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benzen_eigenvalues [2009/11/24 15:47]
jelen
benzen_eigenvalues [2017/03/06 14:55] (current)
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-===== Eigen-spectra =====+===== Eigenvalue ​spectra =====
  
 Once we have obtained the ground state atomic configuration,​ we can perform electronic structure analysis. To obtain the detail information about the eigen-energy spectra of the benzene molecule, we perform one time-step run with the fixed ground state charges (we suppose our optimized structure is stored in  **''​answer.bas''​** file). Our **''​fireball.in''​** file looks like now: Once we have obtained the ground state atomic configuration,​ we can perform electronic structure analysis. To obtain the detail information about the eigen-energy spectra of the benzene molecule, we perform one time-step run with the fixed ground state charges (we suppose our optimized structure is stored in  **''​answer.bas''​** file). Our **''​fireball.in''​** file looks like now:
  
 +<​code>​
   &OPTION   &OPTION
   basisfile = answer.bas   basisfile = answer.bas
Line 14: Line 15:
   iwrteigen = 1   iwrteigen = 1
   &END   &END
 +</​code>​
  
 Once the calculation is done, **''​eigen.dat''​** file appears in the working directory, which lists in ascending order all eigenvalues of molecular orbitals: Once the calculation is done, **''​eigen.dat''​** file appears in the working directory, which lists in ascending order all eigenvalues of molecular orbitals:
  
 +<​code>​
            ​1 ​         36            ​1 ​         36
   ------ the energy eigenvalues ----   ------ the energy eigenvalues ----
Line 29: Line 31:
      ​16.15497 ​    ​17.03885 ​    ​81.57499 ​    ​83.17471      ​16.15497 ​    ​17.03885 ​    ​81.57499 ​    ​83.17471
      ​83.19519 ​    ​86.09707 ​    ​86.11842 ​    ​87.78916      ​83.19519 ​    ​86.09707 ​    ​86.11842 ​    ​87.78916
 +</​code>​
  
 Information about occupancies of individual molecular level can be written into output file, if keyword **''​iwrtefermi''​** is switched on. In this way energy levels of HOMO and LUMO orbitals can be identified. In our particular case we found in output file: Information about occupancies of individual molecular level can be written into output file, if keyword **''​iwrtefermi''​** is switched on. In this way energy levels of HOMO and LUMO orbitals can be identified. In our particular case we found in output file:
  
  
- +<​code>​
   ------ fermi ioccupy_k for k-point =            1   ------ fermi ioccupy_k for k-point =            1
   Band n =    1 k-points: ioccupy =  1   Band n =    1 k-points: ioccupy =  1
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   Band n =   35 k-points: ioccupy =  0   Band n =   35 k-points: ioccupy =  0
   Band n =   36 k-points: ioccupy =  0   Band n =   36 k-points: ioccupy =  0
 +</​code>​
  
 From the list, we can identify the last occupied molecular level (HOMO) is no. 15 and first unoccupied level (LUMO) is no. 16. Let note, the list of eigenvalues can be found in '''​eigen.dat'''​ file accounting appropriate number of levels (in ascending order). From the list, we can identify the last occupied molecular level (HOMO) is no. 15 and first unoccupied level (LUMO) is no. 16. Let note, the list of eigenvalues can be found in '''​eigen.dat'''​ file accounting appropriate number of levels (in ascending order).
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 (i) switch on '''​iwrtdos'''​ keyword in section '''&​OUTPUT''',​ so '''​fireball.in'''​ looks like now:  (i) switch on '''​iwrtdos'''​ keyword in section '''&​OUTPUT''',​ so '''​fireball.in'''​ looks like now: 
  
 +<​code>​
   &OPTION   &OPTION
   basisfile = answer.bas   basisfile = answer.bas
Line 95: Line 98:
   iwrtdos = 1   iwrtdos = 1
   &END   &END
- +</​code>​ 
 (ii) an extra new file called **''​dos.optional''​** has to be created in the working directory with following syntax: (ii) an extra new file called **''​dos.optional''​** has to be created in the working directory with following syntax:
  
