Missing 1.

1
Short User Manual
Riccardo Gusmeroli and Claudia Dallera
Copyright 2004-2007 Riccardo Gusmeroli and Claudia Dallera.
All Rights Reserved
CONTENTS II
Contents
1 Introduction 1
2 Installation procedure 1
3 Initial settings 1
4 Structure of Missing 1
5 How to perform an X-ray absorption calculation 3
5.1 RCN program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
5.2 RCN2 program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
5.3 RCG program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
5.4 Racer program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
6 How to perform a resonant X-ray emission calculation 13
6.1 RCN program for RXES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
6.2 RCN2 program for RXES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
6.3 RCG program for RXES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
6.4 RACER program for RXES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
6.5 TFLUOR program for RXES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
7 Data postprocessing 17
8 Software generalities 18
9 Contact informations 19
Bibliography 20
1. Introduction 1
This document is an introductory guide to the use of the Personal Computer interface to the atomic
multiplet code based on Cowans programs. The name of the interface program is Missing: Multiplet
Inner-Shell Spectroscopy INterface GUI (please note that the code was formerly named RGAss and that
the screenshots contained in this manual were taken before the ofcial name was given). The programs
that are accessed through the interface are listed here below, together with the name of the people who
developed the codes.
All programs listed above can be downloaded from the website
http://www.esrf.fr/UsersAndScience/Experiments/TBS/SciSoft/
where the present manual can also be found.
1 Introduction
In order to perform an Atomic Multiplet calculation several programs must be called subsequently. For
each of them we provide the printout of the screen with the explanation of the parameters that must be
the dened by the user. Many parameters do not need to be adjusted unless in very special cases. For
these parameters (that are not detailed in the present manual) we refer the reader to the original manual
by Robert Cowan, that can be downloaded from the site. Before starting with the use of the programs
some options can be dened through the menus. This is detailed in section 1. When the calculation is
nished the results can be exported to be viewed, as detailed in section How to look at results.
2 Installation procedure
1. Obtain the package rgass.zip fromthe Web site http://www.esrf.fr/UsersAndScience/Experiments/TBS/SciSoft/
2. Unzip the package with your favourite unzip software to a folder called rgass (or any other name).
3. Go to folder rgass.
4. Double-click on Missing.exe
5. In Tools menu item click on the Install shell extensions command so that the Missing program is
automatically loaded when double-clicking on a .rgs le.
6. Again in Tools menu item click on the Re-install RCG command.
3 Initial settings
The les created through Missing are called Workspaces and have the extension .rgs. The initial page of
the program (Fig. 1) allows to create a new Workspace, to open an existing one, and to save the active
Wrokspace. Duplicating an existing workspace must be made from outside the program, infact the Save
as command is not active. The calls to the programs and their activation can be made fromthe Application
menu item as well as from the buttons located below. The Settings menu item gives access to settings
that affect the calculation and the export of the results, that can also be accessed from within the call to
each separate program. They will therefore be detailed in the section dedicated to the specic program.
General note: Missing allows to input the parameters through a user-friendly interface. However it also
allows to edit the input le, as in the origianl version. To do this check the Customcheckbox in the upper
left part of the screen that appears for each program call.
4 Structure of Missing
Missing is organized as a collection of chained calls to external scientic packages. In particular it is able
to manage the following applications:
4. Structure of Missing 2
Figure 1: Empty workspace.
RCN [1] (by R. D. Cowan) calculates single-conguration radial wavefunctions P
nl
(r) for a spher-
ically symmetrized atom via homogeneous-differential-equation approximations to the Hartree-
Fock method.
RCN2 [1] (by R. D. Cowan) accepts radial wavefunctions (for one or more different congura-
tions of one or more atoms or ions) from either RCN, and for each atom calculates various two-
conguration radial integrals: overlap integrals P
nl
|P
n

