exercises:2018_ethz_mmm:bands_ii_2018
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exercises:2018_ethz_mmm:bands_ii_2018 [2018/05/03 07:17] – dpasserone | exercises:2018_ethz_mmm:bands_ii_2018 [2018/05/03 15:26] – dpasserone | ||
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=====Calculation of the bandstructure of Si and of a graphene nanoribbon by means of DFT with different settings===== | =====Calculation of the bandstructure of Si and of a graphene nanoribbon by means of DFT with different settings===== | ||
- | Download the tar file exercise_9.tar [[https:// | + | Download the tar file exercise_9.tar [[https:// |
exercise_9 | exercise_9 | ||
Execute the command | Execute the command | ||
Line 9: | Line 9: | ||
- | **go to your scratch | + | **enter the directory |
- | < | + | |
- | cd / | + | |
- | </ | + | |
- | and copy there the tar file of the exercise: | + | |
- | < | + | |
- | cp / | + | |
- | tar -xvf exercise_11.tar | + | |
- | cd exercise_11 | + | |
- | </ | + | |
- | **You will find a different directory for each TASK | + | **You will find a different directory for each TASK** |
- | ** | + | |
Please have a look at this web page | Please have a look at this web page | ||
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===TASK_0==== | ===TASK_0==== | ||
- | The batch script // **run**// contains the instruction to run a quantum-espresso DFT calculation | + | The script // **run**// contains the instruction to run a quantum-espresso DFT calculation |
for a conventional cell of Si (ibrav=1 for simple cubic cell). | for a conventional cell of Si (ibrav=1 for simple cubic cell). | ||
As you can see in the file, 8 atoms are included in the cell of parameter a=5.43A. | As you can see in the file, 8 atoms are included in the cell of parameter a=5.43A. | ||
The primitive cell (ibrav=2 for fcc) would contain only 2 atoms and would not be cubic. | The primitive cell (ibrav=2 for fcc) would contain only 2 atoms and would not be cubic. | ||
The script is meant to run a calculation to optimize the wavefunction of the system and to compute the total energy. | The script is meant to run a calculation to optimize the wavefunction of the system and to compute the total energy. | ||
- | A single k point, Gamma, is used for the summation over the Brillouin Zone. | + | A single k point, Gamma (0,0,0), is used for the summation over the Brillouin Zone. |
<note important> | <note important> | ||
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* how many occupied eigenvector do we have for each k-point (the occupation is printed in the output for each k-point after the energies of the eigenvalues belonging to the k-point | * how many occupied eigenvector do we have for each k-point (the occupation is printed in the output for each k-point after the energies of the eigenvalues belonging to the k-point | ||
- | Submit | + | run the calculation |
< | < | ||
- | qsub run | + | ./run |
</ | </ | ||
- | **PLEASE NOTE:** | + | Have a look to the output generated: |
- | + | ||
- | < | + | |
- | qstat | grep your_username | + | |
- | </ | + | |
- | if in the 5th column you see | + | |
- | * " | + | |
- | * " | + | |
- | * " | + | |
- | If you do not get anything your job was completed as well | + | |
- | + | ||
- | + | ||
- | + | ||
- | Have a look to the output generated: si.out | + | |
* identify where the symmetry operations used by the code are listed | * identify where the symmetry operations used by the code are listed | ||
* identify the k-points used during the calculations | * identify the k-points used during the calculations | ||
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</ | </ | ||
- | ===TASK_2=== | + | ===TASK_2 |
Here the //**run**// script contains the data to run a calculation for a large Si cell | Here the //**run**// script contains the data to run a calculation for a large Si cell | ||
There are 216 atoms corresponding to 3x3x3 of the conventional cell (8 atoms per cell in the conventional cell thus 3*3*3*8 atoms in total) used in the previous calculations | There are 216 atoms corresponding to 3x3x3 of the conventional cell (8 atoms per cell in the conventional cell thus 3*3*3*8 atoms in total) used in the previous calculations | ||
<note important> | <note important> | ||
- | submit the calculation (it will take ~10 minutes to be completed) | + | |
compare the total energy (**THAT WE CALL E27**)obtained in this calculation with the ones obtained in task_0, | compare the total energy (**THAT WE CALL E27**)obtained in this calculation with the ones obtained in task_0, | ||
* why the total energy obtained in TASK_1 is closer to **E27**/27 compared to the energies obtained in TASKS 0, | * why the total energy obtained in TASK_1 is closer to **E27**/27 compared to the energies obtained in TASKS 0, | ||
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submit the calculation | submit the calculation | ||
< | < | ||
- | qsub run | + | ./run |
</ | </ | ||
- | once THE CALCULATION IS COMPLETED plot the bands | + | once THE CALCULATION IS COMPLETED plot the bands providing the value of the fermi level that you obtain with the command: |
< | < | ||
grep " | grep " | ||
+ | </ | ||
+ | < | ||
python bands.py | python bands.py | ||
</ | </ | ||
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following the procedure of TASK_3 submit the calculation and plot the bandstructure | following the procedure of TASK_3 submit the calculation and plot the bandstructure | ||
< | < | ||
- | qsub run | + | ./run |
</ | </ | ||
wait for all calculations to be cmpleted and | wait for all calculations to be cmpleted and | ||
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Compare the vectors of the simulation cell and the vectors of the reciprocal cell as printed in the output (si.out) with the same quantities present in the output of TASK_3 | Compare the vectors of the simulation cell and the vectors of the reciprocal cell as printed in the output (si.out) with the same quantities present in the output of TASK_3 | ||
</ | </ | ||
+ | |||
+ | **TASK_6 and TASK_7** | ||
+ | In TASK_6 and TASK_7 you will find scf.in and bands.in to compute the bandstructure of a 7AGNR nanoribbon | ||
+ | from it's primitive cell (TASK_6) and in a double cell (TASK_7 containing two units) | ||
+ | |||
+ | use | ||
+ | < | ||
+ | ./ | ||
+ | </ | ||
+ | to plot the bands in TASK_6 | ||
+ | and | ||
+ | < | ||
+ | ./ | ||
+ | </ | ||
+ | to plot teh bands in TASK_7. | ||
+ | |||
+ | Additionally in the TASK_6 directory execution of: | ||
+ | < | ||
+ | ./ | ||
+ | </ | ||
+ | will create a superposition of the two plots | ||
+ | |||
+ | **the accuracy of the calculations is poor to allow execution of the PC** |
exercises/2018_ethz_mmm/bands_ii_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1