exercises:2018_ethz_mmm:ethanol_2018
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revisionNext revisionBoth sides next revision | ||
exercises:2018_ethz_mmm:ethanol_2018 [2018/03/23 06:06] – created dpasserone | exercises:2018_ethz_mmm:ethanol_2018 [2018/03/23 15:37] – dpasserone | ||
---|---|---|---|
Line 17: | Line 17: | ||
<code cp2k> | <code cp2k> | ||
+ | & | ||
+ | | ||
& | & | ||
+ | BASIS_SET_FILE_NAME ./ | ||
& | & | ||
| | ||
Line 24: | Line 27: | ||
&END POISSON | &END POISSON | ||
& | & | ||
- | | + | |
&END QS | &END QS | ||
+ | |||
# | # | ||
# Include the exchange and correlation information | # Include the exchange and correlation information | ||
# | # | ||
- | @INCLUDE './pbe.inc' | + | @INCLUDE './hf.inc' |
& | & | ||
Line 41: | Line 44: | ||
&END CELL | &END CELL | ||
& | & | ||
- | H | + | H |
- | H | + | |
- | | + | H |
- | C | + | |
- | H 5.4118318595 | + | |
- | H | + | |
&END COORD | &END COORD | ||
& | & | ||
Line 53: | Line 53: | ||
&END TOPOLOGY | &END TOPOLOGY | ||
- | | + | |
- | &BASIS | + | |
- | @INCLUDE './ | + | |
- | & | + | |
+ | &POTENTIAL | ||
+ | 4 4 0 | ||
+ | 0.24762086 | ||
+ | & | ||
+ | &END KIND | ||
+ | &KIND H ! potential and basis for H | ||
+ | | ||
| | ||
& | & | ||
1 0 0 | 1 0 0 | ||
0.20000000 | 0.20000000 | ||
- | & | + | & |
&END KIND | &END KIND | ||
&KIND C ! potential and basis for C | &KIND C ! potential and basis for C | ||
- | & | + | BASIS_SET _MYBASIS_ |
- | @INCLUDE ' | + | |
- | & | + | |
| | ||
& | & | ||
Line 78: | Line 83: | ||
& | & | ||
| | ||
- | | + | |
| | ||
&END GLOBAL | &END GLOBAL | ||
- | + | | |
</ | </ | ||
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:// |
- | Copy the files to the created directory in the '' | + | Copy the file to the created directory in the '' |
+ | < | ||
+ | tar xvf exercise_5.tar | ||
+ | </ | ||
<note tip> | <note tip> | ||
In the directory you will find the following files: | In the directory you will find the following files: | ||
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * several '' | + | * '' |
</ | </ | ||
+ | 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, | ||
+ | < | ||
+ | m_replace _MYBASIS_ ' | ||
+ | </ | ||
+ | (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> | + | <note important> |
- | where file.inp has to be replaced by the relevant prefix of the input file (example: '' | + | In the '' |
- | In the '' | + | <note important>> |
- | <note important>> | + | |
- | This will list all the energies. | + | This will list all the energies. |
+ | |||
+ | ^ 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 '' | ||
- | 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 | ||
- | </ | ||
- | When you are done with the three levels of theory, then you can redo the exercise with the larger | + | <note important> |
- | Redo the calculations with the three levels '' | + | |
<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 | + | - Prepare a table with rows and columns: on the rows the basis set, on the columns |
- Compare the results with the published ones (note the conversion factors. You can use the tool at [[http:// | - Compare the results with the published ones (note the conversion factors. You can use the tool at [[http:// | ||
- | - 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? | ||
</ | </ | ||
Line 127: | Line 149: | ||
=== BONUS TRACK === | === BONUS TRACK === | ||
- | <note tip>We may be interested in the visualisation of the electronic density. Copy the '' | + | <note tip>We may be interested in the visualisation of the electronic density. Copy the '' |
Add the following sections: | Add the following sections: |
exercises/2018_ethz_mmm/ethanol_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1