l
, conguration-interaction Coulomb in-
tegrals R
k
and spin-orbit integrals
nln

l
, and radial electric-dipole and electric-quadrupole inte-
grals.
RCG [1] (by R. D. Cowan) computes the angular factor of various matrix elements involved in the
theory of atomic structure and spectra. It computes the XAS spectrum in spherical symmetry.
RACER [2] (by B. T. Thole) calculates all the required quantities involved in point-group calcu-
lations. It computes the XAS spectrum in lower symmetry when the initial and nal state are
characterized by one conguration only.
TotalFluor (by B. T. Thole, H. Ogasawara, M. A. van Veenendaal, P. Ferriani, and C. M. Bertoni)
computes Hamiltonians and Transition matrices in lower symmetry. It computes the XAS spec-
trum in lower symmetry in cases of interacting congurations as well as Resonant Inelastic X-ray
Emission Spectra.
The sequence of the required calls, together with the provided options and data, are collected in a so-
called workspace (which can be stored in a le with extension .rgs). When a workspace is runned, Missing
executes the external calls following three main steps:
1. Builds an input le on the base of user options and data (the user is also allowed to give the input
le directly if needed)
5. How to perform an X-ray absorption calculation 3
2. Runs the external executable in batch-mode grabbing the screen output messages, any error mes-
sage and keeping trace of all the output data les
3. Rearranges all the grabbed data so that they are available to the user in separate windows of the
main program
After running all the required programs related to a specic calculation, the user can access a postprocess
phase where a series of useful plots are generated. In particular this option is available via the export
to an HTML archive: a web-ready hierarchical document is created with links to a summary of the
input/output data of each call and to high quality PDF plots and plot-ready raw les of spectra and
other useful functions.
5 How to perform an X-ray absorption calculation
This section details which steps must be followed to perform a calculation of X-ray absorption in the
case where the initial and the nal state are characterized by one conguration only.
5.1 RCN program
The program RCN allows to dene the congurations of the initial and nal states of the transition.
To call it use the Add RCN call command from the Application menu bar, or the N button (see Fig. 2).
Use the Congure button to dene the congurations of the initial and nal state of the transition. Each
Figure 2: RCN program main panel.
conguration is called Card for obvious historical reasons.
To create a conguration card use the New... button from the screen shown in Fig. 3. Under the General
tab you must specify the element and can give a label to the element that you are investigating, for
instance Ni2+ (see Fig. 4). Do not worry about all the other parameters, they are ne as they are. Under
5.1 RCN program 4
Figure 3: RCN Conguration panel.
Figure 4: RCN General tab in the Conguration panel.
the Conguration tab you now specify the occupation numbers of all orbitals involved in the transition
and can give it a label (like 2p6 3d8, see Fig. 5).
When you have specied all congurations press OK. You can verify that the congurations that you
have created are possible initial and nal states of a dipole transition by looking at their parity (either
the color of the arrow at the most left side, or the Parity column. The Show set arrangment button tells
you whether the congurations have the same ionization state.
To modify a conguration card click on it and use the Conguration button. You can change the order of
the created congurations by using the up and down arrow buttons.
Finally, the Parameters button gives access to a large number of parameters that determine the accuracy
of the calculation. They give origin to all the numbers that apear in the rst row of the input. Some of
5.1 RCN program 5
Figure 5: RCN Conguration tab in the Conguration panel.
them are self-explanatory, many are not. You should not need to change them. In case you really wish
to know their meaning and effect you are welcome to refer to Cowans original manuals.
Now you can press the Done button. You should see something similar to Fig. 6.
Figure 6: RCN Conguration panel after creation of conguration.
One more button, that is present in most of the program calls is the HTML button. This button is to
deny the format and content of the HTML output.
When you have performed all the detailed steps run the program, either through the Run command in
the Applications menu, or through the button with the exclamation mark. It is not mandatory to run each
program separately and you could run everything at the end, when all programs have been dened.
However, it is better if you do it at each step: in fact by doing so you will be able to see the input created
by each program for the following program, and to follow better the instructions.
5.2 RCN2 program 6
5.2 RCN2 program
The program RCN2 computes the average energies, the radial integrals and the spin-orbit parameters
of the electornic congurations dened in RCN. To call the program use the Add RCN2 call command
from the Application menu bar, or the 2 button (see Fig. 7). In this program you can set some parameters
Figure 7: RCN2 program main panel.
that inuence the calculation performe in the subsequent steps: this is done through the The program
RCN allows to dene the congurations of the initial and nal states of the transition. To call it use the
Congure... button.
The General tab (Fig. 8) denes whether the radial integrals are multiplied by the overlap integrals and
whether the inetgrals needed for the computation of an electric quadrupole transition should be calcu-
lated.
The Numeric Parameters tab (Fig. 9)is particularly important. It denes the factor for rescaling the
Slater integral values with respect to their atomic value in order to simulate the effect of the intra-
atomic correlation not accounted for in the HartreeFock approximation. F
k
(l
i
, l
j
), F
k
(l
i
, l
i
), G
k
(l
i
, l
j
)
and R
k
(l
i
, l
j
, l

