MENA 9520 FME Modelling Tutorial 5 ( )

Transcription

1 MENA 9520 FME Modelling Tutorial 5 ( ) Task 5: Understanding type of bonding using charge-density plots Exercise 5.1: Visualizing charge density in Si: 1. mkdir charge 2. Copy a converged CTRL file to this directory 3. Change verbose = 50 in CTRL; Run lmctl 4. Edit the CTRL file; change verbose = 30 again. Select CHARGE = T We need to select the plane in which charge-density is to be visualized. For example, to select the (1 0 0) plane, we need to give origin and two vectors R1 and R2 that make up the plane (shown in the figure below) Here: R1 Origin = R1 = R2 = O R2

2 Scroll down CTRL file: 1. In the PLOT token, we can change origin, R1, R2 etc. For the present case, keep default origin. Give R1 and R2 as shown below. NDELR1 is the number of grid points to calculate charge density. If its more we get finer charge density. As we plot 2-dimensional plots, make NDELR3=0 corresponding to R3. After saving CTRL file, Run lm We get a new file RHO (self-consistent ground-state charge density) Run gnucharge See following example: We get files CHARGE.GNU and CHARGE.DAT Run gnuplot load CHARGE.GNU The output file charge.ps can be viewed with gv. Note: In the CHARGE label, we can select CHARWIN = T to plot charge density within a particular energy interval.

3 Si Charge-density along (100) plane The contours indicate charge density. The dark spheres at four corners and at centre are the Si atoms. By increasing number of grid points more contours can be seen. (Note: we can increase grid points depending on available memory in the machine). Exercise 5.2: Change Origin and see the difference Plot charge density along (010) and (001) planes Change CHARWIN parameters in the CHARGE label and plot charge-density for different energy intervals Note: Every time we change parameters in PLOT label of CTRL, we have to save and run lm to get the charge density corresponding to the given parameters. You may save the CTRL file and respective charge.ps file in the name of your choice for future reference. Exercise 5.3: Check for covalent character in bonding. Note: The characteristic of covalent bonding is sharing of electrons between two atoms. So we have to select a proper plane to visualize charge contours between atoms. Charge density along diagonal plane can provide the desired visualization.

4 In this case: Origin = R1 = R2 = If we double the vectors as shown below and run lm, we can see the charge density between Si atoms. Charge density of Si along diagonal plane. Finite contours between atoms implying covalent character. Exercise 54: 5.4: Establish the type of bonding in Cl using charge-density plots

5 Origin = Cl Cl Task 5.2: Plotting charge density within crystal structure We use a program called Xcrysden (can be opened through the icon shown on the screen). 1. To generate charge density compatible with this program, we have give finite number in NDELR3 and FORMAT = 3 in the CTRL. See the example below: 2. Run lm to get the RHO file. 3. Download an executable lm2xsf from By running lm2xsf, the CTRL and RHO are changed to an format read by Xcrysden. (Note: lm2xsf will generate a file this.xsf.gz in the primitive cell.) 4. Run lm2xsf u (to get the respective file for conventional unit cell) 5. Mv this.xsf.gz to a name of your choice. (eg. Si.xsf.gz; the file extension should always be *.xsf.gz) Note: 1. For running Xcrysden, mkdir xcrys_tmp in your home directory 2. Edit your shell file (eg.vi ~/.cshrc or vi ~/.bashc). Insert the following line: 3. Setenv XCRYSDEN_SCRATCH $HOME/xcrys_tmp 4. save and quit. 5. Type source ~/.cshrc (to enable the setenv command)

6 Plotting charge density using Xcrysden: 1. Open Xcrysden. File Open Structure Open XSF open your *.xsf.gz file 2. We get the crystal structure. (You can change background color, etc) 3. Goto Tools Data Grid (Identifier shows RHO_lm2xsf). Click OK 4. We get a pop-up window (Isosurface/Property ) 5. We can unselect Display Isosurface (or Isovalue should be given) 6. Select Apply to Planes 7. Go to Plane #1, Select display color plane, display isolines, thermometer 8. In Ranges select 0.05 to 1 9. You can choose the color basis, isoline etc of your choic 10. Press Submit 11. You can rotate the crystal structure to see the charge density incorporated within the crystal cell. Exercise 5.5: Plot charge density of Si, Cl and dal using Xcrysden Structure details for Al: Analyze the type bonding using these plots Note: Remember to copy your files to your home machine because your guest user names will be removed in a week. We acknowledge Prof. O.K. Andersen, Max-Planck Institute for Solid-State Research, Stuttgart for kindly providing the TB-LMTO program used in these tutorials.