Added remaining projects.

alpha_spectroscopy/adv_lab.bib

@@ -0,0 +1,8 @@
+@ONLINE{Doe:2009:Online,
+author = {Doe, Ringo},
+title = {This is a test entry of type {@ONLINE}},
+month = jun,
+year = {2009},
+url = {http://www.test.org/doe/}
+}
+

alpha_spectroscopy/report.text

@@ -0,0 +1 @@
+Alpha-partcicle spectroscopy is a method for testing and measuring the properties of any alpha emitter, which is a class of radioactive particles the emit alpha particles, a bound collection of two protons and two neutrons 

alpha_spectroscopy/report/examples.bib

@@ -0,0 +1,230 @@
+
+
+@article{article,
+  author  = {Peter Adams}, 
+  title   = {The title of the work},
+  journal = {The name of the journal},
+  year    = 1993,
+  number  = 2,
+  pages   = {201-213},
+  month   = 7,
+  note    = {An optional note}, 
+  volume  = 4
+}
+
+@book{book,
+  author    = {Peter Babington}, 
+  title     = {The title of the work},
+  publisher = {The name of the publisher},
+  year      = 1993,
+  volume    = 4,
+  series    = 10,
+  address   = {The address},
+  edition   = 3,
+  month     = 7,
+  note      = {An optional note},
+  isbn      = {3257227892}
+}
+
+@booklet{booklet,
+  title        = {The title of the work},
+  author       = {Peter Caxton}, 
+  howpublished = {How it was published},
+  address      = {The address of the publisher},
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@conference{conference,
+  author       = {Peter Draper}, 
+  title        = {The title of the work},
+  booktitle    = {The title of the book},
+  year         = 1993,
+  editor       = {The editor},
+  volume       = 4,
+  series       = 5,
+  pages        = 213,
+  address      = {The address of the publisher},
+  month        = 7,
+  organization = {The organization},
+  publisher    = {The publisher},
+  note         = {An optional note}  
+}
+
+@inbook{inbook,
+  author       = {Peter Eston}, 
+  title        = {The title of the work},
+  chapter      = 8,
+  pages        = {201-213},
+  publisher    = {The name of the publisher},
+  year         = 1993,
+  volume       = 4,
+  series       = 5,
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  note         = {An optional note}
+}
+
+@incollection{incollection,
+  author       = {Peter Farindon}, 
+  title        = {The title of the work},
+  booktitle    = {The title of the book},
+  publisher    = {The name of the publisher},
+  year         = 1993,
+  editor       = {The editor},
+  volume       = 4,
+  series       = 5,
+  chapter      = 8,
+  pages        = {201-213},
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  note         = {An optional note}
+}
+
+@manual{manual,
+  title        = {The title of the work},
+  author       = {Peter Gainsford}, 
+  organization = {The organization},
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@mastersthesis{mastersthesis,
+  author       = {Peter Harwood}, 
+  title        = {The title of the work},
+  school       = {The school of the thesis},
+  year         = 1993,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@misc{misc,
+  author       = {Peter Isley}, 
+  title        = {The title of the work},
+  howpublished = {How it was published},
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@phdthesis{phdthesis,
+  author       = {Peter Joslin}, 
+  title        = {The title of the work},
+  school       = {The school of the thesis},
+  year         = 1993,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@proceedings{proceedings,
+  title        = {The title of the work},
+  year         = 1993,
+  editor       = {Peter Kidwelly},
+  volume       = 4,
+  series       = 5,
+  address      = {The address of the publisher},
+  month        = 7,
+  organization = {The organization},
+  publisher    = {The name of the publisher},
+  note         = {An optional note}
+}
+
+@techreport{techreport,
+  author       = {Peter Lambert}, 
+  title        = {The title of the work},
+  institution  = {The institution that published},
+  year         = 1993,
+  number       = 2,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@unpublished{unpublished,
+  author       = {Peter Marcheford}, 
+  title        = {The title of the work},
+  note         = {An optional note},
+  month        = 7,
+  year         = 1993
+}
+                            
+
+@ONLINE{Doe:2009:Online,
+author = {Doe, Ringo},
+title = {This is a test entry of type {@ONLINE}},
+month = jun,
+year = {2009},
+url = {http://www.test.org/doe/}
+}
+
+@article
+{ahu61,
+
+   author={Arrow, Kenneth J. and Leonid Hurwicz and Hirofumi Uzawa
+},
+   title={Constraint qualifications in maximization problems
+},
+   journal=
+{Naval Research Logistics Quarterly},
+   volume={8},
+   year=1961
+,
+   pages={175-191
+}
+}
+
+@book{ab94,
+   author* = {Charalambos D. Aliprantis and Kim C. Border},
+   year = {1994},
+   title = {Infinite Dimensional Analysis},
+   publisher = {Springer},
+   address = {Berlin}
+}
+
+*A book must have either an author field or an editor field.
+
+@incollection{m85,
+   author={Maskin, Eric S.},
+   year={1985},
+   title={The theory of implementation in {N}ash
+ equilibrium: a survey},
+   booktitle={Social Goals and Social Organization},
+   editor={Leonid Hurwicz and David Schmeidler and Hugo Sonnenschein},
+   pages={173-204},
+   publisher={Cambridge University Press},
+   address={Cambridge}
+}
+
+@inproceedings{ah2006,
+   author={Aggarwal, Gagan and Hartline, Jason D.},
+   year={2006},
+   title={Knapsack auctions},
+   booktitle={Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms},
+   pages={1083-1092},
+   publisher={Association for Computing Machinery},
+   address={New York}
+}
+
+@techreport{arrow48,
+  author = {Arrow, Kenneth J.},
+  title = {The possibility of a universal social welfare function},
+  institution = {RAND Corporation},
+  year = {1948},
+  number = {P-41},
+  type = {Report}
+}
+
+@unpublished{FudenbergKreps1988,
+  title = {A theory of learning, experimentation, and equilibrium in games},
+  author = {Fudenberg, Drew and Kreps, David M.},
+  year = {1988},
+  note = {Unpublished paper}
+}

