13-reference list[1]

harvard reference list example以下是一个基于参考文献列表示例的1500-2000字文章。

文章的主题是关于社交媒体对青少年身心健康的影响。

社交媒体对青少年身心健康的影响引言：社交媒体的普及和广泛应用对青少年的生活方式和心理健康产生了深远影响。

本文将探讨社交媒体如何影响青少年的身心健康，并以相关研究文献为依据，探讨其中的具体影响因素及相关解决方案。

1. 青少年的社交媒体使用情况根据Smith等人的研究结果[1]，80的青少年使用社交媒体以与朋友保持联系、分享照片和视频等。

与此同时，研究指出青少年每天平均使用社交媒体的时间超过6小时[2]。

这种普及的使用行为潜在地影响着青少年的身心健康。

2. 社交媒体与心理健康之间的关系许多研究都发现社交媒体使用与青少年心理健康问题之间存在一定的相关性。

一项研究表明，过度使用社交媒体与孤独感、抑郁和焦虑等心理健康问题密切相关[3]。

此外，社交媒体的曝光还与负面情绪和不满意度增加相关[4]。

这些研究强调了社交媒体使用对青少年心理健康的负面影响。

3. 社交媒体在身体健康方面的影响除了心理健康问题外，社交媒体的使用还与青少年的身体健康问题相关。

研究表明，长时间使用社交媒体与青少年的体重增加和睡眠质量下降密切相关[5]。

此外，青少年在追求社交媒体上的完美形象时可能导致营养失衡和饮食紊乱[6]。

这些身体健康问题需要引起关注并寻找解决方案。

4. 减轻社交媒体对身心健康的影响的方法虽然社交媒体的负面影响已得到广泛研究，但也有一些方法可以减轻这些负面影响。

研究表明，教育和家庭支持是关键。

提供有关社交媒体使用的信息和培养青少年的媒体素养是减轻负面影响的有效方法[7]。

此外，家庭支持和亲密关系的建立被发现能够减轻青少年在社交媒体使用方面的压力[8]。

教育和家庭支持的角色强调了如何缓解和控制社交媒体对身心健康的影响。

结论：社交媒体的广泛使用对青少年的身心健康产生了影响。

harvard reference list example -回复如何使用哈佛引用样式创建参考文献清单。

引用是写作重要的一部分，它使作者能够在其作品中引用和归功于其他人的研究和观点。

在学术写作中，正确引用非常重要，因为它可以确保作者诚实、准确地表达自己的立场，并清楚地显示研究并基于哪些先前的工作。

在引用中，哈佛引用样式是最广泛使用的样式之一。

它不仅包含了作者的姓名和出版物的年份，还提供了文章或章节的标题、出版地点和出版者。

这篇文章将一步一步地解释如何使用哈佛引用样式创建参考文献列表。

1. 标题参考文献清单应该以"参考文献"或"参考书目"为标题，居中放置，并使用加粗字体。

例如：参考文献2. 作者姓名按照"姓，名"的格式列出作者的姓名。

将作者的姓氏排在前面，然后是名字的首字母缩写。

如果有多个作者，用逗号分隔。

例如：Smith, J.Brown, A., Johnson, L.3. 出版日期在作者姓名后面，用括号括起来并紧跟着在逗号后添加出版日期。

出版物的年份应该是在括号内的数字形式，并使用逗号将年、月和日分隔开来。

例如：Smith, J. (2021, January 15).4. 文章或章节标题在出版日期后面，以引号将文章或章节的标题括起来。

标题应使用句子的大小写规则，只有首字母大写，除非标题中包含专有名词或缩写词。

例如：Smith, J. (2021, January 15). "The Importance of Harvard Referencing."5. 期刊名或书名在文章或章节标题后面，使用斜体字列出期刊名或书名。

这应该是斜体文本，例如：Smith, J. (2021, January 15). "The Importance of Harvard Referencing." Journal of Academic Writing.6. 出版地点和出版者在期刊名或书名之后，使用逗号将出版地点和出版者分隔开来。

reference list的格式全文共四篇示例，供读者参考第一篇示例：Reference List的格式是学术写作中十分重要的一部分，它用来列出你在文章中引用或参考的各种资料来源，以便读者可以查证、深入了解你的研究或文章内容。

一个规范的Reference List应该包括作者的姓名、出版年份、题目、出版地点和出版商等信息，按照特定的格式排列在文末。

在不同的学科领域和学术机构中，Reference List的格式也可能有所不同，但一般都遵循国际通用的规范。

为了帮助读者更好地撰写和排列Reference List，以下将为您详细介绍Reference List的格式：1. 作者姓名：在Reference List中，作者姓名的排列顺序应该按照作者在原文中出现的顺序，即第一作者列在第一位，之后的作者依次列出。

如果有多个作者，则用逗号隔开，并在最后一个作者的姓名前加上“&”符号。

如果某个作者的姓名包含有缩写，应当按其原文全称列出，而不是直接使用缩写。

2. 出版年份：在作者姓名之后，应当紧跟着文章或书籍的出版年份。

出版年份应当用小括号括起来，紧跟在作者姓名之后，并在括号内用逗号与出版年份隔开。

如果有多个出版年份，应当按照出版年份的顺序从旧到新排列。

3. 题目：在出版年份的后面，应该列出文章或书籍的题目。

题目应该用斜体或引号标明，以示与其他信息的区分。

在书籍的情况下，应该注明出版地点和出版商。

4. 出版地点和出版商：对于书籍来说，除了作者姓名、出版年份和题目外，还应该包括出版地点和出版商的信息。

这些信息可以帮助读者更好地定位和获取参考资料。

5. 期刊文章：如果引用的是期刊文章，则除了作者姓名、出版年份和题目外，还应该包括期刊的名称、卷号和页码等信息。

6. 网络资源：对于网络资源，应该包括作者姓名、出版年份、题目、网址和获取日期等信息。

网址应该足够具体，以便读者可以直接访问到原始资料。

在排列Reference List时，应该按照字母顺序或出版年份顺序排列各个条目，以方便读者查找。

reference参数用法-回复Reference参数用法是编程中一个重要的概念，可以帮助开发者更好地管理和操作变量。

在编程中，函数通常需要接受参数并返回结果。

Reference参数通过引用传递的方式，让函数可以直接修改原始变量的值，而不是创建副本进行修改。

本文将详细介绍Reference参数的用法，以及它的优缺点，并通过实例进行示范。

一、什么是Reference参数在编程中，参数传递一般有两种方式：值传递（by value）和引用传递（by reference）。

值传递是指函数会创建传递参数的副本进行操作，而引用传递则是直接对原始变量进行操作。

Reference参数就是通过引用传递的方式将变量传递给函数。

二、Reference参数的声明和使用在很多编程语言中，Reference参数的声明方式与普通参数相似，只需要在参数名称前加上特定的符号即可。

例如，在C++中，将参数声明为Reference可以使用&符号，如下所示：void modifyNumber(int &num) {num += 10;}int main() {int number = 5;modifyNumber(number);cout << number; 输出15return 0;}在上面的例子中，函数`modifyNumber`接受了一个Reference参数`num`，并将它加上了10。

在`main`函数中调用`modifyNumber`时，传入的是`number`的引用，因此`number`的值在函数中发生了改变。

三、Reference参数的优点使用Reference参数具有以下几个优点：1. 减少内存消耗：使用Reference参数可以直接对原始变量进行修改，避免了创建副本，减少了内存消耗。

