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Re: XANES for benzene
Dear M. Koshino,
I attacehed the feff.inp file and the output of the feff8.2 for that file.
I modified your input file and changed many cards. I also like the
ATOMS program to make feff.inp files, but typically I do not use the
defaults and modify cards a lot. Here are the changes I made
EXCHANGE 2 1 0
ixc=2 uses no self-energy shifts, and seems to give best agreement
in your case; often the default ixc=0 is the best; for f-elements
often ixc=3 is the best
vr = 1 to see 1 eV below the Fermi level; feff8.2 sometimews puts
Fermi level too high. I never used vr>2.
AFOLP 1.4
this card often produces better potentials for open structures
like hydrocarbon molecules or for tetrahedral coordination.
(default is AFOLP 1.15 seems to better for solid state applications)
DEBYE 100 400
I tried to simulate temperature effects; but in this case of soft
hydrogen bonds between molecules and strong covalent bonds within the
molecules the Correlated Debye model does not seem to work well. The
model assumes that all bonds are of similar strength.
SCF 3.5
You had TOO BIG radius here. Typically I use the Rscf=3.5-4.2 Angstroms
to have about 15-25 atoms in clusters. This is used to calculate the
smooth quantity- charge density and potential. Do not need to use
huge clusters here. Chemical bonds are local, and charge around the atom
should not depend on very distant atoms.
FMS 3.5
This chooses a cluster of 16 atoms with only 6 carbon atoms included.
Effectively it one benzene circle. This seems to be enough here.
To get close to the band structure results we typically need more
that 150 atoms in cluster. The same holds for XANES calculations,
for Si we used as much as 850 atom clusters. (Ankudinov et al.,
PRB 65, 104107 (2002)).
POTENTIALS
* ipot Z element l_scmt l2fms stoichiometry
0 6 C 2 3 0.1
1 6 C 2 3 3.9
2 1 H 2 3 4
Here I always make changes to the ATOMS output. Usually I increase
l_scmt cards ( use -1: the feff8.2 defaults usually better choice)
l_fms I typically make 3, since it in principle how high in energy
you can trust feff8.2
stoichiometry: ATOMS usually puts too small value for the absorber
(0.001) which often causes problems for the self-consistency loop.
The higher relative weight 1-5 % helps self-consistency enormously.
This result I get with these cards (xmu.dat is attached) is closest
I could get to Fig.1 of the Horsley et al paper. The peak A of feff8.2
is too broad. This is typical for pi* resonance and we discussed the
reason for that ealier. (See e.g. paper
on"Shape resonances of oriented molecules: ab initio theory and
experiment on hydrocarbon molecules" , Haack et al., PRL 84 (2000) 614.)
Also the peak C seems to be too big. However the peak positions
look in reasonable agreement to experimental data:
Thus in experiment peak to peak distances are ( AB-3.9; AC 8.5; AD 15 eV),
while in calculation are (4.3 10.2 and 15.5). Since errobar is about 0.5
agreement is not bad.
Let me know if you think agreement is still not satisfactory.
I also used calculation for larger cluster of 102 atoms, to simulate
solid state data; but the agreement gets worse than the calculations
for 16 atoms. Probably bonds between benzene molecules are much softer
than the bonds between atoms of one molecule. Then Debye-Waller factors
then can wash out the the structure due to distant atoms.
Also I did sometimes calculation for Glycine ( unpublished). There two
carbon atoms are not equivalent and to get agreement with experiment
you cannot use the same potential type for 2 carbon atoms. You can use
the same potential type only for carbons that have the same nearest
neighbors.
