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Updates to typesetting codes

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Alex Selimov 2021-03-16 14:12:22 -04:00
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commit ad8ac6cb31
23 changed files with 9546 additions and 48 deletions
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---
title: "<++>"
abstract: ""
author: Alex Selimov
###
### Bibliography settings
###
link-citations: true
###
### Formatting settings
###
documentclass: article
fontsize: 12pt
figPrefix: figure
#geometry: margin=1.0in
geometry: "left=3cm,right=3cm,top=2cm,bottom=2cm"
header-includes:
- \usepackage{mathpazo}
- \usepackage{amsmath}
urlcolor: blue
---
\newpage
# References

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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only">
<info>
<title>IEEE</title>
<id>http://www.zotero.org/styles/ieee</id>
<link href="http://www.zotero.org/styles/ieee" rel="self"/>
<link href="https://ieeeauthorcenter.ieee.org/wp-content/uploads/IEEE-Reference-Guide.pdf" rel="documentation"/>
<link href="https://journals.ieeeauthorcenter.ieee.org/your-role-in-article-production/ieee-editorial-style-manual/" rel="documentation"/>
<author>
<name>Michael Berkowitz</name>
<email>mberkowi@gmu.edu</email>
</author>
<contributor>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</contributor>
<contributor>
<name>Rintze Zelle</name>
<uri>http://twitter.com/rintzezelle</uri>
</contributor>
<contributor>
<name>Stephen Frank</name>
<uri>http://www.zotero.org/sfrank</uri>
</contributor>
<contributor>
<name>Sebastian Karcher</name>
</contributor>
<contributor>
<name>Giuseppe Silano</name>
<email>g.silano89@gmail.com</email>
<uri>http://giuseppesilano.net</uri>
</contributor>
<contributor>
<name>Patrick O'Brien</name>
</contributor>
<contributor>
<name>Brenton M. Wiernik</name>
</contributor>
<category citation-format="numeric"/>
<category field="engineering"/>
<category field="generic-base"/>
<summary>IEEE style as per the 2018 guidelines, V 11.12.2018.</summary>
<updated>2019-12-20T09:14:19+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<locale xml:lang="en">
<terms>
<term name="chapter" form="short">ch.</term>
<term name="presented at">presented at the</term>
<term name="available at">available</term>
</terms>
</locale>
<!-- Macros -->
<macro name="status">
<choose>
<if variable="page issue volume" match="none">
<text variable="status" text-case="capitalize-first" suffix="" font-weight="bold"/>
</if>
</choose>
</macro>
<macro name="edition">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" text-case="capitalize-first" suffix="."/>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="issued">
<choose>
<if type="article-journal report" match="any">
<date variable="issued">
<date-part name="year" form="long" prefix="(" suffix=")" />
</date>
</if>
<else-if type="bill book chapter graphic legal_case legislation motion_picture song thesis" match="any">
<date variable="issued">
<date-part name="year" form="long"/>
</date>
</else-if>
<else-if type="paper-conference" match="any">
<date variable="issued">
<date-part name="month" form="short"/>
<date-part name="year" prefix=" "/>
</date>
</else-if>
<else>
<date variable="issued">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</else>
</choose>
</macro>
<macro name="author">
<names variable="author">
<name and="text" et-al-min="100" et-al-use-first="1" initialize-with=". "/>
<label form="short" prefix=", " text-case="capitalize-first"/>
<et-al font-style="italic"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="editor">
<names variable="editor">
<name initialize-with=". " delimiter=", " and="text"/>
<label form="short" prefix=", " text-case="capitalize-first"/>
</names>
</macro>
<macro name="locators">
<group delimiter="">
<text macro="edition"/>
<group delimiter="">
<number variable="volume" form="numeric" font-weight="bold" />
</group>
<group delimiter=" ">
<number variable="number-of-volumes" form="numeric"/>
<text term="volume" form="short" plural="true"/>
</group>
<group delimiter=" ">
<number variable="issue" form="numeric" prefix="(" suffix=")" />
</group>
</group>
</macro>
<macro name="title">
<choose>
<if type="bill book graphic legal_case legislation motion_picture song" match="any">
<text variable="title" font-style="italic"/>
</if>
<else>
<text variable="title" quotes="false"/>
</else>
</choose>
</macro>
<macro name="publisher">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference song" match="any">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</if>
<else>
<group delimiter=", ">
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</else>
</choose>
</macro>
<macro name="event">
<choose>
<if type="paper-conference speech" match="any">
<choose>
<!-- Published Conference Paper -->
<if variable="collection-editor editor editorial-director issue page volume" match="any">
<group delimiter=", ">
<group delimiter=" ">
<text term="in"/>
<text variable="container-title" font-style="italic"/>
</group>
<text variable="event-place"/>
</group>
</if>
<!-- Unpublished Conference Paper -->
<else>
<group delimiter=", ">
<group delimiter=" ">
<text term="presented at"/>
<text variable="event"/>
</group>
<text variable="event-place"/>
</group>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="access">
<choose>
<if type="webpage post post-weblog" match="any">
<choose>
<if variable="URL">
<group delimiter=" ">
<text variable="URL"/>
<group delimiter=" " prefix="(" suffix=")">
<text term="accessed"/>
<date variable="accessed">
<date-part name="month" form="short" strip-periods="false"/>
<date-part name="day" form="numeric-leading-zeros" prefix=" " suffix=", "/>
<date-part name="year" form="long"/>
</date>
</group>
</group>
</if>
</choose>
</if>
<else-if match="any" variable="DOI">
<text variable="DOI" prefix="doi: "/>
</else-if>
<else>
<group delimiter=". ">
<group delimiter=": ">
<text term="accessed" text-case="capitalize-first"/>
<date variable="accessed">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</group>
<text term="online" prefix="[" suffix="]" text-case="capitalize-first"/>
<group delimiter=": ">
<text term="available at" text-case="capitalize-first"/>
<text variable="URL"/>
</group>
</group>
</else>
</choose>
</macro>
<macro name="page">
<choose>
<if type="article-journal" variable="number" match="all">
<group delimiter=" ">
<text value="Art."/>
<text term="issue" form="short"/>
<text variable="number"/>
</group>
</if>
<else>
<group delimiter=" ">
<text variable="page"/>
</group>
</else>
</choose>
</macro>
<macro name="citation-locator">
<group delimiter=" ">
<choose>
<if locator="page">
<label variable="locator" form="short"/>
</if>
<else>
<label variable="locator" form="short" text-case="capitalize-first"/>
</else>
</choose>
<text variable="locator"/>
</group>
</macro>
<!-- Citation -->
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout delimiter=", ">
<group prefix="[" suffix="]" delimiter=", ">
<text variable="citation-number"/>
<text macro="citation-locator"/>
</group>
</layout>
</citation>
<!-- Bibliography -->
<bibliography entry-spacing="0" second-field-align="flush">
<layout suffix=".">
<!-- Citation Number -->
<text variable="citation-number" prefix="[" suffix="]"/>
<!-- Author(s) -->
<text macro="author" suffix=": "/>
<!-- Rest of Citation -->
<choose>
<!-- Specific Formats -->
<if type="article-journal">
<group delimiter="">
<text macro="title" suffix=". " />
<text variable="container-title" font-style="italic" form="short" suffix="."/>
<text macro="locators" suffix=", "/>
<text macro="page" suffix=" "/>
<text macro="issued"/>
</group>
</if>
<else-if type="paper-conference speech" match="any">
<group delimiter=", ">
<text macro="title"/>
<text macro="event"/>
<text macro="issued"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="status"/>
<text macro="access"/>
</group>
</else-if>
<else-if type="report">
<group delimiter=", ">
<text macro="title"/>
<text macro="event"/>
<text macro="issued"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="status"/>
<text macro="access"/>
</group>
</else-if>
<else-if type="thesis">
<group delimiter=", ">
<text macro="title"/>
<text macro="event"/>
<text macro="issued"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="status"/>
<text macro="access"/>
</group>
</else-if>
<else-if type="webpage post-weblog post" match="any">
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="issued"/>
</group>
<text macro="access"/>
</else-if>
<else-if type="patent">
<group delimiter=", ">
<text macro="title"/>
<text variable="number"/>
<text macro="issued"/>
</group>
</else-if>
<!-- Generic/Fallback Formats -->
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text macro="locators"/>
</group>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued"/>
<text macro="page"/>
</group>
</else-if>
<else-if type="article-magazine article-newspaper broadcast interview manuscript map patent personal_communication song speech thesis webpage" match="any">
<group delimiter=", ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="locators"/>
<text macro="publisher"/>
<text macro="page"/>
<text macro="issued"/>
</group>
</else-if>
<else-if type="chapter paper-conference" match="any">
<group delimiter=", " suffix=", ">
<text macro="title"/>
<group delimiter=" ">
<text term="in"/>
<text variable="container-title" font-style="italic"/>
</group>
<text macro="locators"/>
</group>
<text macro="editor" suffix=" "/>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued"/>
<text macro="page"/>
</group>
</else-if>
<else>
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="locators"/>
</group>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="page"/>
<text macro="issued"/>
<text macro="access"/>
</group>
</else>
</choose>
</layout>
</bibliography>
</style>

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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
<!-- Association for Computing Machinery (ACM), generated from "acm" metadata at https://github.com/citation-style-language/journals -->
<info>
<title>ACM Transactions on Modeling and Computer Simulation</title>
<title-short>TOMACS</title-short>
<id>http://www.zotero.org/styles/transactions-on-modeling-and-computer-simulation</id>
<link href="http://www.zotero.org/styles/transactions-on-modeling-and-computer-simulation" rel="self"/>
<link href="http://www.zotero.org/styles/association-for-computing-machinery" rel="independent-parent"/>
<link href="https://www.acm.org/publications/authors/reference-formatting" rel="documentation"/>
<category citation-format="numeric"/>
<category field="engineering"/>
<issn>1049-3301</issn>
<eissn>1558-1195</eissn>
<updated>2017-07-09T19:14:54+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
</style>

