142 files changed, 12 insertions, 2314 deletions

diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 4ab411f..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,26 +0,0 @@
-
-# auto-generated 
-toc.t2t
-tentative_list_of_topics.t2t
-*.html
-*.pdf
-*.eps
-syllabus*.tex
-lecture*_handouts.tex
-lecture*_presentation.tex
-lecture_names.rem
-
-# tex temporal files
-*.aux
-*.log
-*.nav
-*.out
-*.snm
-*.toc
-
-# html styles and related
-.sass-cache
-*.css
-
-# destination dirs
-web_site_version
diff --git a/Makefile b/Makefile
index 636e44c..9b246cf 100644
--- a/Makefile
+++ b/Makefile
@@ -1,25 +1,15 @@
 # -*- make -*-
+# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
+# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
+# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
+# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
 
-TOPDIR=$(shell pwd)
-
-make = make
-
-class_base_dir = $(shell basename $(CURDIR))
-
-upload_location_wm = physics.wm.edu:public_html/classes/$(class_base_dir)/
-# see 2012_fall_practical_computing_for_scientists for PREVIOUS_YEAR_MATERIALS_DIR usage
-PREVIOUS_YEAR_MATERIALS_DIR = 
-
-
-files4upload = $(html_targets) $(samples)  $(syllabus_dir) $(misc) 
-
-upscr = rsync --delete  -ave ssh
-
+# Default value so one can compile i3-msg standalone
+TOPDIR=..
 include $(TOPDIR)/common.mk
 include ./local.mk
 include $(MAKEINCLUDE_DIR)/t2t.mk
 include $(MAKEINCLUDE_DIR)/tex.mk
-include $(MAKEINCLUDE_DIR)/css.mk
 
 
 dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
@@ -36,21 +26,5 @@ real_clean: $(REAL_CLEAN_TARGETS)
 
 install: $(INSTALL_TARGETS)
 
-upload: upload_location_wm
-
-
-upload_location_wm:
-	$(make) upload2location upload_location=$(upload_location_wm)
-
-upload2location: 
-	$(upscr) $(files4upload) $(upload_location)
-
-last_time_uploaded: $(files4upload) $(weekly_pdf_slides) $(lab_manuals_pdf) $(homeworks_assignments)
-	touch last_time_uploaded
-
-real_clean: clean_all
-
-backup: 
-	rsync -rvze ssh * spiffy.physics.wm.edu:jobs/wm/$(class_base_dir)/
 
