Graduate Texts in Physics Sérgio Luiz Morelhão Computer Simulation Tools for X-ray Analysis Scattering and Diff raction Methods Graduate Texts in Physics SeriesEditors ProfessorRichardNeeds CavendishLaboratory JJThomsonAvenue CambridgeCB30HE,UK [email protected] ProfessorWilliamT.Rhodes DepartmentofComputerandElectricalEngineeringandComputerScience ImagingScienceandTechnologyCenter FloridaAtlanticUniversity 777GladesRoadSE,Room456 BocaRaton,FL33431,USA [email protected] ProfessorSusanScott DepartmentofQuantumScience AustralianNationalUniversity ScienceRoad Acton0200,Australia [email protected] ProfessorH.EugeneStanley CenterforPolymerStudiesDepartmentofPhysics BostonUniversity 590CommonwealthAvenue,Room204B Boston,MA02215,USA [email protected] ProfessorMartinStutzmann WalterSchottkyInstitut TUMünchen 85748Garching,Germany [email protected] Graduate Texts in Physics publishes core learning/teaching material for graduate- andadvanced-levelundergraduatecoursesontopicsofcurrentandemergingfields within physics, both pure and applied. These textbooks serve students at the MS- or PhD-level and their instructors as comprehensive sources of principles, definitions,derivations,experimentsandapplications(asrelevant)fortheirmastery and teaching, respectively. International in scope and relevance, the textbooks correspondtocoursesyllabisufficientlytoserveasrequiredreading.Theirdidactic style, comprehensiveness and coverage of fundamental material also make them suitable as introductions or references for scientists entering, or requiring timely knowledgeof,aresearchfield. Moreinformationaboutthisseriesathttp://www.springer.com/series/8431 Sérgio Luiz Morelhão Computer Simulation Tools for X-ray Analysis Scattering and Diffraction Methods 123 SérgioLuizMorelhão InstituteofPhysics UniversityofSãoPaulo SãoPaulo,Brazil TheauthorwishtoacknowledgeLDDidacticforsponsoringthetranslationofthisbookfrom Portuguese,itsoriginallanguage. ISSN1868-4513 ISSN1868-4521 (electronic) GraduateTextsinPhysics ISBN978-3-319-19553-7 ISBN978-3-319-19554-4 (eBook) DOI10.1007/978-3-319-19554-4 LibraryofCongressControlNumber:2015944087 SpringerChamHeidelbergNewYorkDordrechtLondon ©SpringerInternationalPublishingSwitzerland2016 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade. Printedonacid-freepaper SpringerInternationalPublishingAGSwitzerlandispartofSpringerScience+BusinessMedia(www. springer.com) TomywifeMarilzaanddaughtersThaliaand Larissaforcaringandunderstandingofmy dedicationtothisproject. Book Credits TranslationintoEnglish: LuanaGuedes,GaryFray PrioridadeConsultoriaLtda. ForsponsoringthetranslationofthisbookfromPortuguese,itsoriginallanguage. LDDIDACTICGmbH,Leyboldstr.1,50354Hürth,Germany vii Preface This book is dedicated to students who need to assimilate extensive knowledge in a short period of time. The international scientific production has increased at a breakneck pace, demanding more dynamic approaches and synergies between different areas of knowledge. Mastering X-ray scattering and diffraction methods meanstobecompetenttoworkinaninfinityofareas,studyingthevarioussystems where the organizational understanding of matter at the atomic scale is necessary. SincethediscoveryofX-radiation,itsuseasaninvestigativetoolhasalwaysbeenin wideexpansionprovidedbyadvancesininstrumentalandcomputationalresource. The current development in the fields of medicine and technology has as one of its supporting pillars the structural analysis offered by X radiation. One of the greatest difficulties faced by beginners in the effective use of this fantastic tool is in analyzing the experimental results. Few are the situations where it is possible to extract structural information directly from the experiments. In most situations, computer programs are necessary for simulating the interaction of radiation with matter. The advent of intense radiation sources and the rapid development of nanotechnologyconstantlycreatechallengesforsolutionsbeyondthoseofferedby thealreadysettledtechniques.Preparingnewresearchersforthisscenarioofrapid and drastic changes requires more than teaching physical phenomena theories, it also calls for teaching how to implement them in a simple and efficient way. In this book, the fundamental concepts needed to analyze a wide range of materials (macromolecules,liquids,nanoparticles,polymers,amorphous,polycrystals,small- moleculecrystals,andproteincrystals)usingscatteringanddiffractiontechniques are demonstrated through computer simulation tools. The chapters follow an ascending order going from disordered to ordered matter, covering various types ofsamplesandtargetingaunificationoftheoreticalapproaches.Thereareexercises thatgowitheachtopicpresented,whichareproposedandsolved.Therearemore than80routinesinMatLabdevelopedforsolvingtheexercises.Therefore,besides X-ray physics, this book also offers a practical programming course in modern, high-levellanguagewithaninfinityofgraphicandmathematicalresources. SãoPaulo,SP,Brazil SérgioL.MorelhaQo ix