This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex 2016.7.18)  15 SEP 2016 11:31
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**ug_cat
(./ug_cat.tex
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk12.clo
File: bk12.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
\c@part=\count79
\c@chapter=\count80
\c@section=\count81
\c@subsection=\count82
\c@subsubsection=\count83
\c@paragraph=\count84
\c@subparagraph=\count85
\c@figure=\count86
\c@table=\count87
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 2014/10/28 v1.0g Enhanced LaTeX Graphics (DPC,SPQR)

(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks14
)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2016/01/03 v1.0q Standard LaTeX Graphics (DPC,SPQR)

(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 2016/01/03 v1.10 sin cos tan (DPC)
)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg
File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
)
Package graphics Info: Driver file: pdftex.def on input line 95.

(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty
Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO)
)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
)
\Gread@gobject=\count88
))
\Gin@req@height=\dimen103
\Gin@req@width=\dimen104
)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/epsfig.sty
Package: epsfig 1999/02/16 v1.7a (e)psfig emulation (SPQR)
\epsfxsize=\dimen105
\epsfysize=\dimen106
)
(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty
Package: a4 2004/04/15 v1.2g A4 based page layout
)
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2010/09/12 v5.6 Page Geometry

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty
Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
Package ifpdf Info: pdfTeX in PDF mode is detected.
)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty
Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
Package ifvtex Info: VTeX not detected.
)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
\Gm@cnth=\count89
\Gm@cntv=\count90
\c@Gm@tempcnt=\count91
\Gm@bindingoffset=\dimen107
\Gm@wd@mp=\dimen108
\Gm@odd@mp=\dimen109
\Gm@even@mp=\dimen110
\Gm@layoutwidth=\dimen111
\Gm@layoutheight=\dimen112
\Gm@layouthoffset=\dimen113
\Gm@layoutvoffset=\dimen114
\Gm@dimlist=\toks15
)
(/usr/share/texlive/texmf-dist/tex/latex/tools/afterpage.sty
Package: afterpage 2014/10/28 v1.08 After-Page Package (DPC)
\AP@output=\toks16
\AP@partial=\box26
\AP@footins=\box27
)
(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty
Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols)
\symlasy=\mathgroup4
LaTeX Font Info:    Overwriting symbol font `lasy' in version `bold'
(Font)                  U/lasy/m/n --> U/lasy/b/n on input line 52.
)
(/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty
\UL@box=\box28
\UL@hyphenbox=\box29
\UL@skip=\skip43
\UL@hook=\toks17
\UL@height=\dimen115
\UL@pe=\count92
\UL@pixel=\dimen116
\ULC@box=\box30
Package: ulem 2012/05/18
\ULdepth=\dimen117
)
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty
Package: natbib 2010/09/13 8.31b (PWD, AO)
\bibhang=\skip44
\bibsep=\skip45
LaTeX Info: Redefining \cite on input line 694.
\c@NAT@ctr=\count93
) (./ug_cat.aux

LaTeX Warning: Label `ssec_evolfourier' multiply defined.


LaTeX Warning: Label `eq_jacobian02_Jall' multiply defined.

)
\openout1 = `ug_cat.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 35.
LaTeX Font Info:    ... okay on input line 35.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 35.
LaTeX Font Info:    ... okay on input line 35.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 35.
LaTeX Font Info:    ... okay on input line 35.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 35.
LaTeX Font Info:    ... okay on input line 35.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 35.
LaTeX Font Info:    ... okay on input line 35.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 35.
LaTeX Font Info:    ... okay on input line 35.
 (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count94
\scratchdimen=\dimen118
\scratchbox=\box31
\nofMPsegments=\count95
\nofMParguments=\count96
\everyMPshowfont=\toks18
\MPscratchCnt=\count97
\MPscratchDim=\dimen119
\MPnumerator=\count98
\makeMPintoPDFobject=\count99
\everyMPtoPDFconversion=\toks19
) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO
)