 
diff --git a/manual_source/chapters/HeNelaser.tex b/chapters/HeNelaser.tex
index 9918f80..9918f80 100644
--- a/manual_source/chapters/HeNelaser.tex
+++ b/chapters/HeNelaser.tex
diff --git a/manual_source/chapters/appendices.tex b/chapters/appendices.tex
index d310873..d310873 100644
--- a/manual_source/chapters/appendices.tex
+++ b/chapters/appendices.tex
diff --git a/manual_source/chapters/blackbody.tex b/chapters/blackbody.tex
index 9f6c9bb..9f6c9bb 100644
--- a/manual_source/chapters/blackbody.tex
+++ b/chapters/blackbody.tex
diff --git a/manual_source/chapters/ediffract.tex b/chapters/ediffract.tex
index d03a1d5..d03a1d5 100644
--- a/manual_source/chapters/ediffract.tex
+++ b/chapters/ediffract.tex
diff --git a/manual_source/chapters/emratio.tex b/chapters/emratio.tex
index fc3c716..fc3c716 100644
--- a/manual_source/chapters/emratio.tex
+++ b/chapters/emratio.tex
diff --git a/manual_source/chapters/fabry-perot.tex b/chapters/fabry-perot.tex
index d74745f..d74745f 100644
--- a/manual_source/chapters/fabry-perot.tex
+++ b/chapters/fabry-perot.tex
diff --git a/manual_source/chapters/faraday_rotation.tex b/chapters/faraday_rotation.tex
index 74d351f..74d351f 100644
--- a/manual_source/chapters/faraday_rotation.tex
+++ b/chapters/faraday_rotation.tex
diff --git a/manual_source/chapters/hspect.tex b/chapters/hspect.tex
index 565c64f..565c64f 100644
--- a/manual_source/chapters/hspect.tex
+++ b/chapters/hspect.tex
diff --git a/manual_source/chapters/interferometry.tex b/chapters/interferometry.tex
index 2170fd9..2170fd9 100644
--- a/manual_source/chapters/interferometry.tex
+++ b/chapters/interferometry.tex
diff --git a/manual_source/chapters/intro.tex b/chapters/intro.tex
index a3ca846..a3ca846 100644
--- a/manual_source/chapters/intro.tex
+++ b/chapters/intro.tex
diff --git a/manual_source/chapters/michelson.tex b/chapters/michelson.tex
index 101fa64..101fa64 100644
--- a/manual_source/chapters/michelson.tex
+++ b/chapters/michelson.tex
diff --git a/manual_source/chapters/millikan.tex b/chapters/millikan.tex
index 085c22f..085c22f 100644
--- a/manual_source/chapters/millikan.tex
+++ b/chapters/millikan.tex
diff --git a/manual_source/chapters/mo.tex b/chapters/mo.tex
index 2a52bea..2a52bea 100644
--- a/manual_source/chapters/mo.tex
+++ b/chapters/mo.tex
diff --git a/manual_source/chapters/naspec.tex b/chapters/naspec.tex
index 8f88b83..8f88b83 100644
--- a/manual_source/chapters/naspec.tex
+++ b/chapters/naspec.tex
diff --git a/manual_source/chapters/pe-effect.tex b/chapters/pe-effect.tex
index b28d000..b28d000 100644
--- a/manual_source/chapters/pe-effect.tex
+++ b/chapters/pe-effect.tex
diff --git a/manual_source/chapters/report_template.tex b/chapters/report_template.tex
index c4f2436..c4f2436 100644
--- a/manual_source/chapters/report_template.tex
+++ b/chapters/report_template.tex
diff --git a/manual_source/chapters/sched.tex b/chapters/sched.tex
index 8227a18..8227a18 100644
--- a/manual_source/chapters/sched.tex
+++ b/chapters/sched.tex
diff --git a/manual_source/chapters/spectr.tex b/chapters/spectr.tex
index 634bec0..634bec0 100644
--- a/manual_source/chapters/spectr.tex
+++ b/chapters/spectr.tex
diff --git a/manual_source/chapters/spol.tex b/chapters/spol.tex
index 6c0446e..6c0446e 100644
--- a/manual_source/chapters/spol.tex
+++ b/chapters/spol.tex
diff --git a/manual_source/chapters/supcon.tex b/chapters/supcon.tex
index c74b856..c74b856 100644
--- a/manual_source/chapters/supcon.tex
+++ b/chapters/supcon.tex
diff --git a/manual_source/chapters/two-photon-interference.tex b/chapters/two-photon-interference.tex
index f1c026d..f1c026d 100644
--- a/manual_source/chapters/two-photon-interference.tex
+++ b/chapters/two-photon-interference.tex
diff --git a/common.mk b/common.mk
deleted file mode 100644
index fcb9e73..0000000
--- a/common.mk
+++ /dev/null
@@ -1,17 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/common.mk"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:04 -0400 (evmik)"
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-# $Id:$
-
-ifndef PREFIX
-	PREFIX=web_site_version
-endif
-
-ifndef DESTDIR
-	DESTDIR=$(TOPDIR)/
-endif
-
-INSTALL = install -C
-MAKEINCLUDE_DIR = $(TOPDIR)/make_templates
-
diff --git a/configs/config.t2t b/configs/config.t2t
deleted file mode 100644
index 0609596..0000000
--- a/configs/config.t2t
+++ /dev/null
@@ -1,25 +0,0 @@
-
-%!includeconf: ./this_class_cfg.t2t
-%!postproc: SITEROOT	.
-
-%!style(html): path2root/evmik.css
-%!style(tex): path2root/styles/evmik
-%%!postproc(html): '(?i)<h1>DrEugeniyMikhailov</h1>' '<h1><a class="headerAuthor" href="HmPgURL">Dr. Eugeniy E. Mikhailov</a></h1>'
-%% -- extra settings to make it handheld device compatible
-%!postproc: '(?i)(<head.*$)' '\1\n<meta name="viewport" content="width=device-width, initial-scale=1.0">'
-%% -------------------------------------------------------------------------------------
-%!postproc(html): '(?i)DrEugeniyMikhailov' 'Dr. Eugeniy E. Mikhailov'
-%!postproc(html): EugeniyMikhailov <a class="headerAuthor" href="HmPgURL">Eugeniy E. Mikhailov</a>
-%!postproc(html): HmPgURL http://physics.wm.edu/~evmik/
-%!postproc(txt): EugeniyMikhailov Eugeniy E. Mikhailov
-%!postproc(tex): EugeniyMikhailov Eugeniy E. Mikhailov
-%!postproc(html): 'WM' 'W&M'
-
-%!postproc(html):  {{(.*?)}}  <\1>
-%!preproc(html):  ^%%errata  """ {{div CLASS="errata"}} 
-%!preproc(html):  ^%%/errata  """ {{/div}} 
-%!preproc(html):  ^%%announce  """ {{div CLASS="announce"}} 
-%!preproc(html):  ^%%/announce  """ {{/div}} 
-%!preproc(html):  ^%%zero_p_space  """ {{div CLASS="zero_p_space"}} 
-%!preproc(html):  ^%%/zero_p_space  """ {{/div}} 
-
diff --git a/configs/labs_acronyms_cfg.t2t b/configs/labs_acronyms_cfg.t2t
deleted file mode 100644
index add1571..0000000
--- a/configs/labs_acronyms_cfg.t2t
+++ /dev/null
@@ -1,21 +0,0 @@
-
-
-%!postproc:  PiLab Measure pi
-%!postproc:  Interf Optical interferometry
-%!postproc:  e/m  Charge mass ratio
-%!postproc:  eDiffr Electron diffraction
-%!postproc:  FaradR Faraday rotation
-%!postproc:  bBody  Blackbody radiation
-%!postproc:  SuperC Superconductivity
-%!postproc:  2slit  Single photon interference
-%!postproc:  phElect Photoelectric effect
-%!postproc:  LabTour Lab Tour
-%!postproc:  Spectr  Spectroscopy
-%!postproc:  SpPrW1  Special Project Week 1
-%!postproc:  SpPrW2  Special Project Week 2
-%!postproc:  FallBrk Fall break (no lab)
-%!postproc:  NoLab   No lab
-%!postproc:  NoMtng  No meeting
-%!postproc:  ThankG  Thanksgiving (no lab)
-%!postproc:  SpPrPrs Special project final presentation
-
diff --git a/configs/this_class_cfg.t2t b/configs/this_class_cfg.t2t
deleted file mode 100644
index 133e527..0000000
--- a/configs/this_class_cfg.t2t
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-%% Order is important
-%!postproc(html): '(?i)<H1>ThisClassID' '<H1><a class="headerTitle" href="ThisClassURL">ThisClassID</a>'
-%!postproc(html): ThisClassURL 'path2root'
-%%% ATTENTION
-%% %!postproc: ThisClassTitle and ThisClassID need to be the last
-%!postproc: ThisClassTitle Experimental Atomic Physics
-%!postproc: ThisClassID 'Physics 251'
-
diff --git a/css_styles/evmik.scss b/css_styles/evmik.scss
deleted file mode 100644
index 514d16e..0000000
--- a/css_styles/evmik.scss
+++ /dev/null
@@ -1,328 +0,0 @@
-// ---------  Color definitions start -------------------
-$body_bg: #336699;
-$body_padding: 0px;
-$body_margin: 1%;
-$body_font_family: Sans-Serif;
-
-$toc_width: 20%;
-
-$body_header_bg: $body_bg;
-$body_header_fg: white;
-
-$link_color_cmd_normal:  black;
-$link_color_cmd_visited: $link_color_cmd_normal;
-$link_color_cmd_hover:   $link_color_cmd_normal;
-$link_color_cmd_active:  $link_color_cmd_normal;
-
-$normal_bg: #ffcc99;
-$normal_fg: black;
-
-$sidebar_bg: lighten($body_bg,35%);
-$sidebar_border_clr: $body_bg;
-
-$toc_bg: lighten($body_bg,35%);
-$toc_border_clr: $body_bg;
-
-
-$div_padding: 0.5%;
-$div_margin_vert:  0.5%;
-$div_margin_horiz:  0.5%;
-
-$small_screen: 480px;
-$large_screen: 1200px;
-
-$errormsg_bg:   #ff0000;
-$infomsg_bg:    #ffccff;
-
-$attention_bg:  #8f0000;
-$attention_fg:  white;
-
-
-$Quiz:          #CFECEC;
-$Homework:      #C3FDB8;
-$LabReport:     #82CAFA;
-$MidTerm:       #f0b7f0;
-$FinalExam:     #f08ab6;
-$Participation: #cccc99;
-$Unset:         #cccccc;
-
-$table_hover_bg: #ffeebb;
-
-$controls_bg: #dddddd;
-
-$col_controls_bg: #dddddd;
-$col_controls_fg: black;
-$col_controls_dangerous_bg: red;
-$col_controls_dangerous_fg: black;
-// ---------  Color definitions end   -------------------
-
-
-body {
-	padding: $body_padding;
-	margin:  $body_margin;
-	background-color: $body_bg;
-	color: $normal_fg;
-	font-family: $body_font_family;
-  text-align: justify;
-	/*
-	a {
-		color:              $link_color_cmd_normal;
-		text-decoration:    none;
-		&:visited { color:  $link_color_cmd_visited;  }
-		&:hover   { 
-			color:  $link_color_cmd_hover;    
-			text-decoration:underline;
-			background-color: lighten($controls_bg,20%);
-		}
-		&:active  { 
-			color:  $link_color_cmd_active;   
-			text-decoration:underline;
-			background-color: lighten($controls_bg,20%);
-		}
-	}
-	*/
-
-	div {
-		background-color: $normal_bg;
-		color: $normal_fg;
-		padding: {
-			top:     $div_padding;
-			bottom:  $div_padding;
-			left:    $div_padding;
-			right:   $div_padding;
-		}
-		margin: {
-			top:     $div_margin_vert;
-			bottom:  $div_margin_vert;
-			left:    $div_margin_horiz;
-			right:   $div_margin_horiz;
-		}
-		pre {
-			background-color: lighten($normal_bg,10%);
-			padding: 15px;
-			border: 1px dashed black;
-		}
-		ul {
-			padding-left: 1em;
-		}
-	}
-	div.toc {
-		margin: {
-			right:	$body_margin;
-			left: $div_padding;;
-			top: $div_padding;
-			bottom: $div_padding;
-		}
-		float: right;
-		z-index: 1;
-		background-color: $toc_bg;
-		width		: 15em;
-		border-style: solid;
-		border-width: 1px;
-		border-color: $toc_border_clr;
-		ul {
-			list-style-type : none;
-			padding: {
-				top:     0;
-				bottom:  0;
-				left:    1em;
-				right:   0;
-			}
-			margin: 0;
-		}
-		p { 
-			margin: 0;
-		}
-		h3 {
-			padding: .1em;
-			margin: 0;
-			font-weight: bold;
-		}
-		// small screen/handheld
-		// @media (max-width: $small_screen) { 
-		// above gives hick up to sass
-		// so I have to do hard coded values
-		@media (max-width: 4in) {
-			float: none;
-			width: auto;
-			margin: 0;
-			padding: 0;
-			h3 {
-				display: none;
-			}
-			ul {
-				padding: 0;
-				list-style-type : none;
-				text-align: center;
-			}
-			li {
-				display: inline-block;
-				padding: .4em;
-			}
-		}
-	}
-	// div.toc {
-		// float: left;
-		// width: $toc_width;
-		// font-weight: bold;
-		// a {
-			// color: black;
-			// text-decoration: none;
-		// }
-		// a:hover {
-			// text-decoration: underline;
-		// }
-	// }
-	div.body {
-		// float: right;
-		// width: 100% - $toc_width - 5%;
-		h1 {
-			padding:  {
-				left:  $div_padding;
-				right: $div_padding;
-			}
-			text-align: left;
-			font-size: 150%;
-			font-weight: bold;
-			color: $body_header_fg;
-			background-color: $body_header_bg;
-		}
-		h2 {
-			padding:  {
-				left:  $div_padding;
-				right: $div_padding;
-			}
-			text-align: left;
-			font-size: 130%;
-			font-weight: normal;
-			color: $body_header_fg;
-			background-color: $body_header_bg;
-		}
-		h3 {
-			padding:  {
-				left:  $div_padding;
-				right: $div_padding;
-			}
-			text-align: left;
-			font-size: 115%;
-			font-weight: normal;
-			color: $body_header_fg;
-			background-color: $body_header_bg;
-		}
-		img.myphoto {
-			float: right;
-			text-align: right;
-			width: 10em;
-		}
-		#sidebar {
-			margin: {
-				left:	$div_padding;
-				right: 0;
-				top: 0;
-				bottom: 0;
-			}
-			float: right;
-			z-index: 1;
-			background-color: $sidebar_bg;
-			width		: 10em;
-			border-style: solid;
-			border-width: 1px;
-			border-color: $sidebar_border_clr;
-			ul {
-				list-style-type : none;
-				padding: {
-					top:     0;
-					bottom:  0;
-					left:    1em;
-					right:   0;
-				}
-				margin: 0;
-			}
-			p { 
-				margin: 0;
-			}
-			h3 {
-				padding: .1em;
-				margin: 0;
-				font-weight: bold;
-			}
-		}
-	}
-	div.header {
-		text-align: left;
-		font-family:  Sans-Serif;
-		h1 {
-			margin: 2pt;
-			font-size: 200%;
-			font-weight: bold;
-			a {
-				color: $normal_fg;
-			}
-		}
-		h2 {
-			margin: 2pt;
-			font-size: 120%;
-			font-weight: normal;
-		}
-		h3 {
-			margin: 2pt;
-			font-size: 110%;
-			font-weight: normal;
-		}
-	}
-
-}
-body.home_page {
-	div.zero_p_space {
-	  margin: 0;
-		padding: 0;
-		p { 
-			margin: 0;
-		}
-	}
-	ul {
-		list-style-type : none;
-		padding: 0;
-		margin: 0;
-	}
-}
-
-	
-
-/*
- * print styles
- */
-@media print {
-	* {
-		background-color: white !important;
-		background-image: none !important;
-	}
-	div.controls { 
-		display: none;
-	}
-	div.greetings { 
-		display: none;
-	}
-	div.footer { 
-		display: none;
-	}
-	div.gradestable { 
-		table.gradestable {
-			th {
-				font-weight: bold;
-				valign: top;
-			}
-		}
-		a[href]:after {
-			content:none;
-		}
-		a img {
-			display: none;
-		}
-	}
-}
-
-
-
- 
-// vim: ts=2:sw=2:tw=74:fdm=indent
diff --git a/css_styles/local.mk b/css_styles/local.mk
deleted file mode 100644
index fa5c1a0..0000000
--- a/css_styles/local.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-#PACKAGE_DIR = $(shell basename `pwd`)
-PACKAGE_DIR = .
-
-tex_independent := 
-t2t_fig_files := 
-tex_fig_files := 
-
-REQUIRED_TARGETS   += css
-INSTALL_TARGETS    += install_css
-
diff --git a/manual_source/fig_sources/angle.fig b/fig_sources/angle.fig
index 6076fde..6076fde 100644
--- a/manual_source/fig_sources/angle.fig
+++ b/fig_sources/angle.fig
diff --git a/manual_source/fig_sources/tester.tex b/fig_sources/tester.tex
index fe2ae4f..fe2ae4f 100644
--- a/manual_source/fig_sources/tester.tex
+++ b/fig_sources/tester.tex
diff --git a/index.t2t b/index.t2t
deleted file mode 100644
index 660ab34..0000000
--- a/index.t2t
+++ /dev/null
@@ -1,71 +0,0 @@
-ThisClassID - ThisClassTitle
-by EugeniyMikhailov
-Fall 2013
-
-
-
-%!includeconf: ./configs/config.t2t
-%!postproc: path2root '.'
-%!options(html): --toc --toc-level=1
-% %%mtime(%Y-%m-%d)
-%!postproc(tex): \\date{.*}  \date{}
-%!postproc(tex): EugeniyMikhailov Eugeniy Mikhailov
-%!postproc(html): EugeniyMikhailov <a class="headerAuthor" href="HmPgURL">Eugeniy E. Mikhailov</a>
-%!postproc(html): HmPgURL http://physics.wm.edu/~evmik/
-%!postproc(txt): EugeniyMikhailov Eugeniy Mikhailov
-%!postproc:  _dummy_line_ ''
-%!preproc: ^__Lecture_(..) %!include: ./lecture\1/toc.t2t
-%!preproc: __Notes_(..) [notes ./lecture_notes/lecture_note_\1.pdf]
-%%!preproc: ^__Notes_(..) [presentation ./weekly_pdf_slides/lecture\1_presentation.pdf] and [handouts ./weekly_pdf_slides/lecture\1_handouts.pdf]
-%!preproc: __HW_(..)__ - [HW \1 ./homeworks/hw\1.pdf] (source latex file [hw\1.tex ./homeworks/hw\1.tex])
-%!preproc: __HW_DUE_DATE__ Due date Monday 1pm
-%!preproc: __HW_EMAIL_SUBMISSION__ Please, add **phys256** to the subject line of your email submission
-%!preproc: __HW_SEPARATOR__ \n\n
-
-
-
-
-%%!include: ./announcements.t2t
-
-= General class information =
-Syllabus [html ./syllabus/syllabus_2013_fall_Experimental_Atomic_Physics_251.html] [pdf ./syllabus/syllabus_2013_fall_Experimental_Atomic_Physics_251.pdf]
-
-%%[Sample homework report ./sample_report/]
-%
-%[Tentative calendar ./cal.html]
-%
-%%[Tentative list of topics ./tentative_list_of_topics.html]
-%
-%[Important dates ./important_dates.html]
-%
-%== Grader ==
-%Travis Horrom <tshorrom@email.wm.edu>.
-
-== Grades ==
-Grades are posted into the web [grades book http://physics.wm.edu/~evmik/cgi-bin/GradeBook.tcl/2013_Fall_Phys251]. Make sure that posted grades coincide with their paper one.
-
-For the first time login use your WM official email as "login" and hit the reset password button. You will get a password shortly via email.
-
-If you have any suggestions or comments, please, let me know.
-
-= Lab schedules =
-- [Monday group ./schedule_mon.html]  schedule
-- [Wednesday and Thursday groups ./schedule_wed.html]  schedule
-
-
-= Class materials =
-- Error propagation [note notes/error_propagation_note.pdf]
-- Lab [manual ./manual/manual.pdf]
-
-
-= Lab reports preparation =
-- Lab report [LaTeX template ./labreport_sample/] 
-- [Comments  ./labreport_sample/comments_from_tas.html] from Matt and A.J.
-- Matlab [usage ./matlab_usage/] examples
-
-
-= Lab books =
-A few pages from [an actual lab book ./labbook_sample/labbook_sample.pdf] (courtesy of N. Belcher)
-
-
-% vim: foldmethod=syntax
diff --git a/labbook_sample/labbook_sample.pdf b/labbook_sample/labbook_sample.pdf
deleted file mode 100644
index b0ea3cc..0000000
--- a/labbook_sample/labbook_sample.pdf
+++ /dev/null
diff --git a/labreport_sample_source/Makefile b/labreport_sample_source/Makefile
deleted file mode 100644
index 9b246cf..0000000
--- a/labreport_sample_source/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
-# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
-# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
-
-# Default value so one can compile i3-msg standalone
-TOPDIR=..
-include $(TOPDIR)/common.mk
-include ./local.mk
-include $(MAKEINCLUDE_DIR)/t2t.mk
-include $(MAKEINCLUDE_DIR)/tex.mk
-
-
-dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
-
-.DEFAULT_GOAL := all
-
-all: compile install
-
-compile: $(REQUIRED_TARGETS)
-
-clean: $(CLEAN_TARGETS)
-	
-real_clean: $(REAL_CLEAN_TARGETS)
-
-install: $(INSTALL_TARGETS)
-
-
-
diff --git a/labreport_sample_source/comments_from_tas.t2t b/labreport_sample_source/comments_from_tas.t2t
deleted file mode 100644
index 50c70cb..0000000
--- a/labreport_sample_source/comments_from_tas.t2t
+++ /dev/null
@@ -1,41 +0,0 @@
-ThisClassID - Comments regarding lab reports preparation
-Matt and A.J.
-
-
-%!includeconf: ../configs/config.t2t
-%!options(html): --no-toc
-%!postproc: path2root '..'
-
-
-While we grade your first lab reports, we want to give you some notes in
-general about we expect for the second round of reports:
-
-+ Bring a hard copy of your report to class. STAPLE!
-+ Abstracts should be short and concise, and contain: a sentence or two
-summarizing the lab, and a sentence or two describing the results you
-obtained. Save background information and why you did the experiment for
-the Introduction.
-+ Make sure your report is readable - most of the reports so far looked
-good.  Make sure that your sections have a space in between them, that your
-section titles are not separated from the sections, your tables are intact,
-and equations are clear.
-+ If you use Word find a way to make your equations readable. If anyone needs
-help with LaTeX please let us know - there is a bit of a learning curve
-since it is a very different method of preparing documents than more
-familiar word processors, but once you understand the method it is actually
-easier for scientific papers.
-+ Keep the report to a reasonable # of pages.  There is no hard limit, and
-do make sure you don't leave important information out, but do not print
-out pages and pages of tables of data and calculations. Provide a summary
-of important data and equations.
-A very important skill is being able to explain your experiments and
-results fully and clearly while being as concise as possible - this is an
-important goal of this course.
-
-
-
-If anything about writing the reports is unclear please ask us.
-
-
-
-
diff --git a/labreport_sample_source/index.t2t b/labreport_sample_source/index.t2t
deleted file mode 100644
index 7c22efd..0000000
--- a/labreport_sample_source/index.t2t
+++ /dev/null
@@ -1,45 +0,0 @@
-ThisClassID - LaTeX usage and lab report template.
-by EugeniyMikhailov
-
-
-
-%!includeconf: ../configs/config.t2t
-%!options(html): --toc --toc-level=1
-%!postproc: path2root '..'
-
-
-= Tex source of the sample report =
-
-This template shows how to use section, figures, tables, and citations.
-- Main tex file of the lab report [labreport_template.tex labreport_template.tex]
-- Figure files necessary for successful generation, copy them to the same directory where tex file located.
- - figure 1 [sr_setup.pdf sr_setup.pdf]
- - figure 2 [sr_squeezing_vs_detuning.pdf sr_squeezing_vs_detuning.pdf]
-
-
-Run several times the command: 
-``` pdflatex labreport_template.pdf
-
-Latex  takes care  of the  page numbering  and references  to the  figures,
-tables and citations thus several  executions are required. This is similar
-to  the  execution  of  the  parser, compiler,  and  linker  for  compiling
-languages.
-
-= Results of compillation =
-- Resulting [pdf  labreport_template.pdf]
-
-
-= Note =
-
-I strongly recommend to learn how to use LaTeX for report writing. While it
-is not as obvious to use as conventional word processing software, it saves
-a lot of  time taking formating task  away from you. Note  in above example
-how listing of the program formatted without any effort from the user.
-
-Below is a link to [The not so Short Introduction to LaTeX http://mirrors.ctan.org/info/lshort/english/lshort-letter.pdf].
-
-
-
-
-
-
diff --git a/labreport_sample_source/labreport_guidelines.tex b/labreport_sample_source/labreport_guidelines.tex
deleted file mode 100644
index b684018..0000000
--- a/labreport_sample_source/labreport_guidelines.tex
+++ /dev/null
@@ -1,141 +0,0 @@
-\documentclass{article}

