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SageMD User Manual

1. crecer eese eren eerte esee seta tons seca 79 TA Viewing the results 79 8 FINAL RESULTS DOCUMENTS AND 80 9 HOW TO WORK WITH 3D 80 9 1 The rendering style size and color of the atomistic structure eese 80 9 2 Various parameters of the bonds 80 9 3 The color of the background and selected atoms 80 9 4 The style and form of the contour around the lattice The style of viewing atomic structure orthogonal or perspective 81 10 QUESTIONS AND nnn nnn nnnnn 82 A How cand select Soca MR i Rm tte me ene es sus 82 A2 How I fit the lattice image to the display screen 82 How can I see the coordinates of the 2 82 A4 How can I change the atom position and or atom 82 5 How can I measure the distance between the atoms eee 82 How can I measure the angles between the 5 2 82 A7 How can I measure the torsion angles 82 8 How can I paste the lattice image into MS Word document 83 A9 I save the lattice i
2. d uan 75 5 2 3 Selecting the spherical cylindrical or parallelepipedic 75 5 2 4 Selecting the atoms in concordance with its 75 5 2 5 Selecting the whole structure and inverting selection sees 75 5 5 6 Selecting according a plane iod eret ttr Dro vm ta Ed fax ye 76 o select fixed atoms o oem edes epe 76 5 3 Setting the parameters for the MD simulation and run simulation 76 5 4 Monitoring the simulation toto to op restare epa pa 76 5 9 Viewing tlie rn Uo xen zoe Doe eR eee Donde anch 77 6 SOURCES OF INFORMATION LIBRARIES AND DATABASES 77 6 1 Database SIFUCLUFBS iieri Dec tret erede ruo meon e toan ac apes ban seth 77 6 2 Database on potential parameters 77 7 TUTORIAL MELTING OF THE AL 77 7 1 Building of the Al crystal a eiie etit e ot Eo eere ep rb lere no erlebte M pe ERE ier e DAE OU 77 7 2 Setting the parameters for the MD simulation 78 7 2 1 Setting the potential parameters 78 7 2 2 Setting parameters for RDF and MSD calculation eee 78 7 2 3 Setting the general Parameters ues dada exo qi ec UH EAR 78 7 3 Monitoring the simulation
3. oret ema aba dat send 25 325 Add from file a 25 Operations menura a e lesan aed agi a E EA E A 26 3 2564 Select geom MENUTEN re Ic eda pai e e pd AR EEES 26 22 02 Select aliment item eoo enc o eee en d hcic e beca E 26 3 2 6 3 Select none menu so ects tee de sepe AR RUIN ER NUS 26 3 2 0 4 Select types TUTTI o oo bs acad 26 3 2 6 5 Select invert MENU PORTO 27 3 2 6 6 Select volumes menu 27 3 2 6 7 Select fixed atoms menu items 27 3 2 6 8 Select 27 3 2 6 9 Show selected only menu item uoa io peto aa d etre FER TR Rd quss 21 te etes oe th arcade Nie eos voe 27 Scale ment IE GEO rev Rec vro atate adc osos e 27 3 2 0 12 Move MENU De be s DEOR 27 3 26 13 Copy Menu i os odis d cioe rie e eb cdi We iHe dde bebo eade 27 3 256 T4 Set type men nist yen EU rale i 28 3 26 13 Delete menu ieu o fete etre DAS 28 3 2 6 16 Check lattice menu aa de RT e VER 28 3 250 TT AGG atom ment MEM sc asics utu aa del b Oii ens 28 32 018 Edit atoms menu TET 3 cord ba be tested irc RU tede 28 3 2 6 19 Add bonds menu 28 3 2 6 20 Remove bonds menu auci die i 28 32k Task Tres Lin m aus Siete OM MM blue 29 3 2 7 1 Wall potential melt Im oos Ic Reda ep a
4. 4 ceres esee eene eee ee eren eterne tasto nae 59 4 16 Set QEq parameters dialog DOX ebore sooo aao rro tono atia reu aso nno nata nba 61 4 17 Set Volumes dialog box 62 4 18 Set boundary conditions dialog 63 4 18 1 Moving wall dialog DOS cuneo 64 4 19 Shock waves dialog 65 4 20 Set parameters for run dialog box 66 4 21 Set graph title dialog 68 C RAPIT ECRIRE 69 4 22 1 Axis Scale tab iiec ette dee Oei erts a tes pir sire dao nie deis opas 70 MDD DNR IS FORMAL LAD n Erbe ea rope lade dtt 71 4223 DNO 71 4 23 Lin Dial g T 72 4 24 Pick element dialog DOK iiss scsessdasscdsiactoseccdcsesdsssduseceessasedcdedussueseadsatscecevauseduneadsvacdesusede 73 4 25 Color dialog DOK Suroso sasas 73 5 SIMULATION EXECUTING isis cess cesicesicenscesstasicevadenacenacessiavedenacesacensanvntanaennecenaes 74 S Lattice Bildino 74 5 1 1 Using SageMD Structure database 74 5 1 2 Importing crystals into SageMD from others 74 51 3 B ilding crystal ace mapa an 74 Idein eer 75 5 2 1 Selecting the individual atom 75 5 2 2 Selecting the group OP
5. Set volumes Boundary Cond Shock waves Run Reset Hard Spheres Add Fixed atoms Unfix atoms The Tasks menu offers the following menu items 3 2 7 1 Wall potential menu item Use this command to display Set potential for wall dialog box 4 13 which allows you to specify the potential parameters for the walls used in the MD simulation Note This command is not available while the MD simulation is running 3 2 7 2 Set potential menu item Use this command to display Set potential dialog box 4 14 which allows you to specify the potential and the potential parameters for the interatomic interaction for the MD simulation Note This command is not available while the MD simulation is running or there are no atoms 3 2 7 3 Ewald sum menu item Use this command to display Set Ewald sum parameters dialog box 4 15 which allows you to specify the Ewald sum parameters Note This command is not available while the MD simulation is running or there are no atoms 3 2 7 4 gEq menu item Use this command to display Set qEq parameters dialog box 4 16 which allows you to use the qEq model in the current MD simulation Note This command is not available while the MD simulation is running or there are no atoms 3 2 7 5 Set volumes menu item Use this command to display Set volumes dialog box 4 17 which allows you to select the volumes where you can calculate the thermodynamic parameters Note T
6. The nial_al_al pot file eunit 22 3000 1 000000 5 554982 0 000000E 00 7 524923E 05 7 480864E 05 7 437026E 05 7 393409E 05 7 350010E 05 7 306829E 05 7 263866E 05 7 221119 05 7 178585E 05 7 136267 05 7 094161E 05 DENS 2 3000 1 000000 5 554981 4 567510 11 4 321021E 25 4 317819 25 4 314566E 25 4 311262 25 4 307906E 25 4 304500 25 4 301044E 25 4 297538 25 4 293982 25 4 290377 25 4 286722E 25 EMBED 2 2213 0 000000 2 054483 24 8 057838 14 5 634532E 02 5 423222E 02 4 451216E 02 3 138738E 02 1 632606E 02 1 056015E 01 1 718979E 02 3 505433E 02 5 344154E 02 7 225567E 02 9 142900E 02 Note that nial_ni_al pot file contains only the pair interaction table The other examples of the EAM potentials you can find in the EAM subdirectory of the SageMD installation directory 3 The Basic Operations of SageMD Window 3 1 Starting SageMD Main Window Click the Start button move the mouse pointer sequentially to Programs then to SageMD and click SageMD SageMD will start and the SageMD main window will be displayed lt AL File Edt View Display Latice Operations Tasks Results Graph Window Help Da se Boo 5 lt 882 88 lt For Help press F1 _ Alternative method from My Computer or Windows Explorer double click SageMD icon 3 2 SageMD main window menus 3 2 1 File menu New Open Close Save Save 45 Ctrl N
7. reo Red m Define Custom Colors gt gt ColorlSolid Lum 0 Blue 0 Add to Custom Colors 5 Simulation Executing 5 1 Lattice Building SageMD is a powerful tool for crystal building Using the different visualization tech niques available in SageMD you can create high quality graphics that can be easily pasted into other windows based software programs or saved as bitmaps The next sections describe several ways of the crystal building in SageMD code 5 1 1 Using the SageMD structure database SageMD has the structure database that contains many different types of structures You can open the desired structure using the File menu 3 2 1 or by pressing the button on the toolbar A standard Open dialog box is displayed on the screen Locate the SageMD templates directory usually Program Files SageMD Template Open needed subdirectory select the vnd file and click the Open button The structure will be displayed on your screen Select Create 3 2 5 1 from Lattice menu 3 2 5 and use Super Cell Tab 4 2 6 in Lattice builder dia log box 4 2 to rebuild crystal 5 1 2 Importing crystals into SageMD from others applications You can import the files with format different from SageMD Just open the File menu 3 2 1 and click on Import item to display on the screen a standard Open dialog box Choose the required file format from the dropdown list in the bottom of dialog select the
8. of j 3l 21 1 lo rj where U is the minimum value of the potential represents the interatomic distance when U U and are additional potential parameters derived from theory or experiment Parameters for pair potentials are often derived by fitting the calculated lattice energy at zero temperature to the crystal sublimation energy and by optimizing unit cell parameters and compressibility so they follow experimental data The constant temperature metal compression curves are also used for parameter fitting in the pairwise potentials Currently the interatomic potential parameters for 26 metals representing different types of crystal lattices body centered face centered hexagonal closed packed are incorporated in the code Several different properties of metals are quite well reproduced by us ing these pair potentials as shown in the recent contributions coming from our group 24 To better represent Coulomb interatomic interactions the use of variable atomic charges reflecting changing atom configurations has been suggested The values of charges are com puted with the charge equilibration QEq method and the short term interactions are approxi mated by the two particle Morse potential This approach was successfully applied to the simula tion of the structure and properties of silicon oxide with four quartz and six stishovite coordi nated silicon amorphous silicon oxide an
9. Cartesian Angstoms C Cartesian Reduced Fractional Change Atom Si Close The Add atoms dialog contains the following fields and buttons Edit positions Allows you to modify the atom positions Coordinate system Use this field to choose the coordinate system You can choose Carte sian reduced or fractional coordinate Note the reduced factor equals to the length of a vector of the unit cell 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 system 4 12 List edit atoms position dialog box Path Operations menu 3 2 6 gt Edit atoms menu item 3 2 6 16 List and edit atoms position Atom positions Edit positions N 0 48078 s AE TBS 0 48078 PES anes b 02641 081382 044983 Ap 073559 0 58541 021583 0 84982 026441 0 550167 0 41459 015018 0 9835 v 2 3 4 5 7 8 9 lt Coordinate System Cartesian Angstoms Cartesian Reduced Fractional Add tom Delete Atom Close This dialog allows you to view and edit the atomic position 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 pos
10. stance mass 4 g mole C dia 1 544 12 011 0 187 mond Al 2 863 26 981 6 72 107 Cu 2 556 63 546 4 91 107 W 2 741 183 85 2 69 107 Ar 3 418 39 948 4 63 107 N2 3 749 28 013 5 034 107 2 968 2 016 0 237 Table 1 Numerical values of relation of the de Broglie wave length to the typical intera tomic distance As be seen from the results given in Table 1 the expression 2 a lt lt 1 is satisfied for metals At the room and higher temperatures this condition is also satisfied for many gases The trajectories and velocities of particles calculated by solving equations 3 provide in formation about the thermodynamic and kinetic properties of a substance The thermodynamic parameters of a substance macroscopic parameters in the classical statistical physics are deter mined from mean ensemble values of the respective dynamic functions 4 Symbol denotes the ensemble averaging for the dynamic function A q p with respect to coordi obser nates and momenta The ergodic hypothesis is used to calculate from the velocities and obser trajectories A lim v r r z dv E 8 2 2 2 Approaches to numerical solution of the equations of motion There are several established methods for numerical solution of equations of motion in mo lecular dynamics We will describe the ones implemented in the SAGE MD code One of the early methods for numerical solution of the equations of motion in MD
11. x 2 Global stress Temperature versus time Radial distribution function file allbox3 Sx E Z PRESSURE STRESS 15 20 25 30 35 340 time total potential kinetic 8 Final Results Documents and Files Excuse it s not ready now 9 How to work with 3D graphics You can always change the display style of a current structure Using the options of the Display parameters dialog you can control several stylistic features of the structures displayed in the main window of the SageMD code Some of the characteristics you control in the Display parameters dialog are The rendering style size and color of the atomistic structure Various parameters of the bonds building The color of the background and selected atoms The style and form of the contour around the lattice The style of viewing atomic structure orthogonal or perspective 9 1 The rendering style size and color of the atomistic structure The Atom tab 4 1 1 of the Display parameters dialog box 4 1 controls the graphical rep resentation of atoms Here you can change the atomic sizes colors and the quality of the render ing of the OpenGL graphics Fore example to change the atoms colors just click on the color you want to change The Color dialog box 4 25 will be displayed Pick the desired color and click OK button to close the Color dialog box All the structur
12. However you need to correct the path to al pot file In this tutorial the path is E Program Files SageMD EAM al pot If during installation you choose the default path then you need only to change the drive letter Save the project file in the new directory before you start the simulation All output files will be created in the directory where you saved the project file 7 1 Building of the Al crystal Double click the SageMd icon on your desktop Select Open from the File menu 3 2 1 The Open file dialog will be displayed Locate the SageMD templates directory Usually Program Files SageMD Template Open the elements subdirectory select the Al vnd file and click the Open button The unit cell of the Al structure will be displayed Click the Bl icon on the toolbar The Lattice builder dialog box 4 2 will be displayed Click the SuperCell tab 4 2 6 Make the number of unit cell in all directions equals 5 and click the OK button From the File menu 3 2 1 select the Save as menu item The Save as dialog will be dis played Use it to save your work It is recommended you save the file in new directory because of all input and output files will be located here 7 2 Setting the parameters for the MD simulation 7 2 1 Setting the potential parameters From the Tasks menu 3 2 7 select the Set potential menu item 3 2 7 2 The Set potential dialog box 4 14 will be displayed From the Potential dropdown list se
13. where At is the integration time step z is the relaxation time is the pressure to be main tained constant P is the current pressure value in the ensemble of particles and B is the compres sion bulk modulus The value of the bulk modulus B need not be precisely equal to the real value In SageMD this method is extended to account for the anisotropic case The size of MD box can be therefore changed independently in three directions and in general case the three components of the pressure tensor Pxx Pyy are specified instead of pressure of the scalar In this case Po Py Pyy P22 3 2 3 Interatomic Potentials 2 3 1 Pair Potentials The choice and derivation of interatomic potential parameters is a central problem in mo lecular dynamic simulation The non empirical intermolecular and interatomic interaction poten tials can be developed from the quantum mechanical theory The interatomic interaction is de termined by the solution of the Schr dinger equation for a system of interacting nuclei and elec trons For the multi particle system the Schr dinger equation can only be solved approximately Important simplification is achieved by separating electronic and nuclear motions via adiabatic approximation The approximate solution of the Schr dinger equation provides the adiabatic potential for nuclei This potential is often sufficiently accurate and yields quality values for properties expressing interaction between a