i
, l

j
) are the Slater integrals involving different shells.
i
is the spin-orbit parameter. The
normally used values of the rescaling factors are 0.8 for the Slater integrals and 1 for the spin-orbit
factor.
Note that the order in which these parameters are listed is used to identify them as they appear in the
input of RCG (see following section).
The Output tab (Fig. 10) does not require to be modied.
5.3 RCG program
The program RCG receives as input the output from program RCN2 and computes the eigenvectors and
eigenvalues of the specied congurations. If the calculation is performed in spherical symmetry (we
explain later howto deen the symmetry) then it will also compute the absorption spectrum. Otherwise
5.3 RCG program 7
Figure 8: RCN2 Conguration General tab.
it will produce the input for the next step.
To call the program use the Add RCG call command from the Application menu bar, or the G button. The
main panel will appear as in Fig. 11 if you have not run the previous programs. Otherwise it will look
as in Fig. 12.
The input that appears in the panel is the output of RCN2. As anticipated in the description of the RCN2
parameters, the values listed after each conguration are the average energy, the Slater integrals and the
spin-orbit parameter. They are identied by the last digit, that corresponds to the order in which they
are listed in the Numeric Parameters tab of the Conguration of RCN2: vaules ending with 0 indicate the
average energy, ending with 1 indicate the Slater parameter of type F
k
(l
i
, l
j
), with 2 the Slater parameter
F
k
(l
i
, l
i
), with 3 the Slater parameter G
k
(l
i
, l
j
) and with 4 the Slater parameter R
k
(l
i
, l
j
, l