-\usepackage{tabularx,amsmath,boxedminipage,epsfig}

-    \oddsidemargin  0.0in

-    \evensidemargin 0.0in

-    \textwidth      6.5in

-    \headheight     0.0in

-    \topmargin      0.0in

-    \textheight=9.0in

-

-\begin{document}

-\title{How to Write a Lab Report}

-\author{Irina Novikova}

-\date{}

-\maketitle

-

-One may think that the work of a scientist is done after the experiment is

-completed, and its results are analyzed. This is not true! Any research finding

-have to be communicated to the scientific community and make its contribution

-to the common knowledge ``database''. Therefor, learning how to communicate the

-results of your experiments to others is a very important skill.

-

-In science the most common way to inform the world about your work is to write a paper in a scientific journal.

-A good paper introduce the readers the original research goal and its significance, describes the experimental

-methods used, presents the results and analyze how they fit into the known physical picture, and draw

-conclusions. All important information must be included in the paper: ideally, any person knowledgeable in the

-field should be able reproduce the experiment and obtain similar results.

-

-A lab report serves similar purpose, but for more limited audience (you course instructors and possible your

-classmates). It is important that you learn how to communicate your findings. In you report you have to clearly

-and concisely communicate the purpose, the methods and the results of your experiments.

-

-The format for a lab report you need to follow is similar to a scientific paper in a journal. Your lab report

-must include the following parts.

-\begin{itemize}

-\item \textbf{Title of the experiment}.

-\item \textbf{Authors list}. The person writing the report must be listed

-first; the name of all people participating in the experiments are listed

-afterwards. This is a traditional practice in a research publications.

-\item \textbf{Abstract.} Abstract is a very short summary of your report. The

-challenge is to describe what experiment you were doing and what are the

-important conclusions in less than 100 words.

-\item \textbf{Theory and significant equations.} Give a brief summary of

-theoretical background and the list of equations you will need for the data

-analysis. In a regular scientific publications this is usually a significant

-part of the paper, and usually includes a review of the relevant publications.

-However, for a lab report it is ok to keep it very brief.

-\item \textbf{Error analysis.} In this section please list the equations and

-methods for figuring out the uncertainties for different measured and

-calculated experimental values. Also list any found and suspected systematic

-errors.

-\item \textbf{Experimental setup and procedures.} Sketch the experimental apparatus. Don't forget to label all the

-used equipment! Briefly describe the important steps taken to produce the data,

-and explain what variables are being measured. In this section you may also

-give values of experimental parameters which do not change in the course of the

-experiment (such as room temperature or laser wavelength).

-\item \textbf{Data and the data analysis.} Provide the results of your

-measurements and data analysis in a form of a table(tables) and graphs. Carry

-out explicit ``sample'' calculation (including calculations of an uncertainty)

-to show how the results are obtained from the measured data points. Also, if

-anything strange or unexpected happened during the experiment you should

-mentioned it.

-\item \textbf{Conclusions.} Give a brief summary of main experimental results

-and draw conclusions. If your results disagree with theoretical predictions or

-accepted value, explain possible sources of disagreement.

-\item \textbf{References.} This section is optional. But if you have used any

-external sources during lab preparation or the data analysis, you should add a

-reference to them.

-\end{itemize}

-

-This sectioning is only approximate. Sections can be merged, dropped or broken

-into subsection depending on the particular experiment, as long as all the

-points mentioned above are addressed.

-

-You should turn in a \textbf{hard} copy of your lab report, but you are

-strongly encouraged to prepare your report electronically. While journal

-publisher expand the range of acceptable formats for paper submissions, most

-physicists (and other scientists who type a lot of equations) prefer LaTeX. A

-report template in Latex is available on the course web-site. \emph{Warning}:

-your first couple experiences with LaTeX may not be very satisfactory - in

-fact, you may be very frustrated! But once you get familiar with the system,

-you will find it quite pleasant to work with. Also, try to find an editor you

-are comfortable with - for example, WinEdt(http://www.winedt.com/) is very easy

-to use. This is a shareware program and comes with 30 day free trial.

-

-Similarly, all the graphs should be done electronically. The default data analysis software for this course is

- Igor Pro from Wavemetrics. Additional instructions will be available from the instructor.

- However, if you would like to use a different software (Matlab, for example, or xmgrace for Linux), you can do so \emph{after

- you receive instructor's permission}. Before you ask, however, make sure that this software can:

-\begin{enumerate}

-\item produce a readable graph with normal axes, axes labels and legend (if

-needed);

-\item plot data points with error bars;

-\item fit the plotted data and returns fit parameters with experimental

-uncertainties.

-\end{enumerate}

-

-

-\begin{boxedminipage}{\linewidth}

-Please don't forged: while you are encouraged to do the experimental

-preparation, the data taking and the data analysis as a team, the lab report is

-an individual task. Copying any part of someone else's report is considered

-plagiarism. This also violates the Honor code, and will be reported to the

-Honor council.

-\end{boxedminipage}

-

-\vspace{1cm}

-

-\textbf{Grade points assignment}

-\begin{itemize}

-

-\item \emph{Abstract}: 10 pt - Concise; describes purpose, method and main results in 3-5 sentences.

-

-\item \emph{Theory/Significant equations}: 5 pt - Brief history, theory behind method and analysis of experiment, major

-equations.

-

-\item \emph{Error Analysis} 10 pt - describes what errors were introduced, how they were treated,

-how you will determine the error on your calculated values (include only the equations you will use in terms of

-the variables particular for each experiment).

-

-\item \emph{Set-up/Procedure}: 10 pt - describe set-up and procedure, include a diagram and/or pictures of the set-up.

-

-\item \emph{Data and Analysis}: 20 pts - include data, your manipulation of the data, describe the data and why you

-manipulated it a certain way, include the major values you found (in text) and analyze what it all means.

-

-\item \emph{Conclusion}: 15 pts - restate purpose, results, meaning, remark about errors, anything else of interest.

-Concise but thorough.

-

-\item \emph{Format}: 10 pt - equations are formatted correctly, pages are in order, ordering of information is logical,

-numbers in text have correct units.

-

-\item \emph{Graphs/Tables}: 10 pt - graphs/tables/diagrams are labeled, graphs are correct, all have correct units, all are

-readable.

-

-\item \emph{Lab Journal}: 10 pt - Lab journal pages are attached, all the experimental records are readable, all relevant

-data are included.

-

-\end{itemize}

-

-

-

-\end{document}

diff --git a/labreport_sample_source/labreport_template.tex b/labreport_sample_source/labreport_template.tex
deleted file mode 100644
index 3462d83..0000000
--- a/labreport_sample_source/labreport_template.tex
+++ /dev/null
@@ -1,218 +0,0 @@
-\documentclass[letterpaper,12pt]{article}

-\usepackage{tabularx,amsmath,boxedminipage,graphicx}

-\usepackage[margin=1in,letterpaper]{geometry} % this shaves off default margins which are too big

-\usepackage{cite}

-\usepackage[final]{hyperref} % adds hyper links inside the generated pdf file

-\hypersetup{

-	colorlinks=true,       % false: boxed links; true: colored links

-	linkcolor=blue,          % color of internal links

-	citecolor=blue,        % color of links to bibliography

-	filecolor=magenta,      % color of file links

-	urlcolor=blue         

-}

-

-\begin{document}

-

-\title{Title of the experiment}

-\author{Y. O. Urname, partners:  P. A. RtnerA, and P. A. RtnerB}

-\date{\today}

-\maketitle

-

-\begin{abstract}

-In this experiment we studied a very important physical effect by measuring the

-dependence of a quantity $V$ of the quantity $X$ for two different sample

-temperatures.  Our experimental measurements confirmed the quadratic dependence

-$V = kX^2$ predicted by Someone's first law. The value of the mystery parameter

-$k = 15.4\pm 0.5$~s was extracted from the fit. We found that this value is

-20\% below theoretically predicted $k_{theory}=17.34$~s. We attribute this

-discrepancy to low efficiency of our $V$-detector.

-\end{abstract}

-

-

-\section{Theory overview}

-Here give a brief summary of the physical effect of interest and provide

-necessary equations. Here is how you insert an equation. According to

-references~\cite{melissinos, Cyr, Wiki} the dependence of interest is given

-by

-\begin{equation} \label{eq:aperp}

-u(\lambda,T)=\frac{8\pi hc\lambda^{-5}}{e^{hc/\lambda kT}-1},

-\end{equation}

-where T is temperature in Kelvin, c is the speed of light, etc. Don't forget to

-explain what each variable in the equation means, when you introduce it for the

-first time!

-

-

-

-

-

-\section{Experimental setup and procedures}

-

-{\bf Note:} LaTeX will put figures and tables at the locations

-where it thinks it is the best. Do not fight it,

-unless you really need it.

-

-Give a schematic of the experimental setup(s) used in the experiment (see

-figure~\ref{fig:samplesetup}). Give the description of  abbreviations

-either in the figure caption or in the text. Write a description of what is

-going on. 

-

-\begin{figure}[ht] 

-        % read manual to see what [ht] means and for other possible options

-        \includegraphics[width=1.0\columnwidth]{sr_setup}

-        % note that in above ___________________^^^^^^^^^figure file name

-        % the file extension is missing. LaTeX is smart enough to find

-        % apropriate one (i.e. pdf, png, etc.)

-        % You can add this extention yourself as it seen below

-        % both notations are correct but above has more flexibility

-        %\includegraphics[width=1.0\columnwidth]{sr_setup.pdf}

-        \caption{

-                \label{fig:samplesetup} % spaces are big no-no withing labels

-                % things like fig: are optional in the label but it helps

-                % to orient yourself when you have multiple figures,

-                % equations and tables

-                {\bf  Every figure MUST have a caption.}

-                Experimental setup. 

-                SMPM fiber depicts single-mode polarization-maintaining fiber,

-                $\lambda/2$ is half-wave plate,

-                PhR is phase-retarding wave plate,

-                PBS is polarizing beam splitter,

-                GP is Glan-laser polarizer,

-                and BPD is balanced photodetector.

-        }

-\end{figure}

-

-Don't forget to list all important steps in your experimental procedure!

-

-Use active voice either in past or present through all the report and be

-consistent with it:

-The laser light comes  from to ... and eventually arrived to the

-balanced photodiode as seen in the figure~\ref{fig:samplesetup}.

-

-Sentences in the past voice while correct generally considered hard to read

-in large numbers. The laser light was directed to ..., wave plates were set

-to ... etc.

-

-

-\section{Experimental data and the data analysis}

-

-In this section you will need to show your experimental results. Use tables and

-graphs when it is possible. Table~\ref{tbl:bins} is an example.

