemi, J. and Tiira, T. and Luosto, U. and Komminaho, K. and Giese, R. and Motuza, G. and Nasedkin, V. and Jacyna, J. and Grad, M. and Janik, T. and Guterch, A. and Kharitonov, O.M. and Omelchenko, V.D. and Doody, J.J.},
+ Journal = tectphys,
+ Pages = {193--217},
+ Title = {Seismic velocity structure across the {F}ennoscandia-{S}armatia suture of the {E}ast {E}uropean {C}raton beneath the {EUROBRIDGE} profile through {L}ithuania and {B}elarus},
+ Volume = 314,
+ Year = 1999}
+
+ at article{GarneroEtal1993a,
+ Author = {Garnero, E.J. and Grand, S.P. and Helmberger, D.V.},
+ Journal = grl,
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+ Volume = 20,
+ Year = 1993}
+
+ at article{GarneroEtal1993b,
+ Author = {Garnero, E.J. and Helmberger, D.V. and Grand. S.},
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+ at article{GasperiniEtal1999,
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+ Year = 1997}
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+ at article{GHA98,
+ Author = {Ghose, S. and Hamburger, M.W. and Ammon, C.J.},
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+ at article{GHV98,
+ Author = {Ghose, S. and Hamburger, M.W. and Virieux, J.},
+ Journal = jgr,
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+ Author = {Ghose, S. and Mellors, R.J. and Korjenkov, A.M. and Hamburger, M.W. and Pavlis, T.L. and Omuraliev, M. and Mamyrov, E. and Muraliev, A.R.},
+ Journal = bssa,
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+ Title = {The $M_s=7.3$ 1992 {S}uusamyr, {K}yrgyzstan, earthquake in the {T}ien {S}han 2. {A}ftershock focal mechanisms and surface deformation},
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+ Author = {Giese, P. and Makris, J. and Akashe, B. and Rower, P. and Letz, H. and Mostaanpour, M.},
+ Institution = {Geological Survey Iran},
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+ Pages = {71--84},
+ Title = {Seismic crustal studies in southern {I}ran between {C}entral {I}ran and the {Z}agros belt},
+ Type = {Report},
+ Year = 1983}
+
+ at article{GieseMA+1984,
+ Author = {Giese, P. and Makris, J. and Akashe, B. and Rower, P. and Letz, H. and Mostaanpour, M.},
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+ Author = {Gleason, G.C. and Tullis, J.},
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+ Volume = 247,
+ Year = 1995}
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+ at article{GoesEtal2000,
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+ Journal = jgr,
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+ Volume = 105,
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+ at article{GoesEtal2004,
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+ at article{GombergEtal1988,
+ Author = {Gomberg, J.S. and Priestley, K.F. and Masters, T.G. and Brune, J.N.},
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+ at article{GomezEtal1998,
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+ Date-Modified = {2008-03-24 18:50:41 +0100},
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+ at article{GBD98,
+ Author = {Grabowska, T. and Bojdys, G. and Dolnicki, J.},
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+ at article{GradEtal1995,
+ Author = {Grad, M. and Krzyzanowska, M. and Pirhonen, S.E.},
+ Date-Modified = {2008-03-24 18:51:40 +0100},
+ Journal = gji,
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+ at article{GrevemeyerEtal2001,
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+ Author = {Zhang, J. and Walter, W.R. and Lay, T. and Wu, R.-S.},
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+ Volume = 160,
+ Year = 2003}
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+ Author = {Zhao, L.S. and Helmberger, D.V.},
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+ Volume = 124,
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+
+ at article{ZhaoEtal1997,
+ Author = {Zhao, M. and Langston, C.A. and Nyblade, A.A. and Owens, T.J.},
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+ Author = {Zhao, L. and Jordan, T.H. and Chapman, C.H.},
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+ Author = {Zhao, D.P.},
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+ at article{ZhaoLei2004,
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+
+ at article{ZhaoEtal2005,
+ AUTHOR = {L. Zhao and T. H. Jordan and K. B. Olsen and P. Chen},
+ JOURNAL = bssa,
+ TITLE = {{Fr\'{e}chet kernels for imaging regional earth structure based on three-dimensional reference models}},
+ VOLUME = {95},
+ PAGES = {2066--2080},
+ YEAR = {2005}
+}
+
+ at article{ZhaoJordan2006,
+ Author = {Zhao, L. and Jordan, T.H.},
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+
+ at article{ZhaoEtal2006,
+ Author = {Zhao, L. and Chen, P. and Jordan, T.H.},
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+
+ at article{ZhijunPanza1999,
+ Author = {Zhijun, D. and Panza, G.F.},
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+
+ at article{Zhi02,
+ Author = {Zhijun, D.},
+ Journal = gji,
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+ Year = 2002}
+
+ at article{ZielhuisN1994,
+ Author = {Zielhuis, A. and Nolet, G.},
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+ Year = 1994}
+
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+ Author = {Zhou, Y. and Dahlen, F.A. and Nolet, G.},
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+ Volume = 158,
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+
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+ Author = {Zhu, L.P. and Helmberger, D.V.},
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+ Year = 1998}
+
+ at article{ZH96,
+ Author = {Zhu, L.P. and Helmberger, D.V.},
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+ Volume = 23,
+ Year = 1996}
+
+ at article{ZhuEtal1997,
+ Author = {Zhu, L.P. and Helmberger, D.V. and Saikia, C.K. and Woods, B.B.},
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+ Pages = {22,799--22,813},
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+ Volume = 102,
+ Year = 1997}
+
+ at article{Zoretal2003,
+ Author = {Zor, E. and Sandvol, E. and Gurbuz, C. and Turkelli, N. and Seber, D. and Barazangi, M.},
+ Journal = grl,
+ Note = {10.1029/2003GL017390},
+ Number = 24,
+ Title = {The crustal structure of the {E}ast {A}natolian plateau ({T}urkey) from receiver functions},
+ Volume = 30,
+ Year = 2003}
+
+ at article{vanHeijstEtal1994,
+ Author = {{Van Heijst}, {H.J.} and Snieder, R. and Nowack, R.},
+ Journal = gji,
+ Pages = {333--343},