alpha_spectroscopy/report/report.bib

@@ -0,0 +1,274 @@
+@ARTICLE{2016ApJ...821...56F,
+   author = {{Fausnaugh}, M.~M. and {Denney}, K.~D. and {Barth}, A.~J. and 
+    {Bentz}, M.~C. and {Bottorff}, M.~C. and {Carini}, M.~T. and 
+    {Croxall}, K.~V. and {De Rosa}, G. and {Goad}, M.~R. and {Horne}, K. and 
+    {Joner}, M.~D. and {Kaspi}, S. and {Kim}, M. and {Klimanov}, S.~A. and 
+    {Kochanek}, C.~S. and {Leonard}, D.~C. and {Netzer}, H. and 
+    {Peterson}, B.~M. and {Schn{\"u}lle}, K. and {Sergeev}, S.~G. and 
+    {Vestergaard}, M. and {Zheng}, W.-K. and {Zu}, Y. and {Anderson}, M.~D. and 
+    {Ar{\'e}valo}, P. and {Bazhaw}, C. and {Borman}, G.~A. and {Boroson}, T.~A. and 
+    {Brandt}, W.~N. and {Breeveld}, A.~A. and {Brewer}, B.~J. and 
+    {Cackett}, E.~M. and {Crenshaw}, D.~M. and {Dalla Bont{\`a}}, E. and 
+    {De Lorenzo-C{\'a}ceres}, A. and {Dietrich}, M. and {Edelson}, R. and 
+    {Efimova}, N.~V. and {Ely}, J. and {Evans}, P.~A. and {Filippenko}, A.~V. and 
+    {Flatland}, K. and {Gehrels}, N. and {Geier}, S. and {Gelbord}, J.~M. and 
+    {Gonzalez}, L. and {Gorjian}, V. and {Grier}, C.~J. and {Grupe}, D. and 
+    {Hall}, P.~B. and {Hicks}, S. and {Horenstein}, D. and {Hutchison}, T. and 
+    {Im}, M. and {Jensen}, J.~J. and {Jones}, J. and {Kaastra}, J. and 
+    {Kelly}, B.~C. and {Kennea}, J.~A. and {Kim}, S.~C. and {Korista}, K.~T. and 
+    {Kriss}, G.~A. and {Lee}, J.~C. and {Lira}, P. and {MacInnis}, F. and 
+    {Manne-Nicholas}, E.~R. and {Mathur}, S. and {McHardy}, I.~M. and 
+    {Montouri}, C. and {Musso}, R. and {Nazarov}, S.~V. and {Norris}, R.~P. and 
+    {Nousek}, J.~A. and {Okhmat}, D.~N. and {Pancoast}, A. and {Papadakis}, I. and 
+    {Parks}, J.~R. and {Pei}, L. and {Pogge}, R.~W. and {Pott}, J.-U. and 
+    {Rafter}, S.~E. and {Rix}, H.-W. and {Saylor}, D.~A. and {Schimoia}, J.~S. and 
+    {Siegel}, M. and {Spencer}, M. and {Starkey}, D. and {Sung}, H.-I. and 
+    {Teems}, K.~G. and {Treu}, T. and {Turner}, C.~S. and {Uttley}, P. and 
+    {Villforth}, C. and {Weiss}, Y. and {Woo}, J.-H. and {Yan}, H. and 
+    {Young}, S.},
+    title = "{McGraw-Hill Dictionary of Scientific & Technical Terms}",
+  journal = {ApJ},
+archivePrefix = "arXiv",
+   eprint = {1510.05648},
+ keywords = {galaxies: active, galaxies: individual: NGC 5548, galaxies: nuclei, galaxies: Seyfert},
+     year = 2016,
+    month = apr,
+   volume = 821,
+      eid = {56},
+    pages = {56},
+      doi = {10.3847/0004-637X/821/1/56},
+   adsurl = {http://adsabs.harvard.edu/abs/2016ApJ...821...56F},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2016Natur.535..388K,
+   author = {{Kara}, E. and {Miller}, J.~M. and {Reynolds}, C. and {Dai}, L.
+  },
+    title = "{Relativistic reverberation in the accretion flow of a tidal disruption event}",
+  journal = {\nat},
+archivePrefix = "arXiv",
+   eprint = {1606.06736},
+ primaryClass = "astro-ph.HE",
+     year = 2016,
+    month = jul,
+   volume = 535,
+    pages = {388-390},
+      doi = {10.1038/nature18007},
+   adsurl = {http://adsabs.harvard.edu/abs/2016Natur.535..388K},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+@ARTICLE{2007MNRAS.380..669C,
+   author = {{Cackett}, E.~M. and {Horne}, K. and {Winkler}, H.},
+    title = "{Testing thermal reprocessing in active galactic nuclei accretion discs}",
+  journal = {MNRAS},
+archivePrefix = "arXiv",
+   eprint = {0706.1464},
+ keywords = {galaxies: active, galaxies: nuclei, galaxies: Seyfert},
+     year = 2007,
+    month = sep,
+   volume = 380,
+    pages = {669-682},
+      doi = {10.1111/j.1365-2966.2007.12098.x},
+   adsurl = {http://adsabs.harvard.edu/abs/2007MNRAS.380..669C},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2014A&ARv..22...72U,
+   author = {{Uttley}, P. and {Cackett}, E.~M. and {Fabian}, A.~C. and {Kara}, E. and 
+    {Wilkins}, D.~R.},
+    title = "{X-ray reverberation around accreting black holes}",
+  journal = {A\&ARv},
+archivePrefix = "arXiv",
+   eprint = {1405.6575},
+ primaryClass = "astro-ph.HE",
+ keywords = {Accretion, accretion disks, Black hole physics, Galaxies: active, Galaxies: Seyfert, X-rays: binaries},
+     year = 2014,
+    month = aug,
+   volume = 22,
+      eid = {72},
+    pages = {72},
+      doi = {10.1007/s00159-014-0072-0},
+   adsurl = {http://adsabs.harvard.edu/abs/2014A%26ARv..22...72U},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2013ApJ...777...24Z,
+   author = {{Zoghbi}, A. and {Reynolds}, C. and {Cackett}, E.~M.},
+    title = "{Calculating Time Lags from Unevenly Sampled Light Curves}",
+  journal = {ApJ},
+archivePrefix = "arXiv",
+   eprint = {1308.5852},
+ primaryClass = "astro-ph.HE",
+ keywords = {black hole physics, galaxies: active, galaxies: nuclei, methods: data analysis },
+     year = 2013,
+    month = nov,
+   volume = 777,
+      eid = {24},
+    pages = {24},
+      doi = {10.1088/0004-637X/777/1/24},
+   adsurl = {http://adsabs.harvard.edu/abs/2013ApJ...777...24Z},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2015ApJ...806..129E,
+   author = {{Edelson}, R. and {Gelbord}, J.~M. and {Horne}, K. and {McHardy}, I.~M. and 
+  {Peterson}, B.~M. and {Ar{\'e}valo}, P. and {Breeveld}, A.~A. and 
+  {De Rosa}, G. and {Evans}, P.~A. and {Goad}, M.~R. and {Kriss}, G.~A. and 
+  {Brandt}, W.~N. and {Gehrels}, N. and {Grupe}, D. and {Kennea}, J.~A. and 
+  {Kochanek}, C.~S. and {Nousek}, J.~A. and {Papadakis}, I. and 
+  {Siegel}, M. and {Starkey}, D. and {Uttley}, P. and {Vaughan}, S. and 
+  {Young}, S. and {Barth}, A.~J. and {Bentz}, M.~C. and {Brewer}, B.~J. and 
+  {Crenshaw}, D.~M. and {Dalla Bont{\`a}}, E. and {De Lorenzo-C{\'a}ceres}, A. and 
+  {Denney}, K.~D. and {Dietrich}, M. and {Ely}, J. and {Fausnaugh}, M.~M. and 
+  {Grier}, C.~J. and {Hall}, P.~B. and {Kaastra}, J. and {Kelly}, B.~C. and 
+  {Korista}, K.~T. and {Lira}, P. and {Mathur}, S. and {Netzer}, H. and 
+  {Pancoast}, A. and {Pei}, L. and {Pogge}, R.~W. and {Schimoia}, J.~S. and 
+  {Treu}, T. and {Vestergaard}, M. and {Villforth}, C. and {Yan}, H. and 
+  {Zu}, Y.},
+    title = "{Space Telescope and Optical Reverberation Mapping Project. II. Swift and HST Reverberation Mapping of the Accretion Disk of NGC 5548}",
+  journal = {\apj},
+archivePrefix = "arXiv",
+   eprint = {1501.05951},
+ keywords = {galaxies: active, galaxies: individual: NGC 5548, galaxies: nuclei, galaxies: Seyfert},
+     year = 2015,
+    month = jun,
+   volume = 806,
+      eid = {129},
+    pages = {129},
+      doi = {10.1088/0004-637X/806/1/129},
+   adsurl = {http://adsabs.harvard.edu/abs/2015ApJ...806..129E},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2015ApJ...806..128D,
+   author = {{De Rosa}, G. and {Peterson}, B.~M. and {Ely}, J. and {Kriss}, G.~A. and 
+  {Crenshaw}, D.~M. and {Horne}, K. and {Korista}, K.~T. and {Netzer}, H. and 
+  {Pogge}, R.~W. and {Ar{\'e}valo}, P. and {Barth}, A.~J. and 
+  {Bentz}, M.~C. and {Brandt}, W.~N. and {Breeveld}, A.~A. and 
+  {Brewer}, B.~J. and {Dalla Bont{\`a}}, E. and {De Lorenzo-C{\'a}ceres}, A. and 
+  {Denney}, K.~D. and {Dietrich}, M. and {Edelson}, R. and {Evans}, P.~A. and 
+  {Fausnaugh}, M.~M. and {Gehrels}, N. and {Gelbord}, J.~M. and 
+  {Goad}, M.~R. and {Grier}, C.~J. and {Grupe}, D. and {Hall}, P.~B. and 
+  {Kaastra}, J. and {Kelly}, B.~C. and {Kennea}, J.~A. and {Kochanek}, C.~S. and 
+  {Lira}, P. and {Mathur}, S. and {McHardy}, I.~M. and {Nousek}, J.~A. and 
+  {Pancoast}, A. and {Papadakis}, I. and {Pei}, L. and {Schimoia}, J.~S. and 
+  {Siegel}, M. and {Starkey}, D. and {Treu}, T. and {Uttley}, P. and 
+  {Vaughan}, S. and {Vestergaard}, M. and {Villforth}, C. and 
+  {Yan}, H. and {Young}, S. and {Zu}, Y.},
+    title = "{Space Telescope and Optical Reverberation Mapping Project.I. Ultraviolet Observations of the Seyfert 1 Galaxy NGC 5548 with the Cosmic Origins Spectrograph on Hubble Space Telescope}",
+  journal = {\apj},
+archivePrefix = "arXiv",
+   eprint = {1501.05954},
+ keywords = {galaxies: active, galaxies: individual: NGC 5548, galaxies: nuclei, galaxies: Seyfert},
+     year = 2015,
+    month = jun,
+   volume = 806,
+      eid = {128},
+    pages = {128},
+      doi = {10.1088/0004-637X/806/1/128},
+   adsurl = {http://adsabs.harvard.edu/abs/2015ApJ...806..128D},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{1999MNRAS.302L..24C,
+   author = {{Collier}, S. and {Horne}, K. and {Wanders}, I. and {Peterson}, B.~M.
+  },
+    title = "{A new direct method for measuring the Hubble constant from reverberating accretion discs in active galaxies}",
+  journal = {\mnras},
+   eprint = {astro-ph/9811278},
+     year = 1999,
+    month = jan,
+   volume = 302,
+    pages = {L24-L28},
+      doi = {10.1046/j.1365-8711.1999.02250.x},
+   adsurl = {http://adsabs.harvard.edu/abs/1999MNRAS.302L..24C},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2016MNRAS.462..511K,
+   author = {{Kara}, E. and {Alston}, W.~N. and {Fabian}, A.~C. and {Cackett}, E.~M. and 
+  {Uttley}, P. and {Reynolds}, C.~S. and {Zoghbi}, A.},
+    title = "{A global look at X-ray time lags in Seyfert galaxies}",
+  journal = {\mnras},
+ keywords = {black hole physics, galaxies: active, X-rays: galaxies},
+     year = 2016,
+    month = oct,
+   volume = 462,
+    pages = {511-531},
+      doi = {10.1093/mnras/stw1695},
+   adsurl = {http://adsabs.harvard.edu/abs/2016MNRAS.462..511K},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@INPROCEEDINGS{2006pces.conf...89P,
+   author = {{Peterson}, B.~M. and {Horne}, K.},
+    title = "{Reverberation mapping of active galactic nuclei}",
+booktitle = {Planets to Cosmology: Essential Science in the Final Years of the Hubble Space Telescope},
+     year = 2006,
+   volume = 18,
+   editor = {{Livio}, M. and {Casertano}, S.},
+    month = jan,
+    pages = {89},
+   adsurl = {http://adsabs.harvard.edu/abs/2006pces.conf...89P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2012ARA&A..50..455F,
+   author = {{Fabian}, A.~C.},
+    title = "{Observational Evidence of Active Galactic Nuclei Feedback}",
+  journal = {\araa},
+archivePrefix = "arXiv",
+   eprint = {1204.4114},
+     year = 2012,
+    month = sep,
+   volume = 50,
+    pages = {455-489},
+      doi = {10.1146/annurev-astro-081811-125521},
+   adsurl = {http://adsabs.harvard.edu/abs/2012ARA%26A..50..455F},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{2015PASP..127...67B,
+   author = {{Bentz}, M.~C. and {Katz}, S.},
+    title = "{The AGN Black Hole Mass Database}",
+  journal = {\pasp},
+archivePrefix = "arXiv",
+   eprint = {1411.2596},
+     year = 2015,
+    month = jan,
+   volume = 127,
+    pages = {67-73},
+      doi = {10.1086/679601},
+   adsurl = {http://adsabs.harvard.edu/abs/2015PASP..127...67B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{2014SSRv..183..253P,
+   author = {{Peterson}, B.~M.},
+    title = "{Measuring the Masses of Supermassive Black Holes}",
+  journal = {\ssr},
+ keywords = {Active galactic nuclei, Black hole, Reverberation mapping},
+     year = 2014,
+    month = sep,
+   volume = 183,
+    pages = {253-275},
+      doi = {10.1007/s11214-013-9987-4},
+   adsurl = {http://adsabs.harvard.edu/abs/2014SSRv..183..253P},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{1973A&A....24..337S,
+   author = {{Shakura}, N.~I. and {Sunyaev}, R.~A.},
+    title = "{Black holes in binary systems. Observational appearance.}",
+  journal = {\aap},
+     year = 1973,
+   volume = 24,
+    pages = {337-355},
+   adsurl = {http://adsabs.harvard.edu/abs/1973A%26A....24..337S},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

