exercises:2014_ethz_mmm:mo_ethene
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
exercise:mo_benzene [2014/03/25 17:23] – sclelia | exercises:2014_ethz_mmm:mo_ethene [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== Molecular orbitals of Benzene | + | ====== Molecular orbitals of Ethene |
- | In this exercise, you will perform an electronic structure | + | In this exercise, you will perform an electronic structure |
- | If performed correctly, your calculations will produce a list of occupied and non occupied MOs and a series of *.cube files, that allow the visualization of the oribital with VMD. | + | |
==== 1. Step ==== | ==== 1. Step ==== | ||
Run a calculation with the following (commented) input file. \\ | Run a calculation with the following (commented) input file. \\ | ||
- | Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[exercise:basis_sets|Basis Sets]] | + | Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[basis_sets|Basis Sets]] |
- | <code - benzene.inp > | + | <code - ethene.inp > |
+ | |||
+ | |||
&GLOBAL | &GLOBAL | ||
- | PROJECT | + | PROJECT |
RUN_TYPE ENERGY | RUN_TYPE ENERGY | ||
PRINT_LEVEL MEDIUM | PRINT_LEVEL MEDIUM | ||
Line 16: | Line 17: | ||
& | & | ||
METHOD Quickstep | METHOD Quickstep | ||
- | & | + | &DFT |
& | & | ||
- | NHOMO 3 ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 3. | + | NHOMO 5 ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 5. |
- | NLUMO 3 ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 3. | + | NLUMO 5 ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 5. |
- | &END MO_CUBES | + | &END MO_CUBES |
&END PRINT | &END PRINT | ||
& | & | ||
PERIODIC NONE | PERIODIC NONE | ||
- | PSOLVER | + | PSOLVER |
&END POISSON | &END POISSON | ||
& | & | ||
METHOD GAPW ! Method: gaussian and augmented plane waves | METHOD GAPW ! Method: gaussian and augmented plane waves | ||
&END QS | &END QS | ||
- | | + | |
& | & | ||
- | MAX_ITER_LUMOS | + | MAX_ITER_LUMOS |
EPS_SCF 1.0E-6 | EPS_SCF 1.0E-6 | ||
SCF_GUESS ATOMIC | SCF_GUESS ATOMIC | ||
MAX_SCF 60 | MAX_SCF 60 | ||
- | EPS_LUMOS | + | EPS_LUMOS |
& | & | ||
EPS_SCF 1.0E-6 | EPS_SCF 1.0E-6 | ||
MAX_SCF 6 | MAX_SCF 6 | ||
&END | &END | ||
- | &OT | ||
- | PRECONDITIONER FULL_ALL | ||
- | ENERGY_GAP 0.1 | ||
- | &END OT | ||
&END SCF | &END SCF | ||
- | | + | |
& | & | ||
& | & | ||
Line 57: | Line 54: | ||
&END XC | &END XC | ||
&END DFT | &END DFT | ||
- | | + | |
&SUBSYS | &SUBSYS | ||
&CELL | &CELL | ||
Line 68: | Line 65: | ||
&END | &END | ||
&COORD | &COORD | ||
- | C | + | C -2.15324 |
- | C 6.197400 | + | C -0.83403 |
- | C | + | H -0.25355 |
- | C | + | H -0.33362 4.51626 -0.89682 |
- | C 3.802600 | + | H -2.65364 |
- | C | + | H -2.73371 4.18846 -0.89198 |
- | H 5.000000 | + | |
- | H | + | |
- | H | + | |
- | H 5.000000 | + | |
- | H | + | |
- | H | + | |
&END COORD | &END COORD | ||
- | &KIND H !Potential | + | &KIND H ! Basis set and potential |
- | & | + | |
- | | + | |
- | 1 0 0 | + | 1 0 0 |
- | 75.42300000 | + | 18.73113700 |
- | 11.35000000 | + | 2.82539370 |
- | 2.59930000 | + | 0.64012170 |
- | 0.73513000 | + | |
1 0 0 1 1 | 1 0 0 1 1 | ||
- | 0.23167000 | + | 0.16127780 |
- | | + | |
- | 0.07414700 | + | |
- | 1 1 1 1 1 | + | |
- | 1.60000000 | + | |
- | 1 1 1 1 1 | + | |
- | 0.45000000 | + | |
- | 1 2 2 1 1 | + | |
- | 1.25000000 | + | |
- | | + | |
- | POTENTIAL ALL | + | |