+ Title = {Resolving a low--velocity zone with surface--wave data},
+ Volume = 118,
+ Year = 1994}
+
+ at article{vanderLee1998,
+ Author = {{Van der Lee}, S.},
+ Journal = gji,
+ Pages = {691--699},
+ Title = {Observations and origin of {R}ayleigh--wave amplitude anomalies},
+ Volume = 135,
+ Year = 1998}
+
+ at article{vanderLeeNolet1997a,
+ Author = {{Van der Lee}, S. and Nolet, G.},
+ Journal = jgr,
+ Pages = {22,815--22,838},
+ Title = {Upper mantle {$S$} velocity structure of {N}orth {A}merica},
+ Volume = 102,
+ Year = 1997}
+
+ at article{vanderLeeNolet1997b,
+ Author = {{Van der Lee}, S. and Nolet, G.},
+ Journal = nature,
+ Pages = {266--269},
+ Title = {Seismic image of the subducted trailing fragments of the {F}arallon plate},
+ Volume = 386,
+ Year = 1997}
+
+ at article{vanderLeeEtal2001,
+ Author = {van der Lee, S. and James, D. and Silver, P.},
+ Journal = jgr,
+ Number = 12,
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+ Title = {Upper mantle $S$ velocity structure of central and western {S}outh {A}merica},
+ Volume = 106,
+ Year = 2001}
+
+ at techreport{iris-ida01,
+ Author = {Davis, P. and Berger, J. and Horwitt, D.},
+ Institution = {Scripps Institution of Oceanography},
+ Number = {01-10},
+ Title = {The {IDA} {M}ark 7 {D}ata {A}cquisition {S}sytem filter problem},
+ Type = {Reference Series},
+ Year = 2001}
+
+ at misc{gsi-tectonic91,
+ Author = {Alavi, M.},
+ Institution = {Geological Survey of Iran},
+ Note = {Scale 1:5,000,000},
+ Title = {Tectonic map of the {M}iddle {E}ast, {G}eological {S}urvey of {I}ran},
+ Year = 1991}
+
+ at misc{CandeEtal1989,
+ Author = {Cande, S.C. and LaBrecque, J.L. and Larson, R.L. and Pitmann, W.C. and Golovchenko, X. and Haxby, W.F.},
+ Institution = {American Association of Petroleum Geologists},
+ Note = {Map Series},
+ Title = {Magnetic Lineations of the World's Ocean Basins},
+ Year = {1989}}
+
+ at misc{unesco-sheet9,
+ Author = {Choubert, G. and Faure-Muret, A.},
+ Institution = {Commission for the geological map of the world, UNESCO},
+ Note = {Scale 1:10,000,000},
+ Number = {Sheet 9},
+ Publisher = {International Geological Mapping Bureau, Paris},
+ Title = {Geological World Atlas, {UNESCO}},
+ Year = {1976}}
+
+ at misc{gsi-geological89,
+ Author = {Haghipour, A. and Aghanabati, A.},
+ Edition = 2,
+ Institution = {Ministry of Mines and Metals, Geological Survey of Iran},
+ Note = {Scale: 1:2,500,00},
+ Title = {Geological map of {I}ran, {M}inistry of {M}ines and {M}etals, {G}eological {S}urvey of {I}ran},
+ Year = 1989}
Added: seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/def_base.tex
===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/def_base.tex (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/def_base.tex 2009-03-24 21:21:31 UTC (rev 14433)
@@ -0,0 +1,36 @@
+%
+% $Id: def_base.tex,v 1.1.1.2 2005/09/20 01:20:28 alessia Exp $
+%
+\def\kmps{$\rm km \; s^{-1}$}
+\def\pers{$\rm s^{-1}$}
+\def\deg{$^{\circ}$}
+\def\mwm{$\rm mW \; m^{-2}$}
+\def\pp{${\rm Pp}$}
+\def\ps{${\rm Ps}\;$}
+\def\ppms{${\rm PpP_{m}s}\;$}
+\def\ppsms{${\rm PpS_{m}s \: + \: PsP_{m}s}\;$}
+\def\pg{$\rm P_g$}
+\def\pn{$\rm P_n$}
+\def\pmp{$\rm P_mP$}
+\def\sg{$\rm S_g$}
+\def\sn{$\rm S_n$}
+\def\sms{$\rm S_mS$}
+\def\vp{$\rm V_p$}
+\def\vs{$\rm V_s$}
+\def\vpvs{$\rm V_{p}/V_{s}$}
+\def\degc{$\rm ^{\circ}C$}
+\def\deg{$\rm^{\circ}$}
+\def\degN{$\rm^{\circ}N$}
+\def\degS{$\rm^{\circ}S$}
+\def\degE{$\rm^{\circ}E$}
+\def\degW{$\rm^{\circ}W$}
+\def\degcpkm{${\rm ^{\circ}C\; km}^{-1}$}
+
+\newcommand{\stga}{Stage~A}
+\newcommand{\stgb}{Stage~B}
+\newcommand{\stgc}{Stage~C}
+\newcommand{\stgd}{Stage~D}
+\newcommand{\stge}{Stage~E}
+
+\newcommand{\trange}[2]{\mbox{{#1}--{#2}~s}}
+\newcommand{\rmd}{\mathrm{d}}
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===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/flexwin_manual.tex (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/flexwin_manual.tex 2009-03-24 21:21:31 UTC (rev 14433)
@@ -0,0 +1,63 @@
+\documentclass[11pt]{report}
+%\documentclass[extra]{gji}
+\usepackage{graphicx}
+\usepackage{rotating}
+\usepackage{a4wide}
+\usepackage{setspace}
+\usepackage[utf8]{inputenc}
+\usepackage{amsmath}
+\usepackage{url}
+\usepackage{natbib}
+\pagestyle{headings}
+\usepackage[noend]{algorithmic}
+
+\onehalfspacing
+\setlength\parindent{0in}
+\addtolength{\parskip}{\baselineskip}
+
+\input{def_base}
+
+\graphicspath{
+ {./manual_figures/}
+}
+
+%===================================
+\begin{document}
+%===================================
+
+%\title{FLEXWIN User Manual}
+%\author{Alessia Maggi}
+%\date{}
+%\maketitle
+
+\thispagestyle{empty}
+\begin{center}
+
+\huge {\bf FLEXWIN User's Manual} \\
+
+\vspace{1.0cm}
+\Large Alessia Maggi
+\end{center}
+
+\vspace{1.0cm}
+\hspace{-0.7cm}
+\includegraphics[width=7in]{ABKT.pdf}
+\newpage
+
+%----------------------------------
+
+\tableofcontents
+
+\input{manual_introduction}
+\input{manual_technical}
+\input{manual_tuning}
+\input{manual_other}
+
+\bibliographystyle{plainnat}
+\bibliography{AM-allcitations}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\end{document}
+
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===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_introduction.tex (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_introduction.tex 2009-03-24 21:21:31 UTC (rev 14433)
@@ -0,0 +1,28 @@
+\chapter{Introduction}
+
+The FLEXWIN software package automates the time-window selection problem for
+seismologists. It operates on pairs of observed and synthetic single component
+seismograms, defining windows that cover as much of a given seismogram as
+possible, while avoiding portions of the waveform that are dominated by noise.
+
+FLEXWIN selects time windows on the synthetic seismogram within which the waveform
+contains a distinct energy arrival, then requires an adequate correspondence
+between observed and synthetic waveforms within these windows.
+%This selection paradigm is general, and can be applied to synthetic seismograms regardless of how they have been obtained.
+
+There is no restriction on the type of simulation used to
+generate the synthetics. Realistic Earth models and more complete wave
+propagation theories yield waveforms that are more similar to the observed
+seismograms, and thereby promote the selection of measurement windows covering
+more of the available data. The input seismograms can be measures of
+displacement, velocity or acceleration. There is no requirement
+for horizontal signals to be rotated into radial and transverse directions.