chaos/CFJChaos/Licence.txt

@@ -0,0 +1,39 @@
+READ THE TERMS OF THIS AGREEMENT CAREFULLY BEFORE USING THE SOFTWARE. BY 
+USING THE SOFTWARE, YOU AGREE TO THE TERMS OF THIS AGREEMENT. IF YOU DO 
+NOT AGREE TO ALL THE TERMS, YOU ARE NOT AUTHORIZED TO DOWNLOAD OR USE THE 
+SOFTWARE IN ANY MANNER.
+
+1. LICENCE TO USE. You are granted a non-exclusive licence, for 
+non-commercial use only, of the accompanying Software (Chaos for Java).
+
+2. RESTRICTIONS. The Software is confidential and copyright. Title to the 
+Software and all associated intellectual property rights is retained by 
+the author. Copyright ©1999-2003 Brian Davies.
+
+3. MODIFICATION. Unless enforcement is prohibited by applicable law, or as
+permitted under clause 6 of the LGPL licence in respect of LGPL libraries, 
+you may not modify, decompile, or reverse engineer the Software.
+
+4. REDISTRIBUTION. You are granted permission to redistribute the software
+under this licence, provided that it is complete and accompanied by this 
+Licence Agreement and all other associated documentation and licences.
+
+5. INSTALLATION SCRIPTS. If the Software is provided with installation 
+scripts, then permission is granted to modify those scripts to allow the 
+Software to be installed on a particular computer or class of computers. 
+Permission is also granted to redistribute such modified scripts, provided
+that all changes are documented.
+
+6. DISCLAIMER OF WARRANTY. The Software is provided "AS IS", with no 
+warranty of any kind, including the warranty of design, merchantability 
+and fitness for a particular purpose.
+
+7. INTERPRETATION. This Licence Agreement shall be governed by the laws 
+of the Australian Capital Territory excluding those provisions related to 
+conflict of laws.
+
+8. TERMINATION. This Agreement is effective until terminated by you. You 
+may terminate this Agreement at any time by destroying all copies of the 
+Software.
+
+         -------------------------------------------------------

