FEFF sample input file (feff.inp)
The TITLE, POTENTIALS and ATOMS (and possibly HOLE) are changed
for a new molecule.
NLEG, RPATH and CRITERIA can be modified to change the number of
included paths.
TITLE Ni(en)3
*
ipot
ixsph ifms ipaths igenfmt iff2chi
CONTROL
1 1 1 1 1 1
PRINT
1 1
1 1
1 3
S02 0.0
RPATH 5.0
NLEG 4
CRITERIA 6.0 3.0
HOLE 1
1.0 Ni K edge ( 8.333 keV)
POTENTIALS
* ipot z
label
0 28 Ni
1 7 N
2 6 C
ATOMS
-0.0000300 0.0013073 -0.0001816 0 Ni
-2.4739038 -1.5115305 0.7589044 2 C
-1.0483688 -1.4876796 1.1925291 1 N
-2.5414679 -1.3959899 -0.7588443 2 C
1.8130334 -0.1666801 1.1930930 1 N
-0.7668047 1.6539245 1.1885048
1 N
0.7628770 1.6552526 -1.1886481 1 N
1.0514640 -1.4849035 -1.1924920 1 N
-1.8121621 -0.1708810 -1.1931455 1 N
2.5438814 -1.3911413 0.7591524 2 C
-0.0731131 2.9011505 0.7588294
2 C
0.0678481 2.9014319 -0.7585353 2 C
2.4768456 -1.5073070 -0.7585675 2 C
END
Explanation:
TITLE title_line
Provide the title. You can have up to 10 lines, each starting with TITLE
p. 8 in manual (module 0)
CONTROL ipot ixsph ifms ipaths
igenfmt iff2chi
Which modules to run (0 does not run a module)
Default
CONTROL 1 1 1 1 1 1
p. 7 in manual (module 0)
PRINT ppot pxsph pfms ppaths
pgenfmt pff2chi
Set the print level for each module
Default
PRINT 0 0 0 0 0 0
p. 8 in manual (module 0)
S02 s02
Also (like HOLE) specifies the amplitude reduction factor
S02.
If s02<0.1, then it is estimated by the program. Typical values
0.8-1.0.
Default
S02 1
p. 14 in manual (module 1)
RPATH rpath
Maximum effective (hlaf-path) distance of a fiven path.
Default 2.2 x the nearest neighbor distance.
p. 25 in manual (module 4)
NLEG nleg
Limits the number of scattering paths to nleg.
Default
NLEG 8
p. 26 in manual (module 4)
CRITERIA critcw critpw
Limits the number of scattering paths.
critcw is a cutoff for a full curved wave calculation; default 4%.
critpw is a plane-wave approximation to chi (fast); default 2.5% (only
paths with an amplitude larger than 2.5% of the maximum one is kept)
Default
CRITERIA 4.0 2.5
p. 26 in manual (module 5)
If you intend to use DEBYE keyword, you should have the first number in
CRITERIA lower than the second one (so that you get Debye-Waller
factors for all paths), e.g.
CRITERIA 1.0 2.5
HOLE ihole s02
Gives the hole-code index (i.e. the involed electron; K-shell = 1, see
Table 2.2 in manual p. 13) and the amplitude reduction factor
S02.
If s02<0.1, then it is estimated by the program. Typical values
0.8-1.0.
Default
HOLE 1 1
p. 12 in manual (module 2)
POTENTIALS
* ipot Z [tag lmax1 lmax2 xnatph]
A list which assigns a unique potential index to each distinguishable
atom.
ipot is the potential index
Z is the atom number
tag is an optional 6-character text identifier
p. 12 in manual (module 1)
ATOMS
* x y z ipot
0.0 0.0 0.0 0
Cartesian coordinates in Å followed by unique potential indices
(the rest of the row is a comment).
One atom per line. H atoms are not needed
There is a supplementary code atoms.x, which generates ATOMS list from
crystallographic data.
p. 7 in manual (module 0)
It seems that at least parts of FEFF expects that the absorbing atom is
the first one in the list.
DEBYE temperature
Debye-temperature idwopt
Asks the program to estimate Debye-Waller factors for each paths (given
in the file
s2_em.dat).
There are three methods, given by idwopt=0, 1, or 2.
- idwopt=0 means that the correlated Debye model is used. No
additional input is needed (good for pure metals and other homogenous
systems).
- idwopt=1 mens that the equation of motion is used. Then a file
spring.inp is needed (see below).
