User`s Manual SageMD2 Code
Contents
1. 2 5 2 3 Asymmetric Cell tab w Lattice Builder a Space Groups Cel Asymmetric Cell Cell vectors Unit Cell Super Cell Atom positionsifractional Edit positions e 0 y O75 E 0 125 Ufo 062i 0 0661 0 1953 Change atom ZF Rebuild unit cell on OK command Add ator Delete atom Clear Build unit cell Ok Cancel Apply now Asymmetric Cell tab allows you to build the whole unit cell by using the space group symmetry operations for each atom in the asymmetric cell Asymmetric Cell tab has the following data fields Atom positions fractional Displays the position and type for each atom in the asymmetric cell To edit the atom position or type you can click on the corresponding row in this field Edit positions Allows you to modify the atom positions x y and z are the fractional coordinates of the atom Their values must be numbers from 0 to 1 If you specify the other value the error message will be displayed Change Atom Allows you to modify the current atom type by selecting a new atom from the dropdown list Add Atom Use this button to add new atom to the structure The atom type 1s specified in the Change atom box The default coordinates of the atom are x 0 y 0 z 0 Use the Edit positions boxes to modify these values Delete Atom Click this button to remove an atom from the asymmetric cell Clear Click this button to remove all atoms from the asymmetric cell Build unit cell Click this2. Help use this button to display this page 23 2 5 1 2 Bond tab Use this tab to build the atomic bonds change bond radii show or hide the bonds image v Display Parameters Build bonds min factor max factor Po osf 1 Build Bond radius 104 M Show bonds i Suto rebuild o CPK view Clase Help This tab has the following boxes and buttons Build bonds group box allows you to create bonds between two atoms if the following criteria are met min factor covalent radii sum lt distance lt max factor covalent radii sum where distance distance between two atoms forming the bond To build the bonds click the Build button If no bonds are shown try other values of the min and max factors Bond radius Allows you to specify the bond radius as a fraction of the radius of atoms forming the bond The bond radii are within 0 100 range Show bonds Check this box to display the bond images or uncheck to hide it Auto rebuild Uncheck this box to build or remove the bonds manually How to add or remove bonds manually see Add bonds 2 2 7 17 and Remove bonds 2 2 7 18 checkboxes of Operations 2 2 7 menu CPK view Check this box to display atoms rendered as spheres sized to the van der Waals VDW radii Close use this button to close the dialog Help use this button to display this page 26 2 5 1 3 Misc tab Use this tab to change various miscellaneous parameters v Display Parameters Colors
3. 2 2 7 10 Use this dialog to move selected atoms by the shift vector you define All the vector components are in the fractional coordinate system x is directed along a y along b and z along c vectors of the unit cell The dialog has the following boxes and buttons X shift Allows you to specify the shift along a vector of the unit cell Y shift Allows you to specify the shift along b vector of the unit cell Z shift Allows you to specify the shift along e vector of the unit cell use the same for all directions Check this box to move the selected atoms by the same shift in all directions OK Click this button to move the selected atoms and close the dialog Cancel Click this button to close the dialog without the moving 46 2 5 11 Copy atoms dialog box Path Operations menu 2 2 7 gt Copy menu item 2 2 7 11 This dialog allows you to translate the selected group of atoms in any direction and repeat the displacement one or more times All the displacement vector components are in the fractional coordinate system X is directed along a y along b and z along c vectors of the unit cell pee EE fractional units DK Lancel The dialog has the following boxes and buttons a Allows you to specify the shift along a vector of the unit cell b Allows you to specify the shift along b vector of the unit cell c Allows you to specify the shift along vector of the unit cell rep Allows you to s
4. Background i Selected atoms Top Back M Axis labels Bottom Back M Hide axis labels Bonds color MM Auto bond colors iw Box color Hi Projection Contour Orthogonal Hide C Perspective C Unit cell Lattice Clase Help This tab has the following boxes and buttons Colors group box allows you to change the window background colors and the color used to display the selected atoms Just click the appropriate color box to display Color dialog box 2 5 22 and choose the new color using this dialog Uncheck Auto checkbox for setting bonds color manually Projections Use these radio buttons to switch between orthogonal and perspective projections Contour Allows you to specify how the contour around the crystal will be displayed Select Hide to hide the contour image Select Unit cell to display the contour around the unit cell Select Lattice to display the contour around the whole crystal Close use this button to close the dialog box Help use this button to display this page 2 2 5 2 Lattice Builder dialog box Path Lattice menu 2 2 5 gt Build Rebuild menu item 2 2 5 1 o reer rre ricer errr rrr Space Groups cel Asymmetric Cell Cell Vectors Unit Cell Super Cell space Groups Data Group number Select space group Select groups to show 141 141 amd E Extensions Origin_2 y Ok Cancel Apply now You can use the Lattice Builder dialog to create a new crystal to m
5. a document Exits SAGEMD2 2 2 2 Edit menu Onda i z Redo Ele Copy Cl E Cut Ctx Faste tie Undo Redo Copy Cut Paste Reverse previous editing operation Reverse previous undo command action Copies data from the document to the clipboard Deletes data from the document and moves it to the clipboard Pastes data from the clipboard into the document 2 2 3 View menu Parallel O Perspective w Front Ctl F O Back CUB O Lett CH L O Right CH R 2 Top Cu T O Bottom Ct K Fit Reset Ctu G oom Parallel Switch to parallel projection Perspective Switch to perspective projection Front Front view of the structure Back Back view of the structure Left Left view of the structure Right Right view of the structure Top Top view of the structure Bottom Bottom view of the structure Fit Fit to view of the structure Reset Reset all viewing parameters Zoom Zoom in on area 2 2 4 Display menu Parameters Capture window Capture Image The Display menu offers the following menu items 2 2 4 1 Parameters menu item Parameters menu item opens Display parameters dialog box 2 5 1 which allows you to build the atomic bonds and control the appearance of the OpenGL objects Note This menu item is not available 1f there are no atoms 2 2 4 2 Capture window menu item This menu item copies the SAGEMD screen onto bitmap file and opens Save image dialog box Use it to save the image into the file 10 1
6. button to build the whole unit cell The number of atoms and their positions in the unit cell depend on the space group settings see Space Group tab 2 5 2 1 31 2 5 2 4 Cell Vectors tab iw Lattice Builder Use this tab to see the unit cell vectors The edit boxes of this dialog have the read only permission To edit the unit cell vectors you can use the Cell 2 5 2 2 tab ax ay az bx by bz cx cy cz are the Cartesian components of the a b c unit cell vectors 52 2 5 2 5 Unit Cell tab w Lattice Builder Edit positions 0 x y O75 zZ 0 125 Change atom Add ator Delete atom Ok Cancel Apply now Ok cancel Apply now Unit Cell tab allows you to view and edit atom positions in the unit cell Also you can change the atom type and add atoms to or remove from the unit cell Generally you build the unit cell using the Asymmetric Cell 2 5 2 3 tab You can alternatively define the atom positions and their types using this tab In this case you do not require knowing the space group information and asymmetric cell settings The Unit Cell tab has the following data fields Atom positions fractional Displays the position and type for each atom in the unit cell To edit the atom position or type you can click on the corresponding row in this field Edit positions Allows you to modify the atom positions x y and z are the fractional coordinates of the atom Their values must be numbers fro