chaos/CFJChaos/ReadMe.txt

@@ -0,0 +1,166 @@
+CHAOS FOR JAVA - APPLICATION VERSION.
+
+The software is free for non commercial use without explicit permission 
+from the author. Before downloading or using it it you must read and agree
+to the licence agreement. All other rights reserved.
+
+Copyright ©1999-2003 Brian Davies.
+
+IMPORTANT NOTICE:
+
+Application Version 1.2.2 has no expiry date, but you should visit the website
+
+http://sunsite.anu.edu.au/education/chaos
+
+for information on later versions.
+
+FEATURES:
+
+Features of Application Version, beyond those of the Applet Version
+documented in my book "Exploring Chaos: theory and experiment", are 
+briefly summarised as:
+
+1. After startup there is a window which has menus and buttons. In the 
+MacOS9 version the window may be hidden using the close box (which does 
+not actually close it), in other versions it may be minimized once some
+other window(s) are open, since all windows carry menus (for the MacOS X
+version, menus are at the top of the screen and always present).
+
+2. Documents may be saved and then re-opened. You will be prompted 
+automatically about saving. Note that no computational or graphical 
+information is saved, only the parameter and window settings necessary 
+for exact reconstruction.
+
+3. Pictures/Graphs may be saved in the following cross platform formats:
+
+   (i) GIF - the compression algorithm is subject to patent and you assume
+       responsibility for any use you make of the output. This format may 
+       be omitted from future versions.
+
+   (ii) JPEG - the compression is not lossless but the quality setting is 
+       high, so the files will be quite large. In most circumstances this 
+       will not be the appropriate format to use.
+
+   (iii) PNG - this format was introduced (in part) to circumvent the use 
+       of patented algorithms. There is increasing support for PNG format 
+       in Browsers and Word Processors. The files will be small - probably
+       smaller than the GIF output.
+       
+4. Printing is possible, using the rudimentary printing features of Java 1.1.
+Because of these limitations, printing is not particularly good.  Device and
+resolution independence are supported in Java 1.2 (aka Java 2) and I expect
+to move to this when time permits.
+
+5. Preferences may be saved and re-loaded, ie, all choices available via 
+the Preferences menu. You will be prompted automatically about saving if 
+needed. Note that preferences are application wide, ie, fonts apply to all
+windows, colours to all windows of that type, ie, Bifurcation Diagrams 
+have distinct colour settings from Fourier Analysis, and so on.
+
+BUG REPORTS:
+
+Bug reports may be sent to
+
+Brian.Davies@anu.edu.au
+
+but it is essential to quote all the information in the startup panel, ie
+
+   (i) the platform and operating system - displayed top left,
+   (ii) the virtual machine information - displayed top right,
+   (iii) the Chaos for Java version - displayed bottom.
+
+VERSION HISTORY:
+
+   Version 1.0 - June 30, 1999. Original version released for use with book.
+
+   Version 1.0.1 - August 2, 1999. Resolves an incompatibility with 
+     Internet Explorer 5 for Windows.
+
+   Version 1.0.2 - September 22, 1999. Minor bug fixes.
+
+   Version 1.0.3 - October 1, 1999. Minor changes to allow application 
+     versions.
+
+   Version 1.0.4 - November 1, 1999. Enhancement (animation) of "Graphical
+     Analysis".
+
+   Version 1.0.5 - January 7, 2000. Minor bug fixes.
+
+   Version 1.1 - January 28, 2000. First application version.
+
+   Version 1.1 - March 1, 2000. Common applet/application version.
+
+   Version 1.1.1 - May 5, 2000. Save as png (portable network graphics) 
+     format. 8th order Runge-Kutta integration of ODEs. Enhancements 
+     of application version user interface.
+
+   Version 1.1.2 - November 1, 2000. Minor bug fixes. Enhancements of user 
+     interface and application preferences. Iterate(1d) has animation and 
+     includes 2d maps. Return maps include 1d maps. Saved files not all 
+     compatible with previous versions. 
+
+   Version 1.1.3 - April 24, 2001.
+     (i)  Major enhancement of Iterate(2d) to allow investigation of fixed 
+     points of two dimensional maps and compositions. The zero-curves of 
+     x - f(x,y) and y - g(x,y) may be viewed in the x-y plane, accurate positions 
+     and eigenvalues of fixed points may also be obtained. 
+     (ii)  ODEs: the two-well oscillator [f(x) = x(1-x^2)] and Duffing oscillator 
+     [f(x) = -x(1+x^2)] are included. 
+     (iii)  File format: version 1.1.3 will read and convert files saved from 
+     version 1.1.2 but the new file format is incompatible with earlier ones. 
+     (iv)  Minor bug fixes and user interface enhancements. 
+
+   Version 1.1.4 - October 22, 2001. 
+     (i)  Minor bug fixes and enhancements. 
+     (ii)  Version 1.1.4 will read and convert files saved from versions 1.1.2 
+     and 1.1.3 but the new file format is incompatible with earlier ones.
+
+   Version 1.1.5 - June 1, 2002.
+     (i)  Minor bug fixes. 
+     (ii)  Some features not documented in "Exploring Chaos: Theory and Experiment" 
+     temporarily removed.
+
+   Version 1.2 - June 2, 2003. 
+     (i)  Complete refactorisation of all code.
+     (ii)  Numerous interface improvements.
+     (iii)  Choice of display modes.
+     (iv)  Dual orbits for PoincarŽ sections.
+     (v)  Fixed points and stability analysis for compositions of two-dimensional
+     maps and PoincarŽ sections.
+     (vi)  Graphical visualisation of bifurcations of two-dimensional maps and
+     PoincarŽ sections.
+     (vii)  Basins of attraction for PoincarŽ sections.
+     (viii)  Bifurcation diagrams of stable and unstable orbits for two-dimensional maps.
+     (ix)  Better estimates of accuracy of fixed points of two-dimensional systems.
+     (x)  Variational equations used for Lyapunov exponents of PoincarŽ sections.
+
+   Version 1.2.1 - Septembeer 30, 2003. 
+     (i)  Minor big fixes.
+     (ii)  Improved algorithm for one-dimensional bifurcation diagrams (periodic orbits).
+     (iii)  MacOSX version has "aqua" appearance and Java 2 printing.
+
+   Version 1.2.2 - November 30, 2003. 
+     (i)  Java 2 printing for all platforms.
+     (ii)  Improvements to the graphical user interface.
+     (iii)  Minor bug fixes.
+
+ACKNOWLEDGEMENTS
+
+Development of this software has been assisted by support from the 
+Australian Apple University Consortium, 
+
+http://auc.uow.edu.au/
+
+an international cooperative program between Apple Computer and Australian
+Universities. One of its aims is to develop educational software for the 
+Macintosh environment.
+
+The Gif Encoder is Copyright (1996) by Jef Poskanzer (jef@acme.com).
+
+The Jpeg Encoder is Copyright (1998) by James R. Weeks and BioElectroMech 
+(James@obrador.com).
+
+The Png Encoder is Copyright (2000) by J. David Eisenberg 
+(david@catcode.com) (GNU Lesser General Public License).
+
+         -----------------------------------------------------------------------

chaos/CFJChaos/enc_lic/GIF.txt

@@ -0,0 +1,25 @@
+ Copyright (C) 1996 by Jef Poskanzer <jef@acme.com>.  All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR WISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+ Visit the ACME Labs Java page for up-to-date versions of this and 
+ fine Java utilities: http://www.acme.com/java/

chaos/CFJChaos/enc_lic/JPEG.txt

@@ -0,0 +1,25 @@
+The JpegEncoder and its associated classes are Copyright (c) 1998, James R.
+Weeks and BioElectroMech.  This software is based in part on the work of the
+Independent JPEG Group.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions, all files included with the source code, and the following
+disclaimer. 
+
+2. Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

chaos/CFJChaos/enc_lic/PNG.txt

@@ -0,0 +1,514 @@
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+  This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it.  You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+  When we speak of free software, we are referring to freedom of use,
+not price.  Our General Public Licenses are designed to make sure that
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+restrictions on the recipients' exercise of the rights granted herein.
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+
+
+  11. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
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+If any portion of this section is held invalid or unenforceable under any
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+
+This section is intended to make thoroughly clear what is believed to
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+
+  12. If the distribution and/or use of the Library is restricted in
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+
+  13. The Free Software Foundation may publish revised and/or new
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+Such new versions will be similar in spirit to the present version,
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+Each version is given a distinguishing version number.  If the Library
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+
+  14. If you wish to incorporate parts of the Library into other free
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+
+			    NO WARRANTY
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+  15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
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+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+
+           How to Apply These Terms to Your New Libraries
+
+  If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change.  You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+  To apply these terms, attach the following notices to the library.  It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the library's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This library is free software; you can redistribute it and/or
+    modify it under the terms of the GNU Lesser General Public
+    License as published by the Free Software Foundation; either
+    version 2.1 of the License, or (at your option) any later version.
+
+    This library is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public
+    License along with this library; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the
+  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+  <signature of Ty Coon>, 1 April 1990
+  Ty Coon, President of Vice
+
+That's all there is to it!
+
+
+

feedback/Quasars-and-Galaxies/wmu_feb08.txt

@@ -0,0 +1,10 @@
+        Quasars and the Birth & Evolution of Galaxies
+
+It was on February 5, 1963 (just 8 days before my birth) that astronomer
+Maarten Schmidt ran through the hallways of Caltech announcing that
+he had discovered the high redshift nature of quasars, then known only
+as mysterious points of light recently identified in radio surveys. In
+the interim period our understanding of their place in the universe has
+gone from that of isolated, ultraluminous freaks of nature to crucial
+links in the birth and evolution of massive galaxies. I will present an
+overview of these very recent and dramatic developments.