Best wishes
Dr. Alexei Ankudinov
TITLE BENZENE
* C K edge energy = 284.20 eV
EDGE K
S02 1.0
* pot xsph fms paths genfmt ff2chi
*CONTROL 1 1 1 1 1 1
CONTROL 0 1 1 1 1 1
*PRINT 1 0 0 0 0 0
EXCHANGE 2 1 0
AFOLP 1.4
DEBYE 100 400
*** ixc=0 means to use Hedin-Lundqvist
* rfms1 [lfms1 nscmt ca nmix]
SCF 3.5
* [xkmax xkstep estep]
XANES 4. .05 .3
* r_fms l_fms
FMS 3.5 0
*FMS 6.2 0
RPATH 0.1
POTENTIALS
* ipot Z element l_scmt l2fms stoichiometry
0 6 C 2 3 0.1
1 6 C 2 3 3.9
2 1 H 2 3 4
ATOMS * this list contains 136 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 C1 0.00000 0
0.30362 -1.02460 -0.08652 2 H1 1.07214 1
-1.00188 0.44657 -0.87292 1 C3 1.40185 2
0.57144 0.89604 0.92708 1 C2 1.41029 3
-1.44724 -0.23585 -1.58828 2 H3 2.16166 4
1.37264 0.57319 1.59812 2 H2 2.18327 5
0.15293 2.23478 0.94889 1 C3 2.43270 6
-1.42038 1.78531 -0.85111 1 C2 2.43499 7
-0.84895 2.68135 0.07597 1 C1 2.81356 8
2.28276 -0.23585 -1.85276 2 H3 2.94946 9
-1.44724 -1.91580 1.92872 2 H3 3.07973 10
-2.35736 0.57319 1.99484 2 H2 3.14087 11
1.50841 2.10815 -1.91888 2 H2 3.22517 12
0.59829 2.91720 1.66424 2 H3 3.41141 13
2.28276 -1.91580 1.66424 2 H3 3.41335 14
-2.22159 2.10815 -1.52216 2 H2 3.42005 15
1.37264 -2.72485 -1.91888 2 H2 3.60431 16
-3.42638 -1.12706 0.16249 2 H1 3.61064 17
0.30362 -1.12706 3.43048 2 H1 3.62362 18
2.72812 0.44657 -2.56811 1 C3 3.77323 19
0.30362 -1.12706 -3.60352 2 H1 3.78785 20
-1.00188 -2.59822 2.64408 1 C3 3.84001 21
-1.15257 3.70594 0.16249 2 H1 3.88443 22
2.72812 -2.59822 0.94889 1 C3 3.88507 23
2.30962 1.78531 -2.58992 1 C2 3.90248 24
-2.35736 -2.72485 -1.52216 2 H2 3.91138 25
0.57144 -3.04769 -2.58992 1 C2 4.04013 26
0.00000 -2.15165 3.51700 1 C1 4.12297 27
0.00000 -2.15165 -3.51700 1 C1 4.12297 28
4.03362 -1.12706 0.16249 2 H1 4.19127 29
-3.15856 0.89604 2.66589 1 C2 4.22923 30
3.73000 -2.15165 0.07597 1 C1 4.30677 31
-3.73000 -2.15165 0.07597 1 C1 4.30677 32
-3.15856 -3.04769 -0.85111 1 C2 4.47094 33
2.57743 3.80840 -0.08652 2 H1 4.59941 34
2.30962 -3.93696 0.92708 1 C2 4.65763 35
-3.13171 2.91720 1.92872 2 H3 4.69442 36
1.50841 -4.25981 1.59812 2 H2 4.79325 37
-3.42638 -1.02460 -3.35451 2 H1 4.90333 38
-1.42038 -3.93696 2.66589 1 C2 4.96227 39
-3.57707 2.23478 2.64408 1 C3 4.97803 40
0.59829 4.59715 -1.85276 2 H3 4.99244 41
3.73000 0.00000 -3.44103 1 C1 5.07480 42
-3.73000 0.00000 -3.44103 1 C1 5.07480 43
0.15293 -4.38643 -2.56811 1 C3 5.08521 44
-3.42638 -1.02460 3.67949 2 H1 5.13113 45
4.30144 0.89604 2.66589 1 C2 5.13928 46
3.73000 0.00000 3.59297 1 C1 5.17903 47
-3.73000 0.00000 3.59297 1 C1 5.17903 48
-1.00188 -2.59822 -4.38992 1 C3 5.19864 49
