[Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster
Ganesh Subramanian
gunkanna at gmail.com
Wed Jul 29 17:01:03 CDT 2015
Dear all,
I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for
a cluster and not a crystal. I encountered two problems.
1. *Using the FOLP card*: The actual cluster size is about 180 atoms
extending upto 18 A in radial distance from the central cobalt atom. But
there are quite a few instances of Hydrogen atoms that are too close. I
tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a
syntax type error, that i cant figure out. I checked the crystal structure
and the smallest hydrogen bond distance is 0.89 A. (I have attached the
corresponding input and log file with suffix 'full cluster')
2. *SCF for small cluster*: Since the problem with the hydrogen distances
persisted, I decided to run the calculation for a smaller cluster (about 50
atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1,
FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this
smaller cluster, there were about 3 of them, and none in the first or
second shell of co-ordination) were removed manually. Now, I did not have
the error on distances, did not require the FOLP card to be manually
altered, but the log1 file seems to suggest that the SCF is not calculated.
I cant figure why that is the case. (I have attached the corresponding
input and log file with suffix 'small cluster')
Sorry for the long email, and thank you for any suggestions.
Ganesh
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* This feff8 input file was generated by TkAtoms 3.0beta7
* Atoms written by and copyright (c) Bruce Ravel, 1998-2001
TITLE MeCbl-Groundstate-Kedge
* Co K edge energy = 7712.0 eV
EDGE K
S02 1.0
* pot xsph fms paths genfmt ff2chi
CONTROL 0 1 1 1 1 1
PRINT 1 0 0 0 0 0
*** ixc=0 means to use Hedin-Lundqvist
* ixc [ Vr Vi ]
EXCHANGE 0 0 0.5
*** Radius of small cluster for
*** self-consistency calculation
*** A sphere including 2 shells is
*** a good choice
*** l_scf = 0 for a solid, 1 for a molecule
* r_scf [ l_scf n_scf ca ]
SCF 7.0
*** Upper limit of XANES calculation.
*** This *must* be uncommented to
*** make Feff calculate full multiple
*** scattering rather than a path expansion
* kmax [ delta_k delta_e ]
XANES 7.0 0.05 0.05
*** Radius of cluster for Full Multiple
*** Scattering calculation
*** l_fms = 0 for a solid, 1 for a molecule
* r_fms l_fms
FMS 8 0
*** Energy grid over which to calculate
*** DOS functions
* emin emax eimag
LDOS -30 20 0.1
*** for EXAFS: RMAX 10.0 and uncomment
*** the EXAFS card
RPATH 0.1
*EXAFS 20
POTENTIALS
* ipot Z element l_scmt l_fms stoichiometry
0 27 Cu 3 2 1
1 1 H 3 2 76
2 6 C 3 3 63
3 7 N 3 2 13
4 8 O 3 2 14
5 15 P 3 2 1
FOLP 1 0.8
ATOMS * this list contains 178 atoms
* x y z ipot tag distance
0 0 0 0 Co 0.000 0
-0.73 1.487 0.476 3 N 1.724 1
1.314 0.811 -0.784 3 N 1.732 2
0.708 -1.561 -0.381 3 N 1.756 3
-1.175 -0.832 1.088 3 N 1.805 4