Best
choice for heterogenous and biological systems.
- idwopt=2 means that the recursion method is used (not tested).
Example:
DEBYE 10 0 1
p. 27 in the manual (module 6).
Note that the absorbing atom needs to be first in the ATOMS list.
In order to get Debye-Waller factors for all paths, you need to set the
first number in CRITERIA lower than the second one, e.g.
CRITERIA 1.0 2.5
Note the
running
problems with this keyword.
END
Marks the end of input. All lines after this are ignored
p. 8 in manual
FEFF output
From the
sample
input
file; the calculation took ~20 s.
Files:
atoms.dat
feff0010.dat feff0025.dat feff0040.dat log6.dat
axafs.dat
feff0011.dat feff0026.dat feff0041.dat logdos.dat
chi.dat
feff0012.dat
feff0027.dat files.dat
misc.dat
crit.dat
feff0013.dat
feff0028.dat
fms.bin mod1.inp
feff.bin
feff0014.dat
feff0029.dat
fpf0.dat mod2.inp
feff.inp
feff0015.dat
feff0030.dat
geom.dat mod3.inp
feff0001.dat
feff0016.dat feff0031.dat global.dat
mod4.inp
feff0002.dat
feff0017.dat feff0032.dat
ldos.inp mod5.inp
feff0003.dat
feff0018.dat feff0033.dat
list.dat mod6.inp
feff0004.dat
feff0019.dat feff0034.dat
log.dat paths.dat
feff0005.dat
feff0020.dat feff0035.dat
log1.dat phase.bin
feff0006.dat
feff0021.dat feff0036.dat
log2.dat pot.bin
feff0007.dat
feff0022.dat feff0037.dat
log3.dat xmu.dat
feff0008.dat
feff0023.dat feff0038.dat
log4.dat xsect.bin
feff0009.dat
feff0024.dat feff0039.dat log5.dat
stdout output:
Feff 8.20
Ni(en)3
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
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
muffin tin
radii and interstitial parameters
iph, rnrm(iph)*bohr,
rmt(iph)*bohr, folp(iph)
0
1.45965E+00 1.38788E+00 1.13723E+00
1
1.14307E+00 9.33010E-01 1.15000E+00
2
1.10893E+00 8.58450E-01 1.15000E+00
mu_old=
5.401
Done with module 1:
potentials.
Calculating cross-section
and phases...
absorption
cross section
phase shifts
for unique potential 0
phase shifts
for unique potential 1
phase shifts
for unique potential 2
Done with module 2:
cross-section and phases...
Done with module 3: FMS.
Preparing plane wave
scattering amplitudes...
Searching for paths...
WARNING: rmax
> distance to most distant atom.
Some
paths may be missing.
rmax,
ratx 5.00000E+00 0.00000E+00
Rmax
5.0000 keep and heap limits 0.0000000
0.0000000
Preparing
neighbor table
Paths
found 288 (maxheap,
maxscatt 74 3)
Eliminating path
degeneracies...
Plane wave chi
amplitude filter 3.00%
Unique
paths 41, total
paths 80
Done with module 4:
pathfinder.
Calculating EXAFS
parameters...
Curved wave
chi amplitude ratio 6.00%
path cw
ratio deg nleg reff
1 100.000
2.000 2 2.1753
2 99.891
2.000 2 2.1764
3 99.828
2.000 2 2.1770
4 22.119
1.000 2 2.9975
5 66.339
3.000 2 2.9978
6 44.205
2.000 2 2.9984
7 10.587
2.000 3 3.3318
8 21.150
4.000 3 3.3321
9 10.539
2.000 3 3.3323
10 10.547
2.000 3 3.3323
11 10.533
2.000 3 3.3327
12 7.858
4.000 3 3.5916
13 1.515
1.000 4 3.6652
14 1.514
1.000 4 3.6658
15 1.512
1.000 4 3.6664
16 1.511
1.000 4 3.6668
17 3.018
2.000 4 3.6675
18 12.699
4.000 3 3.7595
19 11.815
6.000 3 3.8164
20 13.914
2.000 3 4.3455
21 13.915
2.000 3 4.3453
22 13.883
2.000 3 4.3467
23 2.109
1.000 4 4.3497
24 2.107
1.000 4 4.3506
25 6.556
2.000 4 4.3517
26 6.557
2.000 4 4.3516
27 4.207
2.000 4 4.3525
28 6.519
2.000 4 4.3534
29 4.203
2.000 4 4.3537
30 3.446
1.000 4 4.4877
31 3.449
1.000 4 4.4878
32 3.453
1.000 4 4.4887
33 3.447
1.000 4 4.4883
34 3.444
1.000 4 4.4884
35 3.451
1.000 4 4.4889
36 3.499
2.000 3 4.8442
37 3.499
2.000 3 4.8437
38 3.532
2.000 3 4.8454
39 3.531
2.000 3 4.8459
40 3.509
2.000 3 4.8454
41 3.508
2.000 3 4.8460
41 paths
kept, 41 examined.