+
+FLEXWIN is a configurable data selection process that can be adapted to
+different tomographic scenarios by tuning a handful of parameters. Although
+the algorithm was designed for use in 3D-3D adjoint tomography, its inherent
+flexibility should make it useful in many data-selection applications.
+
+For a detailed introduction to FLEXWIN as applied to seismic tomography, please consult \cite{MaggiEtal2009}. If you use FLEXWIN for your own research, please cite \cite{MaggiEtal2009}.
+
+
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===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_other.tex (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_other.tex 2009-03-24 21:21:31 UTC (rev 14433)
@@ -0,0 +1,36 @@
+\chapter{Miscellaneous}
+
+\section{Bug reports and suggestions for improvements}
+To report bugs or suggest improvements to the code, please send an email to the CIG Computational Seismology Mailing List (cig-seismo at geodynamics.org) or Alessia Maggi (alessia at sismo.u-strasbg.fr), and/or use our online bug tracking system Roundup (www.geodynamics.org/roundup).
+
+\section{Notes and Acknowledgments}
+The main developers of the FLEXWIN source code are Alessia Maggi and Carl Tape. The following individuals (listed in alphabetical order) have also contributed to the development of the source code: Daniel Chao, Min Chen, Vala Hjorleifsdottir, Qinya Liu, Jeroen Tromp. The following individuals (listed in alphabetical order) contributed to this manual: Sue Kientz, Alessia Maggi, Carl Tape.
+
+The FLEXWIN code makes use of filtering and enveloping algorithms that are part of SAC (Seismic Analysis Code, Lawerence Livermore National Laboratory) provided for free to IRIS members. We thank Brian Savage for adding interfaces to these algorithms in recent SAC distributions.
+
+We acknowledge support by the National Science Foundation under grant EAR-0711177.
+Daniel Chao received additional support from a California Institute of Technology Summer Undergraduate Reseach Fellowship.
+
+
+\section{Copyright}
+Copyright 2009, by the California Institute of Technology (U.S.) and University of Strasbourg (France). ALL RIGHTS RESERVED. U.S. Government Sponsorship Acknowledged.
+
+Any commercial use must be negotiated with the Office of Technology Transfer at
+the California Institute of Technology. This software may be subject to U.S.
+export control laws and regulations. By accepting this software, the user
+agrees to comply with all applicable U.S. export las and regulations, including
+the International Traffic and Arms Regulations, 22 C.F.R 120-130 and the Export
+Administration Regulations, 15 C.F.R. 730-744. User has the responsibility to
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+
+The California Institute of Technology specifically disclaims any warranties,
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+purpose. The software and documentation provided hereunder is on an `as is'
+basis, and the California Institute of Technology has no obligations to provide
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Copied: seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_technical.tex (from rev 14431, seismo/3D/ADJOINT_TOMO/flexwin_paper/latex/manual_technical.tex)
===================================================================
--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_technical.tex (rev 0)
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@@ -0,0 +1,141 @@
+\chapter{Getting started\label{sec:install}}
+
+Here is where you find basic information for obtaining and installing the FLEXWIN package.
+For details of how to tune the algorithm to your seismograms, see chapter~\ref{sec:tuning}.
+
+\section{System requirements}
+In order to install and run, FLEXWIN requires:
+\begin{itemize}
+\item UNIX operating system (Linux, Solaris, MacOS \ldots)
+\item a fortran compiler (gfortran, ifort, etc...)
+\item other packages : SAC (Seismic Analysis Code, available from IRIS); GMT (Generic Mapping Tools) for the plotting scripts
+\end{itemize}
+
+FLEXWIN requires the following libraries external to the package in order to
+compile and run: {\tt libsacio.a} and {\tt libsac.a}. Both libraries
+are distributed by IRIS as part of the SAC package (version 101.2 and above).
+The IRIS download site (as of 30-March-2009) is here:
+\url{http://www.iris.edu/software/sac/sac.request.htm}.
+(To check your version, type sac.)
+
+
+\section{Obtaining the code}
+
+The code is available as a gzipped tarball from CIG (Computational Infrastructure for Geodynamics, \url{http://www.geodynamics.org}). The tarball is unpacked by typing {\tt tar xvzf flexwin.tgz}.
+
+The package contains the flexwin code and documentation, as well as a set of
+test data, examples of user files for different scenarios, and a set of utility
+scripts that may be useful for running flexwin on large datasets.
+
+
+\section{Compilation}
+
+If your compiler of choice is gfortran, then you should be able to use the
+{\tt make\_gfortran} makefiles with only minor modifications (notably you may need to
+change the search path for the {\tt libsacio.a} library). If you prefer another
+compiler, you should modify the OPT and FC lines in the makefiles accordingly. We tested the code using gfortran version 4.1.2
+(To check your version, type {\tt gfortran --version}.)
+
+{\bf Important note}: All the code is compiled with the -m32 option, which makes
+32bit binaries. This option is currently required to enable compatibility with
+SAC. Future versions of the SAC distribution may no longer require this
+compatibility flag.
+
+Steps to compile the flexwin package:
+\begin{enumerate}
+\item Compile {\tt libtau.a} and create {\tt iasp91.hed} and {\tt iasp91.tbl}. In the {\tt flexwin/ttimes\_mod} directory type: {\tt make -f make\_gfortran}. This will compile {\tt libtau.a}, and two programs, {\tt remodl} and {\tt setbrn}. The makefile will also run {\tt remodl} and {\tt setbrn} to create the {\tt iasp91.hed}and {\tt iasp91.tbl} files. You should then type {\tt make -f make\_gfortran install} to install the iasp91 files.
+\item Compile flexwin. Edit the {\tt make\_gfortran} file in the flexwin root directory to ensure the {\tt SACLIBDIR} environment variable points to the location of your SAC libraries (by default {\tt \$SACHOME/lib}). Then type {\tt make -f make\_gfortran}.
+\end{enumerate}
+
+You should end up with the {\tt flexwin} executable. The program requires the {\tt iasp91.hed} and {\tt iasp91.tbl} files (or symbolic links to them) to be present in the directory from which the code is launched.
+
+
+\section{Running the Test case}
+
+You should test your compiled code on the {\tt test\_data} dataset provided. In the
+{\tt flexwin/test\_data} directory, type {\tt ./flexwin < input.test}. The results of your
+run will be found in the {\tt MEASURE} subdirectory, and
+should match those found in the {\tt MEASURE.orig}
+subdirectory.
+
+You can also test the basic plotting script by running {\tt ./plot\_seismos\_gmt.sh
+MEASURE/ABKT.II.LHZ}, whose output will be
+{\tt MEASURE/ABKT.II.LHZ.seis.eps}.
+file. Your result should be identical to what is shown in Figure~\ref{fg:test_data}.
+
+\begin{figure}
+\center \includegraphics[width=7in]{ABKT_II_LHZ_seis.pdf}
+\caption{\label{fg:test_data}
+Windowing results for the test data set, plotted using the {\tt ./plot\_seismos\_gmt.sh} script.