7. the list of the tag names is not empty 17 2 2 9 Results menu Local ROF MSD Temperature Animation Make MPEG The Results menu offers the following menu items 2 2 9 1 Local RDF menu item Use this menu item to display Local RDF dialog box 2 5 20 which allows you to calculate the radial distribution function RDF both for current structure and average result for structures that were defined with the certain time step and saved in the files In the latter case you must import any structure file by Import menu item of File 2 2 1 menu before applying Local RDF menu item It s necessary in order that the program might be able to do the proper intrinsic settings 2 2 9 2 MSD menu item This menu item allows calculating and viewing the graph of mean square displacement MSD of selected atoms versus file number This operation makes sense for variety of structures that were defined with the certain time step and saved in the files At first import one of the structure files by Import menu item of File 2 2 1 menu if you have not done it until now Then select some atoms for which you want to calculate MSD and choose MSD menu item whereupon select the required structure files in the appeared Open files dialog box The graph of MSD versus file number will appear in the MSD Graph 2 5 23 box 2 2 9 3 Temperature menu item Use this menu item to display Calculate temperature 2 5 21 dialog box that all
8. tilt grain boundaries with CSL will be displayed 2 is calculated by volume ratio of CSL elementary cell and crystal elementary cell Maximum value of this parameter 1s limited by the code and equals 49 because grain boundaries 2 gt 49 have no physical application mostly After specifying of 2 parameter and pressing Enumerate button in the field below dialog will appear list of grain boundaries designated by Miller indices and 2 value At selection of any line in this list in the field Tilt CSL vectors coordinates of CSL vectors in matrix form will be displayed in fractional and grain boundaries indices and normal indices will be displayed in the fields Plane h k 1 and Normal U V W It is necessary to choose required plane and press Build button for construction of tilt grain boundary Click Undo Build button and then select a listbox item to build another configuration Note Symmetry of selected crystal must be cubic or hexagonal otherwise the following message box will appear after attempt to calculate possible CSL 61 iw Info During choice of crystal with hexagonal symmetry SAGEMD2 code verifies ratio c a to be rational exception is rotation around axis c otherwise the following alert will appear iw Not rational direction x 62 2 5 24 2 Twist tab The Twist tab allows construction of symmetrical twist grain boundaries Lal Enumerate CSL Symmetrical tilt Twist Options Planech K I 11 Max
9. 1 2 2 4 3 Capture image menu item Use this menu item to copy any part of the SAGEMD screen to the bitmap file To do 1t hold the left mouse button and move mouse to draw the rectangle to select the part of the screen to save After releasing the mouse button the Save image dialog box will be displayed Use it to save the image into the file 2 2 5 Lattice menu Build Rebuild Delete Rebuild 4s Unit Cell Enumerate CSL Build Bicrystal 2 2 5 1 Build Rebuild menu item Use this menu item to display the Lattice Builder dialog box 2 5 2 which allows you to build or rebuild the crystal 2 2 5 2 Delete menu item Use this menu item to delete the current structure Note The command is not available if there is no structure 2 2 5 3 Rebuild as unit cell menu item Use this menu item to transform current super cell to new unit cell and set the structure space group to Pl 2 2 5 4 Enumerate CSL menu item Use this menu item to display the Enumerate SCL dialog box 2 5 24 which allows you to construct symmetrical twist and tilt grain boundaries 2 2 5 5 Create Bicrystal menu item Use this menu item to display the Build interface dialog box 2 5 25 which allows you to construct bi crystal interface 12 2 2 6 Surface menu Cleave SuUnace Add Ato super Cell Make Unit Cell 2 2 6 1 Cleave surface menu item Use this menu item to display the Cleave surface dialog box 2 5 3 which allows you to c
10. 15 22 VO AGE a toms Te MU SO aiii 15 2 sd OA atoms MIC IU Mi Ai A doi 15 22s bE INGOs ponds Chec kD NX ta dl o 15 22 LES Remove bonds checkbox lt s3d caters aiiadieact e ere ed 15 PA A anes E PA TA ested saan E A E E E 16 A C reale tas ment A 16 LS LS CICL DY tas men Ma a E a E A 16 228 5 Deselect Dy tas menu css lidia 16 220 Delete tas ment te o 16 DR INE Sid A a e 17 UA A A 17 DIED boyy MSD mente ds 17 2293 Temperature mMenu isis 17 229 ANMALA MENU E Diso ii 17 22 9 gt Make MPEG check DO ta ia AOS 18 LR LO WIRON MENU sorain ni enan EN E E ENEA EO 19 2 3 SAGEMD2 main window Toolbar ccccccsssssscccccssssssccccssssssscccccssssssccccssssssccsscsssssscosseess 20 2 4 SAGEMD2 main window Control Panel ssseccccsssecccccscecccccssecceccsseccecossecccccssecceccssecceessse 22 PADI OTA DOXES T A A E A EEE A A E E A EA 23 23 1 DISPla parameters didlo DOK anean dada ao 23 A e A senate E laa T A E E E A A A NES 24 ISA MAA O A N a ees 25 AE Ia D ear EE O E eee oe eee es 26 22 Lattice Builder dialog DOK ct o 27 Dy Space OUD taD e cateuaa dei osiece ete au otacat Roane itga lee neaineecle aceieteaen 28 ASIS E E ssc sss cis Seether eat CER teeth Sse nea fed ta Sistine EEEE 29 DIAZ AS MINCE Colts iii di 30 IAE NV ECOS Dr ir ic a 31 22 It Celta Teei mm eis E 32 LI SUPE C Oa De STE 33 215 3 Cleave s rface dialog DO T at cde aeataacdeedainerse 34 23 l Surdeco BOX ID a 35 Bt 2 CO PUONS CAD A Ue a T 36 2 54 AGG atom tO s
11. 5 7 which allows you to select the atoms by the atom type Note This menu item is not available if there are no atoms 14 2 2 7 5 Select invert menu item Use this menu item to toggle the current selection Note This menu item 1s not available 1f there are no atoms 2 2 7 6 Select by plane menu items Use this menu item to display Input plane position dialog box 2 5 9 which allows you to specify a plane to divide the structure into two parts 2 2 7 7 Show selected only menu item Use this menu item to display only the selected atoms and hide all the others Note This menu item is not available if there are no selected atoms 2 2 7 8 Show all menu item Use this menu item to cancel the Show selected only 2 2 7 7 command action and display all atoms of the structure Note This menu item is not available if Show selected only command has not been executed previously 2 2 7 9 Scale menu item Use this menu item to display Scale coordinate of atom dialog box 2 5 8 which allows you to scale the atomic coordinates of the selected atoms Note This menu item 1s not available if there are no selected atoms 2 2 7 10 Move menu item Use this menu item to display Move atoms dialog box 2 5 10 which allows you to move the selected atoms to new positions Note This menu item is not available if there are no selected atoms 2 2 7 11 Copy menu item Use this menu item to display Copy atoms dialog box 2 5 11 which allow
12. Choose units allows choosing the coordinate system in which it is necessary to show separation and positions of the atoms Clear use this button to clear the edit box of this tab Close use this button to close this dialog Torsion angles use this check box to measure the torsion angles 51 2 5 13 3 Surface distance tab The Surface distance tab allows you to measure the distance between atom and specified surface Create the surface and click atom whose separation you wish to measure The edit box of this tab will show the number of selected atoms its type and position The distance will appear in the second line M 4 type lt r x 1 6ol Y 3 900 2 JUy5 Choose units ourface distance 3 3035 amp Angstrom C Reduced C Fractional Clear Close Choose units allows you to choose the coordinate system in which it is necessary to show separation and positions of the atoms Clear use this button to clear the edit box of this tab Close use this button to close this dialog 52 2 5 14 Add atoms dialog box Path Operations menu 2 2 7 gt Add atoms menu item 2 2 7 16 The Add atoms dialog allows you to add new atoms to the structure You can specify the atomic positions and types AE Edit positions Coordinate system Cartesian Angstroms C Cartesian Reduced 3 C Fractional Change Atom Py The Add atoms dialog contains the following fields and buttons Edit positions Allows y