-

-\begin{table}[ht]

-\begin{center}

-\caption{Every table needs a caption}

-\label{tbl:bins} % spaces are big no-no withing labels

-\begin{tabular}{|ccccccc|} \hline

-\multicolumn{1}{|c}{Polarization} & \multicolumn{1}{c}{Target} &

-\multicolumn{1}{c}{Bin} & \multicolumn{1}{c}{$<x>$} &

-\multicolumn{1}{c}{$<Q^2>$} & \multicolumn{1}{c}{$A_{\perp}^{meas}$} &

-\multicolumn{1}{c|}{$\Delta A_{\perp}$} \\

-\hline

-$-$ & LiD     & 1 &   0.0233323 &   0.8429978  &   0.0044151 &   0.0030871 \\

-    &         & 2 &   0.0638046 &   1.5017358  &   0.0021633 &   0.0021343 \\

-    &         & 3 &   0.1892825 &   3.1877837  &   0.0006640 &   0.0022467 \\

-    &         & 4 &   0.4766562 &   7.1827556  &  -0.0197585 &   0.0085528 \\

-    & NH$_3$  & 1 &   0.0232572 &   0.8454089  &   0.0003600 &   0.0018642 \\

-    &         & 2 &   0.0633156 &   1.4870013  &   0.0023831 &   0.0013287 \\

-    &         & 3 &   0.1923955 &   3.1753302  &  -0.0024246 &   0.0013771 \\

-    &         & 4 &   0.4830315 &   7.3245904  &  -0.0284834 &   0.0047061 \\

-$+$ & LiD     & 1 &   0.0233503 &   0.8340932  &  -0.0086018 &   0.0031121 \\

-    &         & 2 &   0.0638688 &   1.4785886  &  -0.0018465 &   0.0021452 \\

-    &         & 3 &   0.1892192 &   3.1277721  &  -0.0017860 &   0.0022525 \\

-    &         & 4 &   0.4778486 &   7.0313856  &  -0.0041773 &   0.0084659 \\

-    & NH$_3$  & 1 &   0.0232964 &   0.8439092  &  -0.0022961 &   0.0018851 \\

-    &         & 2 &   0.0633764 &   1.4814540  &   0.0021355 &   0.0013354 \\

-    &         & 3 &   0.1924094 &   3.1580557  &  -0.0065302 &   0.0013775 \\

-    &         & 4 &   0.4825868 &   7.3191291  &  -0.0290878 &   0.0047329 \\

-\hline

-\end{tabular}

-\end{center}

-\end{table}

-

-\subsection{Error analysis}

-

-Analysis of equation~\ref{eq:aperp} shows ...

-

-Note: this section can be integrated with the previous one as long as you

-address the issue. Here explain how you determine uncertainties for different

-measured values. Suppose that in the experiment you make a series of

-measurements of a resistance of the wire $R$ for different applied voltages

-$V$, then you calculate the temperature from the resistance using a known

-equation and make a plot  temperature vs. voltage squared. Again suppose that

-this dependence is expected to be linear~\cite{Cyr}, and the proportionality coefficient

-is extracted from the graph. Then what you need to explain is that for the

-resistance and the voltage the uncertainties are instrumental (since each

-measurements in done only once), and they are $\dots$. Then give an equation

-for calculating the uncertainty of the temperature from the resistance

-uncertainty. Finally explain how the uncertainty of the slop of the graph was

-found (computer fitting, graphical method, \emph{etc}.)

-

-If in the process of data analysis you found any noticeable systematic

-error(s), you have to explain them in this section of the report.

-

-It is also recommended to plot the data graphically to efficiently illustrate

-any points of discussion. For example, it is easy to conclude that the

-experiment and theory match each other rather well if you look at

-Fig.~\ref{fig:samplesetup} and Fig.~\ref{fig:exp_plots}.

-

-\begin{figure}[ht] 

-        \includegraphics[width=0.5\columnwidth]{sr_squeezing_vs_detuning}

-        % some figures do not need to be too wide

-        \caption{

-                \label{fig:exp_plots}  % spaces are big no-no withing labels

-                % things like fig: are optional in the label but it helps

-                % to orient yourself when you have multiple figures,

-                % equations and tables

-                {\bf Every figure MUST have a caption.}

-                {\bf Every plot MUST have axes labeled.}

-                The dependence of self rotation and squeezing on the laser

-                detunings.

-        }

-\end{figure}

-

-

-\section{Necessary remarks}

-

-Context of this template is out of sync with figures, tables, references,

-etc. It is just a template with examples how to use particular \LaTeX{}

-features.

-

-\section{Conclusions}

-Here your briefly summarize your findings.

-

-%++++++++++++++++++++++++++++++++++++++++

-

-% References section will be created automatically 

-% with inclusion of "thebibliography" environment

-% as it shown below. See text starting with line

-% \begin{thebibliography}{99}

-

-

-

-

-% There is a fancier and in long run more convinient way to do bibliography 

-% with automatic inclusion of references from the bibliography database

-% file. See usage of "bibtex" if you are interested in it.

-% http://www.bibtex.org/

-% but for know we will go with hand formated list.

-% Note: with this approach it is YOUR responsibility to put them in order

-% of appearance.

-\begin{thebibliography}{99}

-

-

-\bibitem{melissinos}

-A.~C. Melissinos and J. Napolitano, \textit{Experiments in Modern Physics},

-(Academic Press, New York, 2003).

-

-\bibitem{Cyr}

-N.\ Cyr, M.\ T$\hat{e}$tu, and M.\ Breton,

-% "All-optical microwave frequency standard: a proposal,"

-IEEE Trans.\ Instrum.\ Meas.\ \textbf{42}, 640 (1993).

-

-\bibitem{Wiki} \emph{Expected value},  available at

-\texttt{http://en.wikipedia.org/wiki/Expected\_value}.

-

-\end{thebibliography}

-

-

-\end{document}

diff --git a/labreport_sample_source/local.mk b/labreport_sample_source/local.mk
deleted file mode 100644
index 7a30c04..0000000
--- a/labreport_sample_source/local.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-PACKAGE_DIR = $(shell basename `pwd`)
-
-tex_independent := labreport_template.tex labreport_guidelines.tex
-t2t_fig_files := 
-tex_fig_files := sr_setup.pdf sr_squeezing_vs_detuning.pdf
-
-REQUIRED_TARGETS   += html_t2t pdf_tex
-INSTALL_TARGETS    += install_html_t2t install_pdf_tex install_tex_src
-
diff --git a/labreport_sample_source/sr_setup.pdf b/labreport_sample_source/sr_setup.pdf
deleted file mode 100644
index b47c137..0000000
--- a/labreport_sample_source/sr_setup.pdf
+++ /dev/null
diff --git a/labreport_sample_source/sr_squeezing_vs_detuning.pdf b/labreport_sample_source/sr_squeezing_vs_detuning.pdf
deleted file mode 100644
index 90d4fc8..0000000
--- a/labreport_sample_source/sr_squeezing_vs_detuning.pdf
+++ /dev/null
diff --git a/local.mk b/local.mk
index fa60706..36fe715 100644
--- a/local.mk
+++ b/local.mk
@@ -2,13 +2,13 @@
 # (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
 
 
-#PACKAGE_DIR = $(shell basename `pwd`)
-PACKAGE_DIR = .
+PACKAGE_DIR = $(shell basename `pwd`)
 
-tex_independent := 
-tex_fig_files := 
+tex_independent := manual.tex
 t2t_fig_files := 
+tex_fig_files := $(wildcard pdf_figs/*.pdf)
+tex_includes  := $(wildcard chapters/*.tex)
 
-REQUIRED_TARGETS   += html_t2t
-INSTALL_TARGETS    += install_html_t2t
+REQUIRED_TARGETS   += pdf_tex
+INSTALL_TARGETS    += install_pdf_tex
 