lag/data/Untitled.ipynb

@@ -0,0 +1,46 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "grid_array = []\n",
+    "\n",
+    "\n",
+    "grid_array_y = []\n",
+    "grid_array.append(grid_array_y)\n",
+    "\n",
+    "grid_array_y.append()\n",
+    "\n",
+    "\n",
+    "\n",
+    "while()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

lag/report/aas_macros.sty

@@ -0,0 +1,106 @@
+%
+%  These Macros are taken from the AAS TeX macro package version 5.2
+%  and are compatible with the macros in the A&A document class
+%  version 7.0
+%  Include this file in your LaTeX source only if you are not using
+%  the AAS TeX macro package or the A&A document class and need to
+%  resolve the macro definitions in the TeX/BibTeX entries returned by
+%  the ADS abstract service.
+%
+%  If you plan not to use this file to resolve the journal macros
+%  rather than the whole AAS TeX macro package, you should save the
+%  file as ``aas_macros.sty'' and then include it in your LaTeX paper
+%  by using a construct such as:
+%   \documentstyle[11pt,aas_macros]{article}
+%
+%  For more information on the AASTeX and A&A packages, please see:
+%       http://journals.aas.org/authors/aastex.html 
+%       ftp://ftp.edpsciences.org/pub/aa/readme.html
+%  For more information about ADS abstract server, please see:
+%       http://adsabs.harvard.edu/ads_abstracts.html
+%
+
+% Abbreviations for journals.  The object here is to provide authors
+% with convenient shorthands for the most "popular" (often-cited)
+% journals; the author can use these markup tags without being concerned
+% about the exact form of the journal abbreviation, or its formatting.
+% It is up to the keeper of the macros to make sure the macros expand
+% to the proper text.  If macro package writers agree to all use the
+% same TeX command name, authors only have to remember one thing, and
+% the style file will take care of editorial preferences.  This also
+% applies when a single journal decides to revamp its abbreviating
+% scheme, as happened with the ApJ (Abt 1991).
+
+\let\jnl@style=\rm
+\def\ref@jnl#1{{\jnl@style#1}}
+
+\def\aj{\ref@jnl{AJ}}                   % Astronomical Journal
+\def\actaa{\ref@jnl{Acta Astron.}}      % Acta Astronomica
+\def\araa{\ref@jnl{ARA\&A}}             % Annual Review of Astron and Astrophys
+\def\apj{\ref@jnl{ApJ}}                 % Astrophysical Journal
+\def\apjl{\ref@jnl{ApJ}}                % Astrophysical Journal, Letters
+\def\apjs{\ref@jnl{ApJS}}               % Astrophysical Journal, Supplement
+\def\ao{\ref@jnl{Appl.~Opt.}}           % Applied Optics
+\def\apss{\ref@jnl{Ap\&SS}}             % Astrophysics and Space Science
+\def\aap{\ref@jnl{A\&A}}                % Astronomy and Astrophysics
+\def\aapr{\ref@jnl{A\&A~Rev.}}          % Astronomy and Astrophysics Reviews
+\def\aaps{\ref@jnl{A\&AS}}              % Astronomy and Astrophysics, Supplement
+\def\azh{\ref@jnl{AZh}}                 % Astronomicheskii Zhurnal
+\def\baas{\ref@jnl{BAAS}}               % Bulletin of the AAS
+\def\bac{\ref@jnl{Bull. astr. Inst. Czechosl.}}
+                % Bulletin of the Astronomical Institutes of Czechoslovakia 
+\def\caa{\ref@jnl{Chinese Astron. Astrophys.}}
+                % Chinese Astronomy and Astrophysics
+\def\cjaa{\ref@jnl{Chinese J. Astron. Astrophys.}}
+                % Chinese Journal of Astronomy and Astrophysics
+\def\icarus{\ref@jnl{Icarus}}           % Icarus
+\def\jcap{\ref@jnl{J. Cosmology Astropart. Phys.}}
+                % Journal of Cosmology and Astroparticle Physics
+\def\jrasc{\ref@jnl{JRASC}}             % Journal of the RAS of Canada
+\def\memras{\ref@jnl{MmRAS}}            % Memoirs of the RAS
+\def\mnras{\ref@jnl{MNRAS}}             % Monthly Notices of the RAS
+\def\na{\ref@jnl{New A}}                % New Astronomy
+\def\nar{\ref@jnl{New A Rev.}}          % New Astronomy Review
+\def\pra{\ref@jnl{Phys.~Rev.~A}}        % Physical Review A: General Physics
+\def\prb{\ref@jnl{Phys.~Rev.~B}}        % Physical Review B: Solid State
+\def\prc{\ref@jnl{Phys.~Rev.~C}}        % Physical Review C
+\def\prd{\ref@jnl{Phys.~Rev.~D}}        % Physical Review D
+\def\pre{\ref@jnl{Phys.~Rev.~E}}        % Physical Review E
+\def\prl{\ref@jnl{Phys.~Rev.~Lett.}}    % Physical Review Letters
+\def\pasa{\ref@jnl{PASA}}               % Publications of the Astron. Soc. of Australia
+\def\pasp{\ref@jnl{PASP}}               % Publications of the ASP
+\def\pasj{\ref@jnl{PASJ}}               % Publications of the ASJ
+\def\rmxaa{\ref@jnl{Rev. Mexicana Astron. Astrofis.}}%
+                % Revista Mexicana de Astronomia y Astrofisica
+\def\qjras{\ref@jnl{QJRAS}}             % Quarterly Journal of the RAS
+\def\skytel{\ref@jnl{S\&T}}             % Sky and Telescope
+\def\solphys{\ref@jnl{Sol.~Phys.}}      % Solar Physics
+\def\sovast{\ref@jnl{Soviet~Ast.}}      % Soviet Astronomy
+\def\ssr{\ref@jnl{Space~Sci.~Rev.}}     % Space Science Reviews
+\def\zap{\ref@jnl{ZAp}}                 % Zeitschrift fuer Astrophysik
+\def\nat{\ref@jnl{Nature}}              % Nature
+\def\iaucirc{\ref@jnl{IAU~Circ.}}       % IAU Cirulars
+\def\aplett{\ref@jnl{Astrophys.~Lett.}} % Astrophysics Letters
+\def\apspr{\ref@jnl{Astrophys.~Space~Phys.~Res.}}
+                % Astrophysics Space Physics Research
+\def\bain{\ref@jnl{Bull.~Astron.~Inst.~Netherlands}} 
+                % Bulletin Astronomical Institute of the Netherlands
+\def\fcp{\ref@jnl{Fund.~Cosmic~Phys.}}  % Fundamental Cosmic Physics
+\def\gca{\ref@jnl{Geochim.~Cosmochim.~Acta}}   % Geochimica Cosmochimica Acta
+\def\grl{\ref@jnl{Geophys.~Res.~Lett.}} % Geophysics Research Letters
+\def\jcp{\ref@jnl{J.~Chem.~Phys.}}      % Journal of Chemical Physics
+\def\jgr{\ref@jnl{J.~Geophys.~Res.}}    % Journal of Geophysics Research
+\def\jqsrt{\ref@jnl{J.~Quant.~Spec.~Radiat.~Transf.}}
+                % Journal of Quantitiative Spectroscopy and Radiative Transfer
+\def\memsai{\ref@jnl{Mem.~Soc.~Astron.~Italiana}}
+                % Mem. Societa Astronomica Italiana
+\def\nphysa{\ref@jnl{Nucl.~Phys.~A}}   % Nuclear Physics A
+\def\physrep{\ref@jnl{Phys.~Rep.}}   % Physics Reports
+\def\physscr{\ref@jnl{Phys.~Scr}}   % Physica Scripta
+\def\planss{\ref@jnl{Planet.~Space~Sci.}}   % Planetary Space Science
+\def\procspie{\ref@jnl{Proc.~SPIE}}   % Proceedings of the SPIE
+
+\let\astap=\aap
+\let\apjlett=\apjl
+\let\apjsupp=\apjs
+\let\applopt=\ao