+}
+\end{figure}
+
+
+\section{Running FLEXWIN}
+
+In general, flexwin is run as follows: {\tt ./flexwin < input} where the {\tt input} file is formatted as follows:
+{\small
+\begin{verbatim}
+327
+RAW_DATA/9627721.CI.ADO.BHR.sac.d.fil
+SYNTH/ADO.CI.BHR.new.fil
+MEASURE/ADO.CI.BHR
+RAW_DATA/9627721.CI.ADO.BHT.sac.d.fil
+SYNTH/ADO.CI.BHT.new.fil
+MEASURE/ADO.CI.BHT
+RAW_DATA/9627721.CI.ADO.BHZ.sac.d.fil
+SYNTH/ADO.CI.BHZ.new.fil
+MEASURE/ADO.CI.BHZ
+....
+\end{verbatim}
+}
+
+i.e. the number of traces to be measured, followed by (in order) the path to
+the raw data sac file, the path to the synthetic sac file and the path and
+basename for the (many!) output files for that trace.
+
+\section{Output files}
+Most output files are in ascii. All file names start with the basename given
+in the input file for that trace:
+\begin{description}
+\item[basename.obs] ascii observed seismogram (filtered)
+\item[basename.syn] ascii synthetic seismogram (filtered)
+\item[basename.obs\_lp.sac] sac observed seismogram (filtered)
+\item[basename.syn\_lp.sac] sac synthetic seismogram (filtered)
+\item[basename.env.obs] ascii envelope of observed seismogram (filtered)
+\item[basename.env.syn] ascii envelope of synthetic seismogram (filtered)
+\item[basename.win] list of windows with theoretical phase arrival times
+\item[basename.win.qual] list of windows with Tshift,CC,dlnA values
+\item[basename.phases] theoretical arrival times of phases
+\item[basename.stalta] STA:LTA timeseries used to select the windows, and
+the time-dependent values of the STA:LTA water level, the cross-correlation
+limit $CC_0$, the time-lag limit $\Delta\tau_0$, amplitude ratio limit
+$\Delta\ln{A}_0$ and the window signal to noise limit $r_0$.
+\item[basename.info] information on the path and some statistics
+\end{description}
+For more details about the file formats, read the {\tt write\_}
+subroutines in {\tt io\_subs.f90}.
+
+\section{Scripts}
+Several plotting routines ({\tt plot\_*.sh}) are provided in the {\tt scripts} subdirectory as examples for plotting seismograms, measurements and adjoint sources. All plotting is
+done using GMT (Generic Mapping Tools). These scripts will need to be modified to suit your particular plotting needs.
+
+The script {\tt extract\_event\_windowing\_stats.sh} extracts statistical
+information on the window selection process, on the measurements. Again,
+you can use use this script as a template for your own information
+extraction needs.
+
+\section{Pre-processing suggestions}
+
+Pre-processing is a subtle procedure that can affect the selection of windows.
+Here we list some suggestions for pre-processing:
+%
+\begin{enumerate}
+\item Interpolate raw data and ``raw'' synthetics using the same time-step.
+
+\item Cut the data and synthetic seismograms based on the data record. If the data record starts before the synthetic record (which is common for local earthquakes), then consider padding zeros before the synthetic record; information prior to the origin time (and P arrival) is useful in assessing the signal-to-noise ratio in the observed records.
+
+\item Bandpass both the data and synthetics over the desired period range, rather than doing this within FLEXWIN, thereby limiting the number of filtering operations. However, for initial determination of the bandpass range of interest, it is simpler to experiment using the FLEXWIN parameters {\tt WIN\_MIN\_PERIOD} and {\tt WIN\_MAX\_PERIOD}.
+\end{enumerate}
+
+%-------------------------------------------------
Copied: seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_tuning.tex (from rev 14431, seismo/3D/ADJOINT_TOMO/flexwin_paper/latex/manual_tuning.tex)
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--- seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_tuning.tex (rev 0)
+++ seismo/3D/ADJOINT_TOMO/flexwin/USER_MANUAL/manual_tuning.tex 2009-03-24 21:21:31 UTC (rev 14433)
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+\chapter{Tuning FLEXWIN for your seismograms\label{sec:tuning}}
+
+FLEXWIN is adapted to your specific problem by modifying the values of the parameters in Table~\ref{tb:params}, and the functional form of those parameters that are time-dependent. We consider the algorithm to be correctly adapted when false positives (windows around undesirable features of the seismogram) are minimized, and true positives (window around desirable features) are maximized. The choice of what makes an adequate set of windows remains subjective, as it depends strongly on the quality of the input model, the quality of the data, and the region of the Earth that the tomographic inversion aims to constrain.
+
+The base values of the various parameters are set in the {\tt PAR\_FILE}, which is read at run time. Examples of base parameter values for the three tomographic scenarios discussed by \cite{MaggiEtal2009} can be found in Table~\ref{tb:example_params}. The functional forms of the time dependent parameters may be adjusted by modifying {\tt user\_parameters.f90} (see next section), and re-compiling the code.
+
+\begin{table}[h]
+\begin{tabular}{lp{0.8\linewidth}}
+\hline
+\multicolumn{2}{l}{Standard tuning parameters:} \\[5pt]
+$T_{0,1}$ & bandpass filter corner periods \\
+$r_{P,A}$ & signal to noise ratios for whole waveform \\
+$r_0(t)$ & signal to noise ratios single windows \\
+$w_E(t)$ & water level on short-term:long-term ratio \\
+$\mathrm{CC}_0(t)$ & acceptance level for normalized cross-correlation\\
+$\Delta\tau_0(t)$ & acceptance level for time lag \\
+$\Delta\ln{A}_0(t)$ & acceptance level for amplitude ratio \\
+$\Delta\tau_{\rm ref}$ & reference time lag \\
+$\Delta\ln{A}_{\rm ref}$ & reference amplitude ratio \\
+\hline
+\multicolumn{2}{l}{Fine tuning parameters:} \\ [5pt]
+$c_0$ & for rejection of internal minima \\
+$c_1$ & for rejection of short windows \\
+$c_2$ & for rejection of un-prominent windows \\
+$c_{3a,b}$ & for rejection of multiple distinct arrivals \\
+$c_{4a,b}$ & for curtailing of windows with emergent starts and/or codas \\
+$w_{\mathrm{CC}}\quad w_{\rm len}\quad w_{\rm nwin}$ & for selection of best non-overlapping window combination \\
+\hline
+\end{tabular}
+\caption{\label{tb:params}
+Overview of standard tuning parameters, and of fine
+tuning parameters. Values are defined in a parameter file, and the
+time dependence of those that depend on time is described by user-defined functions.
+}
+\end{table}
+
+\pagebreak
+\section{User parameters}
+The main user parameters in the {\tt PAR\_FILE} are:
+\begin{description}
+\item[{\tt WIN\_MIN\_PERIOD}]Corresponds to $T_0$ in Table~\ref{tb:params}, and is the short wavelength cut-off for the band-pass filter applied to the raw synthetic and observed seismograms.
