[Ifeffit] Using FEFF8 with Artemis
Scott Calvin
SCalvin at slc.edu
Thu May 24 11:51:44 CDT 2007
Hi all,
I've been having some difficulty using FEFF8 generated files with
Artemis. Here's what I've tried:
I've run a somewhat modified version of FEFF 8.28 on a Mac. It
generates files as it should (I've used them with feffit before).
I open Artemis...I've tried on a pc running Windows XP, and on a
PowerPC Mac running OS 10.4.9. In both cases, the result was similar.
After opening Artemis, I choose "New Feff input template," and then
"Import feff.inp." I choose the feff.inp file from the folder where I
ran Feff. I ask for just the first path, and I get an error (this
one's taken from the pc):
Use of uninitialized value in pattern match (m//) at
/PerlApp/Ifeffit/Path.pm line 1623.
main::_ANON_('Used of uninitialized valye in patern match (m//)
at /PerlApp/If...') called at /PerlApp/Ifeffit/Path.pm line 1623
Ifeffit::Path::pathlabel('Ifeffit::Path=HASH(0x2195580)', 'Path
%i: [%p]') called at artemis line 6150
main::fetch_nnnn(data0.feff2', 'C:\New
ifeffit 2\horae\stash\artemis.project.1\data0.feff2',
'._feff0001.dat') called at artemis line 340
eval {...} called at /PerlApp/Tk.pm line 340
Tk::MainLoop() called at artemis line 2127
The result is that although the feff.inp screen in Artemis looks
fairly normal, the "Data & Paths" screen just shows "Path 0:[]"
beneath the new feff calculation. I can also try adding a new path
from under the theory menu and I get a similar response (different
line numbers in the error message).
I've never tried bringing a Feff8 calculation into Artemis before. Is
there something obvious I'm doing wrong? I've attached the feff.inp
file and one of the path files to aid in diagnosis.
--Scott Calvin
Sarah Lawrence College
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Prussian Blue ICSD23105 Feff 8.20x8
Fe(b)
POT SCF 30 4.0000 0, core-hole, AFOLP (folp(0)= 1.150)
Abs Z=26 Rmt= 1.237 Rnm= 1.297 K shell
Pot 1 Z=26 Rmt= 1.293 Rnm= 1.417
Pot 2 Z= 6 Rmt= 0.725 Rnm= 0.974
Pot 3 Z= 7 Rmt= 0.727 Rnm= 0.970
Pot 4 Z= 8 Rmt= 1.254 Rnm= 1.290
Pot 5 Z= 1 Rmt= 0.517 Rnm= 0.654
Gam_ch=1.309E+00 H-L exch
Mu=-7.096E+00 kf=2.667E+00 Vint=-1.976E+01 Rs_int= 1.360
PATH Rmax= 7.000, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 2.50%
Path 1 icalc 2
-----------------------------------------------------------------------
2 6.000 1.9183 1.9318 -7.09569 nleg, deg, reff, rnrmav(bohr), edge
x y z pot at#
0.0000 0.0000 0.0000 0 26 Fe absorbing atom
0.0000 -1.9183 0.0000 2 6 C
k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@#
