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example:electronic_structure_analysis [2009/11/07 10:20]
jelen created 		example:electronic_structure_analysis [2011/02/18 13:13] (current)
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 Once we have obtained an optimized atomic configuration,​we can perform electronic structure analysis. To obtain the detail information about energy spectra of the molecule, we perform one-time step run with fixed charges (our optimized structure is stored in '''​ answer.bas'''​ file). Our fireball.in file looks like: Once we have obtained an optimized atomic configuration,​we can perform electronic structure analysis. To obtain the detail information about energy spectra of the molecule, we perform one-time step run with fixed charges (our optimized structure is stored in '''​ answer.bas'''​ file). Our fireball.in file looks like:
  
-  &OPTION\\ +  &​OPTION 
-  basisfile = answer.bas\\ +  basisfile = answer.bas 
-  nstepf = 1\\ +  nstepf = 1 
-  icluster = 1\\ +  icluster = 1 
-  iqout = 1\\ +  iqout = 1 
-  ifixcharge = 1\\ +  ifixcharge = 1 
-  dt = 0.5\\ +  dt = 0.5 
-  &END\\ +  &END 
-  &OUTPUT\\ +  &​OUTPUT 
-  iwrteigen = 1\\ +  iwrteigen = 1 
-  &END\\+  &END
  
  
-Finishing the calculation,​ ''​ eigen.dat''​ file appears in the working directory, which lists in ascending order all eigenvalues of molecular orbitals:+Finishing the calculation,​ ''​eigen.dat''​ file appears in the working directory, which lists in ascending order all eigenvalues of molecular orbitals:
  