-2.22159 -4.25981 1.99484 2 H2 5.20200 50
3.88293 2.23478 2.64408 1 C3 5.20217 51
-1.15257 3.80840 -3.35451 2 H1 5.20433 52
2.72812 0.44657 4.46589 1 C3 5.25226 53
2.88105 2.68135 3.51700 1 C1 5.27820 54
2.88105 2.68135 -3.51700 1 C1 5.27820 55
2.30962 1.78531 4.44408 1 C2 5.31710 56
4.30144 -3.04769 -0.85111 1 C2 5.33996 57
4.03362 -1.02460 -3.35451 2 H1 5.34534 58
-4.73188 0.44657 -2.56811 1 C3 5.40234 59
0.57144 -3.04769 4.44408 1 C2 5.41893 60
-1.15257 3.80840 3.67949 2 H1 5.41950 61
0.59829 -5.06885 -1.85276 2 H3 5.42991 62
-3.15856 0.89604 -4.36811 1 C2 5.46441 63
-4.73188 -2.59822 0.94889 1 C3 5.48104 64
-5.17724 -0.23585 -1.85276 2 H3 5.50383 65
5.10264 0.57319 1.99484 2 H2 5.50862 66
4.03362 -1.02460 3.67949 2 H1 5.55505 67
4.32829 2.91720 1.92872 2 H3 5.56454 68
-2.35736 0.57319 -5.03916 2 H2 5.59275 69
2.88105 4.83300 0.00000 1 C1 5.62657 70
2.88105 -4.83300 0.00000 1 C1 5.62657 71
1.37264 0.57319 -5.43588 2 H2 5.63573 72
-1.44724 -0.23585 5.44572 2 H3 5.63968 73
-1.44724 -1.91580 -5.10528 2 H3 5.64169 74
2.28276 -0.23585 5.18124 2 H3 5.66673 75
2.57743 3.70594 3.43048 2 H1 5.66969 76
-3.57707 -4.38643 -0.87292 1 C3 5.72697 77
1.50841 2.10815 5.11512 2 H2 5.73446 78
-5.17724 -1.91580 1.66424 2 H3 5.76574 79
2.57743 3.70594 -3.60352 2 H1 5.77603 80
-3.13171 4.59715 -1.58828 2 H3 5.78481 81
1.50841 5.40619 1.59812 2 H2 5.83577 82
5.23841 2.10815 -1.52216 2 H2 5.84827 83
0.15293 5.27957 -2.56811 1 C3 5.87303 84
3.88293 -4.38643 -0.87292 1 C3 5.92283 85
1.37264 -2.72485 5.11512 2 H2 5.95596 86
5.10264 -2.72485 -1.52216 2 H2 5.98153 87
-0.84895 4.83300 -3.44103 1 C1 5.99327 88
-0.84895 -4.83300 -3.44103 1 C1 5.99327 89
-5.15038 1.78531 -2.58992 1 C2 6.03502 90
-1.42038 -3.93696 -4.36811 1 C2 6.04959 91
-1.15257 -5.96006 0.16249 2 H1 6.07265 92
-0.84895 4.83300 3.59297 1 C1 6.08178 93
-0.84895 -4.83300 3.59297 1 C1 6.08178 94
-3.57707 2.23478 -4.38992 1 C3 6.08778 95
0.59829 2.91720 -5.36976 2 H3 6.14022 96
2.28276 -1.91580 -5.36976 2 H3 6.14130 97
-3.13171 -5.06885 -1.58828 2 H3 6.16632 98
-2.22159 5.40619 1.99484 2 H2 6.17590 99
-4.88257 3.80840 -0.08652 2 H1 6.19281 100
4.30144 0.89604 -4.36811 1 C2 6.19562 101
0.57144 0.89604 -6.10692 1 C2 6.19870 102
END
# BENZENE Feff 8.20
# POT SCF 30 3.5000 0, core-hole, AFOLP (folp(0)= 1.400)
# Abs Z= 6 Rmt= 0.927 Rnm= 1.022 K shell
# Pot 1 Z= 6 Rmt= 0.947 Rnm= 1.046
# Pot 2 Z= 1 Rmt= 0.819 Rnm= 0.894
# Gam_ch=8.676E-02 Gd state Vi= 0.000E+00 Vr= 1.000E+00
# Mu=-9.515E+00 kf=2.662E+00 Vint=-1.582E+01 Rs_int= 1.362
# FMS rfms= 3.5000
# PATH Rmax= 0.100, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 