-1.293 0.017 -1.587 2 C 2.047 5
-1.628 1.352 1.298 2 C 2.483 6
-1.646 0.059 2.026 2 C 2.611 7
1.44 2.014 -0.847 2 C 2.617 8
1.674 -1.773 -1.033 2 C 2.648 9
0.065 -2.651 -0.292 2 C 2.668 10
-0.361 2.622 0.395 2 C 2.676 11
2.151 0.331 -1.562 2 C 2.679 12
-1.518 -1.905 1.163 2 C 2.699 13
0.567 2.92 -0.473 2 C 3.012 14
0.08 0.589 2.961 1 H2 3.020 15
2.423 -0.876 -1.633 2 C 3.050 16
-1.094 -2.832 0.333 2 C 3.054 17
-0.8 0.26 3.233 2 C 3.341 18
3.026 0.892 1.392 1 H5 3.448 19
2.801 -1.786 1.549 1 H4 3.665 20
-0.699 -0.591 3.706 1 H2 3.817 21
-2.038 2.748 1.975 2 C 3.950 22
3.001 1.502 2.085 3 N 3.951 23
2.924 -1.048 -2.449 1 H 3.955 24
-2.994 -0.645 2.527 2 C 3.971 25
0.795 -3.712 -1.166 2 C 3.971 26
2.129 -3.213 -1.116 2 C 4.013 27
-2.497 -2.107 2.332 2 C 4.014 28
2.966 1.351 -2.354 2 C 4.020 29
-1.385 3.613 1.102 2 C 4.023 30
2.808 2.449 -1.53 2 C 4.028 31
-3.946 -0.621 0.726 1 H2 4.060 32
-1.22 0.906 3.817 1 H2 4.108 33
3.601 -1.355 1.522 3 N 4.138 34
0.4 -2.921 -3.025 1 H3 4.224 35
2.795 1.217 2.932 1 H5 4.230 36
3.712 -0.574 1.974 1 H4 4.243 37
2.702 -3.406 0.874 1 H4 4.435 38
4.152 1.702 -0.187 1 H4 4.491 39
1.539 1.977 -3.728 1 H4 4.492 40
-2.692 3.586 -0.467 1 H5 4.508 41
-4.202 -0.405 1.635 2 C 4.527 42
0.992 4.397 -0.487 2 C 4.534 43
-1.711 -4.229 0.511 2 C 4.591 44
0.324 -3.792 -2.611 2 C 4.615 45
2.573 -3.326 -1.961 1 H 4.640 46
-3.249 -2.646 2.035 1 H 4.658 47
0.848 3.782 2.591 1 H5 4.662 48
2.648 3.255 -2.035 1 H 4.663 49
-4.396 0.54 1.668 1 H2 4.733 50
2.434 1.58 -3.774 2 C 4.761 51
3.07 -3.715 0.032 2 C 4.819 52
4.035 2.577 -0.579 2 C 4.823 53
-2.343 4.256 0.132 2 C 4.860 54
0.942 4.76 0.419 1 H5 4.870 55
-2.008 -3.447 -2.876 4 O 4.918 56
2.387 0.722 -4.248 1 H4 4.926 57
1.913 4.468 -0.817 1 H5 4.928 58
3.571 2.835 1.893 2 C 4.937 59
-1.272 -3.474 3.311 1 H3 4.965 60
-2.371 -4.204 1.233 1 H3 4.982 61
4.608 0.219 -1.892 1 H4 4.986 62
2.954 4.008 0.364 1 H4 4.992 63
-2.15 -4.501 -0.323 1 H3 4.999 64
-2.008 -2.903 3.566 2 C 5.018 65
-1.016 -4.862 0.731 1 H3 5.021 66
0.402 4.897 -1.066 1 H5 5.028 67
4.663 -1.852 0.661 2 C 5.061 68
-1.698 -2.269 4.238 1 H3 5.098 69
4.416 0.956 -2.49 2 C 5.159 70
-1.11 -4.263 -2.692 2 C 5.163 71
3.778 3.538 0.562 2 C 5.206 72
-2.527 -0.411 4.554 1 H2 5.224 73
-3.349 -0.384 4.007 2 C 5.236 74
-0.805 4.863 1.856 2 C 5.267 75
0.695 -5.198 -0.718 2 C 5.293 76
-1.873 4.943 -0.384 1 H5 5.300 77
-3.606 3.081 2.397 2 C 5.314 78
0.233 4.451 2.953 2 C 5.347 79
-3.997 2.297 2.804 1 H6 5.396 80
-0.231 -5.406 -0.483 1 H3 5.432 81
0.884 -4.417 -3.085 1 H3 5.460 82
1.27 -5.344 0.058 1 H3 5.493 83
-4.12 3.289 1.597 1 H6 5.508 84
4.504 -3.18 -0.063 2 C 5.514 85
-0.239 4.077 3.714 1 H5 5.520 86
-0.344 5.427 1.215 1 H5 5.572 87
-3.767 0.496 4.091 1 H2 5.583 88
3.081 -4.692 0.037 1 H4 5.613 89
-3.079 4.665 0.624 1 H5 5.624 90
3.353 3.63 2.752 4 O 5.656 91
3.034 2.184 -4.253 1 H4 5.662 92
4.852 2.817 -1.061 1 H4 5.710 93
4.982 1.715 -2.261 1 H4 5.734 94