i
, l

j
) (that is
used only in those cases where interaction among different conguration in the same state is used).
The Congure... button has many tabs, of which we address only the General and the RME ones. The
Printout 1, Printout 2 and Printout 3 tabs do not need to be modied, and the Rearrange tab will be
detailed later when describing how an X-ray emission calculation is performed.
The General (shown in Fig. 13) is to be used in cases that are slightly more sophisticated than the example
that we are giving here, i.e. in the cases where interaction among different congurations must be
taken into account. So, if the initial state (referred to as First parity/lower level or the nal state Second
parity/upper level) is made up by more than one of the congurations listed in RCN, this must be declared
in the Transitions to be included box. We do not detail here the other boxes, which are not of broad use,
apart from the Coupling box, that allows to select between LS and JJ coupling.
The RME tab (RME stands for Reduced Matrix Elements) is extremely important and is needed in all cases
where the calculations are performed in non-spherical symmetry. This tab is shown in Fig. 14. The
terms that must be added to the spherical hamiltonian are specied here in form of Operators: the Shell
operator allows to specify the particular symmetry (cubic Oh, tetrahedral C4h, ...) of the system. The
Spin operator is required to specify the presence of an exchange-split eld. The procedure to include
those operators in the calculation is the following:
5.4 Racer program 8
Figure 9: RCN2 Conguration Numeric Parameters panel.
Choose the operator through the Add... button
Check the box corresponding to the parity (i.e. the initial or nal state, or both) and orbital on which the
operator should act. The order of the orbitals corresponds to the one listed in the input of RCN.
You will need to modify the numbers in the following lines of the panel in some special cases: the
minimum and maximum values of J (for Crystal Field matrix elements calculation) are 4 most of the time
but might be 2 and 6 in some cases (as the one of the present example). We will give some hint about
this point in the section 5.4. The Pole values of the Interaction matrix elements calculation are always 1 for
transitions governed by electric dipole operators, they would be 2 for quadrupolar transitions. Finally,
the number after Number of interacting shells: indicates that only for the specied number of shells in
each state the Slater integrals and spin-orbit parameters will be included in the calculation. Further
shells will be considered to be continuum or ligand shells.
If some operators have been chosen in the RME tab, then the calculation must continue with the Racer
program.
In the case of a system that is well described in spherical symmetry, the calculation ends when running
RCG. After this the spectra can be generated and viewed through the button located to the right of the
exclamation mark (or through the Export as HTML command in the File menu item) as detailed in 7. The
parameters that dene the generated spectrum must be dened through the HTML button on the main
screen.
if only the HTML parameters are changed, there is no need to re-run the calculation, exporting is
enough. The same holds for the Racer program.
5.4 Racer program
The Racer program comes after the RCG program. The call can be added only when Operators have been
selected in RCG, as explained in the previous section (you will get an error otherwise). The input of
Racer is loaded through the Load Standard File... button (Fig. 15). The button gives access to a number
of inputs for calculating the spectra in different symmetries. Each item of the Load Racer Standard File
5.4 Racer program 9
Figure 10: RCN2 Conguration Output panel.
input species the starting symmetry (always spherical O3) and the desired symmetry for the system.
The available inputs are for calculations in the Oh, O2 and C4h symmetry. Note that for an absorption
calculation you have to select among the options without TFluor: these are the input les for emission
calculations and will be explained later.
We give some details about the structure of the input shown in Fig. 16 in order to enable the user of the
programs to modify them.
The input always starts with Y. The next line contains the name of the routine that is called (Butler for
absorption calculation and Racer for resonant inelastic X-ray emission calculations. The labels that fol-
low give the chain of the symmetries (with their parities) through which the calculations goes from the
spherical to the nal symmetry. For more information on how to construct these chains you can refer to
Chapter 12 in the book by P.H. Butler in Ref. [2]. The available inputs should to the job for most cases.
The following blocks describe the structure of the Hamiltonian for the ground and excited state. With
reference to FigureXXX, the Hamiltonian ACTOR, having symmetry 0+ in Butlers notation, is com-
posed by three OPERators (HAMILTONIAN, SHELL2 and SPIN2), that refer respectively to the spherical
part of the Hamiltonian, to the Crystal Field part, and to the magnetic exchange interaction part. Note
that the operators SHELL and SPIN end with a number: this number indicates the shell on which the
operator acts and must correspond to the number specied in the RME tab of the input of RCG.
After each operator comes the keyword BRANCH followed by a list of symbols intercalated by > num-
bers. These symbols express the symmetry (in Butlers group notation) through which the system is
transformed from the initial spherical to the nal desired symmetry (tetrhaedral C4H in the present ex-
ample). Numbers not followed by a + or sign indicate multeplicity (0 means 1).
The last number of each BRANCH line indicates the strength of the operator. The number that ends
the BRANCH lines of the SHELL2 operators is related to the Crystal Field parameters 10Dq, Ds and Dt.
These are among the most important parameters you want to include in the calculation, so they deserve
some precise practical information on how to use them:
in the case of C4H calculation like the present one, 10Dq, Ds and Dt are specied separately. The num-
5.4 Racer program 10
Figure 11: RCG program main panel.
bers that appear in the input of Racer are X
400
, X
420
and X
220
(this is easily remembered by looking at
the BRANCH lines (containing respectively 4+ 0+ 0+, 4+ 2+ 0+, 2+ 2+ 0+). It will be useful to recall here
the relations between the 10Dq, Ds, Dt and the X
400
, X
420
and X
220
:
X
400
=

