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ArticleOutline
•References
VirtualizingaccesstoscientificapplicationswiththeApplicationHostingEnvironment
OriginalResearchArticle
ComputerPhysicsCommunications,Volume180,Issue12,December2009,Pages2513-2525
S.J.Zasada,P.V.Coveney
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Aweb-deployedinterfaceforperformingabinitiomoleculardynamics,optimization,andelectronicstructureinFireball
ComputerPhysicsCommunications,Volume180,Issue3,March2009,Pages418-426
J.BrandonKeith,JacobR.Fennick,ChadE.Junkermeier,DanielR.Nelson,JamesP.Lewis
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AbstractAbstract|Figures/TablesFigures/Tables|ReferencesReferences
Abstract
Fireballisanabinitiotechniqueforfastlocalorbitalsimulationsofnanotechnological,solidstate,andbiologicalsystems.Wehaveimplementedaconvenientinterfacefornewusersandsoftwarearchitectsintheplatform-independentJavalanguagetoaccessFireball'
suniqueandpowerfulcapabilities.ThegraphicaluserinterfacecanberundirectlyfromawebserverorfromwithinalargerframeworksuchastheComputationalScienceandEngineeringOnline(CSE-Online)environmentortheDistributedAnalysisofNeutronScatteringExperiments(DANSE)framework.Wedemonstrateitsuseforhigh-throughputelectronicstructurecalculationsandamulti-100atomquantummoleculardynamics(MD)simulation.
Programsummary
Programtitle:
FireballUI
Catalogueidentifier:
AECF_v1_0
ProgramsummaryURL:
http:
//cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html
Programobtainablefrom:
CPCProgramLibrary,Queen'
sUniversity,Belfast,N.Ireland
Licensingprovisions:
StandardCPClicence,http:
//cpc.cs.qub.ac.uk/licence/licence.html
No.oflinesindistributedprogram,includingtestdata,etc.:
279
784
No.ofbytesindistributedprogram,includingtestdata,etc.:
12
836
145
Distributionformat:
tar.gz
Programminglanguage:
Java
Computer:
PCandworkstation
Operatingsystem:
TheGUIwillrununderWindows,MacandLinux.ExecutablesforMacandLinuxareincludedinthepackage.
RAM:
512MB
Wordsize:
32or64bits
Classification:
4.14
Natureofproblem:
Thesetupandrunningofmanysimulations(allofthesametype),fromthecommandline,isaslowprocess.Butmostresearchqualitycodes,includingtheabinitiotight-bindingcodeFIREBALL,aredesignedtorunfromthecommandline.Thedesireistohaveamethodforquicklyandefficientlysettingupandrunningahostofsimulations.
Solutionmethod:
WehavecreatedagraphicaluserinterfaceforusewiththeFIREBALLcode.Oncetheuserhascreatedthefilescontainingtheatomiccoordinatesforeachsystemthattheyaregoingtorunasimulationon,theusercansetupandstartthecomputationsofuptohundredsofsimulations.
Runningtime:
3to5minutesona2GHzPentiumIVprocessor.
1.Introduction
2.Fireballtheory
2.1.Pseudopotentials
2.2.Exchange–correlationtheoryandtheFdatapregeneratedbasissets
2.3.DOGS:
Aself-consistentfunctional
3.Fireballuserinterface
3.1.Menuandtreedirectory
3.2.Fireballtab
4.Frameworkintegration
5.ExamplesofhowtouseFireballUI
5.1.Downloadingfiles
5.2.High-throughputcomputing
5.3.Abinitiomoleculardynamics
6.Conclusion
Acknowledgements
References
16
AbstractsofRecentArticlesandLiterature
Security,Volume20,Issue1,31January2001,Pages70-74
Chloë
Palmer,HelenMeyer
AbstractAbstract
Lawoncrackingsecuritycodestoughened,AmyHarmon.TheUScopyrightofficehaspassedanewlawmakingitillegaltobreakthesecuritymethodsinplacetopreventthecopyingofdigitalmusic,booksandmovies.Thelawwillupdatetheexisting1998DigitalMillenniumCopyrightActandwillcomeintoeffectimmediately.ThedecisionwasopposedbygroupssuchasUniversities,programmersandlibrarieswhoarguethatcopyrightedworkshouldbearchivedandleantout.Programmersalsoclaimedthatreverse-engineeringwasavalidtechniqueinthecauseoflearninghowtechnologyworks.TheAssociationofAmericanUniversitieshasstatedthatinordertomaintaincivilliberties,theremustbebroadexemptionstoallowfor“fairuse”ofpurchasedcopyrighteddigitalgoods.TheTorontoStar,30October,E3.