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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
<info>
<title>Elsevier (numeric, with titles)</title>
<id>http://www.zotero.org/styles/elsevier-with-titles</id>
<link href="http://www.zotero.org/styles/elsevier-with-titles" rel="self"/>
<link href="http://www.zotero.org/styles/elsevier-without-titles" rel="template"/>
<link href="http://www.elsevier.com/journals/journal-of-hazardous-materials/0304-3894/guide-for-authors#68001" rel="documentation"/>
<author>
<name>Richard Karnesky</name>
<email>karnesky+zotero@gmail.com</email>
<uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
</author>
<contributor>
<name>Rintze Zelle</name>
<uri>http://twitter.com/rintzezelle</uri>
</contributor>
<category citation-format="numeric"/>
<category field="generic-base"/>
<summary>A style for many of Elsevier's journals that includes article titles in the reference list</summary>
<updated>2019-10-15T15:14:08+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="author">
<names variable="author">
<name initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
<label form="short" prefix=", "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="editor">
<names variable="editor">
<name initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
<label form="short" prefix=" (" text-case="capitalize-first" suffix=")"/>
</names>
</macro>
<macro name="year-date">
<choose>
<if variable="issued">
<date variable="issued">
<date-part name="year"/>
</date>
</if>
<else>
<text term="no date" form="short"/>
</else>
</choose>
</macro>
<macro name="publisher">
<text variable="publisher" suffix=", "/>
<text variable="publisher-place" suffix=", "/>
<text macro="year-date"/>
</macro>
<macro name="edition">
<!--TODO: CSL should have low numeric be text (e.g. '3'->'third')-->
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition"/>
</else>
</choose>
</macro>
<macro name="access">
<choose>
<if variable="URL">
<text variable="URL"/>
<group prefix=" (" suffix=")" delimiter=" ">
<text term="accessed"/>
<date variable="accessed" form="text"/>
</group>
</if>
</choose>
</macro>
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout prefix="[" suffix="]" delimiter=",">
<text variable="citation-number"/>
</layout>
</citation>
<bibliography entry-spacing="0" second-field-align="flush">
<layout suffix=".">
<text variable="citation-number" prefix="[" suffix="]"/>
<text macro="author" suffix=", "/>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=", ">
<text variable="title"/>
<text macro="edition"/>
<text macro="publisher"/>
</group>
</if>
<else-if type="chapter paper-conference" match="any">
<text variable="title" suffix=", "/>
<text term="in" suffix=": "/>
<text macro="editor" suffix=", "/>
<text variable="container-title" form="short" text-case="title" suffix=", "/>
<text macro="edition" suffix=", "/>
<text macro="publisher"/>
<group delimiter=" ">
<label variable="page" form="short" prefix=": "/>
<text variable="page"/>
</group>
</else-if>
<else-if type="patent">
<group delimiter=", ">
<text variable="title"/>
<text variable="number"/>
<text macro="year-date"/>
</group>
</else-if>
<else-if type="thesis">
<group delimiter=", ">
<text variable="title"/>
<text variable="genre"/>
<text variable="publisher"/>
<text macro="year-date"/>
</group>
</else-if>
<else>
<group delimiter=" ">
<text variable="title" suffix=","/>
<text variable="container-title" form="short" text-case="title" suffix="."/>
<text variable="volume"/>
<text macro="year-date" prefix="(" suffix=")"/>
<text variable="page" form="short"/>
</group>
</else>
</choose>
<choose>
<if variable="DOI">
<text variable="DOI" prefix=". https://doi.org/"/>
</if>
<else>
<text macro="access" prefix=". "/>
</else>
</choose>
</layout>
</bibliography>
</style>

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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only">
<info>
<title>IEEE</title>
<id>http://www.zotero.org/styles/ieee</id>
<link href="http://www.zotero.org/styles/ieee" rel="self"/>
<link href="https://ieeeauthorcenter.ieee.org/wp-content/uploads/IEEE-Reference-Guide.pdf" rel="documentation"/>
<link href="https://journals.ieeeauthorcenter.ieee.org/your-role-in-article-production/ieee-editorial-style-manual/" rel="documentation"/>
<author>
<name>Michael Berkowitz</name>
<email>mberkowi@gmu.edu</email>
</author>
<contributor>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</contributor>
<contributor>
<name>Rintze Zelle</name>
<uri>http://twitter.com/rintzezelle</uri>
</contributor>
<contributor>
<name>Stephen Frank</name>
<uri>http://www.zotero.org/sfrank</uri>
</contributor>
<contributor>
<name>Sebastian Karcher</name>
</contributor>
<contributor>
<name>Giuseppe Silano</name>
<email>g.silano89@gmail.com</email>
<uri>http://giuseppesilano.net</uri>
</contributor>
<contributor>
<name>Patrick O'Brien</name>
</contributor>
<contributor>
<name>Brenton M. Wiernik</name>
</contributor>
<category citation-format="numeric"/>
<category field="engineering"/>
<category field="generic-base"/>
<summary>IEEE style as per the 2018 guidelines, V 11.12.2018.</summary>
<updated>2019-12-20T09:14:19+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<locale xml:lang="en">
<terms>
<term name="chapter" form="short">ch.</term>
<term name="presented at">presented at the</term>
<term name="available at">available</term>
</terms>
</locale>
<!-- Macros -->
<macro name="status">
<choose>
<if variable="page issue volume" match="none">
<text variable="status" text-case="capitalize-first" suffix="" font-weight="bold"/>
</if>
</choose>
</macro>
<macro name="edition">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" text-case="capitalize-first" suffix="."/>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="issued">
<choose>
<if type="article-journal report" match="any">
<date variable="issued">
<date-part name="month" form="short" suffix=" "/>
<date-part name="year" form="long"/>
</date>
</if>
<else-if type="bill book chapter graphic legal_case legislation motion_picture song thesis" match="any">
<date variable="issued">
<date-part name="year" form="long"/>
</date>
</else-if>
<else-if type="paper-conference" match="any">
<date variable="issued">
<date-part name="month" form="short"/>
<date-part name="year" prefix=" "/>
</date>
</else-if>
<else>
<date variable="issued">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</else>
</choose>
</macro>
<macro name="author">
<names variable="author">
<name and="text" et-al-min="7" et-al-use-first="1" initialize-with=". "/>
<label form="short" prefix=", " text-case="capitalize-first"/>
<et-al font-style="italic"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="editor">
<names variable="editor">
<name initialize-with=". " delimiter=", " and="text"/>
<label form="short" prefix=", " text-case="capitalize-first"/>
</names>
</macro>
<macro name="locators">
<group delimiter=", ">
<text macro="edition"/>
<group delimiter=" ">
<text term="volume" form="short"/>
<number variable="volume" form="numeric"/>
</group>
<group delimiter=" ">
<number variable="number-of-volumes" form="numeric"/>
<text term="volume" form="short" plural="true"/>
</group>
<group delimiter=" ">
<text term="issue" form="short"/>
<number variable="issue" form="numeric"/>
</group>
</group>
</macro>
<macro name="title">
<choose>
<if type="bill book graphic legal_case legislation motion_picture song" match="any">
<text variable="title" font-style="italic"/>
</if>
<else>
<text variable="title" quotes="true"/>
</else>
</choose>
</macro>
<macro name="publisher">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference song" match="any">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</if>
<else>
<group delimiter=", ">
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</else>
</choose>
</macro>
<macro name="event">
<choose>
<if type="paper-conference speech" match="any">
<choose>
<!-- Published Conference Paper -->
<if variable="collection-editor editor editorial-director issue page volume" match="any">
<group delimiter=", ">
<group delimiter=" ">
<text term="in"/>
<text variable="container-title" font-style="italic"/>
</group>
<text variable="event-place"/>
</group>
</if>
<!-- Unpublished Conference Paper -->
<else>
<group delimiter=", ">
<group delimiter=" ">
<text term="presented at"/>
<text variable="event"/>
</group>
<text variable="event-place"/>
</group>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="access">
<choose>
<if type="webpage post post-weblog" match="any">
<choose>
<if variable="URL">
<group delimiter=" ">
<text variable="URL"/>
<group delimiter=" " prefix="(" suffix=")">
<text term="accessed"/>
<date variable="accessed">
<date-part name="month" form="short" strip-periods="false"/>
<date-part name="day" form="numeric-leading-zeros" prefix=" " suffix=", "/>
<date-part name="year" form="long"/>
</date>
</group>
</group>
</if>
</choose>
</if>
<else-if match="any" variable="DOI">
<text variable="DOI" prefix="doi: "/>
</else-if>
<else>
<group delimiter=". ">
<group delimiter=": ">
<text term="accessed" text-case="capitalize-first"/>
<date variable="accessed">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</group>
<text term="online" prefix="[" suffix="]" text-case="capitalize-first"/>
<group delimiter=": ">
<text term="available at" text-case="capitalize-first"/>
<text variable="URL"/>
</group>
</group>
</else>
</choose>
</macro>
<macro name="page">
<choose>
<if type="article-journal" variable="number" match="all">
<group delimiter=" ">
<text value="Art."/>
<text term="issue" form="short"/>
<text variable="number"/>
</group>
</if>
<else>
<group delimiter=" ">
<label variable="page" form="short"/>
<text variable="page"/>
</group>
</else>
</choose>
</macro>
<macro name="citation-locator">
<group delimiter=" ">
<choose>
<if locator="page">
<label variable="locator" form="short"/>
</if>
<else>
<label variable="locator" form="short" text-case="capitalize-first"/>
</else>
</choose>
<text variable="locator"/>
</group>
</macro>
<!-- Citation -->
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout delimiter=", ">
<group prefix="[" suffix="]" delimiter=", ">
<text variable="citation-number"/>
<text macro="citation-locator"/>
</group>
</layout>
</citation>
<!-- Bibliography -->
<bibliography entry-spacing="0" second-field-align="flush">
<layout suffix=".">
<!-- Citation Number -->
<text variable="citation-number" prefix="[" suffix="]"/>
<!-- Author(s) -->
<text macro="author" suffix=", "/>
<!-- Rest of Citation -->
<choose>
<!-- Specific Formats -->
<if type="article-journal">
<group delimiter=", ">
<text macro="title"/>
<text variable="container-title" font-style="italic" form="short"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="issued"/>
<text macro="status"/>
<text macro="access"/>
</group>
</if>
<else-if type="paper-conference speech" match="any">
<group delimiter=", ">
<text macro="title"/>
<text macro="event"/>
<text macro="issued"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="status"/>
<text macro="access"/>
</group>
</else-if>
<else-if type="report">
<group delimiter=". ">
<group delimiter=", ">
<text macro="title"/>
<text macro="publisher"/>
<group delimiter=" ">
<text variable="genre"/>
<text variable="number"/>
</group>
<text macro="issued"/>
</group>
<text macro="access"/>
</group>
</else-if>
<else-if type="thesis">
<group delimiter=", ">
<text macro="title"/>
<text variable="genre"/>
<text macro="publisher"/>
<text macro="issued"/>
</group>
</else-if>
<else-if type="webpage post-weblog post" match="any">
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="issued"/>
</group>
<text macro="access"/>
</else-if>
<else-if type="patent">
<group delimiter=", ">
<text macro="title"/>
<text variable="number"/>
<text macro="issued"/>
</group>
</else-if>
<!-- Generic/Fallback Formats -->
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text macro="locators"/>
</group>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued"/>
<text macro="page"/>
</group>
</else-if>
<else-if type="article-magazine article-newspaper broadcast interview manuscript map patent personal_communication song speech thesis webpage" match="any">
<group delimiter=", ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="locators"/>
<text macro="publisher"/>
<text macro="page"/>
<text macro="issued"/>
</group>
</else-if>
<else-if type="chapter paper-conference" match="any">
<group delimiter=", " suffix=", ">
<text macro="title"/>
<group delimiter=" ">
<text term="in"/>
<text variable="container-title" font-style="italic"/>
</group>
<text macro="locators"/>
</group>
<text macro="editor" suffix=" "/>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued"/>
<text macro="page"/>
</group>
</else-if>
<else>
<group delimiter=", " suffix=". ">
<text macro="title"/>
<text variable="container-title" font-style="italic"/>
<text macro="locators"/>
</group>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="page"/>
<text macro="issued"/>
<text macro="access"/>
</group>
</else>
</choose>
</layout>
</bibliography>
</style>