2. 提高运行效率：使用Reference参数可以避免频繁的值传递，节省了时间和资源。

3. 使函数操作更直观：通过使用Reference参数，函数的操作可以直接影响原始变量，使代码更加简洁和易于理解。

Title Intro—Introduction to base reference manualDescription Remarks and examples Also seeDescriptionThis entry describes the organization of the reference manuals.Remarks and examples The complete list of reference manuals is as follows:[R]Stata Base Reference Manual[ADAPT]Stata Adaptive Designs:Group Sequential Trials Reference Manual[BAYES]Stata Bayesian Analysis Reference Manual[BMA]Stata Bayesian Model Averaging Reference Manual[CAUSAL]Stata Causal Inference and Treatment-Effects Estimation Reference Manual[CM]Stata Choice Models Reference Manual[D]Stata Data Management Reference Manual[DSGE]Stata Dynamic Stochastic General Equilibrium Models Reference Manual[ERM]Stata Extended Regression Models Reference Manual[FMM]Stata Finite Mixture Models Reference Manual[FN]Stata Functions Reference Manual[G]Stata Graphics Reference Manual[IRT]Stata Item Response Theory Reference Manual[LASSO]Stata Lasso Reference Manual[XT]Stata Longitudinal-Data/Panel-Data Reference Manual[META]Stata Meta-Analysis Reference Manual[ME]Stata Multilevel Mixed-Effects Reference Manual[MI]Stata Multiple-Imputation Reference Manual[MV]Stata Multivariate Statistics Reference Manual[PSS]Stata Power,Precision,and Sample-Size Reference Manual[P]Stata Programming Reference Manual[RPT]Stata Reporting Reference Manual[SP]Stata Spatial Autoregressive Models Reference Manual[SEM]Stata Structural Equation Modeling Reference Manual[SVY]Stata Survey Data Reference Manual[ST]Stata Survival Analysis Reference Manual[TABLES]Stata Customizable Tables and Collected Results Reference Manual[TS]Stata Time-Series Reference Manual[M]Mata Reference Manual12Intro—Introduction to base reference manualWhen we refer to“reference manuals”,we mean all manuals listed above.When we refer to the specialty manuals,we mean all the manuals listed above except[R].Arrangement of the reference manualsEach manual contains the following sections:•Contents.A table of contents can be found at the beginning of each manual.•Cross-referencing the documentation.This entry lists all the manuals and explains how they are cross-referenced.•Introduction.This entry—usually called intro—provides an overview of the manual.In the specialty manuals, this introduction suggests entries that you might want to readfirst and provides information about new features.Each specialty manual contains an overview of the commands described in it.•Entries.Entries are arranged in alphabetical order.Most entries describe Stata commands,but some entries discuss concepts,and others provide overviews.Entries that describe estimation commands are followed by an entry discussing postestimation commands that are available for use after the estimation command.For example,the xtlogit entry in the[XT]manual is followed by the xtlogit postestimation entry.•Glossary.A glossary is contained in all the specialty manuals.Tofind information and commands quickly,use Stata’s search command;see[R]search(see the entry search in the[R]manual).Each reference manual does not contain its own author or subject index.A combined author index and a combined subject index for all reference manuals can be found in the Stata Index,[I].This manual also contains a combined subject table of contents for all reference manuals and the User’s Guide,an acronym glossary,and a vignette index.Arrangement of each entryEntries in most of the Stata reference manuals contain the following sections,which are explained below:DescriptionQuick startMenuSyntaxOptionsRemarks and examplesStored resultsMethods and formulasAcknowledgmentsReferencesAlso seeIntro—Introduction to base reference manual3DescriptionThe purpose of the command is briefly described here.Quick startA quick start lists common uses of the command and the corresponding syntax for each.For details on the syntax elements shown in the Quick start examples and to further customize the examples shown,see the Syntax and Options sections of the entry.If you prefer to use the GUI,see the Menu section of the entry.For applied examples of the syntax,see Remarks and examples.MenuA menu indicates how the dialog box for the command may be accessed using the menu system.SyntaxA command’s syntax diagram shows how to type the command,indicates all possible options,andgives the minimal allowed abbreviations for all the items in the command.For instance,the syntax diagram for the summarize command issummarizevarlistifinweight,optionsoptions DescriptionMaindetail display additional statisticsmeanonly suppress the display;calculate only the mean;programmer’s option format use variable’s display formatseparator(#)draw separator line after every#variables;default is separator(5) display options control spacing and base and empty cellsvarlist may contain factor variables;see[U]11.4.3Factor variables.varlist may contain time-series operators;see[U]11.4.4Time-series varlists.by,collect,rolling,and statsby are allowed;see[U]11.1.10Prefix commands.aweight s,fweight s,and iweight s are allowed.However,iweight s may not be used with the detail option;see [U]11.1.6weight.Items in the typewriter-style font should be typed exactly as they appear in the diagram, although they may be abbreviated.Underlining indicates the shortest abbreviations where abbre-viations are allowed.For instance,summarize may be abbreviated su,sum,summ,etc.,or it may be spelled out completely.Items in the typewriter font that are not underlined may not be abbreviated.Square brackets denote optional items.In the syntax diagram above,varlist,if,in,weight,and the options are optional.The options are listed in a table immediately following the diagram,along with a brief description of each.Items typed in italics represent arguments for which you are to substitute variable names,observation numbers,and the like.4Intro—Introduction to base reference manualThe diagrams use the following symbols:#Indicates a literal number,for example,5;see[U]12.2Numbers.Anything enclosed in brackets is optional.At least one of the items enclosed in braces must appear.|The vertical bar separates alternatives.%fmt Any Stata format,for example,%8.2f;see[U]12.5Formats:Controlling how data are displayed.depvar The dependent variable in an estimation command;see[U]20Estimation and postesti-mation commands.exp Any algebraic expression,for example,(5+myvar)/2;see[U]13Functions and ex-pressions.filename Anyfilename;see[U]11.6Filenaming conventions.indepvars The independent variables in an estimation command;see[U]20Estimation and postestimation commands.newvar A variable that will be created by the current command;see[U]11.4.2Lists of new variables.numlist A list of numbers;see[U]11.1.8numlist.oldvar A previously created variable;see[U]11.4.1Lists of existing variables.options A list of options;see[U]11.1.7options.range An observation range,for example,5/20;see[U]11.1.4in range."string"Any string of characters enclosed in double quotes;see[U]12.4Strings.varlist A list of variable names;see[U]11.4varname and varlists.If varlist allows factor variables,a note to that effect will be shown below the syntax diagram;see[U]11.4.3Factorvariables.If varlist allows time-series operators,a note to that effect will be shown belowthe syntax diagram;see[U]11.4.4Time-series varlists.varname A variable name;see[U]11.3Naming conventions.weight A[wgttype=exp]modifier;see[U]11.1.6weight and[U]20.24Weighted estimation. xvar The variable to be displayed on the horizontal axis.yvar The variable to be displayed on the vertical axis.The Syntax section will indicate whether factor variables or time-series operators may be used with a command.summarize allows factor variables and time-series operators.If a command allows prefix commands,this will be indicated immediately following the table of options.summarize allows by.If a command allows weights,the types of weights allowed will be specified,with the default weight listedfirst.summarize allows aweight s,fweight s,and iweight s,and if the type of weight is not specified,the default is aweight s.Intro—Introduction to base reference manual5OptionsIf the command allows any options,they are explained here,and for dialog users the location of the options in the dialog is indicated.For instance,in the logistic entry in this manual,the Options section looks like this:££Model ...££SE/Robust ...££Reporting ...££Maximization ...Remarks and examplesThe explanations under Description and Options are exceedingly brief and technical;they are designed to provide a quick summary.The remarks explain in English what the preceding technical jargon means.Examples are used to illustrate the command.Links to video examples posted on Stata’s YouTube channel are provided at the end of this section.Stored resultsCommands are classified as e-class,r-class,s-class,or n-class,according to whether they store calculated results in e(),r(),s(),or not at all.These results can then be used in subroutines by other programs(ado-files).Such stored results are documented here;see[U]18.8Accessing results calculated by other programs and[U]18.9Accessing results calculated by estimation commands. Methods and formulasThe techniques and formulas used in obtaining the results are described here as tersely and technically as possible.AcknowledgmentsSome Stata commands began as community-contributed commands,or they were enhanced after suggestions by a Stata user.Here we acknowledge these contributions.6Intro—Introduction to base reference manualReferencesPublished sources are listed that either were directly referenced in the preceding text or might be of interest.Also seeOther manual entries relating to this entry are listed that might also interest you.£ Elizabeth L.(“Betty”)Scott(1917–1988)was an astronomer and mathematician trained at the University of California at Berkeley.She published herfirst paper when she was just22years old,and her work was focused on comets for much of her early academic career.During World War II,Scott began working at the statistical laboratory at Berkeley,which had recently been established by Jerzy Neyman,sparking what would be a long and fruitful collaboration with him.After the war,she shifted her focus toward mathematics and statistics, partly because of limited career opportunities as an astronomer,though she still applied her research to astronomical topics.For example,in1949she published a paper using statistical techniques to analyze the distribution of binary star systems.She also published papers examining the distribution of galaxies,and she is the name behind the“Scott effect”,which helps determine the distances to ter in her career,Scott applied her statistical knowledge to problems associated with ozone depletion and its effects on the incidence of skin cancer as well as weather modification.She was also a champion of equality for women graduate students and faculty.Among Scott’s many awards and accomplishments,she was elected an honorary fellow of the Royal Statistical Society and was a fellow of the American Association for the Advancement of Science.In1992,the Committee of Presidents of Statistical Societies established the Elizabeth L.Scott Award,a biannual award to recognize those who have strived to enhance the status of women within the statistics profession.¢¡£ Janet Lippe Norwood(1923–2015)was born in Newark,New Jersey.She obtained her PhD from Tufts University and taught political science at Wellesley College.Norwood made significant contributions while she was thefirst female commissioner for the Bureau of Labor Statistics (BLS).She accomplished the goal of conducting the Consumer Expenditure Survey annually,a long-time goal of the BLS,and saved the National Longitudinal Survey from termination.As commissioner,she would present data on national unemployment before the Joint Economic Committee on a monthly basis,a duty that she performed with unwavering impartiality.Under her direction,the statistical quality of reported indicators improved,as did the cooperation of the BLS with the Census Bureau and the National Center for Health Statistics.After her role as commissioner,she was the Chair of the Advisory Council on Unemployment Compensation,appointed by presidents George H.W.Bush and Bill Clinton.She also held a variety of other leadership positions,including president of the American Statistical Association, board member of the American Economic Association,and chair of a statistical committee for the OECD.Norwood was a trailblazer.In her honor,the University of Alabama at Birmingham created the Janet L.Norwood Award to recognize women in statistics.¢¡Intro—Introduction to base reference manual7Also see[U]1.1Getting Started with StataStata,Stata Press,and Mata are registered trademarks of StataCorp LLC.Stata andStata Press are registered trademarks with the World Intellectual Property Organization®of the United Nations.Other brand and product names are registered trademarks ortrademarks of their respective companies.Copyright c 1985–2023StataCorp LLC,College Station,TX,USA.All rights reserved.。