14. 1 512460 02 1 504188e 02 1 495960e 02 1 487778 02 1 479640e 02 1 471547e 02 1 463498e 02 DENS 1 3000 1 5 7000 5 041442e 01 5 025043e 01 5 008697e 01 4 992404 01 4 976164e 01 4 959977e 01 4 943842 01 4 927760e 01 4 91173 1e 01 EMBED 1 400 0 40 0 000000 0 090532 0 179980 Lines beginning with the sign are comments and must be placed at the beginning of the file The eunit command sets energy units for the potential It can be eV K and erg If this command do not present in the file the energy units are eV PAIR typel type2 table size distancel distance2 The pair PAIR command identifies the table below as pair potential function The typel and type2 are the atom types involved in the interaction The table_size is the number of points in the pair potential tables The distancel and distance2 define the distance range in the angstrom units The distance2 is the cutoff radius for the potential In the example above the pair table has distances from to 5 7 angstroms The first value in the pair table corresponds the 1 angstrom of atoms separation The last value corresponds the cutoff distance 5 7 angstroms After the pair line is the pair potential table The number of values in the table must match the number specified in the pair line The values must be separated by spaces or the new line characters DENS type table size distancel distance2 The DENS or dens command identifies th
15. Ctri o Ctrl 5 Export Import ConvToUnix Print Print Preview Print Setup Ctrl P Recent Files Exit The File menu offers the following commands New Open Close Save Save As Export Import ConvToUnix Print Print Preview 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 Converts a WIN DOS text file to a Unix text file format Prints a document Displays the document on the screen as it would appear printed Selects a printer and printer connection Exits SageMD Print Setup Exit 3 2 2 Edit menu Undo Ctrl Cut Ctrl C Paste Ctrl Capture window Capture image Capture image to file The Edit menu offers the following commands Undo Reverse previous editing operation Redo Reverse previous undo command action Cut Deletes data from the document and moves it to the clipboard Copy Copies data from the document to the clipboard Paste Pastes data from the clipboard into the document Capture window Copies the SageMD screen onto the clipboard After that you can paste the image into the documents of the other applications Capture image Copies the any part of the SageMD screen to the clipboard T
16. Note This command is not available if the new document has not been saved yet Shortcuts Toolbar A 3 2 7 10 Add fixed atoms menu item This command allows to freeze the group of the selected atoms in the current MD simu lation The coordinates of these atoms will not be changed during the whole simulation To fix atoms you must select wanted group of atoms and click once on this menu item Note This command is not available if no atoms were selected 3 2 7 11 Unfix atoms menu item This command allows to unfreeze all atoms which were fixed by Add fixed atoms 3 2 7 10 command Note This command is not available if no atoms were fixed 3 2 8 Results menu Lentview Graph Adf Graph Msd Graph Temp Graph Energy Graph Stess Graph Stress vol Graph temp vol Graph Velocity Graph Lattice The Results menu offers the following commands Lentview Use this command to display the Lentview program s dialog which allows you to view the changes of the structure during simulation process This command is available only after simula tion is done Graph Rdf Allows viewing the radial distribution function RDF graph of the selected volume This graph is not available if before simulation any volume was not selected Graph Msd Allows viewing the mean square deviation MSD function graph of the selected volume This graph is not available if before simulation any volume was not selected Graph Temp Allows viewin
17. Path Tasks menu 3 2 7 gt Wall potential menu item 3 2 7 1 The Set potential for wall dialog allow you to specify the parameters of the Morse potential U r u exp 2 Alfa r R0 2 exp Alfa r R0 on the box walls Set potential for wall potential parameters U ev UES Alfa 1 4 1 062 RO amp 321 Cutoff 22 Cancel The Set potential for wall dialog contains the following fields and buttons U Allows you to specify the deep of the potential pit Alfa Allows you to specify the hardness parameter of the Morse potential RO The distance r to the point where the potential has the minimum value U r u Cutoff Allows you to specify the cutoff radius as the fraction of the RO The real cutoff ra dius Angstrom is cutoff RO OK Click this button to set potential parameters for wall and close the dialog Cancel Click this button to close the dialog without saving the wall potential parameters 4 14 Set potential dialog box Path Tasks menu 3 2 7 gt Set potential menu item 3 2 7 2 The Set potential dialog allows you to specify the potentials of the interatomic interactions Set potential Set interaction between atom types Between types Potential Si and Si Morse Properties Cancel Help The Set potential dialog contains the following fields and buttons Between types Allows you to choose two atoms types between which you want to specify the interatomic pot
18. The dialog has the following fields and buttons Walls offset from boundaries Allows you to specify distance between the crystal edge and the potential wall in reduced units Use the left box to specify the distance from the edge which is the near coordinate system origin Use the right box to specify parameters for the opposite edge of the crystal The negative values mean that the potential wall was moved in the negative direction of the coordinate axe from the crystal edge You specify offset in the reduced units Walls velocity Allows you to specify the value and direction of the wall velocity Use this feature to model the crystal tension or compression Free surface Check the box or boxes to model the free surface or surfaces of the crystal Use for restart only Check this box to set wall positions and velocities between restarts of the MD simulation By default the wall positions and velocities between restarts keep values from previous MD simulation OK Use this button to apply your changes and close the dialog Cancel Use this button to discard your changes and close the dialog 4 19 Shock waves dialog box Path Tasks menu 3 2 7 gt Shock waves menu item 3 2 7 7 Use this dialog box to simulate the propagation of the shock waves in the structure or when you need abruptly to set the new value and direction of the selected atoms velocity the bom barding processes The initial velocity value is applied at the beginning t
19. atoms bonds change bonds radius show or hide the bonds image Display parameters Atom Bond Misc Build bonds min factor max factor ps f Bond radius 0 4 H Display bonds as cylinder Show bonds Auto rebuild This tab has the following boxes and buttons Build bonds group box allows you to create bonds between two atoms if the following cri teria is met min factor covalent radiuses sum lt distance lt max factor covalent radiuses sum where distance distance between the two atoms forming the bond To build the bonds click the Build button If no bonds are shown try another values of the min and max factors Display bonds as cylinder Check this box to display the bonds as a cylinder Uncheck this box to display the bonds as a cone Note If the atoms forming the bond have the same size the bonds will be displayed as a cylinder in both cases Bond radius Allows you to specify the bond radius as a fraction of the radius of the atoms forming the bond If these atoms have different radiuses the minimal radius will be used to dis play the bond thickness The bond radiuses are in 0 1 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 bonds manually How to add or remove bonds manually see Add bonds 3 2 6 19 and Remove bonds 3 2 6 20 menu items Close use this button to close the dialog Help use this button
20. energy of atom i embedded in the environment with the electron density created by the electrons of all other atoms of the system and considered to be additive eG 36 j i p r is the density of electrons in the atom at the distance r from the nucleus The function p r for the given element is derived either from quantum chemical calculations or from empirical information Functions 1 and F p are selected such as to obtain agree ment of calculated values with experimental data for a crystal lattice constant elastic constants sublimation energy and the vacancy formation energy The following functional form of F p is universally used for all metals 37 It allows to interpret the o r as an overlap integral of wave functions of atoms i and j The embedded atom method is successfully used to study structures of metals and alloys as well as investigation of crystal lattice defects surface structures etc The EAM method in SAGE MD was extended for 23 elements 2 3 3 EAM potential file format The example of the EAM potential file is shown below This format is similar to one used XMD code http www ims uconn edu centers simul xmd Johnson s potential for Au cutoff 5 700 A Time step determined for fcc Au 200K Chantrenne DTIME 1 28e 14 s Z Lattice constant 4 08 A eunit eV PAIR 1 1 3000 1 5 7000 1 529143e 02 1 520779 02
21. file and press Open button The crystal will be displayed in the SageMD main window 5 1 3 Building crystal from scratch There is the consecution of action for building alpha quartz crystal SiOz from scratch 1 Start SageMD 2 Select New from the File 3 2 1 menu 3 Select the and then Create 3 2 5 1 menu item of Lattice 3 2 5 menu The Lattice Builder dialog 4 2 will be displayed 4 Under group number enter 154 Make sure that P3221 is displayed in the Select space group combo box 5 Click Cell tab 4 2 2 Enter 4 914 and 5 405 6 Click the Asymmetric Cell tab 4 2 3 Click the Clear button and then the Add Atom button The Pick element 4 24 dialog box will be displayed 7 Click the Si button then OK 8 In the Edit positions group box on Asymmetric Cell tab 4 2 3 enter the values 0 4699 0 7 0 6666667 9 Click the Add atom button choose and click OK 10 Enter the position of O atom x 0 4141 y 0 2681 and z 0 7854 11 Click the Build unit cell button on Asymmetric Cell tab 4 2 3 and then the Unit Cell tab 4 2 5 on Lattice Builder dialog 4 2 Make sure that the full unit cell contains 9 atoms 12 Click the Apply Now button and move the dialog to a screen corner Use the left mouse button to rotate the lattice and right mouse button to move it 13 Click the SuperCell tab 4 2 6 on Lattice Builder dialog 4 2 Make the number cell in all directions equal to 2 Click th
22. lattice image into MS Word document From the Edit menu 3 2 2 select the Capture image menu item Hold the left mouse button and move mouse to draw rectangle around the lattice After releasing the mouse button the lattice image will be copied to the clipboard After that you can paste the image in such applications as Word Power Point Excel Paint using Paste command from Edit menu of this applications A9 Can I save the lattice image in the file Yes you can save the lattice image as the bitmap bmp file From the Edit menu 3 2 2 select the Capture image to file menu item Hold the left mouse button and move mouse to draw rectangle around the lattice After releasing the mouse button the Save as dialog box will be displayed Use this dialog to save the image A10 Can I print the lattice image No you cannot This feature will be implemented soon However you can paste the lattice image in the MS Word document and print it 11 How can I change the atoms colors From the Display menu 3 2 4 select the Parameters menu item 3 2 4 1 The Atom tab 4 1 1 of the Display parameters dialog box 4 1 will be displayed Click on the color you wish to change The Color dialog box 4 25 will be displayed Choose color and click OK button A12 How can I change the atoms sizes From the Display menu 3 2 4 select the Parameters menu item 3 2 4 1 The Atom tab 4 1 1 of the Display parameters
23. open this dialog double click on the desired title Axis dialog box 4 22 Allows to change axis properties To open this dialog double click on the desired axis Line dialog box 4 23 Allows to change graph line style To open this dialog double click on the desired line To copy the graphs data to the MS Excel activate the graph window and use Ctrl C key board shortcut Start MS Excel and use Ctrl V shortcut to paste the graph data on MS Excel sheet To paste the graph to MS Word use Paste special command from the Edit menu of this application 3 2 9 Graph menu Temperature Volumes temp The Graph menu offers the following commands Temperature Allows viewing the Temperature graph Volumes Temp Allows viewing the temperature graph of the selected volume The all aforesaid in the preview section about manipulating with graphical data and setting graph s properties is correctly for this graphs 3 3 SageMD main window Toolbar The toolbar is displayed across the top of the application window below the menu bar The toolbar provides quick mouse access to many tools used in SageMD To hide or display the Toolbar choose Toolbar from the View menu ALT V T ClickTo 5 Open new document Open an existing document SageMD displays the Open dialog box in which you can locate and open the desired file x Save the active document or template with its current name If you have n
24. this button to remove all the atoms from the asymmetric cell Build unit cell Click this button to build the full unit cell The number of atoms and their positions in the unit cell depend on the space group settings see Space Group tab 4 2 1 4 2 4 Cell vectors tab Lattice Builder Space Groups Cell Asymmetric Cell Cell vectors Unit SuperCell Unit cell vectors angstoms Ax 4 2521847 2 4550000 Az 0 0000000 0 0000000 By 4 9100000 Bz 0 0000000 Cx 0 000000 0 0000000 Cz 5 4020000 OK Cancel Apply New Add to existing 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 4 2 2 tab ax ay az bx by bz cx cy cz are the Cartesian components of the a b c unit cell vec tors 4 2 5 Unit cell tab Lattice Builder Space Groups Cell Asymmetric Cell vectors Unit SuperCel Atom positions fractional Edit positions x Y ENSE 0 48078 0 48078 0 0 51922 0 0 666667 DAN n 0 51922 0 33333 0 0 15018 0 41459 0 1165 0 58541 073559 0 793167 0 26441 084982 044983 073559 058541 02168323 Change Atom al si Add Atom Delete Atom Clear 1 2 3 4 5 7 lt OK Cancel Apply New Addto existing Unit Cell tab allows you to v
25. to display this page 4 1 3 Misc tab Use this tab to change various miscellaneous parameters Display parameters Atom Bend Misc Colors Background Selected atoms Projection Contour C Hide Unit cell lattice C Perspective This tab has the following boxes and buttons Colors group box allows you to change the window background color and color which is used to display the selected atoms Just click the appropriate color box to display Color dialog box 4 25 and choose the new color using this dialog Projections Use this radio button to switch between orthogonal and perspective projec tions Contour Allows you to specify how the contour around the crystal will be displayed Se lect 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 4 2 Lattice Builder dialog box Path Lattice menu 3 2 5 Create menu item 3 2 5 1 Lattice Builder Space Groups Cel Asymmetric Cell Cell vectors Unit Cell SuperCell group number Select space group Select groups to show 8 Y Extensions Other Names Monoclinic c2 Em Orthorhombic OK Apply Now Help New Add to existing You can use the Lattice Builder dialog to create new crystal to mo