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8
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@ -22,9 +22,13 @@ fi
case $2 in
"article")
cp ~/typsetting/article.tex ~/typesetting/GTLogo.pdf . ;;
cp ~/typesetting/article.md . ;;
"pres")
cp ~/typesetting/pres.md . ;;
"larticle")
cp ~/typesetting/article.tex ~/typesetting/GTLogo.pdf . ;;
"presentation")
cp ~/typsetting/presentation.tex ~/typesetting/GTLogo.pdf . ;;
cp ~/typesetting/presentation.tex ~/typesetting/GTLogo.pdf . ;;
"notes")
cp ~/typesetting/notes.md . ;;
*)

176
pandoc_lua_filters/author-info-blocks.lua Normal file
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@ -0,0 +1,176 @@
--[[
affiliation-blocks – generate title components
Copyright © 2017–2020 Albert Krewinkel
Permission to use, copy, modify, and/or distribute this software for any purpose
with or without fee is hereby granted, provided that the above copyright notice
and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
THIS SOFTWARE.
]]
local List = require 'pandoc.List'
local utils = require 'pandoc.utils'
local stringify = utils.stringify
local default_marks
local default_marks = {
corresponding_author = FORMAT == 'latex'
and {pandoc.RawInline('latex', '*')}
or {pandoc.Str '✉'},
equal_contributor = FORMAT == 'latex'
and {pandoc.RawInline('latex', '$\\dagger{}$')}
or {pandoc.Str '*'},
}
local function intercalate(lists, elem)
local result = List:new{}
for i = 1, (#lists - 1) do
result:extend(lists[i])
result:extend(elem)
end
if #lists > 0 then
result:extend(lists[#lists])
end
return result
end
--- Check whether the given author is a corresponding author
local function is_corresponding_author(author)
return author.correspondence and author.email
end
--- Create inlines for a single author (includes all author notes)
local function author_inline_generator (get_mark)
return function (author)
local author_marks = List:new{}
if author.equal_contributor then
author_marks[#author_marks + 1] = get_mark 'equal_contributor'
end
local idx_str
for _, idx in ipairs(author.institute) do
if type(idx) ~= 'table' then
idx_str = tostring(idx)
else
idx_str = stringify(idx)
end
author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
end
if is_corresponding_author(author) then
author_marks[#author_marks + 1] = get_mark 'corresponding_author'
end
local res = List.clone(author.name)
res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
return res
end
end
local function is_equal_contributor (author)
return author.equal_contributor
end
--- Create equal contributors note.
local function create_equal_contributors_block(authors, mark)
local has_equal_contribs = List:new(authors):find_if(is_equal_contributor)
if not has_equal_contribs then
return nil
end
local contributors = {
pandoc.Superscript(mark'equal_contributor'),
pandoc.Space(),
pandoc.Str 'These authors contributed equally to this work.'
}
return List:new{pandoc.Para(contributors)}
end
--- Generate a block list all affiliations, marked with arabic numbers.
local function create_affiliations_blocks(affiliations)
local affil_lines = List:new(affiliations):map(
function (affil, i)
local num_inlines = List:new{
pandoc.Superscript{pandoc.Str(tostring(i))},
pandoc.Space()
}
return num_inlines .. affil.name
end
)
return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
end
--- Generate a block element containing the correspondence information
local function create_correspondence_blocks(authors, mark)
local corresponding_authors = List:new{}
for _, author in ipairs(authors) do
if is_corresponding_author(author) then
local mailto = 'mailto:' .. pandoc.utils.stringify(author.email)
local author_with_mail = List:new(
author.name .. List:new{pandoc.Space(), pandoc.Str '<'} ..
author.email .. List:new{pandoc.Str '>'}
)
local link = pandoc.Link(author_with_mail, mailto)
table.insert(corresponding_authors, {link})
end
end
if #corresponding_authors == 0 then
return nil
end
local correspondence = List:new{
pandoc.Superscript(mark'corresponding_author'),
pandoc.Space(),
pandoc.Str'Correspondence:',
pandoc.Space()
}
local sep = List:new{pandoc.Str',', pandoc.Space()}
return {
pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
}
end
--- Generate a list of inlines containing all authors.
local function create_authors_inlines(authors, mark)
local inlines_generator = author_inline_generator(mark)
local inlines = List:new(authors):map(inlines_generator)
local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
local last_author = inlines[#inlines]
inlines[#inlines] = nil
local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
if #authors > 1 then
result:extend(List:new{pandoc.Str ","} .. and_str)
end
result:extend(last_author)
return result
end
return {
{
Pandoc = function (doc)
local meta = doc.meta
local body = List:new{}
local mark = function (mark_name) return default_marks[mark_name] end
body:extend(create_equal_contributors_block(doc.meta.author, mark) or {})
body:extend(create_affiliations_blocks(doc.meta.institute) or {})
body:extend(create_correspondence_blocks(doc.meta.author, mark) or {})
body:extend(doc.blocks)
-- Overwrite authors with formatted values. We use a single, formatted
-- string for most formats. LaTeX output, however, looks nicer if we
-- provide a authors as a list.
meta.author = FORMAT:match 'latex'
and pandoc.MetaList(doc.meta.author):map(author_inline_generator(mark))
or pandoc.MetaInlines(create_authors_inlines(doc.meta.author, mark))
-- Institute info is now baked into the affiliations block.
meta.institute = nil
return pandoc.Pandoc(body, meta)
end
}
}