Manual Reference Pages - samtools (1)NAMEsamtools - Utilities for the Sequence Alignment/Map (SAM) formatbcftools - Utilities for the Binary Call Format (BCF) and VCFCONTENTSSynopsisDescriptionSamtools Commands And OptionsBcftools Commands And OptionsSam FormatVcf FormatExamplesLimitationsAuthorSee AlsoSYNOPSISsamtools view -bt ref_list.txt -o aln.bam aln.sam.gzsamtools sort aln.bam aln.sortedsamtools index aln.sorted.bamsamtools idxstats aln.sorted.bamsamtools view aln.sorted.bam chr2:20,100,000-20,200,000samtools merge out.bam in1.bam in2.bam in3.bamsamtools faidx ref.fastasamtools pileup -vcf ref.fasta aln.sorted.bamsamtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bamsamtools tview aln.sorted.bam ref.fastabcftools index in.bcfbcftools view in.bcf chr2:100-200 > out.vcfbcftools view -vc in.bcf > out.vcf 2> out.afsDESCRIPTIONSamtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly.Samtools is designed to work on a stream. It regards an input file ‘-’ as the standard input (stdin) and an output file ‘-’ as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error output (stderr).Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with ‘ftp://’ or ‘http://’. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entire alignment file unless it is asked to do so.SAMTOOLS COMMANDS AND OPTIONSview samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]Extract/print all or sub alignments in SAM or BAM format. If no region is specified,all the alignments will be printed; otherwise only alignments overlapping the specifiedregions will be output. An alignment may be given multiple times if it is overlappingseveral regions. A region can be presented, for example, in the following format:‘chr2’ (the whole chr2), ‘chr2:1000000’ (region starting from 1,000,000bp) or‘chr2:1,000,000-2,000,000’ (region between 1,000,000 and 2,000,000bp including the endpoints). The coordinate is 1-based.OPTIONS:-b Output in the BAM format.-f INT Only output alignments with all bits in INT present in the FLAG field. INTcan be in hex in the format of /^0x[0-9A-F]+/ [0]-F INT Skip alignments with bits present in INT [0]-h Include the header in the output.-H Output the header only.-l STR Only output reads in library STR [null]-o FILE Output file [stdout]-q INT Skip alignments with MAPQ smaller than INT [0]-r STR Only output reads in read group STR [null]-R FILE Output reads in read groups listed in FILE [null]-S Input is in SAM. If @SQ header lines are absent, the ‘-t’ option is required.-c Instead of printing the alignments, only count them and print the totalnumber. All filter options, such as ‘-f’,‘-F’ and ‘-q’ , are taken intoaccount.-t FILE This file is TAB-delimited. Each line must contain the reference name and thelength of the reference, one line for each distinct reference; additionalfields are ignored. This file also defines the order of the referencesequences in sorting. If you run ‘samtools faidx <ref.fa>’, the resultantindex file <ref.fa>.fai can be used as this <in.ref_list> file.-u Output uncompressed BAM. This option saves time spent oncompression/decomprssion and is thus preferred when the output is piped toanother samtools command.tview samtools tview <in.sorted.bam> [ref.fasta]Text alignment viewer (based on the ncurses library). In the viewer, press ‘?’ forhelp and press ‘g’ to check the alignment start from a region in the format like‘chr10:10,000,000’ or ‘=10,000,000’ when viewing the same reference sequence.mpileup samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped bysample identifiers in @RG header lines. If sample identifiers are absent, each inputfile is regarded as one sample.In the pileup format (without -u or-g), each line represents a genomic position, consisting of chromosome name, coordinate, reference base, read bases, read qualities and alignment mapping qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a ’>’ or ’<’ for a reference skip, ‘ACGTN’ for a mismatch on the forward strand and ‘acgtn’ for a mismatch on the reverse strand. A pattern ‘\+[0-9]+[ACGTNacgtn]+’ indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Similarly, a pattern ‘-[0-9]+[ACGTNacgtn]+’ represents a deletion from the reference. The deleted bases will be presented as ‘*’ in the following lines. Also at the read base column, a symbol ‘^’marks the start of a read. The ASCII of the character following ‘^’ minus 33 gives the mapping quality. A symbol ‘$’ marks the end of a read segment.Input Options:-6Assume the quality is in the Illumina 1.3+ encoding. -A Do not skip anomalous read pairs in variant calling.-B Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base beingmisaligned. Applying this option greatly helps to reduce false SNPs caused bymisalignments.-b FILE List of input BAM files, one file per line [null]-C INT Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generatedfrom the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, therecommended value for BWA is 50. [0]-d INT At a position, read maximally INT reads per input BAM. [250]-E Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit.-f FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null]-l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null]-q INT Minimum mapping quality for an alignment to be used [0]-Q INT Minimum base quality for a base to be considered [13]-r STR Only generate pileup in region STR [all sites]Output Options:-D Output per-sample read depth-g Compute genotype likelihoods and output them in the binary call format (BCF). -S Output per-sample Phred-scaled strand bias P-value-u Similar to -g except that the output is uncompressed BCF, which is preferred for piping.Options for Genotype Likelihood Computation (for -g or -u):-e INT Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20]-h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100]-I Do not perform INDEL calling-L INT Skip INDEL calling if the average per-sample depth is above INT. [250]-o INT Phred-scaled gap open sequencing error probability. Reducing INT leads tomore indel calls. [40]-P STR Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates fromsequencing technologies that have low indel error rate such as ILLUMINA.[all]reheader samtools reheader <in.header.sam> <in.bam>Replace the header in in.bam with the header in in.header.sam. This command is muchfaster than replacing the header with a BAM->SAM->BAM conversion.cat samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]Concatenate BAMs. The sequence dictionary of each input BAM must be identical, althoughthis command does not check this. This command uses a similar trick to reheader whichenables fast BAM concatenation.sort samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. Thiscommand may also create temporary files <out.prefix>.%d.bam when the whole alignmentcannot be fitted into memory (controlled by option -m).OPTIONS:-o Output the final alignment to the standard output.-n Sort by read names rather than by chromosomal coordinates-m INT Approximately the maximum required memory. [500000000]merge samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...] Merge multiple sorted alignments. The header reference lists of all the input BAMfiles, and the @SQ headers of inh.sam, if any, must all refer to the same set ofreference sequences. The header reference list and (unless overridden by -h) ‘@’headers of in1.bam will be copied to out.bam, and the headers of other files will beignored.OPTIONS:-1Use zlib compression level 1 to comrpess the output-f Force to overwrite the output file if present.-h FILE Use the lines of FILE as ‘@’ headers to be copied to out.bam, replacing any header lines that would otherwise be copied from in1.bam. (FILE is actuallyin SAM format, though any alignment records it may contain are ignored.) -n The input alignments are sorted by read names rather than by chromosomalcoordinates-R STR Merge files in the specified region indicated by STR [null]-r Attach an RG tag to each alignment. The tag value is inferred from filenames.-u Uncompressed BAM outputindex samtools index <aln.bam>Index sorted alignment for fast random access. Index file <aln.bam>.bai will becreated.idxstats samtools idxstats <aln.bam>Retrieve and print stats in the index file. The output is TAB delimited with each lineconsisting of reference sequence name, sequence length, # mapped reads and # unmappedreads.faidx samtools faidx <ref.fasta> [region1 [...]]Index reference sequence in the FASTA format or extract subsequence from indexedreference sequence. If no region is specified, faidx will index the file and create<ref.fasta>.fai on the disk. If regions are speficified, the subsequences will beretrieved and printed to stdout in the FASTA format. The input file can be compressedin the RAZF format.fixmate samtools fixmate <Srt.bam> <out.bam>Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.rmdup samtools rmdup [-sS] <input.srt.bam> <out.bam>Remove potential PCR duplicates: if multiple read pairs have identical externalcoordinates, only retain the pair with highest mapping quality. In the paired-endmode, this command ONLY works with FR orientation and requires ISIZE is correctly set.It does not work for unpaired reads (e.g. two ends mapped to different chromosomes ororphan reads).OPTIONS:-s Remove duplicate for single-end reads. By default, the command works forpaired-end reads only.-S Treat paired-end reads and single-end reads.calmd samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>Generate the MD tag. If the MD tag is already present, this command will give awarning if the MD tag generated is different from the existing tag. Output SAM bydefault.OPTIONS:-A When used jointly with -r this option overwrites the original base quality.-e Convert a the read base to = if it is identical to the aligned referencebase. Indel caller does not support the = bases at the moment.-u Output uncompressed BAM-b Output compressed BAM-S The input is SAM with header lines-C INT Coefficient to cap mapping quality of poorly mapped reads. See the pileupcommand for details. [0]-r Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).-E Extended BAQ calculation. This option trades specificity for sensitivity,though the effect is minor.targetcut samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>This command identifies target regions by examining the continuity of read depth,computes haploid consensus sequences of targets and outputs a SAM with each sequencecorresponding to a target. When option -f is in use, BAQ will be applied. This commandis only designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzmanet al. (2010)].phase samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>Call and phase heterozygous SNPs. OPTIONS:-A Drop reads with ambiguous phase.-b STR Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file STR.0.bam and phase-1 reads in STR.1.bam. Phase unknown reads will be randomly allocated toone of the two files. Chimeric reads with switch errors will be saved in STR.chimeric.bam.[null]-F Do not attempt to fix chimeric reads.-k INT Maximum length for local phasing. [13]-q INT Minimum Phred-scaled LOD to call a heterozygote. [40]-Q INT Minimum base quality to be used in het calling. [13]BCFTOOLS COMMANDS AND OPTIONSview bcftools view [-AbFGNQSucgv] [-D seqDict] [-l listLoci] [-s listSample] [-igapSNPratio] [-t mutRate] [-p varThres] [-P prior] [-1nGroup1] [-d minFrac] [-UnPerm] [-X permThres] [-T trioType] in.bcf [region]Convert between BCF and VCF, call variant candidates and estimate allele frequencies.Input/Output Options:-ARetain all possible alternate alleles at variant sites. By default, the viewcommand discards unlikely alleles.-b Output in the BCF format. The default is VCF.-D FILE Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]-F Indicate PL is generated by r921 or before (ordering is different).-G Suppress all individual genotype information.-l FILE List of sites at which information are outputted [all sites]-N Skip sites where the REF field is not A/C/G/T-Q Output the QCALL likelihood format-s FILE List of samples to use. The first column in the input gives the sample namesand the second gives the ploidy, which can only be 1 or 2. When the 2ndcolumn is absent, the sample ploidy is assumed to be 2. In the output, theordering of samples will be identical to the one in FILE. [null]-S The input is VCF instead of BCF.-u Uncompressed BCF output (force -b).Consensus/Variant Calling Options:-cCall variants using Bayesian inference. This option automatically invokesoption -e.-d FLOAT When -v is in use, skip loci where the fraction of samples covered by readsis below FLOAT. [0]-e Perform max-likelihood inference only, including estimating the site allelefrequency, testing Hardy-Weinberg equlibrium and testing associations withLRT.-g Call per-sample genotypes at variant sites (force -c)-i FLOAT Ratio of INDEL-to-SNP mutation rate [0.15]-p FLOAT A site is considered to be a variant if P(ref|D)<FLOAT [0.5]-P STR Prior or initial allele frequency spectrum. If STR can be full, cond2, flator the file consisting of error output from a previous variant calling run.-t FLOAT Scaled muttion rate for variant calling [0.001]-T STR Enable pair/trio calling. For trio calling, option -s is usually needed tobe applied to configure the trio members and their ordering. In the filesupplied to the option -s, the first sample must be the child, the secondthe father and the third the mother. The valid values of STR are ‘pair’,‘trioauto’, ‘trioxd’ and ‘trioxs’, where ‘pair’ calls differences between twoinput samples, and ‘trioxd’ (‘trioxs’) specifies that the input is from the Xchromosome non-PAR regions and the child is a female (male). [null]-v Output variant sites only (force -c)Contrast Calling and Association Test Options:-1 INTNumber of group-1 samples. This option is used for dividing the samples intotwo groups for contrast SNP calling or association test. When this option isin use, the following VCF INFO will be outputted: PC2, PCHI2 and QCHI2. [0] -U INT Number of permutations for association test (effective only with -1) [0]-X FLOAT Only perform permutations for P(chi^2)<FLOAT (effective only with -U) [0.01]index bcftools index in.bcfIndex sorted BCF for random access.cat bcftools cat in1.bcf ["in2.bcf "[..."]]]"Concatenate BCF files. The input files are required to be sorted and have identical samples appearing in the same order.SAM FORMATSequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which arestarted with the ‘@’ symbol, each alignment line consists of:Col Field Description1QNAME Query template/pair NAME2FLAG bitwise FLAG3RNAME Reference sequence NAME4POS1-based leftmost POSition/coordinate of clipped sequence5MAPQ MAPping Quality (Phred-scaled)6CIAGR extended CIGAR string7MRNM Mate Reference sequence NaMe (‘=’ if same as RNAME)8MPOS1-based Mate POSistion9TLEN inferred Template LENgth (insert size)10SEQ query SEQuence on the same strand as the reference11QUAL query QUALity (ASCII-33 gives the Phred base quality)12+OPT variable OPTional fields in the format TAG:VTYPE:VALUEEach bit in the FLAG field is defined as:Flag Chr Description0x0001p the read is paired in sequencing0x0002P the read is mapped in a proper pair0x0004u the query sequence itself is unmapped0x0008U the mate is unmapped0x0010r strand of the query (1 for reverse)0x0020R strand of the mate0x00401the read is the first read in a pair0x00802the read is the second read in a pair0x0100s the alignment is not primary0x0200f the read fails platform/vendor quality checks0x0400d the read is either a PCR or an optical duplicatewhere the second column gives the string representation of the FLAG field.VCF FORMATThe Variant Call Format (VCF) is a TAB-delimited format with each data line consists of the following fields:Col Field Description1CHROM CHROMosome name2POS the left-most POSition of the variant3ID unique variant IDentifier4REF the REFerence allele5ALT the ALTernate allele(s), separated by comma6QUAL variant/reference QUALity7FILTER FILTers applied8INFO INFOrmation related to the variant, separated by semi-colon9FORMAT FORMAT of the genotype fields, separated by colon (optional)10+SAMPLE SAMPLE genotypes and per-sample information (optional)The following table gives the INFO tags used by samtools and bcftools.Tag Format DescriptionAF1double Max-likelihood estimate of the site allele frequency (AF) of thefirst ALT alleleDP int Raw read depth (without quality filtering)DP4int[4]# high-quality reference forward bases, ref reverse, alternate forand alt rev basesFQ int Consensus quality. Positive: sample genotypes different; negative:otherwiseMQ int Root-Mean-Square mapping quality of covering readsPC2int[2]Phred probability of AF in group1 samples being larger (,smaller)than in group2PCHI2double Posterior weighted chi^2 P-value between group1 and group2 samplesPV4double[4]P-value for strand bias, baseQ bias, mapQ bias and tail distancebiasQCHI2int Phred-scaled PCHI2RP int# permutations yielding a smaller PCHI2CLR int Phred log ratio of genotype likelihoods with and without thetrio/pair constraintUGT string Most probable genotype configuration without the trio constraintCGT string Most probable configuration with the trio constraintEXAMPLESo Import SAM to BAM when @SQ lines are present in the header:samtools view -bS aln.sam > aln.bamIf @SQ lines are absent:samtools faidx ref.fasamtools view -bt ref.fa.fai aln.sam > aln.bamwhere ref.fa.fai is generated automatically by the faidx command.o Attach the RG tag while merging sorted alignments:perl -e ’print "@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"’ > rg.txtsamtools merge -rh rg.txt merged.bam ga.bam 454.bamThe value in a RG tag is determined by the file name the read is coming from. In this example, in the merged.bam, reads from ga.bam will be attached RG:Z:ga, while reads from 454.bam will be attached RG:Z:454.o Call SNPs and short INDELs for one diploid individual:samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcfbcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcfThe -D option of varFilter controls the maximum read depth, which should be adjusted to about twice the average read depth. One may consider to add -C50 to mpileup if mapping quality is overestimated for reads containing excessive mismatches. Applying this option usually helps BWA-short but may not other mappers.o Generate the consensus sequence for one diploid individual:samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fqo Call somatic mutations from a pair of samples:samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcfIn the output INFO field, CLR gives the Phred-log ratio between the likelihood by treating the two samples independently, and the likelihood by requiring the genotype to be identical. This CLR is effectively a score measuring the confidence of somatic calls. The higher the better.o Call de novo and somatic mutations from a family trio:samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcfFile samples.txt should consist of three lines specifying the member and order of samples (in the order of child-father-mother). Similarly, CLR gives the Phred-log likelihood ratio with and without the trio constraint. UGT shows the most likely genotype configuration without the trio constraint, and CGT gives the most likely genotype configuration satisfying the trio constraint.o Phase one individual:samtools calmd -AEur aln.bam ref.fa | samtools phase -b prefix - > phase.outThe calmd command is used to reduce false heterozygotes around INDELs.o Call SNPs and short indels for multiple diploid individuals:samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg - > var.raw.bcfbcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcfIndividuals are identified from the SM tags in the @RG header lines. Individuals can be pooledin one alignment file; one individual can also be separated into multiple files. The -P optionspecifies that indel candidates should be collected only from read groups with the @RG-PL tagset to ILLUMINA. Collecting indel candidates from reads sequenced by an indel-prone technologymay affect the performance of indel calling.o Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:samtools mpileup -Igf ref.fa *.bam > all.bcfbcftools view -bl sites.list all.bcf > sites.bcfbcftools view -cGP cond2 sites.bcf > /dev/null 2> sites.1.afsbcftools view -cGP sites.1.afs sites.bcf > /dev/null 2> sites.2.afsbcftools view -cGP sites.2.afs sites.bcf > /dev/null 2> sites.3.afs......where sites.list contains the list of sites with each line consisting of the referencesequence name and position. The following bcftools commands estimate AFS by EM.o Dump BAQ applied alignment for other SNP callers:samtools calmd -bAr aln.bam > aln.baq.bamIt adds and corrects the NM and MD tags at the same time. The calmd command also comes withthe -C option, the same as the one in pileup and mpileup. Apply if it helps.LIMITATIONSo Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.o Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan reads or ends mappedto different chromosomes). If this is a concern, please use Picard’s MarkDuplicate whichcorrectly handles these cases, although a little slower.AUTHORHeng Li from the Sanger Institute wrote the C version of samtools. Bob Handsaker from the BroadInstitute implemented the BGZF library and Jue Ruan from Beijing Genomics Institute wrote the RAZFlibrary. John Marshall and Petr Danecek contribute to the source code and various people from the1000 Genomes Project have contributed to the SAM format specification.SEE ALSOSamtools website: <>samtools-0.1.17samtools (1)05 July 2011。

