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exercise:mo_benzene [2014/03/25 17:07] – scleliaexercise:2014_ethz_mmm:mo_ethene [2014/10/15 13:38] – oschuett
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-====== Molecular orbitals of Benzene ====== +====== Molecular orbitals of Ethene ====== 
-In this exercise, you will perform an electronic structure calculations to obtain the benzene molecular orbitals (MOs).\\ +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. 
-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 benzene+  PROJECT ethene
   RUN_TYPE ENERGY   RUN_TYPE ENERGY
   PRINT_LEVEL MEDIUM   PRINT_LEVEL MEDIUM
Line 16: Line 17:
 &FORCE_EVAL &FORCE_EVAL
   METHOD Quickstep              ! Electronic structure method (DFT,...)   METHOD Quickstep              ! Electronic structure method (DFT,...)
-  &DFT                            +  &DFT
     &PRINT     &PRINT
       &MO_CUBES                 ! Controls the printing of the MOs in the output and in the *.cube files       &MO_CUBES                 ! Controls the printing of the MOs in the output and in the *.cube files
-      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
     &POISSON                    ! Solver requested for non periodic calculations     &POISSON                    ! Solver requested for non periodic calculations
       PERIODIC NONE       PERIODIC NONE
-      PSOLVER  MT               ! Type of solver+      PSOLVER  WAVELET          ! Type of solver
     &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
-  +
     &SCF                        ! Parameters controlling the convergence of the scf. This section should not be changed.      &SCF                        ! Parameters controlling the convergence of the scf. This section should not be changed. 
-      MAX_ITER_LUMOS 5000+      MAX_ITER_LUMOS 10000
       EPS_SCF 1.0E-6       EPS_SCF 1.0E-6
       SCF_GUESS ATOMIC       SCF_GUESS ATOMIC
       MAX_SCF 60       MAX_SCF 60
-      EPS_LUMOS  0.0001+      EPS_LUMOS  0.000001
       &OUTER_SCF       &OUTER_SCF
         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
-    +
     &XC                        ! Parametes needed to compute the electronic exchange potential      &XC                        ! Parametes needed to compute the electronic exchange potential 
       &XC_FUNCTIONAL NONE      ! No xc functional       &XC_FUNCTIONAL NONE      ! No xc functional
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     5.000000     6.382700     5.000000 +    C         -2.15324        3.98235        0.00126 
-C     6.197400     5.691300     5.000000 +    C         -0.83403        4.16252       -0.00140 
-C     6.197400     4.308700     5.000000 +    H         -0.25355        3.95641        0.89185 
-C     5.000000     3.617300     5.000000 +    H         -0.33362        4.51626       -0.89682 
-C     3.802600     4.308700     5.000000 +    H         -2.65364        3.62861        0.89669 
-C     3.802600     5.691300     5.000000 +    H         -2.73371        4.18846       -0.89198
-H     5.000000     7.456100     5.000000 +
-H     7.127000     6.228000     5.000000 +
-H     7.127000     3.772000     5.000000 +
-H     5.000000     2.543900     5.000000 +
-H     2.873000     3.772000     5.000000 +
-H     2.873000     6.228000     5.000000+
     &END COORD     &END COORD
-    &KIND H                                  !Potential and basis sets for H +    &KIND H                    ! Basis set and potential for H 
-      &BASIS +     &BASIS 
-  6 +  2 
-  1  0  0  4  1 +  1  0  0  3  1 
-         75.42300000          0.00240650 +         18.73113700          0.03349460 
-         11.35000000          0.01848700 +          2.82539370          0.23472695 
-          2.59930000          0.08974200 +          0.64012170          0.81375733
-          0.73513000          0.28111000+
   1  0  0  1  1   1  0  0  1  1
-          0.23167000          1.00000000 +          0.16127780          1.00000000 
-  1  0  0  1  1 +     &END 
-          0.07414700          1.00000000 +     POTENTIAL ALL 
-  1  1  1  1  1 +     &POTENTIAL 