13. User s Manual SageMD2 Code PREFACE ici odo aae 5 1 INSTALLATION INSTRUCTIONS 00 ai 6 2 THE BASIC OPERATIONS OF SAGEMD2 MAIN WINDOW 00000 7 ZN VV MING OW sicario 7 2 2 SAGEMD2 Main window menus cccccccccccccccsccccccccscccccccccsccsccccecccecccsccccecccscccecccsccoscccceees 8 A RR A 8 A 0 MO A AS 9 22 IS VIEW MENU As 10 22 A DISPIAYy MENU sao 10 ELA ParaInerers memi ME A iio 10 ZA Capture Window Menu Ms a dial in 10 22 Capire mate ment SM eh een detonate aya a ca tabatonsetiea tudes 11 ZO Late Me arta oca 11 22 51 BUNGIE DUNG ment MEM iS het th po eee ae eet enh ou ead 11 LA LD Delete MS MA sen CTI eRe eee 11 2 Rebuild as umt col ment Mata tai 11 ld Emnumerate CSL Ment eM sides ici 11 225 0 calle Bic ys akmeni Me Mana a E 11 22O SUI ACS MeN aea A 12 ZO CASA Ve surn ace Menu Ha E dsd 12 22 02 Add atoms ment Mc ii ca 12 2200 Per Cell mention 12 2 22d OPErI tons MEN add 13 22 SEL ACEON Menu a 13 De e le Ol aN Te OO 13 Ds IEC NOMS HIS VU drid aa 13 22 Fe SEIS CE LY Pe MMe NU AS Sie teda uaa eienc erecta 13 LOS IEC Ver menu MLCT seo a ii 14 ZO SEEC EOV DIAG mentes as ale salen nice ale aca a N 14 2 2 1 SNOW Selected Only Menu Md Dis ds 14 A A sn tsa OTAI 14 ER AN AS gesesteh ors a tearsseteenink eaecsiecets raat A OA 14 DWE IOV Tile MUNG Ushuaia es eate es tect eii 14 DD dE COP MAS UE MECH ice sirens o 14 2D APA SE Pe MCU We MS AAA 14 AE DA O ee eC Rn E TA 15 2D NA CHECK latice ment Mi A ii
14. aph objects editing and has the obvious sense You may edit the graph objects in two ways For example 1f you want to edit Graph title you may click the title field on the graph or click the corresponding button In both cases Set title text dialog box will appear Set title text Input new text emperature versus File nu Cancel OK 59 2 5 24 Enumerate CSL dialog box Path Lattice menu 2 2 5 gt Enumerate CSL menu item 2 2 5 4 Symmetrical titt Twist Options Planech k I 1 10 Max sigma twin index 492 Enumerate Bormal u Y w 1 10 Mirror plane olga Tit CSL vectors You can use the Enumerate CSL dialog to construct symmetrical twist and tilt grain boundaries In order to activate this dialog a crystal must be constructed opened in the main window of visualizer Dialog consists of three tabs Symmetrical tilt tab 2 5 24 1 Twist tab 2 5 24 2 Options tab 2 5 24 3 60 2 5 24 1 Symmetrical tilt tab Tab Symmetrical tilt allows construction of symmetrical tilt grain boundaries Lal Enumerate CSL Symmetrical titt Twist Options Planech kK Ih a2 50 Max sigma twin index 494 Enumerate Bormal u Y w 1 10 Mirror plane olla Tit CSL vectors Undo Builg How Intenace The only parameter which must be specified by the user in the field Max sigma twin index for calculation of all possible tilt grain boundaries is the 2 maximum value I e up to which value list of
15. ar is displayed across the top of the application window below the menu bar The toolbar provides quick mouse access to many tools used in SAGEMD2 Click to O Create new document z Open document file Fi Save document a Save document to another file Undo G Redo e Print snapshot image de Remove selected data from the document and store it on the clipboard Copy the selection to the clipboard al Insert the contents of the clipboard into the document Switch to perspective projection sol Switch to parallel projection View structure from the front View structure from behind View structure from the left View structure from the right q E P E ii View structure from the top View structure from below i Reset view a it image to be visible 21 22 2 4 SAGEMD2 main window Control Panel Control panel Angles x o m woo oo moo Z oo m zoom colors Settings Background P Top Back P Bottom Back P T Fog T Turbo Display CFK view Low Giuality High enna eA RS Control panel is intended for controlling and setting parameters for image on the screen Control panel consists of four group boxes Angles group box allows you to rotate atomic structure relative to the axes X Y Z by input of the appropriate values of angle in degrees into corresponding fields or turning corresponding dialers and to increase decrease image
16. ated If you set atom number to be O then Rdf is calculated relative to atom which is the nearest to the geometric center of current structure and has the type selected in the dropdown list Typel Typel Allows you to choose the type of the atom relative to which Rdf is calculated If the chosen type does not agree with the type of the specified center atom an error massage will be returned Type2 Allows you to choose the type of the atoms for which Rdf is calculated Rmin A Allows you to specify the minimal distance from the center atom Rmax A Allows you to specify the maximal distance from the center atom dr A Allows you to specify distance increment Coordination numbers Check this box if you want to calculate coordinate numbers Uncheck this box if you want to calculate normalized Rdf Calculate Click this button to calculate Rdf for the input data Rdf graph will appear in the RDF Graph 2 5 23 window From files Allows you to choose list of structure files for Rdf averaging Click this button to open standard dialog box Open files Close Click this button to close this dialog 57 2 5 21 Calculate temperature dialog box Path Results menu 2 2 9 gt Temperature menu item 2 2 9 3 Calculate tem perature Type Temperature selected Calculate Cancel From files The Calculate temperature dialog box has the following fields and buttons Type Allows you to choose the type of atoms for which te
17. by input of the appropriate coefficient into Zoom field Colors group box allows you to set colors and tints of window background top and bottom of background Click the appropriate color box to display Color dialog box 2 5 22 and choose the new color using this dialog Settings group box the fog check box allows you to set fog effect on the structure Use turbo check box to rotate structure quickly Display group box contains controls for governing the appearance of the structure Use the Quality slider to control rendering quality of the OpenGL objects Sometimes high value of this parameter may result in lower performance of your computer In such case you should decrease the value of this parameter Use the check box CPK view to display atoms rendered as spheres sized to the Van der Waals VDW radii 23 2 5 Dialog boxes The most of menu items open the various dialog boxes that enable entering the input data and setting the essential parameters The dialog boxes are itemized below in this chapter All dialog boxes are included into an individual chapter for both hyperlinks and text references usability 2 5 1 Display parameters dialog box Path Display menu 2 2 4 gt Parameters menu item 2 2 4 1 Y Display Parameters atom Bona Misc Low Guality High oa OA Make same size Clase Help Use this dialog box to build the atomic bonds and to control the atom size and colors Also the dialog allows you
18. e second one c Average reducing of the both crystals vectors to average quantity In order to keep the cell volume the same after changing the crystal geometry it is necessary to check Keep Density Constant The volume will be the same because of ranging of atom coordinates along vector normal to boundary plane User can define distance in angstroms between planes of two crystals in interface area in the field Vacuum gap So the distance between two crystals will be set during bi crystal building It is necessary to click OK button after setting of all the parameters for bi crystal building in 3D window 67 2 5 25 2 Options tab Tab Options allows setting additional parameters for interface building These parameters are of the same kind as at grain boundary building Remove atoms by separation Minimum separation Angstri 15 Remove Removal method Random C Crystal C Crustal_2 Translation angstroms A E L 0 0 0 Crystal C Crustal_2 Translate Build Close Help The fields of the tab are the following Minimum separation Angstr sets value of minimum distance for atoms on the different sides of the boundary plane One atom which is closer than this distance 1s removed from each pair of atoms Removal method choice of method of removal for atoms the distance between which is less then value set in the field Minimum separation Angstroms Random atoms are removed randomly Crystal_1 atoms alwa