0.000 3.1373E+00 1.2137E-04 -5.6506E+00 1.005E+00 2.1232E+01 1.8236E+00
0.100 3.1370E+00 7.0186E-02 -6.0241E+00 1.005E+00 2.1262E+01 1.8262E+00
0.200 3.1362E+00 1.3986E-01 -6.3792E+00 1.005E+00 2.1352E+01 1.8340E+00
0.300 3.1348E+00 2.0845E-01 -6.7155E+00 1.005E+00 2.1496E+01 1.8470E+00
0.400 3.1327E+00 2.7535E-01 -7.0335E+00 1.006E+00 2.1689E+01 1.8650E+00
0.500 3.1300E+00 3.3983E-01 -7.3338E+00 1.006E+00 2.1919E+01 1.8879E+00
0.600 3.1264E+00 4.0115E-01 -7.6172E+00 1.006E+00 2.2175E+01 1.9155E+00
0.700 3.1220E+00 4.5857E-01 -7.8847E+00 1.006E+00 2.2440E+01 1.9477E+00
0.800 3.1165E+00 5.1142E-01 -8.1371E+00 1.007E+00 2.2699E+01 1.9842E+00
0.900 3.1099E+00 5.5919E-01 -8.3756E+00 1.007E+00 2.2932E+01 2.0248E+00
1.000 3.1021E+00 6.0152E-01 -8.6012E+00 1.008E+00 2.3121E+01 2.0694E+00
1.100 3.0928E+00 6.3826E-01 -8.8149E+00 1.009E+00 2.3248E+01 2.1176E+00
1.200 3.0820E+00 6.6944E-01 -9.0174E+00 1.009E+00 2.3297E+01 2.1693E+00
1.300 3.0694E+00 6.9524E-01 -9.2095E+00 1.010E+00 2.3256E+01 2.2243E+00
1.400 3.0550E+00 7.1596E-01 -9.3919E+00 1.011E+00 2.3117E+01 2.2824E+00
1.500 3.0386E+00 7.3194E-01 -9.5649E+00 1.012E+00 2.2878E+01 2.3435E+00
1.600 3.0201E+00 7.4356E-01 -9.7290E+00 1.014E+00 2.2541E+01 2.4073E+00
1.700 2.9993E+00 7.5121E-01 -9.8844E+00 1.015E+00 2.2115E+01 2.4738E+00
1.800 2.9761E+00 7.5523E-01 -1.0031E+01 1.017E+00 2.1613E+01 2.5429E+00
1.900 2.9503E+00 7.5594E-01 -1.0170E+01 1.019E+00 2.1050E+01 2.6144E+00
2.000 2.9219E+00 7.5360E-01 -1.0300E+01 1.022E+00 2.0444E+01 2.6882E+00
2.200 2.8564E+00 7.4062E-01 -1.0535E+01 1.027E+00 1.9174E+01 2.8429E+00
2.400 2.7786E+00 7.1754E-01 -1.0734E+01 1.035E+00 1.7945E+01 3.0066E+00
2.600 2.6898E+00 6.8513E-01 -1.0898E+01 1.043E+00 1.6874E+01 3.1793E+00
2.800 2.5920E+00 6.4383E-01 -1.1035E+01 1.036E+00 1.6057E+01 3.3617E+00
3.000 2.4174E+00 5.8912E-01 -1.1109E+01 1.008E+00 1.5568E+01 3.5671E+00
3.200 2.2689E+00 5.8215E-01 -1.1221E+01 1.132E+00 8.3430E+00 3.7564E+00
3.400 2.2089E+00 5.5540E-01 -1.1385E+01 1.182E+00 6.8776E+00 3.9101E+00
3.600 2.1573E+00 5.1234E-01 -1.1547E+01 1.209E+00 6.2318E+00 4.0607E+00
3.800 2.0869E+00 4.6226E-01 -1.1685E+01 1.218E+00 5.8976E+00 4.2200E+00
4.000 2.0105E+00 4.1199E-01 -1.1820E+01 1.220E+00 5.7333E+00 4.3833E+00
4.200 1.9302E+00 3.6481E-01 -1.1953E+01 1.214E+00 5.6702E+00 4.5504E+00
4.400 1.8475E+00 3.2362E-01 -1.2088E+01 1.205E+00 5.6735E+00 4.7207E+00
4.600 1.7632E+00 2.8873E-01 -1.2225E+01 1.195E+00 5.7238E+00 4.8940E+00
4.800 1.6784E+00 2.6066E-01 -1.2366E+01 1.182E+00 5.8093E+00 5.0700E+00
5.000 1.5934E+00 2.3879E-01 -1.2506E+01 1.170E+00 5.9222E+00 5.2484E+00
