# CP2K Open Source Molecular Dynamics

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exercises:2017_ethz_mmm:qmmm

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 exercises:2017_ethz_mmm:qmmm [2017/06/02 03:43]dpasserone exercises:2017_ethz_mmm:qmmm [2020/08/21 10:15] (current) Both sides previous revision Previous revision 2017/06/02 03:54 dpasserone 2017/06/02 03:43 dpasserone 2017/06/02 03:33 dpasserone 2017/06/02 02:28 dpasserone 2017/06/02 02:26 dpasserone 2017/06/02 02:26 dpasserone 2017/06/02 01:40 dpasserone created Next revision Previous revision 2017/06/02 03:54 dpasserone 2017/06/02 03:43 dpasserone 2017/06/02 03:33 dpasserone 2017/06/02 02:28 dpasserone 2017/06/02 02:26 dpasserone 2017/06/02 02:26 dpasserone 2017/06/02 01:40 dpasserone created Line 28: Line 28: * 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. + + + ===== 3. Task: Checking the geometry  ===== + + 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? + + + + ===== 4. Task: Electronic properties  ===== + + + 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: + + > 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 '' + + Plot the ''.dat'' files using gnuplot. The Fermi energy is set to zero eV. + + > 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 + + * **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? - ===== Questions =====