-          1.60000000          1.00000000 +     1    0    0 
-  1  1  1  1  1 +     0.20000000    0 
-          0.45000000          1.00000000 +     &END
-  1  2  2  1  1 +
-          1.25000000          1.00000000 +
-      &END +
-      POTENTIAL ALL +
-      &POTENTIAL +
-          1    0    0 +
-          0.20 0 +
-      &END+
     &END KIND     &END KIND
-    &KIND C                                    !Potential and basis sets for C              +    &KIND C                    ! Basis set and potential for C 
-      &BASIS +     &BASIS 
-  9 +  4 
-  1  0  0  8  2 +  1  0  0  6  1 
-       7857.10000000          0.00056825          0.00000000 +       3047.52490000          0.00183470 
-       1178.70000000          0.00439150         -0.00000059 +        457.36951000          0.01403730 
-        268.32000000          0.02250400         -0.00006275 +        103.94869000          0.06884260 
-         75.94800000          0.08665300         -0.00075773 +         29.21015500          0.23218440 
-         24.55900000          0.24405000         -0.00733080 +          9.28666300          0.46794130 
-          8.62120000          0.44148000         -0.03893200 +          3.16392700          0.36231200 
-          3.12780000          0.35332000         -0.08890800 +  1  0  1  3  1  1 
-          0.82202000          0.00000000          0.21689000 +          7.86827240         -0.11933240          0.06899910 
-  1  0  0  1  1 +          1.88128850         -0.16085420          0.31642400 
-          0.33017000          1.00000000 +          0.54424930          1.14345640          0.74430830 
-  1  0  0  1  1 +  1  0  1  1  1  1 
-          0.11463000          1.00000000 +          0.16871440          1.00000000          1.00000000
-  1  1  1  4  1 +
-         33.77500000          0.00602940 +
-          7.67660000          0.04322800 +
-          2.23570000          0.16301000 +
-          0.76447000          0.36504000 +
-  1  1  1  1  1 +
-          0.26232000          1.00000000 +
-  1  1  1  1  1 +
-          0.08463800          1.00000000+
   1  2  2  1  1   1  2  2  1  1
-          1.40000000          1.00000000 +          0.80000000          1.00000000 
-  1  2  2  1  1 +     &END 
-          0.45000000          1.00000000 +     POTENTIAL ALL 
-  1  3  3  1  1 +     &POTENTIAL 
-          0.95000000          1.00000000 +     4    2    0 
-      &END +     0.34883045    0    
-      POTENTIAL ALL +     &END
-      &POTENTIAL +
-         4    2    0 +
-         0.34883045    0 +
-      &END+
     &END KIND     &END KIND
- 
   &END SUBSYS   &END SUBSYS
 &END FORCE_EVAL &END FORCE_EVAL
Line 151: Line 119:
  
  
 + ==== 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 list of ALL the occupied MOs and 3 (as specified in the input)unoccupied MOs eigenvalues are printed in the output. \\ +The ethene band gap (energy difference between HOMO and LUMO) is also printed. 
-The benzene band gap (energy difference between HOMO and LUMO) is also printed. +
 <code> <code>
  
Line 190: Line 158:
  
  ==== 3. Step ====  ==== 3. Step ====
-In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube orbitals are generated. \\ 
-The number and typology of cubes 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 produced.  \\ 
-*.cube files can be visualized with VMD: 
  
 +In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files is generated. \\
 +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.)  \\
 +∗.cube files report the structure of a given MO and can be visualized with VMD:
  
 +  * 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):\\    Graphics > Representations > Draw style > Drawing Method: CPK
 +  * To visualize the MO structure in VMD:\\    Graphics > Representations > Draw style > Drawing Method: Isosurfaces 
 +  * In  Isosurfaces, set Draw to "Wireframe" (other formats may not be visible with VMD in Brutus)
 +  * 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:
 +{{ 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. 
 +
 +
 +  
  
exercises/2014_ethz_mmm/mo_ethene.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1