26. units Number of unit cells in a directions box size Number of unit cells in b directions 2 box size Number of units cells in directions 2 box size Allow me to change box size manually OK Cancel Apply Now Help New Add to existing The SuperCell 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 in terms of the unit cell vectors For example the fractional coordinates of atoms in 2x2x2 supercell are in 0 1 9999 range The atoms in the original unit cell have their coordinates in 0 0 9999 range The SuperCell tab has the following fields Number of unit cell in a direction Allows you to specify the range of the supercell along the vector of the unit cell Number of unit cell in b direction Allows you to specify the range of the supercell along the b vector of the unit cell Number of unit cell in c direction Allows you to specify the range of the supercell along the c vector of the unit cell Box size Defines the periodic box size for MD simulation Allow to change box size manually By default the box size coincide with the corre sponding values in the left box Check this box to define the box size manually 4 3 Select geom dialog box Path Operatio
27. 0 1d a h cos Tersoff potential works for a wider range of modeling needs than the potential introduced earlier by Stillinger and Weber This does not however come without a price Tersoff potential is difficult to parameterize in the complex angular part and generally suffers from the large num ber of empirical parameters needed The table below lists two sets of potential parameters for Si as suggested by Tersoff version A provides a better description of surface properties while ver sion B models better elastic properties Table 2 Numerical values of the Tersoff potential parameters Si A Si B A eV 3 2647x10 1 8308x10 B eV 9 5373 10 4 7118x10 0 afa 3 2394 2 4799 0 n 1 3258 1 7322 a 0 0 0 0 B 3 3675 10 1 0999x 10 6 n 2 2956x10 4 8381 1 0039x10 d 2 0417 1 6218x10 SOR 5 9826x10 0 ala 1 3258 1 7322 4 3 0 2 85 0 2 0 15 SageMD also incorporates the modifications of the Stillinger Weber potential as suggested by Watanabe et al These are used to model properties of silicon silicon oxide and the inter face between these materials These potential parameters were obtained from quantum chemical calculations In the embedded atom method EAM total energy is represented as follows FQ 35 i gt j where is the pair interatomic interaction energy F p is the
28. 2786 y 1 06849 2 6 57333 dx 1 12432 dy 0 974119 dz 0 629333 dr 1 61526 f Angstrem Reduced Fractional Press shift key to select atoms Release shift key to rotate The Check lattice dialog box contains the following tabs Check Distance tab 4 11 1 Check Angels tab 4 11 2 4 10 1 Check distance tab The Check distance tab allows you to measure the atoms separation Hold the shift key and click the two atoms whose separation you wish to measure In the edit box of this tab will be shown up the number of selected atoms its types and positions In the third line will be appeared the atoms separation Check lattice Check Distance Check Angles 48 type Si 4 25218 0 0943702 2 7 20266 Choose units N 43 type 0 3 12796 1 06849 2 6 57333 dx 1 12432 dy 0 974119 42 0 629333 dr 1 61526 Angstrem Reduced Fractional Press shift key to select atoms Release shift key to rotate The Check distance tab contains the following fields and buttons Chose units allow you to choose the coordinate system in which the atoms separation and positions will be shown Clear use this button to clear the edit box of this tab Close use this button to close this dialog 4 10 2 Check angles tab The Check Angles tab allows you to measure the angles between atoms and the torsion an gles Hold the shift key and click the three atoms to measure the ang
29. Alfa KMAX KMAY KMAZ This button is visible only if use Ewald sum box was checked Edit Charges field Allows you to choose the atom type and specify its charges Cutoff Allows you to specify the real space cutoff forces Radius of long range correction Alfa Allows you to specify the Ewald convergence parameter Alfa KMAY KMAZ Allows you to specify the Ewald sum parameters that effectively define the range of the reciprocal space sum one for each of the three axis directions There are three variables that control the accuracy the Ewald summation they are Alfa the Ewald convergence parameter Cutoff the real space forces cutoff and the KMAX Y Z inte gers that effectively define the range of the reciprocal space sum one integer for each of the three axis directions These variables are not independent and it is usual to regard one of them as pre determined and adjust the other two accordingly The Ewald sum splits the electrostatic sum for the infinite periodic system into a damped real space sum and a reciprocal space sum The rate of convergence of both sums is governed by Alfa Evaluation of the real space sum is truncated at r Cutoff so it is important that Alfa be chosen so that contributions to the real space sum are negligible for terms with r gt Cutoff The recommended value for Alfa is 3 2 Cutoff or greater too large a value will make the reciprocal space sum very slowly convergent The opti mum values for KMAX are
30. MD Chapter 3 acquaints with soft ware s Main Window Menus and ToolBar The base dialog boxes itemize in Chapter 4 Chapter 5 explains how to prepare and execute molecular dynamic simulations with SageMD Chapter 6 tells about libraries and databases used for prepare input data for MD simulation The MD simu lation of Al crystal melting is shown for example in Chapter 7 Chapter 8 describes the result files and documents Chapter 9 explains how to work with 3D graphics Chapter 10 answers the most possible user questions The list of used literature is shown in References Notations used in this Manual All names of menu items dialog boxes controls etc denotes as underlined Example Click the OK button All hyperlinks are accompanied by text references in parentheses to corresponding sec tion It makes this document convenient for work in both electronic and printed version Example Use Set potential 4 14 dialog to set interatomic potential for atoms Warning SageMD development is going on now so some discrepancies between User Manual text and today software s state may take place These discrepancies will have been eliminated in the next visions of the Manual 1 Installation and hardware requirements 1 1 Minimum requirements Computer Intel Pentium or compatible Memory 128 MB RAM Screen resolution 800x600 Color performance 16 bit 65536 colors Operating system Windows 98 Windows Me Windows NT 4 0
31. SageMD User Manual Display parameters Atom Bond Misc Low Quality High size Select Check lattice Box Sphere Cylinder Check Distance Check Angles Input two vertex Coordinate System C Cartesian Angstoms 1 Y1 21 N 60 x 1 12432 8 43349 z 7 832 Choose units 0 0 0 i N 57 type Si y 7 45937 2 7 20268 umi N 58 type 0 0 638593 57635 2 6 03133 ngs Angle 34 8611 2 Y2 z2 C Reduced NN po Fractional Clear Close Torsion angles Press shift key to select atoms Release shift key to rotate Fractional Select Invert Select All Select None Close Help Display program information version number and copyright Sel 3 72 Version 0 9 ALPHA 2000 2003 7 1 INSTALLATION AND HARDWARE REQUIREMENTS 8 1 1 Minimum requirements 8 1 2 WS tal ee 8 1 3 8 2 MAINFRAME PROBLEMS AND METHODS IMPLEMENTED IN 9 2 1 About Prog AM 24 5c0sjuossessonssseasisncouasssoniosvansvossasnsgusedensssssaloobervuccguwosessossnvdeaceuatelesdeseceucseds 9 2 2 Molecular Dynamics Some of the theory eee eee ee eee eres ee eren eee netto nate 10 2 2 1 Principles of MD simulation s o
32. TRL A 3 2 6 3 Select none menu item Use this command to deselect all atoms of the structure Note This command is not available if there are no the selected atoms Shortcuts Toolbar 991 keys SHIFT A 3 2 6 4 Select type menu item Use this command to display Select type dialog box 4 4 which allows you to select the atoms by the atom type Note This command 15 not available if there are no atoms 3 2 6 5 Select invert menu item Use this command to toggle the current selection Note This command is not available if there are no atoms sj Shortcuts Toolbar 99 keys ALT A 3 2 6 6 Select volumes menu item Use this command to select all volumes which have been defined using Set volumes dialog box 4 17 Note This command is not available if no volumes are defined 3 2 6 7 Select fixed atoms menu items This command allows to select the atoms that were fixed by Add fixed atoms menu item 3 2 7 10 in the Task menu 3 2 7 These atoms will be selected by yellow color Note This command is not available if the fixed atoms were not added 3 2 6 8 Select by plane menu items Use this command to display Select by plane dialog box 4 5 allowing to specify a plane that divide the structure into two parts 3 2 6 9 Show selected only menu item Use this command to display only the selected atoms and hide all other Note This command is not available if there are not the selected atoms 3 2 6 10 Sh
33. Windows 2000 Professional Windows XP 1 2 Installation Locate the sagemd exe file and run it Follow the instructions on your screen 1 3 Uninstalling Click the Start button select Settings then Control Panel The Control panel will be displayed Click the Add Remove Programs icon Locate SageMD in the application list and click it SageMD will be removed from your system 2 Mainframe problems and methods implemented in SageMD 2 1 About program Molecular dynamics MD is widely used to study materials structure and properties based on the microscopic atomic scale models The range of possible applications for MD simulation is very broad and is constantly growing with the advances in computer power and accessibility Beside classical monographs see for example refs that describe in detail the theoretical and algorithmic foundations of MD there exist numerous applications and computer codes see for example refs The advent of massively parallel computers immensely expanded the range of possible applications of MD It is currently feasible to study ensembles of 107 10 at oms simple molecules with the MD approaches SageMD is specifically targeted at modeling materials with the wide range of chemical bonding situations including metallic covalent and ionic bonds The goal was to make SageMD a multipurpose flexible and user friendly package easy to use in a typical computing environ ment The major part o
34. al or perspective These two characteristics can be also controlled from the Misk tab 4 1 3 of the Display parameters dialog box 4 1 Just choose wanted projection in the projection field Depending on you choice the projec tion will be orthogonal or perspective Also you can 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 10 Questions and Answers A1 How can I select atoms Hold shift key and click atoms to select Hold ctrl key and the left mouse button Move mouse to draw rectangle around atoms to select From the Operation menu 3 2 6 select the Select geom 3 2 6 1 menu item From the Operation menu 3 2 6 select the Select type menu item 3 2 6 4 To select all atoms use the ctrl A keyboard shortcut A2 How can I fit the lattice image to the display screen Press the spacebar A3 How can I see the coordinates of the atoms From the Operation menu 3 2 6 select the Edit atoms menu item 3 2 6 18 to display the List and edit atom position dialog box 4 12 Select the atom whose position you wish to see The atom coordinates will be displayed in the Edit position group box A4 How can I change the atom position and or atom type From the Operation menu 3 2 6 select the Edit atoms menu item 3 2 6 18 to display the L
35. ba e baba e o ito edens 29 27 2 Set potential eai esi Sodio ena dunt 29 3 2 7 3 Ewald sum menu item so ed ier est n reprae 29 3 241 PIED 29 302 1 5 Set yolumes MENU Item ec eec aei 29 3 2 7 6 Boundary cond menu ue o lt a Secus etes 29 3 2 7 7 Shock waves menu en ce 30 3 2 S R n ment items ee Abr eb ob en rior tae 30 SEPA E MIRI OO UE 30 3 27 10 Add fixed atoms menu item itu eo Denn o her aie eu eec scd da de 30 3 2 7 11 Unfix atoms menu 30 2 2 6 51 uat enrk eeu Labium Lontobud debi ta heit it 31 3 2 0 Graph MENU so eas se kee e a rase 32 3 3 SageMD main window Toolbar eoeeeo ee oho eov rebua 33 4 DIALOG BOXES cias acit EE RERUM CE IR ON REL A DE DIRE S c ER QUE ERN MI EDAM 34 4 1 Display parameters dialog box 34 Be LN A OIL Tao SGre E de sale Natl 35 E T 36 4 13 37 42 Lattice Builder dialog DOX ss ssssecsssasssc sseesecsoisssedtsscescsossdsscessavesustsduncocceavesedasadcvacscensese 38 452 1 Space Group tab Aw aw beds do gu a ute d dads 39 duse utmost ie intem aded tests Der uasa 40 Cel 41 324 CSU seotors
36. be selected after you click on the Select button of this dia log Also you can cancel selection by clicking Close button Input plane position Input line segments on a b c axises a b C E N ooe The Select by plane dialog contains three fields a b and were you can specify the plan position in fractional coordinate system After this you can click the Select button and selected atoms will be displayed in the main window by yellow color If you want to select another part of the structure just click Invert selection button on the toolbar or press in the keyboard or choose this command in the Operation menu 4 6 Scale coordinates of the atoms dialog box Path Operations menu 3 2 6 Scale menu item 3 2 6 11 Use this dialog to scale the coordinates of the selected atoms by the factors you define Scale coordinates of atoms scale factor Y scale factor H _ Cancel Z scale factor 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 at oms Y scale factor Allows you to specify the factor to scale Y coordinates of the selected at oms Z scale factor Allows you to specify the factor to scale Z coordinates of the selected at oms use the same for all directions Check this box to scale all the coordinate components by the same factor OK Click this button to scal
37. cells contain more then 100 atoms but asymmetric cell needed to create such unit cell may contain a few at oms only To build the crystal the SageMD uses the data from Cell 4 2 2 Unit Cell 4 2 5 and SuperCell 4 2 6 tabs The Space Groups 4 2 1 and this tabs need to build the unit cell only In fact you can define the position of atoms in the unit cell manually Then you need to define the cell vectors using the Cell 4 2 2 tab and specify how many times to repeat the unit cell along cell vectors using the SuperCell 4 2 6 tab then press OK button to build the crystal Asymmetric Cell tab has the following data fields Atom positions fractional Displays the position and type for the each atom in the asym metric 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 coor dinates of the atom Their values must be a numbers between 0 and 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 Displays the Pick element 4 25 dialog which allows you to add the new atom to the asymmetric cell The default coordinate of the atom are x 0 y 0 z 0 Use the Edit posi tions boxes to modify these values Delete Atom Click this button to remove an atom from the asymmetric cell Clear Click
38. cylinder you need to define the cylinder axis the coordinates of the cylinder base center the cylinder radius and height Select Sphere Cylinder Coordinate System Cartesian Angstoms C Cartesian Reduced Axis Axis along 2 2 65 4 2E 3 EE Select Inver Select All Select None Close 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 Note the reduced factor equals to the length of the a vector of the unit cell Apply Click this button to select the atoms which are inside of the specified cylinder 4 4 Select type dialog box Path Operations menu 3 2 6 Select type menu item 3 2 6 4 Use this dialog to select atoms by the atom type Select type Select the atomic symbol from the dropdown list and click OK button All atoms which have the selected type will be selected 4 5 Select by plane dialog box Path Operations menu 3 2 6 Select by plane menu item 3 2 6 8 This command of the SageMD code allows specifying a plane that divides the structure into tow parts One of these parts will