  
            ​1 ​        142            ​1 ​        142
-  ------ the energy eigenvalues ​----+   --- the energy eigenvalues ---
       -20.77644 ​   -20.17576 ​   -19.32420 ​   -18.49408       -20.77644 ​   -20.17576 ​   -19.32420 ​   -18.49408
-    ​-18.49262 ​   -17.56440 ​   -17.48782 ​   -16.37893 +     -18.49262 ​   -17.56440 ​   -17.48782 ​   -16.37893 
-    -16.35960 ​   -14.45772 ​   -13.77290 ​   -12.91450 +     ​-16.35960 ​   -14.45772 ​   -13.77290 ​   -12.91450 
-    -12.55894 ​   -12.31129 ​   -11.72733 ​   -10.57604 +     ​-12.55894 ​   -12.31129 ​   -11.72733 ​   -10.57604 
-    -10.47081 ​   -10.27380 ​    ​-9.84700 ​    ​-9.75059 +     ​-10.47081 ​   -10.27380 ​    ​-9.84700 ​    ​-9.75059 
-     ​-9.28453 ​    ​-9.25281 ​    ​-8.86563 ​    ​-8.08602 +      -9.28453 ​    ​-9.25281 ​    ​-8.86563 ​    ​-8.08602 
-     ​-7.86517 ​    ​-7.84647 ​    ​-7.63290 ​    ​-7.56571 +      -7.86517 ​    ​-7.84647 ​    ​-7.63290 ​    ​-7.56571 
-     ​-7.38417 ​    ​-7.07353 ​    ​-6.59935 ​    ​-5.95037 +      -7.38417 ​    ​-7.07353 ​    ​-6.59935 ​    ​-5.95037 
-     ​-5.93908 ​    ​-5.79952 ​    ​-4.77435 ​    ​-3.52791 +      -5.93908 ​    ​-5.79952 ​    ​-4.77435 ​    ​-3.52791 
-     ​-1.31315 ​    ​-0.15600 ​     0.13238 ​     0.36040 +      -1.31315 ​    ​-0.15600 ​     0.13238 ​     0.36040 
-      0.95653 ​     0.98146 ​     1.60240 ​     2.20926 +       ​0.95653 ​     0.98146 ​     1.60240 ​     2.20926 
-      2.36855 ​     2.46027 ​     2.81924 ​     3.35559 +       ​2.36855 ​     2.46027 ​     2.81924 ​     3.35559 
-      4.89158 ​     5.47431 ​     5.80665 ​     5.83704 +       ​4.89158 ​     5.47431 ​     5.80665 ​     5.83704 
-      6.03328 ​     6.93077 ​     6.98308 ​     7.45317 +       ​6.03328 ​     6.93077 ​     6.98308 ​     7.45317 
-      7.80996 ​     9.21705 ​     9.23329 ​     9.72755 +       ​7.80996 ​     9.21705 ​     9.23329 ​     9.72755 
-     ​10.35864 ​    ​10.52539 ​    ​11.11532 ​    ​11.31138 +      10.35864 ​    ​10.52539 ​    ​11.11532 ​    ​11.31138 
-     ​11.34314 ​    ​11.65157 ​    ​11.71850 ​    ​11.98661 +      11.34314 ​    ​11.65157 ​    ​11.71850 ​    ​11.98661 
-     ​12.43798 ​    ​12.47948 ​    ​12.64843 ​    ​13.13170 +      12.43798 ​    ​12.47948 ​    ​12.64843 ​    ​13.13170 
-     ​14.04051 ​    ​14.19757 ​    ​14.55861 ​    ​15.06387 +      14.04051 ​    ​14.19757 ​    ​14.55861 ​    ​15.06387 
-     ​15.21110 ​    ​15.30968 ​    ​15.37279 ​    ​15.99312 +      15.21110 ​    ​15.30968 ​    ​15.37279 ​    ​15.99312 
-     ​16.04862 ​    ​16.43805 ​    ​16.46738 ​    ​16.88387 +      16.04862 ​    ​16.43805 ​    ​16.46738 ​    ​16.88387 
-     ​16.99408 ​    ​17.25263 ​    ​17.61341 ​    ​18.59642 +      16.99408 ​    ​17.25263 ​    ​17.61341 ​    ​18.59642 
-     ​18.93562 ​    ​19.46990 ​    ​19.80628 ​    ​20.31527 +      18.93562 ​    ​19.46990 ​    ​19.80628 ​    ​20.31527 
-     ​20.34526 ​    ​21.40842 ​    ​21.74713 ​    ​22.24177 +      20.34526 ​    ​21.40842 ​    ​21.74713 ​    ​22.24177 
-     ​22.61195 ​    ​22.76252 ​    ​23.34774 ​    ​24.49545 +      22.61195 ​    ​22.76252 ​    ​23.34774 ​    ​24.49545 
-     ​24.59028 ​    ​24.93521 ​    ​25.67988 ​    ​25.78261 +      24.59028 ​    ​24.93521 ​    ​25.67988 ​    ​25.78261 
-     ​26.51534 ​    ​27.32112 ​    ​27.55584 ​    ​28.04580 +      26.51534 ​    ​27.32112 ​    ​27.55584 ​    ​28.04580 
-     ​28.47919 ​    ​28.76664 ​    ​29.50683 ​    ​30.65046 +      28.47919 ​    ​28.76664 ​    ​29.50683 ​    ​30.65046 
-     ​30.90050 ​    ​31.21945 ​    ​33.09324 ​    ​34.44970 +      30.90050 ​    ​31.21945 ​    ​33.09324 ​    ​34.44970 
-     ​35.52433 ​    ​35.86108 ​    ​37.34994 ​    ​37.88428 +      35.52433 ​    ​35.86108 ​    ​37.34994 ​    ​37.88428 
-     ​38.35645 ​    ​41.40826 ​    ​42.20641 ​    ​43.29368 +      38.35645 ​    ​41.40826 ​    ​42.20641 ​    ​43.29368 
-     ​43.70757 ​    ​47.36562 ​    ​48.51939 ​    ​50.04231 +      43.70757 ​    ​47.36562 ​    ​48.51939 ​    ​50.04231 
-     ​56.31003 ​    ​56.38914 ​    ​60.36281 ​    ​66.30143 +      56.31003 ​    ​56.38914 ​    ​60.36281 ​    ​66.30143 
-     ​66.39706 ​    ​73.75972 ​    ​87.06108 ​    ​87.07247 +      66.39706 ​    ​73.75972 ​    ​87.06108 ​    ​87.07247 
-     ​89.24974 ​    ​91.64514 ​    ​93.81909 ​    ​95.64658 +      89.24974 ​    ​91.64514 ​    ​93.81909 ​    ​95.64658 
-     ​95.97695 ​    ​99.09614 +      95.97695 ​    ​99.09614 
-</​pre>​+
 In addition, an occupancy 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: In addition, an occupancy 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:
  