19. equal 0 The last action is remove atoms on both sides of interface whose separation is less then value of minimum separation fields Specify the value of separation and click Remove button You can t close the dialog if you did not click this button If you do not wish to remove atoms then you need to specify the separation value as 0 Close dialog Use Lattice gt Build Rebuild menu item to show the Lattice Builder dialog Use Super Cell tab to build super cell Export structure in cif format The symbol 1 will be added to atoms symbol for labeled atoms and nothing to others For example Sil O1 Also the file with extension tag will be created in the export directory This file is created for all export formats The line which contains means that corresponding atom labeled and 0 is not labeled
20. leave a cryStal in a specified direction to create a surface 2 2 6 2 Add atoms menu item Use this menu item to display the Add atom to surface dialog box 2 5 4 which allows you to add new atoms to the cleave surface 2 2 6 3 Super cell menu item Use this menu item to display the Make super cell dialog box 2 5 5 that allows you to build the super cell defining the size of the super cell in terms of the numbers of the unit cell in each direction of the specified surface 13 2 2 7 Operations menu select geom elect all CHA select none Shift A select type select invert A A select by plane Snow selected only SHO all oCale Hoye Copy Set type Delete Del Check lattice Add atoms Edit atoms O Add bonds CO Remove bonds The Operations menu offers the following menu items 2 2 7 1 Select geom menu item Use this menu item to open Select dialog box 2 5 6 which allows you to select the atoms using the Box 2 5 6 1 Sphere 2 5 6 2 and Cylinder 2 5 6 3 tabs of this dialog box 2 2 7 2 Select all menu item Use this menu item to select all atoms of the structure Note This menu item is not available if all atoms have already been selected 2 2 7 3 Select none menu item Use this menu item to deselect all atoms of the structure Note This menu item 1s not available if there are no selected atoms 2 2 7 4 Select type menu item Use this menu item to display Select type dialog box 2
21. lp Surtace Box tab has the next fields and buttons Miller indexes Specifies the cleave plane using the Miller indices h k and separated by spaces Top Specifies the distance from the origin to the top of the cleave slab as either e Fractional a fraction of the D spacing of the Miller family of the Cleave plane e Angstrom an absolute value in Angstroms Depth Specifies the thickness of the cleave slab either as a fraction of the D spacing or in Angstroms Components In these fields you may see the calculated directions of the generating vectors for the Cleave plane U and V Vectors length In these fields you may see the calculated length of the generating vectors for the Cleave plane U and V Angle In this field you may see the calculated angle between vectors U and V 36 2 5 3 2 Options tab 3 405 4314 6 3602 43914 10 61 90 99 1203 10 81 4314 90 99 1203 3 405 9 626 90 99 1203 4 Aen adna 40 a 1 05 Constrains Mas Length Angle Anglez 16 215 J ag 31 Set vectors Fractional Find ja closest A Angle UV po Find DR Cancel Help The main tool for choosing of surface vectors for two crystals is tab Options dialog Cleave Surface Click Generate button to generate table The table consists of four columns Length U Length V lengths of surface vectors Alpha angle between surface vectors and S area of surface cell Vectors table is generated according to limiting condition
22. lt grain boundaries Lal Enumerate CSL symmetrical tilt Twist Options Remove atoms by separation Minimum separation Angstr 15 OSO EU Removal method C 2D periodic Random Cristal_2 3D periodic C Cristal Width Fractional Distance to label atoms Angstrj 7 J M Translation angstrorns Remove atoms by separation Angstroms specifies a value of minimum distance for atoms on different sides of boundary plane One atom from each pair which is closer than this distance will be removed To remove atoms the user must specify the Removal method and press Remove button Removal method choice of removal method for atoms distance between which closer than specified in the field Remove atoms by separation Angstroms Random remove atoms randomly Crystal_1 remove atoms from crystal 1 always Crystal_2 remove atoms from crystal 2 always 2D 3D periodicity periodicity of grain boundary cell construction 2D periodic choice of 2D periodicity Thickness of crystal on both boundary sides is being specified in the field Width Angstrom in angstroms Super cell of the constructed grain boundary can be changed only in two directions lying in boundary plane Super cell size can be specified in menu Lattice gt Build Rebuild tab Super Cell 3D periodic choice of 3D periodicity Thickness of crystal on both boundary sides is being specified in the field Width Fractional Super cell
23. m 0 to 1 If you specify the other value the error message will be displayed Change Atom Allows you to modify the current atom type by selecting the new atom from the dropdown list Add Atom Use this button to add a new atom to the structure Atom type 1s specified in the Change atom box The default coordinates of the atom are x 0 y 0 z 0 Use the Edit positions boxes to modify these values Delete Atom Click this button to remove an atom from the unit cell Clear Click this button to remove all atoms from the unit cell 33 2 5 2 6 Super Cell tab bl Lattice Builder supertell datathox size in fractional units Mumber of unit cells in a direction E box size Mumber of unit cells in b direction E hox size Number of unit cells in c direction E box size Slow me tai change hos sice manually Ok Cancel Apply now The Super Cell tab allows you to create a supercell crystal from the current unit cell Also you can use this tab to rebuild the supercell You define the size of the supercell in terms of the numbers of the unit cell in each direction The fractional coordinates of the supercell are given in terms of the unit cell vectors For example the fractional coordinates of atoms in 2x2x2 supercell are within the range from O to1 9999 The atoms in the original unit cell have their coordinates within the range from 0 to 0 9999 The Super Cell tab has
24. mperature is calculated Temperature this is the field for temperature output for current structure From files Allows you to choose a list of velocity files for calculating the temperature Click this button to open standard dialog box Open files If you have chosen the list of velocity files the graph of temperature versus file index will appear in the Temperature Graph 2 5 23 window Calculate Click this button to calculate temperature for the current structure Cancel Click this button to close this dialog 2 5 22 Color dialog box 4 Color Dialog a aaa ee ee 8S eee 6 8 ee oe Cancel 58 2 5 23 Graph window All graphs obtained in Results menu 2 2 9 are outputted into Graph window MM MSD Graph MSD Graph Close A Scale Y Scale Export Save image Title Title Y Title MSD 42 Title Font A Title Font Y Title Font Close _kscale _Useele _ Export ave image te Atte ito Tte tont Tie font Y Tte font File number Graph box contains the graph field and some buttons Close Click this button to close Graph box Export Click this button to save graph data in the text file Specify the file name in the appeared Export graph data dialog box Save image Click this button to save graph image in appropriate format bmp ppm xpm gif xbm Specify the file name and type in the appeared Save image dialog box The other buttons are intended for gr
25. n the third line a8 Check lattice Check Distance Check Angles Surface distance M 4 type r x 1 Bol Y 3 900 2 Jo Choose units M 19 pes lt 9 40 Yad 1093 z 3 30393 e dx 2 0885 dy 0 4205 dz 0 0000 dr 2 1304 cla Reduced C Fractional The Check distance tab contains the following fields and buttons Choose units allows you to choose the coordinate system in which it is necessary to show separation and positions of the atoms Clear use this button to clear the edit box of this tab Close use this button to close this dialog 50 2 5 13 2 Check Angles tab The Check Angles tab allows you to measure the angles between atoms and the torsion angles Click three atoms to measure the angle between them At first you need to click the atom which is the vertex of the angle To measure the torsion angle you must check the Torsion angles check box Then click two atoms B and C whose angle you wish to measure Then click two atoms A and D which are bonded to B and C respectively In the edit box of this tab there will be the number of selected atoms their types and positions The last line will show the angle between atoms or the torsion angle bad Check lattice H 15 type 0 lt 1 6017 yeo bodo z 4 5159 Choose units NM 14 type 0 lt 7402 Y 4 0132 z 0 0000 yF Angstrom C Reduced C Fractional Clear Close Torsion angles The Check Angles tab contains the following fields and buttons