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty
Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
)
Package pdftexcmds Info: LuaTeX not detected.
Package pdftexcmds Info: \pdf@primitive is available.
Package pdftexcmds Info: \pdf@ifprimitive is available.
Package pdftexcmds Info: \pdfdraftmode found.
)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf

(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty
Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
Package etexcmds Info: Could not find \expanded.
(etexcmds)             That can mean that you are not using pdfTeX 1.50 or
(etexcmds)             that some package has redefined \expanded.
(etexcmds)             In the latter case, load this package earlier.
)))
Package grfext Info: Graphics extension search list:
(grfext)             [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE
G,.JBIG2,.JB2,.eps]
(grfext)             \AppendGraphicsExtensions on input line 452.

(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
e
))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: a4paper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: twoside 
* h-part:(L,W,R)=(56.9055pt, 483.69687pt, 56.9055pt)
* v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt)
* \paperwidth=597.50787pt
* \paperheight=845.04684pt
* \textwidth=483.69687pt
* \textheight=731.23584pt
* \oddsidemargin=-15.36449pt
* \evensidemargin=-15.36449pt
* \topmargin=-47.23828pt
* \headheight=12.0pt
* \headsep=19.8738pt
* \topskip=12.0pt
* \footskip=30.0pt
* \marginparwidth=57.81621pt
* \marginparsep=7.0pt
* \columnsep=10.0pt
* \skip\footins=10.8pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidetrue
* \@mparswitchtrue
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <14.4> on input line 50.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <7> on input line 50.
LaTeX Font Info:    Try loading font information for U+lasy on input line 50.
(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd
File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions
)
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <5> on input line 50.
 [1


{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2

] (./ug_cat.toc
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <12> on input line 3.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <8> on input line 3.
LaTeX Font Info:    External font `cmex10' loaded for size
(Font)              <6> on input line 3.
 [3])
\tf@toc=\write3
\openout3 = `ug_cat.toc'.

 [4] [5

] [6]
(./chap_evoleq.tex
Chapter 1.
[7

] [8] [9]) [10] [11

] [12] (./chap_cathist.tex
Chapter 2.

Package natbib Warning: Citation `fraedrichetal1998' on page 13 undefined on in
put line 5.


Package natbib Warning: Citation `borthetal2016' on page 13 undefined on input 
line 6.

) (./chap_pseudospec.tex [13

] [14

]
Chapter 3.
[15]
Overfull \hbox (22.24377pt too wide) in paragraph at lines 195--199
\OT1/cmr/m/n/12 On the dis-cretized grid in the phys-i-cal space the modes with
 wave num-bers $(\OML/cmm/m/it/12 k[]; k[]\OT1/cmr/m/n/12 ) = (\OMS/cmsy/m/n/12
 ^^@\OML/cmm/m/it/12 N=\OT1/cmr/m/n/12 2\OML/cmm/m/it/12 ; \OMS/cmsy/m/n/12 ^^@
\OML/cmm/m/it/12 M=\OT1/cmr/m/n/12 2)$
 []

[16] [17] [18]
Overfull \hbox (8.27783pt too wide) in paragraph at lines 673--680
\OT1/cmr/m/n/12 The per-mu-ta-tion ma-trix $\OML/cmm/m/it/12 P[]$ \OT1/cmr/m/n/
12 maps the in-put vec-tor $[]$ to $[]$, a $4$-component
 []

[19] <figures/phys_grid.pdf, id=78, 796.9775pt x 597.23125pt>
File: figures/phys_grid.pdf Graphic file (type pdf)

<use figures/phys_grid.pdf>
Package pdftex.def Info: figures/phys_grid.pdf used on input line 877.
(pdftex.def)             Requested size: 341.72076pt x 256.0748pt.