lag/report/examples.bib

@@ -0,0 +1,230 @@
+
+
+@article{article,
+  author  = {Peter Adams}, 
+  title   = {The title of the work},
+  journal = {The name of the journal},
+  year    = 1993,
+  number  = 2,
+  pages   = {201-213},
+  month   = 7,
+  note    = {An optional note}, 
+  volume  = 4
+}
+
+@book{book,
+  author    = {Peter Babington}, 
+  title     = {The title of the work},
+  publisher = {The name of the publisher},
+  year      = 1993,
+  volume    = 4,
+  series    = 10,
+  address   = {The address},
+  edition   = 3,
+  month     = 7,
+  note      = {An optional note},
+  isbn      = {3257227892}
+}
+
+@booklet{booklet,
+  title        = {The title of the work},
+  author       = {Peter Caxton}, 
+  howpublished = {How it was published},
+  address      = {The address of the publisher},
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@conference{conference,
+  author       = {Peter Draper}, 
+  title        = {The title of the work},
+  booktitle    = {The title of the book},
+  year         = 1993,
+  editor       = {The editor},
+  volume       = 4,
+  series       = 5,
+  pages        = 213,
+  address      = {The address of the publisher},
+  month        = 7,
+  organization = {The organization},
+  publisher    = {The publisher},
+  note         = {An optional note}  
+}
+
+@inbook{inbook,
+  author       = {Peter Eston}, 
+  title        = {The title of the work},
+  chapter      = 8,
+  pages        = {201-213},
+  publisher    = {The name of the publisher},
+  year         = 1993,
+  volume       = 4,
+  series       = 5,
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  note         = {An optional note}
+}
+
+@incollection{incollection,
+  author       = {Peter Farindon}, 
+  title        = {The title of the work},
+  booktitle    = {The title of the book},
+  publisher    = {The name of the publisher},
+  year         = 1993,
+  editor       = {The editor},
+  volume       = 4,
+  series       = 5,
+  chapter      = 8,
+  pages        = {201-213},
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  note         = {An optional note}
+}
+
+@manual{manual,
+  title        = {The title of the work},
+  author       = {Peter Gainsford}, 
+  organization = {The organization},
+  address      = {The address of the publisher},
+  edition      = 3,
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@mastersthesis{mastersthesis,
+  author       = {Peter Harwood}, 
+  title        = {The title of the work},
+  school       = {The school of the thesis},
+  year         = 1993,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@misc{misc,
+  author       = {Peter Isley}, 
+  title        = {The title of the work},
+  howpublished = {How it was published},
+  month        = 7,
+  year         = 1993,
+  note         = {An optional note}
+}
+
+@phdthesis{phdthesis,
+  author       = {Peter Joslin}, 
+  title        = {The title of the work},
+  school       = {The school of the thesis},
+  year         = 1993,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@proceedings{proceedings,
+  title        = {The title of the work},
+  year         = 1993,
+  editor       = {Peter Kidwelly},
+  volume       = 4,
+  series       = 5,
+  address      = {The address of the publisher},
+  month        = 7,
+  organization = {The organization},
+  publisher    = {The name of the publisher},
+  note         = {An optional note}
+}
+
+@techreport{techreport,
+  author       = {Peter Lambert}, 
+  title        = {The title of the work},
+  institution  = {The institution that published},
+  year         = 1993,
+  number       = 2,
+  address      = {The address of the publisher},
+  month        = 7,
+  note         = {An optional note}
+}
+
+@unpublished{unpublished,
+  author       = {Peter Marcheford}, 
+  title        = {The title of the work},
+  note         = {An optional note},
+  month        = 7,
+  year         = 1993
+}
+                            
+
+@ONLINE{Doe:2009:Online,
+author = {Doe, Ringo},
+title = {This is a test entry of type {@ONLINE}},
+month = jun,
+year = {2009},
+url = {http://www.test.org/doe/}
+}
+
+@article
+{ahu61,
+
+   author={Arrow, Kenneth J. and Leonid Hurwicz and Hirofumi Uzawa
+},
+   title={Constraint qualifications in maximization problems
+},
+   journal=
+{Naval Research Logistics Quarterly},
+   volume={8},
+   year=1961
+,
+   pages={175-191
+}
+}
+
+@book{ab94,
+   author* = {Charalambos D. Aliprantis and Kim C. Border},
+   year = {1994},
+   title = {Infinite Dimensional Analysis},
+   publisher = {Springer},
+   address = {Berlin}
+}
+
+*A book must have either an author field or an editor field.
+
+@incollection{m85,
+   author={Maskin, Eric S.},
+   year={1985},
+   title={The theory of implementation in {N}ash
+ equilibrium: a survey},
+   booktitle={Social Goals and Social Organization},
+   editor={Leonid Hurwicz and David Schmeidler and Hugo Sonnenschein},
+   pages={173-204},
+   publisher={Cambridge University Press},
+   address={Cambridge}
+}
+
+@inproceedings{ah2006,
+   author={Aggarwal, Gagan and Hartline, Jason D.},
+   year={2006},
+   title={Knapsack auctions},
+   booktitle={Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms},
+   pages={1083-1092},
+   publisher={Association for Computing Machinery},
+   address={New York}
+}
+
+@techreport{arrow48,
+  author = {Arrow, Kenneth J.},
+  title = {The possibility of a universal social welfare function},
+  institution = {RAND Corporation},
+  year = {1948},
+  number = {P-41},
+  type = {Report}
+}
+
+@unpublished{FudenbergKreps1988,
+  title = {A theory of learning, experimentation, and equilibrium in games},
+  author = {Fudenberg, Drew and Kreps, David M.},
+  year = {1988},
+  note = {Unpublished paper}
+}