diff --git a/make_templates/css.mk b/make_templates/css.mk
deleted file mode 100644
index f705738..0000000
--- a/make_templates/css.mk
+++ /dev/null
@@ -1,33 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-CLEAN_TARGETS      += clean_css
-REAL_CLEAN_TARGETS += real_clean_css
-
-scss_files  = $(wildcard *.scss)
-css_targets = $(scss_files:%.scss=%.css)
-
-css: $(css_targets)
-
-$(css_targets): %.css : %.scss
-	sass $<   > $@
-
-clean_css:
-	rm -rf .sass-cache
-
-real_clean_css:
-	rm -f $(css_targets)
-
-dest_dir_css: 
-	$(INSTALL) -d -m 0755 $(dest_dir)
-
-install_css: dest_dir_css
-ifneq ($(strip $(css_targets)),)
-	$(INSTALL) -m 0644 $(css_targets) $(dest_dir)/
-endif
-
-install_css_src: dest_dir_css
-ifneq ($(strip $(scss_files)),)
-	$(INSTALL) -m 0644 $(scss_files) $(dest_dir)/
-endif
-
diff --git a/make_templates/t2t.mk b/make_templates/t2t.mk
deleted file mode 100644
index 80cf65d..0000000
--- a/make_templates/t2t.mk
+++ /dev/null
@@ -1,77 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-CLEAN_TARGETS      += clean_tex
-REAL_CLEAN_TARGETS += real_clean_tex
-
-t2t_files  = $(wildcard *.t2t)
-tex_from_t2t  = $(t2t_files:%.t2t=%.tex)
-pdf_from_t2t  = $(tex_from_t2t:%.tex=%.pdf)	
-html_from_t2t = $(t2t_files:%.t2t=%.html)
-
-html_t2t: $(html_from_t2t)
-
-pdf_tex:  $(pdf_from_independent_tex)
-
-pdf_t2t:  $(pdf_from_t2t)
-
-tex_t2t: $(tex_from_t2t)
-
-
-
-$(html_from_t2t): %.html : %.t2t $(t2t_fig_files)
-	txt2tags --css-sugar -t html -o $@ $< 
-	
-
-$(pdf_from_t2t): %.pdf : %.tex $(t2t_fig_files)
-	rubber -d  $< 
-
-
-dest_dir_t2t: 
-	$(INSTALL) -d -m 0755 $(dest_dir)
-
-install_t2t_src: dest_dir_t2t install_t2t_fig_files
-ifneq ($(strip $(t2t_files)),)
-	$(INSTALL) -m 0644 $(html_from_t2t) $(dest_dir)/
-endif
-
-install_t2t_fig_files: 
-ifneq ($(strip $(t2t_fig_files)),)
-	$(INSTALL) -m 0644 $(t2t_fig_files) $(dest_dir)/
-endif
-
-install_html_t2t: dest_dir_t2t $(html_from_t2t) install_t2t_fig_files
-ifneq ($(strip $(html_from_t2t)),)
-	$(INSTALL) -m 0644 $(html_from_t2t) $(dest_dir)/
-endif
-
-install_pdf_t2t: dest_dir_t2t $(pdf_from_t2t)
-ifneq ($(strip $(pdf_from_t2t)),)
-	$(INSTALL) -m 0644 $(pdf_from_t2t) $(dest_dir)/
-endif
-
-clean_t2t: clean_t2t_tex
-	
-real_clean_t2t: clean_t2t_tex
-	rm -f $(pdf_from_t2t)
-	rm -f $(html_from_t2t)
-
-clean_t2t_tex:
-	rm -f $(tex_from_t2t)
-
-clean_t2t_aux: $(tex_from_t2t)
-	rm -f $(tex_from_t2t:%.tex=%.dvi)
-	rm -f $(tex_from_t2t:%.tex=%.log)
-	rm -f $(tex_from_t2t:%.tex=%.aux)
-	rm -f $(tex_from_t2t:%.tex=%.nav)
-	rm -f $(tex_from_t2t:%.tex=%.out)
-	rm -f $(tex_from_t2t:%.tex=%.snm)
-	rm -f $(tex_from_t2t:%.tex=%.toc)
-	rm -f $(tex_from_t2t:%.tex=%.vrb)
-	rm -f $(tex_from_t2t:%.tex=%.blg)
-	rm -f $(tex_from_t2t:%.tex=%.bbl)
-	rm -f missfont.log
-	rm -f *Notes.bib
-
-
-
diff --git a/make_templates/tex.mk b/make_templates/tex.mk
deleted file mode 100644
index 61ffce4..0000000
--- a/make_templates/tex.mk
+++ /dev/null
@@ -1,48 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-CLEAN_TARGETS      += clean_t2t
-REAL_CLEAN_TARGETS += real_clean_t2t
-
-pdf_from_independent_tex= $(tex_independent:%.tex=%.pdf)
-
-pdf_tex:  $(pdf_from_independent_tex)
-
-$(pdf_from_independent_tex): %.pdf : %.tex $(tex_fig_files) $(tex_includes)
-	rubber -d  $< 
-
-dest_dir_tex:
-	$(INSTALL) -d -m 0755 $(dest_dir)
-
-install_pdf_tex: dest_dir_tex $(pdf_from_independent_tex)
-ifneq ($(strip $(pdf_from_independent_tex)),)
-	$(INSTALL) -m 0644 $(pdf_from_independent_tex) $(dest_dir)/
-endif
-
-install_tex_src: dest_dir_tex 
-ifneq ($(strip $(tex_independent)),)
-	$(INSTALL) -m 0644 $(tex_independent) $(dest_dir)/
-endif
-ifneq ($(strip $(tex_fig_files)),)
-	$(INSTALL) -m 0644 $(tex_fig_files) $(dest_dir)/
-endif
-
-clean_tex: clean_tex_aux
-
-clean_tex_aux:
-	rm -f $(tex_independent:%.tex=%.dvi)
-	rm -f $(tex_independent:%.tex=%.log)
-	rm -f $(tex_independent:%.tex=%.aux)
-	rm -f $(tex_independent:%.tex=%.nav)
-	rm -f $(tex_independent:%.tex=%.out)
-	rm -f $(tex_independent:%.tex=%.snm)
-	rm -f $(tex_independent:%.tex=%.toc)
-	rm -f $(tex_independent:%.tex=%.vrb)
-	rm -f $(tex_independent:%.tex=%.blg)
-	rm -f $(tex_independent:%.tex=%.bbl)
-	rm -f missfont.log
-	rm -f *Notes.bib
-
-
-real_clean_tex: clean_tex_aux
-	rm -f $(pdf_from_independent_tex)
diff --git a/manual_source/manual.tex b/manual.tex
index 7800da0..7800da0 100644
--- a/manual_source/manual.tex
+++ b/manual.tex
diff --git a/manual_source/Makefile b/manual_source/Makefile
deleted file mode 100644
index 9b246cf..0000000
--- a/manual_source/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
-# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
-# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
-
-# Default value so one can compile i3-msg standalone
-TOPDIR=..
-include $(TOPDIR)/common.mk
-include ./local.mk
-include $(MAKEINCLUDE_DIR)/t2t.mk
-include $(MAKEINCLUDE_DIR)/tex.mk
-
-
-dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
-
-.DEFAULT_GOAL := all
-
-all: compile install
-
-compile: $(REQUIRED_TARGETS)
-
-clean: $(CLEAN_TARGETS)
-	
-real_clean: $(REAL_CLEAN_TARGETS)
-
-install: $(INSTALL_TARGETS)
-
-
-
diff --git a/manual_source/local.mk b/manual_source/local.mk
deleted file mode 100644
index 36fe715..0000000
--- a/manual_source/local.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-PACKAGE_DIR = $(shell basename `pwd`)
-
-tex_independent := manual.tex
-t2t_fig_files := 
-tex_fig_files := $(wildcard pdf_figs/*.pdf)
-tex_includes  := $(wildcard chapters/*.tex)
-
-REQUIRED_TARGETS   += pdf_tex
-INSTALL_TARGETS    += install_pdf_tex
-
diff --git a/matlab_usage_source/Makefile b/matlab_usage_source/Makefile
deleted file mode 100644
index 9b246cf..0000000
--- a/matlab_usage_source/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
-# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
-# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
-
-# Default value so one can compile i3-msg standalone
-TOPDIR=..
-include $(TOPDIR)/common.mk
-include ./local.mk
-include $(MAKEINCLUDE_DIR)/t2t.mk
-include $(MAKEINCLUDE_DIR)/tex.mk
-
-
-dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
-
-.DEFAULT_GOAL := all
-
-all: compile install
-
-compile: $(REQUIRED_TARGETS)
-
-clean: $(CLEAN_TARGETS)
-	
-real_clean: $(REAL_CLEAN_TARGETS)
-
-install: $(INSTALL_TARGETS)
-
-
-
diff --git a/matlab_usage_source/errorbar_plot.png b/matlab_usage_source/errorbar_plot.png
deleted file mode 100644
index ec6ed39..0000000
--- a/matlab_usage_source/errorbar_plot.png
+++ /dev/null
diff --git a/matlab_usage_source/errorbar_with_large_font_plot.png b/matlab_usage_source/errorbar_with_large_font_plot.png
deleted file mode 100644
index cea3333..0000000
--- a/matlab_usage_source/errorbar_with_large_font_plot.png
+++ /dev/null
diff --git a/matlab_usage_source/fitted_data.png b/matlab_usage_source/fitted_data.png
deleted file mode 100644
index 5b37fdc..0000000
--- a/matlab_usage_source/fitted_data.png
+++ /dev/null
diff --git a/matlab_usage_source/fitted_data_improved.png b/matlab_usage_source/fitted_data_improved.png
deleted file mode 100644
index c7dbeb3..0000000
--- a/matlab_usage_source/fitted_data_improved.png
+++ /dev/null
diff --git a/matlab_usage_source/index.t2t b/matlab_usage_source/index.t2t
deleted file mode 100644
index d2f1f94..0000000
--- a/matlab_usage_source/index.t2t
+++ /dev/null
@@ -1,382 +0,0 @@
-ThisClassID - Matlab usage,  short (may be too short) introduction
-by EugeniyMikhailov
-
-
-
-%!includeconf: ../configs/config.t2t
-%!options(html): --toc --toc-level=1
-%!postproc: path2root '..'
-
-= Why Matlab =
-
-At the very least, it is a great replacement of a  hand held calculator. Once
-you need  to process multiple  data point it  became tedious with  a simple
-calculator. Once  you master Matlab  it will not matter  if it is  one data
-point or millions of them. It  can do complex math, plotting, fitting, etc.
-It is also the complete programming language which can stand by itself.
-Also, Matlab has **excellent help documentation** and a lot of tutorials at the web.
-
-There are free alternatives. [Octave  http://www.gnu.org/software/octave/]
-is  one example. This what I personally use
-instead of Matlab all the time. But it is a bit difficult with installation
-and it  might be  scary to  see no  GUI and  only a  command prompt  for a
-beginner.
-
-= Getting Matlab =
-
-Please visit W&M IT [software support page http://www.wm.edu/offices/it/a-z/software/]
-and download Matlab from appropriate "Licensed Software >> Math & Statistics
-Software" section. They have several available versions. Either one is fine.
-Since we are learning Matlab, we will not  have time to go to fancy toolboxes
-which Matlab provides/removes with new releases. 
-
-
-= Statistics functions =
-
-== Mean of a set ==
-Often you will need to find the mean and standard deviation of a particular
-sample set. Let's say we estimated  a resistor value (**R**) with different
-method and obtained the following experimental values.
-
-| **R**  | 1.20 | 1.10 | 1.11 | 1.05 | 1.05 | 1.15 |
-
-First we transfer it to a Matlab vector variable
-``` R=[ 1.20, 1.10, 1.11, 1.05, 1.05, 1.15 ]
-
-Notice that for a vector variable I use **,** as a separator.
-
-Now we ready to calculate mean of this set
-``` mean(R)
-with answer 1.1100
-
-== Standard deviation of a set ==
-Standard deviation normalized with **N-1** samples  (so called unbiased estimator)
-is done with
-``` std(R)
-with answer 0.058310. If you need normalization with **N** samples do
-``` std(R,1)
-with answer 0.053229
-
-In both  cases there is  to many  significant figures which  is unjustified
-from physics point of view. So remember, Matlab just does the math for you,
-the analysis and presentation of results is on you.
-
-
-
-= How to make a simple plot =
-Suppose during the measurements we obtain the following data
-for each current value **I** we measured voltage **V**
-with some uncertainty in voltage measurement **dV**.
-Our experimental data is represented in the following table.
-
-|| I   | V   | dV  |
-|  0.1 | 1.0 | 0.2 |
-|  1.0 | 2.2 | 0.1 |
-|  1.8 | 3.2 | 0.2 |
-|  3.3 | 3.8 | 0.2 |
-|  4.0 | 4.9 | 0.3 |
-
-First of all,  we need to transfer  it to the Matlab column vector variables. Pay
-attention to the delimiter **;** between numbers
-
-``` 
-I  = [  .1; 1.0; 1.8; 3.3; 4.0 ]
-V  = [ 1.0; 2.2; 3.2; 3.8; 4.9 ]
-dV = [ 0.2; 0.1; 0.2; 0.2; 0.3 ]
-```
-
-Now we make a simple plot without error bars to get  the basic, text after
-**%** is considered as a comment and Matlab will disregard it.
-
-```
-figure(1) % all plotting output will go to the particular window
-plot(I,V, 'x') 
-```
-
-[simple_unlabeled_plot.png]
-
-Easy,  is not  it? Here  were mark  our data  point with  crosses and  used
-**'''x'''** parameter to specify this. You can do other markers as well.
-
-
-But  **every plot  must be  present with  title, proper  axes labels  and units**.
-Note **'** for the string specifiers
-
-``` 
-title('Dependence of voltage on current')
-xlabel('Current (A)')
-ylabel('Voltage (V)')
-``` 
-
-[simple_labeled_plot.png]
-
-No our plot is nice and pretty.
-
-
-= Fixing the range of the axes =
-
-Have a look at above plot. We see that one of the axes (y) does not contain
-origin point  (y=0). Such plots are  very common in finances  and design to
-fool a reader, but they are  generally not acceptable in scientific reports
-and  definitely not  in  my class  unless  you  have a  good  reason to  do
-otherwise.
-
-The fix is very easy. Note that we are actually sending a vector [0,5] to the
-**``ylim``** function (fir x-axis we need to use **``xlim``** function).
-``` ylim([0,5])
-
-Now our plot is good to present
-
-[simple_labeled_and_proper_limits_plot.png]
-
-
-= Plotting with error bars =
-Let's open a new window for the plot
-
-``` figure(2)
-
-Now we make plot with error bars assuming that they are the same for up and down parts
-
-```
-errorbar(I,V,dV,'x')
-ylim([0,6])
-```
-
-Yet again we need proper labeling
-
-``` 
-title('Dependence of voltage on current')
-xlabel('Current (A)')
-ylabel('Voltage (V)')
-``` 
-
-[errorbar_plot.png]
-
-= Fixing plots font size =
-
-Honestly Matlab is not the best tool to do presentation quality plots, it
-requires a quite a bit of messing with their GUI. But at least for a quick font
-size fix do the following. This might look like  a magic spell so do read documentation
-on **``set``** command.
-
-```
-fontSize=24;
-set(gca,'FontSize',fontSize );
-
-errorbar(I,V,dV,'x')
-title('Dependence of voltage on current')
-xlabel('Current (A)')
