Software Engine for Configurations of Ionic Liquids User's Guide
Contents
1. Figure 14 Export Wizard The User Information Screen 2 Cluster Information Most tasks on supercomputers or clusters are managed by cluster managers Currently PBS and cluster informations SLURM are supported It is necessary to enter your Choose a Cluster Manager enter a personal system account name and account name of the particular cluster You also sPesify the amount of walltime CPUs and memory for the job specify here wall time number of nodes cores and memory for your runs The default values are Wall Cluster Manager PBS w time 45 min Nodes 1 CPUs 4 Memory Accout Name 1024 MB Walltime hhh mm ss 00 45 00 Nodes 1 CPUs 4 Structure Exporter Memory MB 1024 Figure 15 Export Wizard The Cluster Information Screen 3 File Information This is the Gaussian specific route line information You choose an algorithm and and a basis set tO file informations combine with The two check boxes Fi req Raman Choose a geometrization method suitable basis set Select if the Raman and SCF Tight are enabling a Raman spectrum spectra should be calculated and the SCF convergence should be tight calculation and a tight SCF convergence respectively A gt In the comment line you may want to enter a personal note about the calculation Finally you have to select a folder for saving the comments exported input files i2. SECIL Software Engine for Configurations of Ionic Liquids User s Guide Table of Contents Overall PUD OSC cin AAA 3 2 IMStallationTASTFUCUONS iis ccnsciacaniwacdviesdeveuscinencsnsssunusnunscacnesuscadansianaeuasevausvacsenudnveavsinacussauasanceaanbans 4 2A Requirement S setii eieaa A AAA AAA E AEA 4 PAE DAN PT o UU A AA E EA T A A E ET 4 ZA 20 PONG JOG io 4 22 ANS tala WOM sa T A peeaneee ease rie UIE 4 3 Getting Star O O 5 OU ooo t a 5 A O 5 FL 2 ACUVO PANS he alee sc ie a N E E N 5 Side Me Result Mee ias 5 4 LIDrary Mate a CO iii a 6 FL TIM DOR aiena E weabasnauioaanemanennanne nae 6 4 2 Deleting Library ENIGOS canada 7 d NEGUN PLOP IIC daras do oia 8 ARSS CACAN o R a A A ucbeea he aepiearenes 8 5 Configuration Generatio ssena a aaa aa 10 1 WAGGING Tons MOCOS 10 2 REMOVING LONS MOICCUIES sr me tages rieaaasenneiion earisenl weeianieens 10 5 5 Gencratiho COMMOUNAU ONS morroia ciisenetaaasarcetteudondads cits caweantag vargceeatanes 11 SA Re amindCON QUO aia AA A henteveetenhuiiaries 12 5 5 Previewing CONFIQUFAtiONS cocconcococconeononconennoncononnonconenronnonronen non rn nrn ren ro nrnrrn non rones rra ro nenananarnenenenan 12 6 Configuration EXPOrFINd cnica 13 6 1 Exporting your Configurations to Gaussian03 0O ccoccoccociocionionionionioncononnnononnonnonnrnenronnrnnennennennenes 13 6 2 EXDO WIZI dais 14 3 EON EGLO A E A S 15 Z Additional Informati li A O aa Eai 16 Fe Me POO Ge UNS rrin aare ia 1
3. instance of this entry is updated immediately Spartan File Properties Name Tetrafluoroborate Abbreviation BF4 Form Charge 1 Delete Edit Figure 5 Editing the entry properties 4 4 Sorting and Searching Spartan File Properties Name Tetrafluoroborate Abbreviation BF4 Form standard orientation de Charge 1 In case you can not find a specific entry in the library list you have two options which will help you First you can sort the list alphabetically or by charge where the entries are split in cations and anions see Figure 6 To sort the library click on the Sort by choice box now select either Charge or Alphabetical Order Library Sort by am Hexafluorophosphate a EMI np Lithium EMI pl B12F12 Tetrafluoroborate Figure 6 The library before and after sorted by charge Anions Hexafluorophosphate Tetrafluoroborate Library Maintenance Second you can look up the entry directly by typing its name in the search field The field is case sensitive The search function starts as soon as a single character is entered in the search field usually it is enough with a subsequence of the given name Figure 7 shows a search for the lithium ion All matches containing a subsequence of the entered sequence will be displayed in the list You can reset the library list by clearing the search field Figure 7 Looking up lithium u