39. d atoms in the current MD simulation The coordinates of these atoms will not be changed during the whole simulation Se lect requisite group of atoms and click Add fixed atoms menu item 3 2 7 10 in the Task menu 3 2 7 5 3 Setting the parameters for the MD simulation and run simulation 1 Build lattice by one of the ways described in the section 5 1 2 Use Display parameters 4 1 dialog to change atoms colors sizes rendering quality and build atom bonds if it is necessary Menu path Display Parameters 3 Use Set potential 4 14 dialog to set interatomic potential for atoms You can implement your own pair potential To do it you need prepare your own potential file The format of the file is EAM potential file format 2 2 4 Only the pair section must be presented in this case Choose EAM potential in the Set potential 4 14 dialog box and specify your file as EAM potential file Menu path Tasks gt Set potential 3 Set boundary conditions The periodic boundary conditions in all direction are default settings Use Set boundary conditions 4 17 dialog to change default settings Menu path Tasks gt Boundary condition 4 If you wish calculate the RDF Radial Distribution Function or MSD Mean Square Displacement you need to set volumes Also you must set volumes if you wish monitoring the temperature and stresses in some part of the simulation cell Select atoms which you wish to in sert into a volume and click Se
40. d transition of quartz to stishovite The QEq method has been incorporated in SageMD with potential parameters available for the number of ionic species The Ewald summation is used to calculate the Coulomb interaction energy to avoid problems with necessary cutoff distances for these long range interactions 2 3 2 Many body potentials The many body interaction potentials are different from the pair potentials as the total in teraction energy of the system is not just a sum of all pair interactions There are three main ap proaches to express the many body interactions cluster cluster functional potentials and em bedded atom method In 1985 paper Stillinger and Weber suggested the potential with two and three particle terms for modeling the diamond structure of silicon The work describes a special case of the general expression for the potential interaction energy of N identical particles 1 2 6 2 v j k i a Q2 ovy iN The potential v in this expression is responsible for modeling external forces The expres sions for v and v are given by vies ale vor no e fil c 24 where amp and o are introduced here in order to make the potential and the interatomic dis tance dimensionless The following five parameter function is used for the pairwise term of the potential aler Ped r a 25 0 This function is continuous and has continuous derivatives for all order
41. dialog box 4 1 will be displayed Click the size you wish to change The Change ball size dialog will be displayed Type the new size and click OK button A13 How can I build the bonds From the Display menu 3 2 4 select the Parameters menu item 3 2 4 1 Click the Bond tab 4 1 2 If the min factor and max factor have values equals to zero make it equals to 0 6 and 1 1 respectively Click Build button If no bonds are displayed you need to increase the value of the max factor Make sure the Show bonds and Auto rebuild check boxes are checked 14 How can I add remove the bonds manually Make sure that IN add bond and X remove bond toolbar icons are available If it is not then from the Display menu 3 2 4 select the Parameters menu item 3 2 4 1 Click the Bond tab 4 1 2 and uncheck the Auto rebuild check box Make sure that the Show bonds check box is checked Click the IN icon on the toolbar to build the bonds Hold the shift key and click the two atoms whose bond you wish to build Click the 1 icon the toolbar to remove the bonds Hold the shift key and click the bond you wish to remove A15 How can I change the background color From the Display menu select the Parameters menu item 3 2 4 1 Click Misc tab Click the background color The Choose color dialog will be displayed Choose color and click OK button A16 How can I hide show the contour around the lattice From the Display
42. dify 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 remove atoms from the unit cell or change their types The Lattice Builder dialog contains the following tabs and buttons Space Groups tab 4 2 1 Cell tab 4 2 2 Asymmetric Cell tab 4 2 3 Cell vectors tab 4 2 4 Unit Cell tab 4 2 5 SuperCell tab 4 2 6 OK use this button to build or rebuild the crystal using the data from the dialog tabs and to close the dialog Cancel use this button to close the dialog without the building or rebuilding the crystal Apply Now the same as OK but the dialog will not be closed Help use this button to get the help about the active tab New if this radio button is checked the current crystal will be deleted before the new crys tal will be built Add to existing if this radio button is checked the atoms of the existing structure will not be deleted New atoms will be added to the existing atoms However the existing unit cell set tings will be replaced new one 4 2 1 Space Group tab Lattice Builder Space Groups Cell Asymmetric Cell Cell vectors Unit Cell SuperCell group number Select space group Select groups to show 8 Cm Y Extensions Other Names Tiekie Monoclinic c2 Y Bim Orthorhombic OK Cancel Apply Now Help New Add to existing The Space Groups tab allows you to specif
43. e Deviation The mean square displacement contains information on the atomic diffusivity The MSD branch contains following parameters first_step Allows to specify the initial time step of MSD calculation last_step Allows to specify the final time step of MSD calculation print step Allows to specify the frequency for saving MSD in the trajectory file Stress Not realized yet To change or specify any parameter in the RDF MSD or Stress branches just click once on the required field end enter your value Select and click once on the volume name to rename it the default name is NoName To exclude the volume from the current simulation process just double click on the volume s cross or name near the name will be appeared red cross instead of green tick 4 18 Set boundary conditions dialog box Path Tasks menu 3 2 7 Boundary cond menu item 3 2 7 6 The Set boundary conditions dialog box allows you to set the boundary conditions for the MD simulation By default periodic boundary conditions are in effect this can be altered with this dialog The periodic boundary conditions can be turned off in any direction independently of the others When the periodic boundary conditions are turned off in some direction you need to adjust the position and velocity of the potential wall using the Wall button for this direction Thus you can simulate free surfaces by setting the wall position beyond the wall potential cutoff distance f
44. e OK button 14 From the File 3 2 1 menu select the Save as menu item to save your work The stan dard Save as dialog box will be displayed Enter 5102 as the file name and then choose the di rectory to save the file and click the Save button 5 2 Selecting atoms Many operations in the SageMD operate upon those atoms that are selected in the main window for example adding volumes adding a layer of the fixed atoms deleting atoms and so on Selected atoms in the 3D view window are displayed in yellow There are several ways to select one atom or a group of atoms Selecting the individual atom Selecting the group of atoms Selecting the spherical cylindrical or parallelepipedic areas Selecting the atoms according its type Selecting the whole structure and inverting selection Selecting according a plane Selecting the fixed atoms 5 2 1 Selecting the individual atom Hold shift key and click atoms to select The picked atoms become selected in addition to any atoms already selected If an atom was already selected it becomes unselected 5 2 2 Selecting the group of atoms As an alternative to picking on an individual atom to select it one or more atoms may be selected graphically by drawing a rectangle with the mouse All atoms within this region are con sidered picked Hold CTRL key and the left mouse button Move mouse to draw rectangle around the atoms to select The starting point of the mouse forms one verte
45. e elements in SageMD are given a default color usually defined by the type of atomic element But sometimes it is useful to give a custom color to the chosen element 9 2 Various parameters of the bonds building Use Bond tab 4 1 2 on the Display parameters dialog box 4 1 to build the atoms bonds change bonds radius show or hide the bonds image This tab allows to change parameters for the whole structure But if you wish to build several bonds between some atoms you must carry out the following actions First make sure that in the Bond tab 4 1 2 of the Display parameters dia log 4 1 the Auto rebuild check box is unchecked and the Show bonds check box is checked Then click the IN button on the toolbar Hold the shift key and click the two atoms whose bond you wish to build If you want to remove bound just click the S button in the toolbar and select this atoms Also you can use Add bonds 3 2 6 19 and Remove bonds 3 2 6 20 menu items in the Operations menu 3 2 6 9 3 The color of the background and selected atoms The default color of the background is black As for selected atoms it is yellow But you can change the color manually for example before capturing and importing atomic structure 3D view image You can change these parameters from the Misk tab 4 1 3 of the Display parame ters dialog box 4 1 9 4 The style and form of the contour around the lattice The style of viewing atomic structure orthogon
46. e motion equations The time step interval will be equal to this factor multiplied on Reduced time unit Number steps Allows you to specify the number of simulation steps Initial temperature Allows you to set the initial temperature of the MD simulation Output options field Save step Allows you to specify the frequency for saving of the trajectory files Print step Allows you to specify the frequency for printing and saving other simulation re sults such as temperature energy stresses Constant temperature options field Const temperature Check this box to turn on the constant temperature simulation Temperature Allows you to specify the temperature which will be maintained during the MD simulation Relaxation time Allows specifying the relaxation time constant The greater value of this constant will require to run more steps to reach the desired temperature However the small value of the constant will result in too abrupt changes of the MD quantities The 100 time_step value will be the good value to start Constant pressure options field Constant pressure Check this box to turn on the constant pressure simulation Px Py Pz The Cartesian components of external pressure The positive value of the pres sure will results in compressing the structure To stretch the structure use the negative value of the pressure Isotropy Check this box to choose isotropic external pressure simulation For the non orthog
47. e table below as a electron density function The type specifies to which atom type the table belongs The other parameters the same as in the pair line EMBED type table_size rol ro2 The EMBED or embed command identifies the table below as the embedded energy func tions The rol and ro2 define the electron density range The first value of the table corresponds the rol value of the density the last value of the table corresponds the r02 value If the structure contains 2 different atom types you must prepare 3 files The example of these files is below alloy The nial ni ni pot file eunit PAIR 1 1 3000 1 000000 4 789502 0 000000E 00 9 146377E 05 9 097009E 05 9 047881E 05 8 998996E 05 8 950352E 05 8 901946E 05 8 853778E 05 8 805849E 05 8 758153E 05 8 710694E 05 8 663468E 05 DENS 1 3000 1 000000 4 789501 0 000000E 00 3 775296E 25 3 770337 25 3 765355E 25 3 760348E 25 3 755318E 25 3 750264E 25 3 745187 25 3 740086E 25 3 734963E 25 3 729817E 25 3 724649E 25 EMBED 1 2362 0 0000000 1 705184e 24 1 137440 13 7 041029E 02 9 087178E 02 1 037061E 03 1 127587E 03 1 194739E 03 1 245699E 03 1 284611 03 1 314099E 03 1 335936E 03 1 351383E 03 1 361368E 03 The nial_ni_al pot file eunit K PAIR 1 2 3000 1 100000 5 463932 6 850880E 05 5 270333 05 5 237156 05 5 204156E 05 5 171331 05 5 138681 05 5 106205E 05 5 073902E 05 5 041770E 05 5 009810 05 4 978020E 05 4 946400E 05
48. e the atomic coordinates and close the dialog Cancel Click this button to close dialog without the scaling 4 7 Move atoms dialog box Path Operations menu 3 2 6 Move menu item 3 2 6 12 Use this dialog to move selected atoms by the shift vector you define All the vector com ponents are in the fractional coordinate system x is directed along the along the b z along vectors of the unit cell Move atoms x shift 2 Y shift E _ Z shift use the same for all directions 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 c 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 dialog without the moving 4 8 Copy atoms dialog box Path Operations menu 3 2 6 gt Copy menu item 3 2 6 13 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 z along c vectors of the unit cell Copy atoms Input displacement vector and rep
49. earth ox ac uk keith moldy 7 Molecular Dynamics Software Materials Explorer http www cachesoftware com pdfs MEUserGuide_2 0 pdf Frisch M J Trucks I W Schlegel H B Secures LE Robb M A Cheeseman J R Zakrzewski V I Montgomery J A Stratmann R E Burant J C Dapprich S Millam J M Daniels A D Kudin K N Strain M C Farkas O Tomasi J Barone V Cossi M Cammi R Mennucci B Pomelli C Adamo C Clifford S Ochterski J Petersson I A Ayala Cui Q Morokuma K Malick D K Rabuck A D Raghavachari K Foresman J B Cioslowski J Ortiz J V Stefanov B B Liu L Liashenko A Piskorz P Komaromi Gomperts R Martin R L Fox D J Keith T Al Laham M A Peng C Y Nanayakkara A Gonzalez C Challacombe M Gill P M W Johnson B Chen W Wong M W Andres J L Gonzalez C Head Gordon M Replogle E S Pople J A Gaussian 98 Revision A 3 Gaussian Inc Pittsburgh PA 1998 Abinit new user guide http www abinit org ABINIT Infos v3 4 new user guide htm 10 Software of the SIESTA Project http www uam es departamentos ciencias fismateriac siesta Landau L D Lifshits E M Theoretical Physics V 5 Statistical Physics Nauka Mos cow 1987 E Balesku R Equilibrium and non equilibrium statistical mechanics V 1 Mir Moscow 1978 13 Landau L D Lifshits Theoretical Physics V 3 Quantum Mecha
50. eat number afi b fo cf Cancel The dialog has the following boxes and buttons a Allows you to specify the shift along the a vector of the unit cell b Allows you to specify the shift along the b vector of the unit cell c Allows you to specify the shift along the c vector of the unit cell rep Allows you to specify how many times to repeat this operations OK Click this button to copy the selected atoms and close the dialog Cancel Click this button to close dialog without the copying 4 9 Set type dialog box Path Operations menu 3 2 6 gt Set type menu item 3 2 6 14 Use this dialog to set the type which you define to the selected atoms New Type Select the atomic symbol from the dropdown list or click New Type button to display Pick element 4 24 dialog which allows you to pick the new atom type from the table Then click OK button to set the new type to the all selected atoms or click Cancel button to close the dialog without the setting new type 4 10 Check lattice dialog box Path Operations menu 3 2 6 Check lattice menu item 3 2 6 16 The Check lattice dialog box allows to measure atoms separation angels between atoms and the torsion angels You can see the positions and atoms separation in fractional reduced or Cartesian coordinate systems Check lattice Check Distance Check Angles N 48 type Si 4 25218 y 0 0943702 2 7 20266 Choose units N 43 type D x 3 1
