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exercises:2018_ethz_mmm:ethanol_2018 [2018/03/23 06:06] – created dpasseroneexercises:2018_ethz_mmm:ethanol_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 <code cp2k> <code cp2k>
 +&FORCE_EVAL                           ! This section defines method for calculating energy and forces
  
 +   METHOD Quickstep                   ! Electronic structure method (DFT,...)
    &DFT    &DFT
 +      BASIS_SET_FILE_NAME ./BASIS_C_H_O 
       &POISSON                        ! Solver requested for non periodic calculations       &POISSON                        ! Solver requested for non periodic calculations
          PERIODIC NONE          PERIODIC NONE
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       &END POISSON       &END POISSON
       &QS                             ! Parameters needed to set up the Quickstep framework       &QS                             ! Parameters needed to set up the Quickstep framework
-         METHOD GAPW                  ! Method: gaussian and augmented plane waves+         METHOD GAPW                  ! Method: gaussian and augmented plane waves 
       &END QS       &END QS
 +   
 # #
 # Include the exchange and correlation information # Include the exchange and correlation information
 # #
-@INCLUDE './pbe.inc'+@INCLUDE './hf.inc'
  
    &END DFT    &END DFT
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       &END CELL       &END CELL
       &COORD                          ! This section specify all the atoms and their coordinates       &COORD                          ! This section specify all the atoms and their coordinates
-  H         2.5558925119        4.9201502245        3.9999999733 +  H         2.5558925119        3.0          4.  
-  H         2.5617214834        3.0599837703        4.0000000267 +  O         4.00                3.5          4. 
-  C         3.3235178526        3.9916405319        4.0000000002 +  H         5.4167134504        3.0669045998 4.
-  C         4.6493228423        3.9951429630        3.9999999995 +
-  H         5.4118318595        4.9261779106        4.0000000269 +
-  H         5.4167134504        3.0669045998        3.9999999735+
       &END COORD       &END COORD
       &TOPOLOGY       &TOPOLOGY
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       &END TOPOLOGY       &END TOPOLOGY
  
-      &KIND H                                      ! potential and basis for H +      
-         &BASIS +      &KIND O                                      ! potential and basis for O  
-@INCLUDE './H_631Gdp.inc' +         BASIS_SET _MYBASIS_ 
-         &END+         POTENTIAL ALL 
 +         &POTENTIAL 
 +     4    4    0 
 +     0.24762086    0 
 +         &END  
 +      &END KIND 
 +      &KIND H                                      ! potential and basis for H  
 +         BASIS_SET _MYBASIS_
          POTENTIAL ALL          POTENTIAL ALL
          &POTENTIAL          &POTENTIAL
           1    0    0           1    0    0
           0.20000000    0           0.20000000    0
-         &END+         &END 
       &END KIND       &END KIND
       &KIND C                         ! potential and basis for C       &KIND C                         ! potential and basis for C
-         &BASIS +         BASIS_SET _MYBASIS_
-@INCLUDE './C_631Gdp.inc' +
-         &END+
          POTENTIAL ALL          POTENTIAL ALL
          &POTENTIAL          &POTENTIAL
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 &GLOBAL                             ! Section with general information regarding which kind of simulation to perform an parameters for the whole PROGRAM &GLOBAL                             ! Section with general information regarding which kind of simulation to perform an parameters for the whole PROGRAM
    PRINT_LEVEL LOW                  ! Global print level    PRINT_LEVEL LOW                  ! Global print level
-   PROJECT c2h4                     ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option)+   PROJECT h2o                      ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option)
    RUN_TYPE GEO_OPT                 ! Geometry optimization    RUN_TYPE GEO_OPT                 ! Geometry optimization
 &END GLOBAL &END GLOBAL
-                                                                                                       +                                                                                  
 </code> </code>
  
 The exercise is executed on the virtual machine cluster. After creating a directory as usual, you can download the file from here: The exercise is executed on the virtual machine cluster. After creating a directory as usual, you can download the file from here:
-<note tip></note>+[[https://polybox.ethz.ch/index.php/s/wtxgaO9IEPM7FXs|(tar file)]]
  