4.753 -3.085 -0.99 1 H4 5.752 95
4.594 0.684 -3.408 1 H4 5.761 96
5.741 -1.287 0.682 4 O 5.923 97
-5.504 -1.166 1.925 2 C 5.946 98
-3.965 -1.064 4.316 1 H2 5.957 99
-1.532 5.363 2.25 1 H5 6.014 100
0.986 -5.782 -1.456 1 H3 6.043 101
4.504 4.191 0.625 1 H4 6.184 102
5.093 -3.823 0.371 1 H4 6.379 103
-3.137 -3.745 4.192 2 C 6.437 104
-1.354 -5.657 -2.958 3 N 6.526 105
-6.51 -0.299 0.368 1 H2 6.527 106
-3.728 4.254 3.361 2 C 6.580 107
-3.357 -4.455 3.581 1 H3 6.629 108
-5.673 -1.993 2.814 4 O 6.639 109
-3.922 -3.183 4.359 1 H3 6.672 110
1.04 5.696 3.398 2 C 6.714 111
-6.604 -0.9 1.038 3 N 6.745 112
-0.67 -6.255 -2.898 1 H4 6.926 113
-3.184 4.243 4.455 4 O 6.927 114
-2.205 -5.954 -3.062 1 H4 7.049 115
-2.008 -2.626 6.339 1 H3 7.149 116
2.05 4.854 4.989 1 H 7.256 117
1.146 6.695 2.696 4 O 7.308 118
-2.661 -4.358 5.503 2 C 7.507 119
1.88 5.649 4.578 3 N 7.510 120
-7.399 -1.324 1.159 1 H2 7.605 121
-2.08 -3.52 6.488 3 N 7.669 122
-5.054 5.341 2.22 1 H6 7.681 123
-4.624 5.338 3.025 3 N 7.683 124
-1.79 -3.874 7.269 1 H3 8.429 125
-2.707 -5.556 5.796 4 O 8.473 126
-4.723 6.046 3.601 1 H6 8.475 127
3.657 6.544 4.239 1 H1 8.612 128
2.832 6.767 4.691 2 C 8.707 129
2.453 7.572 4.317 1 H1 9.055 130
2.371 6.047 7.196 4 O 9.694 131
3.109 6.938 6.24 2 C 9.836 132
4.243 4.4 7.706 4 O 9.836 133
2.05 4.336 8.879 4 O 10.092 134
2.487 7.667 6.344 1 H 10.257 135
3.134 5.213 8.292 5 P 10.284 136
5.001 7.829 5.91 1 H3 11.011 137
4.405 7.736 6.675 2 C 11.127 138
4.862 7.25 7.385 1 H3 11.434 139
4.151 8.613 6.996 1 H3 11.847 140
3.704 6.108 9.46 4 O 11.854 141
1.918 6.772 9.906 1 H 12.152 142
2.77 6.616 10.359 2 C 12.600 143
1.926 5.091 11.435 1 H 12.664 144
2.576 5.791 11.594 2 C 13.213 145
3.243 8.973 9.298 1 H5 13.322 146
3.747 5.16 11.995 4 O 13.585 147
4.45 5.645 11.736 1 Ho 13.762 148
3.257 7.86 11.008 2 C 13.913 149
3.026 9.122 10.227 2 C 14.034 150
2.093 9.407 10.314 1 H5 14.116 151
4.226 7.792 11.079 1 H 14.189 152
1.139 6.856 12.625 1 H 14.412 153
0.369 4.49 13.692 1 H 14.414 154
2.102 6.749 12.652 2 C 14.493 155
-0.411 1.976 14.446 1 Hm 14.586 156
2.678 7.948 12.285 4 O 14.875 157
0.876 4.432 14.508 2 C 15.195 158
3.873 10.094 10.746 4 O 15.244 159
-0.602 2.494 15.243 2 C 15.457 160
-1.431 2.98 15.122 1 Hm 15.479 161
2.535 6.358 13.975 3 N 15.561 162
1.962 5.3 14.722 2 C 15.769 163
0.525 3.474 15.488 2 C 15.882 164
3.697 10.21 11.612 1 Ho 15.898 165
-0.685 1.893 16.011 1 Hm 16.137 166
3.591 6.904 14.652 2 C 16.590 167
4.144 7.623 14.332 1 H 16.754 168
2.748 5.246 15.931 2 C 16.996 169
1.317 3.409 16.675 2 C 17.071 170
3.751 6.267 15.816 3 N 17.421 171
2.4 4.291 16.901 2 C 17.602 172
1.334 1.524 17.528 1 Hm 17.645 173
0.955 2.397 17.753 2 C 17.940 174
-0.016 2.324 17.812 1 Hm 17.963 175
2.917 4.228 17.732 1 H 18.461 176
1.301 2.698 18.608 1 Hm 18.848 177
END
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Feff 8.40
XANES:
FOLP:
Expert option, please read documentation carefully and check your results.