51. ential Potential From the dropdown list select the interatomic potential which you wish to set for the pair you selected in Between types box For many body potentials or if you use the Ewald sum you must set the same potential for all interatomic interactions The available poten tials are EAM Morse modified Morse Bukingem Watanabe SW Tersoff B Tersoff C BKS Abinit Gaussian98 To use the Abinit and Gaussian98 potentials you need to install these codes on your computer During the MD simulations the SageMD call those codes to calculate the forces Any pair potential you can represent as EAM potential file which has only the pair part of the interatomic interaction The dens and embed parts of the file you must exclude Thus you have the ability to implement the pair potentials which are not implemented in SageMD code See EAM potential file format 2 3 3 Properties Click this button to display the Set potential parameters dialog box 4 14 1 which allows specifying the potential parameters of the interatomic interactions This button is visible not for all interatomic potentials Poten file This button is available only for EAM potential It allows choosing the potential data file OK Click this button to set potential and close the dialog Cancel Click this button to close the dialog 4 14 1 Set potential parameters dialog box Path Tasks menu 3 2 7 Set potential menu item 3 2 7 2 Set potential dialo
52. ep are almost the same However Beeman method requires more computer memory Since the major part of computer time is spent in step where forces are calculated these methods can be considered equivalent with respect to computation rate While Verlet method requires the least amount of computer memory compared to the other two methods it causes appreciably larger fluctuations of the total energy In SageMD code the velocity Verlet method is used as a default Irrespectively of the integration method however it is necessary to make sure that the total en ergy of the system is preserved or otherwise reduce the integration step The integrator com mand is implemented in the code to select the integration method 2 2 4 MD simulation at constant temperature and constant pressure The method suggested by Berendsen is implemented in SageMD code for simulation at constant temperature and constant pressure Temperature control in this approach is achieved by multiplying atom velocities by a coefficient A defined by the following equation 15 T where At is the integration time step 7 is the typical relaxation time T is the current tem perature and is the defined fixed temperature The pressure is controlled by changing atom coordinates and the size of the MD box At every time step atom coordinates and the size of MD box are rescaled by the coefficient calcu lated from the expression 1 3 16
53. eral parameters From the Tasks menu 3 2 7 select Run menu item 3 2 7 8 The Setting parameters for run dialog box 4 20 will be displayed Type 3000 in the number steps box Type 10 in the Save step box to set frequency for saving the trajectory file Type 10 in the Print step box to set frequency for saving the other output files Check the Stress checkbox to output stresses during the MD simulation Check the Const temperature checkbox and type 1500 in the Temperature and 1 in the Re laxation time boxes Check the Const pressure checkbox and type 1 in the Relaxation time box Click OK button to close the dialog The MD simulation script file will be displayed Close it to start simulation 7 3 Monitoring the simulation After starting the MD simulation click the Graph menu 3 2 9 and select Temperature menu item From the Window menu select Tile vertically menu item You can see the temperature graph and the aluminum structure simultaneously When the simulation is done click the 29 icon on the toolbar 7 4 Viewing the results Use Graph RDF Graph MSD Graph temp Graph energy and Graph stress menu items of the Results menu 3 2 8 to see graphs Use Tile vertically menu item of the Windows menu to see all graphs simultaneously e SageMD eam al vnd File Edit View Display Lattice Operations Tasks Results Graph Window Help 85 660 7 eam_al vnd 6 DER 81 eam_al vnd 4
54. ery N step means that every N step the atomic charges will be recalculated OK click this button to apply current settings and close dialog Cancel Click this button to discard all changes and close dialog The parameters of the QEq model are in the QEq_params dat file The example of such file is following below TR RR SE ZEl QuanNo MinQ MaxQ ElectNeg Hardness GenRadii H 1 1 1 4 52800 6 49205 0 37100 Li 2 1 1 3 00600 2 38600 1 55700 C 2 4 4 5 34300 5 06300 0 75900 N 2 3 5 6 89900 5 88000 0 71500 O 2 2 6 8 74100 6 68200 0 66900 F 2 1 7 10 87400 7 47400 0 70600 Na 3 1 1 2 84300 2 29600 2 08500 Mg 3 1 2 3 95100 3 69300 1 50000 AI 3 5 3 4 06000 3 59000 1 20100 Si 3 4 4 4 16800 3 48700 1 17600 P 3 3 5 5 46300 4 00000 1 10200 S 3 2 6 6 92800 4 48600 1 04700 Cl 3 1 7 8 56400 4 94600 0 99400 K 4 1 1 2 42100 1 92000 2 58600 Br 4 1 7 7 79000 4 42500 1 14100 Ti 4 1 4 3 47000 3 38000 1 60700 Zr 5 1 4 3 40000 3 55000 1 75800 26 To learn more see original paper 4 17 Set Volumes dialog box Path Tasks menu 3 2 7 Set volumes menu item 3 2 7 5 Set Volumes dialog box allows to select any atoms in the current structure into independent group which called volume These volumes are useful if you want to get some parameters not of the whole structure but only of the some part of it You can add up t
55. f the code is written in FORTRAN 90 while some modules are written in MS Graphical User Interface GUI simplifies user interaction with the code and provides for setup of initial data via intuitive and easy to operate dialogues and menus Initial data results parameters MD cell and crystal lattice can be inspected on the computer screen User friendly GUI also allows for analysis of results with a variety of graphs and tools GUI gives the next main features 3 D visualization of the periodic atomic structures Copying moving deletion and changing types of the highlighted atoms Highlighting the crystal lattice fragments as boxes spheres and cylinders Visualization of rotations and displacements Calculations of bonds lengths and angles between atoms Visualization of orthogonal and perspective projections Exporting atom coordinates to car fdf xtl and xyz file formats Support for dynamic visualization of modeling results while calculations are run ning SageMD code can be used to model properties of materials at constant temperature and or constant pressure to study behavior of the crystal lattice under expansion or compression to cal culate Radial Distribution Function RDF and to derive atomic diffusion coefficients The user can choose different boundary conditions namely periodical boundary conditions free surfaces and movable walls In addition the QEq approach for interatomic energy calculation which ta
56. g box 4 14 The Set potential parameters dialog box allows you to specify selected potential parame ters The next figure represents Set potential parameters dialog box for Morse potential Set potential parameters potential parameters Alfa 1 062 RO 3 321 Cutoff 7 3062 4 15 Set Ewald sum parameters dialog box Path Tasks menu 3 2 7 Ewald sum menu item 3 2 7 3 The Set Ewald sum parameters dialog box allows you to specify long range electrostatic potentials methods and to set some parameters Set Ewald sum parameters Ewald sum parameters Cutoff Alfa KMAY use direct columb summation use Ewald sum Calculate m Edit charges Charge 0 66 3 DK Cancel parum The Set Ewald sum parameters dialog contains the following fields Use Ewald sum Check this box to use Ewald summation in the current simulation The Ewald summation is the technique for calculating electrostatic interactions in a periodic or pseudo periodic system Use direct coulomb summation Check this box to use direct Coulomb sum in the current simulation Use of the direct Coulomb sum is sometimes necessary for accurate simulation of isolated nonperiodic systems It is not for periodic systems Calculate Click this button to use automatic calculation of Alfa KMAY KMAZ parameters You can enter only Cutoff parameter to use automatic calculation or you can manu ally specify
57. g the Temperature graph Graph Energy Allows viewing the total Energy graph Graph Stress Allows viewing the graphs of the external Pressure and its components Px Py Pz This graph is available if the stress calcu lation during the MD simulation was turned on to turn on stress calculation use the Set parameters for run dialog box 4 20 Graph Stress vol Allows viewing the external Pressure and its components graphs of the selected volumes This graph is available if the stress calculation during the MD simulation was turned on and before MD simulation volume was selected Graph Temp vol Allows to view the temperature graph of the selected vol umes This graph is not available if before simulation any volume was not selected Graph Velocity Allows viewing the Velocity components graphs Vx Vy Vz This graph is not available if before simulation any volume was not selected Graph Lattice This command allows viewing 3D Lattice structure The Graphs menu items allow you to view all necessary graphs Temperature Energy Pressure Velocity MSD and RDF after the current MD simulation is done The time step of all graphs depends on value Save step parameter which may specified in the Set parameters for run dialog box 4 20 You can easily manipulate with this data copy to the MS Excel or MS Word change the axis line titles properties and so on Set Graph Title dialog box 4 21 Allows to change graph and axis titles and fonts To
58. he equations of motion are given by dr dp dv 5 m F i 1 2 N dt 2 where is an interaction force between particles i and j Adiabatic approximation the Born Oppenheimer approximation further allows us to de scribe interatomic interactions via effective potentials The classic equation of motion 3 can be used to describe the state of microparticles at oms and molecules if A lt lt a where 4 is the de Broglie wavelength for a particle and ais the typical distance between particles De Broglie s wavelength for the particle with the mass m 15 determined by the relation 2mh A 6 Taking into account the values of the fundamental constants Planck constant Boltzmann constant and unit of atomic mass h 1 0546 107 7 5 k 21 3807 10 J K 1 6605 10 7 kg for temperature T 300K the equation 6 can be written as rus M 7 where 15 is the atomic or molecular mass of the particle Table 1 contains calculated values of the relation 4 a for some metals and gases For metals the value of a represents the interatomic interaction between the nearest neighbors in a crystal lattice under normal conditions For gases the value of ais related to the o parameter in the Lennard Jones interparticle potential The numerical values of parameters a and o were taken from refs Sub Molecular or atomic Ala a
59. he step you specify us ing this dialog To add shock wave you must select atoms before clicking on the Add button Shock waves LN Sep Velocty A 8 4 1 0 0 0 1 Shock 2 Shock2 4 1 0 Velocity reduced factor 1 02713 km s Add Del Edit The dialog has the following fields and buttons N The number of the shock wave You have not the possibility to edit this field Name The name of the shock wave You can leave the default name or type the new one This field must not be empty Step The step number at which apply the specified initial velocity to the atoms which were selected for the shock wave Which atoms were selected you can see by clicking on the de sired line The atoms of the selected wave will be highlighted Velocity the value of the atoms velocity of the shockwave This value applied as the initial velocity of the shock wave atoms at the beginning of the specified step You set velocity using the reduced units The real value km s Velocity velocity reduced factor A B C define the vector in fractional units along which the velocity vector of the shock wave atoms will be directed At the example the one shock wave is directed in positive direction of the A vector of the simulation box and another in the negative direction of this vector The value of the vector is no matter The direction means only The 1 1 1 and 5 5 5 vectors have the same direction So you can specify any of
60. his command is not available while the MD simulation is running or there are no atoms 3 2 7 6 Boundary cond menu item Use this command to display Set boundary condition dialog box 4 18 which allows you to set the boundary condition for the MD simulation Note This command is not available while the MD simulation is running or there are no atoms Shortcuts Toolbar ER 3 2 7 7 Shock waves menu item Use this command to open the Shock waves dialog box 4 19 which allows you to set the direction and value of the velocity of the selected atoms You will be able also to define the step at which apply this velocity Note This command is not available if the simulation is running or number of atoms is 0 3 2 7 8 Run menu item Use this command to display Set parameters for run dialog box 4 20 which allows you to specify the MD simulation parameters such as the time step the number of the time steps the output options and start the simulation Note This command is not available while the MD simulation is running or there are no atoms Shortcuts Toolbar S 3 2 7 9 Reset menu item Use this command to delete the current document and open the last saved version of the document When the MD simulation is running you can use this command to abort simulation or detach the simulation process from the GUI shell After finishing the MD simulations you must to do this command otherwise some commands will be unavailable
61. ialog you can show or hide the bonds and choose the background color The Display parameters dialog has the following tabs and buttons Atom tab 4 1 1 Bond tab 4 1 2 Misc tab 4 1 3 Close use this button to close the dialog Help use this button to get the help about the currently active tab 4 1 1 Atom tab Use this tab to change the atomic sizes colors and the quality of the rendering of the OpenGL graphics Display parameters Atom Bond Low Quality High To change the atoms colors just click on the color you wish to change The Color dialog box 4 25 will be displayed Pick the desired color and click OK button to close the Color dia log To change the atoms size click on the value of the atomic radius in the Size column The dialog will be displayed which 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 the rendering quality of the OpenGL objects The high value of this parameter in some cases will results to the decreasing of your computer perform ance In such case you should decrease the value of this parameter Use Make same size button to make the all atomic radiuses be equal to the radius value of the currently selected atom Close use this button to close the dialog Help use this button to display this page 4 1 2 Bond tab Use this tab to build the
62. iew and edit atoms 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 4 2 3 tab Alternatively you can define the atom positions and their types using this tab In this case you do not require knowing the space group informa tion and asymmetric cell settings The Unit Cell tab has the following data fields Atom positions fractional Displays the position and type for the 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 coor dinates of the atom Their values must be a numbers between 0 and 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 Displays the Pick element 4 25 dialog which allows you to add the new atom to the unit cell The default coordinate 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 the atoms from the unit cell 4 2 6 SuperCell tab Lattice Builder Space Groups Cell Asymmetric Cell vectors Unit Cell SuperCell SuperCell data size fractional