•Creating a reference list or bibliographyA numbered list of references must be provided at the end of thepaper. The list should be arranged in the order of citation in the text of the assignment or essay, not in alphabetical order. List only one reference per reference number. Footnotes or otherinformation that are not part of the referencing format should not be included in the reference list.The following examples demonstrate the format for a variety of types of references. Included are some examples of citing electronic documents. Such items come in many forms, so only some examples have been listed here.Print DocumentsBooksNote: Every (important) word in the title of a book or conference must be capitalised. Only the first word of a subtitle should be capitalised. Capitalise the "v" in Volume for a book title.Punctuation goes inside the quotation marks.Standard formatSingle author[1] W.-K. Chen, Linear Networks and Systems. Belmont, CA: Wadsworth,1993, pp. 123-135.[2] S. M. Hemmington, Soft Science. Saskatoon: University ofSaskatchewan Press, 1997.Edited work[3] D. Sarunyagate, Ed., Lasers. New York: McGraw-Hill, 1996.Later edition[4] K. Schwalbe, Information Technology Project Management, 3rd ed.Boston: Course Technology, 2004.[5] M. N. DeMers, Fundamentals of Geographic Information Systems,3rd ed. New York : John Wiley, 2005.More than one author[6] T. Jordan and P. A. Taylor, Hacktivism and Cyberwars: Rebelswith a cause? London: Routledge, 2004.[7] U. J. Gelinas, Jr., S. G. Sutton, and J. Fedorowicz, Businessprocesses and information technology. Cincinnati:South-Western/Thomson Learning, 2004.Three or more authorsNote: The names of all authors should be given in the references unless the number of authors is greater than six. If there are more than six authors, you may use et al. after the name of the first author.[8] R. Hayes, G. Pisano, D. Upton, and S. Wheelwright, Operations,Strategy, and Technology: Pursuing the competitive edge.Hoboken, NJ : Wiley, 2005.Series[9] M. Bell, et al., Universities Online: A survey of onlineeducation and services in Australia, Occasional Paper Series 02-A. Canberra: Department of Education, Science andTraining, 2002.Corporate author (ie: a company or organisation)[10] World Bank, Information and Communication Technologies: AWorld Bank group strategy. Washington, DC : World Bank, 2002.Conference (complete conference proceedings)[11] T. J. van Weert and R. K. Munro, Eds., Informatics and theDigital Society: Social, ethical and cognitive issues: IFIP TC3/WG3.1&3.2 Open Conference on Social, Ethical andCognitive Issues of Informatics and ICT, July 22-26, 2002, Dortmund, Germany. Boston: Kluwer Academic, 2003.Government publication[12] Australia. Attorney-Generals Department. Digital AgendaReview, 4 Vols. Canberra: Attorney- General's Department,2003.Manual[13] Bell Telephone Laboratories Technical Staff, TransmissionSystem for Communications, Bell Telephone Laboratories,1995.Catalogue[14] Catalog No. MWM-1, Microwave Components, M. W. Microwave Corp.,Brooklyn, NY.Application notes[15] Hewlett-Packard, Appl. Note 935, pp. 25-29.Note:Titles of unpublished works are not italicised or capitalised. Capitalise only the first word of a paper or thesis.Technical report[16] K. E. Elliott and C.M. Greene, "A local adaptive protocol,"Argonne National Laboratory, Argonne, France, Tech. Rep.916-1010-BB, 1997.Patent / Standard[17] K. Kimura and A. Lipeles, "Fuzzy controller component, " U.S. Patent 14,860,040, December 14, 1996.Papers presented at conferences (unpublished)[18] H. A. Nimr, "Defuzzification of the outputs of fuzzycontrollers," presented at 5th International Conference onFuzzy Systems, Cairo, Egypt, 1996.Thesis or dissertation[19] H. Zhang, "Delay-insensitive networks," M.S. thesis,University of Waterloo, Waterloo, ON, Canada, 1997.[20] M. W. Dixon, "Application of neural networks to solve therouting problem in communication networks," Ph.D.dissertation, Murdoch University, Murdoch, WA, Australia, 1999.Parts of a BookNote: These examples are for chapters or parts of edited works in which the chapters or parts have individual title and author/s, but are included in collections or textbooks edited by others. If the editors of a work are also the authors of all of the included chapters then it should be cited as a whole book using the examples given above (Books).Capitalise only the first word of a paper or book chapter.Single chapter from an edited work[1] A. Rezi and M. Allam, "Techniques in array processing by meansof transformations, " in Control and Dynamic Systems, Vol.69, Multidemsional Systems, C. T. Leondes, Ed. San Diego: Academic Press, 1995, pp. 133-180.[2] G. O. Young, "Synthetic structure of industrial plastics," inPlastics, 2nd ed., vol. 3, J. Peters, Ed. New York:McGraw-Hill, 1964, pp. 15-64.Conference or seminar paper (one paper from a published conference proceedings)[3] N. Osifchin and G. Vau, "Power considerations for themodernization of telecommunications in Central and Eastern European and former Soviet Union (CEE/FSU) countries," in Second International Telecommunications Energy SpecialConference, 1997, pp. 9-16.[4] S. Al Kuran, "The prospects for GaAs MESFET technology in dc-acvoltage conversion," in Proceedings of the Fourth AnnualPortable Design Conference, 1997, pp. 137-142.Article in an encyclopaedia, signed[5] O. B. R. Strimpel, "Computer graphics," in McGraw-HillEncyclopedia of Science and Technology, 8th ed., Vol. 4. New York: McGraw-Hill, 1997, pp. 279-283.Study Guides and Unit ReadersNote: You should not cite from Unit Readers, Study Guides, or lecture notes, but where possible you should go to the original source of the information. If you do need to cite articles from the Unit Reader, treat the Reader articles as if they were book or journal articles. In the reference list or bibliography use the bibliographical details as quoted in the Reader and refer to the page numbers from the Reader, not the original page numbers (unless you have independently consulted the original).[6] L. Vertelney, M. Arent, and H. Lieberman, "Two disciplines insearch of an interface: Reflections on a design problem," in The Art of Human-Computer Interface Design, B. Laurel, Ed.Reading, MA: Addison-Wesley, 1990. Reprinted inHuman-Computer Interaction (ICT 235) Readings and Lecture Notes, Vol. 1. Murdoch: Murdoch University, 2005, pp. 32-37. Journal ArticlesNote: Capitalise only the first word of an article title, except for proper nouns or acronyms. Every (important) word in the title of a journal must be capitalised. Do not capitalise the "v" in volume for a journal article.You must either spell out the entire name of each journal that you reference or use accepted abbreviations. You must consistently do one or the other. Staff at the Reference Desk can suggest sources of accepted journal abbreviations.You may spell out words such as volume or December, but you must either spell out all such occurrences or abbreviate all. You do not need to abbreviate March, April, May, June or July.To indicate a page range use pp. 111-222. If you refer to only one page, use only p. 111.Standard formatJournal articles[1] E. P. Wigner, "Theory of traveling wave optical laser," Phys.Rev., vol. 134, pp. A635-A646, Dec. 1965.[2] J. U. Duncombe, "Infrared navigation - Part I: An assessmentof feasability," IEEE Trans. Electron. Devices, vol. ED-11, pp. 34-39, Jan. 1959.[3] G. Liu, K. Y. Lee, and H. F. Jordan, "TDM and TWDM de Bruijnnetworks and shufflenets for optical communications," IEEE Trans. Comp., vol. 46, pp. 695-701, June 1997.OR[4] J. R. Beveridge and E. M. Riseman, "How easy is matching 2D linemodels using local search?" IEEE Transactions on PatternAnalysis and Machine Intelligence, vol. 19, pp. 564-579, June 1997.[5] I. S. Qamber, "Flow graph development method," MicroelectronicsReliability, vol. 33, no. 9, pp. 1387-1395, Dec. 1993.[6] E. H. Miller, "A note on reflector arrays," IEEE Transactionson Antennas and Propagation, to be published.Electronic documentsNote:When you cite an electronic source try to describe it in the same way you would describe a similar printed publication. If possible, give sufficient information for your readers to retrieve the source themselves.If only the first page number is given, a plus sign indicates following pages, eg. 26+. If page numbers are not given, use paragraph or other section numbers if you need to be specific. An electronic source may not always contain clear author or publisher details.The access information will usually be just the URL of the source. As well as a publication/revision date (if there is one), the date of access is included since an electronic source may change between the time you cite it and the time it is accessed by a reader.E-BooksStandard format[1] L. Bass, P. Clements, and R. Kazman. Software Architecture inPractice, 2nd ed. Reading, MA: Addison Wesley, 2003. [E-book] Available: Safari e-book.[2] T. Eckes, The Developmental Social Psychology of Gender. MahwahNJ: Lawrence Erlbaum, 2000. [E-book] Available: netLibrary e-book.Article in online encyclopaedia[3] D. Ince, "Acoustic coupler," in A Dictionary of the Internet.Oxford: Oxford University Press, 2001. [Online]. Available: Oxford Reference Online, .[Accessed: May 24, 2005].