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exercises:2017_ethz_mmm:qmmm [2017/06/02 03:43]
dpasserone
exercises:2017_ethz_mmm:qmmm [2017/06/02 03:54] (current)
dpasserone
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   * Run the jobs by giving the command: ''​qsub run -v INP=qm_1l''​ and similarly for the other input files.   * Run the jobs by giving the command: ''​qsub run -v INP=qm_1l''​ and similarly for the other input files.
   * You will also get cube files for hartree potential and electronic density. They can be examined with vmd.   * You will also get cube files for hartree potential and electronic density. They can be examined with vmd.
-  * For each job, a ''​*pos*xyz''​ optimization file is produced, as well as two PDOS files, one for the species 1 (K), the other for the species 2 (Cl).+  * For each job, a ''​*pos*xyz''​ optimization file is produced, as well as two PDOS files, one for the species 1 (K), the other for the species 2 (Cl). All will be prefixed by the ''​PROJECT''​ prefix you set in task 1. 
 +</​note>​ 
 + 
 +===== 3. Task: Checking the geometry ​ ===== 
 +<note important>​ 
 +By direct inspection of the last configuration in each file ''​*pos*xyz''​ (example: **KCl_QM-pos-1.xyz**),​ check the distance between 1-2, 2-3 layers. What are the differences between the three cases? 
 +</​note>​ 
 + 
 + 
 +===== 4. Task: Electronic properties ​ ===== 
 + 
 +<note important>​ 
 +Extract a smeared dos from the ''​pdos''​ files, using the python scripts present in the directory. For each case in task 1 the procedure is: 
 +<code bash> 
 +> python get-smearing-pdos.py KCl_1-PDOS-QMMM-k1-1.pdos 
 +> mv smeared.dat KCl_1.K.dat 
 +> python get-smearing-pdos.py KCl_1-PDOS-QMMM-k2-1.pdos 
 +> mv smeared.dat KCl_1.Cl.dat 
 +> paste KCl_1.K.dat KCl_1.Cl.dat > KCl_1.KCl.dat # all in the same file. The columns are ''​ENERGY PDOS_K ENERGY PDOS_Cl ''​ 
 +</​code>​ 
 +Plot the ''​.dat''​ files using gnuplot. The Fermi energy is set to zero eV. 
 +<code bash> 
 +> gnuplot 
 +gnuplot> set xrange [-5:10] 
 +gnuplot> plot '​KCl_1.KCl.dat'​ u 1:($2+$4) w l, plot '​KCl_QM.KCl.dat'​ u 1:($2+$4) w l, plot '​KCl_2.KCl.dat'​ u 1:($2+$4) w l 
 +</​code>​ 
 +  * **Note the differences you observe** 
 +  * Find the value of the band gap in the ''​*.out''​ files and relate it to what you see in gnuplot. How close is the QMMM to the full QM representation?​
 </​note>​ </​note>​
  
  
  
-===== Questions ===== 
   ​   ​
  
exercises/2017_ethz_mmm/qmmm.txt · Last modified: 2017/06/02 03:54 by dpasserone