(*********************************************************************** Mathematica-Compatible Notebook This notebook can be used on any computer system with Mathematica 3.0, MathReader 3.0, or any compatible application. The data for the notebook starts with the line of stars above. To get the notebook into a Mathematica-compatible application, do one of the following: * Save the data starting with the line of stars above into a file with a name ending in .nb, then open the file inside the application; * Copy the data starting with the line of stars above to the clipboard, then use the Paste menu command inside the application. Data for notebooks contains only printable 7-bit ASCII and can be sent directly in email or through ftp in text mode. Newlines can be CR, LF or CRLF (Unix, Macintosh or MS-DOS style). NOTE: If you modify the data for this notebook not in a Mathematica- compatible application, you must delete the line below containing the word CacheID, otherwise Mathematica-compatible applications may try to use invalid cache data. For more information on notebooks and Mathematica-compatible applications, contact Wolfram Research: web: http://www.wolfram.com email: info@wolfram.com phone: +1-217-398-0700 (U.S.) Notebook reader applications are available free of charge from Wolfram Research. ***********************************************************************) (*CacheID: 232*) (*NotebookFileLineBreakTest NotebookFileLineBreakTest*) (*NotebookOptionsPosition[ 59254, 1697]*) (*NotebookOutlinePosition[ 101545, 3155]*) (* CellTagsIndexPosition[ 100642, 3125]*) (*WindowFrame->Normal*) Notebook[{ Cell[CellGroupData[{ Cell["Scientific Publishing", "Title", CounterAssignments->{{"Title", 0}}], Cell["Formatting Technical Papers", "Subtitle", CounterAssignments->{{"Title", 0}}], Cell[TextData[{ "Paul Abbott\nDepartment of Physics\nUniversity of Western Australia\n\ Nedlands, WA 6907, Australia\n", ButtonBox["http://www.physics.uwa.edu.au/~paul", ButtonData:>{ URL[ "http://www.physics.uwa.edu.au/~paul"], None}, ButtonStyle->"Hyperlink"] }], "Author"], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ". Abstract" }], "Section"], Cell[TextData[{ "Most people know ", StyleBox["Mathematica", FontSlant->"Italic"], " as a tool for teaching or research in mathematics. What is not so \ well-known is that ", StyleBox["Mathematica", FontSlant->"Italic"], " provides an excellent environment for doing professional quality \ scientific publishing. " }], "Text"], Cell[CellGroupData[{ Cell[TextData[{ "This hands-on tutorial will demonstrate how to use ", StyleBox["Mathematica", FontSlant->"Italic"], " to produce high-quality technical documents:" }], "Text"], Cell[TextData[{ StyleBox[" introduction to the ", "Bullet"], StyleBox["Mathematica", "Bullet", FontSlant->"Italic"], StyleBox[" front end;", "Bullet"] }], "SmallText"], Cell[TextData[StyleBox[ "document formatting strategies;", "Bullet"]], "SmallText"], Cell[TextData[{ StyleBox["effective use of ", "Bullet"], StyleBox["Mathematica", "Bullet", FontSlant->"Italic"], StyleBox["'s typesetting;", "Bullet"] }], "SmallText"], Cell[TextData[{ StyleBox["conversion to ", "Bullet"], Cell[BoxData[ StyleBox[ RowBox[{"T", AdjustmentBox["E", BoxMargins->{{-0.075, -0.085}, {0, 0}}, BoxBaselineShift->0.5], "X"}]]], "Bullet"], StyleBox[" using TeXSave;", "Bullet"] }], "SmallText"], Cell[TextData[StyleBox[ "conversion to HTML using HTMLSave.", "Bullet"]], "SmallText"] }, Open ]] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ". References and Tools" }], "Section"], Cell[TextData[{ "For an up to date list of ", StyleBox["Mathematica", FontSlant->"Italic"], " books, see ", ButtonBox["http://www.wolfram.com/bookstore", ButtonData:>{ URL[ "http://www.wolfram.com/bookstore"], None}, ButtonStyle->"Hyperlink"], ". Although ", StyleBox[ButtonBox["The Mathematica Book", ButtonData:>{C, "C100"}, ButtonStyle->"MainBookLink"], FontSlant->"Italic"], " contains some sections on typesetting, presently there is no book that \ fully documents all the ", StyleBox["Mathematica", FontSlant->"Italic"], " typesetting or front end capabilities." }], "Text", CellTags->"references"], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ".", CounterBox["Subsection"], ". The Beginner's Guide to ", StyleBox["Mathematica", FontSlant->"Italic"], ", Version 3" }], "Subsection"], Cell[TextData[{ ButtonBox["The Beginner's Guide to Mathematica Version 3", ButtonData:>{ URL[ "http://store.wolfram.com/view/ISBN0521622026"], None}, ButtonStyle->"Hyperlink"], " by Jerry Glynn and Theodore Gray (Cambridge University Press, 1997), has \ two parts that are especially relevant to this tutorial: " }], "Text"], Cell[CellGroupData[{ Cell[TextData[{ "Part ", StyleBox["12", FontWeight->"Bold"], ": Text and Document Features in ", StyleBox["Mathematica", FontSlant->"Italic"] }], "Subsubsection"], Cell[TextData[Cell[BoxData[ FormBox[GridBox[{ {\(Chapter\ \(46 : \)\), \(Why\ does\ my\ notebook\ look\ different\ printed\ than\ on\ \(screen?\)\), "173"}, {\(Chapter\ \(47 : \)\), RowBox[{"How", " ", "do", " ", StyleBox["I", FontSlant->"Plain"], " ", "use", " ", "style", " ", \(sheets?\)}], "176"}, {\(Chapter\ \(48 : \)\), \(What\ are\ styles, \ style\ sheets, \ and\ style\ \(environments?\)\), "177"}, {\(Chapter\ \(49 : \)\), RowBox[{"How", " ", "do", " ", StyleBox["I", FontSlant->"Plain"], " ", "use", " ", "that", " ", "darn", " ", "Option", " ", "Inspector", " ", \(anyway?\)}], "188"} }], TraditionalForm]]]], "3ColumnTable"] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ "Part ", StyleBox["14", FontWeight->"Bold"], ": Programming the Front End" }], "Subsubsection"], Cell[TextData[Cell[BoxData[ FormBox[GridBox[{ {\(Chapter\ \(54 : \)\), RowBox[{"How", " ", "do", " ", StyleBox["I", FontSlant->"Plain"], " ", "make", " ", "hyperlinks", " ", "in", " ", "and", " ", "between", " ", \(notebooks?\)}], "234"}, {\(Chapter\ \(55 : \)\), RowBox[{"Is", " ", StyleBox["Mathematica", FontSlant->"Italic"], " ", \(\[OpenCurlyDoubleQuote]scriptable\[CloseCurlyDoubleQuote]? \)}], "241"}, {\(Chapter\ \(56 : \)\), RowBox[{"What", " ", "commands", " ", "can", " ", StyleBox["I", FontSlant->"Plain"], " ", "use", " ", "to", " ", "control", " ", "the", " ", StyleBox["Mathematica", FontSlant->"Italic"], " ", "front", " ", \(end?\)}], "246"}, {\(Chapter\ \(57 : \)\), RowBox[{"What", " ", "options", " ", "can", " ", StyleBox["I", FontSlant->"Plain"], " ", "use", " ", "to", " ", "control", " ", "the", " ", StyleBox["Mathematica", FontSlant->"Italic"], " ", "front", " ", \(end?\)}], "281"}, {\(Chapter\ \(58 : \)\), RowBox[{"How", " ", "do", " ", StyleBox["I", FontSlant->"Plain"], " ", "use", " ", "file", " ", "names", " ", "in", " ", \(programs?\)}], "282"} }], TraditionalForm]]]], "3ColumnTable"] }, Closed]] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ".", CounterBox["Subsection"], ". The Help Browser" }], "Subsection"], Cell[TextData[{ "To learn more about ", StyleBox["Mathematica", FontSlant->"Italic"], " ", ButtonBox["The Help Browser", ButtonData:>{"The Help Browser (Macintosh)"}, ButtonStyle->"GettingStartedLink"], " is the primary reference. Choosing ", StyleBox["Help. . .", "Menu"], " from the ", StyleBox["Help", "Menu"], " menu at any time gives you access to ", StyleBox["Mathematica", FontSlant->"Italic"], "\[CloseCurlyQuote]s on-line documentation. " }], "Text", CellTags->{"Help Browser", "on-line documentation"}] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ".", CounterBox["Subsection"], ". Palettes" }], "Subsection"], Cell[TextData[{ "Version 3 of ", StyleBox["Mathematica", FontSlant->"Italic"], " includes palettes and buttons. For more information on palettes see ", ButtonBox["Using Palettes", ButtonData:>{"Using Palettes (Macintosh)"}, ButtonStyle->"GettingStartedLink"], ". These tools make it much easier to use ", StyleBox["Mathematica", FontSlant->"Italic"], " for doing any type of calculation, especially typesetting, by reducing \ the amount of syntax that you need to know. ", ButtonBox["Palettes and Buttons", ButtonData:>{"Palettes and Buttons"}, ButtonStyle->"GettingStartedLink"], " provide a simple but fully customizable point-and-click interface to ", StyleBox["Mathematica", FontSlant->"Italic"], ". " }], "Text"], Cell[CellGroupData[{ Cell[TextData[{ "Here is the ", ButtonBox["International Characters", ButtonData:>{"InternationalCharacters.nb", None}, ButtonStyle->"Hyperlink", ButtonNote->None], " palette for European characters. ", StyleBox["Mathematica", FontSlant->"Italic"], " supports over 700 special