+\item[{\tt WIN\_MAX\_PERIOD}]Corresponds to $T_1$ in Table~\ref{tb:params}, and is the long wavelength cut-off for the band-pass filter applied to the raw synthetic and observed seismograms.
+\item[{\tt SNR\_INTEGRATE\_BASE}]Corresponds to $r_P$ in Table~\ref{tb:params}, and is the minimum signal to noise ratio on the power of the observed seismogram for windowing to continue.
+\item[{\tt SNR\_MAX\_BASE}]Corresponds to $r_A$ in Table~\ref{tb:params}, and is the minimum signal to noise ratio on the modulus of the observed seismogram for windowing to continue.
+\item[{\tt WINDOW\_S2N\_BASE}]Corresponds to $r_0$ in Table~\ref{tb:params}, and is the minimum signal to noise ratio for a window on the observed seismogram to be acceptable.
+\item[{\tt STALTA\_BASE}]Corresponds to $w_E$ in Table~\ref{tb:params}, and is the water level to be applied to the synthetic short-term/long-term average waveform in order to generate candidate time windows. See Figure~\ref{fg:win_composite}a.
+\item[{\tt CC\_BASE}]Corresponds to $CC_0$ in Table~\ref{tb:params}, and is the minimum normalized cross-correlation value between synthetic and observed seismogram for a window to be acceptable.
+\item[{\tt TSHIFT\_BASE}]Corresponds to $\Delta\tau_0$ in Table~\ref{tb:params}, and is the maximum cross-correlation lag (in seconds) between synthetic and observed seismogram for a window to be acceptable.
+\item[{\tt DLNA\_BASE}]Corresponds to $\Delta\ln{A}_0$ in Table~\ref{tb:params}, and is the maximum amplitude ratio ($\Delta\ln{A}$ or $\Delta A/A$) between synthetic and observed seismogram for a window to be acceptable.
+\item[{\tt TSHIFT\_REFERENCE}]Corresponds to $\Delta\tau_{\rm ref}$ in Table~\ref{tb:params}, and allows for a systematic traveltime bias in the synthetics.
+\item[{\tt TSHIFT\_REFERENCE}]Corresponds to $\Delta\ln{A}_{\rm ref}$ in Table~\ref{tb:params}, and allows for a systematic amplitude bias in the synthetics.
+\item[{\tt C\_0}]Corresponds to $C_0$ in Table~\ref{tb:params}, and is expressed as a multiple of $w_E$. No window may contain a local minimum in its STA:LTA waveform that falls below the local value of $C_0 w_E$. See Figure~\ref{fg:win_composite}b.
+\item[{\tt C\_1}]Corresponds to $C_1$ in Table~\ref{tb:params}, and is expressed as a multiple of $T_0$. No window may be shorter than $C_1 T_0$.
+\item[{\tt C\_2}]Corresponds to $C_2$ in Table~\ref{tb:params}, and is expressed as a multiple of $w_E$. A window whose seed maximum on the STA:LTA waveform rises less than $C_2 w_E$ above either of its adjacent minima is rejected. See Figure~\ref{fg:win_composite}c.
+\item[{\tt C\_{3a}}]Corresponds to $C_{3a}$ in Table~\ref{tb:params}, and is expressed as a fraction. It regulates the acceptable height ratio between local maxima in a given window on the STA:LTA waveform. See Figure~\ref{fg:separation}.
+\item[{\tt C\_{3b}}]Corresponds to $C_{3b}$ in Table~\ref{tb:params}, and is expressed as a multiple of $T_0$. It regulates the acceptable time separation between local maxima in a given window on the STA:LTA waveform. See Figure~\ref{fg:separation}.
+\item[{\tt C\_{4a}}]Corresponds to $C_{4a}$ in Table~\ref{tb:params}, and is expressed as a multiple of $T_0$. It limits the length of a window before its first local maximum in STA:LTA.
+\item[{\tt C\_{4b}}]Corresponds to $C_{4b}$ in Table~\ref{tb:params}, and is expressed as a multiple of $T_0$. It limits the length of a window beyond its last local maximum in STA:LTA. See Figure~\ref{fg:win_composite}d.
+\item[{\tt WEIGHT\_AVERAGE\_CC}]Corresponds to $w_{CC}$ in Table~\ref{tb:params}, and is the weight given to the average cross-correlation value in the process of resolving window overlaps. See Figure~\ref{fg:phaseD}.
+\item[{\tt WEIGHT\_SPACE\_COVERAGE}]Corresponds to $w_{\rm len}$ in Table~\ref{tb:params}, and is the weight given to the time span covered by windows in the process of resolving window overlaps.
+\item[{\tt WEIGHT\_N\_WINDOWS}]Corresponds to $w_{\rm nwin}$ in Table~\ref{tb:params}, and is the weight given to the total number of windows in the process of resolving window overlaps.
+\end{description}
+
+\begin{table}
+\begin{center}
+\begin{tabular}{lcccccc}
+\hline
+ & Global & \multicolumn{2}{c}{Japan} & \multicolumn{3}{c}{S. California} \\
+\hline
+$T_{0,1}$ & 50, 150 & 24, 120 & 6, 30 & 6, 30 & 3, 30 & 2, 30 \\
+$r_{P,A}$ & 3.5, 3.0 & 3.5, 3.0 & 3.5, 3.0 & 3.0, 2.5 & 2.5, 3.5 & 2.5, 3.5 \\
+$r_0$ & 2.5 & 1.5 & 3.0 & 3.0 & 4.0 & 4.0 \\
+$w_E$ & 0.08 & 0.11 & 0.12 & 0.18 & 0.11 & 0.07 \\
+$\mathrm{CC}_0$ & 0.85 & 0.70 & 0.73 & 0.71 & 0.80 & 0.85 \\
+$\Delta\tau_0$ & 15 & 12.0 & 3.0 & 8.0 & 4.0 & 3.0 \\
+$\Delta\ln{A}_0$ & 1.0 & 1.0 & 1.5 & 1.5 & 1.0 & 1.0 \\
+$\Delta\tau_{\rm ref}$ & 0.0 & 0.0 & 0.0 & 4.0 & 2.0 & 1.0 \\
+$\Delta\ln{A}_{\rm ref}$& 0.0 & 0.0 & 0.0 & 0.0 & 0.0 & 0.0 \\
+\hline
+$c_0$ & 0.7 & 0.7 & 0.7 & 0.7 & 1.3 & 1.0 \\
+$c_1$ & 4.0 & 3.0 & 3.0 & 2.0 & 4.0 & 5.0 \\
+$c_2$ & 0.3 & 0.0 & 0.6 & 0.0 & 0.0 & 0.0 \\
+$c_{3a,b}$ & 1.0, 2.0 & 1.0, 2.0 & 1.0, 2.0 & 3.0, 2.0 & 4.0, 2.5 & 4.0, 2.5 \\
+$c_{4a,b}$ & 3.0, 10.0 & 3.0, 25.0 & 3.0, 12.0 & 2.5, 12.0 & 2.0, 6.0 & 2.0, 6.0 \\
+$w_{\mathrm{CC}}, w_{\rm len}, w_{\rm nwin}$
+ & 1, 1, 1 & 1, 1, 1 & 1, 1, 1 & 0.5,1.0,0.7 & 0.70,0.25,0.05 & 1,1,1 \\
+\hline
+\end{tabular}
+\caption{\label{tb:example_params}
+Values of standard and fine-tuning parameters for the three seismological
+scenarios discussed \cite{MaggiEtal2009}. This table is identical to Table~3 of that study.
