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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) – external edit 127.0.0.1
@@ Line 19: / Line 19: @@
 <note important>
    *  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>
+===== 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
     #fit to some physical property
-    &MM_KIND K
-      RADIUS 1.52
-    &END MM_KIND
     &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
     &END MM_KIND