report/report.tex

@@ -0,0 +1,275 @@
+
+
+
+\documentclass[11pt,letterpaper]{article}
+
+%\usepackage{aas_macros}
+\usepackage{biblatex}
+\usepackage{graphicx}
+\usepackage[margin=1.in,centering]{geometry}
+\usepackage{hyperref}
+\usepackage{caption}
+\usepackage[export]{adjustbox}
+\usepackage{float}
+\usepackage{gensymb}
+
+\bibliography{/home/caes/wmu/phy-4660/adv_lab.bib}
+
+\begin{document}
+
+
+\newcommand{\FpaO}{$^{19}\textrm{F(p,}\alpha)^{16}\textrm{O}$}
+\newcommand{\LipaHe}{$^7\textrm{Li(p,}\alpha)^4\textrm{He}$}
+
+%\newcommand{}$^7\textrm{Li(p,}\alpha)^4\textrm{He}$ reaction.\\
+
+
+
+
+
+
+\title{The Role of Active Galactic Nuclei in Galactic Evolution and Cosmology}
+\author{Otho Ulrich}
+\maketitle
+
+\begin{abstract}
+AGN Feedback\end{abstract}
+
+
+%─────────────
+\section{Introduction}
+    \label{sec:intro}
+    Bragg diffraction of X-rays is a useful method for characterising the atomic and molecular structure of materials. Many mechanical and electric properties are functions of the atomic structures that constitute materials. Bragg diffraction uses the wave theory of electromagnetic radiation to predict how x-rays will interact with the atomic lattice of a crystal. The spacing between atoms can be measured by inference, and these spacings are called the lattice constants.\\
+
+    We attempt to compute the lattice constant from an x-ray diffractometer reading of a sample of NaCl, or common salt. NaCl forms a cubic crystal structure, so it has a single lattice constant. This will be computed from the diffraction pattern and compared to known values. Three amorphous samples will also be analyzed: plastic of an unknown type; grease; and wood. These materials are not expected to have rigid crystal structures, but the average spacing between atoms can be ascertained from the diffraction pattern. These materials are  made of mostly carbon, with some hydrogen and oxygen. We therefore expect their densities to be nearly that of amorphous carbon.\\
+
+\section{Bragg Diffraction}
+    \label{subsec:bragg}
+    The diffraction angle of x-rays by atoms in a crystal lattice or other molecule depends on the distance between atoms. The lattice constants of a crystal describe the distances and angles between atoms, but in the case of a cubic lattice such as NaCl, there is only one relevant lattice constant. Bragg diffraction predicts strong x-ray signals at diffraction angles that produce constructive interference. Figure~\ref{fig:bragg} illustrates the geometry of Bragg diffraction; the distance between planes d is the lattice constant, and the Bragg condition
+
+        \begin{equation}
+            \centering 2d\sin \theta = n\lambda,
+        \end{equation}
+
+    where $\lambda$ is the photon wavelength of the X-ray and $n$ a positive integer describes the angles at which strong signals should be detected. \cite{advlabxrd} \\
+
+    \begin{figure}
+        \center
+        \includegraphics[width=3in]{braggdiffraction.png}
+        \caption{Bragg diffraction from a cubic crystal lattice. Plane waves incident on a crystal lattice at angle $\theta$ are partially reflected by successive parallel crystal planes of spacing d. The superposed reflected waves interfere constructively if the Bragg condition $2d\sin \theta =n\lambda$ is satisfied. \cite{braggdiff_wiki}} 
+        \label{fig:bragg}
+    \end{figure}
+
+    The modern approach to analyzing materials by Bragg diffraction is to interpret the output as the reciprocal space representation of the lattice positions. An inverse Fourier transform then gives the positions that make the lattice. The HighScore Plus software, associated with the Empyrean XRD, is used to perform these operations. \cite{highscore}\\
+
+    A crystal powder sample will have random orientations across all possible rotations in 3 dimensions; we call this powder diffraction. In a cubic crystal the Miller indices ($h~k~l$) describe the orientation of the planes, predicting periodic lattice points along the z-axis that will produce constructive interference. While the lattice constant does not change, each orientation may result in a different diffraction spacing, so a powder diffraction will result in a diffraction pattern where signals are observed at many angles; observe Figure~\ref{fig:miller}. The lattice constant can be computed in each case.\\
+
+
+%─────────────
+\section{Material Structure}
+    \label{subsec:nacl}
+    The structure of some samples tested here are known. NaCl is a face-centered cubic lattice with lattice constant $a = 564.02 \textrm{pm}$. \cite{naclwiki} This closely agrees with the value reported by Wallace and Barrett: $a = 5.64 \pm 0.0005 \textrm{\AA}$. \cite{10.1021/ja01631a014} The allowed miller indices for a FCC lattice are given in Table~\ref{tab:cubicstructure}, with the computed diffraction spacing, and some of the geometries are shown in Figure~\ref{fig:miller}. \\
+
+    \begin{table}
+        \centering
+        \begin{tabular}{llllll}
+            h & k & l & Spacing () & $2\theta (\degree)$ & Reflected Int. (\%) \\
+            \hline                              
+            1 & 1 & 1 & 3.26 & 27.367 & 8.7        \\
+            0 & 0 & 2 & 2.82 & 31.704 & 100        \\
+            0 & 2 & 2 & 1.99 & 45.449 & 64.3       \\
+            1 & 1 & 3 & 1.70 & 53.87  & 2.2        \\
+            2 & 2 & 2 & 1.63 & 56.474 & 20.2       \\
+            0 & 0 & 4 & 1.41 & 66.229 & 8.7        \\
+            1 & 3 & 3 & 1.29 & 73.072 & 1          \\
+            0 & 2 & 4 & 1.26 & 75.294 & 22.5       \\
+            2 & 2 & 4 & 1.15 & 83.994 & 16.2       \\
+        \end{tabular}
+        \caption{Allowed Miller indices ($h~k~l$) for NaCl. For each, the predicted diffraction spacing along the axis normal to the sample surface is predicted, and the incidence angle with its expected reflected intensity. \cite{10.1021/ja01631a014} \cite{highscore}}
+        \label{tab:cubicstructure}
+    \end{table}
+
+    \begin{figure}[]
+        [A]\includegraphics[width=1.4in]{FCC_002.pdf}
+        [B]\includegraphics[width=1.4in]{FCC_111.pdf}
+        [C]\includegraphics[width=1.4in]{FCC_022.pdf}
+        [D]\includegraphics[width=1.4in]{FCC_133.pdf}
+        \caption{Four of the atomic plane orientations of a face-centered cubic lattice that result in Bragg diffraction. The Miller indices ($h~k~l$) for each structure are [A] (0 0 2) [B] (1 1 1) [C] (0 2 2) [D] (1 3 3). The predicted diffraction spacings are tabulated in Table~\ref{tab:cubicstructure}}
+        \label{fig:miller}
+    \end{figure}
+
+    Amorphous materials consisting of mostly carbon have complex structures. Therefore, they are difficult to analyze in detail. \cite{C3CS60279F} The diffraction pattern peak should reach a maximum at the angle $\theta$ corresponding to the average distance between atoms, and lesser peaks can be expected as indicators of other prominent structures within a sample. These values will be determined and a density computed from the average distance between atoms. \cite{advlabxrd} \\
+
+
+    \begin{table}
+        \centering
+        \begin{tabular}{rlllll}
+        Mat. & Packing Frac. & Density (g/cm$^3$) & Atomic Mass (g) &  MAC (cm$^2$/g) & Pen. Depth ($\mu \textrm{m}$) \\
+        \hline
+        NaCl    & 0.7 & 2.165 & -                       & 73.7 & 206 \\
+        Carbon & 0.6 & 2.0   & $1.99442\times10^{-23}$ & 4.3   & 4460 \\
+        \end{tabular}
+        \caption{Properties of interest for the materials analyzed in this study. Values for the amorphous materials are assumed to be those of amorphous carbon. Packing fractions are rough estimates. The mass attenuation coefficients are taken from the NIST Hubbell and Seltzer database, and used by HighScore Plus to compute the penetration depth. Densities and atomic mass are as reported on Wikipedia, April 17, 2017. \cite{MACNIST} \cite{naclwiki} \cite{carbonwiki}}
+        \label{tab:properties}
+    \end{table}
+
+    \subsection{Penetration Depth}
+        \label{subsec:pendepth}
+
+        The penetration depth of Cu K-$\alpha_1$ is computed for each material. This is the depth in a material by which 98\% of the photons at this energy will have attentuated. The defining formula
+
+        \begin{equation}
+            I_L = I_0 \times e^{-(\frac{\mu}{\rho}\rho L)}
+        \end{equation}
+    
+        is valid for symmetric (gonio) scans. \cite{highscore} The HighScore Plus software computes the penetration depth from the mass attentuation coefficient, specific gravity of the material, and a powder packing fraction. These values are tabulated in Table~\ref{tab:properties} along with the computed penetration depths. Penetration depth is computed for an incidence angle 90\degree, which gives maximum penetration. \\
+
+%─────────────
+
+\section{X-ray Diffractometer}
+    \label{subsec:diffrator}
+    An Empyrean x-ray diffractometer by PANalytical \cite{empyrean} was used to collect a diffraction pattern from each sample. In this machine, an x-ray source emits onto a material sample, and a detector records x-rays diffracted at the angle of incidence; see Figure~\ref{fig:diffractometer}. X-rays are created by accelerating electrons toward a copper anode (Figure~\ref{fig:xraysource}). The X'Celerator detector is an x-ray sensor consisting of 127 single-file barrier detectors with copper K-$\alpha$ efficiency $>94\%$ \cite{xcelerator}.\\
+
+    The sample container depth was not measured during the experiment -- a major oversight. A best guess for the sample tray depth is $1.5\pm.3$ cm. If the penetration depth of a material exceeds this distance, diffraction from the container may be observed, contaminating the results.
+
+    \begin{figure}
+        \center
+        \includegraphics[width=3in]{empyrean_sample.jpg}
+        \includegraphics[width=3in]{empyrean_scanners.pdf}
+        \caption{The PANalytical Empyrean x-ray diffractometer. A sample is placed in a bin at the center. X-rays are generated in the arm on the left, diffracted at an incidence angle $\theta$ by the sample at the center, and detected at a reflected angle $\theta$ by the X'Celerator in the arm on the right. Each scan runs through $\theta = \{5\degree .. 45\degree\}$.}