 +
 +<​code>​
   1.0                   ! scale factor (leave 1.0)   1.0                   ! scale factor (leave 1.0)
   1       ​12 ​           ! list of atoms to analyze DOS   1       ​12 ​           ! list of atoms to analyze DOS
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   0.0     ​0.0 ​          ! leave untouched   0.0     ​0.0 ​          ! leave untouched
   0.05                  ! imaginary part of Green function (controls energy level smearing)   0.05                  ! imaginary part of Green function (controls energy level smearing)
 +</​code>​
  
 In this particular case, all 12 atoms will be involved in the DOS analysis and DOS will be calculated from energy -22.0 until 0.0 eV with energy step 0.05 eV. Several files will appear in the working directory **''​dens_XXX.dat''​** containing projected DOS on each atom labeled ''​XXX''​ and a file **''​dens_TOT.dat''​** including the total DOS. In this particular case, all 12 atoms will be involved in the DOS analysis and DOS will be calculated from energy -22.0 until 0.0 eV with energy step 0.05 eV. Several files will appear in the working directory **''​dens_XXX.dat''​** containing projected DOS on each atom labeled ''​XXX''​ and a file **''​dens_TOT.dat''​** including the total DOS.
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 ===== Real-space electronic density ===== ===== Real-space electronic density =====
    
-Sometimes is more illustrative to visualize the electron density in real-space. This can help as a primitive estimation of STM images or it can provide more information about spatial (de)localization certain molecular levels. Here we'll visualize HOMO and LUMO state of the molecule. To do this, we need to first switch on keyword ''​iwrtewf''​ in **''​fireball.in''​** file (the section **''&​OUTPUT''​**). As a next step, we need to create a new section in **''​fireball.in''​** called **''&​MESH''​** with following keywords:+Sometimes is more illustrative to visualize the electron density in real-space. This can help as a primitive estimation of STM images or it can provide more information about spatial (de)localization certain molecular levels. Here we'll visualize HOMO and LUMO state of the molecule. To do this, we need to first switch on keyword ​**''​iwrtewf''​** in **''​fireball.in''​** file (the section **''&​OUTPUT''​**). As a next step, we need to create a new section in **''​fireball.in''​** called **''&​MESH''​** with following keywords:
  
 +
 +<​code>​
   &MESH   &MESH
   iewform = 1               ! individual levels listed bellow will be plotted in separated files    iewform = 1               ! individual levels listed bellow will be plotted in separated files 
   npbands = 2               ! number of molecular levels to be plotted   npbands = 2               ! number of molecular levels to be plotted
-  pbands =36,37             ! list of molecular levels to be plotted ​+  pbands =15,16             ! list of molecular levels to be plotted ​
   &END   &END
 +</​code>​
  
 Real-space densities of individual molecular levels are stored in **''​bandplot_XXXX.xsf''​** files, where ''​XXXX''​ means number of given molecular orbital. These files are stored in an internal format of visualization program [[http://​www.xcrysden.org |Xcrysden]]. Real-space densities of individual molecular levels are stored in **''​bandplot_XXXX.xsf''​** files, where ''​XXXX''​ means number of given molecular orbital. These files are stored in an internal format of visualization program [[http://​www.xcrysden.org |Xcrysden]].
  
-real density of state of the HOMO molecular state \\+the real-space distribution of the density of state of the HOMO molecular state  
 + 
 +{{:​benzen:​benzen_homo.png|HOMO Benzen}} 
 + 
 +the real-space distribution of the density of state of the LUMO molecular state  
 + 
 +{{:​benzen:​benzen_lumo.png|LUMO benzen}} 
 + 
 +<​code>​ 
 +  &MESH 
 +  iewform = 2            ! sum density in energy window ​   
 +  ewfewin_min = -8.16    ! lower energy bound 
 +  ewfewin_max = -2.16    ! lower energy bound 
 +  &END 
 +</​code>​ 
 + 
  
benzen_eigenvalues.1259074044.txt.gz · Last modified: 2011/02/18 13:14 (external edit)