4. 6 FZ PIOUE TINS O Lo e oe FP E aden 16 S APPENA A ios 17 OLAYA FICFOMa E nren e e a a ds el 17 Overall Purpose 1 Overall Purpose Creating starting structures is a crucial task for any molecular modelling and is very difficult to evaluate a priori For ionic liquids which are amorphous condensed materials composed solely of molecular ions the most correct starting structures leading to the deepest minima the fastest are difficult even to imagine Furthermore in the search for the most correct one there is an obvious risk of bias from the researcher SECIL uses a mindless algorithm to efficiently sample possible starting structures configurations for ionic systems taking into account the packing of cations and anions and automatically parses these to input files for popular computational chemistry packages We hope that the easy use of SECIL to construct molecular level models will benefit the ionic liquids community at large and not be limited to computational studies Installation Instructions 2 Installation Instructions 2 1 Requirements Before you try to install SECIL be sure that your computer system fulfils all necessary requirements as outlined below 2 1 1 Java SECIL is a Java application To run properly on your system it is necessary to have an updated Java Runtime Environment JRE installed currently at least JRE 6 The JRE is not included in the SECIL data files You c
5. allow you to explore its possibilities without importing your own However most likely you will eventually want to use a set which is not listed in the current library Therefore you can import as illustrated in Figure 2 Select File Import in the main menu Here you have the choice to import a Spartan file which is generated by the Titan Spartan molecule modelling software or a XYZ File Select the data file which you want to use via the file chooser As seen in Figure 2 the new molecule is displayed on the screen and a property panel blends in where the library tab used to be El Enter a proper name an abbreviation and the correct charge of this entry you can change the properties later at any time After specifying the properties click Add to Library Afterwards the new entry is displayed in the library list E Now it is ready to use see Adding Molecules Lithium Structurizing Help New File a a 32 El B12F12 Close File l Import s Spartan File XYZ File Spartan File Properties Name B12F12 Abbrevation B12F12 Form Charge 15 Add to Library Figure 2 Adding a new ion to SECIL s library To avoid duplicates SECIL checks if the same ion molecule is already included in the library and if the chosen name abbreviation is occupied A dialogue informs you For consistency and correct functionality only add separate ions molecules as entries i e no pairs o
6. an get a copy of the JRE at java com 2 1 2 OpenGL JOGL SECIL uses the advantages of OpenGL to create a user friendly working environment thus make sure that your graphic card supports OpenGL If you are not sure just install the most recent drivers for your graphic card and take a look at the instructions if they are supporting OpenGL In general all new graphic cards support OpenGL Java applications need the Java OpenGL JOGL libraries to display OpenGL content SECIL is distributing different versions for Mac Linux and Windows Operating Systems The newest version is available at https jogl dev java net Download the correct files for your system Windows Mac Linux etc and unpack them modify your CLASSPATH environment variable to include the full paths to jogl jar and gluegen rt jar C Users myhome jogl version windows i586 lib jogl jar Copy the jogl jar as well as the gluegen rt jar to the SECIL lib folder The lib folder also provides some JOGL libraries which you can use 2 2 Installation SECIL is delivered as Zip archive for different operating systems Windows Mac and Linux After downloading SECIL for your Operation System unpack the zip file and you get the following folder structure Lo SECIL L lib J templates To install SECIL permanently copy the SECIL root folder to a proper location on your hard drive e g CA Program Files SECIL The SECIL folder contains a Java archive file SECIL j