109
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--[[
pagebreak – convert raw LaTeX page breaks to other formats
Copyright © 2017-2020 Benct Philip Jonsson, Albert Krewinkel
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]
local stringify_orig = (require 'pandoc.utils').stringify
local function stringify(x)
return type(x) == 'string' and x or stringify_orig(x)
end
--- configs – these are populated in the Meta filter.
local pagebreak = {
asciidoc = '<<<\n\n',
context = '\\page',
epub = '<p style="page-break-after: always;"> </p>',
html = '<div style="page-break-after: always;"></div>',
latex = '\\newpage{}',
ms = '.bp',
ooxml = '<w:p><w:r><w:br w:type="page"/></w:r></w:p>',
odt = '<text:p text:style-name="Pagebreak"/>'
}
local function pagebreaks_from_config (meta)
local html_class =
(meta.newpage_html_class and stringify(meta.newpage_html_class))
or os.getenv 'PANDOC_NEWPAGE_HTML_CLASS'
if html_class and html_class ~= '' then
pagebreak.html = string.format('<div class="%s"></div>', html_class)
end
local odt_style =
(meta.newpage_odt_style and stringify(meta.newpage_odt_style))
or os.getenv 'PANDOC_NEWPAGE_ODT_STYLE'
if odt_style and odt_style ~= '' then
pagebreak.odt = string.format('<text:p text:style-name="%s"/>', odt_style)
end
end
--- Return a block element causing a page break in the given format.
local function newpage(format)
if format:match 'asciidoc' then
return pandoc.RawBlock('asciidoc', pagebreak.asciidoc)
elseif format == 'context' then
return pandoc.RawBlock('context', pagebreak.context)
elseif format == 'docx' then
return pandoc.RawBlock('openxml', pagebreak.ooxml)
elseif format:match 'epub' then
return pandoc.RawBlock('html', pagebreak.epub)
elseif format:match 'html.*' then
return pandoc.RawBlock('html', pagebreak.html)
elseif format:match 'latex' then
return pandoc.RawBlock('tex', pagebreak.latex)
elseif format:match 'ms' then
return pandoc.RawBlock('ms', pagebreak.ms)
elseif format:match 'odt' then
return pandoc.RawBlock('opendocument', pagebreak.odt)
else
-- fall back to insert a form feed character
return pandoc.Para{pandoc.Str '\f'}
end
end
local function is_newpage_command(command)
return command:match '^\\newpage%{?%}?$'
or command:match '^\\pagebreak%{?%}?$'
end
-- Filter function called on each RawBlock element.
function RawBlock (el)
-- Don't do anything if the output is TeX
if FORMAT:match 'tex$' then
return nil
end
-- check that the block is TeX or LaTeX and contains only
-- \newpage or \pagebreak.
if el.format:match 'tex' and is_newpage_command(el.text) then
-- use format-specific pagebreak marker. FORMAT is set by pandoc to
-- the targeted output format.
return newpage(FORMAT)
end
-- otherwise, leave the block unchanged
return nil
end
-- Turning paragraphs which contain nothing but a form feed
-- characters into line breaks.
function Para (el)
if #el.content == 1 and el.content[1].text == '\f' then
return newpage(FORMAT)
end
end
return {
{Meta = pagebreaks_from_config},
{RawBlock = RawBlock, Para = Para}
}

185
pandoc_lua_filters/scholarly-metadata.lua Normal file
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@ -0,0 +1,185 @@
--[[
ScholarlyMeta – normalize author/affiliation meta variables
Copyright (c) 2017-2020 Albert Krewinkel, Robert Winkler
Permission to use, copy, modify, and/or distribute this software for any purpose
with or without fee is hereby granted, provided that the above copyright notice
and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
THIS SOFTWARE.
]]
local List = require 'pandoc.List'
-- Split a string at commas.
local function comma_separated_values(str)
local acc = List:new{}
for substr in str:gmatch('([^,]*)') do
acc[#acc + 1] = substr:gsub('^%s*', ''):gsub('%s*$', '') -- trim
end
return acc
end
--- Ensure the return value is a list.
local function ensure_list (val)
if type(val) ~= 'table' then
-- create singleton list (or empty list if val == nil).
return List:new{val}
elseif val.t == 'MetaInlines' then
-- check if this is really a comma-separated list
local csv = comma_separated_values(pandoc.utils.stringify(val))
if #csv >= 2 then
return csv
end
return List:new{val}
elseif val.t == 'MetaList' then
return List:new(val)
else
-- MetaBlocks or MetaMap, use as a singleton
return List:new{val}
end
end
--- Returns a function which checks whether an object has the given ID.
local function has_id (id)
return function(x) return x.id == id end
end
--- Copy all key-value pairs of the first table into the second iff there is no
-- such key yet in the second table.
-- @returns the second argument
function add_missing_entries(a, b)
for k, v in pairs(a) do
b[k] = b[k] or v
end
return b
end
--- Create an object with a name. The name is either taken directly from the
-- `name` field, or from the *only* field name (i.e., key) if the object is a
-- dictionary with just one entry. If neither exists, the name is left unset
-- (`nil`).
function to_named_object (obj)
local named = {}
if type(obj) ~= 'table' then
-- if the object isn't a table, just use its value as a name.
named.name = pandoc.MetaInlines{pandoc.Str(tostring(obj))}
named.id = tostring(obj)
elseif obj.t == 'MetaInlines' then
-- Treat inlines as the name
named.name = obj
named.id = pandoc.utils.stringify(obj)
elseif obj.name ~= nil then
-- object has name attribute → just create a copy of the object
add_missing_entries(obj, named)
named.id = pandoc.utils.stringify(named.id or named.name)
elseif next(obj) and next(obj, next(obj)) == nil then
-- the entry's key is taken as the name, the value contains the
-- attributes.
key, attribs = next(obj)
if type(attribs) == "string" or attribs.t == 'MetaInlines' then
named.name = attribs
else
add_missing_entries(attribs, named)
named.name = named.name or pandoc.MetaInlines{pandoc.Str(tostring(key))}
end
named.id = named.id and pandoc.utils.stringify(named.id) or key
else
-- this is not a named object adhering to the usual conventions.
error('not a named object: ' .. tostring(obj))
end
return named
end
--- Resolve institute placeholders to full named objects
local function resolve_institutes (institute, known_institutes)
local unresolved_institutes
if institute == nil then
unresolved_institutes = {}
elseif type(institute) == "string" or type(institute) == "number" then
unresolved_institutes = {institute}
else
unresolved_institutes = institute
end
local result = List:new{}
for i, inst in ipairs(unresolved_institutes) do
result[i] =
known_institutes[tonumber(inst)] or
known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or
to_named_object(inst)
end
return result
end
--- Insert a named object into a list; if an object of the same name exists
-- already, add all properties only present in the new object to the existing
-- item.
function merge_on_id (list, namedObj)
local elem, idx = list:find_if(has_id(namedObj.id))
local res = elem and add_missing_entries(namedObj, elem) or namedObj
local obj_idx = idx or (#list + 1)
-- return res, obj_idx
list[obj_idx] = res
return res, #list
end
--- Flatten a list of lists.
local function flatten (lists)
local result = List:new{}
for _, lst in ipairs(lists) do
result:extend(lst)
end
return result
end
--- Canonicalize authors and institutes
local function canonicalize(raw_author, raw_institute)
local institutes = ensure_list(raw_institute):map(to_named_object)
local authors = ensure_list(raw_author):map(to_named_object)
for _, author in ipairs(authors) do
author.institute = resolve_institutes(
ensure_list(author.institute),
institutes
)
end
-- Merge institutes defined in author objects with those defined in the
-- top-level list.
local author_insts = flatten(authors:map(function(x) return x.institute end))
for _, inst in ipairs(author_insts) do
merge_on_id(institutes, inst)
end
-- Add list indices to institutes for numbering and reference purposes
for idx, inst in ipairs(institutes) do
inst.index = pandoc.MetaInlines{pandoc.Str(tostring(idx))}
end
-- replace institutes with their indices
local to_index = function (inst)
return tostring(select(2, institutes:find_if(has_id(inst.id))))
end
for _, author in ipairs(authors) do
author.institute = pandoc.MetaList(author.institute:map(to_index))
end
return authors, institutes
end
return {
{
Meta = function(meta)
meta.author, meta.institute = canonicalize(meta.author, meta.institute)
return meta
end
}
}

16
pres.md Normal file
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@ -0,0 +1,16 @@
---
title: "<++>"
abstract: ""
author: Alex Selimov
###
### Bibliography settings
###
bibliography:
- /home/aselimov/typesetting/references.bib
csl: /home/aselimov/typesetting/ieee.csl
link-citations: true
---