+}
+\end{center}
+\end{table}
+
+\begin{figure}
+\center \includegraphics[width=6in]{window_composite.pdf}
+\caption{\label{fg:win_composite}
+(a)~Window creation process. The thick black line represents the STA:LTA
+waveform $E(t)$, and the thick horizontal dashed line its water level $w_E(t)$.
+Local maxima are indicated by alternating red and blue dots, windows are
+indicated by two-headed horizontal arrows. The time of the local maximum used
+as the window seed $t_M$ is denoted by the position of the dot. Only windows for the fourth local maximum are shown. (b)~Rejection of candidate windows based on the amplitude of the local minima. The two deep
+local minima indicated by the grey arrows form virtual barriers. All candidate
+windows that cross these barriers are rejected.
+(c)~Rejection of candidate
+windows based on the prominence of the seed maximum. The local maxima
+indicated by the grey arrows are too low compared to the local minima
+adjacent to them. All windows that have these local maxima as their seed are
+rejected (black crosses over the window segments below the time series).
+(d)~Shortening of long coda windows. The grey bar indicates the maximum coda
+duration $c_{4b} T_0$. Note that after the rejection based on prominence represented in (c) and before shortening of long coda windows represented in (d), the algorithm rejects candidate windows based on the separation of distinct phases, a process that is illustrated in Figure~\ref{fg:separation}.
+}
+\end{figure}
+
+\begin{figure}
+\center \includegraphics[width=5in]{window_rejection_separation.pdf}
+\caption{\label{fg:separation}
+Rejection of candidate windows based on the separation of distinct phases.
+(a)~Heights of pairs of local maxima above their intervening minimum.
+(b)~The black line represents the limiting value of $h/h_M$. Vertical bars represent
+$h/h_M$ for each pair of maxima. Their position along the horizontal axis is
+given by the time separation $\Delta T$ between the maxima of each pair. The
+color of the bar is given by the color of the seed maximum corresponding to $h_M$. Bars whose height
+exceeds the line represent windows to be rejected.
+(c)~The windows that have been rejected by this criterion are indicated by black
+crosses.
+}
+\end{figure}
+
+\begin{figure}
+\center \includegraphics[width=5in]{window_overlap.pdf}
+\caption{\label{fg:phaseD}
+The selection of the best non-overlapping window
+combinations. Each grey box represents a distinct group of windows.
+Non-overlapping subsets of windows are shown on separate lines. Only one
+line from within each group will be chosen, the one corresponding to the
+highest weighted score. The resulting optimal set
+of data windows is shown by thick arrows.}
+\end{figure}
+
+\section{Time dependence of user parameters}
+A subset of the FLEXWIN parameters from Table~\ref{tb:params} are time-dependent (where time is measured along the seismogram). This feature enables the user to exercise fine control of the windowing algorithm. The user can modulate the time-dependence of these parameters by editing the {\tt set\_up\_criteria\_arrays} subroutine in the {\tt user\_functions.f90} file. This subroutine is called after the seismograms have been read in, and the following variables have been set:
+\begin{description}
+\item[{\tt npts, dt, b}] Number of points, time step, time of first point with respect to the reference time of both seismograms. The observed and synthetic seismograms should have identical values of these three quantities.
+\item[{\tt evla, evlo, evdp, stla, stlo}] Event latitude, event longitude, event depth (km), station latitude, station longitude, read from the observed seismogram.
+\item[{\tt azimuth, backazimuth, dist\_deg, dist\_km}] Calculated from the event and station locations above.
+\item[{\tt kstnm, knetwk, kcmpnm}] Station name, network name, component name, read from the observed seismogram.
+\item[{\tt num\_phases, ph\_names, ph\_times}] Number, names and arrival times of standard seismic phases calculated through IASPEI91 using the event depth and epicentral distance.
+\end{description}
+
+The {\tt set\_up\_criteria\_arrays} subroutine first sets up non time-modulated versions of the time-dependent parameters using a simple loop over time:
+{\small
+\begin{verbatim}
+! -----------------------------------------------------------------
+! This is the basic version of the subroutine - no variation with time
+! -----------------------------------------------------------------
+ do i = 1, npts
+ time=b+(i-1)*dt
+ DLNA_LIMIT(i)=DLNA_BASE
+ CC_LIMIT(i)=CC_BASE
+ TSHIFT_LIMIT(i)=TSHIFT_BASE
+ STALTA_W_LEVEL(i)=STALTA_BASE
+ S2N_LIMIT(i)=WINDOW_AMP_BASE
+ enddo
+\end{verbatim}
+}
+It is then up to the user to modulate these values for the specific problem at hand. For example, should the user want to discourage the algorithm from picking windows beyond the end of the first surface wave-train $R1$, the following lines should be added to the {\tt user\_functions.f90} file to raise the water level on the STA:LTA waveform by a factor of ten:
+{\small
+\begin{verbatim}
+ ! --------------------------------
+ ! Set approximate end of rayleigh wave arrival
+ R_vel=3.2
+ R_time=dist_km/R_vel
+ ! --------------------------------
+ ! modulate criteria in time
+ do i = 1, npts
+ time=b+(i-1)*dt
+ if (time.gt.R_time) then
+ STALTA_W_LEVEL(i)=STALTA_BASE*10.0
+ endif
+ enddo
+\end{verbatim}
+}
+Should the user want the algorithm to be less stringent in its requirements for the cross-correlation fit for the surface wave portion of the seismograms, and allow a greater travel-time lag for deeper events, the required lines could be:
+{\small
+\begin{verbatim}
+ ! --------------------------------
+ ! Set approximate end of rayleigh wave arrival
+ R_vel=3.2
+ R_time=dist_km/R_vel
+ ! --------------------------------
+ ! Set approximate start of love wave arrival
+ Q_vel=4.2
+ Q_time=dist_km/Q_vel
+ ! --------------------------------
+ ! modulate criteria in time
+ do i = 1, npts
+ time=b+(i-1)*dt
+ ! if we are in the surface wave times, then make the cross-correlation
+ ! criterion less severe
+ if (time.gt.Q_time .and. time.lt.R_time) then
+ CC_LIMIT(i)=0.9*CC_LIMIT(i)
+ endif
+ ! --------------------------------
+ ! modulate criteria according to event depth
+ !