characters with new fonts optimized for both \ screen and printer. You can find all these characters in the ", ButtonBox["Complete Characters", ButtonData:>{"CompleteCharacters.nb", None}, ButtonStyle->"Hyperlink", ButtonNote->None], " palette. All of them have consistent full names; some also have aliases, \ as well as ", Cell[BoxData[ FormBox[ StyleBox[ RowBox[{"T", AdjustmentBox["E", BoxMargins->{{-0.075, -0.085}, {0, 0}}, BoxBaselineShift->0.5], "X"}]], TraditionalForm]]], " and SGML names. For example, have a look at the ", ButtonBox["basic typesetting palette", ButtonData:>{"BasicTypesetting.nb", None}, ButtonStyle->"Hyperlink", ButtonNote->None], ". Also, it is straightforward to develop your own palettes or buttons for \ a particular (typesetting) application: see Section ", ButtonBox["1.10.12", ButtonData:>{"1.10.12", None}, Active->True, ButtonStyle->"MainBookLink"], " of ", StyleBox["The Mathematica Book", FontSlant->"Italic"], ". " }], "Text"], Cell[TextData[{ "Remember to create an ", StyleBox["insertion point", FontSlant->"Italic"], " in your Notebook ", StyleBox["before", FontSlant->"Italic"], " you use a palette." }], "Warning", CellTags->"insertion point"] }, Open ]], Cell[CellGroupData[{ Cell["Selecting Cells by Type", "Subsubsection"], Cell[CellGroupData[{ Cell[TextData[{ "You can select all cells of a particular style using a kernel function. \ Evaluating the input below selects all cells of type ", StyleBox["Subsection", "Subsection"], ": " }], "Text"], Cell[BoxData[ \(NotebookFind[SelectedNotebook[], "\", All, CellStyle]\)], "Input", CellTags->"NotebookFind"] }, Open ]], Cell[CellGroupData[{ Cell["\<\ This functionality can be embedded in a button or palette that uses \ commands executed by the front end, without requiring a kernel. 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Inline and Display Mathematics " }], "Subsection"], Cell[CellGroupData[{ Cell["\<\ Now we demonstrate one easy and powerful way of producing correctly \ formatted two-dimensional inline equations. Consider the following text cell \ containing a valid mathematical expression:\ \>", "Text", CellTags->"two-dimensional inline equations"], Cell["\<\ Here is some text with a formula, Integrate[x Sin[x],x]=Integrate[x \ Sin[x],x]. \ \>", "Continuation"], Cell[CellGroupData[{ Cell[TextData[{ "To convert formulas in text cells into two-dimensional form, first \ highlight the formula and use ", StyleBox["Edit", "Menu"], " \[RightTriangle] ", StyleBox["Expression Input", "Menu"], " \[RightTriangle] ", StyleBox["Start Inline Cell", "Menu"], ". After selecting ", StyleBox["Integrate[x Sin[x],x]=Integrate[x Sin[x],x]", FontColor->RGBColor[1, 0, 0]], " we turn this into an ", StyleBox["inline cell", FontSlant->"Italic"], "." }], "Bullet", CellTags->"inline cell"], Cell[TextData[{ "Here is some text with a formula, ", Cell[BoxData[ \(TraditionalForm \`Integrate[x\ Sin[x], x] = Integrate[x\ Sin[x], x]\)]], ". " }], "Continuation"] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ "Now highlight the expression on the left-hand side of the = sign and use ", StyleBox["Cell", "Menu"], " \[RightTriangle] ", StyleBox["Convert To", "Menu"], " \[RightTriangle] ", StyleBox["TraditionalForm", "Menu"], ". Note that if you double-click on the first ", Cell[BoxData[ FormBox[ StyleBox["Integrate", FontColor->RGBColor[1, 0, 0]], TraditionalForm]]], " it will select this for you automatically. Remove the additional set of \ parens." }], "Bullet"], Cell[TextData[{ "Here is some text with a formula, ", Cell[BoxData[ FormBox[ RowBox[{ FormBox[\(\[Integral]\(x\ \(sin(x)\)\) \[DifferentialD]x\), "TraditionalForm"], "=", \(Integrate[x\ Sin[x], x]\)}], TraditionalForm]]], ". " }], "Continuation"] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ "Now highlight the expression on the right-hand side of the = sign and use \ ", StyleBox["Kernel", "Menu"], " \[RightTriangle] ", StyleBox["Evaluation", "Menu"], " \[RightTriangle] ", StyleBox["Evaluate In Place", "Menu"], ". Remove the additional set of parens." }], "Bullet", CellTags->"in place evaluation"], Cell[TextData[{ "Here is some text with a formula, ", Cell[BoxData[ FormBox[ RowBox[{ FormBox[\(\[Integral]\(x\ \(sin(x)\)\) \[DifferentialD]x\), "TraditionalForm"], "=", FormBox[\(sin(x) - x\ \(cos(x)\)\), "TraditionalForm"]}], TraditionalForm]]], ". " }], "Continuation"] }, Closed]] }, Open ]] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ".", CounterBox["Subsection"], ". Importing Figures" }], "Subsection"], Cell[TextData[{ "You can usually directly insert a graphic at a particular location by \ copying and pasting the graphic from another application. Unfortunately, the \ optimal way to deal with a particular type of graphic is often machine or \ operating system dependent. For example, if you paste a Windows Metafile (or \ a Macintosh PICT) into a Notebook then, even though ", StyleBox["Mathematica", FontSlant->"Italic"], " Notebooks are highly portable, that graphic will only display under the \ originating operating system." }], "Continuation"], Cell[TextData[{ "One way to ensure portability of all images is to do ", StyleBox["Cell", "Menu"], " \[RightTriangle] ", StyleBox["Convert To", "Menu"], " \[RightTriangle] ", StyleBox["Bitmap", "Menu"], "." }], "Warning"], Cell[TextData[{ "Once you import a graphic into the front end, you can use the command ", StyleBox["Cell", "Menu"], " \[RightTriangle] ", StyleBox["Convert To", "Menu"], " \[RightTriangle] ", StyleBox["InputForm", "Menu"], " to convert the graphic to a form which can be manipulated by the kernel. \ In some cases this can be used to convert the graphic to a more portable \ format." }], "Warning"] }, Closed]] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ". Stylesheets" }], "Section"], Cell[TextData[{ StyleBox["Mathematica", FontSlant->"Italic"], " has a very extensive document formatting structure with fully \ programmable style sheets. Importantly, it is straightforward to maintain a \ single document which includes different styles for on-screen display and \ print-out." }], "Text", CellTags->"style sheets"], Cell[TextData[{ StyleBox["Mathematica", FontSlant->"Italic"], " comes with a collection of color and black-and-white style sheets that \ define new styles for all cells. Open a new Notebook and then go to ", StyleBox["Format", "Menu"], " \[RightTriangle] ", StyleBox["Style Sheet", "Menu"], " and choose from the list." }], "Text"], Cell[CellGroupData[{ Cell[TextData[{ "Use ", StyleBox["Edit Style Sheet\[Ellipsis]", "Menu"], " to set up style sheets for ", StyleBox["Mathematica", FontSlant->"Italic"], " notebooks. It is far easier to demonstrate style sheets than write about \ them so I will give a basic demonstration of their capabilities and how they \ can be utilized." }], "Text"], Cell[TextData[{ "When working with style sheets, both the option inspector (", StyleBox["Format", "Menu"], " \[RightTriangle] ", StyleBox["Option Inspector\[Ellipsis]", "Menu"], " ) and direct editing of the raw underlying ", StyleBox["Mathematica", FontSlant->"Italic"], " cell expression (", StyleBox["Format", "Menu"], " \[RightTriangle] ", StyleBox["Show Expression", "Menu"], ") are very useful." }], "Warning", CellTags->{"option inspector", "raw cell expression"}] }, Open ]] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ". Document Structure" }], "Section"], Cell[TextData[{ "The approach taken in this tutorial is to emulate the style of particular \ journal to illustrate how a technical paper can be formatted using ", StyleBox["Mathematica", FontSlant->"Italic"], ". We will spend some time looking at the ", StyleBox[ButtonBox["Theory of N-Beam Diffraction", ButtonData:>{ URL[ "ftp://ftp.physics.uwa.edu.au/pub/EMC/3BeamPaper.nb"], None}, ButtonStyle->"Hyperlink"], FontSlant->"Italic"], " paper which was generated as a ", StyleBox["Mathematica", FontSlant->"Italic"], " Notebook and recently published in ", StyleBox["Acta Cryst.", FontSlant->"Italic"] }], "Text"], Cell[TextData[{ "For more on Notebooks as documents see ", StyleBox["The Mathematica Book", FontSlant->"Italic"], ", Section ", ButtonBox["1.3.5", ButtonData:>{"1.3.5", None}, Active->True, ButtonStyle->"MainBookLink"], "." }], "Text"], Cell[CellGroupData[{ Cell[TextData[{ CounterBox["Section"], ".", CounterBox["Subsection"], ". Automatic Numbering " }], "Subsection"], Cell[TextData[{ "It is very easy to automaticaly number figures, tables, equations, ", StyleBox["etc", FontSlant->"Italic"], ". 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