GamecouldholdkeytoNetsecurity,GarethCook.Accordingtotopmathematicians,thekeytocrackingencryptionalgorithmscouldbelinkedtothepopularMinesweepergamewhichcomesfreewiththeWindowsoperatingsystem.Theproblem,the‘PversusNPconjecture’,askswhysomeproblemsaresodifficulttosolveusingacomputer,whileotherscanbesolvedveryquickly.Problemslikeputtingalistintoalphabeticalorder,whichareeasilysolvedbyacomputerareclassifiedasPproblems,andthosewhichcannotareclassedasNP.AprominentspecialistchallengedtheconjectureinthespringeditionoftheMathematicalIntelligencerjournal,sayingthattheconjecturewouldbeprovedfalseiftheMinesweeperlogicgamecouldbecracked,foranysizedboard,usingacomputerprogram.Iftheconjectureistrue,thencertaintypesofproblemwillalwaysremaininsolublebycomputersandthecurrentsystemofencryptionalgorithmswillcontinuetobeconsideredtobesafe.TheClayMathematicalInstituteconsidersthemattertobesoimportantthattheyhaveofferedaUS$1millionprizeforasolution.Theimpactofsuchadiscoverywouldbetomathematicallymaptheboundarybeyondwhichcomputers,nomatterhowpowerful,cannotsucceed.TheBostonGlobe,1November,B1,B4.
MOJproposesnewlawstocrackdownonhackers.TheJapaneseMinistryofJusticehasannouncedthatitintendstotoughenupTaiwan’sCriminalCodeasitrelatestohackers.Thosewhobreakintogovernment,militaryorfinancialinstitutionswouldfaceupto15yearjailsentences.OfficialsalsosaythatanyformofhackingovertheInternetshouldbemadeillegal.ThecodewilladdressholesinlegislationrelatingtocomputercrimesandwillalsocriminalizethedistributionofpornographyandsellingofprohibitedsubstanceswhileregulatingtheresponsibilitiesofISPs,pornographicwebsitesandthosewhichfacilitategambling.TheChinaPost,23October.
Canada’scomputersecurityloopholescalledthreattoUS.DavidAkin.JamesAdams,seniorsecurityadvisortotheUS,toldthePopTech2000conferencethatCanadaisincapableofdefendingitselfagainstattacksagainstitstelecommunicationsandcomputernetworks.ThisendangerstheUSbecause“CanadaisessentiallythebackdoorintoAmerica”,duetotheamountofmajorUScorporationswhichhaveCanadianoffices.TheprivatesectorintheUSandCanadadonothavetherighttoshareinformationgleanedbythesecurityagencies,whichleavesitmorevulnerablethatthosefromcountrieslikeFrance,Israel,China,RussiaandIndia.Thecriticismcomesas30countriesincludingtheUS,butnotCanada,aregearinguptosimulateinformationwarfareattacks.AdamsalsowarnedagainstpurchasinghardwareandsoftwarefromFrance,China,IndiaorRussia,“WeknowwithoutanyquestionwhatsoeverthatalotofthingsthataresoldintheUnitedStates,beitafirewallorsomesoftware,areinfectedwithimplantsfromthesecountriessothatanythingthatgoesacrosstheirnetworks,orisstoredintheirprogramsissentbacktothecountryofmanufacture.”CanadianNationalPost,30October.
Virusesthenextgeneration,KimZetter.Virusesaregettingfasterandmoreprolific.Theyhavebeenaroundsincetheearly60swhentheyinfectedthroughfloppydisks,the‘sneakernet’.Theycangoaroundtheworldinminutes,sentbyE-mail.Withthetrendwithinindustrytousethesameofftheshelfproducts—Windows,Word,Outlook—virusescanhitmillionsofmachinesinonefellswoop.RonMoritzatSymantec,ananti-viruscompany,said,“Iftheviruswriterseverthoughtthroughtheirprograms,wewouldseemuchmorevirulentvirusesthatwouldreally