26. odify the space group number the unit cell parameters the primitive cell vectors and the box size Also using Lattice Builder dialog box you can add and remove atoms from the unit cell or change their types The Lattice Builder dialog contains the following tabs and buttons Space Groups tab 2 5 2 1 Cell tab 2 5 2 2 Asymmetric Cell tab 2 5 2 3 Cell vectors tab 2 5 2 4 Unit Cell tab 2 5 2 5 SuperCell tab 2 5 2 6 OK use this button to build or rebuild the crystal using data from the dialog tabs and to close the dialog Cancel use this button to close the dialog without building or rebuilding the crystal Apply Now the same as OK but the dialog will not be closed Help use this button for help about the active tab 28 2 5 2 1 Space Group tab wd Lattice Builder nena cen Asymmetric Cell Cell vectors Unit Ce Super Cell space Groups Data Group number select space group Select groups to show 141 5 Jiatvamd y E Extensions Origin_2 Ok Cancel Apply now The Space Groups tab allows you to specify or modify the space group and space group settings for the structure that you wish to build or rebuild The Space Groups tab has the following boxes Group number You can specify a space group number by editing this box or using the spin buttons When you change the group number the contents of the Select space group box will be changed also and vice versa Select space group allo
27. of the constructed grain boundary can be changed in all three directions Super Cell size can be specified in menu Lattice gt Build Rebuild tab Super Cell 64 Width Fractional Angstrom specifies crystal depth on both sides of the boundary If 3D periodicity is chosen parameter is specified in fractional coordinates of CSL cell if periodicity is 2D in angstroms Distance to label atoms Angstroms specifies value determining on which distance from the boundary the atoms will be labeled by tag In order to select these atoms after grain boundary construction it is necessary to enter menu Tags gt Select by Tag and choose Near interface from the list Also user can view labeled atoms by pressing Show interface button While exporting the structure in cif format the 1 symbol will be added to the the atom symbol in the _atom_site_label field for atoms near interface Translation Angstroms this field specifies translation of the atoms coordinates in three directions on both sides of the boundary Where A and B translation along the boundary C translation perpendicular to boundary plane If 2D periodicity is chosen it is impossible to specify translation C User must specify the crystal number Crystal_1 or Crystal_2 and press Translate button to translate the atoms coordinates 2 5 25 Build interface dialog box Path Lattice menu 2 2 5 gt Create Bicrystal menu item 2 2 5 5 Build interface Selec
28. oper cell f 14 Y E DK Lancel This dialog box allows you to create a super sell surface from the current unit cell Set the size of the super cell in terms of the numbers of the unit cell in each direction of surface and click OK button 38 2 5 6 Select dialog box Path Operations menu 2 2 7 gt Select geom menu item 2 2 7 1 This dialog allows you to select atoms which are inside the box sphere or cylinder Box Sphere Cylinder Input two vertex Coordinate systern Cartesian Angstroms i wT Z AAA 0 ro C Cartesian Reduced Fractional X2 Y2 z2 Apply Select Invert Select All Select None Close Help The Select dialog box contains the following tabs and buttons Box tab see 2 5 6 1 Sphere tab see 2 5 6 2 Cylinder tab see 2 5 6 3 Select invert use this button to toggle the current selection Select all use this button to select all atoms of the structure Select none use this button to deselect all atoms of the structure Close use this button to close this dialog Help use this button for help about the currently active tab 39 2 5 6 1 Box tab This tab allows you to specify the box which contains the atoms you wish to select To specify the box you need to define the coordinates of two vertices of this box These vertices are the end points of the largest diagonal of the box Box Sphere Cylinder Input two vertes coordinate system amp Carte
29. ou to modify the atom positions Coordinate system Use this field to choose the coordinate system You can choose Cartesian reduced or fractional coordinates Change Atom Allows you to modify the current atom type by selecting the new atom from the dropdown list Add Use this button to add the new atom to the structure Close Click this button to close this dialog 53 2 5 15 List and edit atom positions dialog box Path Operations menu 2 2 7 gt Edit atoms menu item 2 2 7 15 we List and edit atoms positions Atom positions Edit positions en CS e 1 AI 9 2043 i 0 0000 3 7368 Apply 3 700 0 2043 Change atom 16517 243 Fy 16517 0 40 coordinate system Cartesian Angstroms C Cartesian Reduced Fractional Add atom Delete atom Close This dialog allows you to view and edit the atomic positions and types Also it allows you to add and remove the atoms Using this dialog you can see and edit the position of individual atom in the opened document Just click on the atom in the structure image and you can see the selected line with atomic position in the Atom positions field You can edit the coordinates of the selected atom using the Edit positions boxes and change the atom type using the Change atom dropdown list Also you can select the individual atom in the Atom positions field and it will be selected in the structure image The List and edit atoms position dialog contains the following fields and but
30. ows you to calculate temperature of specified atoms For this command it s necessary to have the velocity file with extension v for current structure or files if you want to calculate temperature for a set of structures that were defined with the certain time step and saved in the files The velocity file must contain the conversion factor into m sec in the first string and the array of velocity components for all atoms of structure 2 2 9 4 Animation menu item This menu item allows you to animate structure transformation This operation makes sense for variety of structures that were defined with the certain time step and saved in the files At first import one of the structure files by Import menu item of File 2 2 1 menu if you have not done it until now Then click Animation menu item and select required structure files in appeared Open files dialog box 2 2 9 5 Make MPEG check box If you want to save MPEG formatted movies in mpg mpg file check this box then click Animation 2 2 9 4 menu item 18 2 2 10 Window menu Tile Horizontally Tile Yertically Cascade Toolbar Control panel 1 quartz Use this menu for the desired layout of windows if you are working with a few documents simultaneously Toolbar checkbox Check this box if you want to see Toolbar in Main Window Control panel checkbox Check this box 1f you want to see Control panel in Main Window 19 2 3 SAGEMD2 main window Toolbar The toolb
31. pecify how many times to repeat this operation OK Click this button to copy the selected atoms and close the dialog Cancel Click this button to close the dialog without the copying 4 2 5 12 Set type dialog box Path Operations menu 2 2 7 gt Set type menu item 2 2 7 12 Use this dialog to set the type which you assign to the selected atoms Cancel Select the atomic symbol from the dropdown list Then click OK button to set the new type to all selected atoms or click Cancel button to close the dialog without setting of a new type 48 2 5 13 Check lattice dialog box Path Operations menu 2 2 7 gt Check lattice menu item 2 2 7 14 The Check lattice dialog box allows you to measure interatomic distance angles between atoms and the torsion angles You can see the positions and interatomic distance in fractional reduced or Cartesian coordinates e Check lattice Check Distance check Angles Surface distance Choose units Angstrom C Reduced C Fractional The Check lattice dialog box contains the following tabs Check Distance tab 2 5 13 1 Check Angles tab 2 5 13 2 Surface distance tab 2 5 13 3 49 2 5 13 1 Check distance tab The Check distance tab allows you to measure the interatomic distance Click two atoms whose separation you wish to measure The edit box of this tab will show the number of selected atoms their types and positions The interatomic distance will appear i