5.200 1.5081E+00 2.2319E-01 -1.2645E+01 1.159E+00 6.0575E+00 5.4289E+00
5.400 1.4232E+00 2.1245E-01 -1.2779E+01 1.148E+00 6.2113E+00 5.6113E+00
5.600 1.3382E+00 2.0574E-01 -1.2904E+01 1.138E+00 6.3809E+00 5.7953E+00
5.800 1.2530E+00 2.0164E-01 -1.3017E+01 1.128E+00 6.5644E+00 5.9809E+00
6.000 1.1674E+00 1.9882E-01 -1.3119E+01 1.119E+00 6.7601E+00 6.1678E+00
6.500 9.5121E-01 1.9094E-01 -1.3328E+01 1.098E+00 7.2954E+00 6.6400E+00
7.000 7.3486E-01 1.7484E-01 -1.3497E+01 1.077E+00 7.8866E+00 7.1179E+00
7.500 5.2551E-01 1.4977E-01 -1.3660E+01 1.057E+00 8.5251E+00 7.6001E+00
8.000 3.2967E-01 1.2100E-01 -1.3838E+01 1.039E+00 9.2052E+00 8.0857E+00
8.500 1.4685E-01 9.5183E-02 -1.4039E+01 1.023E+00 9.9230E+00 8.5739E+00
9.000 -3.0454E-02 7.6771E-02 -1.4243E+01 1.008E+00 1.0676E+01 9.0640E+00
9.500 -2.0734E-01 6.6319E-02 -1.4408E+01 9.958E-01 1.1461E+01 9.5559E+00
10.000 -3.8352E-01 6.1606E-02 -1.4507E+01 9.849E-01 1.2277E+01 1.0049E+01
11.000 -7.1576E-01 5.8191E-02 -1.4612E+01 9.672E-01 1.3996E+01 1.1038E+01
12.000 -1.0098E+00 4.9168E-02 -1.4793E+01 9.583E-01 1.5823E+01 1.2030E+01
13.000 -1.2870E+00 3.6529E-02 -1.5127E+01 9.531E-01 1.7754E+01 1.3024E+01
14.000 -1.5458E+00 3.0037E-02 -1.5382E+01 9.481E-01 1.9781E+01 1.4019E+01
15.000 -1.7775E+00 2.7783E-02 -1.5361E+01 9.466E-01 2.1902E+01 1.5016E+01
16.000 -1.9988E+00 2.5317E-02 -1.5397E+01 9.457E-01 2.4113E+01 1.6013E+01
17.000 -2.2040E+00 2.1202E-02 -1.5676E+01 9.446E-01 2.6410E+01 1.7011E+01
18.000 -2.3912E+00 1.8051E-02 -1.5954E+01 9.450E-01 2.8792E+01 1.8009E+01
19.000 -2.5714E+00 1.4820E-02 -1.5969E+01 9.449E-01 3.1255E+01 1.9007E+01
20.000 -2.7374E+00 1.0934E-02 -1.5885E+01 9.445E-01 3.3797E+01 2.0006E+01
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* This feff8 input file was generated by Artemis 0.8.006
* Atoms written by and copyright (c) Bruce Ravel, 1998-2001
TITLE Prussian Blue ICSD23105
TITLE Fe(b)
* Fe K edge energy = 7112.0 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 3
*** ixc=0 means to use Hedin-Lundqvist
* ixc [ Vr Vi ]
EXCHANGE 0
RPATH 7.0
EXAFS 20
NLEG 4
*** 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 4.0
*** 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 4.0
*** Radius of cluster for Full Multiple
*** Scattering calculation
*** l_fms = 0 for a solid, 1 for a molecule
* r_fms l_fms
*FMS 4.22023 0
*** Energy grid over which to calculate
*** DOS functions
* emin emax eimag
* LDOS -30 20 0.1
POTENTIALS
* ipot Z element l_scmt l_fms stoichiometry
0 26 Fe 2 2 0.001
1 26 Fe 2 2 7
2 6 C 1 1 18
3 7 N 1 1 18