+        \label{fig:diffractometer}
+    \end{figure}
+
+    \begin{figure}
+        \center
+        [A]\includegraphics[width=3in]{xraytube.png}
+        [B]\includegraphics[width=3in]{Copper_K_Rontgen.png}
+        \caption{[A] X-rays are generated when collisions with accelerated electrons knock electrons in the copper atoms of the anode out of the K shell. When the electrons fall back to the K shell, x-rays are emitted with energies indicated in [B]. These energy values are important for predicting the x-ray diffraction pattern from Bragg diffraction. \cite{advlabxrd} \cite{xraytubephoto}}
+        \label{fig:xraysource}
+    \end{figure}
+
+    \begin{table}
+        \centering
+        \begin{tabular}{cccc}
+            Copper Emission & Energy (eV) & Frequency (Hz) & Wavelength ($\textrm{\AA}$)\\
+            \hline
+            K-$\alpha_1$ & 8046 & 1.946$\times 10^{18}$ & 1.541\\
+            K-$\alpha_2$ & 8027 & 1.941$\times 10^{18}$ & 1.393\\
+            K-$\beta$    & 8903 & 2.153$\times 10^{18}$ & 1.545\\
+        \end{tabular}
+        \caption{Copper K-$\alpha$ and K-$\beta$ x-ray photon properties. The K-$\alpha_1$ is the primary driver of x-ray diffraction in this study, but the other x-rays are also present in smaller numbers.}
+        \label{tab:kalpha}
+    \end{table}
+
+
+    \subsection{Computational Details}
+        \label{sec:compdets}
+        The phases of the x-rays cannot be measured, so the HighScore Plus software from PANalytical determines the phase by fitting predicted profiles. To identify the NaCl pattern, a background is determined using the minimum 2nd derivative method with ``bending factor'' = 5, ``granularity'' = 20, and using smoothed input data. Peaks are located with ``minimum significant'' = 10.00, ``minimum tip width'' = 0.01, ``maximum tip width'' = 1.00, and ``peak base width'' = 2.00. \cite{highscore}.\\
+
+        The lattice constant $a$ is computed by
+
+        \begin{equation}
+            a = \textrm{diffraction spacing}\times\sqrt{h^2 + k^2 + l^2}.
+        \end{equation}
+
+        For the amorphous samples, peaks are identified by hand to within a standard error of $\pm0.05\degree$. We use the copper K-$\alpha$ wavelength from table \ref{tab:kalpha}: $\lambda = 1.541\times10^{-10} \textrm{\AA}$. The spacing is calculated as
+
+        \begin{equation}
+            d/n = \lambda / \left(2\sin\theta\right)
+        \end{equation}
+
+        with n = 1. Using the atomic mass and packing fraction from Table~\ref{tab:properties} allows the density $\rho$ to be computed as
+
+        \begin{equation}
+            \rho = \frac{\textrm{atomic mass}}{\textrm{unit cell volume}\times\textrm{packing fraction}}
+        \end{equation}
+
+        where the unit cell is assumed to be face-centered cubic with side length equal to the computed average distance.
+%─────────────    
+\section{Results}
+    \label{sec:results}
+
+    \begin{figure}
+        \centering
+        [A]\includegraphics[width=6.5in]{nacl_bumps.pdf}
+        [B]\includegraphics[width=6.5in]{nacl_compare_bumps.pdf}
+        \caption{[A] HighScore Plus identified the characteristic NaCl diffraction pattern from Cu K-$\alpha$ emission, and this is used to fit the phase and in turn determine the lattice constant. [B] At the most prominent peak, the detector measurements (red) strongly correlate with the computed diffraction lines (blue).}
+        \label{fig:nacldiffraction}
+    \end{figure}
+
+    \begin{table}
+    \centering
+        \begin{tabular}{llrlllc}
+            2$\theta$ (\degree) & Spacing ($\textrm{\AA}$) & Refl. Int. (\%) & h & k & l & Lattice Const. ($\textrm{\AA}$)\\
+            \hline
+            27.369~(0.000)&3.2588~(0.000)&2.32~(0.73)
+                &1&1&1&5.64$\pm0.35$\\
+            31.638~(0.002)&2.8258~(0.002)&100 ~(0.00)
+                &0&0&2&5.65$\pm0.40$\\
+            45.385~(0.001)&1.9967~(0.004)&16.75~(0.74)
+                &0&2&2&5.65$\pm0.56$\\
+            53.873~(0.000)&1.7004~(0.000)&0.58~(0.74)
+                &1&1&3&5.64$\pm0.66$\\
+            56.430~(0.000)&1.6293~(0.000)&4.36~(0.78)
+                &2&2&2&5.64$\pm0.69$\\
+            66.180~(0.000)&1.4109~(0.000)&8.96~(0.03)
+                &0&0&4&5.64$\pm0.80$\\
+            75.291~(0.000)&1.2612~(0.000)&5.54~(0.75)
+                &0&2&4&5.64$\pm0.89$\\
+            83.949~(0.000)&1.1518~(0.002)&2.42~(0.85)
+                &2&2&4&5.64$\pm0.98$\\
+        \end{tabular}
+    \caption{Observed peaks from the NaCl sample. Diffraction spacings and the reflected intensity ratios are computed for each. The Miller indices are determined by matching angular position with Table~\ref{tab:cubicstructure}. In parentheses is the ratio difference from predicted values in that table. These values are best matches reported by the HighScore software, but uncertainties were not reported. An inspection by eye gives approximately $\pm0.05\degree$ for 98\% confidence in the observed angle $2\theta$, and the computed standard error for the diffraction spacing is $\pm 0.20 \textrm{\AA}$.}
+    \label{tab:naclobs}
+    \end{table}
+
+    \begin{figure}[]
+    	[A] \includegraphics[width=1.9in]{plastic_peaks.pdf} 
+    	[B] \includegraphics[width=1.9in]{grease_peaks.pdf}  
+    	[C] \includegraphics[width=1.9in]{wood_peaks.pdf} 
+    	\caption{Diffraction curves observed from the three amorphous samples, presented on log scales: [A] unknown plastic; [B] grease; [C] wood. The largest peak should correspond to the average distance between atoms. Secondary peaks may indicate a secondary structure. An interpretation is attempted in Section~\ref{sec:conclusion}.}
+    	\label{fig:amorphous_peaks}
+    \end{figure}
+
+    \begin{table}
+        \centering
+        \begin{tabular}{lrrrl}
+            Sample & 2$\theta \pm 0.5$ ($\degree$) & Spacing ($\textrm{\AA}$) & Density (g/cm$^3$) & Ratio (2g/cm$^3$)\\
+            \hline
+            Plastic*&14.0&$6.32\pm0.45$&$0.136\pm0.029$&$0.07\pm0.02$\\
+            Plastic &30.5&$2.93\pm0.09$&$0.549\pm0.038$&$0.27\pm0.04$\\
+            Plastic &42.5&$2.13\pm0.05$&$3.451\pm0.243$&$1.73\pm0.24$\\
+            Grease* &12.0&$7.37\pm0.62$&$0.087\pm0.021$&$0.04\pm0.02$\\
+            Grease  &20.0&$4.44\pm0.22$&$0.385\pm0.057$&$0.19\pm0.06$\\
+            Wood    &16.0&$5.54\pm0.35$&$0.200\pm0.038$&$0.10\pm0.04$\\
+            Wood*   &22.5&$3.95\pm0.17$&$0.545\pm0.070$&$0.20\pm0.07$\\
+            Wood    &34.5&$2.60\pm0.07$&$1.899\pm0.153$&$0.95\pm0.15$\\
+            Wood    &46.0&$1.97\pm0.04$&$4.359\pm0.265$&$2.18\pm0.27$\\
+        \end{tabular}
+        \caption{Observed peaks in diffraction pattern in amorphous samples. * indicates greatest peak, likely the peak associated with the average spacing between atoms. The ratio relative to the known carbon density 2.0 g/cm$^3$ is also tabulated.}  
+        \label{tab:amorph_spacings}
+    \end{table}
+
+
+    The penetration depths of NaCl and amorphous carbon are 206 $\mu \textrm{m}$ and 4,460 $\mu \textrm{m}$, respectively. 98\% of all photons will have attentuated at this depth in the material.
+
+    The observed diffraction pattern from NaCl is presented in Figure~\ref{fig:nacldiffraction}. The HighScore software was able to identify the copper Bragg diffraction pattern, which was prominent by inspection. Table~\ref{tab:naclobs} contains the values obtained by the program, with divergence from predicted values. The lattice constant for NaCl's face-centered cubic structure is computed from each value, all returning approximately 5.64, with relative error between 7\% and 18\%.
+
+    Several peaks were identified for each amorphous sample. In each case, a spacing was determined and a density computed. These are reported in Table~\ref{tab:amorph_spacings}. The densities ran from 0.087 to 4.359 g/cm$^3$, which is a run of about 1.5 orders of magnitude. The median value is 2.22 g/cm$^3$.
+
+
+%─────────────
+\section{Conclusion}
+    \label{sec:conclusion}
+
+The penetration depths fall short of the 1.2 cm limit imposed by the sample container tray depth, so we do not expect that there are significant signals observed from the sample container over these collections. Signals observed may therefore reliably be considered emergent from Bragg diffraction by the samples.
+
+The diffraction pattern of NaCl was easily and clearly identified by the HighScore Plus program. The angles of incidence and reflection deviate from predictions only in the fourth order of precision or less, as do the diffraction spacings. The reflection intensities, however, deviate by a large amount from predictions: many showing approximately $\frac{1}{4}$ the predicted intensity. It's suspicious that each of these errors falls within a small range around $\frac{1}{4}$, and this may indicate a computational error rather than an experimental one.
+
+The lattice constant for NaCl was computed in each case, and all agree to within 3 orders of precision with the known lattice constant 5.64 $\textrm{\AA}$. This method of measuring the lattice constant appears to be very reliable.
+
+The amorphous samples present several peaks from which to compute an average diffraction spacing. Only one of the computed densities falls precisely around the density of amorphous carbon (wood, 46.0$\degree$). Considering a cubic structure using the average distance is a rudimentary approach, and the fact that computed densities are all within 1.5 orders of magnitude of carbon's density is remarkable. It should also be noted that the median value across all of these densities is 2.22 g/cm$^3$, which only differs from carbon by about 10\%. It may be reasonable to consider that each of these peaks indicates a prominent component to the structure, so taking them all into account provides a better estimation of the density.
+
+\printbibliography
+
+\end{document}