[4] W. D. Nance, "Management information system," in The BlackwellEncyclopedic Dictionary of Management Information Systems,G.B. Davis, Ed. Malden MA: Blackwell, 1999, pp. 138-144.[E-book]. Available: NetLibrary e-book.E-JournalsStandard formatJournal article abstract accessed from online database[1] M. T. Kimour and D. Meslati, "Deriving objects from use casesin real-time embedded systems," Information and SoftwareTechnology, vol. 47, no. 8, p. 533, June 2005. [Abstract].Available: ProQuest, /proquest/.[Accessed May 12, 2005].Note: Abstract citations are only included in a reference list if the abstract is substantial or if the full-text of the article could not be accessed.Journal article from online full-text databaseNote: When including the internet address of articles retrieved from searches in full-text databases, please use the Recommended URLs for Full-text Databases, which are the URLs for the main entrance to the service and are easier to reproduce.[2] H. K. Edwards and V. Sridhar, "Analysis of software requirementsengineering exercises in a global virtual team setup,"Journal of Global Information Management, vol. 13, no. 2, p.21+, April-June 2005. [Online]. Available: Academic OneFile, . [Accessed May 31, 2005].[3] A. Holub, "Is software engineering an oxymoron?" SoftwareDevelopment Times, p. 28+, March 2005. [Online]. Available: ProQuest, . [Accessed May 23, 2005].Journal article in a scholarly journal (published free of charge on the internet)[4] A. Altun, "Understanding hypertext in the context of readingon the web: Language learners' experience," Current Issues in Education, vol. 6, no. 12, July 2003. [Online]. Available: /volume6/number12/. [Accessed Dec. 2, 2004].Journal article in electronic journal subscription[5] P. H. C. Eilers and J. J. Goeman, "Enhancing scatterplots withsmoothed densities," Bioinformatics, vol. 20, no. 5, pp.623-628, March 2004. [Online]. Available:. [Accessed Sept. 18, 2004].Newspaper article from online database[6] J. Riley, "Call for new look at skilled migrants," TheAustralian, p. 35, May 31, 2005. Available: Factiva,. [Accessed May 31, 2005].Newspaper article from the Internet[7] C. Wilson-Clark, "Computers ranked as key literacy," The WestAustralian, para. 3, March 29, 2004. [Online]. Available:.au. [Accessed Sept. 18, 2004].Internet DocumentsStandard formatProfessional Internet site[1] European Telecommunications Standards Institute, 揇igitalVideo Broadcasting (DVB): Implementation guidelines for DVBterrestrial services; transmission aspects,?EuropeanTelecommunications Standards Institute, ETSI TR-101-190,1997. [Online]. Available: . [Accessed:Aug. 17, 1998].Personal Internet site[2] G. Sussman, "Home page - Dr. Gerald Sussman," July 2002.[Online]. Available:/faculty/Sussman/sussmanpage.htm[Accessed: Sept. 12, 2004].General Internet site[3] J. Geralds, "Sega Ends Production of Dreamcast," ,para. 2, Jan. 31, 2001. [Online]. Available:/news/1116995. [Accessed: Sept. 12,2004].Internet document, no author given[4] 揂憀ayman抯?explanation of Ultra Narrow Band technology,?Oct.3, 2003. [Online]. Available:/Layman.pdf. [Accessed: Dec. 3, 2003].Non-Book FormatsPodcasts[1] W. Brown and K. Brodie, Presenters, and P. George, Producer, 揊rom Lake Baikal to the Halfway Mark, Yekaterinburg? Peking to Paris: Episode 3, Jun. 4, 2007. [Podcast television programme]. Sydney: ABC Television. Available:.au/tv/pekingtoparis/podcast/pekingtoparis.xm l. [Accessed Feb. 4, 2008].[2] S. Gary, Presenter, 揃lack Hole Death Ray? StarStuff, Dec. 23, 2007. [Podcast radio programme]. Sydney: ABC News Radio. Available: .au/newsradio/podcast/STARSTUFF.xml. [Accessed Feb. 4, 2008].Other FormatsMicroform[3] W. D. Scott & Co, Information Technology in Australia:Capacities and opportunities: A report to the Department ofScience and Technology. [Microform]. W. D. Scott & CompanyPty. Ltd. in association with Arthur D. Little Inc. Canberra:Department of Science and Technology, 1984.Computer game[4] The Hobbit: The prelude to the Lord of the Rings. [CD-ROM].United Kingdom: Vivendi Universal Games, 2003.Software[5] Thomson ISI, EndNote 7. [CD-ROM]. Berkeley, Ca.: ISIResearchSoft, 2003.Video recording[6] C. Rogers, Writer and Director, Grrls in IT. [Videorecording].Bendigo, Vic. : Video Education Australasia, 1999.A reference list: what should it look like?The reference list should appear at the end of your paper. Begin the list on a new page. The title References should be either left justified or centered on the page. The entries should appear as one numerical sequence in the order that the material is cited in the text of your assignment.Note: The hanging indent for each reference makes the numerical sequence more obvious.[1] A. Rezi and M. Allam, "Techniques in array processing by meansof transformations, " in Control and Dynamic Systems, Vol.69, Multidemsional Systems, C. T. Leondes, Ed. San Diego: Academic Press, 1995, pp. 133-180.[2] G. O. Young, "Synthetic structure of industrial plastics," inPlastics, 2nd ed., vol. 3, J. Peters, Ed. New York:McGraw-Hill, 1964, pp. 15-64.[3] S. M. Hemmington, Soft Science. Saskatoon: University ofSaskatchewan Press, 1997.[4] N. Osifchin and G. Vau, "Power considerations for themodernization of telecommunications in Central and Eastern European and former Soviet Union (CEE/FSU) countries," in Second International Telecommunications Energy SpecialConference, 1997, pp. 9-16.[5] D. Sarunyagate, Ed., Lasers. New York: McGraw-Hill, 1996.[8] O. B. R. Strimpel, "Computer graphics," in McGraw-HillEncyclopedia of Science and Technology, 8th ed., Vol. 4. New York: McGraw-Hill, 1997, pp. 279-283.[9] K. Schwalbe, Information Technology Project Management, 3rd ed.Boston: Course Technology, 2004.[10] M. N. DeMers, Fundamentals of Geographic Information Systems,3rd ed. New York: John Wiley, 2005.[11] L. Vertelney, M. Arent, and H. Lieberman, "Two disciplines insearch of an interface: Reflections on a design problem," in The Art of Human-Computer Interface Design, B. Laurel, Ed.Reading, MA: Addison-Wesley, 1990. Reprinted inHuman-Computer Interaction (ICT 235) Readings and Lecture Notes, Vol. 1. Murdoch: Murdoch University, 2005, pp. 32-37.[12] E. P. Wigner, "Theory of traveling wave optical laser,"Physical Review, vol.134, pp. A635-A646, Dec. 1965.[13] J. U. Duncombe, "Infrared navigation - Part I: An assessmentof feasibility," IEEE Transactions on Electron Devices, vol.ED-11, pp. 34-39, Jan. 1959.[14] M. Bell, et al., Universities Online: A survey of onlineeducation and services in Australia, Occasional Paper Series 02-A. Canberra: Department of Education, Science andTraining, 2002.[15] T. J. van Weert and R. K. Munro, Eds., Informatics and theDigital Society: Social, ethical and cognitive issues: IFIP TC3/WG3.1&3.2 Open Conference on Social, Ethical andCognitive Issues of Informatics and ICT, July 22-26, 2002, Dortmund, Germany. Boston: Kluwer Academic, 2003.[16] I. S. Qamber, "Flow graph development method,"Microelectronics Reliability, vol. 33, no. 9, pp. 1387-1395, Dec. 1993.[17] Australia. Attorney-Generals Department. Digital AgendaReview, 4 Vols. Canberra: Attorney- General's Department, 2003.[18] C. Rogers, Writer and Director, Grrls in IT. [Videorecording].Bendigo, Vic.: Video Education Australasia, 1999.[19] L. Bass, P. Clements, and R. Kazman. Software Architecture inPractice, 2nd ed. Reading, MA: Addison Wesley, 2003. [E-book] Available: Safari e-book.[20] D. Ince, "Acoustic coupler," in A Dictionary of the Internet.Oxford: Oxford University Press, 2001. [Online]. Available: Oxford Reference Online, .[Accessed: May 24, 2005].[21] H. K. Edwards and V. Sridhar, "Analysis of softwarerequirements engineering exercises in a global virtual team setup," Journal of Global Information Management, vol. 13, no. 2, p. 21+, April-June 2005. [Online]. Available: AcademicOneFile, . [Accessed May 31,2005].[22] A. Holub, "Is software engineering an oxymoron?" SoftwareDevelopment Times, p. 28+, March 2005. [Online]. Available: ProQuest, . [Accessed May 23, 2005].[23] H. Zhang, "Delay-insensitive networks," M.S. thesis,University of Waterloo, Waterloo, ON, Canada, 1997.[24] P. H. C. Eilers and J. J. Goeman, "Enhancing scatterplots withsmoothed densities," Bioinformatics, vol. 20, no. 5, pp.623-628, March 2004. [Online]. Available:. [Accessed Sept. 18, 2004].[25] J. Riley, "Call for new look at skilled migrants," TheAustralian, p. 35, May 31, 2005. Available: Factiva,. [Accessed May 31, 2005].[26] European Telecommunications Standards Institute, 揇igitalVideo Broadcasting (DVB): Implementation guidelines for DVB terrestrial services; transmission aspects,?EuropeanTelecommunications Standards Institute, ETSI TR-101-190,1997. [Online]. Available: . [Accessed: Aug. 17, 1998].[27] J. Geralds, "Sega Ends Production of Dreamcast," ,para. 2, Jan. 31, 2001. [Online]. Available:/news/1116995. [Accessed Sept. 12,2004].[28] W. D. Scott & Co, Information Technology in Australia:Capacities and opportunities: A report to the Department of Science and Technology. [Microform]. W. D. Scott & Company Pty. Ltd. in association with Arthur D. Little Inc. Canberra: Department of Science and Technology, 1984.AbbreviationsStandard abbreviations may be used in your citations. A list of appropriate abbreviations can be found below:。

