FDMNES

User’s Guide

Yves Joly

[email protected]
Institut Néel, CNRS, BP 166
38042 Grenoble Cedex 9, France

November 2023

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Outline

Introduction 5

A) General Presentation 7
B) Some advices to make the best possible simulation 11
C) Main input file 15
D) Convolution 61
E) Parameter optimization 71
F) Extraction of DAFS scan and spectra 77
G) Unit cell modification 79
H) FDMX user’s guide 81
I) 2D diffraction 85

List of the fdmnes keywords 95

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Introduction
The FDMNES program calculates the spectra of different spectroscopies related to the
real or virtual absorption of x-ray in material. It gives the absorption cross sections around the
ionization edges, that is in the XANES energy range. Calculations can be performed along all
the conditions of linear or circular polarization. In the same way, it calculates the structure
factors and intensities of anomalous or resonant diffraction spectra (DAFS or RXD) for 3D
diffraction and for surface diffraction (SRXRD). FDMNES also allows the comparison of the
simulated spectra to experimental ones with the help of objective criteria.
FDMNES is mainly a fully relativistic DFT-LSDA code. Optionally Hubbard correction
(LSDA+U) can be used. It uses two techniques. The first one is based on the Finite Difference
Method (FDM) to solve the Schrödinger equation. In that way the shape of the potential is free
and in particular avoid the muffin-tin approximation. The second one uses the Green formalism
(multiple scattering) on a muffin-tin potential. This approach can be less precise but is faster.
The program includes also a multi-electronic extension using the “Time-Dependent DFT” with
a local kernel. The program is symmetrized. Symmetry operations are calculated automatically.

The FDMNES program can be freely downloaded at the web address:

https://fdmnes.neel.cnrs.fr

In case of publication related to the use of the program thanks to cite:

O. Bunau and Y. Joly
Self-consistent aspects of x-ray absorption calculations
J. Phys. : Condens. Matter 21, 345501 (2009).

The FDMNES program highly benefited from the scientific contribution of Calogero
Natoli who has provided a constant and essential help. He is in particular at the origin of all the
developments using the multiple scattering theory and the extensions to resonant diffraction
and magnetism. Oana Bunau realized the extension towards TD-DFT and participated to the
inclusion of self-consistency and Hubbard correction and now Yvonne Soldo-Olivier develops
the surface x-ray diffraction. The program also benefited from the expertise of Delphine
Cabaret, Hubert Renevier, Sergio Di Matteo, Christian Brouder, Aline Ramos, Stéphane
Grenier, Emilio Lorenzo and Yvonne Gründer, without whom different advances would have
not been realized. Finally, this work has been made greatly easier with the support of Denis
Raoux.

From March 2015, Guda, Soldatov et al. (Rostov-on-Don, Russia) make the code far
faster by the use of the MUMS library which solves systems of linear equations for sparse
matrices. This method is now the default option used when running in the finite difference
method mode. When using it thanks to cite also:
Sergey A. Guda, Alexander A. Guda, Mikhail A. Soldatov, Kirill A. Lomachenko, Aram
L. Bugaev, Carlo Lamberti, Wojciech Gawelda, Christian Bressler, Grigory Smolentsev,
Alexander V. Soldatov, Yves Joly
"Optimized Finite Difference Method for the Full-Potential XANES Simulations: Application
to Molecular Adsorption Geometries in MOFs and Metal-Ligand Intersystem Crossing
Transients" J. Chem. Theory Comput. 11, 4512-4521 (2015).
and
P. R. Amestoy, A. Guermouche, J.-Y. L'Excellent and S. Pralet
Hybrid scheduling for the parallel solution of linear systems

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Parallel Computing Vol 32 (2), pp 136-156 (2006).

From October 2015, the code also includes the FDMX extension from J. Bourke and
Ch. Chantler. When using it, thanks to cite also:

Jay Daniel Bourke, Christopher Thomas Chantler and Yves Joly

"Extended X-ray Absorption Fine Structure Calculations Using the Finite Difference Method"
J. Synchrotron Rad. 23, 551-559 (2016).

To have an overview of X-ray absorption spectroscopy, we recommend the reading of:

X-Ray Absorption and X-ray Emission Spectroscopy: Theory and Applications
Edited by J. A. van Bokhoven and C. Lamberti, Wiley (2016).
ISBN: 978-1-118-84423-6.

The work presented here concerns more specifically the chapter 4:

"Theory of X-ray Absorption Near Edge Structure" by Yves Joly and Stéphane Grenier.

Another of our publications gives the main concepts of resonant diffraction:

"Basics of Resonant Elastic X-ray Scattering theory"
by S. Grenier and Y. Joly, J. Phys.: Conference Series 519, 012001 (2014).

Surface resonant x-ray diffraction and x-ray Raman spectroscopy are respectively given
in:
Yves Joly, Antoine Abisset, Aude Bailly, Maurizio De Santis, Farid Fettar, Stéphane Grenier,
Danny Mannix, Aline Y. Ramos, Marie-Claire Saint-Lager, Yvonne Soldo-Olivier, Jean-Marc
Tonnerre, Sergey A. Guda, and Yvonne Gründer.
"Simulation of surface resonant x-ray diffraction"
J. Chem. Theory Comput. 14, 973-980 (2018).
DOI: 10.1021/acs.jctc.7b01032.

Yves Joly, Chiara Cavallari, Sergey A. Guda, and Christoph J. Sahle

"Full potential simulation of x-ray Raman scattering spectroscopy"
J. Chem. Theory Comput. 13, 2172-2177 (2017).
DOI: 10.1021/acs.jctc.7b00203.

The FDMNES code and the Finite Difference method are presented in 2 sections of the
International Tables for Crystallography, Volume I: X-ray Absorption Spectroscopy and
Related Techniques (2021 & 2022)
ISBN: 978-1-119-43394-1

The FDMNES code

by O. Bunău, A. Y. Ramos, and Y. Joly
DOI: 10.1107/S1574870720003304

Finite-difference method for the calculation of X-ray spectroscopies

by Y. Joly, A. Y. Ramos, and O. Bunău
DOI: 10.1107/S1574870722001598

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A- General presentation

I- Computer configuration
FDMNES run on all the computers, under LINUX, Mac or Windows. The programming
language is Fortran 2003. Executables are furnished for Windows 32 and 64 bits, Linux 64 bits
for sequential calculations and for parallel calculations under MPI.
Users can also compile the code themselves. The code needs then MUMPS, LAPACK
and BLAS libraries (and MPI for parallel). When they are not available, it is possible, but not
recommended to use a gaussian solver routine furnished with the other routines

II- The packages

Different packages for the different operating systems (Windows 32, Windows 64,
Linux 64, Mac) can be downloaded. They contain the corresponding executable, a set of
examples of input files, the user’s guide and other information:

- fdmnes_win64.exe: executable for Windows 64 bits,

- fdmnes_win32.exe: executable for Windows 32 bits,
- fdmnes_linux64: executable for linux 64 bits,
- fdmnes_mac.exe: executable for Mac OS,
- run_fdmnes_command: command for Mac OS to execute fdmnes_mac. When clicking
on it, the working directory of fdmnes_mac is the current.
- fdmfile.txt: input file,
- Sim/Test_stand/in: directory containing a set of examples of fdmnes input files.
- Doc: directory containing information on the code, the manual, the file
"FDMNES_Modifications.txt" where are listed the modifications done in the code
along the time. For Mac contains also “Instructions_for_Mac” which gives
explanations to make the mac version running

The fortran routines with example of makefile can also be downloaded as well as an executable
for the parallel version of the code

IV- Compilation
For those who do not want or cannot use the executables of the package, it is possible
to compile the fortran routines. The code is more efficient when running with MUMPS library.
All the furnished routines, but mat_solve_gaussian.f90, sub_util.f and not_mpi.f90, must then
be compiled and linked with the call to this library and the ones whom it depends (SCOTCH,
METIS, BLAS, LAPACK…). The files included in this step (mpif.h, …) must be set in the
same directory (or in a dedicated one).
When this library is not available, one exchanges mat_solve_MUMPS.f90 by
mat_solve_gaussian.f90, sub_util.f and not_mpi.f90, and one compiles and links without call to
external library. Nevertheless by this way, calculations will be far more CPU consuming.
sub_util.f can be replaced by BLAS and LAPACK.
Two examples of "makefile" for linux are provided.

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V- Parallelization
Thanks to Sergey Guda, Keisuke Hatada, Kuniko Hayakawa and Rainer Wilcke, the
users having the access to a cluster of computers can, using the MPI library, run the program in
parallel mode. For this purpose, one has to delete the files "mpif.h" and "not_mpi.f" when
compiling and makes the call to the corresponding library.

VI- Running

After compilation, the program can be run following the usual procedure available on
your system.
As soon as the program is running, it calls the file "fdmfile.txt". This file must also be in
the same directory than the executable file. It only contains the number of independent
calculation to perform, followed the name of the input file of each of these calculations. For
example:

! Input file for fdmnes

1  number of input files
Sim/cu/in/cu_inp.txt  name of the input file

When running in parallel, with MPI, one can use the executable given for this purpose,
or another one compiled by the user with the MUMPS library. There are 2 levels of
parallelization in FDMNES. The first one is a simple one inside the loop over energy. The
second one, optional works inside the MUMPS library. It is useful only when working using
the finite difference method.

Typically, in the first case, the command to send the job is:

mpirun -np 16 fdmnes

The calculation uses then 16 processors in parallel.

To use the 2 parallelism one typically must write:

mpirun -np 16 -x HOST_NUM_FOR_MUMPS=2 fdmnes

In that case, 16 processors are used, 8 energies will be calculated in parallel. For each of them,
2 processors run the MUMPS library.

VII- Troubleshooting
When the program stops without reason, check if an “fdmnes_error.txt” file has been
created. When created, this file contains a message explaining the trouble. Most often it is due
to an error in the input file. It can also be due to the fact that the input file is not found. One has
to check several points:
1) The called files are in the good directory. The name must contain all the paths.
2) The extensions are correct.
3) Their names are OK (under Linux, upper and lower cases must be respected).

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4) When using downloaded input files, some problems of compatibility between

systems can occur. It can be better to write again completely these files.

When the program stops without “fdmnes_error.txt” file, it can be due to a problem of
space memory. Sometimes one gets a message with “stacking fault”. In this case try again
putting in the input file the keyword “Memory_save”. This keyword can be useful when there
are many non-equivalent atoms. An approximation (in fact very good) is then done on the
potential calculation. This option saves some memory space.

VIII- Structure of the calculation

For a complete calculation one has the following scheme:

Choose of the parameters, input file reading

Loop over the position or

charge parameters
Calculation of the XANES spectra and DAFS amplit.

Loop over the shift and

convolution parameters

Convolution and calculation of the DAFS intensities

Comparison with the experimental spectra

Calculation of the final XANES and DAFS amplit.

Convolution and calculation of the final DAFS

Extraction of DAFS azimuth scan or spectra

The program allows the calculation of spectra from a grid of parameters (position,
charge…), to convolute them with other parameters (convolution width, energy shift…), then
to compare them to experimental spectra with the help of objective criteria. These different
steps can be performed together or separately. The comparison with the experimental spectra is
also not mandatory. When used, the parameter fit must be performed with care. In practice

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many calculations are limited to the step “XANES and DAFS calculation” and “Convolution
and calculation of DAFS intensities”. These two steps can also be performed together or
separately.

In the output files, the absorption cross section are in Mbarn (1 Mbarn = 10-18 cm2) and
summed up over the atoms of same chemical specie in the unit cell or in the cluster. To convert
ħ
in number of electron one has to multiply by 𝐶 = = 0.004555352 × ħ𝜔 , where
R,  and a0 are respectively the Rydberg constant, the fine structure constant and the Bohr
radius in Angstrom, ħ𝜔 is the photon energy in eV. One has also to divide by the number of
atoms if one wants the result per atom. The intensities of the reflections are in square of number
of electrons.

The next chapter treats about the principal input file for the step “XANES and DAFS
calculation”. Generally, this file is sufficient to describe all the necessary data for the calculation
because the program calculates its atomic bases and the potential. Nevertheless, the user can
prefer use its own atomic bases or uses directly the potential calculated by the band structure
program FLAPW WIEN-2k. In both cases, some other files must be furnished. They are
described further in the manual. The input necessary for the steps “Convolution”, “comparison
with the experimental spectra” and “Extraction of azimuth scan or spectra” can be set in the
same input file, but they are explained separately in the sections D, E and F.

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B-Some advices to make the best possible simulation

The purpose of this little section is to help the user of this code to obtain the best possible
simulation, considering the limitations of the program.

1) DFT

FDMNES is a DFT program with a TDDFT extension. DFT is a ground state theory. It is thus
in principal false to calculate the exciting states, the ones probed by x-ray absorption
spectroscopies …
But we do it anyway. Indeed, at least for the K-edges of all elements and the L2 and L3 edges
of heavy elements (that is from, say, Z = 31), and with some tried and tested options, it is
possible to obtain very satisfactory agreement. This leads to the following setting:

 The simulation of K (or L1) edge of all elements or L2 or L3 edges of heavy elements
must give a convenient result

By convenient, one means that most features of the data must be reproduced when the atomic
structure is known. They must be reproduced in intensity at typically less than 10% and in
position at less than some eV. Often the agreement can be even better.

We can anyway also calculate the other edges. For example L23 edges of the first half of the 3d
elements is improved by the use of the theory (and keyword) "TDDFT", especially for the ratio
L2/L3. One nevertheless must not expect a reproduction of the excitonic states which gives the
so-called "multiplet" features often observed for example in oxides.
We can also get interesting results playing with screening parameters and option of self-
consistency for the heavier elements.

2) First calculation

For the first calculation of a new material, one must always start with the simplest input file,
that is:
1) Keep all the fdmnes default options and so describing only the atomic structure, the
energy range and terminating with a "Convolution"
2) Make the calculation with a small radius ("Radius" = 3, for example)
3) Use the multiple scattering theory (keyword "Green")
4) No self-consistent calculation

An example for magnetite:

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Filout
Sim/Test/Fe3O4

Range
-5. 0.1 5. 0.2 10. 0.5 20. 1. 30. 2. 60. 4. 100.

Radius
3.0

Green

Spgroup
Fd-3m:1

Crystal
8.3940 8.3940 8.3940 90.0 90.0 90.0

26 .6250 .6250 .6250

26 .0000 .0000 .0000
8 .3800 .3800 .3800

Convolution

End

One must remember that by default:

- The absorbing chemical specie is the first one in the list under "Crystal" (or "Molecule").
If it is not the case, use the keyword "Z_absorber" and below write the absorbing atomic
number.
- The absorption edge is K, in the other case use the keyword "Edge".

The spectrum one gets by such a calculation must already "look like" the experimental
spectrum. Pre-edges can be not well reproduced, some structures can be missing or shifted, but
the general envelope of the spectra must be good. In the other case, there is a problem…
If it is the case, the first thing to check is the atomic structure. It can be the case for example
when the structure comes from a cif file obtained by the use of "Cif_file" keyword. Cif files
often come from structural refinements and they may contain multiple configurations with
occupancy rate less than 1. This leads to atoms apparently too close, and the XANES
calculation takes all the atoms…
In any event, the output file with the extension "bav" contains all the useful information on the
structure.
- Looking for "Symsite" one finds the information related to the space group, the number
of non-equivalent atoms and for each of them the symmetry operations making the
relation to its equivalent atoms.
- Further, and for each absorbing atom, non-equivalent by symmetry, one finds the cluster
description around it. For this, search "Agregat". Just below it is written the punctual
group and a bit further the cluster arranged by increasing distance from its center. When
there is a mistake in the structure, very often pathological positions are evident (for

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example the number of first neighbors are not conform, or interatomic distances are
evidently false because not physical.

 For any new calculation check in the "bav" file the structure

This checking is in any case interesting because you can find there the distances, the number of
atoms and the chemical species of the different shells.

3) Following calculations

The previous step being done, one has now to improve the result. For this try the following
procedures roughly in this order (see in the manual the significance and the precise syntax of
the keywords given below):

1) When there are heavy elements in the structure (say Z >50) (not necessarily the
absorbing atom) use the keyword "Relativism" or "Spinorbit" (with this last, the
calculation is more expensive…)

2) For the calculation of molecules which are not in gas phase, use the keyword "Vmax"
with typical value -6 eV written below.

3) Progressively increase the calculation radius, up to convergence (after convolution).

Typically, one needs to go up to 5-7 Å.

4) Try the exchange-correlation potential GGA, PBE96, in principle better with the
keyword « PBE96 ».

5) If agreement is insufficient, use the finite difference method mode (suppressing the
keyword "Green"); begin again with the small radius then increase it…

6) Make a self-consistent calculation with keyword "SCF". In most cases at this stage, the
agreement is already sufficient, but possibly at the very beginning of the edge.

7) By default, in fdmnes, at the K, L1, M1 and O1 edges, self-consistency is done without

core-hole, the core-hole plus its screening charge being added just at the XANES step.
When the agreement is not yet sufficiently good, particularly at the rising edge, this can
be modified using "SCFexc" (core-hole already present during the SCF), then "SCFexcv
plus a screening smaller than 1 with the keyword "Screening". For insulating
compounds, this last mode can be better. Some software for XANES use the equivalent
of "SCFexc" and "Screening" = 0 as default option. Note that for L23, M23 and M45 edges
the complete calculation is done by default in the ground state (no core-hole). Check in
the manual the significance of "SCFexc", "Nonexc" and "Excited" options to modify all
this. Finally, there is no half core-hole option in fdmnes, because the author does not
understand what this means…
Sometimes, and specifically for oxides, it can be noted that SCF leads to solutions not
converging versus the cluster radius. One observes for instance a beating phenomenon
on the atomic charges, versus the number of atomic shells incoming in the calculation
area. This can be overcome by the use of the keyword "Full_atom" which suppress an
approximation, taking the cluster atoms equivalent by the space group symmetry instead
of the punctual group symmetry.

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8) For the K-edge of 3d, 4d or 5d elements or L23 edges of heavy elements, test the
occurrence of quadrupolar transitions (keyword "Quadrupole").

9) Convolution can be improved. This one has a default width a bit too large. One can
reduce it by the keyword "Gamma_max". When comparing with an experiment
recorded in fluorescence high resolution mode, one must reduce the core level width
with the keyword "Gamma_hole". Sometimes it is convenient to shift the Fermi level
(or cutting energy) which is badly defined due to the core-hole, using the keyword
"E_cut". This is especially the case when using "Screening" option. The temperature
effect can be roughly considered with the keyword "Abs_U_iso". Note that it is
automatically considered when the mean square displacement, U, is included in the cif
file. One must remember that the efficient U in XANES is smaller than in diffraction.
Finally note that the convolution can be performed a part from the main calculation. It
is a way to save a lot of time (see chapter Convolution).