-<pre> + 
- ... +  ... 
- Band n =   24 k-points: ioccupy =  1 +  Band n =   24 k-points: ioccupy =  1 
- Band n =   25 k-points: ioccupy =  1 +  Band n =   25 k-points: ioccupy =  1 
- Band n =   26 k-points: ioccupy =  1 +  Band n =   26 k-points: ioccupy =  1 
- Band n =   27 k-points: ioccupy =  1 +  Band n =   27 k-points: ioccupy =  1 
- Band n =   28 k-points: ioccupy =  1 +  Band n =   28 k-points: ioccupy =  1 
- Band n =   29 k-points: ioccupy =  1 +  Band n =   29 k-points: ioccupy =  1 
- Band n =   30 k-points: ioccupy =  1 +  Band n =   30 k-points: ioccupy =  1 
- Band n =   31 k-points: ioccupy =  1 +  Band n =   31 k-points: ioccupy =  1 
- Band n =   32 k-points: ioccupy =  1 +  Band n =   32 k-points: ioccupy =  1 
- Band n =   33 k-points: ioccupy =  1 +  Band n =   33 k-points: ioccupy =  1 
- Band n =   34 k-points: ioccupy =  1 +  Band n =   34 k-points: ioccupy =  1 
- Band n =   35 k-points: ioccupy =  1 +  Band n =   35 k-points: ioccupy =  1 
- Band n =   36 k-points: ioccupy =  1 +  Band n =   36 k-points: ioccupy =  1 
- Band n =   37 k-points: ioccupy =  0 +  Band n =   37 k-points: ioccupy =  0 
- Band n =   38 k-points: ioccupy =  0 +  Band n =   38 k-points: ioccupy =  0 
- Band n =   39 k-points: ioccupy =  0 +  Band n =   39 k-points: ioccupy =  0 
- Band n =   40 k-points: ioccupy =  0 +  Band n =   40 k-points: ioccupy =  0 
- Band n =   41 k-points: ioccupy =  0 +  Band n =   41 k-points: ioccupy =  0 
- Band n =   42 k-points: ioccupy =  0 +  Band n =   42 k-points: ioccupy =  0 
- Band n =   43 k-points: ioccupy =  0 +  Band n =   43 k-points: ioccupy =  0 
- ... +  ... 
-</​pre>​+
  
 It means last occupied level (HOMO) is no. 36 and first unoccupied level is no. 37. Their eigenvalues can be found in '''​eigen.dat'''​ file accounting appropriate number of levels (in ascending order). It means last occupied level (HOMO) is no. 36 and first unoccupied level is no. 37. Their eigenvalues can be found in '''​eigen.dat'''​ file accounting appropriate number of levels (in ascending order).
  
----- + 
-== Density Of States (DOS) ==+===== Density Of States (DOS) ===== 
 Another way how to analyze energy spectra of molecule in Fireball is to calculate Density Of State (DOS). In addition, ​ Another way how to analyze energy spectra of molecule in Fireball is to calculate Density Of State (DOS). In addition, ​
 projected DOS on each atom is provided. To run this task for particular atomic configuration,​ two steps are necessary:</​br> ​ projected DOS on each atom is provided. To run this task for particular atomic configuration,​ two steps are necessary:</​br> ​
 (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: 
-<pre> + 
-&​OPTION +  &​OPTION 
-basisfile = answer.bas +  basisfile = answer.bas 
-nstepf = 1 +  nstepf = 1 
-icluster = 1 +  icluster = 1 
-itdse = 0 +  iqout = 1 
-iqout = 1 +  ifixcharge = 1 
-ifixcharge = 1 +  dt = 0.5 
-dt = 0.5 +  &END 
-&END +  &​OUTPUT 
-&​OUTPUT +  iwrtdos = 1 
-iwrtdos = 1 +  &END 
-&END + 
-</​pre> ​+
 (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:
-<pre> + 
-1.0                   ! scale factor (leave 1.0) +  1.0                   ! scale factor (leave 1.0) 
-1       ​22 ​           ! list of atoms to analyze DOS +  1       ​22 ​           ! list of atoms to analyze DOS 
-441                   ! number of energy steps +  441                   ! number of energy steps 
--22.0   ​0.05 ​         ! initial energy, energy step  +  -22.0   ​0.05 ​         ! initial energy, energy step  
-0                     ! leave untouched +  0                     ! leave untouched 
-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) 
-</​pre>​+
  
 In this particular case, all 22 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.  ​ In this particular case, all 22 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.  ​
Line 121: Line 121:
 [[Image:​DOS.png]] [[Image:​DOS.png]]
  
----- 
  
-== Real-space electronic density ==+=====  
 +Real-space electronic density ===== 
 + 
 Sometimes is more illustrative visualize electron density in real-space. This can help can be of use as primitive estimation of STM images or it can provide more information about spacial (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 visualize electron density in real-space. This can help can be of use as primitive estimation of STM images or it can provide more information about spacial (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:
  
-&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 =36,​37 ​            ! list of molecular levels to be plotted  
-&END +  &END 
-</​pre>​ + 
-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 \\ 
  
-real density of state of the HOMO molecular state <br\> 
-[[Image:​HOMO.png]]<​br\>​ 
-real density of state of the LUMO molecular state <br\> 
-[[Image:​LUMO.png]]<​br\>​ 
  
example/electronic_structure_analysis.1257585606.txt.gz · Last modified: 2011/02/18 13:14 (external edit)

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