-Copy the files to the created directory in the ''EXERCISES'' path.+Copy the file to the created directory in the ''EXERCISES'' path, and execute 
 +<code> 
 +tar xvf exercise_5.tar 
 +</code>
 <note tip> <note tip>
 In the directory you will find the following files: In the directory you will find the following files:
-  * ''h2o.inp'' for the geometry optimization of water +  * ''h2o_template.inp'' for the geometry optimization of water 
-  * ''ethanol.inp'' for the geometry optimization of ethanol +  * ''ethanol_template.inp'' for the geometry optimization of ethanol 
-  * ''ethylene.inp'' for the geometry optimization of ethylene (ethene) +  * ''ethylene_template.inp'' for the geometry optimization of ethylene (ethene) 
-  * ''run'' to launch the jobs to the queue +  * ''hf.inc'' file describing the level of theory (exchange and/or correlation functional), in this case Hartree Fock 
-  * several ''*.inc'' file describing the level of theory (exchange and/or correlation functional) and the basis sets.+  * ''BASIS_H_C_O'' a repository file for basis sets.
 </note> </note>
  
 +First you have to modify the input files in order to prescribe a certain basis set. You have, from the simplest to the most advanced:
 +
 +  - 3-21G*
 +  - 6-31G*
 +  - 6-31Gxx
 +  - 6-31++Gxx
 +  - 6-311Gxx
 +  - 6-311++Gxx
 +
 +For example, 
 +<code>
 +m_replace _MYBASIS_ '6-31G*' < h2o_template.inp > h2o_BASIS1.inp
 +</code>
 +(note: **use the quote, because the star is a bash special character!!!**)
 The command to launch the job is The command to launch the job is
-<note important>> qsub run -v INP=file </note> +<note important> cp2k.ssmp -i h2o_BASIS1.inp > h2o_BASIS1.out </note> 
-where file.inp has to be replaced by the relevant prefix of the input file (example: ''h2o''). +In the ''*.out'' files you can look for the final energies by the following command: 
-In the ''*.xyz'' files you can look for the final energies by the following command: +<note important>> grep 'ENERGY|' myoutput.out </note>. 
-<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.+This will list all the energies. Then you can redo the exercise with different basis set, reusing the command **m_replace**. 
 + 
 +^ Basis set                  ^ Energy H2O [$E_h$] ^ Energy Ethylene [$E_h$] ^ Energy Ethanol [$E_h$]^ Distance CC Ethanol [$Å$] ^ Reaction energy [$E_h$] ^ 
 +| BASIS 1(Name)              | ....             | ....              | ....            | ....                       | ....                      | 
 +| BASIS 2(Name)| ....             | ....              | ....            | ....                       | ....                      | 
 +| BASIS 3(Name)| ....             | ....              | ....            | ....                       | ....                      | 
 +| BASIS 4(Name)| ....             | ....              | ....            | ....                       | ....                      | 
 +| BASIS 5(Name)| ....             | ....              | ....            | ....                       | ....                      | 
 +| BASIS 6(Name)| ....             | ....              | ....            | ....                       | ....                      |
  
-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. +<note important>The binding energy is only significant if all terms were calculated with the same basis-set.</note>
-Redo the calculations with the three levels ''pbe'', ''b3lyp'' and ''hf''.+
    
 <note warning> <note warning>
 Assignments: Assignments:
   - Compute the reaction energy for the dehydration reaction of ethanol   - 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)+  - Prepare a table with rows and columns: on the rows the basis set, on the columns different quantities (see above).
   - 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]]   - 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)+  - Comment on the dependence on the basis set 
   - Is this information enough to determine the rates of reaction? Why?   - Is this information enough to determine the rates of reaction? Why?
 </note> </note>
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 === BONUS TRACK === === BONUS TRACK ===
  
-<note tip>We may be interested in the visualisation of the electronic density. Copy the ''ethanol.inp'' into ''ethanol_dens.inp''.</note>+<note tip>We may be interested in the visualisation of the electronic density. Copy the ''ethanol_BASIS1.inp'' into ''ethanol_dens_BASIS1.inp''.</note>
  
 Add the following sections: Add the following sections:
exercises/2018_ethz_mmm/ethanol_2018.1521785214.txt.gz · Last modified: 2020/08/21 10:15 (external edit)