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exercises:2018_ethz_mmm:bands_ii_2018

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exercises:2018_ethz_mmm:bands_ii_2018 [2018/05/03 07:14] – created dpasseroneexercises:2018_ethz_mmm:bands_ii_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-=====Calculation of the bandstructure of Si 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=====
  
-<note important> +Download the tar file exercise_9.tar [[https://polybox.ethz.ch/index.php/s/CH5VdcI40YdELez|here]]  and move it to the directory where you would like to have the 
-connect to hypatia:+exercise_9 
 +Execute the command
 <code> <code>
-ssh -X EMPA-USER@jump1.empa.ch +tar -cvf exercise_9.tar
-ssh -X hypatia +
-</code>  +
-<code> +
-module load python/2.7.12 +
 </code> </code>
  
  
-**go to your scratch directory:** +**enter the directory exercise_9**
-<code> +
-cd /mnt/scratch/your_username +
-</code> +
-and copy there the tar file of the exercise: +
-<code> +
-cp /home/cpi/exercise_11.tar ./ +
-tar -xvf exercise_11.tar +
-cd exercise_11 +
-</code>+
  
-**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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 [[http://www.quantum-espresso.org/]] [[http://www.quantum-espresso.org/]]
-</note>+
  
 ===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 the calculation to the queue+run the calculation (you can find output examples in the directory **./done**)
 <code> <code>
-qsub run+./run
 </code> </code>
  
  
-**PLEASE NOTE:** +Have a look to the output generated: **si.out**
- +
-<code> +
-qstat | grep your_username +
-</code> +
-if in the 5th column you see    +
-  * "Q" it means that your job is still waiting in the queue +
-  * "R" your job is running +
-  * "C" your job is completed +
-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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 </note> </note>
  
-===TASK_2===+===TASK_2 DO NOT EXECUTE THE SCRIPT RUN it requires too much memory si.out is already present===
 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_0,0b,0c,1   compare the total energy (**THAT WE CALL E27**)obtained in this calculation with the ones obtained in task_0,0b,0c,1  
   *  why the total energy obtained in TASK_1 is closer to **E27**/27 compared to the energies obtained in TASKS 0,0b,0c?     *  why the total energy obtained in TASK_1 is closer to **E27**/27 compared to the energies obtained in TASKS 0,0b,0c?  
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 submit the calculation submit the calculation
 <code> <code>
-qsub run+./run
 </code> </code>
-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:
 <code> <code>
 grep "Fermi" si.out grep "Fermi" si.out
 +</code>
 +<code>
 python bands.py python bands.py
 </code> </code>
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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
 <code> <code>
-qsub run+./run
 </code> </code>
 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
 </note> </note>
 +
 +**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 
 +<code>
 +./plot_qe_bands.py 7agnr_1uc.save
 +</code> 
 +to plot the bands in TASK_6
 +and
 +<code>
 +./plot_qe_bands.py 7agnr_2uc.save
 +</code>
 +to plot teh bands in TASK_7.
 +
 +Additionally in the TASK_6 directory execution of:
 +<code>
 +./plot_qe_bands.py 7agnr_1uc.save  --add_dir ../TASK_7/7agnr_2uc.save --fold 2
 +</code>
 +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_2018.1525331695.txt.gz · Last modified: (external edit)