4) Other outputs

1) Dichroism can be calculated using keyword « Polarized ». For the calculation of

XMCD and for magnetic material in general, the magnetic configuration state must be
imposed (with keywords "Magnetism" or "Spinorbit" and "Atom_conf " or "Atom"). We
recall here that without spin-orbit (on the conduction band states), there is no XMCD at
K or L1 edges.

2) Because the absorption spectroscopy calculations need first the calculation of the
density of states, this one can be given as extra output of the code. The projected density
of states can be obtained by keyword the "Density" and "Density_all". The Crystal
overlap orbital population can be obtained with keywords "COOP".

3) When a main calculation has been done (with a specific radius), many results on the
absorbing atoms are in the bav file. Consequently, new calculations on the same
structure and with the same radius can be done very quickly reading this bav file with
the keyword "Extract". By this way one can calculate specific polarizations (or DAFS
reflections), suppress or include the calculation of quadrupole, or, dipole, demand for
output of the Density (but not the COOP).

4) Results on XES (only valence to core), X-ray Raman, resonant diffraction and surface
resonant diffraction can also be obtained (see the corresponding sections).

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C- Main input file

I- General Structure
It contains most of the inputs necessary for the calculation. All the data in input and
output are in Angstrom and electron-Volt. Many options are chosen by default. One can modify
or add other options using keywords. Text can be in upper or lower case. Blank lines or
beginning by “!” are not considered. Between number, one must put at least one blank. When
getting problem when opening these input files, one has to check if their name is correct.
Moreover, some compilers do not like files written under other system (MAC, DOS,
LINUX…). In case of difficulties when the program wants to open one of these downloaded
files, it can be useful to completely write them again.
The input file contains several blocks of data, each one starting with a specific keyword.
The end of the input file is noted by the keyword "End". Whatever is after is not red. Here
comes an example of input file:

! Fdmnes input file

! Calculation for the copper K-edge in copper cfc

Filout
Sim/Cu/Cu_out  Name of the output files (without extension)

Range
-2. 0.2 5. 0.5 10. 1. 40.

Radius  Cluster radius

3.0

Crystal  crystal structure

3.610 3.610 3.610 90. 90. 90.  Unit cell parameters (Å and degrees) : a, b, c, 
29 0.0 0.0 0.0  Atomic number, position
29 0.5 0.5 0.0
29 0.5 0.0 0.5
29 0.0 0.5 0.5

Convolution  to get convoluted spectra

End  end of the input file

Two blocks are necessary for any calculations. The first one starts with the keyword
“Radius” followed by the value of the radius of the sphere surrounding the area of calculation.
The second one is necessary to describe the material structure. Which can be a molecule or a
3D or 2D periodical structure. This description follows respectively the keywords "Molecule",
"Crystal" or "Surface".

All the keywords related to the convolution or to the fit of the parameters are treated in
chapter C and D.

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Output file names

By default the output file name is fdmnes_out. This name can be modified by the use of
the keyword "filout" followed by the name we want (without extension). Then one gets several
output files with the extensions:
_bav.txt output file giving details
.txt contains only the spectra by column
_nrixs.txt contains only the spectra by column for NRIXS simulations
If a calculation is performed on several non-equivalent crystallographic sites, one gets the
extensions:
_i.txt, _j.txt … in which i and j are the index of the sites (see keyword absorber)

In option or depending on the type of calculation, one can also get the files:
_conv.txt convoluted spectra scan (keyword Convolution).
_scan.txt dafs versus angles for azimuthal scan (keyword DAFS).
_sda.txt state density for the atom number a (keyword Density).
_atoma.txt results for one atom at position number ’a’ (keyword Allsite).
_atoma_scan.txt DAFS scan results for the atom a (keyword Allsite and DAFS).
_tddft.txt output with the TDDFT option (keyword Tddft).
_tddft_scan.txt azimuthal scan in the TDDFT option (keyword DAFS and Tddft).
_tddft_conv.txt convoluted spectra in TDDFT (keyword Convolution and Tddft).

For the analysis of the spherical tensors (keyword Spherical and Sphere_all)
_sph_atoma.txt spherical tensors of the atom a.
_sph_atoma_int.txt integral of the spherical tensors of the atom a.
_sph_signal_atoma_xan.txt contribution of each atomic spherical tensor on the
average xanes signal.
_sph_signal_atoma_poli.txt contribution of each atomic spherical tensor on the xanes
polarisation number i.
_sph_signal_atoma_rxsi.txt contribution of each atomic spherical tensor on the DAFS
reflection number i.
_sph_signal_xtal_xan.txt contribution of the crystal spherical tensor on the average
xanes signal.
_sph_signal_xtal_rxsi.txt contribution of the crystal spherical tensor on the DAFS
reflexion number i.
_sph_xtal.txt spherical tensors of the crystal.
_sph_xtal_int.txt integral of the spherical tensors of the crystal.
_sph_xtal_rxsi.txt spherical tensor of the crystal for the DAFS reflexion number i.

For the analysis of the cartesian tensors (keyword cartesian):

_car_atoma.txt cartesian tensors of the atom a.
_car_xtal.txt cartesian tensors for the crystal
_car_xtal_rxsi.txt cartesian tensors for the crystal for the DAFS reflection number i.

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II- Basic keywords

1) Output file names

The different output files have names with the same root. The extensions automatically
added depending on the chosen option. To define this root use :

Filout  or "File_out"
Sim/Cu/Cu_out  Name of the output files (without extension)

The files can eventually be in a subdirectory.

2) Radius of the cluster

The final states are calculated inside a sphere, whose radius is defined with the keyword
"Radius". Only the atoms inside this sphere are considered. By default, the sphere is centered
on the absorbing atom.

Radius  Mandatory keyword preceding the radius of the cluster.

3.5  value in Angstrom of the cluster radius.

For calculations on large energy range (typically used in EXAFS), it can be convenient
using a decreasing radius when energy increases. For this purpose, one can set energy ranges
with decreasing radius:

Radius
8.3 100 7 250 5 500 4  8.3: radius up to 100 eV, 7 radius between 100 and 250 eV…
4 : radius beyond 500 eV

3) Cluster or crystal structure

Under "Crystal" or "Molecule" stand all the data describing respectively the unit cell or
the molecule. If the calculation is done using the FLAPW output, this block is useless because
the structure is red in one of the FLAPW output files. Under the keyword, come the mesh
parameters (Å) and the angles (degrees). Then come all the atoms (and not only the non-
equivalent ones, but when is specified the space group using the keyword "Spgroup"). By
default and in the absence of the keyword "Absorber", the absorbing atom chemical specie
corresponds to the first atom in the list.

Example 1: cfc copper crystal:

Crystal  Crystal structure

3.610 3.610 3.610 90. 90. 90.  a, b, c, 
29 0.0 0.0 0.0  Atomic number, position
29 0.5 0.5 0.0
29 0.5 0.0 0.5
29 0.0 0.5 0.5

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Example 2: FeO6 octahedron:

Molecule
1.900 1.900 1.900 90. 90. 90.  a, b, c, 
26 0.0 0.0 0.0  Atomic number, position
8 1.0 0.0 0.0
8 -1.0 0.0 0.0
8 0.0 1.0 0.0
8 0.0 -1.0 0.0
8 0.0 0.0 1.0
8 0.0 0.0 -1.0

The atomic structure can also be given in cylindrical or spherical coordinates. To use
cylindrical coordinates, it is sufficient to give only two numbers under "Molecule". The program
will understand they are a and c and that the positions of the atoms are given by r,  and z. Thus
to describe the same octahedron as previously:

Molecule
1.900 1.900  a, c
26 0.0 0.0 0.0  Atomic number, position (r,  and z)
8 1.0 0.0 0.0
8 1.0 180.0 0.0
8 1.0 90.0 0.0
8 1.0 -90.0 0.0
8 0.0 0.0 1.0
8 0.0 0.0 -1.0

To use spherical coordinates, only one number (a) must be set after "Molecule". The
position of the atoms is then given by r, . For the same octahedron:

Molecule
1.900 a
26 0.0 0.0 0.0  Atomic number, position (r, )
8 1.0 90.0 0.0
8 1.0 90.0 90.0
8 1.0 90.0 180.0
8 1.0 90.0 270.0
8 1.0 0.0 0.0
8 1.0 180.0 0.0

When working with 2D film, one just has to replace « Crystal » by « Film ».

It is possible, in the non-magnetic case, to specify only the non-equivalent atoms. Then
one has to give the space group under the keyword "Spgroup". The complete name, as in the
international table, must be given. For example, for magnetite, one gets:

Spgroup
Fd-3m:1  it is also possible to write 227:1

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Crystal
8.3940 8.3940 8.3940 90.0 90.0 90.0

26 .6250 .6250 .6250 ! Fe 16d

26 .0000 .0000 .0000 ! Fe 8a
8 .3800 .3800 .3800 ! O 32e

Note that for the calculation of the symmetry, it is important de define the atom position
with a sufficient number of digits (say 10). For instance, for graphite one has to write:

Spgroup
P63mc

Crystal
2.456 2.456 6.696 90. 90. 120. = a, b, c, alpha, beta, gamma
6 0.0 0.0 0.0
6 0.3333333333 0.6666666667 0.0

Writing for example 0.3333 in the last line, would create false atoms. Program would stop
immediately with an error message.

It is also possible to have an occupancy rate not full for the atoms. For this one must write the
keyword “Occupancy” and a fifth column after the atom position containing this weight:

Occupancy

Crystal  or Molecule or Film or Surface or Interface

2.456 2.456 6.696 90. 90. 120.
6 0.0 0.0 0.0 0.8  weight 80 %
6 0.25 0.25 0.0 1.  weight 100%

During the building of the cluster, when 2 atoms are at the same position, only the one
with the highest weight is kept. The final signal is taken with the given weights.

It is possible to use directly the structure given in pdb or cif files. These ones contain all
the geometry, the space group… In this case use, one of the following way:

Pdb_file (or Film_Pdb_file, when working with a 2D film)

File_name.pdb

Cif_file (or Film_Cif_file, when working with a 2D film)

File_name.cif

It is also possible to describe a surface structure with a 2D periodicity using the

keywords « Surface », « Film » or « Bulk ». See these keywords presented in section “2D
Diffraction”. They can also be used for XANES.

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4) Atomic electronic densities

An electronic configuration is used by default for all the atoms. It is possible to modify
it by the use of the keywords "Atom" or "Atom_conf". Moreover under "Crystal" or "Molecule"
one must not anymore put the atomic number, by the atom type number. For example in case
of a FeO6 octahedron with the Fe 3d64s2 and O 2s22p4 configuration:

Atom  keyword preceding the atomic electronic densities

26 2 3 2 6. 4 0 2.  atomic number of the chemical specie of type 1, number
8 2 2 0 2. 2 1 4. of valence orbital and (n,l,pop) of each of these orbitals

molecule
1.900 1.900 1.900 90. 90. 90.  a, b, c, 
1 0.0 0.0 0.0  Atom type, position
2 1.0 0.0 0.0
2 -1.0 0.0 0.0
2 0.0 1.0 0.0
2 0.0 -1.0 0.0
2 0.0 0.0 1.0
2 0.0 0.0 -1.0

Important remark: contrary to what one can think, the formal charges attributed to the atoms in
the ionic compounds are far from the true charge. Thus one has to perform exchange of charge
between atoms with care and in a moderate way. A good technique is, for example for 3 d
elements, the good number of “d” electron, following the formal charge, but keeping the
neutral atom, putting electrons in the large radius 4s or 4p orbitals.

Another possibility permits to keep the atomic number in front of each atom in the list
after Crystal or Molecule and to give the electronic configuration only for some of them. For
this use the keyword “Atom_conf” with just below
the number of atom with the following configuration (nbr)
the indexes of these atoms in the list under “Crystal” or “Molecule” (ind1,ind2…)
the number of atomics orbitals with a specific configuration (no)
the quantum numbers ni and ℓi and the occupancy, pi, for each specific orbital i.

Atom_conf
2 1 2 2 3 2 5. 4 1 1.  nbr, ind1, ind2, no, n1, ℓ1, p1, n2, ℓ2, p2
1 3 2 3 2 6. 4 1 0.  another configuration for the third atom in the list below

Crystal
4. 4. 4. 90 90 90
26 0. 0. 0.
26 0.5 0. 0.
26 0. 0.5 0.
26 0. 0. 0.5

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In the example above the atoms 1 and 2 of the list under « Crystal » have the configuration
3d54p1. The atom 3 has the configuration 3d6. The remaining atoms have the default
configuration.

When one wants to give a configuration for a doping element (see keyword
« Doping »), one must write « 0 » for the atom index:
Atom_conf
1 0 2 3 2 5. 4 1 1.  nbr of atom (1), then index = 0

5) Absorbing atoms

All the atoms present in the structure participate to the absorption or scattering. By
default, the calculated spectra correspond to the sum of the scattering produced by all the atoms
of the same atomic number than the first one in the list under "Crystal" or "Molecule".
When one wants to select some of the absorbing atoms, one has to use the keyword
"Absorber". For example, if one wants that the absorbing atom is the nth of the list and only this
one (under "Crystal" or "Molecule"), put:

Absorber
3  absorbing atom number (here the 3rd in the list).

If this example goes with the FeO6 structure defined just above, the result in the output file
would correspond to a calculation of an oxygen atom summed over the 6 atoms because they
are equivalent by symmetry. If one wants the result from a unique site, use the keyword
"Symsite" or "Allsite" (see further on).

If there are non-equivalent sites, one has to perform independent calculations. For this,
one must specify each atom number under "Absorber". The name of each of the corresponding
output file get the suffix "_n" in which n it the atom number.

Filout
copper_out

Absorber
15  atom numbers whom results will in output file copper_out_1 and copper_out_5

The summation over these different sites and the eventual energy shifts is to be
performed during a following step.

Another possibility is to define the atomic numbers of the absorbing atoms. We can have
1 or several atomic numbers (but of the same edge, K…) This is done with the keyword:

Z_absorber
26  all the atoms with Z = 26 are absorbing atoms

Z_absorber
26 27  all the atoms with Z = 26 or Z = 27 are absorbing atoms

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6) Energy range

The energy range E that one defines in the input is the energy of the photoelectron
relative to the Fermi level.
By default the energy range is -5 to 60 eV by 0.5 eV step. One can change the range,
the step or even have a variable step using:

Range  keyword for the energy range

1. 0.5 60.  Emin, step, Emax

Other example with variable step:

Range
1. 0.1 10. 0.5 20. 1. 60.00  E min, step, E intermediate, step …

To get a continuously increasing step (k step constant) put:

Rangel
1. 0.1 200.  E min, step at the Fermi level, E max

By default, the output energy range is relatively to the Fermi level. If one wants that the
output energy is the photon energy put the keyword:

Energpho

7) Multiple scattering mode

If one wants to calculate in the multiple scattering mode use the keyword:

Green

Then the potential is automatically a muffin-tin one. The mode is faster than the finite difference
method, so one has to use it first.

8) Threshold type

By default the threshold is the K one. For other threshold put the keyword:

Edge  keyword preceding the threshold type

L1  threshold (K, L1, L2, L3, M1 …)

It is possible in a single run to calculate 2 edges with the same initial (n,l), that is the edges L2
and L3 or M2 and M3 or M4 and M5 … For this write:

Edge  keyword preceding the threshold type

L23  threshold L2 and L3, or M23, M45, N23, N45.

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9) Multipolar expansion

By default only the transition electric dipolar component (E1E1) is calculated. This is
modified by the keywords:

Quadrupole  quadrupolar calculation (E1E2 and E2E2)

Octupole  octupolar calculation (E1E3 and E3E3)
Dipmag  magnetic dipole calculation (E1M1) and (M1M1)
E1E2  calculation of E1E2
E1E3  calculation of E1E3
E2E2  calculation of E2E2
E3E3  calculation of E3E3
E1M1  calculation of E1M1
M1M1  calculation of M1M1
No_E1E1  No calculation of the dipolar-dipolar component (E1E1)
No_E2E2  No calculation of the quadrupolar-quadrupolar component
No_E1E2  No calculation of the dipolar-quadrupolar component
No_E1E3  No calculation of the dipolar-octupolar component
Dip_rel  To take into account the spin-orbit transition term in E1E1

10) Polarization and dichroism

By default the calculation is performed along 1, 2 or 3 orthogonal polarizations in the

dipole mode (and up to six in quadrupolar) depending of the symmetry, and only the average
corresponding to a powder is given. To get the spectra for the different polarizations, use:

Polarize

To get linear or circular dichroism, one must specifies polarization and wave vector (in
quadrupolar) orientations. These vectors must then be given in the non-orthogonal, but
normalized crystal basis. For example if (𝛼 = 𝛽 = 𝛾 = 90°), for 3 polarizations in the (a,b)
plane at 0, 30 and 45° from a :

Polarize
1 0 0
0.866025404 0.5 0
0.707106781 0.707106781 0

Note that the normalization is performed in the code thus for an orthogonal unit cell
(0.707106781, 0.707106781, 0) is equivalent to (1,1,0). For a non-orthogonal unit cell, correct
coordinates must be given. For example in the hexagonal case (𝛾 = 120°), the coordinates of a
vector in the (a,b) plane, at the angle 𝛿 from a are cos 𝛿 + sin 𝛿 ⁄√3 , cos(120 − 𝛿) +
sin(120 − 𝛿)⁄√3 , 0 .

For a quadrupolar calculation, one has to specify the wave vector after the polarization:

Polarize
1.0 1.0 0.0 0.0 0.0 1.0
1.0 -1.0 0.0 0.0 0.0 1.0

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0.0 0.0 1.0 0.0 0.0 0.0

Each line contains the polarization vector, the wave vector. If the wave vector is zero
(or omitted) this case is calculated in the dipolar approximation.

It is possible to perform an average on different polarizations adding a new number at

the end of the line is the corresponding weight. If at least two weights are non-zero, in the
output, there will be a new column with the weighted average of the different polarization.

Polarize
1.0 1.0 0.0 0.0 0.0 1.0 1.
1.0 -1.0 0.0 0.0 0.0 1.0 1.
0.0 0.0 1.0 0.0 0.0 0.0 0.

If one wants to have a circular polarization, one just has to put this one to zero followed
by the value of the wave vector:

Polarize
0.0 0.0 0.0 0.0 0.0 1.0

In the output one will have the calculation the sum right plus left polarizations, then the
difference. In this example, in orthogonal coordinates, the calculation corresponds to the
polarization x+iy and x-iy.