-ylabel('Voltage (V)')
-```
-
-[errorbar_with_large_font_plot.png]
-
-
-= Fitting and data reduction =
-
-Modern experiments generate  a lot of data, while humans  can keep in their
-mind only  about 7 things.  So there is no  way to intelligently  work with
-large  data set.  We  need  to extract  essential  information  out of  our
-data  i.e. do  data  reduction.  Often we  have  some  idea for  analytical
-representation/model of  the experimental  data but we  are not  sure about
-the  model parameters  values. The  process  of extracting  them is  called
-**fitting**.
-
-So let's  look at  above Voltage  vs Current  dependence. According  to the
-Ohm's law  such dependence  must be linear  i.e **``V =  R*I``**. Where
-**``R``** is constant coefficient called resistance.
-
-So first  we need to  define the model for  Matlab. We **must**  specify an
-independent variable name  unless it is called **``x``**, which  is not our
-choice  here. Also,  notice  that **``fittype``**  function  wants to  know
-independent variable //name// thus **``I``** is surrounded by **``' '``**
-
-```
-f=fittype( @(R,I) R*I, 'independent', 'I' )
-%______________^ independent variable must be last in the function arguments
-%____________^ even though R is supposed to be fixed it is still a variable
-%              from fitting point of view
-```
-
-Now  our job is simple, we need to specify a guessed value of the R as starting point
-for the fit function.
-
-``` param_guessed = [ 4 ]
-
-You might  have a  model with  multiple parameters  than it  is a  bit more
-evolved. Please, do read help file about fitting.
-
-Finally, we fit.
-```
-[fitobject, goodness_of_fit] = fit (I, V, f, 'StartPoint', param_guessed)
-```
-
-You will see the following
-```
-fitobject = 
-
-     General model:
-     fitobject(I) = R*I
-     Coefficients (with 95% confidence bounds):
-       R =       1.291  (0.8872, 1.695)
-
-goodness_of_fit = 
-
-           sse: 2.6340
-       rsquare: 0.7050
-           dfe: 4
-    adjrsquare: 0.7050
-          rmse: 0.8115
-```
-
-The most interesting part is **``R =       1.291  (0.8872, 1.695)``**, 
-where 1.291 is the mean for the extracted parameter ``**R**``
-and **``(0.8872, 1.695)``** is the interval within one standard deviation. 
-So we get our error bars as well: 
-one sigma is equal ``1.695 - 1.291 = 0.4040``
-
-So our conclusion is that **``R = 1.3 +/- 0.4``**.
-
-== Checking the fitting result ==
-
-We should not trust computed fit parameters blindly. For our simple case it
-is probably  OK, but  for more evolved  nonlinear fitting  functions result
-might  go way  off  if we  specify starting  point  significantly far  from
-optimal.
-
-One way  to see check  fit quality  is to look  at Root Mean  Squared error
-(**``rmse``**) parameter from above output.  It reflect what is the typical
-deviation of the model/fit from experimental points. It should be about the
-size  of your  experimental error  bars. If  it is  much smaller  then most
-likely you are over fitting (you model has to many free parameters). If it is 
-much bigger your fit model is not good enough.
-
-
-Another way to check consistency of the fit it to look at plotted data and the fit
-simultaneously. Let's open yet one more window and plot our data first
-```
-figure(3)
-fontSize=24;
-set(gca,'FontSize',fontSize );
-
-errorbar(I,V,dV, 'x')
-
-hold on
-```
-
-notice **``hold on``** statement, now next plotting command will draw over presented plot i.e. graphics window //holds on// to already present content.
-
-Now we the plot corresponding to our model/fit. There are multiple way to do it,
-the simplest is
-```
-plot( fitobject )
-
-title('Dependence of voltage on current')
-xlabel('Current (A)')
-ylabel('Voltage (V)')
-```
-
-[fitted_data.png]
-
-This is not a very good fit since the fit line most of the times more than a typical experimental error away.
-
-== More elaborated fit ==
-
-It looks like our  voltage has some offset. We need to  update our model to
-include **``Vb``** the biasing voltage term: **``V = R*I +Vb``**. So in our
-fit/model should include two unknown parameters **``R``** and **``+Vb``**
-
-```
-f=fittype( @(R, Vb, I) R*I+Vb, 'independent', 'I' )
-```
-
-We need provide initial
-guess for two parameters
-
-```
-param_guessed = [ 4, .5 ]
-%_________________^           R value
-%____________________^^       Vb value
-```
-
-The rest of the procedure is the same as above
-
-```
-[fitobject, goodness_of_fit] = fit (I, V, f, 'StartPoint', param_guessed)
-```
-
-and we see fit parameters **``R``** and **``+Vb``** below
-```
-
-fitobject = 
-
-     General model:
-     fitobject(I) = R*I+Vb
-     Coefficients (with 95% confidence bounds):
-       R =      0.9094  (0.5556, 1.263)
-       Vb =       1.165  (0.2817, 2.048)
-
-goodness_of_fit = 
-
-           sse: 0.3832
-       rsquare: 0.9571
-           dfe: 3
-    adjrsquare: 0.9428
-          rmse: 0.3574
-```
-
-Let's see how our new fit looks like
-
-```
-figure(4)
-fontSize=24;
-set(gca,'FontSize',fontSize );
-
-errorbar(I,V,dV, 'x')
-hold on
-
-plot( fitobject )
-
-title('Dependence of voltage on current')
-xlabel('Current (A)')
-ylabel('Voltage (V)')
-```
-
-[fitted_data_improved.png]
-
-This seems to be a much better fit.
-
-
-= Saving your Matlab plots =
-
-Well it nice to have Matlab  plots.  But as soon as you close Matlab they will go away.
-How to save them for a future use? Actually, quite easy with **``print``** command. Unlike the name suggest it does not make a carbon copy but actually an electronic one.
-
-For figure saved in png format do
-``` print('-dpng', 'V_vs_I.png')
-
-If you find that you figures are to large specify resolution in dots per inch 
-with **``-r``** option. For example
-``` print('-dpng', '-r50',  'V_vs_I.png')
-
-or if you need a pdf (Matlab usually make very bad pdfs without a lot of tweaking)
-``` print('-dpdf', 'V_vs_I.pdf')
-
-The **``-d``** stands for output driver option, i.e png or pdf in above examples.
-
-Make sure that you read documentation for **``print``** command there are some
-useful parameters.
-
-
-
-= Where to learn more =
-
-At W&M Physics 256 class teaches how scientists use computers. Matlab was a language of
-choice for this class. Feel free to read and use
-[my Physics 256 materials http://physics.wm.edu/~evmik/classes/2012_fall_practical_computing_for_scientists/]
-make sure that you read at least Lecture 02 slides. Also lecture 15 slides discuss
-data reduction and fitting.
-
-
-
-
diff --git a/matlab_usage_source/local.mk b/matlab_usage_source/local.mk
deleted file mode 100644
index 1cd94e5..0000000
--- a/matlab_usage_source/local.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-PACKAGE_DIR = $(shell basename `pwd`)
-
-tex_independent := 
-tex_fig_files := 
-t2t_fig_files := errorbar_plot.png errorbar_with_large_font_plot.png fitted_data_improved.png fitted_data.png simple_labeled_and_proper_limits_plot.png simple_labeled_plot.png simple_unlabeled_plot.png
-
-REQUIRED_TARGETS   += html_t2t
-INSTALL_TARGETS    += install_html_t2t
diff --git a/matlab_usage_source/simple_labeled_and_proper_limits_plot.png b/matlab_usage_source/simple_labeled_and_proper_limits_plot.png
deleted file mode 100644
index 54871d4..0000000
--- a/matlab_usage_source/simple_labeled_and_proper_limits_plot.png
+++ /dev/null
diff --git a/matlab_usage_source/simple_labeled_plot.png b/matlab_usage_source/simple_labeled_plot.png
deleted file mode 100644
index c43f077..0000000
--- a/matlab_usage_source/simple_labeled_plot.png
+++ /dev/null
diff --git a/matlab_usage_source/simple_unlabeled_plot.png b/matlab_usage_source/simple_unlabeled_plot.png
deleted file mode 100644
index f39bce6..0000000
--- a/matlab_usage_source/simple_unlabeled_plot.png
+++ /dev/null
diff --git a/notes/Makefile b/notes/Makefile
deleted file mode 100644
index 9b246cf..0000000
--- a/notes/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
-# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
-# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
-
-# Default value so one can compile i3-msg standalone
-TOPDIR=..
-include $(TOPDIR)/common.mk
-include ./local.mk
-include $(MAKEINCLUDE_DIR)/t2t.mk
-include $(MAKEINCLUDE_DIR)/tex.mk
-
-
-dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
-
-.DEFAULT_GOAL := all
-
-all: compile install
-
-compile: $(REQUIRED_TARGETS)
-
-clean: $(CLEAN_TARGETS)
-	
-real_clean: $(REAL_CLEAN_TARGETS)
-
-install: $(INSTALL_TARGETS)
-
-
-
diff --git a/notes/error_propagation_note.tex b/notes/error_propagation_note.tex
deleted file mode 100644
index 19413ed..0000000
--- a/notes/error_propagation_note.tex
+++ /dev/null
@@ -1,90 +0,0 @@
-\documentclass[letterpaper,11pt]{article}
-\usepackage{units}
-\begin{document}
-
-\section*{A note on error propagation}
-
-We are trying to find the change (uncertainty) in some function $f(x,y,z)$ when $x,y$ and $z$ are subject to change (i.e., have some uncertainty). Assuming first that only $x$ has an uncertainty $\delta x$ and that our measured values (distinct from the variables $x,y$ and $z$)  are $x_0, y_0, z_0$, we have:
-
-\begin{eqnarray}\label{eq:delta_f}
-|\delta f(x_0,y_0,z_0)| & = & \left| f(x_0+\delta x, y_0, z_0) - f(x_0,y_0,z_0) \right | \\
- & \approx & \left|[f(x_0,y_0,z_0) + \frac{\partial f}{\partial x}\Big|_{x=x_0} (x_0+\delta x  - x_0)] \right. \nonumber \\
-& & \left. -f(x_0,y_0,z_0)  \right| \\
-& = &  \left| \frac{\partial f}{\partial x}\Big|_{x=x_0} (\delta x) \right|
-\end{eqnarray}
-
-For uncorrelated uncertainties on $x,y$ and $z$, this leads to the general formula:
-
-\begin{equation}
-(\delta f)^{2} = \left(\frac{\partial f}{\partial x}\right)^{2} (\delta x)^{2} 
- + \left(\frac{\partial f}{\partial y}\right)^{2} (\delta y)^{2} 
- + \left(\frac{\partial f}{\partial z}\right)^{2} (\delta z)^{2} 
-\end{equation}
-
-Where we evaluate $f()$ and it's derivatives at $(x_0,y_0,z_0)$.
-
-\subsection*{Example from the e/m lab}
-
-We'd like to propagate errors on $e/m$.  First we write down a function for $e/m$ in terms of the measured variables:
-
-\begin{equation}
-\frac{e}{m}=\left[\frac{125}{32}\frac{a^2}{\mu_{0}^2 N^{2}}\right]\frac{V}{I^2 r^2} = C \frac{V}{I^2 r^2}
-\end{equation}
-where $C$ is a constant and $V,I,r$ are the measured variables. We can now propagate errors and find the uncertainty $(e/m)_{j}$, the measured value of $e/m$ for trial $j$. We set $e/m = f(V,I,r)$ and then $(e/m)_j= f(V_j, I_j, r_j)\equiv f_j$. The uncertainty in $f_j$ is:
-\begin{eqnarray}
-(\delta f_j)^2 & = & \left(\frac{\partial f}{\partial V}\Big|_j \right)^{2} (\delta V)^{2} 
- + \left(\frac{\partial f}{\partial I}\Big|_j \right)^{2} (\delta I)^{2} 
- + \left(\frac{\partial f}{\partial r}\Big|_j \right)^{2} (\delta r)^{2} \\
-& = & \left(\frac{C}{I_j^2 r_j^2}\right)^2 (\delta V_j)^2 
-    + \left(\frac{-2C V_j}{I_j^3 r_j^2}\right)^2 (\delta I_j)^2
-    + \left(\frac{-2C V_j}{I_j^2 r_j^3}\right)^2 (\delta r_j)^2 \\
-    & & \mbox{now we can rearrange a little bit} \nonumber \\
-& = & \left(\frac{CV_j}{I_j^2 r_j^2}\right)^2 \left(\frac{\delta V_j}{V_j}\right)^2 
-    + \left(\frac{CV_j}{I_j^2 r_j^2}\right)^2  \left(2\frac{\delta I_j}{I_j}\right)^2
-    + \left(\frac{CV_j}{I_j^2 r_j^2}\right)^2  \left(2\frac{\delta r_j}{r_j}\right)^2
-\end{eqnarray}
-
-But $\left(\frac{CV_j}{I_j^2 r_j^2}\right)^2 = (f_j)^2$, so we have 
-
-\begin{equation}\label{eq:final_em} 
-(\delta f_j)^2 =   (f_j)^2 \left(\frac{\delta V_j}{V_j}\right)^2 
-    +  (f_j)^2 \left(2\frac{\delta I_j}{I_j}\right)^2
-    + (f_j)^2 \left(2\frac{\delta r_j}{r_j}\right)^2
-\end{equation}
-The terms $\frac{\delta V_j}{V_j}$, $\frac{\delta I_j}{I_j}$, $\frac{\delta r_j}{r_j}$ are just fractional uncertainties in the measured voltage, current and radius. In this case, you had something like $\frac{\delta V_j}{V_j}\approx\frac{\unit[0.05]{V}}{\unit[250]{V}}=0.02\%$, something similar for $I$, but $\frac{\delta r_j}{r_j}\approx \frac{\unit[0.3]{cm}}{\unit[4.0]{cm}}=7.5\%$, so the last term in Eq.~\ref{eq:final_em} completely dominates the other two. Therefore:
-
-\begin{equation}\label{eq:approx_err}
-|\delta f_j| \approx |f_j| \left|2\frac{\delta r_j}{r_j}\right| = 15\%|f_j|
-\end{equation}
-
-This is the sort of analysis I'd like to see in a report and Eq.~\ref{eq:approx_err} is what you'd code into an Igor or Excel spreadsheet. Of course Eq.~\ref{eq:final_em} would also work, you'd just miss out on some intuition about what was driving the uncertainties in your experiment and could be more vulnerable to typos in the formula. 
-
-\subsection*{A slightly different approach}