646
references.bib
View File

@ -68,7 +68,7 @@
@article{Anciaux_2018,
author = {Anciaux, G. and Junge, T. and Hodapp, M. and Cho, J. and Molinari, J. -F. and Curtin, W. A.},
title = {The Coupled Atomistic/Discrete-Dislocation method in 3d part I: Concept and algorithms},
title = {The Coupled Atomistic/Discrete-Dislocation method in 3d part {I}: Concept and algorithms},
journal = {Journal of the Mechanics and Physics of Solids},
publisher = {Elsevier BV},
year = {2018},
@ -309,6 +309,116 @@
keyword = {Nanoindentation, Nanoscale, Transmission electron microscopy (TEM)}
}
\relax
\bibstyle{IEEEtran}
\citation{*}
\bibdata{Xiang_2018}
This is BibTeX, Version 0.99d (TeX Live 2020/Arch Linux)
Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
The top-level auxiliary file: bib2html19b8ac.aux
I couldn't open style file IEEEtran.bst
---line 2 of file bib2html19b8ac.aux
: \bibstyle{IEEEtran
: }
I'm skipping whatever remains of this command
I found no style file---while reading file bib2html19b8ac.aux
You've used 0 entries,
0 wiz_defined-function locations,
85 strings with 520 characters,
and the built_in function-call counts, 0 in all, are:
= -- 0
> -- 0
< -- 0
+ -- 0
- -- 0
* -- 0
:= -- 0
add.period$ -- 0
call.type$ -- 0
change.case$ -- 0
chr.to.int$ -- 0
cite$ -- 0
duplicate$ -- 0
empty$ -- 0
format.name$ -- 0
if$ -- 0
int.to.chr$ -- 0
int.to.str$ -- 0
missing$ -- 0
newline$ -- 0
num.names$ -- 0
pop$ -- 0
preamble$ -- 0
purify$ -- 0
quote$ -- 0
skip$ -- 0
stack$ -- 0
substring$ -- 0
swap$ -- 0
text.length$ -- 0
text.prefix$ -- 0
top$ -- 0
type$ -- 0
warning$ -- 0
while$ -- 0
width$ -- 0
write$ -- 0
(There were 2 error messages)
\relax
\bibstyle{IEEEtran}
\citation{*}
\bibdata{Xiang_2018}
This is BibTeX, Version 0.99d (TeX Live 2020/Arch Linux)
Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
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publisher = {EDP Sciences},
year = {1993},
@ -767,6 +917,19 @@
keyword = {Grain boundaries, Crystal plasticity, Finite element, HCP materials, Heterogeneities}
}
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author = {Dikken, R and Khajeh Salehani, Mohsen},
title = {Edge dislocation impingement on interfaces between dissimilar metals},
year = {2017},
month = {August},
url = {https://hal.archives-ouvertes.fr/hal-01572509},
note = {working paper or preprint},
hal_id = {hal-01572509},
hal_version = {v1},
keyword = {defects, interfaces, molecular dynamics, dislocation impingement, aluminum, nickel},
pdf = {https://hal.archives-ouvertes.fr/hal-01572509/file/impingAlNi.pdf}
}
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author = {Ding, Zhigang and Li, Shuang and Liu, Wei and Zhao, Yonghao},
title = {Modeling of {Stacking} {Fault} {Energy} in {Hexagonal}-{Close}-{Packed} {Metals}},
@ -781,6 +944,32 @@
keyword = {Stacking fault energy, hcp, SFE}
}
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author = {Dobson, Matthew and Fox, Ian and Saracino, Alexandra},
title = {Cell list algorithms for nonequilibrium molecular dynamics},
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journal = {Acta Materialia},
publisher = {Elsevier BV},
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month = {jun},
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url = {https://doi.org/10.1016%2Fj.actamat.2019.04.016},
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author = {Dupraz, Maxime and Rao, Satish I. and Swygenhoven, Helena Van},
title = {Large scale 3-dimensional atomistic simulations of screw dislocations interacting with coherent twin boundaries in Al, Cu and Ni under uniaxial and multiaxial loading conditions},
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doi = {10.1016/j.commatsci.2017.07.043}
}
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title = {Study on mechanical and magnetic properties of {Cu}/{Ni} multilayer composite fabricated by accumulative roll bonding process},
@ -1086,6 +1284,20 @@
keyword = {Dislocation, Dislocations, Interfaces, Extended finite element method, Nonlinear, Peach-Koehler force, XFEM}
}
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keyword = {Dislocations, Grain Boundary}
}
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}
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author = {Huang, Shan and Chen, Dengke and Song, Jun and McDowell, David L. and Zhu, Ting},
title = {Hydrogen embrittlement of grain boundaries in nickel: an atomistic study},
journal = {npj Computational Materials},
publisher = {Springer Science and Business Media LLC},
year = {2017},
month = {jul},
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volume = {3},
url = {https://doi.org/10.1038%2Fs41524-017-0031-1},
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}
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author = {Huang, Wen and Mura, T.},
title = {Elastic fields and energies of a circular edge disclination and a straight screw disclination},
@ -1318,6 +1570,20 @@
issn = {1359-6454}
}
@article{Jian_2020,
author = {Jian, Wu-Rong and Zhang, Min and Xu, Shuozhi and Beyerlein, Irene J.},
title = {Atomistic simulations of dynamics of an edge dislocation and its interaction with a void in copper: a comparative study},
journal = {Modelling and Simulation in Materials Science and Engineering},
publisher = {IOP Publishing},
year = {2020},
month = {apr},
number = {4},
volume = {28},
pages = {045004},
url = {https://doi.org/10.1088%2F1361-651x%2Fab8358},
doi = {10.1088/1361-651x/ab8358}
}
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author = {Kacher, Josh and Zhu, Ting and Pierron, Olivier and Spearot, Douglas E.},
title = {Integrating in situ TEM experiments and atomistic simulations for defect mechanics},
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doi = {10.1080/01418610208240448}
}
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author = {Kuhr, Bryan and Farkas, Diana and Robertson, Ian M.},
title = {Atomistic studies of hydrogen effects on grain boundary structure and deformation response in FCC Ni},
journal = {Computational Materials Science},
publisher = {Elsevier BV},
year = {2016},
month = {sep},
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pages = {92--101},
url = {https://doi.org/10.1016%2Fj.commatsci.2016.05.014},
doi = {10.1016/j.commatsci.2016.05.014}
}
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author = {Kumar M D German C F Shih, Authors V},
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doi = {10.1016/j.scriptamat.2010.04.005}
}
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author = {Li, Yang and Fan, Zhaochuan and Li, Weixuan and McDowell, David L. and Chen, Youping},
title = {A multiscale study of misfit dislocations in PbTe/PbSe(001) heteroepitaxy},
journal = {Journal of Materials Research},
publisher = {Cambridge University Press (CUP)},
year = {2019},
month = {apr},
number = {13},
volume = {34},
pages = {2306--2314},
url = {https://doi.org/10.1557%2Fjmr.2019.69},
doi = {10.1557/jmr.2019.69}
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author = {Li, Nan and Wang, Jian and Misra, Amit and Huang, Jian Yu},
title = {Direct {Observations} of {Confined} {Layer} {Slip} in {Cu}/{Nb} {Multilayers}},
@ -1529,6 +1822,19 @@
keyword = {Dislocation, Molecular dynamics, Fracture, Crack, Interface}
}
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author = {Liu, Xuying and Hao, Rui and Mao, Shimin and Dillon, Shen J.},
title = {Shear strengths of FCC-FCC cube-on-cube interfaces},
journal = {Scripta Materialia},
publisher = {Elsevier BV},
year = {2017},
month = {mar},
volume = {130},
pages = {178--181},
url = {https://doi.org/10.1016%2Fj.scriptamat.2016.11.038},
doi = {10.1016/j.scriptamat.2016.11.038}
}
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author = {Liu, Z. and Monclús, M. A. and Yang, L. W. and Castillo-Rodríguez, M. and Molina-Aldareguía, J. M. and LLorca, J.},
title = {Tensile deformation and fracture mechanisms of Cu/Nb nanolaminates studied by in situ TEM mechanical tests},
@ -1717,7 +2023,7 @@
}
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@ -2097,6 +2417,20 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
keyword = {molecular dynamics, hardness, nanoindentation}
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author = {Ryu, Seunghwa and Kang, Keonwook and Cai, Wei},
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author = {Sangid, Michael D. and Ezaz, Tawhid and Sehitoglu, Huseyin},
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author = {Shao, Shuai and Wang, Jian and Beyerlein, Irene J. and Misra, Amit},
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author = {Song, J. and Curtin, W. A.},
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year = {2011},
school = {Georgia Institute of Technology}
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@ -2776,6 +3198,20 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
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author = {Wang, J. and Beyerlein, I. J. and Tomé, C. N.},
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author = {Wang, Jian},
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publisher = {Springer Science and Business Media LLC},
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author = {Wang, Jian and Zhou, Qing and Shao, Shuai and Misra, Amit},
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journal = {Materials Science and Engineering: A},
publisher = {Elsevier BV},
year = {2017},
month = {jun},
volume = {696},
pages = {503--510},
url = {https://doi.org/10.1016%2Fj.msea.2017.04.111},
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author = {WANG, Lin and DU, Qing-lin and LI, Chang and CUI, Xiao-hui and ZHAO, Xing and YU, Hai-liang},
title = {Enhanced mechanical properties of lamellar Cu/Al composites processed via high-temperature accumulative roll bonding},
@ -2953,7 +3416,7 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
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author = {Williams, P L and Mishin, Y and Hamilton, J C},
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publisher = {IOP Publishing},
year = {2006},
@ -3091,9 +3554,22 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
doi = {10.1016/j.ijplas.2017.12.005}
}
@article{Xie_2021,
author = {Xie, Zhou-Can and Li, Chen and Wang, Hai-Ying and Lu, Chunsheng and Dai, Lan-Hong},
title = {Hydrogen induced slowdown of spallation in high entropy alloy under shock loading},
journal = {International Journal of Plasticity},
publisher = {Elsevier BV},
year = {2021},
month = {apr},
volume = {139},
pages = {102944},
url = {https://doi.org/10.1016%2Fj.ijplas.2021.102944},
doi = {10.1016/j.ijplas.2021.102944}
}
@article{Xiong_2012,
author = {Xiong, Liming and McDowell, David L. and Chen, Youping},
title = {Nucleation and growth of dislocation loops in Cu, Al and Si by a concurrent atomistic-continuum method},
title = {Nucleation and growth of dislocation loops in {Cu}, {Al} and {Si} by a concurrent atomistic-continuum method},
journal = {Scripta Materialia},
publisher = {Elsevier BV},
year = {2012},
@ -3105,6 +3581,19 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
doi = {10.1016/j.scriptamat.2012.07.026}
}
@article{Xiong_2015,
author = {Xiong, Liming and Xu, Shuozhi and McDowell, David L. and Chen, Youping},
title = {Concurrent atomistic–continuum simulations of dislocation–void interactions in fcc crystals},
journal = {International Journal of Plasticity},
publisher = {Elsevier BV},
year = {2015},
month = {feb},
volume = {65},
pages = {33--42},
url = {https://doi.org/10.1016%2Fj.ijplas.2014.08.002},
doi = {10.1016/j.ijplas.2014.08.002}
}
@article{xiong_concurrent_2012,
author = {Xiong, Liming and Deng, Qian and Tucker, Garritt and McDowell, David L. and Chen, Youping},
title = {A concurrent scheme for passing dislocations from atomistic to continuum domains},
@ -3127,6 +3616,20 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
year={2016},
school={Georgia Institute of Technology}
}
@article{Xu_2017,
author = {Xu, Shuozhi and Xiong, Liming and Chen, Youping and McDowell, David L.},
title = {Comparing EAM Potentials to Model Slip Transfer of Sequential Mixed Character Dislocations Across Two Symmetric Tilt Grain Boundaries in {Ni}},
journal = {JOM},
publisher = {Springer Science and Business Media LLC},
year = {2017},
month = {mar},
number = {5},
volume = {69},
pages = {814--821},
url = {https://doi.org/10.1007%2Fs11837-017-2302-1},
doi = {10.1007/s11837-017-2302-1}
}
@article{Xu_2018,
author = {Xu, Shuozhi and Latypov, Marat I. and Su, Yanqing},
title = {Concurrent atomistic-continuum simulations of uniaxial compression of gold nano/submicropillars},
@ -3154,11 +3657,26 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
doi = {10.1016/j.actamat.2019.05.030}
}
@article{Xu_2020a,
author = {Xu, Shuozhi and Mianroodi, Jaber R. and Hunter, Abigail and Svendsen, Bob and Beyerlein, Irene J.},
title = {Comparative modeling of the disregistry and Peierls stress for dissociated edge and screw dislocations in Al},
journal = {International Journal of Plasticity},
publisher = {Elsevier BV},
year = {2020},
month = {jun},
volume = {129},
pages = {102689},
url = {https://doi.org/10.1016%2Fj.ijplas.2020.102689},
doi = {10.1016/j.ijplas.2020.102689}
}
@article{Xu_2020,
author = {Xu, Shuozhi and Li, Yang and Chen, Youping},
title = {Si/Ge (111) Semicoherent Interfaces: Responses to an In-Plane Shear and Interactions with Lattice Dislocations},
title = {{Si}/{Ge} (111) Semicoherent Interfaces: Responses to an In-Plane Shear and Interactions with Lattice Dislocations},
journal = {physica status solidi (b)},
publisher = {Wiley},
volume = {257},
issue = {12},
year = {2020},
month = {aug},
pages = {2000274},
@ -3196,14 +3714,14 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
}
@article{xu_pycac_2018,
author = {Xu, Shuozhi and Payne, Thomas G and Chen, Hao and Liu, Yongchao and Xiong, Liming and Chen, Youping and Mcdowell, David L},
title = {{PyCAC} : {The} concurrent atomistic-continuum simulation environment},
year = {2018},
number = {i},
pages = {857--871},
doi = {10.1557/jmr.2018.8},
file = {/home/aselimov/docs/My Library/files/657/Xu et al. - 2018 - PyCAC The concurrent atomistic-continuum simulation environment.pdf},
issn = {0884-2914}
title={PyCAC: The concurrent atomistic-continuum simulation environment},
author={Xu, Shuozhi and Payne, Thomas G and Chen, Hao and Liu, Yongchao and Xiong, Liming and Chen, Youping and McDowell, David L},
journal={Journal of Materials Research},
volume={33},
number={7},
pages={857},
year={2018},
publisher={Cambridge University Press}
}
@article{xu_quasistatic_2015,
@ -3269,6 +3787,33 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
keyword = {molecular dynamics method, nanostructured materials, nucleation, plastic deformation, slip, stress-strain relations, tungsten, twin boundaries, yield strength}
}
@article{Yang_2015,
author = {Yang, Shengfeng and Chen, Youping},
title = {Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
publisher = {The Royal Society},
year = {2015},
month = {mar},
number = {2175},
volume = {471},
pages = {20140758},
url = {https://doi.org/10.1098%2Frspa.2014.0758},
doi = {10.1098/rspa.2014.0758}
}
@article{Yang_2020a,
author = {Yang, Hui and Zhu, Linggang and Zhang, Ruifeng and Zhou, Jian and Sun, Zhimei},
title = {Influence of high stacking-fault energy on the dissociation mechanisms of misfit dislocations at semi-coherent interfaces},
journal = {International Journal of Plasticity},
publisher = {Elsevier BV},
year = {2020},
month = {mar},
volume = {126},
pages = {102610},
url = {https://doi.org/10.1016%2Fj.ijplas.2019.09.016},
doi = {10.1016/j.ijplas.2019.09.016}
}
@article{Yang_2020,
author = {Yang, Hui and Zhu, Linggang and Zhang, Ruifeng and Zhou, Jian and Sun, Zhimei},
title = {Shearing dominated by the coupling of the interfacial misfit and atomic bonding at the FCC (111) semi-coherent interfaces},
@ -3409,6 +3954,32 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
keyword = {NMM}
}
@article{Zhang_2014,
author = {Zhang, R. F. and Germann, T. C. and Liu, X. Y. and Wang, J. and Beyerlein, I. J.},
title = {Layer size effect on the shock compression behavior of fcc–bcc nanolaminates},
journal = {Acta Materialia},
publisher = {Elsevier BV},
year = {2014},
month = {oct},
volume = {79},
pages = {74--83},
url = {https://doi.org/10.1016%2Fj.actamat.2014.07.016},
doi = {10.1016/j.actamat.2014.07.016}
}
@article{Zhang_2017,
author = {Zhang, Xiaoman and Zhang, Bin and Mu, Yang and Shao, Shuai and Wick, Collin D. and Ramachandran, B. Ramu and Meng, W. J.},
title = {Mechanical failure of metal/ceramic interfacial regions under shear loading},
journal = {Acta Materialia},
publisher = {Elsevier BV},
year = {2017},
month = {oct},
volume = {138},
pages = {224--236},
url = {https://doi.org/10.1016%2Fj.actamat.2017.07.053},
doi = {10.1016/j.actamat.2017.07.053}
}
@article{zhang_length-scale-dependent_2011,
author = {Zhang, J. Y. and Zhang, X. and Wang, R. H. and Lei, S. Y. and Zhang, P. and Niu, J. J. and Liu, G. and Zhang, G. J. and Sun, J.},
title = {Length-scale-dependent deformation and fracture behavior of Cu/X (X = Nb, Zr) multilayers: The constraining effects of the ductile phase on the brittle phase},
@ -3510,6 +4081,33 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
doi = {10.1038/srep15428}
}
@article{Zheng_2020,
author = {Zheng, Yuanyuan and Yu, Ping and Zhang, Kaiyu and Wen, Mao and Zheng, Jinyang and Zhou, Chengshuang and Zhang, Lin},
title = {Coupling effect of grain boundary and hydrogen segregation on dislocation nucleation in bi-crystal nickel},
journal = {International Journal of Hydrogen Energy},
publisher = {Elsevier BV},
year = {2020},
month = {jul},
number = {38},
volume = {45},
pages = {20021--20031},
url = {https://doi.org/10.1016%2Fj.ijhydene.2020.04.291},
doi = {10.1016/j.ijhydene.2020.04.291}
}
@article{Zheng_2021,
author = {Zheng, Zhouqi and Chen, Jiawei and Zhu, Yaxin and Zhao, Lv and Huang, Minsheng and Liang, Shuang and Li, Zhenhuan},
title = {An atomistically-informed phase-field model for quantifying the effect of hydrogen on the evolution of dislocations in FCC metals},
journal = {International Journal of Plasticity},
publisher = {Elsevier BV},
year = {2021},
month = {mar},
volume = {138},
pages = {102937},
url = {https://doi.org/10.1016%2Fj.ijplas.2021.102937},
doi = {10.1016/j.ijplas.2021.102937}
}
@article{zherebtsov_loss_2010,
author = {Zherebtsov, Sergey and Salishchev, Gennady and Lee Semiatin, S.},
title = {Loss of coherency of the alpha/beta interface boundary in titanium alloys during deformation},
@ -3549,6 +4147,20 @@ Nanolaminate materials, also referred to as “superlattices” or “multilayer
doi = {10.1016/s1359-6454(99)00127-5}
}
@article{Zhou_2003,
author = {Zhou, Min},
title = {A new look at the atomic level virial stress: on continuum-molecular system equivalence},
journal = {Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences},
publisher = {The Royal Society},
year = {2003},
month = {sep},
number = {2037},
volume = {459},
pages = {2347--2392},
url = {https://doi.org/10.1098%2Frspa.2003.1127},
doi = {10.1098/rspa.2003.1127}
}
@article{Zhou_2018,
author = {Zhou, Qing and Ren, Yue and Du, Yin and Hua, Dongpeng and Han, Weichao},
title = {Cracking and Toughening Mechanisms in Nanoscale Metallic Multilayer Films: A Brief Review},