To calculate the transmission through a sample of a specific thickness and to check

change in polarization to the sample, it is necessary to calculate an absorption - matrix. This
is done with the keyword:

Mat_polar
0. 0. 1. 1. 0. 0.  polarization  and wave vector

See also the keywords: “Sample_thickness”, “Stokes” and “Stokes_name” to define the sample
thickness, incoming polarization matrix and analyzer angles.

II-10) Doping

It is possible, more specifically for crystal to calculate the absorption of a doping

element set in substitution in place of another one. For this one uses the keyword « Doping »,
followed by the atomic number of the doping element and the index of the atom to substitute in
the list under « Crystal »:

Doping
27 1  substitution by Cobalt of the atom in the first site.

The doping atom is supposed to be at low concentration, thus the cluster built around it, is the
same than the one given by the crystal. Symmetries are kept.

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II-11) Getting back the electronic structure from a previous calculation

It is possible to get back the electronic structure of the absorbing atoms from a previous
calculation (it is in the fdmnes_out_bav.txt type file) and to compute other polarizations, or ask
for the density of state (keyword Density), or make a TDDFT calculation different or not done
in the previous calculation, putting the key word “Extract” followed by the corresponding
name:

Extract
Sim/calcul_prec_bav.txt

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III- Non resonant X-ray inelastics scattering (NRIXS)

The non-resonant inelastic scattering (NRIXS or X-Raman) is very close to XANES.
The first order term is equivalent to the dipolar approximation in XANES. One can obtain a
more precise simulation, depending on the momentum transfer q, using the keyword:

NRIXS
3. 5.5 9.  the different values of the modulus of q in Å-1

The corresponding output file will have the extension "_nrixs".

When one wants to simulate an experiment performed on a mono-crystal one must

specify also the direction of vector q. This is done replacing the keyword “NRIXS” by
“NRIXS_mono”, followed line by line by the modulus of q and the direction of q which is
expressed in the unit cell basis. This direction does not need to be normalized:

NRIXS_mono
3. 1. 0. 0.  modulus of q, then direction of q
3. 1. 1. 1.
3. 1. 2. 2.5
3.  when the direction vector is not given (or equal to (0,0,0)) this
5. 1. 0. 0. corresponds to the calculation of powder, like when using « NRIXS »
5. 1. 1. 1.

If one wants the results resolved in ℓ, the Bessel quantum number associated to the
expansion of 𝑒𝑥𝑝(𝑖𝒒. 𝒓) in the transition operator, write:

All_nrixs

By default the maximum value of ℓ is 2. To change it, write :

Lmax_nrixs
3  ℓ maximum value.

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IV- Anomalous or resonant diffraction

1) Reflections and polarization

In case of anomalous (or resonant) diffraction (DAFS, DANES, RXS, RXD)

calculation, put the keyword "DAFS" (or "RXS") followed by the index of the beams to
calculate. The orientation of the polarization and wave vector can be described by different
way. When working in  or s, or in circular polarization, put the number 1, 2,
3, 4 or 5 for the polarization respectively , , circular right, circular left or linear along a
general direction, in input then in output.

DAFS
0 0 2 1 2 45.  reflection indices, , , azimuth
0 0 2 1 1 45.  reflection indices, , , azimuth

When the polarization is linear but not  or , but with an angle  such that  = 0° when it is 
and 90° when it is , one must write:

DAFS
0 0 2 1 0. 5 10. 45.  reflection indices, , angle, rectilinear, angle, azimuth
0 0 2 1 0. 5 -10 45.

Note that in this case, one must specify both incoming and outgoing polarization angles, even
when one of them is ,  or circular. When it is circular, the angle is not taken into account.

Let’s take a, b and c, the unit cell vectors, 𝒊𝒂 = 𝒂⁄|𝒂|, 𝒊𝒄 = 𝒄⁄|𝒄|, and Q the normalized
diffraction vector. We define the azimuthal angle, , using the base (I,J,Q) such that:

𝑰 = 𝑸 × 𝒊𝒄 × 𝑸⁄|𝒊𝒄 × 𝑸|, 𝑱=𝑸×𝑰

When 𝑸 is along c, 𝒊𝒄 is substituted by 𝒊𝒂 . One then gets, versus the Bragg angle B the incoming
and outgoing
 wave vectors:
  
k i  cos B cosI  cos B sin J  sin  B Q ,
   
k s  cos B cosI  cos B sin J  sin  B Q .
For the  and  polarizations, one gets:
  
  sin  I  cos J
     
 i  ki     sin  B cosI  sin  B sin J  cos B Q
     
 s  k s      sin  B cosI  sin  B sin J  cos B Q

By this way,  increases when the sample is rotated trigonometrically. For example with an
orthogonal unit cell: reflection (h,0,0), (I,J,Q) =(𝒊𝒄 ,−𝒊𝒃 , 𝒊𝒂 )
1 1 0.  corresponds to - with polarization along −𝒊𝒃 .
1 1 90.  corresponds to - with polarization along 𝒊𝒄 .
reflexion (0,0,ℓ), (I,J,Q) =(𝒊𝒂 , 𝒊𝒃 , 𝒊𝒄 )
1 1 0.  corresponds to - with polarization along 𝒊𝒃 .
1 1 90.  corresponds to - with polarization along 𝒊𝒂 .

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i

ki
s
Q
ks
B J
I


If one does not put the angle, this implies that one performs a  scan and all the
amplitudes are calculated for all the angles by 2° step. There is then a supplementary output
files with the extension "_scan.txt".

It is also possible to perform a 360° scan by 2° step for the tilinear incoming or outgoing
polarizations. For this, one has to write 10 in place of the  notification:

DAFS
0 0 2 10 1 45.  incoming polarization is scanned
0 0 2 2 10 45.  outgoing polarization is scanned

The first value (angle = 0°) corresponds to the  polarization. 90° corresponds to  polarization.

It is possible to write the exact polarization directions. This can be useful for peculiar
uses as in photoemission. In case of linear polarization write:

DAFS
000  Reflection index
0. 0. 1. 0. 1. 0  i, ki
0. 0. 1. 0.7071 0.7071 0.  s, ks

For circular polarization, it is complex:

DAFS
000  reflection index
0.7071 0.7071 0. 0. 0. 0. 0. 1. 0.  i, ki (xr xi yr yi zr zi kix kiy kiz)
0.7071 -0.7071 0. 0. 0. 0. 0. 1. 0.  s, ks

When one does not want phase term between atoms, for example to simulate
photoemission, just write 0 0 0 as reflection index.

Note that it is possible to choose any other origin for the azimuth, just using another
vector than 𝒊𝒄 to define the basis vector I and J. For this just write:

Zero_azim
0. 1. 1.  vector in the direct crystal base

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In some cases, as in biology, one has a very large number of diffracted beams. It is then
simpler to specify the beams to calculate using experimental files. In this case one must give
the corresponding file names containing the experimental spectra, the orientation matrix giving
the incoming polarization versus the unit cell and for each file the rotation angle. One thus has
to write:

DAFS_exp
11.231547 3.519121 -71.823997  matrix
12.573563 -170.027649 -6.364535
-86.558281 -5.978752 -11.279972
0.  angle for the first file
MoFe/Refl_R5to2_1.txt  name of the first file
10.  angle for the second file
MoFe/Refl_R5to2_2.txt  name of the second file …

Each experimental file contains some number of spectra in column along the format :
-1 16 28 -1 20 18  (h,k,l) for each reflections (integer)
Energy D[-1,16,28] D[-1,20,18]  one line of comment
7080 -3.19 -7.96  Energy, intensity for each reflections
7100 9.75 16.65

One must have at least one space between each number, but no tabulation or coma between the
numbers. The number of digit or space between the numbers is free.

For a calculation with DAFS_exp, by default one calculates and compares to the data, the
value : 𝐼 (𝑄) + 𝐼 (𝑄) − 𝐼 (−𝑄) + 𝐼 (−𝑄). If one wants to calculate and compare
other values related to the intensity, write “DAFS_exp_type “ with below a number between 1
and 4:

DAFS_exp_type
1  𝐼 (𝑄) + 𝐼 (𝑄)
2  𝐼 (𝑄) + 𝐼 (𝑄)
3  𝐼 (𝑄) + 𝐼 (𝑄) − 𝐼 (−𝑄) − 𝐼 (−𝑄)
4  default case : 𝐼 (𝑄) + 𝐼 (𝑄) − 𝐼 (−𝑄) + 𝐼 (−𝑄)

It is now possible to calculate the self-absorption corresponding to the incoming and

outgoing photon polarizations. For this put the keyword:

Self_abs

Then one gets in the output files, after each reflection two new columns containing the
linear absorption coefficients, the unit being the m-1. They contain after the convolution also
the absorption coming from the other atoms and the other edges. That is that the absorption
before the edge is not zero. The new data allows the correction due to the self-absorption in
order to compare with experimental spectra. The corrected spectra are, after convolution in
columns following the non-corrected spectra. Their names begin with “Ic”.

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One can make a more sophisticated correction taking into account the birefringence. For
this put the keyword:

Full_self_abs

It is then necessary to calculate all the reflections along the 4 polarizations , ,  and 
and in this order:

DAFS
2 0 0 1 1 0.
2 0 0 1 2 0.
2 0 0 2 1 0.
2 0 0 2 2 0.

In first approximation, this correction is equivalent to Self_abs. It allows the taking into
account of the rotation of the polarization when the electromagnetic wave propagates into the
media.

Note that from this, it is possible to calculate circular polarizations reflection intensity
for any value of the Stokes parameters. This part is performed in the “convolution” step. See
thus the corresponding paragraph.

By default the scan step is 2°. To modify it, use:

Step_azim
0.5  step in degrees of the azimuthal scan

2) Non resonant magnetic scattering

The non-resonant magnetic scattering is taken into account for the DAFS. This term can
be decreased, or put to zero, using a multiplicative factor:

No_res_mag
0.8  factor

An additional factor can be applied to the contribution from the orbital moment. This
factor corresponds to L/2S (and not L/S):

No_res_mom
-0.3  factor for the orbital moment

By default, this factor is calculated using the Hund rules and multiplied by 0.2.

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3) Temperature

It is possible to take into account the thermic disorder using the Debye model. For this purpose
use the keyword :

Atom_B_iso

After keyword "Crystal", one then must add a fifth column after the atom positions the Debye
parameter (8𝜋 〈𝑢 〉) in Ų. If no number are given, the default zero value is given. When using
also "Occupancy" keyword, the fifth and sixth columns contain the 2 corresponding parameters
in the order given by the order of the keywords in the input file.

For the same purpose but using as Debye parameter 〈𝑢 〉 instead of 8𝜋 〈𝑢 〉 use:

Atom_U_iso

Debye disorder can also be anisotropic with keywords "Atom_B_ani" or "Atom_U_ani". Up to

now only 3 values can be given for xx, yy et zz. When ony 2 values are given, the code sets
𝑈 = 𝑈 ≠ 𝑈 . When a unique value is given 𝑈 = 𝑈 = 𝑈 . Columns adds as for "iso"
When using also "Occupancy" it is better to have "Atom_U_ani" or "Atom_B_ani" after.

Atom_U_ani

4) Occupancy

In the same way, one can use an occupancy rate on each sites. For this purpose write:

Occupancy

Then after keyword “Crystal” in the fifth column, after the atom position, the occupancy rates,
between 0 and 1 are given. When no number value, the default 1 value is used. When using also
"Atom_B_iso" or "Atom_U_iso" (or ani), see just above for the order.

5) Common keywords with SRXRD

"DAFS_2D" allows the definition of reflections and polarizations using the operation modes
corresponding to the diffractometer geometry with up to 6 circles. It is described in chapter
SRXRD.

"No_analyzer" allows the calculation of reflections without analyzer. See also the chapter
SRXRD.

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V- Potential, magnetism and calculation technique

1) Relativistic calculation

By default, simulations are non-relativistic, without spin-orbit and non-magnetic for the
valence and conduction band states (but relativistic with spin-orbit for core states). For heavy
atoms (say Z > 36), in the structure, including when they are not absorbing atoms, it is
recommended to make a relativist calculation using the keyword:

Relativism

To be more precise, it can be useful, to start from the Dirac equation, which contains
the spin-orbit interaction. Such a calculation, fully relativistic can be done with the keyword:

Spinorbit

Note that then the simulations are typically 4 to 8 times longer and need 2 times more memory
space. Beside the relativistic aspect, when scattering or absorption depend on conduction band
electron spin-orbit, this keyword is mandatory. A spin-polarized simulation can then be done
using this keyword plus the keyword "Atom_conf " or "Atom" (see further on).
With the keyword “Spinorbit”, simulation is automatically relativistic. For a non-
relativistic simulation without spin-orbit use the keyword:

Nonrelat

2) Spin polarized calculation

To make a spin polarized calculation, one can use the “Spinorbit” keyword, see above,
or more simply, when spin-orbit can be neglected (what can be the case of L23 edges but never
of the K edges) put the keyword:

Magnetism

If the polarized potential comes from LAPW, "Spinorbit" or "Magnetism" must be before
"Flapw". When the calculation does not use the Wien-2k output, the use of the keywords
"Atom" or "Atom_conf " is mandatory to specify the electronic configuration, different for the
spin up and spin down parts. The orbital occupancy must be given for each spin in doubling the
corresponding columns.

Example of metal fcc nickel:

Magnetism

Atom
28 2 3 2 5. 4. 4 0 0.5 0.5

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Crystal
3.52387 3.52387 3.52387 90. 90. 90.
1 0.0 0.0 0.0
1 0.5 0.5 0.0
1 0.5 0.0 0.5
1 0.0 0.5 0.5

The configuration is 3d94s1 with 5 electrons 3d up and 4 electrons 3d down, 0.5 electron
4s up and 0.5 electron 4s down.
In case of an antiferromagnetic structure, one must put a minus sign in front of the atom
type number to specify the atom with the reverse spin. For example:

Atom
23 2 3 2 2. 0. 4 1 0.5 0.5
8 0

Crystal
7.255 5.002 5.548 90.0 96.75 90.0
1 0.34380 0.00080 0.29910
1 0.65620 0.99920 0.70090
-1 0.84380 0.50080 0.79910
-1 0.15620 0.49920 0.20090

2 0.40700 0.84500 0.65200

2 0.09300 0.84500 0.34800
2 0.59300 0.15500 0.34800
2 0.90700 0.15500 0.65200

Alternatively, it is possible to use the keyword « Atom_conf » which allows to specify

the orbital occupancy of only some of the a atoms:

Atom_conf
2 1 2 2 3 2 2. 0. 4 1 .5 .5  nbr of atoms with the configuration, then index of these atoms
2 3 4 2 3 2 0. 2. 4 1 .5 .5  then nbr of orb, then n,l occ up, occ down for each orbital…

Crystal
7.255 5.002 5.548 90.0 96.75 90.0 / a, b, c, alfa, beta, gamma
23 0.34380 0.00080 0.29910 V8
23 0.65620 0.99920 0.70090 V6
23 0.84380 0.50080 0.79910 V4
23 0.15620 0.49920 0.20090 V5

8 0.40700 0.84500 0.65200 O 1 8f

8 0.09300 0.84500 0.34800 O 2 8f

3) Spin axis

By default the spin axe is along the c axis but in the trigonal unit mesh in which it is
along the c axis of the associated hexagonal unit mesh. This axis can be orientated along any
(but uniform) direction:

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Axe_spin
-0.08909 0. -0.15025  in unit mesh

Another way to specify this axis is using the Euler angles. The orthogonal basis to do that is
such that 𝒛 is along 𝒄, but for trigonal system in which 𝒛 is along the hexagonal axis, 𝒙 is along
𝒃 × 𝒄 and 𝒚 is along 𝒛 × 𝒙. One then has to write:

Ang_spin
45. 90. 0.  rotation around 𝒛, then around new 𝒚, then around new 𝒛. In this case spin axis
is along (1,1,0) in the internal basis

Note that it is possible to define non collinear spin using atomic local basis. In this case
one has to define the Euler local angles after the keyword “crystal” or “molecule”, in the line
just before the corresponding atoms. See “non-spherical atom”. Example:

Crystal
7.7400 7.7400 3.8400 90. 90. 90.
45. 90. ! spin axis along (1 1 0)
1 0.0 0.0 0.0
2 0.25 0.25 0.5
135. 90. ! spin axis along (-1 1 0)
1 0.5 0.0 0.0
2 0.75 0.25 0.5
315. 90. ! spin axis along (1 -1 0)
1 0.0 0.5 0.0
2 0.25 0.75 0.5
225. 90. ! spin axis along (-1 -1 0)
1 0.5 0.5 0.0
2 0.75 0.75 0.5

4) Self-consistent calculations

By default a calculation cycle is performed over the occupied states to determine the
Fermi energy. The XANES calculation corresponds to the cycle 2, but this one is done with the
initial potential. To avoid this Fermi (non SCF) energy determination, use the keyword :

No_Fermi

To perform a self-consistent calculation, use the keyword:

SCF

The calculation is then really self-consistent. The potential is calculated again at each cycle.
The final XANES calculation uses this SCF potential. By default the convolution uses the
calculated Fermi energy as cutting energy.

When using SCF calculation, the cluster radius for the SCF is the same than the one for the
XANES. For a single evaluation in one cycle of the Fermi energy the radius is equal to the

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minimum between the XANES cluster radius and 3.5 A. In both cases, this radius can be change
using the keyword :

R_self
3.  Value of the radius for the SCF and/or Fermi energy evaluation.

With SCF calculation, the maximum number of cycle is fixed to 100. To modify this number
use the keyword:

N_self
20

The electronic density of the cycle n+1 is interpolated between the electronic density of the two
previous cycles. The initial weight of the cycle is 0.1. This weight decreases or increases
according to the quality of the convergence between 4 and 0.25 times the initial value. To
change this initial weight use:

P_self
0.05  Initial weight.

The convergence is considered as realized when the variation of the total energy is less than Na
x Econv, in which Na is the number of atom and Econv a criteria fixed at 0.1 eV. To modify
Econv put:

Delta_E_conv
2.  Value of Econv.

It can happend, that when the weight increase up to 2 or 4 times the p_self, value, the calculation
become very unstable (it can be seen on the orbital occupancy). On can then limit this increase
by the parameter p_self_max:

P_self_max
0.05  value of the maximum weight. When used, the best is to put it equal to p_self.

The SCF calculation is done with a non-excited cluster. The excited potential of the absorbing
atom is taken into account only in the K and L1 edges in the XANES final calculation by
difference. If one wants to perform a SCF calculation with an excited cluster, use the keyword:

SCF_exc

If one wants perform a simulation with SCF in excited state but without any screening, that is
with a cluster charged +1, with SCF_EXC one has to use keyword “Screening” with the value
0 (see this keyword).

