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--- exercises:2017_ethz_mmm:reaction_energy_2017 [2017/04/27 17:00] – dpasserone
+++ exercises:2017_ethz_mmm:reaction_energy_2017 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 84: / Line 84: @@
 </code>
-The exercise is executed on the ''hypatia'' cluster. The instructions to connect are found [[exercises:2017_ethz_mmm:replica_2017|here]]. After creating a directory as usual, you can copy the files from the following location.
+The exercise is executed on the ''hypatia'' cluster. The instructions to connect are found [[exercises:2017_ethz_mmm:replica_2017|here]]. After creating a directory as usual, you can copy the files from the following location:
+<note tip>~psd/Exercise_8/</note>
+Copy the files to the created directory in the ''/mnt/project/yourusername/'' path.
 <note tip>
 In the directory you will find the following files:
@@ Line 94: / Line 96: @@
   * several ''*.inc'' file describing the level of theory (exchange and/or correlation functional) and the basis sets.
 </note>
+The command to launch the job is
+<note important>> qsub run -v INP=file </note>
+where file.inp has to be replaced by the relevant prefix of the input file (example: ''h2o'').
+In the ''*.xyz'' files you can look for the final energies by the following command:
+<note important>> grep i c2h6o-pos-1.xyz  </note>.
+This will list all the energies. Pick the last one for the optimized structure. You can also visualize it with vmd.
+You will run the calculation by changing in **ALL THREE INPUT FILES** the ''@INCLUDE'' lines, in the following way:
+At the line concerning the exchange and correlation potential, you prescribe the level of theory:
+<note important>
+  * hf.inc for Hartree-Fock
+  * pbe.inc for DFT/PBE, with gradient corrected local density
+  * b3lyp.inp for hybrid functional containing a percentage of exact exchange
+</note>
+When you are done with the three levels of theory, then you can redo the exercise with the larger basis set, and change EVERYWHERE in the input file the instances of ''H_631Gdp.inc'' to ''H_6311++G2d2p.inc'' and the same for the O_* and C_* instances.
+Redo the calculations with the three levels ''pbe'', ''b3lyp'' and ''hf''.
+<note warning>
+Assignments:
+  - Compute the reaction energy for the dehydration reaction of ethanol
+  - Prepare a table with rows and columns: on the rows the level of theory, on the columns the basis set (3x2 table)
+  - Compare the results with the published ones (note the conversion factors. You can use the tool at [[http://www.colby.edu/chemistry/PChem/Hartree.html|Energy converter]]
+  - Comment on the dependence on the basis set and on the level of theory (hint: this also need the next theory lecture)
+  - Is this information enough to determine the rates of reaction? Why?
+</note>
+=== BONUS TRACK ===
+<note tip>We may be interested in the visualisation of the electronic density. Copy the ''ethanol.inp'' into ''ethanol_dens.inp''.</note>
+Add the following sections:
+**under &DFT**
+<code cp2k>
+       &PRINT
+          &E_DENSITY_CUBE
+          &END
+       &END
+       &SCF
+          SCF_GUESS RESTART
+       &END
+</code>
+This tells to read the old wavefunction and to print the cubefile of the density.
+At the end of the input file:
+<code cp2k>
+&EXT_RESTART
+     RESTART_FILE_NAME ./c2h6o-1.restart
+&END
+</code>
+Then, change ''RUN_TYPE GEO_OPT'' to ''RUN_TYPE ENERGY'' to only run a single point calculation. It will generate a cubefile with the density which you may visualize with VMD.