Done with module 5: F_eff.
Calculating chi...
feffdt, feff.bin to
feff.dat conversion Feff 8.20
Ni(en)3
Feff
8.20
POT Non-SCF,
core-hole, AFOLP (folp(0)= 1.150)
Abs Z=28 Rmt=
1.388 Rnm= 1.460 K shell
Pot 1 Z= 7 Rmt= 0.933 Rnm=
1.143
Pot 2 Z= 6 Rmt= 0.858 Rnm=
1.109
Gam_ch=1.576E+00 H-L exch
Mu= 5.401E+00 kf=2.312E+00
Vint=-1.496E+01 Rs_int= 1.569
PATH Rmax=
5.000, Keep_limit= 0.00, Heap_limit 0.00 Pwcrit= 3.00%
41
paths to process
path filename
1
feff0001.dat
2
feff0002.dat
3
feff0003.dat
4
feff0004.dat
5
feff0005.dat
6
feff0006.dat
7
feff0007.dat
8
feff0008.dat
9
feff0009.dat
10 feff0010.dat
11 feff0011.dat
12 feff0012.dat
13 feff0013.dat
14 feff0014.dat
15 feff0015.dat
16 feff0016.dat
17 feff0017.dat
18 feff0018.dat
19 feff0019.dat
20 feff0020.dat
21 feff0021.dat
22 feff0022.dat
23 feff0023.dat
24 feff0024.dat
25 feff0025.dat
26 feff0026.dat
27 feff0027.dat
28 feff0028.dat
29 feff0029.dat
30 feff0030.dat
31 feff0031.dat
32 feff0032.dat
33 feff0033.dat
34 feff0034.dat
35 feff0035.dat
36 feff0036.dat
37 feff0037.dat
38 feff0038.dat
39 feff0039.dat
40 feff0040.dat
41 feff0041.dat
Use all paths
with cw amplitude ratio 6.00%
S02
0.953 Global sig2 0.00000
Done with module 6: DW +
final sum over paths.
Sample spring.inp file
This file is described in
Anna
Poiarkova's
thesis and not in the FEFF manual.
The file is needed only if idwopt=1 or 2 in DEBYE keyword (i.e. if
Debye-Waller factors should be calculated).
turbo2feff generates this file automatically if a hessian is present in
the control file.
* BACDUE.pdb, spring.inp
* force constants from UFF
*
res wmax dosfit acut
VDOS 0.02
1 1.2 3
PRINT 5
STRETCHES
* i j
k_ij dR_ij(%)
0
1
102 1
0
2
140 1
3
5
454 2
2
7
1019 1
2
11
715 1
5
6
677 1
7
8
510 4
ANGLES
* i j k
ktheta dtheta(%)
1
0 16
51.84137 1
1
0 23
73.29867 1
0
1
2 34.96747 1
1
2
6 90.01431 1
2
6 24
91.09171 1
2
6
7 81.96911 1
Note that the units of the force constants are N/m. Thus, force
constants in kJ/mole/Å^2 should be divided by 6.0221367
(Avogadros number without any exponent).
1 N/m = 0.1 nN/Å = 0.01 mdyne/Å = 6.0221367
kJ/mole/Å^2 = 6.42294 10^-4 H/Bohr^2
In addition, they should be multiplied by 2, because they are real
force constants U=k/2(x-x0)^2 => f=k(x-x0) and not the
energy-derived force constants used by define (and Amber and CNS):
U=k'(x-x0)^2 => f=2k'(x-x0)
The numbering of the atoms is the same as in the feff.inp file, but the
absorber is #0 and the rest of the atoms are numbered starting from 1
(turbo2feff gives this numbering in the last column).
The last parameter in the row dR_ij is the tolerance in the bond lenght
when searchin for a similar bond, measured in percentage deviation in
the bond length.