Thermo-Calc®User’s GuideVersion PThermo-Calc Software ABStockholm Technology ParkBjörnnäsvägen 21SE-113 47 Stockholm, SwedenCopyright © 1995-2003 Foundation of Computational ThermodynamicsStockholm, Sweden目录第1部分一般介绍 (12)1.1 计算热力学 (12)1.2 Thermo-Calc软件/数据库/界面包 (12)1.3 致谢 (13)1.4 版本历史 (13)1.5 Thermo-Calc软件包的通用结构 (13)1.6 各类硬件上Thermo-Calc软件包的有效性 (14)1.7 使用Thermo-Calc软件包的好处 (14)第2部分如何成为Thermo-Calc专家 (14)2.1 如何容易地使用本用户指南 (14)2.2 如何安装和维护Thermo-Calc软件包 (16)2.2.1 许可要求 (16)2.2.2 安装程序 (16)2.2.3 维护当前和以前版本 (16)2.2.4 使TCC执行更方便 (16)2.3 如何成为Thermo-Calc专家 (16)2.3.1 从TCSAB与其世界各地的代理获得迅速技术支持 (17)2.3.2 日常使用各种Thermo-Calc功能 (17)2.3.3 以专业的和高质量的标准提交结果 (17)2.3.4 通过各种渠道相互交换经验 (17)第3部分Thermo-Calc软件系统 (17)3.1 Thermo-Calc软件系统的目标 (17)3.2 一些热力学术语的介绍 (18)3.2.1 热力学 (18)3.2.2 体系、组元、相、组成、物种（System, component, phases, constituents and species） (18)3.2.3 结构、亚点阵和位置 (19)3.2.4 成分、构成、位置分数、摩尔分数和浓度(composition, constitution, site fractions, molefractions and concentration) (19)3.2.5 平衡态和状态变量 (19)3.2.6 导出变量 (22)3.2.7 Gibbs相规则 (25)3.2.8 状态的热力学函数 (25)3.2.9 具有多相的体系 (25)3.2.10 不可逆热力学 (26)3.2.11 热力学模型 (26)3.2.12 与各种状态变量有关的Gibbs能 (27)3.2.13 参考态与标准态 (27)3.2.14 溶解度范围 (28)3.2.15 驱动力 (28)3.2.16 化学反应 (28)3.2.17 与平衡常数方法相对的Gibbs能最小化技术 (28)3.2.18 平衡计算 (29)3.3 热力学数据 (30)3.3.1 数据结构 (30)3.3.3 数据估价 (32)3.3.6 数据加密 (33)3.4 用户界面 (34)3.4.1 普通结构 (34)3.4.2 缩写 (34)3.4.3 过程机制（history mechanism） (35)3.4.4 工作目录和目标目录(Working directory and target directory) (35)3.4.5 参数转换为命令 (36)3.4.6 缺省值 (36)3.4.7 不理解的问题 (36)3.4.8 帮助与信息 (36)3.4.9 出错消息 (36)3.4.10 控制符 (36)3.4.11 私人文件 (36)3.4.12 宏工具 (37)3.4.13 模块性 (37)3.5 Thermo-Calc中的模块 (37)3.5.1 基本模块 (37)3.7 Thermo-Calc编程界面 (39)3.7.1 Thermo-Calc作为引肇 (39)3.7.2 Thermo-Calc应用编程界面：TQ和TCAPI (40)3.7.3 在其它软件包中开发Thermo-Calc工具箱 (43)3.7.4 材料性质计算核材料工艺模拟的应用 (43)3.8 Thermo-Calc的功能 (44)3.9 Thermo-Calc应用 (44)第4部分Thermo-Calc数据库描述 (45)4.1 引言 (45)4.2 Thermo-Calc数据库描述形式 (45)第5部分数据库模块（TDB）——用户指南 (55)5.1 引言 (55)5.2 TDB模块中用户界面 (56)5.3 开始 (56)5.3.1 SWITCH-DATABASE (56)5.3.2 LIST-DATABASE ELEMENT (56)5.3.3 DEFINE_ELEMENTS (56)5.3.4 LIST_SYSTEM CONSTITUENT (56)5.3.5 REJECT PHASE (56)5.3.6 RESTORE PHASE (56)5.3.7 GET_DATA (56)5.4 所有TDB监视命令的描述 (56)5.4.1 AMEND_SELACTION (56)5.4.6 DEFINE_SPECIES (58)5.4.7 DEFINE_SYSTEM (58)5.4.8 EXCLUDE_UNUSED_SPECIES (58)5.4.9 EXIT (58)5.4.10 GET_DATA (58)5.4.11 GOTO_MODULE (59)5.4.12 HELP (59)5.4.13 INFORMA TION (59)5.4.14 LIST_DATABASE (60)5.4.15 LIST_SYSTEM (60)5.4.16 MERGE_WITH_DA TABASES (61)5.4.17 NEW_DIRECTORY_FILE (61)5.4.18 REJECT (61)5.4.19 RESTORE (62)5.4.20 SET_AUTO_APPEND_DA TABASE (62)5.4.21 SWITCH_DA TABASE (63)5.5 扩展命令 (64)第6部分数据库模块（TDB）——管理指南 (64)6.1 引言 (64)6.2 TDB模块的初始化 (65)6.3 数据库定义文件语法 (66)6.3.1 ELEMENT (67)6.3.2 SPECIES (67)6.3.3 PHASE (67)6.3.4 CONSTITUENT (67)6.3.5 ADD_CONSTITUENT (68)6.3.6 COMPOUND_PHASE (68)6.3.7 ALLOTROPIC_PHASE (68)6.3.8 TEMPERA TURE_LIMITS (68)6.3.9 DEFINE_SYSTEM_DEFAULT (69)6.3.10 DEFAULT_COMMAND (69)6.3.11 DATABASE_INFORMATION (69)6.3.12 TYPE_DEFINITION (69)6.3.13 FTP_FILE (70)6.3.14 FUNCTION (70)6.3.15 PARAMETER (72)6.3.16 OPTIONS (73)6.3.17 TABLE (73)6.3.18 ASSESSED_SYSTEMS (73)6.3.19 REFERENCE_FILE (74)6.3.20 LIST_OF_REFERENCE (75)6.3.21 CASE与ENDCASE (76)6.3.22 VERSION_DA TA (76)6.5 数据库定义文件实例 (77)6.5.1 例1：一个小的钢数据库 (77)6.5.2 例2：Sb-Sn系个人数据库 (78)第7部分制表模块（TAB） (81)7.1 引言 (81)7.2 一般命令 (81)7.2.1 HELP (81)7.2.2 GOTO_MODULE (81)7.2.3 BACK (82)7.2.4 EXIT (82)7.2.5 PATCH (82)7.3 重要命令 (82)7.3.1 TABULATE_SUBSTANCE (82)7.3.2 TABULATE_REACTION (85)7.3.3 ENTER_REACTION (86)7.3.4 SWITCH_DA TABASE (87)7.3.5 ENTER_FUNCTION (88)7.3.6 TABULATE_DERIV A TIVES (89)7.3.7 LIST_SUBSTANCE (91)7.4 其它命令 (92)7.4.1 SET_ENERGY_UNIT (92)7.4.2 SET_PLOT_FORMAT (92)7.4.3 MACRO_FILE_OPEN (92)7.4.4 SET_INTERACTIVE (93)7.5 绘制表 (93)第8部分平衡计算模块（POL Y） (94)8.1 引言 (94)8.2 开始 (95)8.3 基本热力学 (95)8.3.1 体系与相 (95)8.3.2 组元（Species） (95)8.3.3 状态变量 (96)8.3.4 组分 (97)8.3.5 条件 (98)8.4 不同类型的计算 (98)8.4.1 计算单一平衡 (98)8.4.2 性质图的Steping计算 (99)8.4.3 凝固路径模拟 (99)8.4.4 仲平衡与T0温度模拟 (99)8.4.5 相图的Mapping计算 (101)8.4.6 势图计算 (101)8.4.7 Pourbaix图计算 (101)8.4.8 绘制图 (101)8.5.4 更高阶相图 (104)8.5.5 性质图 (104)8.6 普通命令 (104)8.6.1 HELP (104)8.6.2 INFORMA TION (104)8.6.3 GOTO_MODULE (105)8.6.4 BACK (105)8.6.5 SET_INTERACTIVE (105)8.6.6 EXIT (106)8.7 基本命令 (106)8.7.1 SET_CONDITION (106)8.7.2 RESET_CONDITION (107)8.7.3 LIST_CONDITIONS (107)8.7.4 COMPUTE_EQUILIBRIUM (107)8.7.6 DEFINE_MATERIAL (108)8.7.6 DEFINE_DIAGRAM (111)8.8 保存和读取POL Y数据结构的命令 (112)8.8.1 SA VE_WORKSPACES (112)8.8.2 READ_WORKSPACES (113)8.9 计算与绘图命令 (114)8.9.1 SET_AXIS_V ARIABLE (114)8.9.2 LIST_AXIS_V ARIABLE (114)8.9.3 MAP (114)8.9.4 STEP_WITH_OPTIONS (115)8.9.5 ADD_INITIAL_EQUILIBRIUM (117)8.9.6 POST (118)8.10 其它有帮助的命令 (118)8.10.1 CHANGE_STA TUS (118)8.10.2 LIST_STA TUS (119)8.10.3 COMPUTE_TRANSITION (120)8.10.4 SET_ALL_START_V ALUES (121)8.10.5 SHOW_V ALUE (122)8.10.6 SET_INPUT_AMOUNTS (122)8.10.7 SET_REFERENCE_STA TE (122)8.10.8 ENTER_SYMBOL (123)8.10.9 LIST_SYMBOLS (124)8.10.10 EV ALUATE_FUNCTIONS (124)8.10.11 TABULATE (124)8.11 高级命令 (125)8.11.1 AMEND_STORED_EQUILIBRIA (125)8.11.3 DELETE_INITIAL_EQUILIBRIUM (126)8.11.4 LIST_INITIAL_EQUILIBRIA (126)8.11.5 LOAD_INITIAL_EQUILIBRIUM (126)8.11.10 SELECT_EQUILIBRIUM (128)8.11.11 SET_NUMERICAL_LIMITS (128)8.11.12 SET_START_CONSTITUTION (129)8.11.13 SET_START_V ALUE (129)8.11.14 PATCH (129)8.11.15 RECOVER_START_V ALUE (129)8.11.16 SPECIAL_OPTIONS (129)8.12 水溶液 (132)8.13 排除故障 (133)8.13.1 第一步 (133)8.13.2 第二步 (133)8.13.3 第三步 (133)8.14 频繁提问的问题 (134)8.14.1 程序中为什么只得到半行？ (134)8.14.2 在已经保存之后为什么不能绘图？ (134)8.14.3 为什么G.T不总是与-S相同？ (134)8.14.4 如何获得组元偏焓 (135)8.14.5 为什么H(LIQUID) 是零而HM(LIQUID)不是零 (135)8.14.6 即使石墨是稳定的为什么碳活度小于1？ (135)8.14.7 如何获得过剩Gibbs能？ (135)8.14.8 当得到交叉结线而不是混溶裂隙时什么是错的？ (135)8.14.9 怎么能直接计算最大混溶裂隙？ (136)第9部分后处理模块（POST） (136)9.1 引言 (136)9.2 一般命令 (137)9.2.1 HELP (137)9.2.2 BACK (137)9.2.3 EXIT (137)9.3 重要命令 (137)9.3.1 SET_DIAGRAM_AXIS (137)9.3.2 SET_DIAGRAM_TYPE (138)9.3.3 SET_LABEL_CORVE_OPTION (139)9.3.5 MODIFY_LABEL_TEXT (139)9.3.6 SET_PLOT_FORMAT (140)9.3.7 PLOT_DIAGRAM (141)9.3.8 PRINT_DIAGRAM (142)9.3.9 DUMP_DIAGRAM (143)9.3.10 SET_SCALING_STA TUS (144)9.3.11 SET_TITLE (144)9.3.12 LIST_PLOT_SETTINGS (144)9.4 实验数据文件绘图命令 (144)9.4.1 APPEND_EXPERIMENTAL_DA TA (144)9.4.2 MAKE_EXPERIMENTAL_DA TAFILE (145)9.5.3 SET_AXIS_LENGTH (147)9.5.4 SET_AXIS_TEXT_STATUS (147)9.5.5 SET_AXIS_TYPE (147)9.5.6 SET_COLOR (147)9.5.7 SET_CORNER_TEXT (148)9.5.8 SET_FONT (148)9.5.9 SET_INTERACTIVE_MODE (149)9.5.10 SET_PLOT_OPTION (149)9.5.11 SET_PREFIX_SCALING (149)9.5.12 SET_REFERENCE_STA TE (149)9.5.13 SET_TIELINE_STA TE (150)9.5.14 SET_TRUE_MANUAL_SCALING (150)9.5.15 TABULATE (150)9.6 奇特的命令 (150)9.6.1 PATCH_WORKSPACE (150)9.6.2 RESTORE_PHASE_IN_PLOT (150)9.6.3 REINIATE_PLOT_SETTINGS (151)9.6.4 SET_AXIS_PLOT_STATUS (151)9.6.5 SET_PLOT_SIZE (151)9.6.6 SET_RASTER_STATUS (151)9.6.8 SUSPEND_PHASE_IN_PLOT (151)9.7 3D图标是：命令与演示 (151)9.7.1 CREATE_3D_PLOTFILE (153)9.7.2 在Cortona VRML Client阅读器中查看3D图 (154)第10部分一些特殊模块 (155)10.1 引言 (155)10.2 特殊模块生成或使用的文件 (156)10.2.1 POL Y3文件 (156)10.2.2 RCT文件 (156)10.2.3 GES5文件 (156)10.2.4 宏文件 (157)10.3 与特殊模块的交互 (157)10.4 BIN模块 (157)10.4.1 BIN模块的描述 (157)10.4.2 特定BIN模块数据库的结构 (161)10.4.3特定BIN计算的演示实例 (162)10.5 TERN 模块 (162)10.5.1 TERN 模块的描述 (162)10.5.2 特殊TERN模块数据库的结构 (166)10.5.3 TERN模块计算的演示实例 (167)10.6 POT模块 (167)10.7 POURBAIX 模块 (167)10.8 SCHAIL 模块 (167)11.2 热化学 (168)11.2.1 一些术语的定义 (168)11.2.2 元素与物种（Elements and species） (168)11.2.3 大小写模式 (169)11.2.4 相 (169)11.2.5 温度与压力的函数 (169)11.2.6 符号 (170)11.2.7 混溶裂隙 (170)11.3 热力学模型 (170)11.3.1 标准Gibbs能 (171)11.3.2 理想置换模型 (171)11.3.3 规则溶体模型 (171)11.3.4 使用组元而不是元素 (172)11.3.5 亚点阵模型—化合物能量公式 (172)11.3.6 离子液体模型，对具有有序化趋势的液体 (172)11.3.7 缔合模型 (173)11.3.8 准化学模型 (173)11.3.9 对Gibbs能的非化学贡献（如铁磁） (173)11.3.10 既有有序-无序转变的相 (173)11.3.11 CVM方法：关于有序/无序现象 (173)11.3.12 Birch-Murnaghan模型：关于高压贡献 (173)11.3.13 理想气体模型相对非理想气体/气体混合物模型 (173)11.3.14 DHLL和SIT模型：关于稀水溶液 (173)11.3.15 HKF和PITZ模型：对浓水溶液 (173)11.3.16 Flory-Huggins模型：对聚合物 (173)11.4 热力学参数 (173)11.5 数据结构 (175)11.5.1 构造 (175)11.5.2 Gibbs能参考表面 (175)11.5.3 过剩Gibbs能 (175)11.5.4 存储私有文件 (175)11.5.5 加密与不加密数据库 (176)11.6 GES系统的应用程序 (176)11.7 用户界面 (176)11.7.1 模块性和交互性 (177)11.7.2 控制符的使用 (177)11.8 帮助与信息的命令 (177)11.8.1 HELP (177)11.8.2 INFORMATION (177)11.9 改变模块与终止程序命令 (178)11.9.1 GOTO_MODULE (178)11.9.2 BACK (178)11.9.3 EXIT (178)11.10 输入数据命令 (178)11.10.4 ENTER_SYMBOL (180)11.10.5 ENTER_PARAMETER (181)11.11 列出数据的命令 (183)11.11.1 LIST_DATA (183)11.11.2 LIST_PHASE_DA TA (183)11.11.3 LIST_PARAMETER (184)11.11.4 LIST_SYMBOL (185)11.11.5 LIST_CONSTITUENT (185)11.11.6 LIST_STATUS (185)11.12 修改数据命令 (185)11.12.1 AMEND_ELEMENT_DA TA (185)11.12.2 AMEND_PHASE_DESCRIPTION (186)11.12.3 AMEND_SYMBOL (188)11.12.4 AMEND_PARAMETER (189)11.12.5 CHANGE_STATUS (191)11.12.6 PATCH_WORKSPACES (191)11.12.7 SET_R_AND_P_NORM (191)11.13 删除数据的命令 (192)11.13.1 REINITIATE (192)11.13.2 DELETE (192)11.14 存储或读取数据的命令 (192)11.14.1 SA VE_GES_WORKSPACE (192)11.14.2 READ_GES_WORKSPACE (193)11.15 其它命令 (193)11.15.1 SET_INTERACTIVE (193)第12部分优化模块（PARROT） (193)12.1 引言 (193)12.1.1 热力学数据库 (194)12.1.2 优化方法 (194)1 2.1.4 其它优化软件 (195)12.2 开始 (195)12.2.1 试验数据文件：POP文件 (195)12.2.2 图形试验文件：EXP文件 (197)12.2.3 系统定义文件：SETUP文件 (197)12.2.4 工作文件或存储文件：PAR文件 (198)12.2.5 各种文件名与其关系 (198)12.2.6 交互运行PARROT模块 (199)12.2.6.3 绘制中间结果 (199)12.2.6.4 实验数据的选择 (199)12.2.6.6 优化与连续优化 (200)12.2.7 参数修整 (200)12.2.8 交互完成的变化要求编译 (201)12.3 交替模式 (201)12.4 诀窍与处理 (201)12.4.4 参数量 (201)12.5 命令结构 (201)12.5.1 一些项的定义 (201)12.5.2 与其它模块连接的命令 (201)12.5.3 用户界面 (201)12.6 一般命令 (201)12.7 最频繁使用的命令 (202)12.8 其它命令 (203)第13部分编辑-实验模块（ED-EXP） (203)第14部分系统实用模块（SYS） (203)14.1 引言 (203)14.2 一般命令 (203)14.2.1 HELP (203)14.2.2 INFORMA TION (204)14.2.4 BACK (205)14.2.5 EXIT (205)14.2.6 SET_LOG_FILE (205)14.2.7 MACRO+FILE_OPEN (205)14.2.8 SET_PLOT_ENVIRONMENT (206)14.3 Odd命令 (207)14.3.1 SET_INTERACTIVE_MODE (207)14.3.2 SET_COMMAND_UNITS (207)14.3.4 LIST_FREE_WORKSPACE (207)14.3.5 PATCH (207)14.3.6 TRACE (207)14.3.7 STOP_ON_ERROR (208)14.3.8 OPEN_FILE (208)14.3.9 CLOSE_FILE (208)14.3.10 SET_TERMINAL (208)14.3.11 NEWS (208)14.3.12 HP_CALCULATOR (208)14.4 一般信息的显示 (209)第15部分数据绘图语言（DATAPLOT） (215)第1部分一般介绍1.1 计算热力学在近十年内与材料科学与工程相联系的计算机计算与模拟的研究与发展已经为定量设计各种材料产生了革命性的方法，热力学与动力学模型的广泛结合使预测材料成分、各种加工后的结构和性能。

