# CP2K Open Source Molecular Dynamics

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exercises:2015_ethz_mmm:mo_ethene

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 exercises:2015_ethz_mmm:mo_ethene [2015/04/17 09:34]oschuett exercises:2015_ethz_mmm:mo_ethene [2020/08/21 10:15] (current) Both sides previous revision Previous revision 2015/04/17 15:36 oschuett 2015/04/17 15:33 oschuett 2015/04/17 09:34 oschuett 2015/02/06 17:49 external edit Next revision Previous revision 2015/04/17 15:36 oschuett 2015/04/17 15:33 oschuett 2015/04/17 09:34 oschuett 2015/02/06 17:49 external edit Line 1: Line 1: - ====== Molecular orbitals of Ethene ====== + ======= Molecular orbitals of Ethene ======= - In this exercise, you will perform an electronic structure calculation to obtain the ethene molecular orbitals (MOs). 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 orbitals with VMD. + In this exercise, you will perform an electronic structure calculation to obtain the ethene molecular orbitals (MOs). 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 the calculation ===== 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: [[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]] Line 17: Line 17: &DFT &DFT &PRINT &PRINT - &MO_CUBES                 ! Controls the printing of the MOs in the output and in the *.cube files + &MO_CUBES                 ! Controls which MOs are written to cube-files. - NHOMO 5                   ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 5. + NHOMO 5 - NLUMO 5                   ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 5. + NLUMO 5 &END MO_CUBES &END MO_CUBES + &PDOS                     ! Controls which MOs are included in the pdos-files. + NLUMO 5 + &END &END PRINT &END PRINT &POISSON                    ! Solver requested for non periodic calculations &POISSON                    ! Solver requested for non periodic calculations Line 113: Line 116: &END SUBSYS &END SUBSYS &END FORCE_EVAL &END FORCE_EVAL - - ==== 2. Step ==== + ===== 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. \\ + If the calculation was performed correctly, a number of new files should have been written: - The ethene band gap (energy difference between HOMO and LUMO) is also printed. + - + $ls *.pdos *.cube - **** **** ****** ** PROGRAM STARTED AT + ethene-k1-1.pdos ethene-WFN_00004_1-1_0.cube ethene-WFN_00006_1-1_0.cube ethene-WFN_00008_1-1_0.cube ethene-WFN_00010_1-1_0.cube ethene-WFN_00012_1-1_0.cube - ***** ** *** *** ** PROGRAM STARTED ON + ethene-k2-1.pdos ethene-WFN_00005_1-1_0.cube ethene-WFN_00007_1-1_0.cube ethene-WFN_00009_1-1_0.cube ethene-WFN_00011_1-1_0.cube ethene-WFN_00013_1-1_0.cube - ** **** ****** PROGRAM STARTED BY + - ***** ** ** ** ** PROGRAM PROCESS ID + - **** ** ******* ** PROGRAM STARTED IN + - + - ..... + - Eigenvalues of the occupied subspace spin 1 + - --------------------------------------------- + - list of eigenvalues + - .... + - + - Lowest Eigenvalues of the unoccupied subspace spin 1 + - ----------------------------------------------------- + - list of eigenvalues + - ..... + - + - HOMO - LUMO gap [eV] : + - ...... + - + - + - **** **** ****** ** PROGRAM ENDED AT + - ***** ** *** *** ** PROGRAM RAN ON + - ** **** ****** PROGRAM RAN BY + - ***** ** ** ** ** PROGRAM PROCESS ID + - **** ** ******* ** PROGRAM STOPPED IN + - Note that the eigenvalues are given in Eh , while the Band gap is given in eV. + First have a look at the *.pdos files. PDOS stands for Projected Density of States. These files list the energies and occupation of the MOs. Furthermore, they show how the MOs are compose from basis-functions of different atoms (one pdos-file for each atomic kind) and angular momentum (s,p,d). Hence, these numbers always sum up to 1.0. + ===== 3. Step ===== - ==== 3. Step ==== + Now look at the *.cube files. + Each cube-file contains the electronic density of one MO mapped onto a regular 3D-grid. Not all MOs were written to a cube-file, this is controlled by the PRINT_MO section. Their filenames tell you to which MO a cube-file belongs. For example ''ethene-WFN_00005_1-1_0.cube'' contains the 5th orbital. - In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files is generated. \\ + Use VMD to visualize the cube-files: - The number of cubes strictly depends on what you have specified in the PRINT_MO section. No extra files are generated (while in the output a default list of all the occupied MOs eigenvalues is anyway produced.) \\ + - To run ''vmd ethene-WFN_00008_1-1_0.cube'' - ∗.cube files report the structure of a given MO and can be visualized with VMD: + - To visualize the molecule (sometimes it's not visible by default):\\ **Graphics > Representations > Draw style > Drawing Method=CPK** - + - Add a second representation by clicking on **Create Rep** - * To run vmd: vmd ethene-WFN_00008_1-1_0.cube + - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe** - * To visualize the molecule (sometimes the default settings are not visible with VMD in Brutus):\\ Graphics > Representations > Draw style > Drawing Method: CPK + - Finally set the **Isovalue** of to a reasonable value, eg. 0.1 . - * To visualize the MO structure in VMD:\\ Graphics > Representations > Draw style > Drawing Method: Isosurfaces + - To visualize the positive and the negative part of an orbital simultaneously, you will have to add a third representation with a negative **Isovalue**, e.g. -0.1 . - * In Isosurfaces, set Draw to "Wireframe" (other formats may not be visible with VMD in Brutus) + - To give the two representations different colors, set their **Coloring Method=ColorID** and choose different ids. - * In Isosurfaces, set Isovalue to 0.1, 0.01 ... + - * To visualize the positive and the negative part of an orbital simultaneously, add a second isosurface representation with isovalues -0.1, -0.01, ... + - * To give the two representations different colors, set their "Coloring Method" to "ColorID" and choose different ids. + What you get should look similar to this: What you get should look similar to this: {{ ethene_pi_orbital.png |}} {{ ethene_pi_orbital.png |}} - ==== Questions ==== - - - 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. - + ===== Questions ===== + - Quickly sketch the energy distribution of the MOs. + - What's the energy of the HOMO, LUMO, and the band-gap? + - Use VMD to identify the shape and energy of the$\pi$and$\pi^*\$ orbitals. -