32. planar sigma 43 5 Enumerate PMormal u Y w 11 olga 2 Angle Planar sigma Twist CoL vectors Undo Builg How Intenace User can specify indices hkl for boundary plane or indices UVW for rotation axis in the fields Plane h k 1 or Normal U V_ W accordingly for construction of symmetrical twist grain boundaries These fields are interconnected so the indices of one field are recalculated automatically after changing indices in another one The second parameter necessary for determination is specified in the field Max planar sigma Its value limits list of possible angles for construction of 3D CSL cell and determined by the density of coincident sites on the grain boundary plain After specifying of the parameters it is necessary to press Enumerate button List of possible CSL cells will appear in the left lower field of the tab The cells in this list are determined by the rotation angle around normal UVW and surface After selection of any line in this list in the field Twist CSL vectors coordinates of CSL vectors will be displayed in matrix form each column specifies CSL vector and value specifying volume ratio of CSL cell and elementary crystal cell will be displayed in the field Sigma It is necessary to press Build button for construction of required twist grain boundary 63 2 5 24 3 Options tab The Options tab allows specifying additional parameters of grain boundaries construction general for twist and ti
33. r 1 W use the same for all directions The dialog has the following boxes and buttons X scale factor Allows you to specify the factor to scale X coordinates of the selected atoms Y scale factor Allows you to specify the factor to scale Y coordinates of the selected atoms Z scale factor Allows you to specify the factor to scale Z coordinates of the selected atoms use the same for all directions Check this box to scale all the coordinate components by the same factor OK Click this button to scale the atomic coordinates and close the dialog Cancel Click this button to close the dialog without the scaling 44 2 5 9 Input plane position dialog box Path Operations menu 2 2 7 gt Select by plane menu item 2 2 7 6 This command of the SAGEMD2 code allows you to specify a plane that divides the structure into two parts One of these parts will be selected after you click the Select button of this dialog Also you can close this dialog by clicking Close button e EE The Input plane position dialog box contains three fields a b and c where you can specify the plane position in fractional coordinate system After that you can click the Select button and the selected atoms will be displayed by the main window in yellow color If you want to select another part of the structure just click Select invert menu item of the operation menu 45 2 5 10 Move atoms dialog box Path Operations menu 2 2 7 Move menu item
34. rfacedialog DOX iii de 37 29 Make superceldialog DOK id 37 2 930 ao as o A A 38 SA BOX Ger O AO 39 230 2 Sphere fa Deuie a a a a 40 LIO Ed ADe tr are tree re mn Te eee eee RT men eRe rene renee ere one haere 41 2 07 Select type dialog DOS A AA enecensorks 42 2 5 8 Scale coordinates of atoms dialOg DOX ccccoocccncnocononacononanonnonacononarononanonnonaconenaronananonos 43 2 5 9 Input plane POSITION ALOE DOK iia A AAA 44 29 LOUWIOVE atOMS ara O EDO Sos 45 2 5 11 Copy atomsdlal02 DOK id awseeeaae Radek 46 2a 2 SOUL DC AIOE DON dad 47 Za 13 Checklatticedialog DOX sii A os 48 CAMBADOS 49 201392 Encck Ano les tab aia ai aos 50 2S Sace di tance A Dies 51 2 5 24 Add atoms dialog DO ibid 52 29 15 List and edit atom positions dialog DO di ia 53 291G Create tag didlog DON ista 54 Z7 electa gala lo DO ain a a a ta 55 2 59 18 Deselect tas didlOg DO iii 55 75 19 Delete tae dialog WOK incaico ecatseete 55 25972 0 Oca RODEOS OOK ira Geese eee 56 2 3021 Calculate temperature didlo DOK ama 57 2 35 22 Color dialog DOK a A A 57 A pa lolo A o e e UA 58 29 24 EnUmerate COL CAI 2 0 OX veias 59 Ze ell yy MN CAL TIO i a AAA O O oo ot A E EE 60 a SUT eects ica 62 A e ro O EA 63 20 23 B ild nterface dialog DO noc oa 65 De IEEE SHUI GAD co dada 66 ES r IOUS 1d A a e e e oo semtaeteueedeeams aoa 67 2 5 26 Search structure dialog box SUTURA Siri 69 3 1 Consecution of actions to build the grain DOUNCATLIES ssscssccccccsssssssssss
35. s which are to be entered in the fields MaxLength maximum vector length Angell and Angel2 minimum and maximum angle between vectors In order to display vectors coordinates instead of their lengths in the table it is necessary to select click check box Fractional In order to find the cell most similar to another cell by dimensions area or angle the search by set parameters is realized in another crystal dialog It is necessary to enter vector parameters in the dialog field Find vectors closest to and click Find button The cell with the most similar parameters will be highlighted in the table The table lines are always sorted by area of surface cell this makes search of cells with similar area easier After the most similar vectors are found it is necessary to click button Set vectors You will be automatically switched to tab Surface Box from Options and initial cell will be displayed on visualizer screen Note it is recommended to keep dialogs Cleave surface open until both surfaces are built 37 2 5 4 Add atom to surface dialog box Path Surface menu 2 2 6 Add atoms menu item 2 2 6 2 Add atoms to surface H v Add atom Fractional Angstrom 7 a 4 4055 This dialog box allows you to specify the type and coordinates of the atom that you wish to add to the specified cleave surface 2 5 5 Make super cell dialog box Path Surface menu 2 2 6 gt Super cell menu item 2 2 6 3 Ca Make super cell
36. s you to copy the selected atoms to new positions Note This menu item is not available if there are no selected atoms 2 2 7 12 Set type menu item Use this menu item to display Set type dialog box 2 5 12 which allows you to set the new type to the selected atoms 15 Note This menu item is not available if there are no selected atoms 2 2 7 13 Delete menu item Use this menu item to delete the currently selected atoms Note This menu item is not available if there are no selected atoms 2 2 7 14 Check lattice menu item Use this menu item to display Check lattice dialog box 2 5 13 which allows you to measure the interatomic separation the angles between atoms and the torsion angles 2 2 7 15 Edit atoms menu item Use this menu item to display List and edit atoms position dialog box 2 5 15 which allows you to view and edit the atomic position and types Also it allows you to add and remove the atoms 2 2 7 16 Add atoms menu item Use this menu item to display Add atoms dialog box 2 5 14 which allows you to add new atoms to the structure Also you can use List and edit atoms position dialog box 2 5 15 to add atoms to the current structure 2 2 7 17 Add bonds checkbox To add the bond check this box and then click the two atoms whose bond you wish to build 2 2 7 18 Remove bonds checkbox To remove the bond check this box and then click the bond which you wish to remove 16 2 2 8 Tags menu If you in
37. sccccssssseees 69 FAQs Preface This SAGEMD2 code is useful as pre processor and post processor for atomistic simulation methods 1 e codes such as molecular dynamics MD Monte Carlo MC and quantum density functional theory DTF SAGEMD includes an efficient and easy to use graphical user interface GUI to enable various manipulations with atomic structures This GUI provides a set of tools for a user to design the material for calculation and to prepare the input for computations and analyze the computational results The User Manual provided below will help you to become familiar with this software This User Manual consists of 2 Chapters Chapter 1 explains requirements for using SAGEMD2 and describes the procedures for its installing and uninstalling Chapter 2 acquaints with software s Main Window Menus 2 1 ToolBar 2 2 Control panel 2 3 and Dialog boxes 2 4 Notations used in this Manual All names of menu items dialog boxes controls etc indicated as underlined Example Click the OK button All hyperlinks are accompanied by text references in parentheses to corresponding sections This makes the Manual easy to handle in both electronic and printed formats Example Use this menu item to display the Lattice Builder dialog box 2 5 2 which allows you to build or rebuild the crystal Warning SAGEMD is in development process now so some discrepancies may occur between User Manual contents and the c