2.50%
# S02=1.000 Temp= 100.00 Debye_temp= 400.00 Global_sig2= 0.00000
# Curved wave amplitude ratio filter 4.000%
# file sig2 tot cw amp ratio deg nlegs reff inp sig2
# 0/ 0 paths used
# xsedge+ 50, used to normalize mu 7.1036E-03
# -----------------------------------------------------------------------
# omega e k mu mu0 chi @#
272.180 -15.125 -1.100 9.43792E-04 7.27191E-03 -6.32811E-03
272.980 -14.325 -1.000 1.45615E-03 9.46132E-03 -8.00516E-03
273.704 -13.601 -0.900 2.30825E-03 1.25946E-02 -1.02863E-02
274.351 -12.954 -0.800 3.76520E-03 1.72359E-02 -1.34707E-02
274.923 -12.382 -0.700 6.31706E-03 2.44113E-02 -1.80942E-02
275.418 -11.887 -0.600 1.08529E-02 3.61245E-02 -2.52716E-02
275.837 -11.468 -0.500 1.89109E-02 5.66786E-02 -3.77678E-02
276.180 -11.125 -0.400 3.31276E-02 9.66043E-02 -6.34767E-02
276.447 -10.858 -0.300 5.94801E-02 1.86971E-01 -1.27491E-01
276.490 -10.815 -0.281 6.72557E-02 2.17026E-01 -1.49770E-01
276.790 -10.515 0.000 5.96658E-01 2.77056E+00 -2.17390E+00
277.090 -10.215 0.281 1.20633E+00 4.92526E+00 -3.71893E+00
277.390 -9.915 0.397 1.38086E+00 4.61816E+00 -3.23730E+00
277.690 -9.615 0.486 1.59059E+00 4.29252E+00 -2.70193E+00
277.990 -9.315 0.561 1.85562E+00 4.00202E+00 -2.14640E+00
278.290 -9.015 0.627 2.16948E+00 3.74887E+00 -1.57939E+00
278.590 -8.715 0.687 2.48038E+00 3.52852E+00 -1.04814E+00
278.890 -8.415 0.742 2.68205E+00 3.33601E+00 -6.53965E-01
278.933 -8.372 0.750 2.69220E+00 3.31045E+00 -6.18257E-01
279.228 -8.077 0.800 2.67002E+00 3.14696E+00 -4.76949E-01
279.542 -7.763 0.850 2.47052E+00 2.99322E+00 -5.22700E-01
279.876 -7.429 0.900 2.19843E+00 2.84973E+00 -6.51294E-01
280.228 -7.077 0.950 1.95244E+00 2.71594E+00 -7.63504E-01
280.600 -6.705 1.000 1.77382E+00 2.59187E+00 -8.18052E-01
280.990 -6.315 1.050 1.66472E+00 2.47676E+00 -8.12036E-01
281.400 -5.905 1.100 1.61630E+00 2.37042E+00 -7.54122E-01
281.828 -5.477 1.150 1.62053E+00 2.27207E+00 -6.51539E-01
282.276 -5.029 1.200 1.67152E+00 2.18120E+00 -5.09677E-01
282.743 -4.562 1.250 1.75331E+00 2.09729E+00 -3.43982E-01
283.229 -4.076 1.300 1.81315E+00 2.01967E+00 -2.06521E-01
283.733 -3.572 1.350 1.78007E+00 1.94810E+00 -1.68030E-01
284.257 -3.048 1.400 1.67975E+00 1.88189E+00 -2.02135E-01
284.800 -2.505 1.450 1.60867E+00 1.82077E+00 -2.12106E-01
285.362 -1.943 1.500 1.61165E+00 1.76407E+00 -1.52420E-01
285.943 -1.362 1.550 1.69657E+00 1.71165E+00 -1.50835E-02
286.543 -0.762 1.600 1.87093E+00 1.66311E+00 2.07819E-01
287.162 -0.143 1.650 2.14662E+00 1.61803E+00 5.28583E-01
287.801 0.496 1.700 2.51781E+00 1.57628E+00 9.41531E-01
288.458 1.153 1.750 2.91103E+00 1.53745E+00 1.37358E+00