Lecture 13PointersRelated Chapter: Chapter 13Objectives:•To appreciate the importance of being able to use addresses as data values•To know how to declare pointer variables.•To be able to use the & (address) and *(indirection) operators.•To recognize the relationship between pointers and arrays•To understand in detail how to use the ++ and --operatorsIntroductionToday we start on one of the most important features of C: pointers. To become a good C programmer, you have to understand pointers and be adept at using them.PointersPointer variables are variables that store memory addresses.Pointers variables are useful in passing storage addresses in function calls (call-by-reference) and for applications involving dynamic data structures (e.g., linked lists)Example: int *intPtr;float *floatPtr;declares intPtr to be a pointer variable to an object of type integer. and floatPtr to be a pointer variable to an object of type float.Pointer Declaration-Syntax We can write the pointer variable declaration as int* intPtr;or as int * intPtr;Note that when we declare more than two pointer variables in one line each pointer name requires an asterisk:int *ptr1, *ptr2;otherwise we are just declaring a regular variable , not a pointer variable.Pointer: Address Data Our first observationis simply that sinceaddresses arenumbers, they canbe stored in memoryas data.Int x,*ptr;x=2;ptr=&x;ptrPointer to a VariableWhen one variable holdsthe address of another, wesay that it is a pointer tothe other variable.In our memory diagrams,we often draw arrows torepresent pointers. Theactual address of x isirrelevant to ourunderstanding of theconcept. We will usearbitrary addresses in thislecture to illustrate themechanics of pointers.ptrDeclaration PointerTo have a variable thatis a pointer, we need todeclare it as a pointer.The syntax for doingthis is to place anasterisk (which we readas "star") in front of thevariable name.In this declaration, wecreate a variable x,which is an integer, andpx a variable px, which is apointer to an integer.FAQ A bout Pointers Answering these questions will get us going on understanding pointers.How can we get the address of x into px?How can we use the px to access or change the value of x?px=&x;*px=10;There are two C operators that are necessary when using pointer variables.& -the address operator returns the address of a variable ptrX holds the address of x .We say ptrX “points” to x.We will apply the & operator only to variables, e.g. &77 or &(x+1) are not valid.The declaration of ptrX initializes the variable ptrX = &x;Example:int x = 3;int * ptrX = &x;31000x 1000ptrX 1004&operatorExample:int x;int * pt;pt = &x; /* another way to assign an address to a pointer variable */ Suppose the address of the variable x is 9640Then, the effect of pt = &x;will be:Address9640x pt 9640&Operatorint x;int * pt;pt = &x;To assign the value “3” to the variable x in C: x = 3;We can use the “ * ” operator to indirectly reference x. We can assign “3” to x by:*pt = 3;Here we use the fact that “pt” points to integer values.xAddress 9640pt 96403*-means "a pointer to" and is called an indirectionoperator or dereferencing operator, since a pointer "indirectly" references a value in a storage location. Example:*Operatordouble *ptr;ptr = NULL;Assigning a NULL value (zero) to a pointerA null pointer points to nothing. We often depict it asptr/*called a null pointer*/NULL PointerExample-Call by Reference1. Problem DefinitionWrite a function “swap”that has two input integer arguments.This function should swap the values of the variables.2. Refine, Generalize, Decompose the problem definition(i.e., identify sub-problems, I/O, etc.)Input = two integersOutput= no value is returned to the calling function, but the values of the called variables should be swapped.3. Develop AlgorithmPass the addresses of the variables and not their values. In theswap function the parameters that hold the addresses are pointers.Use the indirection operator to swap the values.Example-Good Swap /* C Function to swap values. */#include <stdio.h>void swap(int * , int *);void main(void){/* function header */int x = 1;int y = 2;swap(&x,&y); /* pass the addresses of x and y */ printf(“x = %d , y = %d \n”,x,y);/* prints x = 2 , y = 1 */ }void swap(int *ptrX , int *ptrY){ /* pointer variables */ int temp = *ptrX;*ptrX = *ptrY ;*ptrY = temp;return;}Main Memory before call to swap110002xy1004Main Memory while executing swap , after temp = *ptrX; but before *ptrX = *ptrY ;12xy 1000ptrX 100030001004300830041004ptrYtemp1Example-Good SwapMain Memory while executing swap, after *ptrX = *ptrY ;but before *ptrY = temp;xyptrX ptrY temp1000 210003000 2100430083004 10041Example-Good SwapMain Memory while executing swap , after *ptrY = temp;but before return;2xy 1000ptrX 1000300011004300830041004ptrY temp1Example-Good SwapThe array name in C is assigned the address of the first element of the array.The following code will assign the address of xArray[0]to xArrayPtr :float xArray[50];float * xArrayPtr; xArrayPtr = xArray;The assignment statement above is equivalent to:xArrayPtr = &xArray[0];Array Names are ConstantPointersPointer Arithmetic Pointer Arithmetic Rule:If p is a pointer to the initial element in an array arr,and k is an integer, thefollowing identity always holds: p+k is defined to be &arr[k];int arr[Max],*p,n;p=&arr[0];n=*(p+k);Pointer Arithmeticlong *p1,*p2,list[N],k; p1=&list[2];p2=&list[1];k=p1-p2;printf(“%d”,k);1000List[0]1008List[1] 1016List[2] 10241016P1 10281008p2Incrementing and Decrementingpointers*p++;The expression could be equivalent to*(p++)Because unary operators in C areevaluated in right-to-left order.Thus the ++ takes precedence over the *.If p originally pointed to arr[0],for example,the increment operation would cause it point to arr[1].The relationship between pointersand arraysThe name of an array is treated as beingsynonymous with a pointer to the initialelement in that array.For example:void SortIntegerArray(int array[],int n);is equivalent to :void SortIntegerArray(int *array,int n);String Literals pointer to an ArrayA string literal (e.g. “A –your course grade\n”) is actuallyrepresented in C by a pointer to an address in memory that holds the first byte of the array of characters.Therefore the following declaration of the pointer variable “string” is valid:char * string = “A –your course grade\n”;and to print the value of “string” , use the “%s” conversion specifier, printf(“%s”,string);Although a pointer can be used as an array name, we cannot modify the values of “string” by using the square brackets of array notation. string[0] = …B‟; /* error !!! */The error is due to the fact that the literal “A –your course grade\n” is stored in a location in memory that cannot be accessed by pointers.Strings as pointersAs with any array in C,a character array can also be interpreted as a pointer to its first element.In this case,the for loop control line to access the character in the string could be :for(cp=word;*cp!=…\0‟;cp++)Strings as pointers(cont.)if you declare an array by writing thelinechar carray[MaxChars];char *cptr;cptr=carray;At this assignment, you can use cptr as if it were a character array.Differences between pointer andarray variableschar carray[6]; char *cptr; carray=“hello”; cptr=“world”;Because the name of the arraycorresponds to the entirecollection of boxes and cannotbe used like one.It is illegal towrite an assignment statementlike this.There is no such restriction if you declare a string as a pointer.The computer puts the characters for “world” somewhere in memory,and the assignment statement stores the address of the first character of the string in cptr.Assignment: P486 No.3++ and--operatorsmain(){int x,y;x=5;y=++x;printf(“x=%d,y=%d\n”,x,y);}main(){int x,y;x=5;y=x++;printf(“x=%d,y=%d\n”,x,y);}x=6,y=6x=6,y=5Quiz:What‟s the result with the following program?( ) sub(int x,int y,int *z){ *z=y-x;}main(){ int a,b,c;sub(10,5,&a);sub(7,a,&b);sub(a,b,&c);Printf(“%4d,%4d,%4d\n”,a,b,c); }A)5,2,3B)-5,-12,-7C)-5,-12,-17D)5,-2,-7BAssuming there are statementsint *p,m=5,n;which program fragment is correctbelow?( )DA)p=&n;scanf(“%d”,&p);B)p=&n;scanf(“%d”,*p);C)scanf(“%d”,&n);*p=n;D)p=&n;*p=m;What’s the result with thefollowing program?C #include<string.h>main(){char *p=“abcdefgh”;printf(“%d\n”,strlen(strcpy(p+3,”ABCD”))); puts(p);}A)8 B)12C)4 D)7What’s the result with the followingprogram?bcdABCD #include<string.h>main(){char s[20]=“abcd”;char *sp=s;sp++;puts(strcat(sp,”ABCD”));}#include<string.h>main(){char a[ ]=“12345678”,*p;int i=0;p=a;while(*p){if(i%2==0) *p=…*‟;p++;i++;}puts(a);}What’s the result with the following program?*2*4*6*8*What’s the result with the following program?#include<string.h>1 main(){char *s1=“AbcdEf”,*s2=“aB”;s1++;t=(strcmp(s1,s2)>0);printf(“%d\n”,t);}。