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exercises:2017_ethz_mmm:qmmm [2017/06/02 03:33]
dpasserone
exercises:2017_ethz_mmm:qmmm [2020/08/21 10:15] (current)
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 <note important>   <note important>  
     Make three copies of **input.inp** and call them **qm_1l.inp**, **qm_2l.inp** and **qm.inp**.      Make three copies of **input.inp** and call them **qm_1l.inp**, **qm_2l.inp** and **qm.inp**. 
-   * **qm_1l.inp** should have ''PROJECT KCl_1'' and one QM layer. Modify accordingly by looking first at the ''kcl.xyz'' coordinate files. +   * **qm_1l.inp** should have ''PROJECT KCl_1'' and one QM layer. Modify accordingly the MM_INDEX lines by looking first at the ''kcl.xyz'' coordinate files. 
-   * **qm_2l.inp** should have ''PROJECT KCl_2'' and two QM layers. Modify accordingly by looking first at the ''kcl.xyz'' coordinate files. +   * **qm_2l.inp** should have ''PROJECT KCl_2'' and two QM layers. Modify accordingly the MM_INDEX lines by looking first at the ''kcl.xyz'' coordinate files. 
-   * **qm.inp** should have ''PROJECT KCl_QM'' and the full QM treatment. For this, it is sufficient to change ''QMMM'' at the beginning to ''QS''.+   * **qm.inp** should have ''PROJECT KCl_QM'' and the full QM treatment. For this, it is sufficient to change ''QMMM'' at the beginning to ''QS''. Change also the input coordinates from kcl.xyz to kcl_opt.xyz: these are the already optimized coordinates for the full QM treatment. In this way you will spare time.
 </note> </note>
  
 +===== 2. Task: Run the jobs  =====
 +<note important>
 +  * 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.
 +  * 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>
  
  
  
-===== Questions ===== 
      
  
Line 69: Line 101:
     #but should be treated as parameters in general     #but should be treated as parameters in general
     #fit to some physical property     #fit to some physical property
-    &MM_KIND K +
-      RADIUS 1.52 +
-    &END MM_KIND+
     &MM_KIND Cl     &MM_KIND Cl
-      RADIUS 1.67 
-    &END MM_KIND 
-    #define the model 
-    &QM_KIND K 
-      MM_INDEX 25..32 41..48 
-    &END QM_KIND 
-        &MM_KIND Cl 
       RADIUS 1.67       RADIUS 1.67
     &END MM_KIND     &END MM_KIND
exercises/2017_ethz_mmm/qmmm.1496374387.txt.gz · Last modified: 2020/08/21 10:15 (external edit)