The force constant of the angles is in 100*mdynÅ/rad^2. Once
again, force constants in kJ/mole/rad^2 should be divided by 6.0221367.
The angle force constants are usually not needed, but they have a clear
influence on the DW factors and may make the fit more stable (less
warnings).
VDOS command (needed only if idwopt=1):
- res is the VDOS spectral resolution width (default 0.05, i.e. 5%
of the band withdth). The smaller the more fine structure and the
longer the computational time.
- wmax is a multiplication factor used to increase the maximum
frequency to which VDOS is calculated (default 1).
- dosfit governes how much of the low frequency part of the BDOS is
to be fitted to Debye-like behavious. The higher the number, the more
of BDOS will be fitted. Default = 1 (about 10% of the total
width). Useful to eliminate low frequency noise.
- acut is the time integration cutoff arameter. Default = 3 is
nearly always OK and it can be omitted.
PRINT gives the number of prdenNNNN.dat files to be written (read
only if idwopt=1).
Sample output
file of DEBYE keyword, file s2_em.dat
If check0 is > 10% then the result is unreliable. Reduce disfit or
increas wmax in the VDOS command (spring.inp file; e.g. to disfit=0.5
and wmax=3 ).
CuS2N2 complex, BP/RI, SVP,
7/4-05
temperature =
10.00 N_at = 25
-----------------------------------------------------------------------
ipath nleg sig2
mu_ipath check0(%)
1
2 0.00385
11.477 0.91
2
2 0.00348
21.311 3.59
3
2 0.00618
10.101 0.08
4
2 0.00370
10.101 2.57
5
3 0.00378
9.423 2.45
6
3 0.00539
9.062 0.31
7
2 0.00401
10.101 0.61
8
4 0.00483
6.476 2.59
10
2 0.00385
10.101 1.62
12
3 0.00383
10.193 0.05
13
2 0.00525
10.101 5.06
15
3 0.00398
8.697 1.66
16
3 0.00401
8.439 0.87
18
3 0.00579
8.918 0.17
20
3 0.00502
9.908 6.37
21
3 0.00573
8.748 0.68
23
3 0.00388
9.755 1.04
24
4 0.00626
6.139 1.52
25
4 0.00832
2.530 4.23
26
4 0.00590
5.474 2.17
27
4 0.01388
2.609 1.24
30
2 0.00536
10.101 0.08
31
3 0.00553
9.920 0.02
32
3 0.00512
9.895 0.29
34
4 0.00594
9.149 0.16
35
4 0.00515
9.928 0.43
36
4 0.00516
8.740 0.96
39
4 0.00551
7.715 1.38
44
2 0.00499
10.101 0.78
45
2 0.00401
21.311 7.18
46
3 0.00506
10.058 0.42
48
4 0.00520
9.763 0.04
Compilation
Feff9.03
Failed to compile it with gfortran locally
(the program compiled when all options were removed, but the program
did not work).
Instead compiled it with ifort on milleotto:
unzip feff90.zip
cd feff90
./Compile
cd bin
inserted FeffPath=/sw/pkg/bio/FEFF/feff90/bin in feff
cd /sw/pkg/bio/Bin
ln -fs /sw/pkg/bio/FEFF/feff90/bin/feff feff9
It does not seem possible to run spring any longer.
Feff82 and 8.3
The program is compiled by simply typing:
g77 feff82.f
mv a.out feff82
Works also with gfortran (17/2-11):
gfortran -o
feff82 feff82.f
Running problem
with DEBYE keyword
The program cannot run (if compiled with g77) with DEBYE keyword, owing
to oversized unit numbers.
Do the following changes to feff82.f and recompile it:
15943c15943
< iem = 31
---
> iem = 111
15949c15949
< irm1 = 41
---
> irm1 =113
15953c15953
< irm2 = 42
---
> irm2 = 112
24418c24418
< iem = 31
---
> iem = 111
24422c24422
< irm1 = 41
---
> irm1 =111
24425c24425
< irm2 = 42
---
> irm2 = 112
24430c24430
< icum = 43
---
> icum = 113
Moreover, the parameter
nsprx
is set much too low for many complexes if the Seminario method is used
(gives Segmentation fault or Memory fault, without any warnings):
27172c27172
< parameter (nsprx = 400)
---
> parameter (nsprx = 40)
A version without changes is feff82_original.f. It is compiled
as feff82.x.
The version with the changes is feff82.f and feff82.