4 8 O 1 1 14
5 1 H 1 1 28
ATOMS * this list contains 251 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 Fe(b) 0.00000 0
1.91828 0.00000 0.00000 2 C 1.91828 1
-1.91828 0.00000 0.00000 2 C 1.91828 2
0.00000 1.91828 0.00000 2 C 1.91828 3
0.00000 -1.91828 0.00000 2 C 1.91828 4
0.00000 0.00000 1.91828 2 C 1.91828 5
0.00000 0.00000 -1.91828 2 C 1.91828 6
* 2.50828 0.63977 0.63977 5 H 2.66647 7
* -2.50828 0.63977 0.63977 5 H 2.66647 8
* 0.63977 2.50828 0.63977 5 H 2.66647 9
* -0.63977 2.50828 0.63977 5 H 2.66647 10
2.50828 -0.63977 0.63977 5 H 2.66647 11
* -2.50828 -0.63977 0.63977 5 H 2.66647 12
0.63977 -2.50828 0.63977 5 H 2.66647 13
* -0.63977 -2.50828 0.63977 5 H 2.66647 14
* 0.63977 0.63977 2.50828 5 H 2.66647 15
* -0.63977 0.63977 2.50828 5 H 2.66647 16
* 0.63977 -0.63977 2.50828 5 H 2.66647 17
* -0.63977 -0.63977 2.50828 5 H 2.66647 18
* 2.50828 0.63977 -0.63977 5 H 2.66647 19
* -2.50828 0.63977 -0.63977 5 H 2.66647 20
* 0.63977 2.50828 -0.63977 5 H 2.66647 21
* -0.63977 2.50828 -0.63977 5 H 2.66647 22
* 2.50828 -0.63977 -0.63977 5 H 2.66647 23
* -2.50828 -0.63977 -0.63977 5 H 2.66647 24
* 0.63977 -2.50828 -0.63977 5 H 2.66647 25
* -0.63977 -2.50828 -0.63977 5 H 2.66647 26
* 0.63977 0.63977 -2.50828 5 H 2.66647 27
* -0.63977 0.63977 -2.50828 5 H 2.66647 28
* 0.63977 -0.63977 -2.50828 5 H 2.66647 29
* -0.63977 -0.63977 -2.50828 5 H 2.66647 30
3.06579 0.00000 0.00000 3 N 3.06579 31
-3.06579 0.00000 0.00000 3 N 3.06579 32
0.00000 3.06579 0.00000 3 N 3.06579 33
0.00000 -3.06579 0.00000 3 N 3.06579 34
0.00000 0.00000 3.06579 3 N 3.06579 35
0.00000 0.00000 -3.06579 3 N 3.06579 36
* 1.80759 1.80759 1.80759 4 O(f) 3.13084 37
* -1.80759 1.80759 1.80759 4 O(f) 3.13084 38
1.80759 -1.80759 1.80759 4 O(f) 3.13084 39
* -1.80759 -1.80759 1.80759 4 O(f) 3.13084 40
* 1.80759 1.80759 -1.80759 4 O(f) 3.13084 41
* -1.80759 1.80759 -1.80759 4 O(f) 3.13084 42
* 1.80759 -1.80759 -1.80759 4 O(f) 3.13084 43
* -1.80759 -1.80759 -1.80759 4 O(f) 3.13084 44
2.53875 2.53875 2.53875 4 O(c) 4.39724 45
-2.53875 2.53875 2.53875 4 O(c) 4.39724 46
* 2.53875 -2.53875 2.53875 4 O(c) 4.39724 47
* -2.53875 -2.53875 2.53875 4 O(c) 4.39724 48
* 2.53875 2.53875 -2.53875 4 O(c) 4.39724 49
* -2.53875 2.53875 -2.53875 4 O(c) 4.39724 50
2.53875 -2.53875 -2.53875 4 O(c) 4.39724 51
-2.53875 -2.53875 -2.53875 4 O(c) 4.39724 52
* 3.26991 3.26991 1.80759 4 O(f) 4.96508 53
* -3.26991 3.26991 1.80759 4 O(f) 4.96508 54
* 3.26991 -3.26991 1.80759 4 O(f) 4.96508 55
-3.26991 -3.26991 1.80759 4 O(f) 4.96508 56
* 3.26991 1.80759 3.26991 4 O(f) 4.96508 57
* -3.26991 1.80759 3.26991 4 O(f) 4.96508 58