5380
references.xml Normal file
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File diff suppressed because it is too large Load Diff

12
scripts/captionify
View File

@ -12,7 +12,7 @@ Help(){
echo "-h: Print this help message"
echo '-d: Open image defined in $VIEWER'
echo "-o: Specify output file, otherwise the output gets written to caption_infile"
echo "-s: Specify font size"
echo "-s: Specify font size in pixels"
echo "infile: The file to be processed"
echo "message: The message to be added"
}
@ -71,7 +71,10 @@ else
fi
if [ "$size" = "" ]; then
size=48
ih=$(identify -format %h $infile)
echo "Height is $ih"
size=$(echo "scale=0; $ih*10/100" | bc )
echo "Size is $size"
fi
#Now add some small padding
@ -83,9 +86,8 @@ else
infile=$outfile
fi
#Now run the actual imagemagick command
montage -background '#ffffffa0' -label "$message" $infile \
-fill black -font Helvetica -pointsize $size \
-geometry +0+0 $outfile
convert -gravity center $infile \( -background '#FFF' -fill black -font Helvetica -size x$size label:"$message" \)\
-append $outfile
if [ $display -eq 1 ]; then

13
scripts/colorbar
View File

@ -20,7 +20,7 @@ Help(){
outfile='colorbar.png'
args=()
declare -a args
argnum=0
x=0
y=0
@ -28,7 +28,7 @@ while [ $# -gt 0 ]; do
unset OPTIND
unset OPTARG
#Parse Flags
while getopts ':hox:y:' options; do
while getopts ':ho:x:y:' options; do
case $options in
h)
Help
@ -49,19 +49,22 @@ while [ $# -gt 0 ]; do
break
fi
;;
?)
esac
done
shift $((OPTIND-1))
args+=("$1")
(( argnum++ ))
shift
(( argnum++ ))
shift
done
#Now pull out the required arguments
if [ "$args" = "" ]; then
Help
elif [ $argnum -ne 3 ]; then
echo "colorbar requires three positional arguments, please view help"
echo "colorbar requires three positional arguments, you have supplied $argnum. Please view help"
echo ${args[0]} ${args[1]}
else
msg="${args[0]}"
lobd="${args[1]}"

