exercises:2018_ethz_mmm:bf3
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exercises:2018_ethz_mmm:bf3 [2018/03/16 11:17] – created dpasserone | exercises:2018_ethz_mmm:bf3 [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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{{ : | {{ : | ||
- | and this is the pictorial view in the gas phase: | ||
- | {{ : | ||
- | In the supplementary material of the paper, which can be found [[http:// | ||
- | |||
- | |||
- | We will compare our results with the published ones. | ||
The input file structure is shown below: | The input file structure is shown below: | ||
<code cp2k> | <code cp2k> | ||
+ | & | ||
+ | | ||
& | & | ||
+ | &SCF | ||
+ | SCF_GUESS RESTART | ||
+ | &END | ||
& | & | ||
| | ||
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&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' |
+ | & | ||
+ | & | ||
+ | | ||
+ | &END | ||
+ | & | ||
+ | | ||
+ | NHOMO 5 | ||
+ | NLUMO 4 | ||
+ | &END MO_CUBES | ||
+ | & | ||
& | & | ||
Line 39: | Line 48: | ||
& | & | ||
| | ||
- | ABC 10 10 10 ! Lengths of the cell vectors A, B, and C | + | ABC 10 10 10 |
&END CELL | &END CELL | ||
- | & | ||
- | H | ||
- | H | ||
- | C | ||
- | C | ||
- | H | ||
- | H | ||
- | &END COORD | ||
& | & | ||
+ | COORD_FILE_NAME BF3.xyz | ||
+ | COORD_FILE_FORMAT XYZ | ||
& | & | ||
&END | &END | ||
&END TOPOLOGY | &END TOPOLOGY | ||
- | & | + | & |
- | & | + | & |
- | @INCLUDE './H_631Gdp.inc' | + | @INCLUDE './B_631GX.inc' |
- | & | + | & |
| | ||
& | & | ||
- | | + | |
- | 0.20000000 | + | |
- | & | + | & |
&END KIND | &END KIND | ||
- | & | + | & |
& | & | ||
- | @INCLUDE './C_631Gdp.inc' | + | @INCLUDE './F_631GX.inc' |
& | & | ||
| | ||
& | & | ||
- | | + | 4 |
- | 0.34883045 | + | |
& | & | ||
&END KIND | &END KIND | ||
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& | & | ||
| | ||
- | | + | |
- | | + | |
&END GLOBAL | &END GLOBAL | ||
- | + | | |
</ | </ | ||
- | The exercise | + | As usual, you can take the tar file of the exercise |
- | <note tip>~psd/ | + | [[https:// |
+ | Copy it to the directory **$HOME/ | ||
- | Copy the files to the created directory in the ''/ | ||
- | <note tip> | ||
- | In the directory you will find the following files: | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | * several '' | ||
- | </ | ||
- | The command to launch the job is | ||
- | <note important>> | ||
- | where file.inp has to be replaced by the relevant prefix of the input file (example: '' | ||
- | In the '' | ||
- | <note important>> | ||
- | 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** | + | |
- | At the line concerning the exchange and correlation potential, | + | Copy the files to the created directory |
- | <note important> | + | <note tip> |
- | * hf.inc for Hartree-Fock | + | In the directory |
- | * pbe.inc for DFT/PBE, with gradient corrected local density | + | * '' |
- | * b3lyp.inp for hybrid functional containing a percentage | + | * '' |
+ | * several '' | ||
</ | </ | ||
- | When you are done with the three levels of theory, then you can redo the exercise with the larger basis set, and change EVERYWHERE | + | The operations |
- | Redo the calculations with the three levels '' | + | <code bash> |
+ | . / | ||
+ | a=$1 | ||
+ | m_xyzrescale $a < BF3.opt.xyz > BF3.xyz | ||
+ | cp BF3.xyz BF3.$a.xyz | ||
+ | m_replace _SCALE_ $a < BF3.0.inp > BF3.$a.inp | ||
+ | cp2k.ssmp -i BF3.$a.inp | ||
+ | |||
+ | mkdir ORB_$a | ||
+ | for b in 12 13 14 15 16 | ||
+ | do | ||
+ | | ||
+ | vmd BF3-" | ||
+ | | ||
+ | | ||
+ | mv out1.tga ORB_$a/ | ||
+ | | ||
+ | |||
+ | | ||
+ | do | ||
+ | | ||
+ | vmd BF3-" | ||
+ | ST=LUMO+" | ||
+ | | ||
+ | mv out1.tga ORB_$a/ | ||
+ | | ||
+ | vmd BF3-" | ||
+ | | ||
- | <note warning> | + | mv dens1.tga ORB_$a/dens1.tga |
- | Assignments: | + | |
- | - Compute the reaction energy for the dehydration reaction of ethanol | + | mv BF3-" |
- | - Prepare | + | |
- | - Compare the results with the published ones (note the conversion factors. You can use the tool at [[http://www.colby.edu/chemistry/PChem/ | + | |
- | - Comment on the dependence on the basis set and on the level of theory (hint: this also need the next theory lecture) | + | rm *bak* |
- | | + | |
- | </ | + | |
+ | </ | ||
- | === BONUS TRACK === | ||
- | <note tip>We may be interested in the visualisation | + | The command to launch |
+ | < | ||
- | Add the following sections: | + | <note important> |
- | **under & | + | Assignments: |
- | <code cp2k> | + | - Run the script with ALPHA=1.0 (meaning: no expansion of the molecule) |
- | & | + | - Look into the BF3.ALPHA.out file to verify |
- | & | + | - What is the homo-lumo gap (distance between highest occupied and lowest unoccupied orbital (remember: it is in Hartree --- write it in eV |
- | &END | + | - The script produces a directory ORB_ALPHA with the orbitals and the density. Compare the orbitals what the illustration above. |
- | & | + | |
- | & | + | - What do you observe in the plots? Which differences? |
- | | + | </note> |
- | & | + | |
- | </ | + | |
- | This tells to read the old wavefunction and to print the cubefile | + | |
- | + | ||
- | At the end of the input file: | + | |
- | <code cp2k> | + | |
- | & | + | |
- | | + | |
- | &END | + | |
- | </code> | + | |
- | Then, change '' | ||
exercises/2018_ethz_mmm/bf3.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1