63. ion the angles between atoms and the torsion angles Note This command is not available if Check lattice dialog box is open 3 2 6 17 Add atom menu item Use this command to display Add atom dialog box 4 11 which allows you to add new atom to the structure Also you can use List and edit atoms position dialog box 4 12 to add at oms to the current structure Note This command is not available if Add atom dialog box or List and edit atoms posi tion dialog box is open 3 2 6 18 Edit atoms menu item Use this command to display List and edit atoms position dialog box 4 12 which allows you to view and edit the atomic position and types Also it allows you to add and remove the atoms Note This command is not available if List and edit atoms position dialog or Add atom dialog are open 3 2 6 19 Add bonds menu item To add the bond hold the shift key and click the two atoms whose bond you wish to build Note This command is not available if the Auto rebuild check box of the Bond tab 4 1 2 of the Display Parameters dialog box 4 1 is checked Shortcuts toolbar 3 2 6 20 Remove bonds menu item To remove the bond hold the shift key and click the bond which you wish to remove Note This command is not available if the Auto rebuild check box of the Bond tab 4 1 2 in the Display Parameters dialog box 4 1 is checked Shortcuts toolbar 3 2 7 Tasks menu Wall potential Set potential Ewald sum
64. ist and edit atom position dialog box 4 12 Select the atom whose position you wish to change The atom coordinates will be displayed in the Edit position group box Enter the new atom position coordinates and click the Apply button To change the atom type use the combo box under the Change atom group box 5 How can I measure the distance between the atoms From the Operation menu 3 2 6 select the Check lattice menu item 3 2 6 16 to display the Check lattice dialog box 4 10 Hold the shift key and click the two atoms whose separation you wish to measure A6 How can I measure the angles between the atoms From the Operation menu 3 2 6 select the Check lattice menu item 3 2 6 16 to display the Check lattice dialog box 4 10 Click the Check angles tab 4 10 2 Make sure that the Torsion angles check box is not checked Hold the shift key and click the three atoms to measure the angle between them At first you need to click the atom which is the vertex of the angle AT How can I measure the torsion angles From the Operation menu 3 2 6 select the Check lattice menu item 3 2 6 16 to display Check lattice dialog box 4 10 Click the Check angles tab 4 10 2 Make sure the Torsion angles check box is checked Hold the shift key and click the two atoms B and C whose torsion angle you wish to measure Then click the two atoms A and D which are bonded to B and C respectively A8 How can I paste the
65. ition 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 Change atom drop down list Also you can select the individual atom in the Atom positions field and it will be se lected in the structure image The List and edit atoms position dialog contains the following fields and buttons Atom positions Displays the position and type for the each atom of the current structure To see the location of the atom in 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 the new atom from the dropdown list Coordinate system Use this field to choose the coordinate system You can choose Carte sian reduced or fractional coordinate system Add Atom Use this button to add the new atom to the structure Atom type is specified in the Change atom box The default coordinate of the atom are x 0 y 0 z 0 Use the Edit posi tions boxes to modify these values Delete Atom Click this button to remove an atom from the unit cell Close Click this button to close this dialog 4 13 Set potential for wall dialog box
66. kes into account atomic charge distribution has been incorporated into SageMD code for mod eling the properties of materials with covalent chemical bonds For derivation of atomic charges and other parameters of force fields used in SageMD quantum chemical programs e g GAUSSIAN and SIESTA have been used 2 2 Molecular Dynamics Some of the theory 2 2 1 Principles of MD simulation In classical dynamics the motion is fully determined if a Hamiltonian is known for the sys tem Hamilton equations 1 determine the ensemble evolution dq OH q p dt Pi 1 dp O0H Qp wy dt For the ensemble of structureless particles interacting with each other via an effective po tential that depends only on their mutual position the generalized coordinates and momenta the Hamiltonian is determined by the following relations N Sn H r r p 2 t U r 2 where U r is the total potential energy of the ensemble of particles under consideration Note U r depends only on the spatial coordinates of the particles r r r ry Hence the system of equations 1 is given by dr m dv U r e m dt Or 90 r By introducing the force that affects the particle with a number i the system of equations 2 can be rewritten as dr _ dt dv 0 me E i 1 2 N dt For the additive pairwise interactions t
67. lcu lated from equation v t At v t 0 541 0 5 a t 14 The total size of the arrays necessary to implement this algorithm is 9 N where is the number of particles To calculate the amount of required computer memory it is necessary to multiply this number by the number by the size of the computer word In SageMD these arrays are of type double precision type i e each array element takes 8 bytes The main advantage of this algorithm 1 that particle coordinates and velocities are calculated at the same time step This method like all methods considered here is the second order method The Gear and Beeman algorithms are also implemented in the SageMD code for numerical solution of the equations of motion 2 2 3 Optimal choice of the method to integrate equations of motion The most accurate of the above integration methods is the Gear method However it re quires a large amount of computer memory The testing done for integration methods showed that the Gear method gives the lowest fluctuations of the total energy as compared to the other two methods However to hold the total energy at constant value the size of the integration step needs to be smaller than for Verlet or Beeman approach This leads to the increase of computer time needed to conduct the MD simulation The fluctuations of the total energy in the Beeman method are much smaller than in the Verlet method while the requirements to the integration st
68. le 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 radio button Then hold the shift key and click the two atoms B and C whose angle you wish to measure Then click the two atoms A and D which are bonded to B and C respectively In the edit box of this tab will be shown up the number of selected atoms its types and positions In the last line will be appeared the angle between atoms or torsion angle Check lattice Check Distance Check Angles N 48 type Si x 4 25218 0 0943702 2 7 20266 Choose units N 51 type 0 5 3765 1 06849 z 7 832 N 43 3 12786 1 06849 2 6 57333 Angle 105 819 Angstrem C Reduced Fractional Clear Torsion angles Press shift key to select atoms Release shift key to rotate The Check Angles tab contains the following fields and buttons Chose units allows choosing the coordinate system in which the atoms separation and po sitions will be shown Clear use this button to clear the edit box of this tab Close use this button to close this dialog Torsion angels use this check box to measure the torsion angles 4 11 Add atoms dialog box Path Operations menu 3 2 6 Add atoms menu item 3 2 6 17 The Add atom dialog allows you to add new atom to the structure You can specify the atomic positions and type Add atoms Edit positions Coordinate System
69. lect EAM Embedded Atom Method and click the Poten file button The Set EAM potential file dialog will be displayed Type the full path to the al pot file or use Browse button to locate this file Usually Program Files SageMD EAM al pot Click OK button to close Set EAM potential file dialog box and then OK button to close Set potential dialog box 7 2 2 Setting parameters for RDF and MSD calculation We wish to run the 3000 steps of the MD simulation The RDF function will be calculated using the 500 last steps The MSD we will calculate using all steps We wish to calculate the RDF function and MSD using all atoms of the crystal Thus we need to select all atoms Hold Ctrl and press C keys to select all atoms From the Tasks menu 3 2 7 select the Set volumes menu item 3 2 7 5 The Set volumes dialog box 4 17 will be displayed Click the Add volume button Click NoName and type the volume name for example Box or Box1 txt Click the mark to expand the list tree Click the mark to expand the RDF tree Click the mark to expand the first_step tree Click the 1 box to select it then click it again to edit 2500 and click the mark to expand last step tree Click the 1 box to select it then click it again to edit 3000 and click the mark to expand Msd tree Set the last step to 3000 and click Close button to close the Set volumes dialog box 7 2 3 Setting the gen
70. log box 4 2 which allows you to build or rebuild the crystal Note This command is not available if the Lattice Builder dialog is opened Shortcuts Toolbar 5 3 2 5 2 Delete menu item Use this command to delete the current structure Note The command is not available if there is not a structure Shortcuts Keys Ctrl Del 3 2 5 3 Add from file menu item Use this command to display the standard Open dialog box Use it to locate the vnd file on your computer or network from which you wish extract the structure and add to the existing one Note Only the atoms will be added The unit cell parameters and other data will be not changed 3 2 6 Operations menu Select geom Select all Ckrl A Select none Shift A Select type Select invert Alt A Select volumes Select Fixed atoms Select by plane Show selected only Show all Scale Move Copy Set type Delete Del Check lattice Add atoms Edit atoms Add bonds Remove bond The Operations menu offers the following menu items 3 2 6 1 Select geom menu item Use this command to open Select geom dialog box 4 3 which allows you to select the atoms using the Box 4 3 1 Sphere 4 3 2 and Cylinder 4 3 3 tabs of this dialog box 3 2 6 2 Select all menu item Use this command to select all atoms of the structure Note This command is not available if all atoms have already been selected LT Shortcuts Toolbar 28 keys C
71. luster configuration depends on the molecular structure Interaction energy be tween two particles and j depends not only upon their own coordinates but also on the coordi nates of all n 2 particles in the a cluster Tersoff potential is a typical example of a potential based on the cluster functional method The many particle potentials suggested by Tersoff are widely used for modeling silicon and other covalent materials Here the energy is calculated as a sum of pseudo pair interactions with the attraction term being dependent on the local environment of the atom via the bond order factor Y 29 i iz j Felt Nay J By 30 where E is the total energy consisting of individual pair contributions The repulsive ie r and the attractive f r forces are approximated by exponential functions similar to the Morse potential fylr Ar 31 f r Bexp 4 r 32 r lt R D fee E E R D lt r lt R D 33 0 gt Function f r confines the interactions to be within the atomic radius which greatly reduces computational effort Bond order parameters and b are the monotonic functions of the coordination number of atoms and depend on the valence angle 8 with the neighboring atoms a n gt n yj 7 felt exp 5 k i by me 34 Z felelnek k i j g 0 1
72. mage in the Tile Jae eoe y t as hs ela doc E Ren es 83 A10 Can I print the lattice 83 A11 How can I change the atoms colors 83 12 How can I change the atoms sizes ost ecran La RR rtl 83 Ale How Cand Build the bonds 4 ase et Deo 83 A14 How can I add remove the bonds manually ssssseeee 84 15 How can I change the background color sssssssseeeeeeen 84 16 How can I hide show the contour around the lattice sss 84 A17 Can I paste the atoms positions into the Notepad or Word documents 84 A18 How can T delete atoms ood on ms MEM te 85 A19 How T rotate the lattice image i e ned tcr cede Ree eias 85 A20 How can 1 move the lattice Image 85 21 How can I export the lattice to Siesta code eese 85 REFERENCES e M 87 Preface Thank you for your choice of SageMD the molecular dynamics simulation software allow ing you to perform molecular dynamics MD calculations on your computer We hope that you will find SageMD useful for your research and this User Manual will help you to become famil iar with this software This User Manual consists of 10 Chapters Chapter 1 explains requirements for using SageMD and describes the procedures for it s installing and uninstalling Chapter 2 describes mainframe problems and methods implemented in Sage
73. menu 3 2 4 menu select the Parameters menu item Click Misc tab 4 1 3 Check the Hide radio button to hide the contour Check the Unit cell radio button to draw contour around the unit cell Check the lattice radio button to draw contour around the crystal A17 Can I paste the atoms positions into the Notepad or Word documents Yes you can Select the atoms whose positions you wish to paste You can select all atoms From the Edit menu 3 2 2 select Copy or use the ctrl C keyboard shortcut to copy the atoms positions to the clipboard After that you can paste the positions into the applications using their the Paste command from the Edit menu The following example is the pasting of the SiC cubic unit cell into MS Word document NumberAtoms 8 5000 Si 0 2 174 2 174 51 2 174 0 2 174 51 2 174 2 1740 1 087 1 087 1 087 1 087 3 261 3 261 3 261 3 261 1 087 3 261 1 087 3 261 If you place the text in such format to the clipboard then you can paste these atoms into SageMD document A18 How can I delete atoms Select the atoms to delete Press the Del key To delete all atoms use the ctrl Del keyboard shortcut A19 How can I rotate the lattice image Hold the left mouse button and move the mouse to rotate the lattice image A20 How can I move the lattice image Hold the right mouse button and move the mouse to move the lattice image A21 How can I export the lattice to Siesta code Fr
74. messages that describe the actions of toolbar buttons as you depress them before releasing them If after viewing the description of the toolbar button command you wish not to execute the command then release the mouse button while the pointer is off the toolbar button The right areas of the status bar indicate the following Sel The number of the currently selected atoms N The number of atoms in the lattice 3 2 4 Display menu Parameters Zoom The Display menu offers the menu items 3 2 4 1 Parameters menu item Parameters menu item opens Display parameters dialog box 4 1 which allows you to build the atoms bonds and control the appearance of the OpenGL objects Note This command is not available if there are no atoms 3 2 4 2 Zoom menu item Use this command to magnify or miniaturize the structure image on your screen Hold the left mouse button and move mouse in the direction indicated by the mouse pointer to increase or decrease the structure image Hold the right mouse button to rotate the image To cancel this command uncheck the Zoom menu item or use the toolbar shortcut To fit the structure image to the screen press the spacebar Note This command is not available if there are no atoms amp Shortcuts toolbar 3 2 5 Lattice menu Create Delete Ctrl Del Add from The Lattice menu offers the following menu items 3 2 5 Create menu item Use this command to display the Lattice Builder dia