7. ar that contains the basic SECIL software The lib folder is keeping the molecule library for the program lib xml and a sub folder containing a System dependent version of the necessary OpenGL Library files To Install SECIL properly read and follow the OpenGL instructions in chapter 2 1 2 carefully Make sure to unpack the OpenGL library files into a folder on your hard drive see chapter 2 1 2 and link your System CLASSPATH to the library file location Also create a copy of the two files jog jar and gluegen rt jar inthe SECIL 1ib folder Getting Started 3 Getting Started 3 1 GUI Figure 1 shows the basic Graphical User Interface GUI of SECIL with its three main working elements the Library El the active area PA and the Results tree ES SECIL a File Generating Exporting Help Library Properties Structure 0 2 A Results Sort by v Y de Results 9 Je Li BF4 Hexafluorophosphate a vV MSI EMI np LiBF41 e LiBF42 e LiBF43 EMI pl Aa LiBF44 B12F12 Tetrafluoroborate Al j El p v Selected Cations Li 1 Anions BF4 1 Structures found 5 Progress Figure 1 The Graphical User Interface 3 1 1 Library The library is divided in a list a sorting menu and a search field The list displays the individual entries stored in the library file When you start SECIL the list is sorted chronological from top to bottom and whenever you import a new en
8. configuration Q 2 Figure 9 Deleting a molecule from the configuration 10 Configuration Generation 5 3 Generating Configurations A set of configurations based on the active area can be generated if at least one anion and one cation entry exists The status bar gives information about how many and which entries currently are active Start the generation of configurations by selecting Generating Run in the Main menu or by clicking the Generate button in the toolbar EN A setup dialogue appears to allow you to decide on the number of configurations Click on the check box type a number in the input field and accept by clicking on the Generate button Pl The generation process starts During this process the active area is locked Elunti all configurations are generated or you press the Cancel button to cancel the process Upon successful generation a list of the resulting configurations is displayed in the result tree El Figure 10 schematically shows all the necessary steps to generate configurations Generation Setup Remember an unspecified amount of results can cause a Java heap space error on your computer Especially for big molecular system Define maximum results 5 Running Cancel Figure 10 Guiding through the different structure creation steps Remember The computational effort of configuration generation rapidly increases with the number of entries and numb
9. dix A 8 AppendixA 8 1 XYZ File Format The XYZ file format is a chemical file format There is no formal standard and several variations exist but a typical XYZ format specifies the molecule geometry by giving the number of atoms with cartesian coordinates that will be read on the first line a comment on the second and the lines of atomic coordinates in the following lines The file format is used in computational chemistry programs for importing and exporting geometries The units are generally in Angstroms Some variations include using atomic numbers instead of atomic symbols or skipping the comment line Files using the XYZ format conventionally have the xyz extension Example 1 ethyl 3methyl imidazolium 19 EMI N 0620630 De DLL IDO Doo do 667 E Uig Ad LOZ US 1 346 00 LOOO N SAA 40 O ELE 65 0 040034 E 1 187244 O OZ DSUSSLLS E 0 132086 Ue LL OGUZ SUsTSO652 Z V32 0 14 ALDO DOS E 2 888449 ULLOA O 0 693027 E 401 Ldod USO OOO Oi 2233 15 H 35 01630 LSO OZ O 299641 H 12922204 1992996 o eoi H Ooo 10 alive 36 23103 9510 0 187044 H Zoo OF Oa TIIG IDO H Ze Loo e DO Ly A 943520 H SOLIS a 143 Oi AGUS H Lge 202 0 907467 i AOD H 2 924043 0 769143 MEON ONS H o 50502 0 414594 Le LOIS 6 H ALA LODO A 1 751144 0 121609 H 31D OO A S162 62 504 UieO 30015 4 Source http en wikipedia org wiki XYZ_ file format 17
10. er of configurations specified Do small test runs first 11 Configuration Generation 5 4 Renaming Configurations By default configurations are named on the entries included This naming may not be the best You can easily rename your set of configurations by a right mouse click on the group folder El An input field shows up where you can enter a new name Figure 11 All configurations in this folder will be updated with the new names automatically El A de Results E di Results Da S Fd REE pue P zi F Lithium BF40 E LiBF41 Lithium BF4 els ithi E a LiBF42 A a ithi E LiBF43 d ithi 3 E de LiBF44 E ithi E LiBF45 Figure 11 Renaming set of configurations 5 5 Previewing Configurations By double clicking on a specific configuration in the Result tree the Preview Tab opens up and the selected configuration is displayed You can now scan through the configurations within the folder by using the arrow keys E Preview Tab E de EMIPF6 3 E EMIPF6 4 Preview Mode Figure 12 Selecting a structure and previewing it on the screen You can mark each result by pressing ed 12 Configuration Exporting 6 Configuration Exporting 6 1 Exporting your Configurations to Gaussian03 09 There are two ways to create Gaussian input and setup files from your generated configurations either by using a wizard or an editor The export wiza