-
-What if derivatives of $f$ are messy to evaluate? For example as in the electron diffraction lab when you are trying to propagate uncertainties on $\sin\theta$ which involves a double angle formula, sines and inverse sines of the quantities you measured. There is a simple thing you can do, going back to Eq.~\ref{eq:delta_f}:
-
-\begin{equation}
-|\delta f(x_0,y_0,z_0)|  =  \left| f(x_0+\delta x, y_0, z_0) - f(x_0,y_0,z_0) \right |
-\end{equation}
-
-which can be generalized to multiple dimensions as:
-
-\begin{eqnarray}
-(\delta f(x_0,y_0,z_0))^2  & = & \left[f(x_0+\delta x, y_0, z_0) - f(x_0,y_0,z_0) \right ]^2 \nonumber \\
-& + & \left[f(x_0, y_0+\delta y, z_0) - f(x_0,y_0,z_0) \right ]^2 \nonumber \\
-& + & \left[f(x_0, y_0, z_0+\delta z) - f(x_0,y_0,z_0) \right ]^2 \nonumber
-\end{eqnarray}
-
-That is, we just reevaluate $f$ when we shift $x_0,y_0,z_0$. The shifts are independent so long as the uncertainties themselves are independent, and we add all shifts in quadrature. This avoids taking derivatives and may, or may not, be less messy. Also, note, I claim it's a little better to do this:
-
-\begin{eqnarray}
-(\delta f(x_0,y_0,z_0))^2  & = & \left[\frac{1}{2}|f(x_0+\delta x, y_0, z_0) - f(x_0,y_0,z_0)| \right. \\
-& + & \left. \frac{1}{2}\left|f(x_0-\delta x, y_0, z_0) - f(x_0,y_0,z_0)\right| \right]^2 \nonumber \\
-& + & \quad \mbox{similar terms for $y$ and $z$}
-\end{eqnarray}
-That is, average the effect of shifting by $\pm \delta x$.
-
-\subsection*{Final Note} 
-Whatever you do, be clear about what you are assuming for input uncertainties and the specific formula for $\delta f$! We don't need to see all steps in deriving $\delta f$ but we must be able to plug your $x_i, y_i, z_i$ and $\delta x_i, \delta y_i, \delta z_i$  into your formula to get your $\delta f_i$. 
-
-\end{document}
diff --git a/notes/local.mk b/notes/local.mk
deleted file mode 100644
index 8d6d951..0000000
--- a/notes/local.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-PACKAGE_DIR = $(shell basename `pwd`)
-
-tex_independent := error_propagation_note.tex
-t2t_fig_files := 
-tex_fig_files := 
-tex_includes  := 
-
-REQUIRED_TARGETS   += pdf_tex
-INSTALL_TARGETS    += install_pdf_tex
-
diff --git a/manual_source/pdf_figs/BECinterferfometer.pdf b/pdf_figs/BECinterferfometer.pdf
index d431d61..d431d61 100644
--- a/manual_source/pdf_figs/BECinterferfometer.pdf
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diff --git a/manual_source/pdf_figs/HeNelevels.pdf b/pdf_figs/HeNelevels.pdf
index fb044da..fb044da 100644
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diff --git a/manual_source/pdf_figs/HeNesetup.pdf b/pdf_figs/HeNesetup.pdf
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diff --git a/manual_source/pdf_figs/LIGO.pdf b/pdf_figs/LIGO.pdf
index 18d0102..18d0102 100644
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diff --git a/manual_source/pdf_figs/LISA.pdf b/pdf_figs/LISA.pdf
index f97bc35..f97bc35 100644
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index babe91a..babe91a 100644
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index 078e76e..078e76e 100644
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index 6f39ca7..6f39ca7 100644
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diff --git a/manual_source/pdf_figs/pic4i.pdf b/pdf_figs/pic4i.pdf
index b996c4a..b996c4a 100644
--- a/manual_source/pdf_figs/pic4i.pdf
+++ b/pdf_figs/pic4i.pdf
diff --git a/manual_source/pdf_figs/scnut.pdf b/pdf_figs/scnut.pdf
index 6fd60c6..6fd60c6 100644
--- a/manual_source/pdf_figs/scnut.pdf
+++ b/pdf_figs/scnut.pdf
diff --git a/manual_source/pdf_figs/series.pdf b/pdf_figs/series.pdf
index 068d1b9..068d1b9 100644
--- a/manual_source/pdf_figs/series.pdf
+++ b/pdf_figs/series.pdf
diff --git a/manual_source/pdf_figs/sinxox.pdf b/pdf_figs/sinxox.pdf
index 687d338..687d338 100644
--- a/manual_source/pdf_figs/sinxox.pdf
+++ b/pdf_figs/sinxox.pdf
diff --git a/manual_source/pdf_figs/solapp.pdf b/pdf_figs/solapp.pdf
index f46e2ab..f46e2ab 100644
--- a/manual_source/pdf_figs/solapp.pdf
+++ b/pdf_figs/solapp.pdf
diff --git a/manual_source/pdf_figs/spec.pdf b/pdf_figs/spec.pdf
index 2388adf..2388adf 100644
--- a/manual_source/pdf_figs/spec.pdf
+++ b/pdf_figs/spec.pdf
diff --git a/manual_source/pdf_figs/tcube.pdf b/pdf_figs/tcube.pdf
index a42f1af..a42f1af 100644
--- a/manual_source/pdf_figs/tcube.pdf
+++ b/pdf_figs/tcube.pdf
diff --git a/manual_source/pdf_figs/test.pdf b/pdf_figs/test.pdf
index a8dc96e..a8dc96e 100644
--- a/manual_source/pdf_figs/test.pdf
+++ b/pdf_figs/test.pdf
diff --git a/manual_source/pdf_figs/thermopile.pdf b/pdf_figs/thermopile.pdf
index c6f8555..c6f8555 100644
--- a/manual_source/pdf_figs/thermopile.pdf
+++ b/pdf_figs/thermopile.pdf
diff --git a/manual_source/pdf_figs/tradcube.pdf b/pdf_figs/tradcube.pdf
index 5bee5ef..5bee5ef 100644
--- a/manual_source/pdf_figs/tradcube.pdf
+++ b/pdf_figs/tradcube.pdf
diff --git a/manual_source/pdf_figs/tsisetup.pdf b/pdf_figs/tsisetup.pdf
index 889bc9b..889bc9b 100644
--- a/manual_source/pdf_figs/tsisetup.pdf
+++ b/pdf_figs/tsisetup.pdf
diff --git a/manual_source/pdf_figs/tungsten.pdf b/pdf_figs/tungsten.pdf
index e87c635..e87c635 100644
--- a/manual_source/pdf_figs/tungsten.pdf
+++ b/pdf_figs/tungsten.pdf
diff --git a/manual_source/pdf_figs/up.pdf b/pdf_figs/up.pdf
index d43ef28..d43ef28 100644
--- a/manual_source/pdf_figs/up.pdf
+++ b/pdf_figs/up.pdf
diff --git a/manual_source/pdf_figs/w_res.pdf b/pdf_figs/w_res.pdf
index 85b393c..85b393c 100644
--- a/manual_source/pdf_figs/w_res.pdf
+++ b/pdf_figs/w_res.pdf
diff --git a/schedule_mon.t2t b/schedule_mon.t2t
deleted file mode 100644
index eeb2afc..0000000
--- a/schedule_mon.t2t
+++ /dev/null
@@ -1,34 +0,0 @@
-ThisClassID - Monday group schedule
-by EugeniyMikhailov
-
-
-
-%!includeconf: ./configs/config.t2t
-%!includeconf: ./configs/labs_acronyms_cfg.t2t
-%!postproc: path2root '.'
-%!options(html): --no-toc
-%!style(tex): ./evmik
-%!style(html): ./evmik.css
-
-== Lab Schedule ==
-
-||  Week         | Sec 1/2 | Sec 3/4 | Sec 5/6 | Sec 7/8 |
-| Aug 25 Week01  | NoMtng  | NoMtng  | NoMtng  | NoMtng  |
-| Sep 1  Week02  | PiLab   | PiLab   | PiLab   | PiLab   |
-| Sep 8  Week03  | Interf  | Interf  | e/m     | e/m     |
-| Sep 15 Week04  | e/m     | e/m     | Interf  | Interf  |
-| Sep 22 Week05  | eDiffr  | eDiffr  | bBody   | bBody   |
-| Sep 29 Week06  | bBody   | bBody   | phElect | phElect |
-| Oct 6  Week07  | phElec  | phElect | eDiffr  | 2slit   |
-| Oct 13 Week08  | FallBrk | FallBrk | FallBrk | FallBrk |
-| Oct 20 Week08  | LabTour | LabTour | LabTour | LabTour |
-| Oct 27 Week10  | FaradR  | Spectr  | 2slit   | eDiffr  |
-| Nov 3  Week11  | Spectr  | 2slit   | Spectr  | FaradR  |
-| Nov 10 Week12  | 2slit   | FaradR  | FaradR  | Spectr  |
-| Nov 17 Week13  | SuperC  | SuperC  | SuperC  | SuperC  |
-| Nov 24 Week14  | SpPrW1  | SpPrW1  | SpPrW1  | SpPrW1  |
-| Dec 1  Week15  | SpPrW2  | SpPrW2  | SpPrW2  | SpPrW2  |
-| Finals Week    | SpPrPrs | SpPrPrs | SpPrPrs | SpPrPrs |
-                  
-
-
diff --git a/schedule_wed.t2t b/schedule_wed.t2t
deleted file mode 100644
index 116c0f7..0000000
--- a/schedule_wed.t2t
+++ /dev/null
@@ -1,34 +0,0 @@
-ThisClassID - Wednesday and Thursday groups schedule
-by EugeniyMikhailov
-
-
-
-%!includeconf: ./configs/config.t2t
-%!includeconf: ./configs/labs_acronyms_cfg.t2t
-%!postproc: path2root '.'
-%!options(html): --no-toc
-%!style(tex): ./evmik
-%!style(html): ./evmik.css
-
-== Lab Schedule ==
-
-||  Week         | Sec 1/2 | Sec 3/4 | Sec 5/6 | Sec 7/8 |
-| Aug 25 Week01  | PiLab   | PiLab   | PiLab   | PiLab   |
-| Sep 1  Week02  | Interf  | Interf  | e/m     | e/m     |
-| Sep 8  Week03  | e/m     | e/m     | Interf  | Interf  |
-| Sep 15 Week04  | eDiffr  | eDiffr  | bBody   | bBody   |
-| Sep 22 Week05  | bBody   | bBody   | phElect | phElect |
-| Sep 29 Week06  | phElec  | phElect | eDiffr  | 2slit   |
-| Oct 6  Week07  | FaradR  | Spectr  | 2slit   | eDiffr  |
-| Oct 13 Week08  | LabTour | LabTour | LabTour | LabTour |
-| Oct 20 Week08  | Spectr  | 2slit   | Spectr  | FaradR  |
-| Oct 27 Week10  | 2slit   | FaradR  | FaradR  | Spectr  |
-| Nov 3  Week11  | SuperC  | SuperC  | SuperC  | SuperC  |
-| Nov 10 Week12  | SpPrW1  | SpPrW1  | SpPrW1  | SpPrW1  |
-| Nov 17 Week13  | SpPrW2  | SpPrW2  | SpPrW2  | SpPrW2  |
-| Nov 24 Week14  | ThankG  | ThankG  | ThankG  | ThankG  |
-| Dec 1  Week15  | SpPrPrs | SpPrPrs | SpPrPrs | SpPrPrs |
-| Finals Week    | NoMtng  | NoMtng  | NoMtng  | NoMtng  |
-
-
-
diff --git a/styles/evmik.sty b/styles/evmik.sty
deleted file mode 100644
index 95c53d7..0000000
--- a/styles/evmik.sty
+++ /dev/null
@@ -1,10 +0,0 @@
-% -*- latex -*-
-% FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/styles/evmik.sty"
-% LAST MODIFICATION: "Tue, 27 Aug 2013 16:11:58 -0400 (evmik)"
-% (C) 2008 by Eugeniy Mikhailov, <evgmik@gmail.com>
-% $Id:$
-
-\usepackage[margin=1in,letterpaper]{geometry}
-%\usepackage{setspace} %to adjust line spacing adjust parameter in the next line
-%\setstretch{1.0}
-
diff --git a/styles/evmikcompact.sty b/styles/evmikcompact.sty
deleted file mode 100644
index 640c428..0000000
--- a/styles/evmikcompact.sty
+++ /dev/null
@@ -1,189 +0,0 @@
-%%
-%% This is file `fullpage.sty',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% fullpage.dtx  (with options: `package')
-%% =============================================
-%% IMPORTANT NOTICE:
-%% 
-%% This program can be redistributed and/or modified under the terms
-%% of the LaTeX Project Public License Distributed from CTAN
-%% archives in directory macros/latex/base/lppl.txt; either
-%% version 1 of the License, or any later version.
-%% 
-%% This is a generated file.
-%% It may not be distributed without the original source file fullpage.dtx.
-%% 
-%% Full documentation can be obtained by LaTeXing that original file.
-%% Only a few abbreviated comments remain here to describe the usage.
-%% =============================================
-%% by Eugeniy E. Mikhailov
-%%  this package try to shrink all unnesesary spaces
-%%  it is all very crude and suitable only for very tailored cases
-\NeedsTeXFormat{LaTeX2e}[1994/06/01]
-\ProvidesPackage{evmikcompact}
-         [2010/09/17 1.0]
-
-\def\maketitle{%
-{\flushleft\Large \bf \@title\par}%
-\vskip 1em
-}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% section definition
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\def\section{\@ifstar\unnumberedsection\numberedsection}
-\def\numberedsection{\@ifnextchar[%]
-  \numberedsectionwithtwoarguments\numberedsectionwithoneargument}
-\def\unnumberedsection{\@ifnextchar[%]
-  \unnumberedsectionwithtwoarguments\unnumberedsectionwithoneargument}
-\def\numberedsectionwithoneargument#1{\numberedsectionwithtwoarguments[#1]{#1}}
-\def\unnumberedsectionwithoneargument#1{\unnumberedsectionwithtwoarguments[#1]{#1}}
-\def\numberedsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-  \refstepcounter{section}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \large
-  \bfseries
-  \thesection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{section}{%
-    \protect\numberline{\thesection}%
-    #1}%
-  }
-\def\unnumberedsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-%  \refstepcounter{section}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \large
-  \bfseries
-%  \thesection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{section}{%
-%    \protect\numberline{\thesection}%
-    #1}%
-  }
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% subsection definition
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\def\subsection{\@ifstar\unnumberedsubsection\numberedsubsection}
-\def\numberedsubsection{\@ifnextchar[%]
-  \numberedsubsectionwithtwoarguments\numberedsubsectionwithoneargument}
-\def\unnumberedsubsection{\@ifnextchar[%]
-  \unnumberedsubsectionwithtwoarguments\unnumberedsubsectionwithoneargument}
-\def\numberedsubsectionwithoneargument#1{\numberedsubsectionwithtwoarguments[#1]{#1}}
-\def\unnumberedsubsectionwithoneargument#1{\unnumberedsubsectionwithtwoarguments[#1]{#1}}
-\def\numberedsubsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-  \refstepcounter{subsection}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \bfseries
-  \thesubsection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{subsection}{%
-    \protect\numberline{\thesubsection}%
-    #1}%
-  }
-\def\unnumberedsubsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-%  \refstepcounter{subsection}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \bfseries