87
scripts/coords Executable file
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@ -0,0 +1,87 @@
#!/bin/bash
##This creates a red to blue divergent colorbar with specified label and bounds.
####
#Help
####
Help(){
echo "This creates a coordinate axis image file with specified x and y labels"
echo
echo "Syntax: colorbar [-h|-o outfile|-x width|-y height] xlabel ylabel"
echo "options:"
echo "-h: print this help"
echo "-o: Specify file to write to"
echo "-x: Specify width of image. Cannot be used with -y"
echo "-y: Specify height of mage. Cannot be used with -x"
echo "xlabel: Label for x axis"
echo "ylabel: Label for y axis"
}
outfile='coords.png'
declare -a args
argnum=0
x=0
y=0
while [ $# -gt 0 ]; do
unset OPTIND
unset OPTARG
#Parse Flags
while getopts ':ho:x:y:' options; do
case $options in
h)
Help
break;;
o)
outfile="$OPTARG";;
x)
x="$OPTARG"
if [ $y -ne 0 ]; then
echo "Cannot use both -x and -y options"
break
fi
;;
y)
y="$OPTARG"
if [ $x -ne 0 ]; then
echo "Cannot use both -x and -y options"
break
fi
;;
esac
done
shift $((OPTIND-1))
args+=("$1")
(( argnum++ ))
shift
done
#Now pull out the required arguments
if [ "$args" = "" ]; then
Help
elif [ $argnum -ne 2 ]; then
echo "coords requires three positional arguments, you have supplied $argnum. Please view help"
echo ${args[0]} ${args[1]}
else
xlabel="${args[0]}"
ylabel="${args[1]}"
#First copy colorbar file to current directory
cp ~/typesetting/figure_templates/coords.png $outfile
#Now create lower and upper labels
convert -background " #FFF " -fill "#ff0000" -font Helvetica -size x180 label:"$xlabel" tmp.png
convert +append -gravity south $outfile tmp.png $outfile
convert -background " #FFF " -fill "#00ff00" -font Helvetica -size x180 label:"$ylabel" tmp.png
convert -append -gravity west tmp.png $outfile $outfile
#Final step is resizing
if [ $x -gt 0 ]; then
convert -scale "$x"x $outfile $outfile
fi
if [ $y -gt 0 ]; then
convert -scale x"$y" $outfile $outfile
fi
rm tmp.png
fi

62
scripts/fig_grid
View File

@ -25,7 +25,7 @@
Help(){
echo "fig_grid combines images into a grid, useful for creating complex figures that can be moved between pandoc/latex and other sources such as word or powerpoint."
echo
echo "Syntax: fig_grid [-h|-o filename|-c captionfile | -s size | -b | -p padding] style inputs"
echo "Syntax: fig_grid [-h|-o filename|-c captionfile | -s size | -b | -p padding | -n] style inputs"
echo "options:"
echo "-h: Prints this help"
echo "-o: Specify output file as filename"
@ -33,6 +33,7 @@ Help(){
echo "-s: Font size for captions in pixels"
echo "-b: Add thin black border around images"
echo "-p: Add padding around images before combining them "
echo "-n: Prevents resizing the images"
echo "style: Represents the style of the output figure. Currently only accepts:"
echo " - nxm (example: 3x2): Arranges a grid into n rows and m columns populating the rows first"
echo "inputs: Input files to be processed"
@ -75,12 +76,13 @@ csize=0
cpad=0
border=0
pad=0
resize=1
output="output.png"
while [ $# -gt 0 ]; do
unset OPTIND
unset OPTARG
#Parse Flags
while getopts ':ho:c:s:bp:' options; do
while getopts ':ho:c:s:bp:n' options; do
case $options in
h)
Help
@ -95,6 +97,8 @@ while [ $# -gt 0 ]; do
border=2;;
p)
pad=$OPTARG;;
n)
resize=0;;
esac
done
shift $((OPTIND-1))
@ -144,7 +148,6 @@ for i in $(seq 1 $((argnum-1)) ); do
fi
done
echo "Resizing all images to $max_x $max_y"
#Get caption size
@ -158,28 +161,49 @@ if [ $pad -eq 0 ]; then
cpad=$(echo "scale=0; $csize/2" | bc)
fi
#Now resize all of the images
for i in $(seq 1 $((argnum-1)) ); do
info=$(identify ${args[$i]} ) || fail "Failed to identify image ${args[$i]}"
x=$(identify -format '%w' ${args[$i]})
y=$(identify -format '%h' ${args[$i]})
if [ $resize -eq 1 ]; then
echo "Resizing all images to $max_x $max_y"
for i in $(seq 1 $((argnum-1)) ); do
info=$(identify ${args[$i]} ) || fail "Failed to identify image ${args[$i]}"
x=$(identify -format '%w' ${args[$i]})
y=$(identify -format '%h' ${args[$i]})
if [ $x -gt $y ]; then
convert -scale "$max_x"x ${args[$i]} $tmp$i.png || fail "Failed to scale image"
fi
if [ $y -gt $x ]; then
convert -scale x"$max_y" ${args[$i]} $tmp$i.png || fail "Failed to scale image"
fi
convert -extent "$max_x"x"$max_y" -gravity center -border "$border"x$border -bordercolor black $tmp$i.png $tmp$i.png || fail "Failed to add padding to image"
done
diffx=$(echo " $max_x - $x" | bc )
diffy=$(echo "$max_y - $y " | bc )
if [ $diffx -eq 0 ]; then
cp ${args[$i]} $tmp$i.png
elif [ $diffy -eq 0 ]; then
cp ${args[$i]} $tmp$i.png
elif [ $diffy -gt $diffx ]; then
convert -scale "$max_x"x ${args[$i]} $tmp$i.png || fail "Failed to scale image"
elif [ $diffx -gt $diffy ]; then
convert -scale x"$max_y" ${args[$i]} $tmp$i.png || fail "Failed to scale image"
fi
convert -extent "$max_x"x"$max_y" -gravity center -border "$border"x$border -bordercolor black $tmp$i.png $tmp$i.png || fail "Failed to add padding to image"
done
else
for i in $(seq 1 $((argnum-1)) ); do
cp ${args[$i]} $tmp$i.png
done
fi
cap_num=1
if [ "${captions[0]}" = "each" ]; then
for i in $(seq 1 $((argnum-1)) ); do
add_caption $tmp$i.png "${captions[$cap_num]}" $cpad $csize || fail "Couldn't add caption"
(( cap_num++ ))
done
fi
k=$(( i+1 ))
cap_num=1
#Now build the actually images based on style
if [[ "$style" == *"x"* ]]; then
vertappend=""
rows=${style%x*}
columns=${style#*x}
echo "Combining images into an $rows by $columns grid"
echo "Combining images into a $rows by $columns grid"
l=1
for i in $(seq 1 $rows); do
horizappend=""
@ -189,13 +213,13 @@ if [[ "$style" == *"x"* ]]; then
done
convert $horizappend +append $tmp$k.png
if [ "${captions[0]}" = "rows" ]; then
add_caption $tmp$k.png ${captions[$cap_num]} $cpad $csize || fail "Couldn't add caption"
add_caption $tmp$k.png "${captions[$cap_num]}" $cpad $csize || fail "Couldn't add caption"
(( cap_num++ ))
fi
vertappend="$vertappend $tmp$k.png"
(( k++ ))
done
convert $vertappend -append $output
convert -gravity center $vertappend -append $output
fi
rm $tmp*.png

10
scripts/md2beamer Executable file
View File

@ -0,0 +1,10 @@
#!/bin/bash
#This script is used to compile md file using markdown
if [ "$2" = '' ]; then
out=${1/md/pdf}
else
out=$2
fi
pandoc -t beamer --citeproc --pdf-engine xelatex pres.md --bibliography /home/aselimov/typesetting/references.bib --csl /home/aselimov/typesetting/csl/custom_beamer_ref.csl --template press -V theme:auriga -V colortheme:auriga -o $out

10
scripts/md2doc Normal file
View File

@ -0,0 +1,10 @@
#!/bin/bash
#This script is used to compile md file using markdown
if [ "$2" = '' ]; then
out=${1/md/docx}
else
out=$2
fi
pandoc $1 --lua-filter="$HOME"/typesetting/pandoc_lua_filters/scholarly-metadata.lua --lua-filter="$HOME"/typesetting/pandoc_lua_filters/author-info-blocks.lua --lua-filter="$HOME"/typesetting/pandoc_lua_filters/pagebreak.lua --filter=pandoc-crossref --bibliography /home/aselimov/typesetting/references.bib --csl /home/aselimov/typesetting/csl/ieee.csl --citeproc -o $out

10
scripts/md2docx Executable file
View File

@ -0,0 +1,10 @@
#!/bin/bash
#This script is used to compile md file using markdown
if [ "$2" = '' ]; then
out=${1/md/docx}
else
out=$2
fi
pandoc $1 --lua-filter="$HOME"/typesetting/pandoc_lua_filters/scholarly-metadata.lua --lua-filter="$HOME"/typesetting/pandoc_lua_filters/author-info-blocks.lua --lua-filter="$HOME"/typesetting/pandoc_lua_filters/pagebreak.lua --filter=pandoc-crossref --citeproc -o $out

10
scripts/md2pdf Executable file
View File

@ -0,0 +1,10 @@
#!/bin/bash
#This script is used to compile md file using markdown
if [ "$2" = '' ]; then
out=${1/md/pdf}
else
out=$2
fi
pandoc $1 --lua-filter="$HOME"/typesetting/pandoc_lua_filters/scholarly-metadata.lua --lua-filter="$HOME"/typesetting/pandoc_lua_filters/author-info-blocks.lua --filter=pandoc-crossref --citeproc --bibliography=/home/aselimov/typesetting/references.bib --csl=/home/aselimov/typesetting/csl/els.csl -o $out