11. nto You can also save the completed data in a template file by using the Save Template button Structure Exporter Freg Raman SCF Tight F Select an output directory Figure 16 Export Wizard The File Information Screen 14 Configuration Exporting 6 3 Export Editor The Export Editor allows you to create detailed input files and if necessary cluster manager files In Figure 17 you see the icons New _ Open Save PY and Cluster Setup Creating Files The content for the GAUSSIAN setup files is to be entered in the text area of the Gaussian Input tab In most cases you need to create an Cluster manager information file as well Thus click the Cluster Setup icon in the toolbar to enable the Cluster Manager Info tab A It is often required to add the file name into your files e g for a check file which is created by GAUSSIAN Hence you can click the F Jicon and a FILENAME text mark will appear in between the data This token used at the right position will change to the real file name during the exporting process In the end of the data add a single blank line by pressing the enter button on your keyboard SECIL will auto complete the files in the exporting process You find the GAUSSIAN syntax at their website Look up the manual pages of the cluster manager for the corresponding syntax Export File Editor _ New Open Y save cluster setup lt F gt Gaussian Inp
12. r higher aggregates 1 Titan 1 0 1 Wavefunction Inc and Schrodinger Inc Irvine CA and Portland OR 1999 2 See Appendix A Library Maintenance A 4 2 Deleting Library Entries There are two ways to delete a entry from the library a Via the popup menu right click on the name in the library list and you get the option Delete El Select and accept the safety dialogue by pressing Yes P4 Figure 3 b Open the molecule in a display tab see Adding Molecule select it Elto open the properties panel Click the Delete button Bas shown in Figure 3 A safety dialogue asks for confirmation El Delete Molecule Delete this Molecule from the Library 1 Tetrafluoroborate Add K Delete Figure 3 Deleting an unwelcome entry from the library Spartan File Properties Mame Tetrafluoroborate El Abbreviation BF4 Delete Molecule Form Charge 1H Figure 4 Deleting an entry using the properties panel Library Maintenance 4 3 Editing Properties Every library entry is editable name abbreviation form and charge Figure 5 illustrates the steps to change the properties After adding a molecule to the screen select it by clicking on it The properties panel appears Now use the Edit button PJ to enable the input fields After editing the corresponding fields you can save the data by clicking the Save Button El After saving the library and every other
13. rd allows you to follow a step by step procedure and provides a fast solution but is quite limited in possibilities The export editor is more advanced and versatile You need to know Gaussian03 09 input file syntax and if applicable also the syntax of the cluster manager of your computer system for setup files Common to both paths to exporting is that you first select the folder and the specific configurations you want to export by using the check boxes Figure 13 Then you either open the Export Wizard q the Export Editor gt by clicking on their icons in the toolbar or by using Main menu Exporting F Ly Results El a Je LiBFa n i Ae LiBF40 o E de LiBF4 1 2 W de LiBF42 laa LiBF44 i E de LiBF45 Figure 13 Selecting configurations in the result tree 13 Configuration Exporting 6 2 Export Wizard The exporting wizard consists of three input screens for user cluster and file information 1 User Information Here you specify a valid email address Depending on system this might allow you to receive information user informations about the status of a job e g when it is started Enter your email address Receive a notification mail when an job is finished or cancelled Here you can also load started ended or aborted complete templates from previous exports Structure Exporter Email Notification Notify me if a job is started finished
