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--- exercises:2017_ethz_mmm:bands_2 [2017/05/17 09:35] – dpasserone
+++ exercises:2017_ethz_mmm:bands_2 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 11: / Line 11: @@
 </code>
-go in the directory where you want to put the exercise and do:
+**go to your scratch directory:**
+<code>
+cd /mnt/scratch/your_username
+</code>
+and copy there the tar file of the exercise:
 <code>
 cp /home/cpi/exercise_11.tar ./
@@ Line 36: / Line 41: @@
 ===TASK_0====
-The batch script run contain the instruction to run a quantum-espresso DFT calculaiton
+The batch script // **run**// contains the instruction to run a quantum-espresso DFT calculation
 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.
 The primitive cell (ibrav=2 for fcc) would contain only 2 atoms and would not be cubic.
-The scirpt is ment to run a calculation to optimize the wavefuntion 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 sinlge k point, Gamma, is used for the summation over the Brillouin Zone.
+A single k point, Gamma, is used for the summation over the Brillouin Zone.
 <note important>
-edit the script //run//
+edit the script //**run**//
 and identify the sections where
-  * Unordered List Itemthe lattice parameter is specified
+  * the lattice parameter is specified
-  * Unordered List Itemthe type of lattice (ibrav) is specified
+  * the type of lattice (ibrav) is specified
   * the coordinates of the atoms are provided in crystal coordinates
-  * the Monkhorst-Pack grid (in this case only Gamma point) is specifyed for the BZ sums
+  * the Monkhorst-Pack grid (in this case only Gamma point) is specified for the BZ sums
+  * how many electrons do we have in the system?
+  * 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
+<code>
+qsub run
+</code>
+**PLEASE NOTE:**
+<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 the k-points used during the calculations
+  * find where the eigenvalues (provided in eV) for each k-point are printed
+  * find the total energy of the system
+to find  the total energy of the system you can also type:
+<code>
+grep "\!" si.out
+</code>
+to  find the Fermi energy of the system you can also type:
+<code>
+grep "Fermi" si.out
+</code>
 </note>
+===TASK_0b, TASK_0c, TASK_1===
+The three tasks repeat the calculation of TASK_0 with a different sampling of the BZ
+in 0b a non shifted grid of 2x2x2 k-points is used, thus containing high symmetry points
+(so not ideal to have a accurate integration) in 0c the 2x2x2 grid is shifted
+and in TASK_1 a non shifted 3x3x3 grid is used.
+<note important>
+have a look at the three different //**run**// files and submit all of them
+then write down the total energy that you get from the three different outputs
+</note>
+===TASK_2===
+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
+<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
+  *  why the total energy obtained in TASK_1 is closer to **E27**/27 compared to the energies obtained in TASKS 0,0b,0c?
+  *  Compare the eigenvalues that you have now at the Gamma k-point with the eigenvalues you had on the different k-points for the calculation of TASK_1. All the eigenvalues obtained in TASK_1, that are subdivided in different k-points are now grouped in a single k-point.
+  * How many k-points are used in the calculation of TASK_1 as listed in si.out? why not 27?
+</note>
+===TASK_3===
+The script //**run**// performs an accurate calculation (Monkhorst-Pack grid 8x8x8) to obtain a accurate estimate of the charge density (thus the hamiltonian) of the system (si.out).
+We use here for the simulation the primitive cell with two atoms per cell.
+The data obtained are used to compute the bandstructure of Si along the symmetry lines
+L-G and G-X. (the output is written in the file sibands.out, where you will find all the eigenvalues for the 100 k-points specified to sample the symmetry lines)
+In the input I specified in "crystal coordinates" (but units of the reciprocal lattice vectors not units of the unit cell vectors)
+the 100 k-points used to sample the L-G and G-X symmetry lines.
+The k-points in sibands.out are given in cartesian coordinates in units of 2pi/a.(as will be used in TASK_5)
+<note important>
+submit the calculation
+<code>
+qsub run
+</code>
+once THE CALCULATION IS COMPLETED plot the bands
+<code>
+grep "Fermi" si.out
+python bands.py
+</code>
+you will obtain the png file bands.png
+</note>
+=== TASK_4 TASK_5===
+The aim of tasks 4 and 5 is to get familiar with what happens to the representation of bandsturctures
+if we change the simulation cell.
+In task 4 I assign to the conventional cell of Si a large lattice parameter,
+the 8 Si atoms of the cell will then be quite far one each other and will almost not interact
+This is of course not a correct representation of Bulk Si, it is instructive to see
+that the bands will reduce to flat lines corresponding to the s and p orbitals of the isolated Si atoms
+<note important>
+following the procedure of TASK_3 submit the calculation and plot the bandstructure
+<code>
+qsub run
+</code>
+wait for all calculations to be cmpleted and
+<code>
+grep "Fermi" si.out
+python bands.py
+</code>
+</note>
+In TASK_5, instead, we use a correct conventional cell (8 atoms in fcc positions with a=5.43A) to compute the bandstructure.
+In order to be able to compare the bandstructure of TASK_5 with the one obtained in TASK_3 (where the primitive cell
+with only two atoms per cell was used) **here i specify in the input
+the k-points of the path in BZ directly in cartesian coordinates.(in units of 1*pi/a)** This is the simplest way
+to be sure that, despite the shape of the BZ in TASK_3 will be different from the one in TASK_5
+we are computing the bandstructure in an equivalent region of the reciprocal space.
+<note important>
+run the calculation, plot the bands and compare with the bands obtained in TASK_3:
+how many filled bands do you have now (number of bands below fermi level) and why?
+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>