MeCbl-Groundstate-Kedge
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 20 24
20 3.02600E+00 8.92000E-01 1.39200E+00
24 3.00100E+00 1.50200E+00 2.08500E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 21 35
21 2.80100E+00 -1.78600E+00 1.54900E+00
35 3.60100E+00 -1.35500E+00 1.52200E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 24 37
24 3.00100E+00 1.50200E+00 2.08500E+00
37 2.79500E+00 1.21700E+00 2.93200E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 35 38
35 3.60100E+00 -1.35500E+00 1.52200E+00
38 3.71200E+00 -5.74000E-01 1.97400E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 106 114
106 -1.35400E+00 -5.65700E+00 -2.95800E+00
114 -6.70000E-01 -6.25500E+00 -2.89800E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 106 116
106 -1.35400E+00 -5.65700E+00 -2.95800E+00
116 -2.20500E+00 -5.95400E+00 -3.06200E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 107 113
107 -6.51000E+00 -2.99000E-01 3.68000E-01
113 -6.60400E+00 -9.00000E-01 1.03800E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 113 122
113 -6.60400E+00 -9.00000E-01 1.03800E+00
122 -7.39900E+00 -1.32400E+00 1.15900E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 117 123
117 -2.00800E+00 -2.62600E+00 6.33900E+00
123 -2.08000E+00 -3.52000E+00 6.48800E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 118 121
118 2.05000E+00 4.85400E+00 4.98900E+00
121 1.88000E+00 5.64900E+00 4.57800E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 123 126
123 -2.08000E+00 -3.52000E+00 6.48800E+00
126 -1.79000E+00 -3.87400E+00 7.26900E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 124 125
124 -5.05400E+00 5.34100E+00 2.22000E+00
125 -4.62400E+00 5.33800E+00 3.02500E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 125 128
125 -4.62400E+00 5.33800E+00 3.02500E+00
128 -4.72300E+00 6.04600E+00 3.60100E+00
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 148 149
148 3.74700E+00 5.16000E+00 1.19950E+01
149 4.45000E+00 5.64500E+00 1.17360E+01
Run continues in case you really meant it.
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 160 166
160 3.87300E+00 1.00940E+01 1.07460E+01
166 3.69700E+00 1.02100E+01 1.16120E+01
Run continues in case you really meant it.
-------------- next part --------------
* This feff8 input file was generated by TkAtoms 3.0beta7
* Atoms written by and copyright (c) Bruce Ravel, 1998-2001
TITLE MeCbl-Groundstate-Kedge
* Co K edge energy = 7712.0 eV
EDGE K
* S02 1.0
* pot xsph fms paths genfmt ff2chi
CONTROL 1 1 1 1 1 1
PRINT 1 0 0 0 0 0
*** ixc=0 means to use Hedin-Lundqvist
* ixc [ Vr Vi ]
EXCHANGE 0 0 0.5
*** Radius of small cluster for
*** self-consistency calculation
*** A sphere including 2 shells is
*** a good choice
*** l_scf = 0 for a solid, 1 for a molecule
* r_scf [ l_scf n_scf ca ]