* 1.80759 3.26991 3.26991 4 O(f) 4.96508 59
* -1.80759 3.26991 3.26991 4 O(f) 4.96508 60
* 3.26991 -1.80759 3.26991 4 O(f) 4.96508 61
* -3.26991 -1.80759 3.26991 4 O(f) 4.96508 62
* 1.80759 -3.26991 3.26991 4 O(f) 4.96508 63
* -1.80759 -3.26991 3.26991 4 O(f) 4.96508 64
* 3.26991 3.26991 -1.80759 4 O(f) 4.96508 65
* -3.26991 3.26991 -1.80759 4 O(f) 4.96508 66
* 3.26991 -3.26991 -1.80759 4 O(f) 4.96508 67
* -3.26991 -3.26991 -1.80759 4 O(f) 4.96508 68
3.26991 1.80759 -3.26991 4 O(f) 4.96508 69
* -3.26991 1.80759 -3.26991 4 O(f) 4.96508 70
* 1.80759 3.26991 -3.26991 4 O(f) 4.96508 71
-1.80759 3.26991 -3.26991 4 O(f) 4.96508 72
* 3.26991 -1.80759 -3.26991 4 O(f) 4.96508 73
* -3.26991 -1.80759 -3.26991 4 O(f) 4.96508 74
* 1.80759 -3.26991 -3.26991 4 O(f) 4.96508 75
* -1.80759 -3.26991 -3.26991 4 O(f) 4.96508 76
5.07750 0.00000 0.00000 1 Fe(a) 5.07750 77
-5.07750 0.00000 0.00000 1 Fe(a) 5.07750 78
0.00000 5.07750 0.00000 1 Fe(a) 5.07750 79
0.00000 -5.07750 0.00000 1 Fe(a) 5.07750 80
0.00000 0.00000 5.07750 1 Fe(a) 5.07750 81
0.00000 0.00000 -5.07750 1 Fe(a) 5.07750 82
4.43774 2.56921 0.63977 5 H 5.16756 83
-4.43774 2.56921 0.63977 5 H 5.16756 84
2.56921 4.43774 0.63977 5 H 5.16756 85
-2.56921 4.43774 0.63977 5 H 5.16756 86
* 4.43774 -2.56921 0.63977 5 H 5.16756 87
-4.43774 -2.56921 0.63977 5 H 5.16756 88
* 2.56921 -4.43774 0.63977 5 H 5.16756 89
-2.56921 -4.43774 0.63977 5 H 5.16756 90
* 4.43774 0.63977 2.56921 5 H 5.16756 91
* -4.43774 0.63977 2.56921 5 H 5.16756 92
* 0.63977 4.43774 2.56921 5 H 5.16756 93
* -0.63977 4.43774 2.56921 5 H 5.16756 94
* 4.43774 -0.63977 2.56921 5 H 5.16756 95
* -4.43774 -0.63977 2.56921 5 H 5.16756 96
* 0.63977 -4.43774 2.56921 5 H 5.16756 97
* -0.63977 -4.43774 2.56921 5 H 5.16756 98
* 2.56921 0.63977 4.43774 5 H 5.16756 99
* -2.56921 0.63977 4.43774 5 H 5.16756 100
* 0.63977 2.56921 4.43774 5 H 5.16756 101
* -0.63977 2.56921 4.43774 5 H 5.16756 102
* 2.56921 -0.63977 4.43774 5 H 5.16756 103
* -2.56921 -0.63977 4.43774 5 H 5.16756 104
* 0.63977 -2.56921 4.43774 5 H 5.16756 105
* -0.63977 -2.56921 4.43774 5 H 5.16756 106
4.43774 2.56921 -0.63977 5 H 5.16756 107
-4.43774 2.56921 -0.63977 5 H 5.16756 108
2.56921 4.43774 -0.63977 5 H 5.16756 109
-2.56921 4.43774 -0.63977 5 H 5.16756 110
4.43774 -2.56921 -0.63977 5 H 5.16756 111
-4.43774 -2.56921 -0.63977 5 H 5.16756 112
2.56921 -4.43774 -0.63977 5 H 5.16756 113
-2.56921 -4.43774 -0.63977 5 H 5.16756 114
* 4.43774 0.63977 -2.56921 5 H 5.16756 115
* -4.43774 0.63977 -2.56921 5 H 5.16756 116
* 0.63977 4.43774 -2.56921 5 H 5.16756 117