+ ! if an intermediate depth event
+ if (evdp.ge.70 .and. evdp.lt.300) then
+ TSHIFT_LIMIT(i)=TSHIFT_BASE*1.4
+ ! if a deep event
+ elseif (evdp.ge.300) then
+ TSHIFT_LIMIT(i)=TSHIFT_BASE*1.7
+ endif
+ enddo
+ \end{verbatim}
+}
+ The above examples illustrate the power of the {\tt user\_functions.f90} file. The user can choose to include/exclude any portion of the seismogram, and to make the rejection criteria for windows more or less stringent on any other portion of the seismogram. All the seismogram-dependent variables whose values are known when the {\tt set\_up\_criteria\_arrays} subroutine is executed may be used to inform these choices, leading to an infinite number of windowing possibilities. The careful user will use knowledge of the properties of the observed data set, the limitations of the synthetic waveforms, and the final use to which the selected windows will be put in order to tailor the subroutine to the needs of each study.
+
+ For a given set of data and synthetics, the {\tt PAR\_FILE} and {\tt user\_functions.f90} files uniquely determine the windowing results.
+
+\subsection{Examples of user functions\label{ap:user_fn}}
+
+%As concrete examples of how the time dependence of the tuning parameters can be exploited, we present here the functional forms of the time dependencies used for the three example tomographic scenarios (global, Japan and southern California) described in \cite{MaggiEtal2009}.
+Here we present the time dependencies of tuning parameters used for three tomographic scenarios \citep{MaggiEtal2009}: global, Japan and southern California.
+In each example we use predicted arrival times derived from 1D Earth models to help modulate certain parameters. Note, however, that the actual selection of individual windows is based on the details of the waveforms, and not on information from 1D Earth models.
+
+\subsubsection{Global scenario\label{ap:user_global}}
+
+In the following, $h$ indicates earthquake depth, $t_Q$ indicates the approximate start of the Love wave predicted by a group wave speed of 4.2~\kmps, and $t_R$ indicates the approximate end of the Rayleigh wave predicted by a group wave speed of 3.2~\kmps. In order to reduce the number of windows picked beyond R1, and to ensure that those selected beyond R1 are a very good match to the synthetic waveform, we raise the water level on the STA:LTA waveform and impose stricter criteria on the signal-to-noise ratio and the waveform similarity after the approximate end of the surface-wave arrivals. We allow greater flexibility in cross-correlation time lag $\Delta\tau$ for intermediate depth and deep earthquakes. We lower the cross-correlation value criterion for surface-waves in order to retain windows with a slight mismatch in dispersion characteristics.
+
+We therefore use the following time modulations:
+\begin{align}
+w_E(t) & =
+ \begin{cases}
+ w_E \text{$t \leq t_R$} ,\\
+ 2 w_E \text{$t > t_R$},
+ \end{cases}
+\\
+r_0(t) & =
+ \begin{cases}
+ r_0 & \text{$t \leq t_R$}, \\
+ 10r_0 & \text{$t > t_R$} ,
+ \end{cases}
+\\
+\mathrm{CC}_0(t) & =
+ \begin{cases}
+ \mathrm{CC}_0 & \text{$t \leq t_R$}, \\
+ 0.9 \mathrm{CC}_0 & \text{$t_Q < t \leq t_R$}, \\
+ 0.95 & \text{$t > t_R$} ,
+ \end{cases}
+\\
+\Delta\tau_0(t) & =
+ \begin{cases}
+ \begin{cases}
+ \tau_0 & \text{$t \leq t_R$}, \\
+ \tau_0/3 & \text{$t > t_R$} ,
+ \end{cases}
+ & \text{$h \leq$ 70~km} \\
+ 1.4\tau_0 & \text{70~km $< h <$ 300~km}, \\
+ 1.7\tau_0 & \text{$h \geq$ 300~km},
+ \end{cases}
+ \\
+\Delta \ln A_0(t) & =
+ \begin{cases}
+ \Delta \ln A_0 & \text{$t \leq t_R$}, \\
+ \Delta \ln A_0/3 & \text{$t > t_R$} .
+ \end{cases}
+\end{align}
+
+%--------------------------
+
+\subsubsection{Japan scenario\label{ap:user_japan}}
+In the following, $t_P$ and $t_S$ denote the start of the time windows for $P$- and $S$ waves, as predicted by the 1-D IASPEI91 model \citep{KennettEngdahl1991}, and $t_{R1}$ indicates the end of the surface-wave time window. For the \trange{24}{120} data, we consider the waveform between the start of the $P$ wave to the end of the surface-wave. We therefore modulate $w_E(t)$ as follows:
+
+%
+\begin{align}
+w_E(t) & =
+ \begin{cases}
+ 10 w_E & \text{$t < t_P$}, \\
+ w_E & \text{$t_P \le t \leq t_{R1}$}, \\
+ 10 w_E & \text{$t > t_{R1}$}.
+ \end{cases}
+\end{align}
+
+For the \trange{6}{30} data, the fit between the synthetic and observed surface-waves is expected to be poor, as the 3D model used to calculate the synthetics cannot produce the required complexity. We therefore want to concentrate on body-wave arrivals only, and avoid surface-wave windows altogether by modulating $w_E(t)$ as follows:
+%
+\begin{align}
+w_E(t) & =
+ \begin{cases}
+ 10 w_E & \text{$t < t_P$}, \\
+ w_E & \text{$t_P \le t \leq t_S$}, \\
+ 10 w_E & \text{$t > t_S$}.
+ \end{cases}
+\end{align}
+
+We use constant values of $r_0(t)=r_0$, $\mathrm{CC}_0(t)=\mathrm{CC}_0$ and $\Delta \ln A_0(t)=\Delta \ln A_0$ for both period ranges. In order to allow greater flexibility in cross-correlation time lag $\Delta\tau$ for intermediate depth and deep earthquakes we use:
+
+\begin{align}
+\Delta\tau_0(t) & =
+ \begin{cases}
+ 0.08 \text{$t_P$} & \text{$h \leq$ 70~km}, \\
+ \max(0.05 \text{$t_P$}, 1.4\tau_0) & \text{70~km $< h <$ 300~km}, \\
+ \max(0.05 \text{$t_P$}, 1.7\tau_0) & \text{$h \geq$ 300~km}.
+ \end{cases}
+\end{align}
+%--------------------------
+
+\subsubsection{Southern California scenario\label{ap:user_socal}}
+
+In the following, $t_P$ and $t_S$ denote the start of the time windows for the crustal P wave and the crustal S wave, computed from a 1D layered model appropriate to Southern California \citep{Wald95}. The start and end times for the surface-wave time window, $t_{R0}$ and $t_{R1}$, as well as the criteria for the time shifts $\Delta\tau_0(t)$, are derived from formulas in \cite{KomatitschEtal2004}. The source-receiver distance (in km) is denoted by $\Delta$.