For a magnetic calculation, by default the spin polarization is kept fixed in amplitude. The total
number of spin up and spin down electron is fixed along the self-consistent (for an anti-ferro,
for the total on the atoms, the number of majoritarian spin and minoritarian spin electron are
kept fixed). To have it free (equivalent to version before 7th of June 2012), use the keyword:

SCF_mag_free

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It can happen that convergence is difficult to reach. A smoothing procedure is possible using:

SCF_smooth

5) Hubbard correction

To include a Hubbard correction applied to the “localized valence orbitals”, use the keyword
"Hubbard_z" with below the atomic number and the Hubbard parameter value (U-J) of the
corresponding chemical specie.

Hubbard_z
23 5.  value in eV of the Hubbard parameter (U-J).
26 4.5  in case of 2 chemical species with such a correction

It is possible to have several chemical species with such a correction. It is also possible to have
this correction with the keyword:

Hubbard
5. 4.5  value of the Hubbard parameters in the order of the atom types

The order of the atom type is the one of the chemical species appearing under the keyword
“crystal” or “molecule” or under “atom” if used. Most often, it is convenient to perform also a
self-consistent calculation. Note that in principal this correction can be applied only on
insulating compounds.

6) TDDFT calculations

TDDFT calculations can be performed using the keyword:

TDDFT

Then a first mono-electronic (LSDA) calculation is performed, followed by the TDDFT cycle.
Then a correction is performed making a mixing between the edges. This can be useful for the
L23 edges of the transition 3d elements. Calculations use a local Kernel with its Coulomb and
exchange-correlation parts. To have only the Coulomb part, use the keyword:

RPA

The TDDFT simulation contains a matrix inversion whom dimension is proportional to the
number of spherical harmonics characterized by a l maximum equal to lmax. In optics lmax =
2 when Z < 21 and 3 in the other cases. To save time, especially in optics, it can be useful to
limit it with the keyword:

Lmax_tddft
2  maximum l value for this part of the calculation.

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7) Conter-ion and Helmholtz layer

It is possible to add a potential simulating the effect of counter-ions in the case of a charged
molecule imbedded in a solvent or to consider a non-ordered Helmholtz layer on top of an
electrochemical interface (see the section on 2D diffraction). The corresponding potential is
√
given by : ∆𝑉 = 𝑉 erf ∆ ∆
where z is the radial coordinate or the
coordinate perpendicular to the surface, 𝑧 is the distance between counter_ion (or Helmholtz
layer and most outer atom and ∆ is the half height width, with avec  = 0.285925223. When
finite different method is used, this potential is also added on all the grid of point inside the
interval. For the surfaces ans for 𝑧 < 𝑧 , where 𝑧 is the surface atom position, a correcting
factor (𝑧 − 𝑧 )⁄(𝑧 − 𝑧 ) is applied to avoid a modification of the potential in the bulk part
with 𝑧 the position of the top most bulk atom, the closest to the surface. All this is obtained
with:

Helmholtz
-10. 2. 8.  𝑉 ,∆ ,𝑃 (en eV et Å)

If , ∆ is omitted, its default value is : ∆ = 2𝑧 , which corresponds to an added potential

on the most outer atom equal to 𝑉 . Alternatively one can use another potential shape for
𝑧 ∈ [𝑧 , 𝑧 + 𝑃 ] with ∆𝑉 = 𝑉 1 + cos 𝜋 ∆ and ∆𝑉 = 0 outside. For is write:

Helm_cos
-10. 2. 3.  𝑉 ,𝑧 ,∆ (en eV et Å)

The Helmholtz potential shape is not known inside the material. It can be suspected that a
screening effect decreases it. For 𝑧 < 𝑧 , the formula with the erf function can be substituted
par parabolic « Helm_mix » or linear « Helm_lin » functions., the second giving the strongest
decrease. One gets them with the keywords :

Helm_mix
-10. 2. 4.  𝑉 ,𝑧 ,∆ (en eV et Å)

Helm_lin
-10. 2. 4.  𝑉 ,𝑧 ,∆ (en eV et Å)

For the Pt(111) surface case, these different options are illustrated in the figure below:

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8) Exchange-correlation potential

By default the calculations are done using the real Hedin, Lundqvist and Von Barth
potential. If one wants to use the Xalpha potential, one must introduce the keyword "Xalpha"
followed by the value of the corresponding parameter:

Xalpha
0.3333  value of the Xalpha parameter

Remark : the value of the Xalpha parameter the closest to the other models is 2/3.
In the case of using the exchange-correlation potential coming from "Flapw", if one
wants to keep this potential independent of the energy put the keyword "Xalpha" with any value
beneath. The potential will not be Xalpha but the one calculated by flapw.

If one prefers to use the Perdew and Wang’s potential or the one from Perdew, Burke et
Ernzerhof PBE96, but keeping the energy dependency proposed by Hedin and Lundqvist, write
respectively the keywords:

Perdew

or

PBE96

9) Screening

By default, the screening is one electron on the first non-full valence orbital of the
absorber. If one wants to modify this value or the number of the orbital, use the keyword
“Screening“ followed by the quantum numbers of the valence orbital and the value in number
of electron (better inferior to 1 !) of the screening. In this case the cluster is not anymore
necessary neutral.

Screening
3 2 0.2  n, l, and screening on the valence orbital

One can omit the orbital quantum number. In this case the code, by default will choose the first
non-full valence orbital and one just write:

Screening
0.2  Screening on the valence orbital
For magnetic calculations, screening is by default the half of the total screening electron on
both spin states. Note that the occupancy rate cannot exceed 2 ℓ+1 for each spin state. If it is
the case the exceeding amount is set on the other spin state. Whatever, one can impose a
different screening, polarized in spin, just writting 2 numbers below “Screening“, eventueally
following n and ℓ :

Screening
0.5 0.3  screening 0.5 up, 0.3 down

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VI- Sophisticated keywords

1) Calculation of the Crystal Overlap Occupation Population (bounding)

The overlap between orbitals of neighboring atoms can be obtained using the keyword:

COOP
1 2 4  indices of the selected atoms. If no index, only COOP with the absorbing atom.

The selected atoms are the ones around which one looks for the first neighbors up to a default
distance equal to the sum of the atomic radii. It is between these couples of atom that are
calculated the orbital overlaps. When no atoms are specified, the COOP are calculated only
around the absorbing atoms.
These ones are given by the formula 𝑛 = 𝑆 ∫ 𝜑 (𝒓)𝜑 (𝒓)𝑑𝒓, where 𝑆 is the overlap
integral and a and b, 2 neighboring atoms. 𝑛 , positive or negative gives the bounding and
antibonding. Results are in files of the type « _coop_n_m » where n and m are the indices of
the 2 neighboring atoms. The correspondence between these file names and the atom in the
structure is given in the “bav” files looking for: “File_coop_name”. The files contain versus
energy, 𝑛 total, followed by 𝑛 (ℓ , ℓ ), then 𝑛 (ℓ , 𝑚 , ℓ , 𝑚 ).

We can modify the limit distance between 2 neighboring atoms to search for second neighbors
for instance. This is done with:

COOP_dist
4  Maximum distance in Angström

For calculation with spin-orbit, the harmonics basis for the COOP is such that the z axis is along
the z axis of the cluster. For the calculations without spin-orbit, the basis is by default along the
bond direction. To have a z axis, as in the spin-orbit case, along the z axis of all the calculation
cluster, use the keyword:

COOP_z_axis

2) Uses of atomic electronic densities of Clementi and Roetti

By default the program calculate the atomic basis using a Hartree-Fock-Dirac

procedure. If you prefer the Clementi and Roetti basis use the keyword:

Clementi

Note that the Clementi basis exists only for Z < 55. When using this basis, the self-
consistent calculations are not anymore possible as well as the automatic evaluation of the
Fermi level (The program takes automatically the option « No_Fermi »).

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3) Non spherical atomic electronic densities

When calculating using the finite difference method, it is possible to define non-
spherical atomic electronic densities. This is done with the keywords "Atom_conf" and
“Atom_nsph". For each non-spherical atom one performs an expansion in spherical harmonics
of these non-spherical orbitals. In practice, one writes an expansion in (l,m) of each of these
orbitals with at the end the number of electron it contains. Optionally a rotation of the local
atomic basis can be performed using the Euler angles (see keyword “Ang_spin”, for the Euler
angle definition). In this case, the Euler angles must be given in the line in front of the atom.
Example:

Atom_conf
1 1 1 3 2 3.

Atom_nsph
1 1 1 ! nbr of atoms, index of the atoms, nbr of orbitals
0. 0. 0. 0. 0. 0. 1. 0. 0. 1.  (l,m) in natural order, here (l=2,m=0) has 1 electron

Molecule
1.9 1.9 1.9 90. 90. 90.  a, b, c, 
0. 45. 0.  45° rotation around the Oy axis
23 0.0 0.0 0.0
8 1.0 0.0 0.0
8 -1.0 0.0 0.0
8 0.0 1.0 0.0
8 0.0 -1.0 0.0

Note that the code does not take into account the eventual decrease in symmetry induced by
this configuration. One thus must take care.

4) Mesh or molecule charge

The unit mesh must be neutral. A molecule is also often neutral. A test is performed in
the program to verify this neutrality. If one wants to omit it, put:

Chfree

5) Orbital dilatation

It is possible to modify the valence orbitals defined above expanding or contracting

them. This can be very useful for ionic material, for instance oxygen 2-, in which the atomic
bases are calculated for neutral atoms. For this purpose introduce "Dilatorb" then for each
orbital one wants to dilate, the atomic type (number in the list "Atom" or "Atom_conf"), the
valence orbital number and the expansion coefficient. For the absorbing atom, add the same
lines, but with “0” in first column, in order both excited and non-excited atoms are expanded:

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Dilatorb
3 2 0.3
0 2 0.3  for the “excited absorbing atom

6) Reference of the photoelectron wave vector

By default the reference of the electronic wave vector (and so of the kinetic energy
outside the sphere of calculation and the muffin-tin ground in case of muffin-tin calculation) is
taken as the average of the potential between the absorbing atom and the first crown when
calculating in green and at the outer sphere frontier in FDM. It is possible to impose this ground
potential at the Fermi energy. The dependence versus the kinetic photoelectron energy is then
added automatically to this term. Put then the keyword:

V0imp
-11.5  value of the ground potential at the Fermi energy.

7) Maximum potential

For a calculation performed on a molecule, the potential increases when going away
from the atoms. When this molecule is not in the gaz phase, but in solution or in any relatively
dense surrounding, this incease is artificial. In case of calculation under the finite difference
mode, this reach to faulse bounded states very thin in energy. It can be usefull to give a
maximum value to this potential to avois this phenomena with the use of the keyword "Vmax",
followed by the value of this potential :

Vmax
-6.

8) Complex energy

It is possible to use a complex energy when working in the multiple scattering mode
(green). For this, one has to specify the imaginary part (positive) of this energy in a table versus
the photoelectron energy, under the keyword "Eimag":

Eimag
0. 0.5
10. 0.7
30. 3.
50. 5.
100. 6.

When a uniform broadening is sufficient, it is not necessary to specify the photoelectron

energy:

Eimag
0.1  value of the uniform width (eV)

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The use of a small width (0.1 eV) is sometimes useful for the calculations at low kinetic
energy of the photoelectron because the localized level (3d or 4f) can be too thin in energy to
be correctly evaluated. It is even more true for X-ray emission calculation (see keyword "XES").
If this broadening is small it has no effect on the forthcoming convolution to take into account
the widths of the hole and final states.

9) Radius of the cluster for the superposition of the potential

The potential inside the sphere of calculation with a radius Rs set under the keyword
"radius", is calculated by superposition. To avoid frontier problems, the atoms taken into
account for the superposition are all the atoms inside the calculation sphere plus an outer shell.
By default this outer shell is 2.5 Å thick, giving thus a new sphere with a Rs + 2.5 radius. This
new radius define also the cluster for the calculation of the punctual group. If one wants a bigger
radius (useful for the oxides) put the keyword:

Rpotmax
15.  radius of the cluster for superposition in Angstrom

10) ℓ+1 approximation for the selection rule

If one wants to make the ℓ +1 approximation in which only the transition  ℓ = +1 is

authorized (so one neglects  ℓ = -1, for example for the threshold L2 and L3, the transitions
are only toward the d states), put the keyword:

lplus1

In the same way if you want only the ℓ -1 states put:

lminus1

11) Rydberg series

One can add an outer sphere having a -1/r potential to analyze Rydberg series. In this
case put the keyword "Rydberg":

Rydberg

12) Cluster origin

By default, the cluster origin is set on the absorbing atom. If one wants that this origin
is not changed from the input file put the keyword:

Noncentre

If one wants to impose a specific center put:

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Center
0 0.25 1  coordinates in unit cell parameter unit of the center

The center can be automatically chosen at the center of the cluster when writing nothing
after the keyword center:

Center

The center can be chosen at the center of the cluster considering only the chemical specie
of the absorbing atoms with the keyword:

Center_abs

To have the center on an axis parallel to c, (usefull for surfaces) write the keyword:

Center_s
0.124 0.5  coordinates (x,y) in unit cell parameter unit of the axis

13) Cut of the potential

To get a cut of the potential in specific output files (Filename_trace.txt), along a line or
a plan inside the FDM grid of points (does not work when using the multiple scattering theory
(Green)), put:

Trace
1 1. 0. 0. 0. 0. 0.  n, a, b, c, p, q, r
n = 1, cut along a line with vector (a,b,c) crossing the point
(p,q,r) in unit mesh parameter
n = 2, cut along the plane ax + by + cz = p
n = 3, gives all the points

Trace
4  To have all the points in the format "cube" : "Filename_den.cube"
or "Filename_pot.cube" respectively for the density and the potential

14) Density of state

To get the partial projection of the density of states and their integral for the harmonics
on the absorbing atom, put the keyword:

Density

Then one gets a new output file with the extension _sd0.txt. (if the absorbing atom is excited)
or _sd1.txt in the other case. By default they are expressed using the cubic harmonics, that is:
s, px, py, pz, dx²-y², dz²… For magnetic calculation, the expansion is split between the "up"
and "dn" components.

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One can prefer the standard tesseral (or real) harmonics. In that case for ℓ=1 and ℓ=2,
the order of the harmonics is modified. From ℓ=3 they are different and when they have no
simple expression their corresponding column name is replaced by the conventional "(ℓ,m)".
For this, with "Density", write also:

Harm_tess

It can be interesting, for example to get the orbital magnetic moment, to prefer output
with the usual complex spherical harmonics. All column names are then of "(ℓ,m)" type. For
this, use the keyword:

Density_comp

General remark on the values one gets: Usually for a transition metal, at the end of the
d band, the integral must be close to 10 (because there are 10 d electrons!). At the end of the
rather un-localized s and p bands, the integrals rarely reach 2 or 6, because the electrons are
counted only inside the atomic sphere of radius Rmstd (see in the bav file for its value). These
orbitals having a rather big radius they are not all inside such atomic sphere. Calculation being
performed in the continuum one also has to recall that n is not anymore a "good" quantum
number. Consequently the integral continue to increase indefinitely with energy. At the end of
a d (or f) band, rather localized, one nevertheless reaches more or less at 10 (or 14). In this case
one can find the Fermi level energy just looking the energy in which the integral reach the
supposed number of electron in the corresponding level of the atom. Sometimes the integral
never reach 10 (or 14) or goes far higher. One of the reasons can be that the starting energy is
too high, one thus loses the beginning of the band, and another reason can be the energy grid is
not sufficiently thin. One has, in this case to take a path smaller (down to 0.01 eV or even less
for 4f elements). In order to avoid such a thin grid, it is also possible de broaden a bit these
localized states using the keyword "Eimag" (this works only in "Green" mode).

To get the projection on all the atoms in the cluster (or unit cell) put the keyword “Density_all”
in place of "Density". Then one gets n new output files with the extensions _sdi.txt, "i" being
the atom number. The correspondence between these files and the atoms of the material can be
found in the "bav" file looking for : "Output file name for the projected density of
state".

Density_all

15) Spherical tensors

To get the spherical tensors (in number of electron) put the keyword:

Spherical

One gets new files with the extension _sph_atom1.txt and _sph_xtal.txt for the atom and
crystal. If one uses such file as input for the convolution process, with the keyword "fprime",
one gets the f’ and f” of each tensor component of the atom. Another file _sph_int_atom1.txt
contains the integral of the spherical tensors.

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To get the contributions of the tensor components on each polarization and reflections,
put in place of "spherical" the keyword:

Sphere_all

Then one gets a series of output files with the extensions _sph_signal_xan.txt,
_sph_signal_pol1.txt, _sph_signal_rxs1.txt for the contributions on each polarization and
reflections. The number after pol or rxs is the number of the polarization or reflection.

16) Cartesian tensors

To get the atomic cartesian tensors put the keyword:

Cartesian

One gets a new output file with the extension _car.txt. Then, one can use other keywords making
that from this output file will be calculated f’ and f” for any tensor component. For this purpose
put the keyword "fprime" in the input file.

17) Calculation area boundary

By default in FDM, the meshing is performed in a sphere extending up to the last atom
inside the sphere of radius given under "Radius" plus the atomic radius (by default 0.65 Å) plus
one inter-point distance (0.2 Å by default). In order to use a bigger sphere use:

Overad
1.2  distance over the last atom + its radius to take into account.

18) Displacement of the absorbing atom

To move the absorbing atom in reference to its position given under "molecule" or
"crystal" use:

Dpos
0.2 0.0 0.0  displacement vector in Angstrom

19) Getting back the tensor components from a previous calculation

It is possible to extract the tensor component from the “bav” file of a previous
calculation. At this step, the tensors must had been written thanks the use of “check_coabs”
keyword with the number 2 below. To get them one must write:

Extract_tens
Sim/calcul_prec_bav.txt

In case of calculations for different absorber position whose number is the number of output
files, one has to extract the tensors from these n files if there are n nonequivalent absorbing

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atoms. This is automatic. If the calculation is to be performed on only one or some of the non-
equivalent atom sites, this must be specified by the keyword "Absorber" followed by the
keyword “extractpos” to select in the bav file the corresponding atom:

Absorber
48

Extractpos
23  in the bav file, the prototypical atoms 2 and 3 are chosen. Their tensors are used
respectively by the atoms 4 and 8 in the list in the input file.

It is possible to make rotations of the local repair. It can be useful when using tensor calculated
in a different base. It is possible de make 1, 2 or 3 rotations around the axes Oz, then Ox, then
Oy. Each rotation defines a new local base, starting point of the next rotation. For this write:

Rotsup
30. 0. 45.  30° rotation around Oz, 0° around Ox then 45° around Oy.

