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exercises:2016_ethz_mmm:bs [2016/05/24 13:39] – pshindeexercises:2016_ethz_mmm:bs [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ===== 1. Running an SCF job and calculating the band structure and DOS of graphene ===== ===== 1. Running an SCF job and calculating the band structure and DOS of graphene =====
-Here we give some notes on how to use [[http://www.quantum-espresso.org|QUANTUM ESPRESSO]] to perform one of the standard tasks e.g. band structure calculation. In this exercise, we calculate the band structure of graphene along the high-symmetry lines (Γ-M-K-Γ) of the Brillouin zone (BZ). First, we do a self-consistent field (scf) calculation and then 'bands' calculation with a set of k-points (along high-symmetry lines). Please have a look at the end of the input files, scf.in and bands.in. In general, to study the electronic band structure one must 'relax' the ions in the system (not required to this exercise!) and then do the post-processing.+Here we give some notes on how to use [[http://www.quantum-espresso.org|QUANTUM ESPRESSO]] to perform one of the standard tasks e.g. band structure calculation. In this exercise, we calculate the band structure of graphene along the high-symmetry lines (Γ-M-K-Γ) of the Brillouin zone (BZ). First, we do a self-consistent field (scf) calculation and then 'bands' calculation with a set of k-points (along high-symmetry lines). Please have a look at the end of the input files, **scf.in**, and **bands.in**. In general, to study the electronic band structure one must 'relax' the ions in the system (not required for this exercise!) and then do the post-processing.
  
 Steps: Steps:
  
 1. Before starting the calculations please load following modules. Please type the commands at the terminal. 1. Before starting the calculations please load following modules. Please type the commands at the terminal.
-   $ module load intel/12.1.2 +   $ module load intel/14.0.1 open_mpi/1.6.5 
-   $ module load open_mpi/1.4.5 +   $ module load quantum_espresso
-   $ module load espresso/5.0.2_openmpi+
  
-2. Create a new directory and download all the **commented** files from the media manager: {{exercise_11.2.tar.gz|}}, copying them to the newly created directory.+2. Download all the **commented** files from the media manager: {{exercise-12.tar.gz|}} or 
 +<note important> wget http://www.cp2k.org/_media/exercises:2016_ethz_mmm:exercise-12.tar.gz</note>
  
 **Self-Consistent Field (SCF) calculation:** **Self-Consistent Field (SCF) calculation:**
  
-The SCF calculation means that the program iteratively updates the orbitals unit certain criterion is reached. Inspect the input file “scf.in” for graphene. The most important input parameters in scf.in are: definition of crystal system, lattice constant, k-grid, and vacuum region to avoid interactions between two graphene sheets. In our case the vacuum is of 12 Å. The symmetry has been included (ibrav) to reduce the number of calculations.+The SCF calculation means that the program iteratively updates the orbitals until certain criterion is reached. Inspect the input file “scf.in” for graphene. The most important input parameters in scf.in are: definition of a crystal system, lattice constant, k-grid, and vacuum region to avoid interactions between two graphene sheets. In our case, a vacuum along the perpendicular direction is ~12 Å. The symmetry has been included (ibrav) to reduce the number of calculations.
  
-   ibrav = 4                                  ! definition of the crystal system (hexagonal for graphene)+   ibrav = 4                                  ! definition of the crystal system (hexagonal for graphene
    celldm(1) = 4.65303296132007217931         ! lattice constant in a.u. (2.462/0.529117249) where 2.462 is the lattice const. in Angstroms    celldm(1) = 4.65303296132007217931         ! lattice constant in a.u. (2.462/0.529117249) where 2.462 is the lattice const. in Angstroms
    celldm(3) = 4.87408610885458976441         ! c/a (12/2.462), where c is the vacuum along z-direction    celldm(3) = 4.87408610885458976441         ! c/a (12/2.462), where c is the vacuum along z-direction
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    K_POINTS automatic    K_POINTS automatic
    KX KY KZ 0 0 0    KX KY KZ 0 0 0
-3. Insert the Γ-centred k-grid KX KY KZ (e.g. 10 10 1). As we are dealing with two-dimensional (2D) system (and so 2D BZ), KZ should be 1. There are two choices for the centre of the mesh: 1) centred on Γ (Γ belongs to the mesh) and 2) centred around Γ (Γ does not belong to the mesh). The second choice can break the symmetry!!. Here we used Γ centred k-grid.+3. Insert the Γ-centred k-grid KX KY KZ (e.g. 10 10 1). As we are dealing with two-dimensional (2D) system (and so 2D BZ), KZ should be 1. There are two choices for the centre of the mesh: 1) centred on Γ (Γ belongs to the mesh) and 2) centred around Γ (Γ does not belong to the mesh). The second choice can break the symmetry!!. Here we use Γ centred k-grid.
        
 4. Run the ground-state calculation using pw.x code of the QUANTUM ESPRESSO suit, 4. Run the ground-state calculation using pw.x code of the QUANTUM ESPRESSO suit,
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    $ grep “Fermi energy”  SCF.out | tail -1    $ grep “Fermi energy”  SCF.out | tail -1
  
-6. Copy the mol.save directory to scf-mol.save. The scf-mol.save is required for 'bands' calculation+6. Copy the mol.save directory to scf-mol.save. The scf-mol.save is required for the 'bands' calculation
    $ cp -rf mol.save/ scf-mol.save/    $ cp -rf mol.save/ scf-mol.save/
  
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 8. and then use dos.in input file to get the density of states from -20 to 10 eV. 8. and then use dos.in input file to get the density of states from -20 to 10 eV.
    $ bsub -n 4 " mpirun dos.x < dos.in > DOS.out "    $ bsub -n 4 " mpirun dos.x < dos.in > DOS.out "
-First column of "graphene.dos" file is the energy and second column is the total DOS. Open plot_dos.plt script to add Fermi energy and save the plot using gnu plot. The DOS should look like this,+First column of "graphene.dos" file is the energy and second column is the total DOS. Open plot_dos.plt script to add Fermi energy and save the plot using gnuplot. The DOS should look like this,
  
 {{ graphene_dos.png?500 | }} {{ graphene_dos.png?500 | }}
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 {{ Graphene-BZ.png?500 | }}  {{ Graphene-BZ.png?500 | }} 
  
-   $ gcc –Wall kpoints.c –o kpoints+   $ gcc -Wall kpoints.c -o kpoints
 and then  and then 
    $ ./kpoints    $ ./kpoints
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   - Repeat steps 3-11 for different k-grids (10 10 1, 20 20 1, 30 30 1 and 40 40 1) and plot the band structures and DOS.   - Repeat steps 3-11 for different k-grids (10 10 1, 20 20 1, 30 30 1 and 40 40 1) and plot the band structures and DOS.
   - What changes do you see in the band structure and DOS? Why?   - What changes do you see in the band structure and DOS? Why?
 +  - Repeat the exercise with a larger unit cell and a smaller number of k points. To this end you can use the provided script ** copy_crystal ** in the following way: 
 +  - copy the crystal coordinates in a file crys.in, then run ./copy_crystal crys.in 4 . In the file crys.in.4 you have the 4x4 cell coordinates. Repeat the calculation by changing the lattice parameter in the input file... 
 </note> </note>
  
-Don't forget to visit [[http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html/|QUANTUM ESPRESSO]] for more details about the input parameters!+Don't forget to visit [[http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html|QUANTUM ESPRESSO]] for more details about the input parameters!
exercises/2016_ethz_mmm/bs.1464097185.txt.gz · Last modified: 2020/08/21 10:15 (external edit)