exercises:2017_ethz_mmm:bands_2
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exercises:2017_ethz_mmm:bands_2 [2017/05/17 09:58] – dpasserone | exercises:2017_ethz_mmm:bands_2 [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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</ | </ | ||
- | go in the directory where you want to put the exercise | + | |
+ | **go to your scratch directory: | ||
+ | < | ||
+ | cd / | ||
+ | </ | ||
+ | and copy there the tar file of the exercise: | ||
< | < | ||
cp / | cp / | ||
Line 36: | Line 41: | ||
===TASK_0==== | ===TASK_0==== | ||
- | The batch script // **run**// | + | The batch script // **run**// |
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 scirpt | + | The script |
- | A sinlge | + | A single |
<note important> | <note important> | ||
Line 49: | Line 54: | ||
* the type of lattice (ibrav) is specified | * the type of lattice (ibrav) is specified | ||
* the coordinates of the atoms are provided in crystal coordinates | * the coordinates of the atoms are provided in crystal coordinates | ||
- | * the Monkhorst-Pack grid (in this case only Gamma point) is specifyed | + | * the Monkhorst-Pack grid (in this case only Gamma point) is specified |
* how many electrons do we have in the system? | * how many electrons do we have in the system? | ||
- | * how many occupied | + | * how many occupied |
Submit the calculation to the queue | Submit the calculation to the queue | ||
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</ | </ | ||
- | Have a look to th eoutput | + | |
+ | **PLEASE NOTE:** | ||
+ | |||
+ | < | ||
+ | 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 | ||
* 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 | ||
* find where the eigenvalues (provided in eV) for each k-point are printed | * find where the eigenvalues (provided in eV) for each k-point are printed | ||
- | * find the total energy of teh system | + | * find the total energy of the system |
to find the total energy of the system you can also type: | to find the total energy of the system you can also type: | ||
Line 88: | Line 107: | ||
===TASK_2=== | ===TASK_2=== | ||
- | Here the //**run**// script contains | + | Here the //**run**// script contains |
- | There are 216 atoms corresponding to 3x3x3 of the conventional cell used in the previuos | + | 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) |
<note important> | <note important> | ||
submit the calculation (it will take ~10 minutes to be completed) | 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, |
* 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. | * 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? | ||
</ | </ | ||
+ | |||
+ | ===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, | ||
+ | In the input I specified in " | ||
+ | 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 | ||
+ | < | ||
+ | qsub run | ||
+ | </ | ||
+ | once THE CALCULATION IS COMPLETED plot the bands | ||
+ | < | ||
+ | grep " | ||
+ | python bands.py | ||
+ | </ | ||
+ | you will obtain the png file bands.png | ||
+ | </ | ||
+ | |||
+ | === 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 | ||
+ | < | ||
+ | qsub run | ||
+ | </ | ||
+ | wait for all calculations to be cmpleted and | ||
+ | < | ||
+ | grep " | ||
+ | python bands.py | ||
+ | </ | ||
+ | |||
+ | </ | ||
+ | |||
+ | 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, | ||
+ | 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 | ||
+ | </ | ||
+ | |||
+ | |||
exercises/2017_ethz_mmm/bands_2.1495015088.txt.gz · Last modified: 2020/08/21 10:15 (external edit)