517
templates/press.beamer Normal file
View File

@ -0,0 +1,517 @@
% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
\PassOptionsToPackage{hyphens}{url}
$if(colorlinks)$
\PassOptionsToPackage{dvipsnames,svgnames*,x11names*}{xcolor}
$endif$
$if(dir)$
$if(latex-dir-rtl)$
\PassOptionsToPackage{RTLdocument}{bidi}
$endif$
$endif$
$if(CJKmainfont)$
\PassOptionsToPackage{space}{xeCJK}
$endif$
%
\documentclass[
14pt,
$if(lang)$
$babel-lang$,
$endif$
$if(papersize)$
$papersize$paper,
$endif$
$if(beamer)$
ignorenonframetext,
$if(handout)$
handout,
$endif$
$if(aspectratio)$
aspectratio=$aspectratio$,
$endif$
$endif$
$for(classoption)$
$classoption$$sep$,
$endfor$
]{$documentclass$}
$if(beamer)$
$if(background-image)$
\usebackgroundtemplate{%
\includegraphics[width=\paperwidth]{$background-image$}%
}
$endif$
\usepackage{pgfpages}
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
\setbeamerfont{footnote}{size=\scriptsize}
\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
$for(beameroption)$
\setbeameroption{$beameroption$}
$endfor$
% Prevent slide breaks in the middle of a paragraph
\widowpenalties 1 10000
\raggedbottom
$if(section-titles)$
\setbeamertemplate{part page}{
\centering
\begin{beamercolorbox}[sep=16pt,center]{part title}
\usebeamerfont{part title}\insertpart\par
\end{beamercolorbox}
}
\setbeamertemplate{section page}{
\centering
\begin{beamercolorbox}[sep=12pt,center]{part title}
\usebeamerfont{section title}\insertsection\par
\end{beamercolorbox}
}
\setbeamertemplate{subsection page}{
\centering
\begin{beamercolorbox}[sep=8pt,center]{part title}
\usebeamerfont{subsection title}\insertsubsection\par
\end{beamercolorbox}
}
\AtBeginPart{
\frame{\partpage}
}
\AtBeginSection{
\ifbibliography
\else
\frame{\sectionpage}
\fi
}
\AtBeginSubsection{
\frame{\subsectionpage}
}
$endif$
$endif$
$if(beamerarticle)$
\usepackage{beamerarticle} % needs to be loaded first
$endif$
$if(fontfamily)$
\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
$else$
\usepackage{lmodern}
$endif$
$if(linestretch)$
\usepackage{setspace}
$endif$
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
$if(mathspec)$
\ifxetex
\usepackage{mathspec}
\else
\usepackage{unicode-math}
\fi
$else$
\usepackage{unicode-math}
$endif$
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
$if(mainfont)$
\setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
$endif$
$if(sansfont)$
\setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
$endif$
$if(monofont)$
\setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$}
$endif$
$for(fontfamilies)$
\newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
$endfor$
$if(mathfont)$
$if(mathspec)$
\ifxetex
\setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
\else
\setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
\fi
$else$
\setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
$endif$
$endif$
$if(CJKmainfont)$
\ifxetex
\usepackage{xeCJK}
\setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
\fi
$endif$
$if(luatexjapresetoptions)$
\ifluatex
\usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
\fi
$endif$
$if(CJKmainfont)$
\ifluatex
\usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
\setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
\fi
$endif$
\fi
$if(beamer)$
$if(theme)$
\usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$}
\definecolor{red}{RGB}{181, 23, 0}
\definecolor{blue}{RGB}{0, 118, 186}
\definecolor{gray}{RGB}{146, 146, 146}
$endif$
$if(colortheme)$
\usecolortheme{$colortheme$}
$endif$
$if(fonttheme)$
\usefonttheme{$fonttheme$}
$endif$
$if(mainfont)$
\usefonttheme{serif} % use mainfont rather than sansfont for slide text
$endif$
$if(innertheme)$
\useinnertheme{$innertheme$}
$endif$
$if(outertheme)$
\useoutertheme{$outertheme$}
$endif$
$endif$
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
\usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(indent)$
$else$
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
\KOMAoptions{parskip=half}}
\makeatother
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\setlength{\abovecaptionskip}{0pt}
\hypersetup{
$if(title-meta)$
pdftitle={$title-meta$},
$endif$
$if(author-meta)$
pdfauthor={$author-meta$},
$endif$
$if(lang)$
pdflang={$lang$},
$endif$
$if(subject)$
pdfsubject={$subject$},
$endif$
$if(keywords)$
pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
$endif$
$if(colorlinks)$
colorlinks=true,
linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
filecolor=$if(filecolor)$$filecolor$$else$Maroon$endif$,
citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
$else$
hidelinks,
$endif$
pdfcreator={LaTeX via pandoc}}
\urlstyle{same} % disable monospaced font for URLs
$if(verbatim-in-note)$
\VerbatimFootnotes % allow verbatim text in footnotes
$endif$
$if(geometry)$
$if(beamer)$
\geometry{$for(geometry)$$geometry$$sep$,$endfor$}
$else$
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
$endif$
$if(beamer)$
\newif\ifbibliography
$endif$
$if(listings)$
\usepackage{listings}
\newcommand{\passthrough}[1]{#1}
\lstset{defaultdialect=[5.3]Lua}
\lstset{defaultdialect=[x86masm]Assembler}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
$if(beamer)$
%\usepackage{caption}
% Make caption package work with longtable
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
$else$
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$
$endif$
$if(graphics)$
\usepackage{graphicx}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
% Set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother
$endif$
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% Avoid problems with \sout in headers with hyperref
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
$else$
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
$endif$
$if(beamer)$
$else$
$if(block-headings)$
% Make \paragraph and \subparagraph free-standing
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
$endif$
$endif$
$if(pagestyle)$
\pagestyle{$pagestyle$}
$endif$
$for(header-includes)$
$header-includes$
$endfor$
$if(lang)$
\ifxetex
% Load polyglossia as late as possible: uses bidi with RTL langages (e.g. Hebrew, Arabic)
\usepackage{polyglossia}
\setmainlanguage[$for(polyglossia-lang.options)$$polyglossia-lang.options$$sep$,$endfor$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
\setotherlanguage[$for(polyglossia-otherlangs.options)$$polyglossia-otherlangs.options$$sep$,$endfor$]{$polyglossia-otherlangs.name$}
$endfor$
\else
\usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
$if(babel-newcommands)$
$babel-newcommands$
$endif$
\fi
$endif$
\ifluatex
\usepackage{selnolig} % disable illegal ligatures
\fi
$if(dir)$
\ifxetex
% Load bidi as late as possible as it modifies e.g. graphicx
\usepackage{bidi}
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\TeXXeTstate=1
\newcommand{\RL}[1]{\beginR #1\endR}
\newcommand{\LR}[1]{\beginL #1\endL}
\newenvironment{RTL}{\beginR}{\endR}
\newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$
$if(natbib)$
\usepackage[$natbiboptions$]{natbib}
\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(csl-refs)$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
{% don't indent paragraphs
\setlength{\parindent}{0pt}
% turn on hanging indent if param 1 is 1
\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
% set entry spacing
\ifnum #2 > 0
\setlength{\parskip}{#2\baselineskip}
\fi
}%
{}
\usepackage{calc} % for \widthof, \maxof
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\maxof{\widthof{#1}}{\csllabelwidth}}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth}{#1}}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$
$if(title)$
\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
$endif$
$if(subtitle)$
$if(beamer)$
$else$
\usepackage{etoolbox}
\makeatletter
\providecommand{\subtitle}[1]{% add subtitle to \maketitle
\apptocmd{\@title}{\par {\large #1 \par}}{}{}
}
\makeatother
$endif$
\subtitle{$subtitle$}
$endif$
\author{$for(author)$$author$$sep$ \and $endfor$}
\date{$date$}
$if(beamer)$
$if(institute)$
\institute{$for(institute)$$institute$$sep$ \and $endfor$}
$endif$
$if(titlegraphic)$
\titlegraphic{\includegraphics{$titlegraphic$}}
$endif$
$if(logo)$
\logo{\includegraphics{$logo$}}
$endif$
$endif$
\begin{document}
$if(has-frontmatter)$
\frontmatter
$endif$
$if(title)$
$if(beamer)$
\frame{\titlepage}
$else$
\maketitle
$endif$
$if(abstract)$
\begin{abstract}
$abstract$
\end{abstract}
$endif$
$endif$
$for(include-before)$
$include-before$
$endfor$
$if(toc)$
$if(toc-title)$
\renewcommand*\contentsname{$toc-title$}
$endif$
$if(beamer)$
\begin{frame}[allowframebreaks]
$if(toc-title)$
\frametitle{$toc-title$}
$endif$
\tableofcontents[hideallsubsections]
\end{frame}
$else$
{
$if(colorlinks)$
\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
$endif$
\setcounter{tocdepth}{$toc-depth$}
\tableofcontents
}
$endif$
$endif$
$if(lot)$
\listoftables
$endif$
$if(lof)$
\listoffigures
$endif$
$if(linestretch)$
\setstretch{$linestretch$}
$endif$
$if(has-frontmatter)$
\mainmatter
$endif$
$body$
$if(has-frontmatter)$
\backmatter
$endif$
$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(has-chapters)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
$if(beamer)$
\begin{frame}[allowframebreaks]{$biblio-title$}
\bibliographytrue
$endif$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
$if(beamer)$
\end{frame}
$endif$
$endif$
$endif$
$if(biblatex)$
$if(beamer)$
\begin{frame}[allowframebreaks]{$biblio-title$}
\bibliographytrue
\printbibliography[heading=none]
\end{frame}
$else$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
$endif$
$endif$
$for(include-after)$
$include-after$
$endfor$
\end{document}