<figures/cmplx_real_spec_grid.pdf, id=79, 796.9775pt x 597.23125pt>
File: figures/cmplx_real_spec_grid.pdf Graphic file (type pdf)

<use figures/cmplx_real_spec_grid.pdf>
Package pdftex.def Info: figures/cmplx_real_spec_grid.pdf used on input line 89
1.
(pdftex.def)             Requested size: 417.6533pt x 312.9803pt.
 [20] [21 <./figures/phys_grid.pdf> <./figures/cmplx_real_spec_grid.pdf

pdfTeX warning: pdflatex (file ./figures/cmplx_real_spec_grid.pdf): PDF inclusi
on: multiple pdfs with page group included in a single page
>] <figures/cmplx_cent_grid.pdf, id=119, 796.9775pt x 597.23125pt>
File: figures/cmplx_cent_grid.pdf Graphic file (type pdf)

<use figures/cmplx_cent_grid.pdf>
Package pdftex.def Info: figures/cmplx_cent_grid.pdf used on input line 934.
(pdftex.def)             Requested size: 417.6533pt x 312.9803pt.
 [22 <./figures/cmplx_cent_grid.pdf>]
Overfull \hbox (0.47232pt too wide) in paragraph at lines 989--995
\OT1/cmr/m/n/12 and the cor-re-spond-ing ve-loc-ity fields $[](\OML/cmm/m/it/12
 k[]; k[]; t\OT1/cmr/m/n/12 )$ and $[](\OML/cmm/m/it/12 k[]; k[]; t\OT1/cmr/m/n
/12 )$ once the vor-tic-ity field $[](\OML/cmm/m/it/12 k[]; k[]; t\OT1/cmr/m/n/
12 )$
 []

[23] [24] [25] <figures/diss_mask.pdf, id=151, 796.9775pt x 597.23125pt>
File: figures/diss_mask.pdf Graphic file (type pdf)

<use figures/diss_mask.pdf>
Package pdftex.def Info: figures/diss_mask.pdf used on input line 1418.
(pdftex.def)             Requested size: 379.68704pt x 284.52756pt.
) (./chap_sims.tex [26] [27 <./figures/diss_mask.pdf>] [28

]
Chapter 4.
) [29] [30] [31

] [32] (./chap_impcat.tex
Chapter 5.
) (./chap_runcat.tex [33

] [34

]
Chapter 6.
) (./chap_catoutput.tex [35] [36

]
Chapter 7.
) (./chap_modifycat.tex [37] [38

]
Chapter 8.
) [39] [40

] [41] [42] (./app_namelists.tex
Appendix A.

Underfull \hbox (badness 10000) in paragraph at lines 2--6

 []


Underfull \hbox (badness 10000) in paragraph at lines 7--12

 []

) (./app_modulsvariables.tex
Underfull \vbox (badness 10000) has occurred while \output is active []

 [43

]
[44]
Appendix B.
) (./app_codestruct.tex [45

] [46

]
Appendix C.
) (./ug_cat.bbl [47] [48

])

Package natbib Warning: There were undefined citations.

[49] (./ug_cat.aux)

LaTeX Warning: There were multiply-defined labels.

 ) 
Here is how much of TeX's memory you used:
 2718 strings out of 494953
 38626 string characters out of 6180977
 117251 words of memory out of 5000000
 5926 multiletter control sequences out of 15000+600000
 11515 words of font info for 45 fonts, out of 8000000 for 9000
 14 hyphenation exceptions out of 8191
 38i,12n,32p,424b,256s stack positions out of 5000i,500n,10000p,200000b,80000s
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></us
r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/public/amsfonts/cm/cmmi6.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
ublic/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmr6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl12.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on ug_cat.pdf (49 pages, 328058 bytes).
PDF statistics:
 304 PDF objects out of 1000 (max. 8388607)
 204 compressed objects within 3 object streams
 0 named destinations out of 1000 (max. 500000)
 21 words of extra memory for PDF output out of 10000 (max. 10000000)