14. sing the search function Tip When you are looking for a family of chemical compounds e g imides just type imide in the search field This is a convenient starting point to create various imide based configurations Configuration Generation 5 Configuration Generation 5 1 Adding Ions Molecules A configuration is built directly from library entries The library list displays all the accessible entries ions molecules You can add a entry to a new or existing by double clicking on its name In case no display tab is selected a new display tab will be created including the selected entry s If you want to add more than one molecule of the same kind it is more convenient to right click on the entry name and choose Add Allin the popup menu A dialogue will appear After specifying the amount n press Ada Elto insert n entries to your working configuration All entries will be displayed in the same display tab E Cancel the dialogue by pressing Cancel BF4 py Add 5 Delete Figure 8 1 the popup menu selected is Add 2 the add dialog 3 a displayed molecule 5 2 Removing Ions Molecules To remove an ion molecules from a configuration by using the remove button in the upper right corner of the active area Select the particular molecule by left clicking with the mouse followed by pressing the Remove button 2 The status bar shows the updated amount of entries for the active
15. try it is displayed at the bottom of the list You might want to sort the list alphabetically or by charge thus you use the drop down menu which is located above the list saying Sort by If you cannot find a particular entry but you know that it is included find it by typing its name a sub string of it or even only the first letter into the search field Since the search field is directly connected to the list the search results will appear immediately To display all entries again just erase the search expression 3 1 2 Active Area You find the active area n the center of SECIL s GUI Figure 1 shows a 1 1 ion pair of lithium Li and tetrafluoroborate BF in 3D Located in the top left and right corner of the 3D display are buttons to move x y Z dimension rotate or remove a single molecule Multiple displays are managed by tabs You can switch from tab to tab to focus different active areas 3 1 3 The Result Tree The result tree arranges the generated configurations as shown in Figure 1 Every time a configuration generation is finished a new folder node containing the seperate configurations is created and displayed in the result tree with an appropriate name due to the included ions molecules etc You can collapse a folder by doubleclicking it and open it the same way Library Maintenance 4 Library Maintenance 4 1 Importing SECIL includes a couple of entries ions molecules in its library by default to
16. ut Cluster Manager Info Figure 17 The Export File Editor To prevent of losing content save the files you are working on before you use the New file function 3 Gaussian 09 documentation http www gaussian com g tech g09ur htm La Additional Information 7 Additional Information 7 1 About SECIL SECIL was created at Applied Physics Chalmers University of Technology in Goteborg Sweden The SECIL project software creation and first examples of usage was made possible by a grant from Stiftelsen J Gust Richert to Dr Patrik Johansson 2009 2010 which is most gratefuly acknowledged SECIL is written in Java and ifreeware 7 2 About the Creators Knut Angenendt studied computer science at the Carl von Ossietzky University of Oldenburg Germany He wrote his diploma thesis at the Chalmers University of Technology in Goteborg Sweden After graduating he was employed by Chalmers to work on the SECIL project He has written all the code developed all the algorithms and the software design of SECIL Dr Patrik Johansson is Assoc Prof at Applied Physics at Chalmers University of Technology One of his major research areas is the physics of ionic liquids especially for applications such as electrolytes for batteries and fuel cells and more specifically the role of the ion ion interactions He initiated the SECIL project with the main idea and aims 16 Appen
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