289.134 1.829 1.800 3.16335E+00 1.50139E+00 1.66196E+00
289.829 2.524 1.850 3.14893E+00 1.46783E+00 1.68110E+00
290.544 3.239 1.900 2.92694E+00 1.43650E+00 1.49044E+00
291.277 3.972 1.950 2.64880E+00 1.40754E+00 1.24126E+00
292.030 4.725 2.000 2.41416E+00 1.38035E+00 1.03381E+00
292.801 5.496 2.050 2.25959E+00 1.35506E+00 9.04536E-01
293.592 6.287 2.100 2.18845E+00 1.33145E+00 8.57001E-01
294.401 7.096 2.150 2.17911E+00 1.30940E+00 8.69709E-01
295.230 7.925 2.200 2.16623E+00 1.28878E+00 8.77449E-01
296.078 8.773 2.250 2.06130E+00 1.26951E+00 7.91785E-01
296.945 9.640 2.300 1.86422E+00 1.25146E+00 6.12762E-01
297.830 10.525 2.350 1.65864E+00 1.23455E+00 4.24089E-01
298.735 11.430 2.400 1.49433E+00 1.21870E+00 2.75634E-01
299.659 12.354 2.450 1.37393E+00 1.20382E+00 1.70114E-01
300.602 13.297 2.500 1.28571E+00 1.18984E+00 9.58777E-02
301.564 14.259 2.550 1.21911E+00 1.17671E+00 4.24037E-02
302.545 15.240 2.600 1.16725E+00 1.16432E+00 2.93490E-03
303.545 16.240 2.650 1.12613E+00 1.15266E+00 -2.65250E-02
304.564 17.259 2.700 1.09321E+00 1.14164E+00 -4.84283E-02
305.603 18.298 2.750 1.06681E+00 1.13121E+00 -6.44057E-02
306.660 19.355 2.800 1.04572E+00 1.12133E+00 -7.56092E-02
307.736 20.431 2.850 1.02907E+00 1.11194E+00 -8.28710E-02
308.832 21.527 2.900 1.01620E+00 1.10300E+00 -8.67967E-02
309.946 22.641 2.950 1.00662E+00 1.09446E+00 -8.78358E-02
311.080 23.775 3.000 9.99912E-01 1.08627E+00 -8.63598E-02
312.232 24.927 3.050 9.95673E-01 1.07842E+00 -8.27469E-02
313.404 26.099 3.100 9.93343E-01 1.07083E+00 -7.74918E-02
314.594 27.289 3.150 9.92187E-01 1.06349E+00 -7.13006E-02
315.804 28.499 3.200 9.91241E-01 1.05636E+00 -6.51234E-02
317.033 29.728 3.250 9.89356E-01 1.04939E+00 -6.00378E-02
318.280 30.975 3.300 9.85617E-01 1.04256E+00 -5.69467E-02
319.547 32.242 3.350 9.79618E-01 1.03585E+00 -5.62274E-02
320.833 33.528 3.400 9.71627E-01 1.02920E+00 -5.75699E-02
322.138 34.833 3.450 9.62465E-01 1.02260E+00 -6.01383E-02
323.462 36.157 3.500 9.53095E-01 1.01602E+00 -6.29289E-02
324.805 37.500 3.550 9.44352E-01 1.00943E+00 -6.50766E-02
326.167 38.862 3.600 9.36807E-01 1.00281E+00 -6.59988E-02
327.548 40.243 3.650 9.30725E-01 9.96125E-01 -6.54000E-02
328.948 41.643 3.700 9.26167E-01 9.89374E-01 -6.32075E-02
330.368 43.063 3.750 9.23021E-01 9.82524E-01 -5.95034E-02
331.806 44.501 3.800 9.21108E-01 9.75575E-01 -5.44672E-02
333.263 45.958 3.850 9.20130E-01 9.68471E-01 -4.83409E-02
334.740 47.435 3.900 9.19834E-01 9.61239E-01 -4.14051E-02
336.235 48.930 3.950 9.19895E-01 9.53853E-01 -3.39572E-02
337.749 50.444 4.000 9.20001E-01 9.46297E-01 -2.62958E-02