-%  \thesubsection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{subsection}{%
-%    \protect\numberline{\thesubsection}%
-    #1}%
-  }
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% subsubsection definition
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\def\subsubsection{\@ifstar\unnumberedsubsubsection\numberedsubsubsection}
-\def\numberedsubsubsection{\@ifnextchar[%]
-  \numberedsubsubsectionwithtwoarguments\numberedsubsubsectionwithoneargument}
-\def\unnumberedsubsubsection{\@ifnextchar[%]
-  \unnumberedsubsubsectionwithtwoarguments\unnumberedsubsubsectionwithoneargument}
-\def\numberedsubsubsectionwithoneargument#1{\numberedsubsubsectionwithtwoarguments[#1]{#1}}
-\def\unnumberedsubsubsectionwithoneargument#1{\unnumberedsubsubsectionwithtwoarguments[#1]{#1}}
-\def\numberedsubsubsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-  \refstepcounter{subsubsection}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \bfseries
-  \thesubsubsection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{subsubsection}{%
-    \protect\numberline{\thesubsubsection}%
-    #1}%
-  }
-\def\unnumberedsubsubsectionwithtwoarguments[#1]#2{%
-  \ifhmode\par\fi
-  \removelastskip
-  \vskip 3ex\goodbreak
-%  \refstepcounter{subsubsection}%
-  \noindent
-  \leavevmode
-  \begingroup
-  \bfseries
-%  \thesubsubsection\ 
-  #2.\quad
-  \endgroup
-  \addcontentsline{toc}{subsubsection}{%
-%    \protect\numberline{\thesubsubsection}%
-    #1}%
-  }
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% list  items config  
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\def\@listi{\leftmargin\leftmargini
-	    %\parsep 5\p@  \@plus2.5\p@ \@minus\p@
-	    %\topsep 2.5\p@ \@plus4\p@   \@minus6\p@
-	    %\itemsep0.0\p@  \@plus2.5\p@ \@minus\p@}
-%\let\@listI\@listi
-
-\AtBeginDocument{%
-  \renewcommand{\@listi}
-    {\setlength{\leftmargin}{\leftmargini}
-     \setlength{\topsep} {0pt}
-     \setlength{\parsep} {\parskip}
-     \setlength{\itemsep}{0pt}}
-  \renewcommand{\@listii}
-    {\setlength{\leftmargin}{\leftmarginii}
-     \setlength{\labelwidth}{\leftmarginii}
-     \addtolength{\labelwidth}{-\labelsep}}
-  \renewcommand{\@listiii}
-    {\setlength{\leftmargin}{\leftmarginiii}
-     \setlength{\labelwidth}{\leftmarginiii}
-     \addtolength{\labelwidth}{-\labelsep}}}
-\makeatother
-
diff --git a/styles/listing_defs.tex b/styles/listing_defs.tex
deleted file mode 100644
index 893f88b..0000000
--- a/styles/listing_defs.tex
+++ /dev/null
@@ -1,20 +0,0 @@
-% -*- latex -*-
-% FILE: "/home/evmik/jobs/wm/2011_fall_practical_computing_for_scientists/styles/listing_defs.tex"
-% LAST MODIFICATION: "Fri, 16 Sep 2011 11:03:13 -0400 (evmik)"
-% (C) 2010 by Eugeniy Mikhailov, <evgmik@gmail.com>
-% $Id:$
-
-
-% {{{ listing color schem definitions
-\definecolor{listcommentcolor}{rgb}{0.0,0.4,0} %dark green
-%\definecolor{listbg}{rgb}{0.67,0.90,0.64} %pale green
-\definecolor{listbg}{rgb}{0.90,0.90,0.90} %light grey
-\lstset{backgroundcolor=\color{listbg}}
-\lstset{commentstyle=\color{listcommentcolor}}
-\lstset{keywordstyle=\color{blue}}
-\lstset{stringstyle=\color{magenta}}
-\lstset{language=matlab}
-\lstset{tabsize=2}
-\lstset{showstringspaces=false}
-\lstset{basicstyle = \ttfamily}
-% }}}
diff --git a/syllabus_source/Makefile b/syllabus_source/Makefile
deleted file mode 100644
index 9b246cf..0000000
--- a/syllabus_source/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# -*- make -*-
-# FILE: "/home/evmik/jobs/wm/2013_fall_Experimental_Atomic_Physics_251/syllabus_source/Makefile"
-# LAST MODIFICATION: "Wed, 11 Sep 2013 13:54:57 -0400 (evmik)"
-# (C) 2001 by Eugeniy Mikhailov, <evmik@tamu.edu>
-# $Id: Makefile,v 1.3 2003/04/23 20:40:19 evmik Exp $
-
-# Default value so one can compile i3-msg standalone
-TOPDIR=..
-include $(TOPDIR)/common.mk
-include ./local.mk
-include $(MAKEINCLUDE_DIR)/t2t.mk
-include $(MAKEINCLUDE_DIR)/tex.mk
-
-
-dest_dir = $(DESTDIR)$(PREFIX)/$(PACKAGE_DIR)
-
-.DEFAULT_GOAL := all
-
-all: compile install
-
-compile: $(REQUIRED_TARGETS)
-
-clean: $(CLEAN_TARGETS)
-	
-real_clean: $(REAL_CLEAN_TARGETS)
-
-install: $(INSTALL_TARGETS)
-
-
-
diff --git a/syllabus_source/local.mk b/syllabus_source/local.mk
deleted file mode 100644
index c599855..0000000
--- a/syllabus_source/local.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- make -*-
-# (C) 2013 by Eugeniy Mikhailov, <evgmik@gmail.com>
-
-
-PACKAGE_DIR = $(shell basename `pwd`)
-
-tex_independent := 
-tex_fig_files := 
-t2t_fig_files := 
-
-REQUIRED_TARGETS   += html_t2t
-INSTALL_TARGETS    += install_html_t2t
-
diff --git a/syllabus_source/syllabus_2013_fall_Experimental_Atomic_Physics_251.t2t b/syllabus_source/syllabus_2013_fall_Experimental_Atomic_Physics_251.t2t
deleted file mode 100644
index 74ad41a..0000000
--- a/syllabus_source/syllabus_2013_fall_Experimental_Atomic_Physics_251.t2t
+++ /dev/null
@@ -1,186 +0,0 @@
-ThisClassID - Syllabus, fall 2013
-
-27 August 2013
-
-%!includeconf: ../configs/config.t2t
-%!postproc: path2root '..'
-%!options(html): --toc --toc-level=1
-%!style(tex): fullpage,../styles/evmikcompact
-% %% parskip remove indent of the paragraphs
-%!style(tex): parskip
-%!postproc(tex): ,a4paper ,letter
-%!postproc(tex): \\date{.*}  \date{}
-% %!postproc(tex): \\maketitle  %\maketitle
-%!postproc(tex): \\clearpage  %\clearpage
-%!postproc(tex): LaTeX  \LaTeX{}
-
-
-= Instructor: Eugeniy E. Mikhailov =
-- Office: Small Hall 253
-%- Lab: Small 032 and 065 
-%- Phones: 221-3571 (office), 251-3560 (lab)
-- Email: eemikh@wm.edu
-- Office Hours:  MWR  9:30-10:30 and by appointment.
-- Web: http://physics.wm.edu/~evmik/ all class materials and announcements will be posted here
-
-
-== Lab assistants ==
-Matt T. Simons <mtsimons@email.wm.edu> and  Aj Pyle <ajpyle@email.wm.edu>
-
-= What will we learn =
-- Experimental techniques
-- Lab report writing
-- Uncertainty analysis
-
-
-= What will we do =
-You will be conducting a new experiment every week, using the 170 minutes we have in class.
-
-== Reading Ahead ==
-The standard experiments have lab "manuals" which I will post at the website. You should reserve about half an hour to read over them **before** coming to lab.
-
-
-== Lab book ==
-
-Your lab book should be a  regular style notebook without rings with either
-line or quadrangle  ruling or a computation log/lab book. It  can be obtained at
-most stationary stores (i.e. Staples, etc ...)
-
-You need to keep a good lab book, with your raw data, sketches or pictures of
-the equipment, notes on your experimental methodology, calculations, etc.
-Everything you do goes into this book and it provides the foundation for your
-lab reports. You need to bring it every week (if you forget you'll have to run
-home to get it).
-
-Diagrams,  data,
-graphs, and other notes on separate pieces of paper should be glued, taped,
-or stapled into the lab book. If something falls out of the lab book during
-reading/shaking/transporting, it is  not the part of the log  book and will
-be discarded. All  notes should be written in **pen**.  Mistakes and errors
-in design,  data, and analysis will  occur, and they should  be crossed out
-neatly.
-
-The  lab book  will be  graded primarily  on completeness  and to  a lesser
-extent on neatness (i.e. better to be complete than neat, though doing both
-is better yet). It  should also feature a table of  contents. The lab books
-will be turned in every week or two and returned before the next lab.
-
-You should  enter you  lab notes  and data  directly into  the lab  book. A
-"scratch" lab book that is neatly copied  into the lab book at a later time
-is not appropriate and will result  in a significantly reduced grade. It is
-OK though  to use  scratch paper  which is  glued into  the lab  book prior
-submission.
-
-
-== Lab reports ==
-You will need to write a report for each of the standard labs. Though you will
-do the experiments in collaboration with a partner, your lab report is your own
-work. They are due at the start of class the following week. Late reports will
-be docked 5% per day.
-
-In physics and mathematics LaTeX is the standard program used to format
-papers. It's great, especially for mathematical forumlae, figures with
-captions, and tables. It's available on Windows/Mac/Linux. A previous student
-says:
-
-	"Just letting you know I used LaTeX using TeXnicCenter as my editor.
-	At first I was a bit skeptical because I felt Word could do just as
-	much without having to build the Document to view it. But as
-	experiments began to need more figures and equations I really started
-	to enjoy latex because it was so simple. I could make gigantic
-	equations like the Schrodinger's equation in just a minute whereas
-	word would have taken me quite a while. Anyways I'm really happy I
-	learned to use LaTeX and look forward to using it in the future."
-
-I **strongly** encourage you to try it but do not require it.
-
-== Analysis software ==
-It might be tempting to use MSExcel for you analysis. I strongly suggest to
-**keep away** from  it. Moreover, I will  not accept plots made in  Excel or its
-analog. They are  easy to spot, since  they are ugly and have  no notion of
-proper axes limits.
-
-I suggest you to use Matlab which is very powerful and free for W&M students.
-
-Usually there is  no "silver bullet" software which does  good analysis and
-presentation,  and you  might  invest some  time to  find  a good  plotting
-software as well. My personal choice is Gnuplot, though Matlab will do good
-enough job most of the time.
-
-**Do not use jpeg** format for the graph representation, use png
-or better yet eps or pdf formats.
-
-
-== Lab visit ==
-
-One week,  instead of doing  experiments, you will visit physics  and applied
-science research labs, and maybe even   talk with a theorist or
-two. You'll write up a summary of your visit.
-
-
-
-
-
-
-= Textbook =
-There is no required text for this class. However, as supplements I suggest:
-- Melissinos and Napolitano, "Experiments in Modern Physics", 2nd Ed., Academic Press.
-- G. L. Squires, "Practical Physics", 4th Ed., Cambridge.
-
-
-= Sections =
-There  are several  independent sections  for this  class. In  general, you
-cannot switch between them after the first experiment since you will have a
-lab partner and some of the experiments require at least two people.
-
-
-= Physics 201 corequisite =
-Physics  201  is a  corequisite  of  this  class. However,  unlike  Physics
-101/102, the two classes  are separate and we do not try  very hard to keep
-them in sync or make sure that  201 covers the theory behind a topic before
-251 does  the experiment. This  is, more or  less, how progress  in physics
-really occurs!  Experimenters usually do  their work at the  frontier where
-there is no theory or where there are multiple competing theories.
-
-
-= Evaluations =
-Your final grade for the course will be determined from the following grading weight distribution:
-- Lab reports and lab visit:			75% 
-- Special project:		15%
-- Logbook evaluation:		5%
-- Lab participation:		5%
-- Occasionally I will make mistakes: typos, etc. If you report them or prove me wrong,
-you will get an extra bonus.
-
-
-I will drop the lowest lab score. However, in order to pass the class, 
-**you** **must** **do** **and** **turn** **in** **a** **report** **for** **all** **labs**. 
-You must also do the special
-project.  Makeup labs are only allowed with prior permission and for a good
-reason or due to illness with a doctor's note. Unlike 101/102 labs there is no
-reserved date. We'll just deal with this as necessary.
-
-= Grading =
-|| Grade | Score percentage | Grade | Score percentage | Grade | Score percentage |
-|        |                  | A     |  94-100          |  A-   |     90-94        |
-| B+     | 87-90            | B     |  84-87           |  B-   |     80-84        |
-| C+     | 77-80            | C     |  74-77           |  C-   |     70-74        |
-| D+     | 67-70            | D     |  64-67           |  D-   |     60-64        |
-| F      | <60              |       |                  |       |                  |
-
-
-
-== Final exam ==
-There is no final exam but the final presentation of you special project. Please, reserve the following dates and time.
-
-- Monday section:     December 10, 2pm
-- Wednesday section:  December 4, 2pm (during normal class time)
-- Thursday section:   December 5, 2pm  (during normal class time)
-
-
-
-%= Important dates =
-% exams, break etc.
-%%!include: ../important_dates.t2t
-
-