* -0.63977 4.43774 -2.56921 5 H 5.16756 118
* 4.43774 -0.63977 -2.56921 5 H 5.16756 119
* -4.43774 -0.63977 -2.56921 5 H 5.16756 120
* 0.63977 -4.43774 -2.56921 5 H 5.16756 121
* -0.63977 -4.43774 -2.56921 5 H 5.16756 122
* 2.56921 0.63977 -4.43774 5 H 5.16756 123
* -2.56921 0.63977 -4.43774 5 H 5.16756 124
* 0.63977 2.56921 -4.43774 5 H 5.16756 125
* -0.63977 2.56921 -4.43774 5 H 5.16756 126
* 2.56921 -0.63977 -4.43774 5 H 5.16756 127
* -2.56921 -0.63977 -4.43774 5 H 5.16756 128
* 0.63977 -2.56921 -4.43774 5 H 5.16756 129
* -0.63977 -2.56921 -4.43774 5 H 5.16756 130
5.07750 2.01171 0.00000 4 O 5.46150 131
-5.07750 2.01171 0.00000 3 N 5.46150 132
2.01171 5.07750 0.00000 3 N 5.46150 133
-2.01171 5.07750 0.00000 3 N 5.46150 134
5.07750 -2.01171 0.00000 3 N 5.46150 135
-5.07750 -2.01171 0.00000 4 O 5.46150 136
2.01171 -5.07750 0.00000 3 N 5.46150 137
-2.01171 -5.07750 0.00000 3 N 5.46150 138
5.07750 0.00000 2.01171 3 N 5.46150 139
-5.07750 0.00000 2.01171 3 N 5.46150 140
0.00000 5.07750 2.01171 4 O 5.46150 141
0.00000 -5.07750 2.01171 3 N 5.46150 142
2.01171 0.00000 5.07750 4 O 5.46150 143
-2.01171 0.00000 5.07750 3 N 5.46150 144
0.00000 2.01171 5.07750 3 N 5.46150 145
0.00000 -2.01171 5.07750 3 N 5.46150 146
5.07750 0.00000 -2.01171 3 N 5.46150 147
-5.07750 0.00000 -2.01171 3 N 5.46150 148
0.00000 5.07750 -2.01171 3 N 5.46150 149
0.00000 -5.07750 -2.01171 4 O 5.46150 150
2.01171 0.00000 -5.07750 3 N 5.46150 151
-2.01171 0.00000 -5.07750 4 O 5.46150 152
0.00000 2.01171 -5.07750 3 N 5.46150 153
0.00000 -2.01171 -5.07750 3 N 5.46150 154
* 5.07750 3.15922 0.00000 2 C 5.98011 155
-5.07750 3.15922 0.00000 2 C 5.98011 156
3.15922 5.07750 0.00000 2 C 5.98011 157
-3.15922 5.07750 0.00000 2 C 5.98011 158
5.07750 -3.15922 0.00000 2 C 5.98011 159
* -5.07750 -3.15922 0.00000 2 C 5.98011 160
3.15922 -5.07750 0.00000 2 C 5.98011 161
-3.15922 -5.07750 0.00000 2 C 5.98011 162
5.07750 0.00000 3.15922 2 C 5.98011 163
-5.07750 0.00000 3.15922 2 C 5.98011 164
* 0.00000 5.07750 3.15922 2 C 5.98011 165
0.00000 -5.07750 3.15922 2 C 5.98011 166
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5.71727 2.56921 0.63977 5 H 6.30058 179
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2.56921 0.63977 5.71727 5 H 6.30058 195
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2.56921 -0.63977 5.71727 5 H 6.30058 199
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0.63977 -5.71727 -2.56921 5 H 6.30058 217
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* -2.50828 -4.43774 -4.43774 5 H 6.75859 250
END
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