38. sian Angstroms 1 41 ro 0 ro C Cartesian Reduced C Fractional x2 Y2 22 0 0 0 Apply Select Invert Select All Select None Close Help This tab has the following data fields X1 Y1 Z1 Allows you to specify the coordinates of the first vertex in the currently active coordinate system X2 Y2 Z2 Allows you to specify the coordinates of the second vertex in the currently active coordinate system Coordinate system Allows you to specify which coordinate system to use to define the box Apply Click this button to select the atoms which are inside the specified box 40 2 5 6 2 Sphere tab This tab allows you to specify the sphere which contains the atoms you wish to select To specify the sphere you need to define coordinates of the sphere center and the sphere radius a oa Box Sphere cylinder Input center location and radius coordinate system Cartesian Angstroms xE C Cartesian Reduced VC ae R ro NA AA NA Apply Select Invert Select All Select None Close Help This tab has the following data fields XC yc zc Allows you to specify the coordinates of the sphere center R Allows you to specify the sphere radius Coordinate system Allows you to specify which coordinate system to use to define the sphere Apply Click this button to select the atoms which are inside the specified sphere 41 2 5 6 3 Cylinder tab This tab allows you to specify
39. t structure Options Crystal_1 Crystal zroz y Unit Cell as C Crustal 1 C Crystal Average Unit Cell Parameters Gamma Mismatch 3 0413 9 073 103 14 097 vacui ge Lo W Keep Density Constant Build Close Help 65 After building of surface cells similar by geometry and dimensions user needs to open Build interface dialog in which it is necessary to choose two windows with structures built surfaces which will form bi crystal The windows are selected in drop down menus Crystal_1 and Crystal_2 It is necessary to note that window name corresponds to opened saved file Dialog consists of two tabs Select structure tab 2 5 25 1 Options tab 2 5 25 2 66 2 5 25 1 Select structure tab select structure Options Crystal_1 Crystal foe y Unit Cell as C Crustal 1 C Crystal amp Average Unit Cell Parameters Gamma Mismatch 3 0413 9 073 103 14 097 Welt Eje Lo W Keep Density Constant Build Close Help In order to provide periodical boundary conditions of obtained bi crystal 1t 1s necessary to change translation vectors and angle between them so that their values will coincide Dialog Build interface offers the following options for bi crystal building in field Unit Cell as a Crystal_1 reducing of the second crystal vectors to the dimensions of the first one b Crystal_2 reducing of the first crystal vectors to the dimensions of th
40. tend to manipulate with the certain groups of atoms it 1s convenient to assign the tag name to each group Use the commands of Tags menu for work with the groups of atoms Pate Tag select by Tag Deselect hy Tag Delete Tag The Tags menu consists of the following menu items 2 2 8 1 Create tag menu item Use this menu item to display Create tag dialog box 2 5 16 which allows you to assign the tag name and tag number to the group of selected atoms Note This menu item is available 1f some atoms are selected Use one of Select geom 2 2 7 1 Select type 2 2 7 4 or Select by plane 2 2 7 6 menu items of Operations 2 2 7 menu to select atoms A different way of atoms selecting is to click directly the necessary atoms in the current structure or holding Shift key and left key of the mouse to select a rectangle region Then all atoms in the interior of this region will be selected 2 2 8 2 Select by tag menu item Use this menu item to display Select by tag dialog box 2 5 17 which allows you to select the atoms by the tag name Note This menu item is available if the list of the tag names is not empty 2 2 8 3 Deselect by tag menu item Use this menu item to deselect atoms which were selected by Select by tag command 2 2 8 4 Delete tag menu item Use this menu item to display Delete tag dialog box 2 5 19 which allows you to delete the tag name from the list Note This menu item is available if
41. the cylinder which contains the atoms you wish to select To specify the cylinder you need to define the cylinder axis the coordinates of the cylinder base center the cylinder radius and height AO OOOO Box Sphere Cylinder coordinate system Cartesian Angstroms C Cartesian Reduced Select Invert select All Select None Close Help This tab has the following data fields Axis along z Allows you to select from dropdown list the axis along which the cylinder will be orientated XC yc zc Allows you to specify the coordinates of the cylinder base center R Allows you to specify the cylinder radius H Allows you to specify the cylinder height Coordinate system Allows you to specify which coordinate system to use to define the sphere Apply Click this button to select the atoms which are inside the specified cylinder 42 2 5 7 Select type dialog box Path Operations menu 2 2 7 gt Select type menu item 2 2 7 4 Use this dialog to select atoms by the atom type Cancel Select the atomic symbol from the dropdown list and click OK button All atoms of the selected type will be selected 43 2 5 8 Scale coordinates of atoms dialog box Path Operations menu 2 2 7 gt Scale menu item 2 2 7 9 Use this dialog to scale coordinates of the selected atoms by the factor you defined bd Scale coordinates of atoms A scale factor 1 DR Y scale factor 1 Cancel Z scale facto
42. the following fields Number of unit cells in a direction Allows you to specify the range of the supercell along a vector of the unit cell Number of unit cells in b direction Allows you to specify the range of the supercell along b vector of the unit cell Number of unit cells in c direction Allows you to specify the range of the supercell along c vector of the unit cell Box size Defines the periodic box size for MD simulation Allow me to change box size manually This option will be realized in the next SAGEMD2 version 34 2 5 3 Cleave surface dialog box Path Surface menu 2 2 6 gt Cleave surface menu item 2 2 6 1 Cleave quartz low Surface Box Options Miller indexes surface position Fractional Angstrom Top 0 D Depth 14 3 61654 Surface vectors Components 010 Vectors length a 914 Angle 30 DR Cancel Help Cleave surface dialog box has the following tabs and buttons Surface Box tab 2 5 3 1 Options tab 2 5 3 2 OK use this button to build or rebuild cleave surface using data from the dialog tabs and to close the dialog Cancel use this button to close the dialog without building or rebuilding the cleave surface 35 2 5 3 1 Surface Box tab Surface Box Options Miller indexes ourtace position Fractional Angstrom Top 1 1 Depth 14 3 61654 Suitace vectors U components 010 Vectors length a 914 Angle 90 DR Cancel He
43. to assign to the group of selected atoms By default this name is GroupN where N is number of tag name in the list but you may input your own name Tag number is the number of a tag name in the list OK Click this button to assign the tag number to selected atoms and close the dialog Cancel Click this button to close the dialog without the assigning tag number 55 2 5 17 Select tag dialog box Path Tags menu 2 2 8 gt Select by tag menu item 2 2 8 2 Lancel Use this dialog box to select atoms by the tag name Choose the tag name from dropdown list and click OK button 2 5 18 Deselect tag dialog box Path Groups Tags menu 2 2 8 gt Deselect by tag menu item 2 2 8 3 Deselect tag DK Lancel Use this dialog box to deselect atoms by the tag name Choose the tag name from dropdown list and click OK button 2 5 19 Delete tag dialog box Path Tags menu 2 2 8 gt Delete tag menu item 2 2 8 4 Group ORK Lancel Use this dialog box to delete a tag name from the list Choose the tag name from dropdown list and click OK button 56 2 5 20 Local RDF dialog box Path Results menu 2 2 9 Local RDF menu item 2 2 9 1 w Local RDF Central atom AA Riri O Calculate From files Close Coordination numbers The Local Rdf dialog box has the following fields and buttons Central atom Allows you to specify a number of an atom relative to which Rdf is calcul