75. nics Nonrelativ istic Theory Nauka Moscow 1987 14 Physical values Reference book edited by Grigoryev I S Meylikhov E Z Moscow Energoisdat 1991 5 Girshfelder J Kertiss Ch R Molecular theory of gases and liquids Inostran naya Literatura Moscow 1961 16 Cubo Statistical mechanics Mir Moscow 1967 17 Verlet L Phys Rev 1967 159 98 18 Verlet L Phys Rev 1968 165 201 Swope W C Andersen Berens Wilson J Chem Phys 1982 76 637 cited from work Berendsen H J C Postma J P M VanGunstern W F Di Nola A Haak J R J Chem Phys 1984 81 3684 cited from work 1 Kaplan I G Introduction in the intermolecular interactions theory Nauka Moscow 1982 2 Selezenev A A Golubev V K Ganchuk N S Chem Phys Reports 1998 17 295 Selezenev A A Golubev V K Aleinikov A Yu Butnev O I Barabanov R A Vo ronin B L In Proceedings of the conference on Shock Compression of Condensed Matter Part 1 Atlanta 2001 374 24 Golubev V K Selezenev Khimicheskay Fizika 2002 21 61 23 Demiralp E Cagin T Goddard III W A Phys Rev Lett 1999 82 1708 2 Rappe A K Goddard W A J Phys Chem 1991 95 3358 2 Valuyev Kaklugin A S Norman Successes of Chemistry 1995 64 7 643 28 Stillinger Weber Phys Rev 1985 31 5262 29 Tersoff J Phys Rev B 1988 37 6991 3 Ter
76. ns menu 3 2 6 gt Select geom menu item 3 2 6 1 This dialog allows you to select atoms which are inside the box sphere or cylinder Select Box Sphere Cylinder m Input two vertex r Coordinate System Cartesian Angstoms x1 Y1 21 0 0 0 Cartesian Reduced f Fractional x2 Y2 22 d ME Apply Select Invert Select None Close The Select geom dialog contains the following tabs and buttons Box tab see 4 3 1 Sphere tab see 4 3 2 Cylinder tab see 4 3 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 to get the help about the currently active tab 4 3 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 the two vertex of this box These vertexes are the end points of the largest diagonal of the box Box Sphere Cylinder m Input two vertex Coordinate System C Cartesian Angstoms xi y1 21 0 0 0 C Cartesian Reduced Fractional x2 Y2 22 _ Apply Select Invert 5 Select None Close This tab has the following data fields Y1 Z1 Allows you to specify
77. o do it hold the left mouse button and move mouse to draw the rec tangle After releasing the mouse button the part of the screen that lies inside the rectangle will be copied to the clipboard After that you can paste the image into the documents of the other applica tions Capture image to file Copies the any part of the SageMD screen to the bitmap file To do it 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 standard Save as dialog will be displayed Use it to save the image into the file 3 2 3 View menu v Toolbar v Status Bar The View menu offers the following menu items 3 2 3 1 Toolbar menu item Use this command to display and hide the Toolbar 3 3 which includes buttons for some of the most common commands in SageMD A check mark appears next to the menu item when the Toolbar is displayed 3 2 3 2 Status Bar menu item Use this command to display or hide the Status Bar which describes the action to be exe cuted by the selected menu item or pressed toolbar button A check mark appears next to the menu item when the Status Bar is displayed The status bar is displayed at the bottom of the SageMD window To display or hide the status bar use the Status Bar command in the View menu The left area of the status bar describes actions of menu items as you use the arrow keys to navigate through menus This area similarly shows
78. o 20 volumes To add new volume you must select atoms see the FAQs Q1 and click Add volume button Set volumes first step f last step dr Rmax 5 47 first step f last step print step w Stress Add volume Delete volume Close The Set volumes dialog contains the following buttons Add volume Allows to add selected group to the new volume Delete volume Allows to delete selected volumes from the volumes list Close Click this button to close Set volumes dialog Set volumes dialog realized in tree type structure In the root we can see the selected vol umes The second branches rdf msd and stress contain the parameters to the calculation of the radial distribution function mean square deviation and stress To open the second branches click once on the cross RDF Radial Distribution Function Radial distribution function is a statistical function about the atomic distribution around an atom in a structure This function describes fluctuations in density around given atom You can think of it as the average number of atoms found at given distance in all directions The RDF branch contains following parameters first_step Allows to specify the initial time step of RDF calculation last_step Allows to specify the final time step of RDF calculation dr Allows to specify the radial step width of RDF Rmax Allows to specify the maximum value of the RDF radius MSD Mean Squar
79. o tmt eto aee BUE II e hee NUES ae a d 10 2 2 2 Approaches to numerical solution of the equations of motion 11 2 2 3 Optimal choice of the method to integrate equations of motion 12 2 2 4 MD simulation at constant temperature and constant 13 2 3 Interat mic Potenfials 13 2 3 Pair Potentials nannini netus ier hae Sat Jacl ea tia 13 2 3 2 Many body potentials ie 16 9 33 EAM potential file format aca trate 19 3 THE BASIC OPERATIONS OF MAIN WINDOW 22 3 1 Starting SageMD Main Window 22 3 2 SageMD main window MENUS 23 3 2 l S eL E EU 23 3 2 2 Edit tenus rec ir tre t aer D Pose iet veo staat Ate Sea e ai dar dads 23 3 2 3 View MENU essi et Hates epa oe teg base goku died ute Maas 24 32 31 Toolbar men TEM eee oe o OO Sd Sponso o ea tla De ay 24 3 2 3 2 Status Bar menu oc deren as Coe Dose md emus last enc E eds 24 ZZA Display THE Pe dide dM NDS 29 524 0 Parameters menu it M euo tac 25 25 32 5 Lattice ea lei ied iai o RA P sued 25 Create men YO o ite rette e ide bue rd te Putus rais 25 TIS DU
80. om the File menu 3 2 1 select the Export menu item The Save as dialog will be displayed Select the fdf extension in the Save as type box Type the file name in the File name box and save the file The following example shows the fdf file generated by SageMD NumberOfAtoms 9 NumberOfSpecies 2 block Chemical Species label 1 14 Si 2 80 endblock Chemical Species label LatticeConstant 1 Ang block LatticeVectors 4 2522 2 455 0 0 4 9 0 0 0 5 402 endblock LatticeVectors AtomicCoordinatesFormat ScaledCartesian block AtomicCoordinatesAndAtomicSpecies 2 0444 1 1803 0 0000 0 6386 1 6669 0 6293 3 1279 1 0685 1 1713 0 0000 2 5494 1 8007 1 1243 3 5235 2 4300 3 6136 0 7881 2 9720 2 2078 1 2747 3 6013 2 4893 2 1746 4 2307 1 7629 0 2804 4 7727 endblock AtomicCoordinatesAndAtomicSpecies NNR NNR NN include default fdf Use include directives to include the other Siesta data References Allen Tildesley D J Computer Simulation of Liquids Clarendon Press Ox ford 1987 Rapaport D C The Art of Molecular Dynamics Simulation Cambridge University Press Cambridge 1995 3 Frenkel D Smit Understanding Molecular Simulation Academic Press New York 1996 Leach Molecular Modelling Principe and Applications Longman New York 1996 Molecular Dynamics Software DISCOVER http www accelrys com insight discover html 5 Molecular Dynamics Software MOLDY http www
81. onal lattices you must check this box Relaxation time Allows setting the relaxation time constant The more value you set to this constant the more steps you need to run to reach the desired value of the pressure However the small value of the constant will result in too abrupt changes of the MD quantities The 100 time_step value will be the good value to start Bulk module Allows you to specify the bulk elastic modulus The value of the bulk elastic modulus should not be necessarily equal to exact real value In most cases you do not need to change the default value Neighbors list options field Use Neighbors list Check this box to use the neighbors list in MD simulation Max neighbors This value is used to build the neighbors list Increase this value if you re ceive the error message the neighbors list too small Cutoff factor All atoms whose separation less then factor cutoff will be included in the neighbors list The cutoff is the potential cutoff radius The factor must be more 1 Restart Check this box to continue the previous MD simulation You can change some pa rameters of the MD simulation Stress Check this box to turn on the stress calculation during the MD simulation Include thermal stress Check this box to include the velocity dependent part of the stress tensor in the stress calculation UX The reduced factor for energy RX The reduced factor for a distance AMX The reduced factor for a mass Reduced
82. ot named the document SageMD displays the Save As dialog box e 88 88 88 APT 5 2 bases Print the active document Remove selected data from the document and stores it on the clipboard Copy the selection to the clipboard Insert the contents of the clipboard into the SageMD document Reverse the last editing Reverse the last undo command action Create or rebuild the crystal Delete the current document and open the last saved version of the document Set the boundary condition for the MD simulation Run the MD simulation Zoom the lattice image Select all atoms Deselect all atoms Toggle the selection Add the bond manually Remove the bond manually 4 Dialog Boxes The most of menu items opens the various dialog boxes that allow entering input data and setting essential parameters The base dialog boxes itemize below in this chapter All dialog boxes were extracted into the individual chapter for both hyperlinks and text references usability So this chapter may be omitted in User Manual reading 4 1 Display parameters dialog box Path Display menu 3 2 4 Parameters menu item 3 2 4 1 Display parameters Atom Bond Misc LN Atom ee Low Quality High Make same size Use this dialog box to build the atomic bonds and to control the atoms size and colors Also the dialog allows you to change the appearance the bonds and their radiuses Using this d
83. ow all menu item Use this command to cancel the Show selected only 3 2 6 9 command action and display all atoms of the structure Note This command is not available if Show selected only command has not been exe cuted previously 3 2 6 11 Scale menu item Use this command to display Scale coordinate of atom dialog box 4 6 which allows you to scale the atomic coordinates of the selected atoms Note This command is not available if there are no the selected atoms 3 2 6 12 Move menu item Use this command to display Move atoms dialog box 4 7 which allows you to move the selected atoms to the new positions Note This command is not available if there are no the selected atoms 3 2 6 13 Copy menu item Use this command to display Copy atoms dialog box 4 8 which allows you to copy the selected atoms to the new positions Note This command is not available if there the selected atoms 3 2 6 14 Set type menu item Use this command to display Set type dialog box 4 9 which allows you to set the new type to the selected atoms Note This command is not available if there are no the selected atoms 3 2 6 15 Delete menu item Use this command to delete the currently selected atoms This command is not available if there are no the selected atoms Shortcuts keys Del 3 2 6 16 Check lattice menu item Use this command to display Check lattice dialog box 4 10 which allows you to measure the atoms separat
84. rom the crystal free surface Also you can simulate the processes of compression or tension of the crystal by setting none zero wall velocities Set boundary condition size fractional units E Periodic boundary a direction b direction c direction OK Cancel The dialog has the following fields and buttons Box size Allows you to change the size of the simulation box This option is not available if periodic boundary condition is not set Periodic boundary Allows you to set or unset periodic boundary conditions in a b and c directions of the unit cell If in some direction the periodic boundary is turned off you can use the button below to display Moving wall dialog box 4 18 1 which allows you to set the potential wall position and velocity OK Use this button to apply your changes and close the dialog Cancel Use this button to discard your changes and close the dialog 4 18 1 Moving wall dialog box Path Tasks menu 3 2 7 Boundary cond menu item 3 2 7 6 Set boundary condi tions 4 18 dialog box The Moving wall dialog box allows you to set the potential wall at specified distance from crystal surface Moving wall Walls offset from boundaries reduced units DAI 11000 DA2 1000 Reduced factor for distance 4 05 Walls velocity reduced units 0 surface Velocity reduced factor 1 02713 km s use for restart only OK Cancel
85. s at point It is a useful feature for many MD calculations that potential and all its derivatives are smooth func tions with respect to coordinates of atoms The three particle interactions are calculated from the following formula 1 2 E E SCAR 27 3 where is the angle between 7 and vectors 4 and are the potential parameters b ik The function is calculated when the vector lengths both and are smaller than the cutoff radius a and it is equal to zero otherwise The potential parameters for silicon obtained from the ref are given below 7 049556277 0 6022245584 4 0 1 8 21 0 1 2 2 0951 4 2167374937 eV gt M Stillinger and Weber conducted molecular dynamic calculations to model the silicon properties in particular silicon melting temperature The potential which they suggested pro vides good description of the crystal silicon but it cannot be applied to the non tetrahedral crys tals formed at high pressures Moreover this approach was unable to provide an accurate esti mate of the phase transfer temperature and the crystal cohesive energy when used with the single common set of parameters In the cluster functional method the interaction energy is represented as o o0 i jkea 28 i gt j Each pair of interacting particles i j is considered a part of the cluster a composed of n particles The c
86. se Tile vertically menu item of the Windows menu to see all graphs simultaneously To scale graphs double click on the desired axis Double click on the line to change line properties Double click on titles to change the title text and font You can copy the graphs data to the MS Excel Activate the graph window and use Ctrl C keyboard shortcut to copy the graph to the clipboard Start MS Excel and use Ctrl V shortcut to paste the graph data on MS Excel sheet To paste the graph to MS Word use Paste special command from the Edit menu of this application The print command will be realized soon 6 Sources of information Libraries and Databases 6 1 Database on structures SageMD database on structures represent the library of ready for use files with extension vnd that contains unit cell structures for many different elements and crystalline materials This library is located in SageMD templates directory usually Program Files SageMD Template See in section 5 1 1 how to build lattice using the SageMD structure database You may to supplement database by your own unit cell structures See in section 5 1 3 how to build unit cell structure using the SageMD 6 2 Database on potential parameters Excuse it s not ready now 7 Tutorial Melting of the Al crystal The eam_al vnd file is the ready for use the project file for this tutorial You can find it in the Template subdirectory of the SageMD installation directory