For the same purpose on can apply symmetry operation on the extracted tensors. They are
codified as explained in the manual with the “symsite” keyword. They must be given in the
same order than the extracted files. These codes are given after the keyword extractsym:

Absorber
48

Extractsym
1 25  code 1 for identity, 25 for inversion.

When keyword “Extract” or “Extract_ten” are used, no “bav” file is created, but when
one also uses keyword “check”.

20) Energy shift of the spectra

If one has gotten a reference for the initial orbital, it is possible to give it under the
keyword "Epsii". This will produce a shift of the output spectra equal to the difference between
this energy and the energy calculated in the program. It is safer to perform this operation with
the shift parameters during the convolution step.

Epsii
6253.1  positive value in eV.

21) Spectra by atom

If one wants to get the signal coming from each atom one has to add the keyword:

Allsite

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One then gets, at most of the usual output files, new output files of the type atom1.txt,
atom2.txt, etc… The suffixes _atom1, _atom2 correspond to the number of the atom.

22) Use of densities and potential coming from FLAPW

If the potential is imported from a FLAPW calculation, one has to introduce the keyword
"flapw". The keyword “Crystal” or “Molecule” becomes also unnecessary. Then must stand the
names of the 5 FLAPW output files in case of spin un-polarized calculation and the 7 files in
case of spin polarized calculation:

Flapw  names of the output FLAPW files

tio2.struct structure and symmetry
tio2.vcoul coulombian potential
tio2.r2v exchange-correlation potential
tio2.clmsum electronic density
tio2.ti1s initial wave function

In case of polarized calculation, the keyword "magnetism" must be before the keyword
"Flapw":

Magnetism

Flapw
tio2.struct structure and symmetry
tio2.vcoul coulombian potential
tio2.r2v exchange-correlation potential spin up and spin down
tio2.clmsum total electronic density
tio2.clmup valence electron electronic density, spin up
tio2.clmdn valence electron electronic density, spin down
tio2.ti1s initial wave function

The last file contains the wave function of the initial core orbital. If one is ok with the
initial wave function calculated internally, one can avoid it. One must in this case substitute the
keyword "Flapw" by "Flapw_psi".
If one wants to have an energy dependent exchange-correlation potential, one must add
the keyword "Hedin".
By default, the absorbing atom is the first one in the ”struct” file list. If one wants that
it is the nth, put the keyword:

absorber
n

For the actual version of Wien2k and magnetic calculations, the exchange-correlation
potential for spin up and spin down is given in two different files. In this case one must use the
keyword:

Flapw_n
tio2.struct
tio2.vcoul

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 FDMNES User’s Guide

tio2_up.r2v exchange-correlation spin up

tio2_dn.r2v exchange-correlation spin down
tio2.clmsum
tio2.clmup
tio2.clmdn
tio2.ti1s

when not using the wien2k core state use :

Flapw_n_p
tio2.struct
tio2.vcoul
tio2_up.r2v
tio2_dn.r2v
tio2.clmsum
tio2.clmup
tio2.clmdn

Note also that sometimes, it is necessary to increase the value of number of point in the radial
mesh. In this case the value to put is given in an error message. It is possible using the keyword
nrato.

Nrato
950  new value given in the error message

23) Jump in the input file

It is possible to jump over a part of the information written in the input file with the
keywords "Jump" and "Endjump". All what is between them is not red. For example:

Jump

Quadrupole
Spinorbit

Endjump  the keywords "Quadrupole" and "Spinorbit" are not considered.

24) Comment

It is possible to introduce a line of comment which will be copied in the output files. For
this purpose write:

Comment
Iron K-edge in magnetite  line of comment

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25) Atomic spectra

To get in last column the atomic absorption spectra (without the neighbour atoms), put
the keyword:
Xan_atom

26) Different absorbing atoms calculated in one run

The electronic structure is calculated in all the cluster of calculation and thus in all atoms
in it. Consequently, it is in principal possible to get the absorption spectra of all the atoms in
only one run. In principal, the absorbing atom is nevertheless “excited”, thus becomes
intrinsically different and one calculation must be performed for each absorbing atom. When
neglecting this difference, it is possible to get all the absorption spectra of the all the atoms,
equivalent and non-equivalent by symmetry operation, of the same chemical specie in only one
run using the keyword:

One_run

For the L23 and M45 edges, the default calculation is such that the absorbing atom is not
excited, thus the result in one run is in principal good. With “One_run” all the absorbing atoms
are calculated, one thus must take care that they are all in the sphere of calculation. The use of
keyword “Center” or “Center_abs” is sometimes helpful is this context.

For surface studies, with the use of “Surface” keyword, the calculation of all non-equivalent
atom inside a layer is possible using the keyword:

One_run_s

The code calculates then automatically, for each layer of thickness by default 0.3 Å, the center
of the spheres of calculation surrounding all the non-equivalent atoms of each layer. To change
the default value, just add the corresponding number in the next line.

27) Increase the L maximum for the writing of the DOS and COOP

By default the pDOS and COOP are given in the output files up to :
L = 1 for Z ≤ 18,
L = 2 for 19 ≤ Z ≤ 54 et
L = 3 for Z ≥ 55.
To increase these L maximum, use the keyword « Lmax_DOSout » :

Lmax_DOSout
2 ! maximum value which replaces the default value when it is bigger.

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28) Optimisation of self-consistency

The calculation is performed on a cluster and the atom symmetry corresponds thus to
the punctual group of this cluster. It has nevertheless been observed that a faster self-
consistency, by imposing at each SCF cycle, that the potential of all the atoms equivalent by
symmetry of the space group, be identical. The chosen potential among all the equivalent atoms,
is the one of the atom the closest to the cluster center, where it is supposed to be the best.
It nevertheless appears, more specifically for the oxides, that this way can leads to a
beating phenomenon versus the cluster radius on the Fermi level value. This can be improved,
keeping the potential identical only for the atoms equivalent by symmetry of the punctual group.
This is done by the use of the keyword:

Full_atom

29) Core state energy

The core state energy (E_core) are used to perform the relative shift between the spectra
of the different absorbing atoms. By default, these energies are the Kohn-Sham energies, that
is 𝐸 = ⟨𝜑|𝐻|𝜑⟩⁄⟨𝜑|𝜑⟩. In order these energies are the total energy of the corresponding state,
use the keyword:

Core_energy_tot

Note that this energy is not the edge energy, because this one takes also into account the loss of
total energy of all the other atom states during the photon absorption process.

30) Buiding cylinder clusters

For surfaces with charges, and specifically for surface diffraction, it can be helpful to
build cylindrical cluster instead of spherical cluster between the absorbing atom and the surface.
It remains half-spherical below the absorbing atom. The radius of the cylinder is the same than
the one of the sphere and by default the absorber is on the axis of the cylinder. To have this
structure only for the superposition of the atomical potentials use the keyword:

Cyl_pot

To have this structure also for the self-consistent calculation uses:

Cyl_SCF

The calculation of absorption and scattering remains done as usual in the sphere.

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VII- Technical keywords

Here stand the technical keywords necessary for specific tests and optimization of the
code, for expert users.

1) Details on the calculations

To get details on the calculations done in every routine, put the keyword:

Check
3333111211
112

Up to 30 numbers can be given. The correspondence between the number and the routine is
given by :

1 : Lecture 2 : Atom / Dirac 3 : Symsite 4 : Init-run

5 : Agregat 6 : Polarization 7 : Atom_selec 8: Etafin
9 : Reseau 10 : Potato 11 : Orbval 12 : Pot0
13 : Potentiel 14: Enrgseuil 15 : Ylm 16 : Potex
17 : 18 : Sphere 19 : Mat / MSM 20 : Tenseur
21 : Coabs 22 : Tddft – sphere 23 : Tddft – Kernel 24 : Tddft - Chi_0
25 : Tddft – Chi 26 : Hubbard 27 : SCF 28: State
30 : Convolution

Values can go from 0 to 4 giving more and more for each routine. By default, there is 1 for all
the routines. One can also write:

check_all  equivalent to icheck = 3 for all the subroutines

no_check  equivalent to icheck = 0 for all the subroutines
check_conv  équivalent to icheck = 3 for the convolution
check_pot  equivalent to icheck = 3 for all the subroutines concerning the potential
check_mat  equivalent to icheck = 3 for the matrices MSM or FDM
check_sph  equivalent to icheck = 3 for the subroutine “sphere”
check_coabs  equivalent to icheck = 3 for the subroutine “coabs”
check_tens  equivalent to icheck = 3 for the subroutine “tenseur”

check_mpi  for parallel computation, gives also n_bav files containing the output of the not-
central computer. “n” is the index of the computer. No index is the central computer.

2) Symmetry

The point symmetry is calculated automatically. Anyway the expert users can impose it
by the keyword:

Sym

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2/m  Schoenflies coefficient or international table of crystallography coefficient. Be

careful that these symmetries are possible only for the mesh axis defined in the input.

3) Calculation basis

By default the connection to the continuum is performed in real base (neuman, bessel).
To use a complex base (bessel, hankel) put:

Basecomp

4) Equivalent atoms

The program automatically calculates the total signal resulting from the equivalent
atoms by symmetry. It is nevertheless possible, for the expert fdmnes user, to impose the
symmetry relation between the atoms and thus to impose this summation. One must then use
the keyword "Symsite". Following this keyword, stands the number of non-equivalent atoms
(or number of group of atoms), then for each of them, the number of equivalent atoms followed
the list of the relative symmetry to the first atom of the list and the atomic position in mesh unit.
The symmetry are codified by number going from 1 to 64, see the list given bellow.

Symsite
3 ! Number of non-equivalent atoms (or group of atoms)
4 ! Number of equivalent atoms, group 1
1 0.2500 0.2500 0.2500
24 0.7500 0.7500 0.2500
23 0.7500 0.2500 0.7500
22 0.2500 0.7500 0.7500
4 ! Number of equivalent atoms, group 2
1 0.0000 0.0000 0.0000
22 0.0000 0.5000 0.5000
23 0.5000 0.0000 0.5000
24 0.5000 0.5000 0.0000
4 ! Number of equivalent atoms, group 3
1 0.5000 0.5000 0.5000
23 0.0000 0.5000 0.0000
22 0.5000 0.0000 0.0000
24 0.0000 0.0000 0.5000

The negative indices correspond to the same symmetry plus time reversal (in case of
magnetism).

Symmetry code:

1: identity 5: rot 43 around (1,-1,1)

6: rot 23 around (-1,1,1)
2: rot 2/3 around (1,1,1) 7: rot 43 around (-1,1,1)
3: rot 4/3 around (1,1,1) 8: rot 23 around (1,1,-1)
4: rot 23 around (1,-1,1) 9: rot 43 around (1,1,-1)

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36: rot 23 around (-1,1,1) and inversion

10: rot 22 around (1,1,0) 37: rot 43 around (-1,1,1) and inversion
11: rot 22 around (-1,1,0) 38: rot 23 around (1,1,-1) and inversion
12: rot 22 around (1,0,1) 39: rot 43 around (1,1,-1) and inversion
13: rot 22 around (-1,0,1) 40: plane perpendicular with 0x
14: rot 22 around (0,1,1) 41: plane perpendicular with 0y
15: rot 22 around (0,-1,1) 42: plane perpendicular with 0z

16: rot 24 around 0x 43: diagonal plane y = z containing Ox

17: rot 24 around 0y 44: diagonal plane x = z containing Oy
18: rot 24 around 0z 45: diagonal plane x = y containing Oz
19: rot -24 around 0x 46: diagonal plane y = -z containing Ox
47: diagonal plane x = -z containing Oy
20: rot -24 around 0y
48: diagonal plane x = -y containing Oz
21: rot -24 around 0z
49: rot 2/3 around 0z
22: rot 22 around 0x
50: rot 4/3 around 0z
23: rot 22 around 0y
51: rot 2/6 around 0z
24: rot 22 around 0z
52: rot 10/6 around 0z
25: inversion 53: rot 2/3 around 0z, negative axe
54: rot 4/3 around 0z, negative axe
26: rot 24 around 0x and mirror 55: rot 2/6 around 0z, negative axe
27: rot 24 around 0y and mirror 56: rot 10/6 around 0z, negative axe
28: rot 24 around 0z and mirror
57: plane at 30° containing 0z
29: rot -24 around 0x and mirror
58: rot 2/2 around axe at 30° perp. 0z
30: rot -24 around 0y and mirror
59: plane at 60° containing 0z
31: rot -24 around 0z and mirror
60: rot 2/2 around axe at 60° perp. 0z
61: plane at 120° containing 0z
32: rot 23 around (1,1,1) and inversion
62: rot 2/2 around axe at 120° perp. 0z
33: rot 43 around (1,1,1) and inversion
63: plane at 150° containing 0z
34: rot 23 around (1,-1,1) and inversion
64: rot 2/2 around axe at 150° perp. 0z
35: rot 43 around (1,-1,1) and inversion

5) Bounded states

If one wants to make positive the kinetic energy for the calculation of bounded states
(beneath the average potential), put the keyword "E_out_min" followed by the kinetic energy
in eV:

E_out_min
0.05 0.5

The first value is for the atomic scattering, the second one only used in FDM is for the cluster
scattering. Default values are respectively 0.2 and 1 eV.

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 Manuel FDMNES

6) Inversion of the matrix in the multiple scattering mode

By default one inverts the matrix (-1+i + G) in which  corresponds to the Neuman-
Bessel normalization. To avoid eventual convergence problems (not seen yet), one can prefer
to calculate (1 + G)-1. For this use the keyword:

Normaltau

7) Muffin-tin potential

If one wants to use the muffin-tin approximation in FDM put the keyword:

Muffintin

8) Non excited absorbing atom

At the K, L1, M1 edges the absorbing atoms is calculated excited that is with a hole in
the core level and an extra electron in the first non-occupied valence state. To perform a
calculation with a non-excited absorbing atom, that is with an absorbing atom without a hole in
its core level and without screening put:

Nonexc

At the other edges, the absorbing atom is not excited. To make it excited put the
keyword:

Excited

9) Modification of the grid of point parameters

By default the finite difference calculation is performed at order 4 with an inter point
distance equal to 0.25 Å, the radius of the spherically symmetric area is around 0.65 Å (less for
the light elements). To modify them write:

Rmt  to modify the muffin-tin radius

0.65

Iord  To modify the order of the Taylor expansion.

2

Adimp  to modify the interpoint distance

0.20

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 Manuel FDMNES

It is possible to use inter-point distance, , decreasing with energy. This can be useful in
EXAFS, because at high photoelectron kinetic energy, lower  are necessary to get the same
precision. For this, write :

Adimp
0.24 100. 0.20 250. 0.16 400. 0.12 500. 0.08

  = 0.24 up to 100 eV,  = 0.2 between 100 and 250 eV,…  = 0.08
beyond 500 eV

Remark: when using different cluster radius, the energy values in which  change, can be the
same than for the radius (see "Radius" keyword).

10) Expansion in spherical harmonics

An expansion in spherical harmonics is performed in the atoms both in the multiple

scattering mode and in the finite difference mode, but with a smaller radius. The maximum
value of ℓ is obtained from the formula 𝑘𝑅 = ℓ (ℓ + 1), in which k is the photo
electron wave vector and R the muffin-tin radius (Rmtg in the bav file) in atomic units. By
default, to this value one adds 1. To fix a value of ℓmax independent of energy just write:

Lmax  The ℓmax value is fixed at 3

3

If one wants to keep the energy dependent formula but adding 1, 2 or more to this
formula, put a negative sign in from of l :

Lmax  The ℓmax value is now given by the formula plus 2.

-2

When the energy is increasing, ℓmax increases. By default the maximum value of ℓmax is
set at 2 for Z = 1, at 3 for Z = 2 then at 4 for Z ≤ 18, then at 5 for Z ≤ 36, then at 6 for Z ≤ 54,
then at 7 for Z ≤ 86 and 8 for Z over. To avoid this limitation put the keyword:

Lmaxfree

When working using the finite difference mode, the connection to the outer sphere also
needs an expansion in spherical waves. This one uses the same formula that for the atom but R
is now the radius of the outer sphere. To modify this ℓmax one proceeds exactly in the same way
with positive value to fix an energy independent value, and negative value to keep the formula
but adding to the formula. By default the additional value is 5. The key word is now "Lmaxso":

Lmaxso
15

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 Manuel FDMNES

It is possible to give a maximum value to the ℓmax of the outer sphere writing:

Lmaxso_max
28  maximum value

11) Muffin-tin radius

By default the muffin-tin radius (used in multiple scattering theory, for the electronic
density calculation and for the SCF) is calculated to have a jump of potential the smallest as
possible and closed between the atoms. One can modify it by the use of 3 different keywords.
If one wants that this radius is calculated using the Norman procedure introduce the
keyword:

Norman

By default there is a 10% overlap between the spheres. If one wants modify this put the
keyword "Overlap" followed by the value of the overlap:

Overlap
0.15  15% overlap

If one wants that the muffin-tin radius be determined by the value it gets when the atomic
potential is equal to the interstitial potential, put the keyword "Rmtv0", followed by the value
of this potential ( takes place the one define by the keyword "V0imp"):

Rmtv0
-12.

If one wants to impose the radius for each chemical species put "Rmtg_Z" followed by
the atomic number and the radius in Angstrom for each of them, and line after line:

Rmtg_Z
8 0.65  Z = 8, Oxygen, radius = 0.65 A
26 1.1  Z = 26, Iron, radius = 1.1 A

12) Continuity of the potential at the muffin-tin radius

To limit potential jump between the interstitial area and the muffin-tin sphere, a linear
interpolation on the potential is performed in the last 10% of the radius. For this put:

Supermuf

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 Manuel FDMNES

13) Atomic charge

The program gives in the output file the atomic charge integrated up to the muffin-tin
radius. If one wants to get this value for a different radius put:

Rcharge  corresponding keyword

1.2 0.7  radius value for each type of atom

To have this parameter define versus the atomic number, write:

Rcharge_Z  corresponding keyword

26 1.2  atomic number and value of the radius for this chemical specie
8 0.9

In both cases it is not necessary to define all the radius. The other ones keep the value defined
by the code.

The code also gives the charge integrated up to the ionic radius. These ones are tabulated in
FDMNES versus the atomic number. To select another radius use:

Rionic
74 0.62  atomic number and value of the radius for this chemical specie
8 1.50

14) Line length

When reading a file, the maximum number of columns of number is by default 10001.
This number can be insufficient for example when making resonant diffraction. It can thus been
increased using the keyword:

Length_line
20000  maximum number of columns in one line

15) Resolution in initial state

The outputs are resolved in initial states only for magnetic calculation. For a non-
magnetic calculation, it is possible to get anyway the output resolved be initial state using the
keyword:

Core_resolved

It is then possible in the step convolution to select one of these states.

