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example:electronic_structure_analysis [2009/11/07 10:20] jelen created |
example:electronic_structure_analysis [2009/11/07 10:30] jelen |
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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 | ||
Line 83: | Line 83: | ||
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]. | ||