- | & | + | |
- | 1 0 0 | + | |
- | 0.20 0 | + | |
- | &END | + | |
&END KIND | &END KIND | ||
- | &KIND C !Potential | + | &KIND C ! Basis set and potential |
- | & | + | |
- | | + | |
- | 1 0 0 | + | 1 0 0 |
- | 7857.10000000 | + | 3047.52490000 |
- | 1178.70000000 | + | 457.36951000 |
- | | + | |
- | 75.94800000 | + | 29.21015500 |
- | 24.55900000 | + | |
- | 8.62120000 | + | 3.16392700 |
- | 3.12780000 | + | 1 0 1 |
- | 0.82202000 | + | |
- | 1 | + | |
- | 0.33017000 | + | 0.54424930 |
- | 1 0 0 | + | 1 |
- | | + | 0.16871440 |
- | 1 1 1 4 1 | + | |
- | | + | |
- | | + | |
- | 2.23570000 | + | |
- | 0.76447000 | + | |
- | 1 1 1 1 1 | + | |
- | 0.26232000 | + | |
- | 1 1 1 1 1 | + | |
- | 0.08463800 | + | |
1 2 2 1 1 | 1 2 2 1 1 | ||
- | | + | 0.80000000 |
- | 1 2 2 1 1 | + | |
- | 0.45000000 | + | |
- | 1 3 3 1 1 | + | |
- | | + | |
- | &END | + | |
- | POTENTIAL ALL | + | |
- | & | + | |
- | | + | |
- | | + | |
- | &END | + | |
&END KIND | &END KIND | ||
- | |||
&END SUBSYS | &END SUBSYS | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
Line 150: | Line 118: | ||
</ | </ | ||
- | <note tip> this calculation can be fairly expensive, a run on multiple nodes is reccomended. </ | ||
- | To run on multiple nodes: | + | ==== 2. Step ==== |
- | < | + | If the calculation was performed correctly, a list of ALL the occupied MOs and 3 (as specified in the input) unoccupied MOs eigenvalues are printed in the output. \\ |
- | bsub -n 16 mpirun cp2k.popt -i benzene -o benz.out | + | The ethene |
- | </ | + | |
- | + | ||
- | ==== 2. Step ==== | + | |
- | If the calculation was performed correctly, a list of ALL the occupied MOs and 3 (as specified in the input)unoccupied MOs eigenvalues are printed in the output. \\ | + | |
- | The benzene | + | |
< | < | ||
Line 197: | Line 159: | ||
==== 3. Step ==== | ==== 3. Step ==== | ||
- | In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files are generated. \\ | + | In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files is generated. \\ |
- | The number | + | The number of cubes strictly |
- | *.cube files report the structure of a given MO and can be visualized with VMD: | + | ∗.cube files report the structure of a given MO and can be visualized with VMD: |
- | * To run vmd: vmd benzene-WFN_00021_1-1_0.cube | + | |
- | * To visualize the MO structure in VMD : Graphics > Representations > Draw style > Drawing Method: Isosurfaces | + | * To run vmd: vmd ethene-WFN_00008_1-1_0.cube |
+ | * To visualize the molecule (sometimes the default settings are not visible with VMD in Brutus): | ||
+ | * To visualize the MO structure in VMD:\\ | ||
+ | * In Isosurfaces, | ||
* In Isosurfaces, | * In Isosurfaces, | ||
+ | * To visualize the positive and the negative part of an orbital simultaneously, | ||
+ | * To give the two representations different colors, set their " | ||
+ | What you get should look similar to this: | ||
+ | {{ ethene_pi_orbital.png |}} | ||
==== Questions ==== | ==== Questions ==== | ||
- | Quickly sketch the energy distribution for the 21 occupied MOs and the three unoccupied MOs. | ||
+ | - Quickly sketch the energy distribution for the occupied MOs and the five unoccupied MOs. \\ | ||
+ | - By using VMD, identify the shape and energy of the π and π* orbitals. | ||
| | ||
exercises/2014_ethz_mmm/mo_ethene.1395768204.txt.gz · Last modified: 2020/08/21 10:14 (external edit)