16) Memory save

For low symmetrical material, it can be useful to save some memory space. This makes an
approximation (but a good one) on the potential calculation. For this use the following keyword:

Memory_save

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 Manuel FDMNES

17) Radius of the Dirac orbitals

By default, the atomic orbitals, are calculated solving a spherical Hartree-Fock-Dirac equation,
up to a radius equal to 20 a.u. = 10.58 Å. In some very rare cases, this radius can be insufficient
and an error message is shown, asking for an increased radius. This can be done with:

Ray_max_dirac
12.  value of the radius of the new atomic orbitals in Å.

18) Header

It is possible to have a header at the beginning of the output files giving the code release, the
date and time of calculation. It also gives for the file after convolution the convolution
parameters and the edge energy.

Header

19) Output files format

The output files containing the spectra of x-ray absorption cross sections and diffracted
intensities have column names containing parenthesis. Some soft-wares used for plotting
misunderstand these parentheses. It is thus possible to substitute them by underlines “_” using
the keyword:

Python

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Manuel FDMNES

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 Manuel FDMNES

D- Convolution

I- Introduction
The fdmnes program allows performing:

1) the convolution by a lorentzian of absorption spectra eliminating the occupied states.

For the anomalous diffraction, it makes the integration over energy of the unoccupied states
then calculates the intensity of the diffracted peaks.

2) a weighted summation over different outputs of the fdmnes program. This summation
can include a relative shift between the spectra.

This step of the calculation can be done together with the previous one, just adding the
corresponding keywords. It can also be done independently, writing another input file contains
only the keywords related to the convolution. Here comes an example:

Calculation  To give the file name resulting from the previous step.
g_rs43  name of the file (extension “.txt” is not necessary)

Conv_out  To give the file name of the convoluted spectra

g_rs43_conv  name of the file

Convolution  keyword to specify an “arctangent” shape for the broadening”

E_cut  keyword to specify a cutting energy

-1.5

II- Keywords for the convolution

1) File names

The input files for the convolution step are the output files of the previous step whose
names are defined under "Filout". When the convolution is performed together with the main
calculation, it is not necessary to specify again this name. In the other cases one has to introduce
it or them with the keyword "Calculation":

Calculation  To give the file names resulting from the previous step.
g_rs43  name of the file

When the main calculation contains several non-equivalent absorbing sites and has thus
produced several output files: "File_name_1", "File_name_2", …, it is not anymore necessary
to specify all of the but only "File_name".

It is not true in the following example where we want to have 2 different relative shifts
or weights between the spectra different:

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 Manuel FDMNES

Calculation  To give the file names resulting from the previous step.
Fe_rs64_01  name of the file 1
1.0 0.2  weight, shift
Fe_rs64_02  name of the file 2
1.0 -0.2  weight, shift

The weight is applied on the XANES and the anomalous scattered amplitudes. For the
DAFS calculations, the output files, before convolution contain in second line the Thomson
factors plus the anomalous part of the non-resonant atoms. By this way it is possible to take
into account an average configuration for substitutions of atoms of different chemical specie on
the same sites.

The name of the convolution output file is by default the input file name with the added
suffix "_conv.txt". Anyway it is possible to impose another name with the keyword:

Conv_out
Fe_rs64_sum_conv  name of the convoluted spectra file

To specify a working directory put the keyword "Directory" followed by the directory
name with at the end the separator "/":

Directory
C:/Documents and Settings/joly/Mes documents/xanes/xanout/v2o3/

When there are more than one absorbing sites, it is possible to have not only the total
convoluted file but also the individual convolutions. For this write the keyword:

All_conv

Before the edge, the absorption is zero. It is possible to take into account the background
coming from the edges of lower energy from all the chemical elements in the material. For this
use the keyword:

Abs_before

2) Fermi level

The zero of the energy is set at the Fermi level. The states beneath the Fermi level are
occupied. At the beginning of the convolution step, the cross section is thus set to zero, for
negative energies. It is possible to change this cutting energy with the keyword:

E_cut  keyword to specify the new cutting energy ("EFermi" keyword in previous
-1.5 versions)

The cutting value is applied without additional shift because in principle this last is used
to simulate the core level shift. Anyway it is possible to apply it added with the E_cut value by
the keyword:

Dec

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 Manuel FDMNES

It is also possible to have different values of the cutting energy for the different files.
This is written in third column after each file name:

Calculation  To give the file names resulting from the previous step.
Fe_rs64_01  name of the file 1
1.0 0.2 -2.  weight, shift, cutting energy
Fe_rs64_02  name of the file 2
1.0 -0.2 -1.9  weight, shift, cutting energy

The cutting energy written under "E_cut" when specified, is then not considered.

3) Convolution width

The convolution to apply depends on the core level width (Hole) and the final state
width. There are different ways to calculate the resulting energy dependent broadening. The
first one uses an arctangent formula:
    1 
  Hole  m  12  1 arctan 3 m  e  2   
  E L arg  e   
 
E  EF
with: e  in which m, Ecent and Elarg are respectively the maximum width (at high
Ecent
energy) of the final state, the center and the width of the arctangent function. The depth at the
center of the arctangent is m/Elarg. A typical curve is given bellow:

Width_(eV)
lambda_(A)
20

15
max
E
cent
10

5
hole
0
E
F 0 20 40 60 80 100
Energy (eV)

Such a convolution is introduced with the keyword:

Convolution

The Hole values come by default from the tables of M. O. Krauze and J. H. Oliver, (J. Phys.
Chem. Ref. Data 8, 329 (1979)). Nevertheless, it is possible to modify them, especially in case
of simulation of high energy resolution experiments, with the keyword:

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 Manuel FDMNES

Gamma_hole
2.05  Core level width (Hole) in eV.

To have different values of Hole for a double edge like L23, just put 2 numbers:

Gamma_hole
1.5 1.  First edge L2 then L3

Default values for Elarg , Ecent and m are respectively: 30, 30 and 15 eV. It is possible to modify
them with the keywords:

Ecent
30.  Ecent

Elarg
30.  Elarg

Gamma_max
20.  m

In the convolution, along the integration it is the width of the running energy which is
taken. It is possible to use the width of the final state energy corresponding to the energy of the
elastic photon. One then makes the integration with a constant width. This procedure improves
the agreement with experiment especially in the pre-edge range in which the other procedure
increases the background. To impose nevertheless a variable width along the integration in
XANES uses the keyword :

Gamma_var

It is also possible to use the Seah-Dench formula for the calculation of the broadening.
In this case one gets:
Am E p 1 Ep
  Hole ,   , with: Ep = E – EF.
m  AE p A Ep m
This is performed with the keyword:

Seah
1. 20.  A,m

One can also use a simple table with the keyword "Table":

Table
0.0 1.  Energy (E-EF) and broadening (E-EF)
10.0 1.5
20.0 2.
30.0 3.5
100.0 5.

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When the keyword "E_cut" is used without the keywords "Convolution" or "Seah", the
width of the convolution is constant and equal to the width of the core hole. In all cases, the
curve shape is written in the talkative "bav" file when the convolution is done in the same run
than the main calculation. When convolution is done alone, to get this curve write the keyword:

Check_conv

To simulate the experimental resolution, it is also possible to convolute by a Gaussian.

This convolution is performed after the lorentzian. For this write:

Gaussian  keyword
1.  width of the gaussian

4) Starting energy

To get output spectra starting at a lower energy put:

Estart
-8.  Value of the starting energy (eV)

5) X-ray emission spectroscopy

With the keyword "XES", it is the emission spectrum which is calculated, and more
accurately the valence to core decays. In such calculation the cutting is simply above the Fermi
level and not beneath it as in XANES. The convolution broadening is the independent of energy
and is fixed by default to the hole width. This with can nevertheless been modified by the use
of the keyword "Gamma_hole". Note that would have interest having previously performed a
calculation in "green" mode with a minimum energy width (keyword "Eimag") at least 0.1 eV,
all this within an energy range convenient for emission:

XES

6) Damping due to multi-electronic effects

In a simple approach, the multi-electronic phenomena can be seen as a simple damping

in the absorption cross section and in the anomalous scattering amplitude in diffraction. This
damping not taken into account, by default, can be introduced using the keyword "S0_2". It is
typically around 0.8.

S0_2
0.8  value of the damping

When setting S0_2 = 0, in diffraction, one keeps only the non-resonant term.

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7) Selection of the transition from a peculiar initial state

The fdmnes output files, before convolution, contain the spectra by transition from all
initial states when the calculations are magnetic and by threshold in the other case. It is possible
to perform the convolution for only one, or some, of these components (avoiding thus their total
summation) with the keyword "Selec_core" with below the selected state. The order of these
states goes from jz = -j to j ; for example at a L3 edge: -3/2, -1/2, 1/2, 3/2. For a L23 edge, L2 is
before L3. For example, applied to a K edge, the 1s state with jz = -1/2 is selected. It is purely
spin down and after transition probes the valence down states:

Selec_core
12  the transitions from the first and second core state are selected.

8) Sample thickness

When the "Mat_polar" keyword in the main calculation has been used, in order to
calculate the transmission through a sample, the sample thickness in m must be given. This is
done with the keyword:

Sample_thickness
100.  Sample thickness in m

See also the "Stokes" and "Stokes_name" keyword, below, which also apply in absorption when
the "Mat_polar" keyword have been used.

8) Thermal disorder

It is possible to take into account the thermic disorder using the Debye model. For this purpose
use the keyword:

Abs_B_iso
0.72  Debye parameter (8𝜋 〈𝑢 〉) in Ų

For the same purpose but using as Debye parameter 〈𝑢 〉 instead of 8𝜋 〈𝑢 〉 use:

Abs_U_iso
0.01  Debye parameter (〈𝑢 〉) in Ų

When these parameters are already given in the input file of the main calculation (using
"Atom_U_iso" or "Atom_B_iso"), they are replaced for this part of the calculation by these new
ones.

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III- Keywords specific for resonant diffraction

1) Azimuthal scan

If there is an azimuthal scan in anomalous diffraction, one has also to give the
corresponding input file names (type _scan.txt) and the new output file. This is set after the
keyword "scan_file":

Scan_file
Fe_rs64_01_scan.txt  name of the input dafs file 1
Fe_rs64_02_scan.txt  name of the input dafs file 2

Scan_conv
Fe_rs64_scan_conv.txt  name of the new output file with the convoluted scan

When the convolution file is included in the “main” calculation file, it is not necessary
to specify the scan file names because they are known by the code. In this case, if one wants to
convolute also these files just uses the “Scan” keyword:

Scan

2) Thomson

Thomson term is calculated by default. It is possible to modify it using the following

keywords.

To eliminate the Thomson factor f0 (as for a forbidden beam) put:

Forbidden

It can be useful to impose specific value for each DAFS reflections for the non-resonant
(Thomson) structure factors and the resonant one of the other atoms. That is: ∑ 𝑝 (𝑓 +
𝑓′ + 𝑖𝑓′′ )𝑒𝑥𝑝(𝑖𝑸. 𝑹 ), with 𝑓′ and 𝑓′′ considered only for the other chemical species
and in which 𝑝 is the site a occupancy rate. This is the case for example for occupancy rate non
equal to one. These complex terms taken as a constant in all the energy range can be introduced
through the keyword:

Thomson
1.1670478E+02 1.0583769E+02 1.1477827E+02 -8.2670689E+01

In the second line stand these terms, here for 2 reflections. They replace the values calculated
by the program and placed in the second line of the output file.

3) Getting f’ and f”

To get in the output file, the f’ and f” values, put the keyword:

Fprime

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 Manuel FDMNES

In the output file for each reflection, there are three columns, f’, f” then intensity. The
intensity is for the mesh, f’ and f” are for one atom of the mesh. f’ contains also f0. To get only
f’, put also the keyword "forbidden".

It is also possible to get the atomic (but in the solid) f’ and f” values without DAFS
simulations. For this the best is to run the main simulation with the keyword "spherical". In a
second step one convolute with the keyword fprime the corresponding output file
“…_sph_atom1.txt”

To get the isolated atomic f’ and f”:

Fprime_atom

The values of the atomic f’ and f” are then in the talkative “bav” file, eventually created
at this time when the convolution is done in an independent job.

4) Corrections

It is possible to make a double absorption correction, corresponding to a measurement

done at the maximum of the « rocking curve » and thus not integrated over it. For this write the
keyword:

Double_cor

This correction is effective only with self_abs or Full_self_abs in the main calculation step.
One gets then in the output file after convolution a new column with ‘Id’ which contains the
intensity doubly corrected.

Another correction is possible to take into account a dead layer, that is a disordered layer
at the surface, not participating to the diffraction, but damping the signal in the incoming and
in the outgoing. This is done with the keyword:

Dead_layer
150  thickness in Angstrom of the dead layer.

This correction is also done during the convolution part of the calculation.

The absorption correction depends on the incidence and exit angles with the surface. Be
default one uses the (rather good) approximation of taking the average angles. To use the
exact angles, one must define the surface plane. This is done with :

Surface_plane
120  indices of the surface plane

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 Manuel FDMNES

III- Getting other polarization conditions

One can be interested by material with birefringence or rotating power properties with
effect in resonant diffraction or in absorption measured in transmission mode and with an
analyser not necessarily parallel to the incoming polarization. One can make this choice on the
analyser condition at the convolution step calculation when in the previous step, the main
calculation had been performed with all , ,  and  polarization conditions. In
absorption calculation this is done when using the keyword "Mat_polar".

In that case, to get the intensities (only for diffraction) corresponding to incoming
polarization right and left, add the keyword:

Circular

It is also possible to get the intensity corresponding to any Stokes parameters (S1= +/-1
sigma and pi, S2 diagonal S3 = +1(-1) circular right (left)) or with or without analyzer, this one
with any angle. For example without analyzer one writes:

Stokes
0 0 1  S1, S2, S3
0 0 -1
0 0.31 0.95
0 0.31 -0.95

Stokes
0 0 1 30. 50.  S1, S2, S3, rotation and Bragg analyzer angles

If the Bragg angle analyzer is not specify, it is supposed perfect, that is 45°:

Stokes
0 0 1 30  S1, S2, S3, rotation analyzer angle (0 = , 90 = )

Note that when using the "check_conv" keyword, the Stokes parameters of the
transmitted beam are printed in the "File_name_bav.txt” file.

It is possible then to specify column name in the output file to make simplest the column
identification, writing:

Stokes_name
no_name  default name
no_name
+00+31+95  name appearing in the first line, in the corresponding column
+00+31-95

In absorption one can check the different contributions on the transmitted signal coming
from birefringence or from dichroism alone. For this purpose, write:

Check_biref

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 Manuel FDMNES

Then for each polarization condition one gets 3 new columns in the output file with in their
name “nB” for “no birefringence”, “nD” for “no dichroism” and “nO” for no off-diagonal
components.

To have the weighted average between 2 sets of spectra (𝐽 , 𝐽 ), giving (𝐼 , 𝐼 ), using the
formulas: 𝐼 = 𝑤𝐽 + (1 − 𝑤)𝐽 and 𝐼 = (1 − 𝑤)𝐽 + 𝑤𝐽 , use the keyword:

Weight_co
0.7  weight
1 2 5 6 8 9  couple of spectra (column index in the output file, without energy) to
average

When using the default value (0.5) for the average, it is not necessary to specify its value:

Weight_co
1 2 56 89

IV- Independent convolution by a gaussian

Independently from any calculation the fdmnes code makes possible to perform a simple
convolution by a gaussian of a table of data. This table must have in first column the abscissa
then a set of column with the ordinates. All the columns must have the same number of
elements. These data can be of any type, for example experimental spectra. Any number of text
lines can be before the data.
The input file asking for such a convolution is of the type:

File_in  keyword demanding the file name containing the data to convolute
File_name_data  name of the file

Conv_gaus  keyword demanding the width of the gaussian

2.5  width in the same unit that the abscissa in the first column of the data
file

File_out  keyword demanding the output file name of the convoluted data
File_name_out_conv  name of the file

End

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 Manuel FDMNES

E- Parameter optimization

It is possible to compare the calculated spectra to the experimental ones with the help
of metric distances and R factor. The metric distance to compare the individual theoretical,
𝐼 , (𝐸), and experimental, 𝐼 , (𝐸), spectra is given by:
1 1 1
𝐷 = 𝐼 , (𝐸) − 𝐼 , (𝐸) 𝑑𝐸
2 𝑐, 𝑐,
with the normalization factors: 𝑐 = ∫ 𝐼 (𝐸)𝑑𝐸

The R factor is a conventional one (see E. Zanazzi and F. Jona, Surf. Sci. 62, 61 (1977)) given
by:
∑ 𝑐 𝐼, 𝐸 −𝐼, 𝐸
𝑅 =
∑ 𝐼, 𝐸
With the normalization factor, 𝑐 , such that: =0

Then for n different spectra, one gets the total metric distance or R factor by:

𝐷 =∑ , 𝑝𝐷 and 𝑅 =∑ , 𝑝𝑅

In which pi is the relative weight for the spectra ″i″ given by 𝑝 = ∑

,

It is possible to vary some parameters in order to optimize the agreement between

calculation and experiment. Then results are given for a multi-dimensional grid of parameters.
The values of the metric distances are given in a special output file. By default, for a complete
calculation, the file name is the fdmnes conventional output file name with the suffix _fit.txt.
For a calculation starting calculating the convoluted spectra, the default output file name is
fdmfit_out.txt. This name can be modified using a specific keyword.

To do this task different keyword must be added in the main input file:

Experiment  Keyword preceding the file names containing the experimental

Nom_exp spectra.

Gen_shift  Minimum and maximum energy shift between calculation and

7108 7114 21 experiment and number of value to test

Metric_out  Keyword preceding the output file name containing the metric
File_name_fit.txt distances

Parameter  Keyword preceding any group of correlated parameters

Par_Gamma_max  Keyword to specify the convolution broadening m as a parameter
15. 25. 5  First and last values and number of values
Parameter
Par_Posx
-0.05 0.05 3

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 Manuel FDMNES

Par_Posy
-0.05 0.05 3

In the previous example the parameters Posx and Posy of the atom 1 are completely correlated.
Thus the atom is displaced along the diagonal.