SCF 5 1
*** Upper limit of XANES calculation.
*** This *must* be uncommented to
*** make Feff calculate full multiple
*** scattering rather than a path expansion
* kmax [ delta_k delta_e ]
XANES 4.5
*** Radius of cluster for Full Multiple
*** Scattering calculation
*** l_fms = 0 for a solid, 1 for a molecule
* r_fms l_fms
FMS 5 1
*** Energy grid over which to calculate
*** DOS functions
* emin emax eimag
LDOS -30 20 0.1
*** for EXAFS: RMAX 10.0 and uncomment
*** the EXAFS card
RPATH -1
EXAFS 20
POTENTIALS
* ipot Z element l_scmt l_fms stoichiometry
0 27 Cu 3 2 1
1 1 H 3 2 14
2 6 C 3 3 25
3 7 N 3 2 6
* 4 8 O 3 2 14
* 5 15 P 3 2 1
* FOLP 1 0.8
ATOMS * this list contains 178 atoms
* x y z ipot tag distance
0 0 0 0 Co 0.000 0
-0.73 1.487 0.476 3 N 1.724 1
1.314 0.811 -0.784 3 N 1.732 2
0.708 -1.561 -0.381 3 N 1.756 3
-1.175 -0.832 1.088 3 N 1.805 4
-1.293 0.017 -1.587 2 C 2.047 5
-1.628 1.352 1.298 2 C 2.483 6
-1.646 0.059 2.026 2 C 2.611 7
1.44 2.014 -0.847 2 C 2.617 8
1.674 -1.773 -1.033 2 C 2.648 9
0.065 -2.651 -0.292 2 C 2.668 10
-0.361 2.622 0.395 2 C 2.676 11
2.151 0.331 -1.562 2 C 2.679 12
-1.518 -1.905 1.163 2 C 2.699 13
0.567 2.92 -0.473 2 C 3.012 14
0.08 0.589 2.961 1 H2 3.020 15
2.423 -0.876 -1.633 2 C 3.050 16
-1.094 -2.832 0.333 2 C 3.054 17
-0.8 0.26 3.233 2 C 3.341 18
-0.699 -0.591 3.706 1 H2 3.817 21
-2.038 2.748 1.975 2 C 3.950 22
3.001 1.502 2.085 3 N 3.951 23
2.924 -1.048 -2.449 1 H 3.955 24
-2.994 -0.645 2.527 2 C 3.971 25
0.795 -3.712 -1.166 2 C 3.971 26
2.129 -3.213 -1.116 2 C 4.013 27
-2.497 -2.107 2.332 2 C 4.014 28
2.966 1.351 -2.354 2 C 4.020 29
-1.385 3.613 1.102 2 C 4.023 30
2.808 2.449 -1.53 2 C 4.028 31
-3.946 -0.621 0.726 1 H2 4.060 32
-1.22 0.906 3.817 1 H2 4.108 33
3.601 -1.355 1.522 3 N 4.138 34
0.4 -2.921 -3.025 1 H3 4.224 35
2.702 -3.406 0.874 1 H4 4.435 38
4.152 1.702 -0.187 1 H4 4.491 39
1.539 1.977 -3.728 1 H4 4.492 40
-2.692 3.586 -0.467 1 H5 4.508 41
-4.202 -0.405 1.635 2 C 4.527 42
0.992 4.397 -0.487 2 C 4.534 43
-1.711 -4.229 0.511 2 C 4.591 44
0.324 -3.792 -2.611 2 C 4.615 45
2.573 -3.326 -1.961 1 H 4.640 46
-3.249 -2.646 2.035 1 H 4.658 47
0.848 3.782 2.591 1 H5 4.662 48
2.648 3.255 -2.035 1 H 4.663 49
-4.396 0.54 1.668 1 H2 4.733 50
END
-------------- next part --------------
Calculating potentials ...
free atom potential and density for atom type 0
free atom potential and density for atom type 1
free atom potential and density for atom type 2
free atom potential and density for atom type 3
initial state energy
overlapped potential and density for unique potential 0
overlapped potential and density for unique potential 1
overlapped potential and density for unique potential 2
overlapped potential and density for unique potential 3
muffin tin radii and interstitial parameters
iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph)
0 1.24151E+00 1.13966E+00 1.15000E+00
1 9.41337E-01 6.67025E-01 1.15000E+00
2 1.43160E+00 1.26080E+00 1.15000E+00
3 9.18708E-01 5.74238E-01 1.15000E+00
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