+
+%CHT modified
+
+For the \trange{6}{30} and \trange{3}{30} data, we use constant values of $r_0(t)=r_0$, $\mathrm{CC}_0(t)=\mathrm{CC}_0$, $\Delta\tau_0(t)=\Delta\tau_0$, and $\Delta \ln A_0(t)=\Delta \ln A_0$. We exclude any arrivals before the $P$ wave and after the Rayleigh wave. This is achieved by the box-car function for $w_E(t)$:
+%
+\begin{align}
+w_E(t) & =
+ \begin{cases}
+ 10 w_E & \text{$t < t_P$}, \\
+ w_E & \text{$t_P \le t \leq t_{R1}$}, \\
+ 10 w_E & \text{$t > t_{R1}$},
+ \end{cases}
+\end{align}
+%For the \trange{6}{30} data, we exclude any arrivals before the $P$ wave and reduce the number of windows picked beyond R1 by modulating $w_E(t)$. We use constant values of $r_0(t)=r_0$, $\mathrm{CC}_0(t)=\mathrm{CC}_0$ and $\Delta \ln A_0(t)=\Delta \ln A_0$, but modulate the cross-correlation time lag criterion so that it is less strict at larger epicentral distances and for surface-waves. We therefore use:
+%
+%\begin{align}
+%w_E(t) & =
+% \begin{cases}
+% 10 w_E & \text{$t < t_P$}, \\
+% w_E & \text{$t_P \le t \leq t_{R1}$}, \\
+% 2 w_E & \text{$t > t_{R1}$},
+% \end{cases}
+%\\
+%\Delta\tau_0(t) & =
+% \begin{cases}
+% 3.0 + \Delta/80.0 & \text{$t \le t_{R0}$}, \\
+% 3.0 + \Delta/50.0 & \text{$t > t_{R0}$},
+% \end{cases}
+%\end{align}
+
+For the \trange{2}{30} data, we avoid selecting surface-wave arrivals as the 3D model used to calculate the synthetics cannot produce the required complexity. The water-level criteria then becomes:
+
+\begin{align}
+w_E(t) & =
+ \begin{cases}
+ 10 w_E & \text{$t < t_P$}, \\
+ w_E & \text{$t_P \le t \leq t_S$}, \\
+ 10 w_E & \text{$t > t_S$}.
+ \end{cases}
+%\\
+%\Delta\tau_0(t) & = \Delta\tau_0.
+\end{align}
+
+
+%-----------------------
+
+
+\section{Tuning considerations}
+FLEXWIN is not a black-box application and should not be applied blindly
+to any given dataset or tomographic scenario. The data windowing required by
+any given problem will differ depending on the inversion method, the scale of
+the problem (local, regional, global), the quality of the data set, the quality of the model,
+and the accuracy of the method used to calculate the synthetic seismograms. The user
+must configure and tune the algorithm for the given problem. Here we
+discuss general considerations the user should bear in mind.
+
+We suggest the following as a practical starting sequence for tuning the algorithm.
+Keep in mind that this process may need to be repeated and refined several times before
+converging on the optimal set of parameters for a given problem and data-set.
+
+$T_{0,1}$ : In setting the corner periods of the bandpass filter, the
+user is deciding on the frequency content of the information to be used in the
+tomographic problem. Values of these corner periods should reflect the
+information content of the data, the quality of the Earth model and the
+accuracy of the simulation used to generate the synthetic seismogram. The
+frequency content in the data depends on the spectral characteristics of the
+source, on the instrument responses, and on the attenuation
+characteristics of the medium. As $T_{0,1}$ depend on the source and station
+characteristics, which may be heterogeneous in any given data-set, these filter
+periods can be modified dynamically by constructing an appropriate user
+function (e.g. {\em if station is in list of stations with instrument X then
+reset T0 and T1 to new values}).
+
+$r_{P,A}$ : In setting the signal-to-noise ratios for the entire seismogram, the
+user is applying a simple quality control on the data. Note that these criteria
+are applied after filtering. No windows will be defined on data that fail this
+quality control.
+
+$w_E(t)$ : For a constant signal the short-term average long-term average ratio, $E(t)$,
+converges to a constant value when
+the length of the time-series is greater than the effective averaging length of
+the long-term average. This value is 0.08 for the short-term average long-term average ratio used in FLEXWIN (it has a small dependence on $T_0$, which can be ignored in most applications). We suggest the user start with a constant
+level for $w_E(t)$ equal to this convergence value. The time dependence of
+$w_E(t)$ should then be adjusted to exclude those portions of the waveform the
+user is not interested in, by raising $w_E(t)$ (e.g. to exclude the fundamental
+mode surface-wave: {\em if t $>$ fundamental mode surface-wave arrival time then set $w_E(t)=1$}).
+We suggest finer adjustments to $w_E(t)$ be made after $r0(t)$,
+$CC_0(t)$, $\Delta T_0(t)$ and $\Delta \ln A_0(t)$ have been configured.
+
+$r_0(t)$, $\mathrm{CC}_0(t)$, $\Delta \tau_{\rm ref}$, $\Delta
+\tau_0(t)$, $\Delta \ln A_{\rm ref}$ and $\Delta \ln A_0(t)$ : These parameters ---
+window signal-to-noise ratio, normalized cross-correlation value between
+observed and synthetic seismograms, cross-correlation time lag, and amplitude
+ratio --- control the degree of well-behavedness of the data within accepted
+windows. The user first sets constant values for these four parameters, then
+adds a time dependence if required. Considerations that should be taken into
+account include the quality of the Earth model used to calculate the synthetic
+seismograms, the frequency range, the dispersed nature of certain arrivals (e.g.
+{\em for t corresponding to the group velocities of surface-waves, reduce
+$CC_0(t)$}), and {\em a priori} preferences for picking certain small-amplitude seismic phases
+(e.g. {\em for t close to the expected arrival for $P_{\rm diff}$, reduce $r_0(t)$}).
+$\Delta \tau_{\rm ref}$ and $\Delta \ln A_{\rm ref}$ should be set to zero at first, and only
+reset if the synthetics contain a systematic bias in traveltimes or amplitudes.
+
+
+$c_{0-4}$ : These parameters control the process by which the suite of all possible data windows is pared down using criteria on the shape of the STA:LTA $E(t)$ waveform alone. We suggest the user start by setting these values to those used in our global example (see Table~\ref{tb:example_params}). Subsequent minimal tuning should be performed by running the algorithm on a subset of the data and closely examining the lists of windows rejected at each stage to make sure the user agrees with the choices made by the algorithm.
+
+$w_{\mathrm{CC}}$, $w_{\rm len}$ and $w_{\rm nwin}$ : These parameters control the overlap resolution stage of the algorithm. Values of $w_{\mathrm{CC}}= w_{\rm len} = w_{\rm nwin} = 1$ should be reasonable for most applications.
+
+The objective of the tuning process summarized here should be to maximize the selection of windows around desirable features in the seismogram, while minimizing the selection of undesirable features.
+Of course, the desirability or undesirability of a given feature is subjective, and it depends on how the user subsequently intends to use the information contained within the data windows.
+
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