The parameters can be fitted are:

For the convolution:
Par_ecent  Central energy for the arctangent
Par_elarg  Energy width for the arctangent
Par_efermi  Fermi (or cutting) energy
Par_gamma_hole  Hole width
Par_gamma_max  Maximum width for the final states
Par_gauss  Gaussian width (or resolution)
Par_shift  Energy shift
Par_weight  weight
Par_weight_co  weight for the average weight between 2 sets of calculated spectra
Par_aseah  First parameter of the Seah-Dench formula
Par_abs_u_iso  Mean square displacement of the absorbing atoms

For the spectra calculation:

Par_a  Contraction or expansion of the mesh parameter a in %
Par_b  Contraction or expansion of the mesh parameter b in %
Par_c  Contraction or expansion of the mesh parameter c in %
Par_abc  General contraction or expansion in %
Par_anga  Value of the unit mesh angle 
Par_angb  Value of the unit mesh angle 
Par_angc  Value of the unit mesh angle 
Par_poporb  Orbital occupancy
Par_posx  Atom position along x
Par_posy  Atom position along y
Par_posz  Atom position along z
Par_occup  occupancy of the atom
Par_dposx  shift of the atom position along x from the original position
Par_dposy  shift of the atom position along y from the original position
Par_dposz  shift of the atom position along z from the original position
Par_theta  position along  for an atom in spherical coordinate
Par_phi  position along  for an atom in spherical or cylindrical coordinate
Par_v_helm  Helmholtz potential
Par_delta_hel  Distance of the Helmholtz layer from the topmost atom layer
Par_width_hel  Width of the Helmholtz layer
Par_cion_ch  charge of the counter ion
Par_cion_w  Gaussian width of the counter ion
Par_cion_x  x position of the counter ion
Par_cion_y  y position of the counter ion
Par_cion_z  z position of the counter ion
Par_cdip_m  moment of the counter dipole
Par_cdip_w  Gaussian width of the counter dipole
Par_cdip_x  x position of the counter dipole
Par_cdip_y  y position of the counter dipole

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 Manuel FDMNES

Par_cdip_z  z position of the counter dipole

Under each parameter must be written the first and last values of the parameter followed
by the number of values. For the parameters Par_posx, Par_posy, Par_posz, Par_theta,
Par_phi, the number of the atom must also be specified in fourth position. In the same way, for
the parameters with "cion" or "cdip" it must be respectively the number of the counter ion or of
the counter dipole. Under the parameter Par_poporb, Par_occup must be also set the number
of the orbital found in the order given under the keyword "Atom", or "Atom_conf".

For example, to specify an exchange of charge between two atoms (titanium and
oxygen), one has to write:

Atom
22 2 3 2 2. 4 0 2.  Ti initial occupancy: 3d2-4s2
8 1 2 1 4.  Oxygen initial occupancy: 2p4

Parameter
Par_poporb
2. 0. 3 1  The first orbital under atom (or Atom_conf) is the 3d titanium.
Par_poporb
4. 6. 3 3  The third orbital under atom (or Atom_conf) is the 2p oxygen.

By default the metric distances are calculated in all the energy range is the intersection
between the experimental and calculated spectra. It is possible to cut the lower or and the higher
energy part of the spectra by the use of the keyword:

Emin
-10.  Minimum energy for all the spectra

Emax
100.  Maximum energy for all the spectra

It is possible to have different values for the different spectra:

Emin
-10. -5. -20. -20.  Minimum energy for each spectra

Emax
45. 100. 100. 100.  Maximum energy for each spectra

If the energy of the experimental spectra is in keV and not in eV, put the keyword:

Kev

When there are several spectra to compare simultaneously, for the calculation they must
be in the same output file. One then must give the number of the column contains the calculated
spectra and associate it at the corresponding experimental file. This is done adding a line after
each experimental file contains the number of the column. If there are 2 numbers, the first one
is the number of the column in the experimental file, the second one being the number of the

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 Manuel FDMNES

column in the calculated file. When there is no number, this means than in both experimental
and calculated file, the spectra are in the second column, the first one being the energy.
Example:

Experiment  keyword
Nom_exp_1.txt  Name of the file containing the first experimental spectra
2  Number of the column in the calculated file containing the corresponding spectra
Nom_exp_2.txt  Name of the file containing the second experimental spectra
3  Number of the column in the calculated file containing the corresponding spectra
Nom_exp_2.txt  Name of the file containing the third experimental spectra
4 3  Numbers of the column in the experimental file Nom_exp_2.txt,
followed by the number of the column in the calculated file

By default, 2 confidence factors are used (D1 and RX). By default, D1 is used for
searching the minimum in the space of parameters. If one wants it is Rx, use the keyword:

Rx

A third one "Rxg" can also be calculated. It is equivalent to Rx but with the spectra set
in n group. In each group the normalization factor between theory and data is the same. When
there is a single spectrum, Rxg is equivalent to Rx. To get this confidence factor put the
keyword:

Rxg
1 2 3 ! index of the spectra with the same normalization factor
4 6 ! second set
5 ! this spectrum has a specific normalization factor

The indexes correspond to the order under "experiment".

When nothing is written under Rxg, there is a single normalization factor for all the spectra.

It is also possible to compare spectra without "fit". In that case we use the keyword
"File_met". When followed by 2 file names, the comparison is done between the 2 set of spectra
included in the files (they must have the same number of columns):

File_met
File_1_conv  name of file number 1
File_2_conv  name of file number 2

The keyword "Gen_shift" or "Metric_out "can be used with "File_met" as usual. This keyword
can be used alone when both files are existing.

To compare one set of spectra with others in a series of files, we use "File_met" followed by a
single file name. Its set of spectra is then compared with the ones given under the keyword
"Experiment", with the column attribution as described in this keyword description. For
example:

File_met
File_conv  File name with several columns, first energy, then the spectra

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 Manuel FDMNES

Experiment
Nom_exp_1.txt  Name of the file containing the 1er spectra
2  Number of the column of the file File_conv
Nom_exp_2.txt  Name of the file containing the 2ème spectra
3  Number of the column of the file File_conv
Nom_exp_2.txt  Name of the file containing the 3ème spectra
4 3  Number of the column of Nom_exp_2 then of File_conv

When the data are given with the errors in 3rd column, the R-factor Rx can be calculated in
order the decrease the weight of the spectra with a large error. One uses 𝐾 = 1/ ∑ 𝑒 , , where
𝑒 , are the errors, j index the energy points and i the reflections. The weight is then given by
𝑤 = 𝐾 / ∑ 𝐾 For this, use the keyword:

Error

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Manuel FDMNES

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 Manuel FDMNES

F- Extraction of DAFS scans and spectra

When realizing a DAFS simulation with azimuth dependence (scan), the output scan file
after convolution contains the intensity of all the reflections at all energies and all azimuth
angles. Often, it is useful to extract from this big file some spectra at specific azimuth angle or
some scan at specific energy. It is what is done in this part with the following input file:

! Input file for FDMNES, Selection part

Selec_inp  keyword for the input file name (output of the convolution part)
xanout/fe3o4/2008_bland/cc_1221_1221_orig_1m10_scan_conv.txt

Selec_out  keyword for the output file name

xanout/test/fe3o4_scan_selec_conv.txt

Energy  keyword for the selected energy for the scan

4.  value of the energy for the scan in eV.

Reflection  keyword for the selected reflections

2569  number of the selected reflections

End

The azimuth scan is extracted at the energy (in eV) given after keyword “Energy”.
It is also possible to extract spectra at a given azimuth angle. For this, no keyword
“Energy” but the keyword “Azimuth” and next line the value of the selected azimuth:
Azimuth
30.  Value of the azimuth

It is possible to have several reflections in the output file at one energy (or one azimuth).
It is also possible to have several energies but only one reflection for the scan or several azimuth
angles but one reflection for the spectra.

Energy
4 7.5  selected energy for the scan

Reflection
2  reflection number 2 selected

or:

Reflection
2  reflection number 2 selected

Azimuth
30. 60. 90.  Azimuth selected

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 Manuel FDMNES

Without the keyword « Reflection », all reflections are given when there is only one energy or
one azimuth asked.

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 Manuel FDMNES

G – Unit cell modification

FDMNES contains a tool to build the list of atoms of a unit cell superstructure from
the atom list of a simple unit cell. This can be used as the starting list corresponding to a unit
cell corresponding to a decrease in symmetry or to specific magnetic order.

Filout  Output file in which is given the list of atom of the superstructure unit cell
xanout/test_stand/mult_out

Mult_cell  Multiplication factor along a, b and c

221  Here one buids a (2a, 2b, c) unit cell

Atomic_nu  Atomic number corresponding to the atom type under "Unit_cell"

26 38 33

Unit_cell  to introduce the original unit cell

3.92430 3.92430 12.36440 90. 90. 90.  a, b, c, 
1 0.50000 0.00000 0.25000  list of all the atoms of the unit cell
1 0.00000 0.50000 0.25000
1 0.50000 0.00000 0.75000
1 0.00000 0.50000 0.75000
2 0.00000 0.00000 0.00000
2 0.50000 0.50000 0.50000
3 0.00000 0.00000 0.36000
3 0.00000 0.00000 0.64000
3 0.50000 0.50000 0.86000
3 0.50000 0.50000 0.14000

The original unit cell is introduced with the keyword "Unit_cell" under which are given
the unit cell parameters, and the list and the list of all the atoms in it. In first column is set the
atomic number, but if using the optional keyword "Atomic_nu". In this case, first column
contains the atom type number and the correspondence between atom type number and atomic
number is given under "Atomic_nu".

To tranform a cubic unit cell in a hexagonal one with:

(1,0,-1) new x axis
(-1,1,0) new y axis,
(1,1,1) new z axis, use the keyword:

Cub_hexa

For the general transformation case, use:

Mat_cul
1 0 -1  new x axis
-1 1 0  new y axis
1 1 1  new z axis, with this matrix the transformation is equivalent to "Cub_hexa"

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H - FDMX User’s guide

FDMX is an extension from J. Bourke and C. Chantler, University of Melbourne,

Australia. When using it, thanks to cite:

Jay Daniel Bourke, Christopher Thomas Chantler and Yves Joly

"Extended X-ray Absorption Fine Structure Calculations Using the Finite Difference Method"
J. Synchrotron Rad. 23, 551-559 (2016).

FDMX is an enhanced approach to calculating both XANES and XAFS spectra using
the finite difference method and the core routines of FDMNES. The easiest way to use FDMX
is to simply include the keyword fdmx in your regular input file, and the code will automatically
optimize computational parameters to ensure accuracy over a wide energy range. FDMX will
process the spectrum to include thermal effects and electron/hole lifetimes, and add background
absorption from more loosely bound electrons. The code is currently designed for use with K-
edge calculations only, however most functionality will also work with other edges (note
keywords for hole widths and background absorption). Additional (optional) controls for
FDMX are possible with specific keywords.

As calculations using FDMX may take several hours, particularly for structures with few or no
axes of symmetry, it is strongly recommended that you compile and run the code using the
MUMPS libraries.

fdmx

Activates FDMX computation and optimization of parameters with respect to energy,

allowing for accurate EXAFS spectra, and triggers the processing routine at the end of the
calculation. When this keyword is used, the Radius keyword is no longer required.

fdmx_proc

Use to activate a post-processing routine from FDMX, implementing thermal, inelastic

scattering, background, and other effects without explicitly calculating the absorption spectra.
This requires an existing output file with absorption cross sections from a previous calculation.

E_cut
4.0 ! Val

Similar to the keyword for convolution in FDMNES, this will suppress transitions below the
nominated Fermi level, expressed in eV. Some absorption will still be possible below this level
due to the hole width and IMFP effects, and background absorption from other edges. Use of
this keyword is strongly recommended.

Radius
8.3 100. 7. 250. 5. 400. 4. ! Val, En, Val …

Allows the user to specify how the cluster radius changes with energy. By default when using
fdmx procedure, the radius is set (as above) to 8.3 Å for energies up to 100 eV, then 7 Å for
energies up to 250 eV, then 5 Å etcetera. Using a high or constant radius at high energies may

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 Manuel FDMNES

result in very long calculations, while low radii will cause XANES and XAFS structure to be
missing.

adimp
0.24 0. 100. 0.20 250. 0.16 400. 0.12 500. 0.08 ! Val, En, Val …

Allows the user to specify how the inter-point distance (grid density) changes with energy. By
default, the inter-point distance is set (as above) to 0.25 Å for energies up to 0 eV, then 0.22 Å
for energies up to 10 eV, then 0.18 Å etcetera. Using a high or constant inter-point distance at
high energies may produce inaccurate results, while low values will lead to long calculations.

Gamma_hole
2.3 ! Val

By default, FDMX will include a core-hole relaxation based on K-shell tabulations from
Scofield and Kostroun (Z=21-50) and “B” (Z=51-100)? Alternatively one may provide an
explicit core-hole lifetime (in eV) with the keyword Gamma_hole or suppress this effect by
using the keyword:

nohole

It is required that you use either Gamma_hole or nohole for calculations involving edges other
than K.

IMFPin
imfpdatafile.txt ! Filename

By default, FDMX will include photoelectron lifetime broadening based on the electron
inelastic mean free path (IMFP) of the absorbing material. For elements the IMFP values are
tabulated from optical data model calculations, while for compounds they are estimated using
the TPP-2M equation. Users may instead include their own IMFP values with the IMFPin
keyword followed by a filename that contains IMFPs in the format:

En Val

where En is in eV and Val is in Å. Alternatively, IMFPs can be calculated directly from optical
energy loss data (i.e. optical ELFs), which may be obtained from band structure packages such
as WIEN2k (in WIEN2k this data is obtainable using the optic routines and is output to a file
named case.eloss). To use ELF data to compute the IMFP, use the keyword:

ELFin
elfdatafile.txt

where the data is formatted the same as for an IMFP input file, excepting that the values are
unitless. The use of ELFin will overwrite other IMFP values up to the maximum energy of the
ELF provided (or 120 eV, whichever is lower), after which default IMFP values will be used.
By default, the IMFP is calculated from the ELF using a Lindhard (fast) representation of the

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 Manuel FDMNES

dielectric function. However, it is recommended that you use an additional keyword for a
Mermin representation:

Mermin
1 ! Val

The number following the Mermin keyword specifies an iteration value, with 0 corresponding
to a Lindhard representation, 1 to a standard Mermin representation (recommended), and higher
values to successive iterations of a self-consistent Mermin model. This calculation may take
some hours, and iteration values higher than 3 will not normally be useful for XAFS. For more
information see Bourke & Chantler, J. Phys. Chem. Lett. 6 314 (2015).

Use of the ELFin keyword will generate an additional output file with the extension _ELF.txt
containing the energy- and momentum-dependent ELF of the system. Use of Mermin without
ELFin will produce no effect.

noIMFP

Use to omit the effects of photoelectron lifetime, and hence represent an infinite IMFP.

Tmeas
298 ! Val

Use to define the temperature, in Kelvin, at which the absorption is being calculated. This value
will affect the Debye-Waller Factor, and is set to 0 by default.

TDebye
345 ! Val

Use to define a Debye temperature (in Kelvin). This is strongly recommended for compound
structures.

DWfactor
0.13 ! Val

Use to define an effective Debye-Waller factor (in Å). By default, this will otherwise be
calculated based on the dominant oscillators contributing to the high energy XAFS spectrum.

noDW

Use to omit thermal effects – effectively a zero Debye-Waller factor.

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 Manuel FDMNES

noBG

By default, FDMX will include background absorption from more loosely bound electrons (i.e.
L, M edges etc). Use this keyword to omit such contributions. Note that the background
absorption currently only works properly for K-edge calculations, and therefore for other edges
this keyword is required.

For comparison with experimental data, it is useful to define an extra function to address the
edge jump discrepancy (triangle effect). This function comes in two flavors, and is implemented
by the following relation:

𝜇 (𝐸) → 𝜇 (𝐸)(1 + 𝑓(𝐸))

where 𝜇 is the atomic (or atom-like) background absorption.

Victoreen
0.8 0.4 ! Val A, Val B

Adds a background function from the Victoreen Equation with A and B parameters following:
𝐸 𝐸
𝑓(𝐸) = 𝐴 +𝐵
𝐸 𝐸
This applies to all energies above the absorption edge E0. A+B provides the relative edge jump
correction, while A/B controls the rate of decay.

Expntl
0.1 100. ! Val A, Val B

Adds a background function of an exponential form with A and B parameters following:

( )
𝑓(𝐸) = 𝐴𝑒
This applies to all energies above the absorption edge E0. A provides the relative edge jump
correction, while B controls the rate of decay.

cm2g

Output results in units of cm2/g instead of Mbarn.

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 Manuel FDMNES

I - 2D Diffraction

FDMNES can simulate 2D – resonant diffraction experiments. The corresponding

output are (h,k,l) peaks with non-integer indices. Truncation rods at a specific energy can be
given as well as spectra at specific points of the truncation rods.

1) Surface structure description

The surface is supposed perpendicular to the (a,b) plane, thus eventually, the unit cell
must be especially written in this way. Note that c is not necessarily perpendicular to the surface.
The surface to simulate must contain some atomic layers that we call “surface” and most often
a substrate taken as semi-infinite crystal that we call “bulk”.

The substrate is taken into account with the keyword:

Bulk ! Structure of the substrate

8.1724 8.1724 4.0862 90. 90. 90. ! a, b, c, alpha, beta, gamma
47 0.0 0.0 0.0 ! Z, x, y, z
47 0.5 0.5 0.0
47 0.5 0.0 0.5
47 0.0 0.5 0.5

On top of the bulk atoms, the surface atoms are set using keyword "Surface":

Surface
8.1724 8.1724 4.0862 90. 90. 90. = a, b, c, alpha, beta, gamma
27 0.0 0.5 0.2 ! Z, x, y, z
…..

Note that the unit cell parameters are not necessary the same than the bulk unit cell parameters.
The distances between the top most bulk atom and the bottom less atom of the surface is given
by the lowest z value (in the 4th column). This can be change using keyword "Surface_shift".
When using it, this distance is given under this keyword:

Surface_shift
1.25  distance between bottom most surface atom and top most bulk layer (A)

To give a shift in the 3 directions one writes:

Surface_shift
0 0.23 1.25  shifts along a and b and distance between bulk and surface (A)

When there is many surface atoms, it can be convenient to consider it as a film which is
considered as “bulk-like” along some unit cell length. In such a film the atomic form factor are
calculated as in a 3D material. For this purpose, one uses the keyword "Film":

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 Manuel FDMNES

Film  Set a simulation on a 2D film, followed by the unit cell description

8.1724 8.1724 4.0862 90. 90. 90. = a, b, c, alpha, beta, gamma
47 0.0 0.0 0.0 ! Z, x, y, z
….

By default the film thickness is equal to the ‘c’ unit cell parameter, eventually multiplied
by the cosines of the angle between c and the basal plane. One can use a specific thickness using
the "Film_thickness" keyword, followed by its value in Angstrom not necessarily equal to a
multiple of c.

Film_thickness
75

The interlayer distance between the topmost substrate layer and the bottom film layer is
by default zero. This can (and must) be changed with the following keyword:

Film_shift
3.5  z when only one number is given (in Angström), z is perpendicular to the surface,
direction outwards.

Film_shift
0. 0. 3.5  x, y, z, all in Angstöm, x and y are along a and b of the film.