44. to change the appearance of the bonds and their radii Using this dialog you can show or hide the bonds and choose the background color The Display parameters dialog has the following tabs and buttons Atom tab 2 5 1 1 Bond tab 2 5 1 2 Misc tab 2 5 1 3 Close use this button to close the dialog Help use this button for help about the currently active tab 24 2 5 1 1 Atom tab Use this tab to change the atom sizes colors and rendering quality of the OpenGL graphics v Display Parameters atom Bona Misc atom eoor se ill 0 5 Low Guality High BABA RARAS EE Make same size Clase Help To change the atom colors just click on the color you wish to change The Color dialog box 2 5 22 will be displayed Set the desired color and click Accept button to close the Color dialog To change the atom size click on the value of atomic radius in the Size column The dialog will be displayed that allows you to specify the new atomic radius Note The atomic size is in Angstrom units The default atomic radius equals its covalent radius Use the Quality slider to control rendering quality of the OpenGL objects Sometimes high value of this parameter may result in lower performance of your computer In such case you should decrease the value of this parameter Use Make same size button to make all atomic radii equal to the radius value of the currently selected atom Close use this button to close the dialog
45. tons Atom positions Displays the position and type for each atom of the current structure To see location of the atom in the structure image or to edit the atom position and type you can click on the corresponding row in this field Edit positions Allows you to modify the atom positions Note you need to click Apply button to apply your edit action Apply Use this button to change the atom position accordingly to the values in the Edit positions boxes Change atom Allows you to modify the current atom type by selecting a new atom from the dropdown list Coordinate system Use this box to choose the coordinate system You can choose Cartesian reduced or fractional coordinates Add Atom Use this button to add a new atom to the structure The atom type is specified in the Change atom box The default coordinates of the atom are x 0 y 0 z 0 Use the Edit positions boxes to modify these values Delete Atom Click this button to remove an atom from the structure Close Click this button to close this dialog 54 2 5 16 Create tag dialog box Path Tags menu 2 2 8 gt Create group Tag menu item 2 2 8 1 The Create tag dialog box allows you to assign a tag name to the group of selected atoms and to add this tag name to the list Create tags Tag name Group Tag number 1 OE Cancel The Create Tag dialog contains the following fields and buttons Tag name Use this box to input a tag name that you wish
46. urrent software s state These discrepancies will be eliminated in the next versions of the Manual 1 Installation Instructions Run sagemd2_setup exe and follow instructions on your screen 2 The Basic Operations of SAGEMD2 Main Window 2 1 Main Window After starting SAGEMD2 and opening Zircon SageMD2 file you will see window that is shown below 9 SageMD woe File Edit View Display Lattice Surface Operations Orientations Tags Tasks Results Graphs Windows Help Debs Se 6 amp 8 SS 00 RAG GARA oarvn BS A 28 Ss quartz_low Ol X amp sioz_ stishovite O X Control panel Animation m Angles x 45 320 Mo ei Y 70 018 MENTE Z 41 425 M n Zoom 0 8 Colors Settings Background M Fog Top Back M Turbo Bottom Back M Display CPK view Low Quality High N Ready Sel o Num 72 amp 2 2 SAGEMD2 main window menus 2 2 1 File menu Ci Mew CHN E Open Ct O i Save Cts Close a Save As Import Export Database Exit The File menu offers the following menu items Close Save Save As Export Import Database Print Exit Creates a new document Opens an existing document Closes an opened document Saves an opened document using the same file name Saves an opened document to a specified file name Saves an opened document to a specified file format Opens a document using a specified file format Opens Search structure dialog box Prints
47. utorials 3 1 Consecution of actions to build the grain boundaries A So ae 10 11 112 13 14 la 16 17 18 19 20 Open or import the structure Open Lattice menu and select Enumerate CSL menu item Switch to Options tab of the Enumerate CSL dialog Fill width distance to label atoms fields and select 2D or 3D periodicity Switch to Symmetrical tilt or Twist tab Fill the available fields Click Enumerate button Select required grain boundary configuration from the list and click on it If you will select the configuration with large 2 the time to build interface may be long Click on Build button The interface will be shown Rotate structure to see the interface Click Show Interface button to see the labeled atoms Click Hide Interface to hide selection If you wish to choose another configuration or change the fields on Option tab then click Undo Build Then click another configuration or change values on Option tab and click again on Build button After building interface switch to Option tab To specify translation fill the A and B fields in case of 3D periodicity or A B and C fields in case of 2D periodicity Choose side of interface to move Note the Crystal_1 1s original crystal and Crystal_2 1s the rotated in case of twist or reflected in case of tilt one Crystal_1 has fractional coordinate z from 0 5 up to 1 You can move atoms along A vector then along B or simultaneously if values A and B not
48. ws you to select the required space group from the dropdown list Note the contents of Group number box will be changed to show the number of the selected space group Select groups to show use this box to select the crystal system which space groups you wish to see in the Select space group box Note that the contents of the group number box will be restricted to show the space group numbers of the selected crystal system 29 2 5 2 2 Cell tab e Lattice ETA Cell data a E C 6 607 6 607 93 30 Angstroms alpha betta gamma 30 30 30 Degrees Crystal system Tetragonal Ok Cancel Apply now The Cell tab allows you to specify the length and relative orientation of the unit cell vectors in space The whole crystal can be built by means of translation of the unit cell along the unit cell vectors see Super Cell tab 2 5 2 6 The space group symmetry can restrict the lattice parameters to the predefined values In such cases some parameters will not be available for editing a b c The length of the unit cell vectors a b c alpha The angle between b and e vectors beta The angle between a and e vectors gamma The angle between a and b vectors Crystal system Can be one of the seven crystal systems triclinic monoclinic orthorhombic tetragonal trigonal hexagonal or cubic Some of the space groups of the trigonal crystal system can have extensions such as hexagonal or rhombohedral axes 30
49. ys removed from crystal 1 Crystal_2 atoms always removed from crystal 2 Translation Angstroms this field sets shift of the atom coordinates in three directions from the both sides of the boundary Where A and B shift along the boundary C shift perpendicular to the boundary plane 7 2 5 26 Search structure dialog box This dialog allows you to find and open structure in the SageMD2 structure database 68 Search structure Structure contains following elements si D Go Search metod Y Only this elements Formula C Structure name _ Formula Name File name Coesite SiO2_ Coesite smd Cristobalite high SiO2_ Cristobalite_h Cristobalite low SiO2_ Cristobalite_Ic Keatite SiO2_ Keatite smd Quartz high SiO2_ Quartz_high Quartz low SiO2 Quartz low Stishovite SiO2_ Stishovite srr The dialog has the following boxes and buttons Structure contains following elements Type the elements symbol separated by space to specify the chemical formula of the structure if the Formula field is checked or the structure name if the Structure name field is cheked Search method Allows you to specify the search structure method Select Formula or Structure name fields The Only this elements field is available only if Formula field is cheked Go Click this button to search structures Open Click this button to open the selected structure Close Click this button to close the dialog 69 3 T
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