87. simulations was the Ver let method 5 for which the difference equations for the particle coordinates and velocities are given by r t At 2r t r t At a t At 9 v t r t At r t Ad 2At In terms of computer time and memory the most effective method is the leap frog ap proach The difference equations are given here by v t 0 5At v t 0 5At a t At 10 r t At r t v t 0 540 At The particle velocities at time can be calculated from the equation v t v t 0 546 v t 0 548 2 11 Velocity Verlet method was also derived It allows the calculation of coordinates and par ticle velocities in one time step The difference equations for this case are given by r t At r t v t At 0 5 a t At 12 v t At v t 0 5 a t a t At At This approach however requires that acceleration vectors for two time steps are stored in the computer memory SageMD code uses this approach to calculate the velocity vector The velocity vector is calculated in two steps At first the intermediate value of velocity is calculated v t 0 5At v t 0 5 a t At 13 and at the second step the new acceleration vector a t At is calculated and stored in the computer memory utilizing the already unneeded array which was freed after previously storing the acceleration vector a t Subsequently velocity values at the time moment Ar are ca
88. soff J Phys Rev 1988 38 9902 Watanabe T Fujiwara Noguchi H Hoshino Ohdomari I Jpn J Appl Phys 1999 38 L366 3 Daw 5 Baskes Phys Rev 1984 29 6443 33 Baskes Phys Rev 1992 46 2727
89. t the active tab 4 22 1 Axis Scale tab The Axis Scale tab allows changing the axis initial and finite value the major and minor division scale factor Axis Scale Axis format Grid Maximum value 165 Minimum value 5 Major divisions Minor divisions The Axis Scale tab contains the following fields Maximum value Allows changing the axis finite value Minimum value Allows changing the axis initial value Major division Allows changing the major division scale factor Minor division Allows changing the minor division scale factor 4 22 2 Axis Format tab The Axis Format tab allows changing the axis style color and weight Axis Scale Axis format Grid Style Color Weight E Font The Axis Format tab contains the following fields Style Use this box to select the axis line style from dropdown list Color Use this box to select the axis line color from dropdown list Weight Use this box to select the axis line weight from dropdown list 4 22 3 Grid tab The Grid tab allows changing the major or minor grid style color and weight Axis Scale Axis format Grid Major divisions 4 r Minor divisions Sye f Style Color Color Black Weight The Grid tab contains the following fields Style Use this box to select the major or minor line style from dropdown list Color Use this box to selec
90. t the major or minor line color from dropdown list Weight Use this box to select the major or minor line weight from dropdown list 4 23 Line Dialog box Path Results menu 3 2 8 gt one of menu items or Path Graph menu 8 2 9 one of menu items The Line dialog allows changing the graph line style color and weight Line format Style Color E Weight Style Use this box to select the graph line style from dropdown list Color Use this box to select the graph line color from dropdown list Weight Use this box to select the graph line weight from dropdown list OK Click this button to apply current settings and close dialog Cancel Click this button to discard all changes and close dialog Apply Now The same as OK but the dialog will not be closed Help Use this button to get the help 4 24 Pick element dialog box Use this dialog to pick the element from the periodic table of elements or to see element s properties Click on the element symbol button and then click OK button to pick element or click Properties button to see the elements properties Pick element Bjc Al si Gal Ge in HBAS REE BREE La Ce Pr Nd Pm Sm Eu Gd Er Tm vb Sn 5 Lu Th Pa U Np Pu Am Cm Cf Es Fm Lr 4 25 Color dialog box Basic colors NENNEN Custom colors 11 PUO
91. t volumes menu item 3 2 7 5 from Tasks 3 2 7 menu to display Set volumes dialog box 4 17 which allows you to set the volume parameters To calculate RDF and MSD for the whole simulation cell select all atoms as the volume You can create up to 20 volumes Menu path Tasks Set volumes 5 Use Ewald sum parameters 4 15 dialog box if your pair potential has Coulumb item Also you can use qEq model in this case However the number of atoms must be less then 600 to use qEq model Menu path Tasks Ewald sum and Tasks qEq 6 Optionally you can fix the selected atoms positions during MD simulation The posi tions of the fixed atoms are not updated during the MD simulation and their velocities will be set to 0 Menu path Tasks Add fixed atoms 7 Use Set parameters for run 4 20 dialog to set other parameters and start the MD simula tion Menu path Tasks Run 8 Click OK button to close the dialog The MD simulation script file will be displayed Close it to start simulation 5 4 Monitoring the simulation After starting the MD simulation click the Graph menu 3 2 9 and select Temperature menu item or Volumes Temp menu item if any volumes were selected You may observe repre sentation of selected quantity on graph When the simulation 15 done click the 29 icon on the toolbar 5 5 Viewing the results Use some of menu items of the Results menu 3 2 8 in concordance with your task to see graphs U
92. tab to on ien nte e 42 35 MICE bleue 42 4 2 6 SuperCell eae AA ES 43 4 3 Select geom dialog DOK 44 dade esca en e iat 45 43 2 Spliere bibe buses eto e 46 4 3 3 Cylinder tabu et e to ve re t erede nite ten ode aaa 47 4 4 Select type dialog Rp n ORE BOE 48 4 5 Select by plane dialog DOx iere peto 48 4 6 Scale coordinates of the atoms dialog 48 4 7 MOVE atoms dial bs os eu ve 50 4 8 atoms dialog DOK 51 4 9 Set type dialog 51 4 10 Check lattice dialog DOX vs scsicsssecsssospassoonpsecedesspidevsodeedessstpvessoniondcesespecevasaperocsersasseeupeee 52 4 10 1 Check distance tab 53 rei 54 4 11 Add atoms do qm x 55 4 12 List edit atoms position dialog ee eren neta S6 4 13 Set potential for wall dialog box eee ee eren eee eene tease tese tn nae 57 4 14 Set potential dialog DOX ssiscsccsscesossssassseccisesescsessseconnsseonensipnccsssesndennssestacseatusssessceesaate 58 4 14 1 Set potential parameters dialog box 59 4 15 Set Ewald sum parameters dialog box
93. 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 ac tive coordinate system Coordinate system Allows you to specify which coordinate system to use to define the box Note the reduced factor equals to the length of the a vector of the unit cell Apply Click this button to select the atoms which are inside of the specified box 4 3 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 the coordinates of the sphere center and the sphere radius Select Box Sphere Cylinder Input center location and radius Coordinate System Cartesian Angstoms xc 0 5 Cartesian Reduced yc 0 5 2c 0 5 Select Invert Select All Select None Close 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 Note the reduced factor equals to the length of the a vector of the unit cell Apply Click this button to select the atoms which are inside of the specified sphere 4 3 3 Cylinder tab This tab allows you to specify the cylinder which contains the atoms you wish to select To specify the
94. the smallest values that reproduce the correct Coulombic energy and virial at the value of Alfa to be used in the simulation Note that one needs to specify the three integers KMAX KMAY KMAZ referring to the three spatial directions to ensure the recipro cal space sum is equally accurate in all directions The values of KMAX KMAY KMAZ must be commensurate with the cell geometry to ensure the same minimum wavelength is used in all directions For a cubic cell set KMAX KMAY KMAZ However for example in a cell with dimensions 2 2 i e a tetragonal cell longer in the c direction than the a and b directions use 2KMAX 2KMA Y KMAZ If the values for the KMAX used are too small the Ewald sum will produce spurious results If values that are too large are used the results will be correct but the calculation will consume unnecessary amounts of cpu time The amount of cpu time in creases with KMAX KMAY KMAZ 4 16 Set parameters dialog box Path Tasks menu 3 2 7 menu item 3 2 7 4 Use this dialog box to turn on the QEq method for the MD simulation Rappe and Goddard suggested the charge equilibration QEq model to predict the atoms charge distribution in dependence of the molecular geometry Set qEq parameters Use gEq every 10 step The dialog has the following fields and buttons Use qEq check this box to use the qEq method during the MD simulation Call geq ev
95. them Add use this button to specify new shock wave from the currently selected atoms Del use this button to delete the currently selected shock wave Edit use this button to change the shock wave parameters Also you can double click on the line you wish to edit Close use this button to close the dialog 4 20 Set parameters for run dialog box Path Tasks menu 3 2 7 gt Run menu item 3 2 7 8 The Set parameters for run dialog box allow you to specify the MD simulation parame ters Set parameters for run General options Constant temperature options Nieghbours list options Time step Temperature Max neighbors 0 01 1200 Const temperature 300 Number steps Relaxation time Cutoff factor o 0 for Initial temperature Hmin 293 Constant pressure options 0 01 Px Isotropy Const pressure Dutput opti Bin utput options pulus 0 0 01 Save step Py Mbar Relaxation time T po i m eue 3 use neighbors list Print step Pz Bulk module Mbar Stress po D Restart eV 0 295 4 91 amu 28 086 Note time in reduced units Reduced time units 4 87712e 013 s Cancel Help The Set parameters for run dialog contains the following fields and buttons General options field Time step Allows you to set the time step interval for performing numerical integration of th
96. time unit The reduced factor for a time The real time reduced time reduced time unit OK Click this button to start simulation with the current parameters Cancel Click this button to exit the dialog and discard all changes 4 21 Set graph title dialog box Path Results menu 3 2 8 one of menu items or Path Graph menu 8 2 9 one of menu items Set graph title Temperature versus time Font Cancel In the text field of this dialog you can enter or change the title of the graph or desired axis Font Click this button to open the font dialog which allows to change the font type size and color OK Click this button to apply current settings and close dialog Cancel Click this button to discard all changes and close dialog 4 22 Axis dialog box Path Results menu 3 2 8 one of menu items or Path Graph menu 3 2 9 one of menu items Axis Scale Axis format Grid Maximum value fics Minimum value Major divisions Minor divisions Auto The Axis dialog allows changing or specifying the axis format scale and grid The Axis dialog contains the following tabs Axis Scale tab 4 22 1 Axis Format tab 4 22 2 Grid tab 4 22 3 OK Click this button to apply current settings and close dialog Cancel Click this button to discard all changes and close dialog Apply Now The same as OK but the dialog will not be closed Help Use this button to get the help abou
97. toms and molecules De novo calculation of the po tential for the many electron system is however a complex problem Therefore semi empirical approaches which contain parameters fitted to the experimental data are often used in practice Due to proximity of atoms in the condensed matter under normal conditions it is almost impossible to derive potentials for two particle interactions from experimental data Potentials in fact are not the pair potentials but represent effective potentials which include effects of many particle interactions These effective potentials are widely used to study properties of liquids and solids Such potentials fitted over a number of experimentally measured characteristics al low us to calculate quantitatively or semi quantitatively many important crystal properties The equation of state crystal elasticity modulus adhesion energy and the crystal structure are the examples of data used for fitting the parameters that enter effective potentials The types of interatomic pair potentials that are incorporated in the SAGE MD code are de scribed below Lennard Jones potential U r Uo 16 17 n m r r Morse and Morse modified potential U r U 2a r 2 exp a 9 18 U r E exp ma exp a r 19 Buckingham and Buckingham modified potential Uo 6 dan 1 P es jJ a 20 6 ces
98. x of the rectangle and the current location of the mouse is the opposite vertex 5 2 3 Selecting the spherical cylindrical or parallelepipedic areas Some tasks for crystal building or interface constructing needs geometrical figures to be se lected The Select geom 4 3 dialog box of the Operations 3 2 6 menu item allows to select areas with spherical cylindrical or parallelepipedic form 5 2 4 Selecting the atoms in concordance with its type If you want to select all the same type atoms of the current crystal structure use the Select type 4 4 dialog box of the Operations 3 2 6 menu item 5 2 5 Selecting the whole structure and inverting selection You can select all atoms by pressing the CTRL A keyboard buttons or choose Select all ae 3 2 6 2 menu item of the Operations 3 2 6 menu or click once 199 button on the toolbar Also you can invert your selection by pressing ALT A or choosing Select invert 3 2 6 5 menu item of the Operations 3 2 6 menu or clicking once button the toolbar 5 5 6 Selecting according plane Sometimes it is necessary to select some region that should be limited by a plane With the help of the Select by plane dialog box 4 5 you can specify a plane that divides the structure into two parts One of the parts will be selected after you click on the Select button of this dialog 5 5 7 Selecting fixed atoms Sometimes it is necessary to freeze the group of the selecte
99. y Now Help New Add to existing 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 the translation of the unit cell along the di rections of the unit cell vectors see SuperCell tab The space group symmetry can constrain the lattice parameters to predefined values In such cases some parameters will not be available to a b The length of the unit cell vectors b alpha The angle between b and vectors beta The angle between a and c vectors gamma The angle between a and b vectors Crystal system Can be one of the seven crystal systems triclinic monoclinic orthorhom bic tetragonal trigonal hexagonal or cubic Some of the space groups of the trigonal crystal sys tem can have extensions such as hexagonal or rhombohedral axes 4 2 3 Asymmetric Cell Tab Lattice Builder Atom positions fractional Edit positions M Atom x Y Z 0 48078 1 Si 0 48078 0 48078 0 2 0 0 15018 0 41459 0 1165 0 48078 0 Change Atom Si v Add Atom Delete Atom Clear Build unit cell OK Apply Now Help New Addto existing Asymmetric Cell tab allows you to build the full unit cell by means of applying the space group symmetry operations for the each atom in the asymmetric cell It results to the decreasing the amount of the work you need to do for the building of the crystal Some unit
100. y or modify the space group and space group settings for the structure which you wish to build or rebuild The Space Groups tab has the following boxes Group number You can specify a space group number by means of editing this box or us ing the spin buttons When you change the group number the contents of the Select space group box will be changed too and vice versa Select space group Enter the space group symbol into this box or 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 groups numbers of the selected crystal system Extensions Allows you to select the space group settings from dropdown list This box will not be displayed if there is nothing to show Other names Displays the alternate the space group name if any exists This box will not be displayed if there is not the alternate name for the selected space group edit 4 2 2 Cell Tab Lattice Builder Space Groups Cell Asymmetric Cell Cell vectors Unit Cell SuperCell data 4 91 5 402 Angstoms alpha beta gamma 5 12 degrees Cristal system Trigonal Hexagonal axes OK Appl

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