Film_shift
0. 0. 3.5 45. ! x, y, z, angle

A fourth number can be added. It is the angle between the a film axis and the a bulk axis.
Can be useful for epitaxial growth when the a film corresponds to the (a,b) diagonal of the bulk

By default, the bottom atom in the film is the one defined with the lowest z position under
the keyword "Crystal". This can be changed defining a new zero, in reduced unit. The atoms
between z = 0 and this value are just shifted by +1.

Film_zero
0.25  The bottom atom will be the next one with z >= 0.25. Then the stacking is as
usual.

Note that the keyword "Spgroup" can be used for a film, but not for the description of
"Surface" or "Interface" as seen bellow. It is possible to use only a film and a bulk. To improve
the calculation it is possible to add some surface layer atoms on top of the film. For this purpose,
we just use the same "Surface" keyword as before. Because there is a "film", the code
understands that the "surface" is on top of the film and not on top of the bulk.

It is also possible to consider an interface between the bulk and the film. This is done
with the same format than with the surface, film or bulk atoms but with the keyword:

Interface
8.1724 8.1724 4.122 90. 90. 90. = a, b, c, alpha, beta, gamma
26 0.0 0.0 0.0
….

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 Manuel FDMNES

The interface distance from the bulk is given in the same format than with the “surface” using
the keyword:

Inter_shift
1.26

One can add a cap layer with:

Cap_layer
2.8837228875 2.8837228875 7.0636496 90. 90. 120.
79 0. 0. 0. 1.
79 0.6666666667 0.3333333333 0.3333333333
79 0.3333333333 0.6666666667 0.6666666667

Cap_thickness
17.1

A Debye disorder in Angström can be given using "Cap_B_iso" or "Cap_U_iso". This disorder
is the same for all the atoms of the cap layer:

Cap_B_iso
80.0  = 8𝜋 〈𝑢 〉 in Ų

Cap_U_iso
1.0  = 〈𝑢 〉 in Ų

By default the distance between film and cap is the sum of the atom radii. This can be changed
with:

Cap_shift
3.0

The roughness of the « bulk » or the interface bulk/film, of the film or the interface
film/cap layer and of the cap layer can be taken into account. They are described by the function
0.5 erfc 𝑧 − 𝑧0⁄√2𝑅 , where z0 is the origin taken at the middle in the inter-layer above the
last atomic layer. This is done with :

Bulk_roughness  roughness at the bulk surface or at the interface bulk/film

1.5 R

Film_roughness  roughness at the film surface or at the interface film/cap layer

4.

Cap_roughness  roughness at the cap layer surface

17.1

With the keywords "Occupancy" and/or "Atom_B_iso" (or "Atom_U_iso",

"Atom_U_ani", "Atom_B_ani") another 1 or 2 other columns, in the 5th and 6th columns, can be

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 Manuel FDMNES

added for surface, film, inter-face and bulk slabs, containing the occupancy rate (between 0 and
1) and the Debye parameter, 8𝜋 〈𝑢 〉, in Ų. The column order of these parameter corresponds
to the order of these keywords in the input file.

Atom_B_iso

47 0.0 0.0 0.0 0.82 ! Z, x, y, z

….

Occupancy
Atom_B_iso

47 0.0 0.0 0.0 0.8 0.82 ! Z, x, y, z, Occupancy, Debye

z
z0 cap roughness

Cap Cap thickness used

unit cell
Cap shift

z0 film roughness
Surface shift

Film thickness used

Film
unit cell

Film shift

z0 bulk roughness Interface shift

O
x
Bulk
unit cell Semi-infinite bulk

Fig. The most complete possible description with film, cap, interface, surface and semi-infinite
bulk. All the elements are optional. For example only “surface” and “bulk” atoms can be given.
Cap and Film thickness used = distance between topmost and bottommost atoms inside Film
Thickness or Cap Thickness. The origin z0 of the roughness function is at half of the interreticular
distance on top of the considered slab.

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 Manuel FDMNES

2) Reflection choice
DAFS
0 0 0.04 0.04 8.16 1 1 0. ! h, k, l_min, lstep, lmax, sigma, sigma, azimuth
0 0 8.18 0.002 8.24 1 1 0.
0 0 8.28 0.04 10.00 1 1 0.

There is thus a scan along the rod from lmin of to lmax.

Note that h and k can be used as non-integer when the (a,b) film periodicity is rational (and not
equal) to the bulk periodicity.

It can be more convenient to use the experimental operation mode as the one defined in "Spec".
In that case use :

DAFS_2D
0 0 0. 0.05 5. 4 1 4 0 0 0. 0. ! h, k, l_min, lstep, lmax, Operation mode, Angle
0 0 0. 0.05 5. 4 1 4 0 0 90. 0. ! h, k, l_min, lstep, lmax, Operation mode, Angle
0 1 0. 0.05 5. 2 1 2 0 0 30. 10.
0 0 1. 4 1 4 0 0 90. 0. ! h, k, l, Operation mode, Angle

After h,k,l (with or without scan along a truncature rod), one gives the 5 integers of the operation
mode of the same table than in "Spec" (and nearly corresponding to the You’th paper (J. Appl.
Cryst, 32, 614 (1999)), then the values of the fixed angles :

Detector Reference Sample Sample Sample

1 delta alfa = beta eta eta Eta
2 nu Alfa mu mu Mu
3 Qaz Beta chi chi Chi
4 Naz Psi phi phi Phi
5 x X eta = delta / 2 eta = delta / 2 eta = delta / 2
6 x X mu = nu / 2 mu = nu / 2 mu = nu / 2

delta = : detector polar angle

nu = : azimuthal detector angle (independent from mu)
Qaz : azimuth of the rotation of the diffraction vector / laboratory
Naz : azimuth of the rotation of the normal to the surface / laboratory. Naz = 0 when
normal is horizontal. Specular case: polarizations  et   Naz = 90 and 0°.
alfa = : incidence angle
beta = : outgoing angle
psi = : azimuthal angle of the sample rotation around the diffraction vector. Its zero is
when the reference vector is in the incidence plane in the positive direction of
the incoming beam; diffraction vector is then horizontal. By default the reference
vector (in reciprocal space) is (0,0,1). To change it, see keword "Setaz".
eta = : polar angle of the sample
mu = : azimuthal angle of the sample

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 Manuel FDMNES

chi = : second angle of the sample

phi = : azimuthal angle of the sample

Figure from You’s paper showing the angle definitions corresponding to a « 4+2 » diffractometer
when all angles are 0

For example, the operation mode 4 1 4 0 0 means « Naz fixed, alfa=beta, phi fixed ».
The following angles are the values of the fixed angles. For example :
"4 1 4 0 0 0. 0." means « Naz =0., alfa=beta, phi =0 ».
"4 1 4 0 0 90. 0." means « Naz =0., alfa=beta, phi =90 ».
"2 1 2 0 0 30. 10. " means « nu =30., alfa=beta, mu =90 ».

Note that the "z-axis mode" used on 4-circles needs to take chi = eta = 0. The free angle can
then be the incidence angle alpha, which is equal to mu. This gives: "0 2 3 1 0 alpha 0. 0. "

Some operation modes are not possible or not coded:

40ij0 for any i and j
i0130 for i = 1, 2 or 3
i0140 for i = 1, 2 or 3

For the specular reflection, one may only use :

41400
01340 with only chi = 0 or 90
01430 with only chi = 0 or 90

With the same keyword, it is possible to have circular polarization writing with a negative
sign one of the 2 first number in the operation mode. For example:

DAFS_2D
0 0 0. 0.05 5. -4 1 4 0 0 0. 0. ! h, k, ℓmin, ℓstep, ℓmax, Operation mode, Angle

Then one obtains in the output file, 2 columns with respectively right and left incoming
circular polarization.

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 Manuel FDMNES

When the experimental orientation matrix (U) times the (h,k,l)Q matrix
transformation (B) is known (the so call UB matrix), this one can be used:

Mat_UB
-0.6713131898 -0.331076068 -0.005363453371
0.331087442 -0.6713288502 -0.0004569418448
-0.004608158701 -0.002782139698 0.7485135622

By default, the reference axis from which the psi angle is defined is the normal to the
surface. It is possible to define another direction, as in the experiment using:

Setaz
1 1 0  direction (in reciprocal space coordinate)

It can be interesting in the convolution part of the calculation to get not only the spectra
but also the scan along the rod at specific energies. To get the corresponding new file (with
extension "_tr"), write:

Transpose_file
15. 17.
The new file is in fact just a transpose of the standard output file, taken in the example
at the energies 15 and 17 eV.

The film, surface, interface and bulk unit cell parameters can be all different. By default
the (h,k,l) indices correspond to the bulk parameters. One can makes that it corresponds to the
film ones with keyword:

hkl_film

Note that when film and unit cell parameters with components parallel to the surface not
rational between them, film and bulk non-specular reflections do not interfere.

By default the code calculate the intensity for well-defined outgoing polarization. Using
"DAFS_2D" keyword, one thus obtains output spectra for both  and  outgoing conditions. To
have only the sum of them, that is as being without analyzer, use the keyword:

No_analyzer

In SRXRD, it is possible to consider a Helmholtz layer. See the keyword "Helmholtz"

in another section of this manual.

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 Manuel FDMNES

Because the bulk is often a dense simple metal, it can be faster to simplify the calculation
in this part. It is possible to avoid the SCF calculation and/or the finite difference method. For
this use:

No_SCF_bulk  no SCF calculation in the bulk, whatever it is SCF or not in the

surface

Green_bulk  in the bulk, the calculation is done using the multiple scattering
theory, whatever is the calculation mode in the surface.

Bulk_atom_not_recalculated  With this option the potential of the bulk atoms inside the
area of calculation of a surface atom are not recalculated. Their
potential obtained at the bulk step is kept.

To mimic the effect of a layer of counter-ions, it is possible to fix a layer (or several
layer) of charge, above the topmost surface layer. This can be done instead of the Helmholtz
potential (see this keyword). Each of these punctual charges give a coulombic potential,
convoluted by a gaussian distribution, which results in a 𝑉 = 2𝑞 𝑒𝑟𝑓 𝑟⁄𝜎√2 ⁄𝑟 potential (in
Rydberg). To keep neutrality, it is better (but not mandatory) to fix the opposite charge on the
reference surface atom. For this purpose, use the keyword "Counter_ion":

Counter_ion
1 3. 0.3 0.5  index of the refence atom (in the list under "Surface" keyword), the
counter ion is above it), distance from it (3 Å), charge q = 0.3, positive
number for a cation, width of the gaussian distribution 𝜎 = 0.5 Å.

Atom_conf  To have the reference atom with the opposite charge (see this keyword).
1 1 1 5 2 8.3 ! For this occupancy, the corresponding Pt atomic charge is -0.3

Surface
2.77482843 2.77482843 6.796913779 90.0 90.0 120.0
78 0.0000000000 0.0000000000 1.00489999999
78 0.3333333333 0.6666666667 0.66666666666
78 0.6666666667 0.3333333333 0.33333333333
78 0.0000000000 0.0000000000 0.0000000000

Note that several counter ions can be given:

Counter_ion
1 3. 0.3 0.5
2 5.5 -0.2 0.5 ! reference atoms can be the same or different

It is also possible to shift the counter ion parallelly to the surface from the reference atom. One
just have to write to more numbers:

Counter_ion
1 0.1 0.15 3. 0.3 0.5  0.1, 0.15 and 3 are the displacements in Å versus the reference atom
along "a" et "b" et "c" defined in the surface unit cell.

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 Manuel FDMNES

In the same way, it is possible to simulate dipoles with the keyword "Counter_dip". The
writing is exactly the same, but instead of charge, one gives the electric moment expressed in
Debye. 2 opposite charges +/-q, with q = e by a space of 1 Å gives moment  = 4.80320 D =
1.602176334 x 10-29 C.m. Examples of molecules: HF = 1.826 D; H2O = 1.855 D; CO = 0.110
D, NO = 0.159 D; SO2 = 1.633 D… The dipoles are perpendicular to the surface. A positive
moment expresses a dipole oriented outward from the surface.

Counter_dip
1 2.5 1.855 0.5  index of referent atom (in the list under "Surface"), the counter-dipole is
just above it), distance from reference atom (2.5 Å), moment,  = 1.855 D,
positive number when dipole outward from the surface, width of the gaussian
distribution 𝜎 = 0.5 Å.

It is also possible to make a displacement along the 3 directions defined by the surface unit cell:

Counter_dip
1 0.1 0.15 2.5 1.855 0.5  0.1, 0.15 and 2.5 are the displacements in Å versus the reference
atom along the directions "a", "b" and "c".

To have a screening of the counter ions and counter dipoles below the surface atomic
plane, like for the counter-ions and counter-dipole potentials, use the keyword:

Counter_linear

This screening leads to a linear decreasing of the counter-ion and counter-dipole

potentials such that at 3 Å below the surface atomic plane, they are zero. To modify this
parameter just set the new value below the keyword:

Counter_linear
2.8  thickness of the linear decreasing, down to zero.

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 Manuel FDMNES

List of fdmnes keywords

Abs_B_iso 66 cm2g 84
Abs_U_iso 66 Comment 49
Abs_before 62 Conv_gaus 70
Absorber 21, 45, 47 Conv_out 62
Adimp 55, 56, 82 Convolution 61, 63
All_conv 62 COOP 40
All_nrixs 27 COOP_dist 40
Allsite 48 COOP_z_axis 40
Ang_spin 35 Core_energ_tot 51
Atom 19, 33, 34, 72 Core_resolved 58
Atom_B_ani 32, 88 Counter_dip 93
Atom_B_iso 32, 88 Counter_ion 92
Atom_conf 20, 41 Counter_linear 93
Atom_U_ani 32, 88 Crystal 17, 31, 40
Atom_U_iso 32, 88 Crystal _p 19
Atom_nsph 41 Cub_hexa 79
Atomic_nu 79 Cyl_pot 51
Axe_spin 35 Cyl_SCF 51
Azimuth 77 Dafs 28, 29, 31, 89
Basecomp 53 DAFS_2D 89
Bulk 85 Dafs_exp 30
Bulk_atom_not_recal 92 Dafs_exp_type 30
Bulk_roughness 87 Dead_layer 68
Calculation 61 Density 44
Cap_B_iso 87 Density_comp 45
Cap_layer 87 Density_all 45
Cap_roughness 87 Dec 63
Cap_shift 87 Delta_E_conv 36
Cap_thickness 87 Dilatorb 42
Cap_U_iso 87 Dip_rel 23
Cartesian 46 Dipmag 23
Center 45 Directory 62
Center_abs 45 Doping 24
Center_s 45 Double_cor 68
Check 52 Dpos 46
Check_all 52 DWfactor 83
Check_biref 69 E_cut 62
Check_coabs 52 E_out_max 53
Check_conv 64 E1E2 23
Check_mat 52 E1E3 23
Check_mpi 53 E1M1 23
Check_pot 52 E2E2 23
Check_sph 52 E3E3 23
Check_tens 52 Ecent 64
Chfree 41 Edge 22
Circular 69 Eimag 42
Clementi 40 Elarg 64

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 Manuel FDMNES

Emax 73 Helm_mix 38
Emin 73 Helmholtz 38
End 15 hkl_film 91
Endjump 49 Hubbard 37
Energpho 22 Hubbard_Z 37
Energy 77 IMFPin 82
Epsii 47 Interface 86
Error 74 Inter_shift 87
Estart 65 iord 55
ELFin 82 Jump 49
Excited 55 Kev 73
Experiment 71, 73 Length_line 58
Expntl 84 Lmax 56
Extract 25 Lmax_DOSout 50
Extract_tens 47 Lmax_nrixs 27
Extractpos 47 Lmax_tddft 37
Extractsym 47 Lmaxfree 56
File_in 70 Lmaxso 14
File_out, Filout 17, 70, 79 Lmaxso_max 56
File_met 74 Lminus1 43
Fdmx 81 Lplus1 43
Fdmx_proc 81 M1M1 23
Film 18, 86 Magnetism 32, 48
Film_Cif_file 19 Mat_mul 79
Film_Pdb_file 19 Mat_polar 24
Film_roughness 87 Mat_UB 91
Film_shift 86 Memory_save 58
Film_thickness 86 Mermin 82
Film_zero 86 Metric_out 71
Flapw 48 Molecule 17, 38
Flapw_n 49 Muffintin 55
Flapw_n_p 49 Mult_cell 79
Flapw_psi 47 N_self 36
Forbidden 67 No_analyzer 91
Fprime 68 No_check 50
Fprime _atom 68 No_E1E1 23
Full_potential 50 No_E1E2 23
Full_self_abs 29 No_E1E3 23
Gamma_hole 64 No_E2E2 23
Gamma_var 64 No_Fermi 35
Gamma_max 64 No_res_mag 32
Gaussian 64 No_res_mom 32
Gen_shift 73 No_SCF_bulk 91
Green 22 noBG 84
Green_bulk 91 noDW 83
Harm_tess 44 noIMFP 83
Header 59 Noncentre 44
Hedin 40, 47 Nonexc 55
Helm_cos 38 Nonrelat 33
Helm_lin 38 Normaltau 55

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 Manuel FDMNES

Norman 57 SCF 35
Nrato 49 SCF_exc 36
NRIXS 27 SCF_mag_free 37
NRIXS_mono 27 SCF_smooth 37
Occupancy 19, 32, 88 Screening 39
Octupole 23 Seah 64
One_run 50 Selec_core 66
One_run_s 50 Selec_inp 77
Overad 46 Selec_out 77
Overlap 57 Self_abs 30
P_self 36 Setaz 88
P_self_max 36 Spgroup 18
Parameter 71 Sphere_all 46
PBE96 39 Spherical 44
Perdew 39 Spinorbit 32
Polarize 23 Step_azim 31
Python 59 Stokes 69
Quadrupole 23 Stokes_name 69
R_self 36 Supermuf 57
Radius 17 Surface 85
Range 22 Surface_plane 68
Rangel 22 Surface_shift 85
Ray_max_dirac 59 Sym 52
Rcharge 58 Symsite 53
Rcharge_Z 58 Table 64
Reflection 75 TDDFT 37
Relativism 33 TDebye 83
Rionic 58 Thomson 67
Rmtg_Z 57 Tmeas 83
Rmt 55 Trace 44
Rmtv0 57 Transpose_file 91
Rotsup 47 Unit_cell 79
RPA 37 V0imp 42
Rpotmax 43 Victoreen 84
Rx 74 Vmax 42
Rxg 74 Weight_co 70
Rydberg 43 Xalpha 39
S0_2 65 Xan_atom 50
Sample_thickness 66 XES 63
Scan 67 Z_absorber 21
Scan_conv 67 Zero_azim 29
Scan_file 67

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