30 (6Dq
7
2
Dt)
X
420
=
7
2

42 (Dt)
X
220
=

70 (Ds)
In case of cubic Oh symmetry only the 10Dq parameter needs to be specied. In this case the rela-
tionship between 10Dq and X
400
is:
X
400
=

30 (6Dq)
In practice, in the case of Oh symmetry, in order to specify the value of 10Dq in eV , you must multiply
it by 6/10

30, i.e. by 3.286335345. In the input le of the example, the value given for X
400
indicates
that 10Dq was 1 eV (Ds and Dt are 0 in the example).
The number that ends the BRANCH lines of the SPIN2 operators gives the value (in eV ) of the magnetic
exchange interaction.
Similar blocks are repeated for the initial ground and the excited nal state.
The last block in the input le describes the transition, in particular the symmetry of the operators that
5.4 Racer program 11
Figure 12: RCG program main panel completed with input.
Figure 13: RCG Conguration General tab.
give rise to the absorption. The symbols following the keyword ACTOR indicate the symmetry and
5.4 Racer program 12
Figure 14: RCG Conguration RME tab.
Figure 15: Racer Load Standard File input.
parity of the transition operator: the symmetry of the light in an electric dipolar transition is described
by three components, usually referred to as q, which take the value 1, 0, 1. The sign that follows
indicates that the dipolar transition operator has odd parity.
Warning: if the input contains names that are not recognized by the Racer program, the Screen Output
will show the error message PIPPPO (Italian for Foo): this tells you that the input needs to be modied.
Side warning: the names following ACTOR are labels that can be chosen freely. We suggest however to
make as little as possibile modications to the input we provide, in order to reduce the risk of mistakes.
The names following OPER cannot be chosen freely.
Important hint: As might be clear by now, building the input of Racer, for instance for a new symme-
try, not listed among the standard input les, is not without risk. Especially the construction of the
BRANCH lines from scratch can be tricky. Of great help can be the Tape Output of Racer, some part of
6. How to perform a resonant X-ray emission calculation 13
Figure 16: Racer standard input.
which are meaningful also when the program has ended with errors: the section starting with REP-
RESENTATIONS (not far from the beginning), contains all branches for the specied symmetry. As is
clear from the standard inputs, branchings of the HAMILTONIAN actor must end with 0+, branchings
of the MULTIPOLE actors start with 1 (the representation of the dipolar light operator in spherical
symmetry) and end with the same symmetry as the operator (i.e. 1+ for the light operator q = 1+ and
so on). The branches representation listed in that le can be very helpful when trying to deal with a new
symmetry.
After successufully running the Racer calculation, you can export the results through the button located
to the right of the exclamation mark (or through the Export as HTML command in the File menu item)
as detailed in 7. The parameters that dene the generated spectrum must be dened through the HTML
button on the main screen. The panel opened by the HTML button (Fig. 17) has two tabs: the General
tab denes self-explanatory parameters very similar to those of the RCG program. The often forgotten
Operators tab (Fig. 18) allows to dene how the elementary spectra are combined to build the nal re-
sults. The Load C4H-LZR button loads the 7 most used combinations, that appear in the bottom part of
the panel. Blank spectra allow to dene any other possible combination. If no spectral combination is
dened, no spectrumwill be computed. As already said in the RCG programsection, if only the HTML
parameters are changed, there is no need to re-run the calculation, exporting is enough.
6 How to perform a resonant X-ray emission calculation
This section explains how to calculate resonant X-ray emission spectra (RXES). We underline that this
part is for resonant spectra: in fact for non-resonant, i.e. uorescent spectra, good results can be obtained
by performing a reversed X-ray absorption calculation, where the excited state is the initial state and the
nal state is the less-excited state in the transition. In the resonant case the Kramers-Heisenberg formula
6.1 RCN program for RXES 14
Figure 17: Racer General tab in the HTML button.
must be included. This is done by performing an additional step in the calculation. We here explain the
whole program sequence: in fact all programs detailed before must be used in a sligthly different way,
as three states (initial, intermediate, nal) must be specied. We will explain here only the differences
with respect to absorption calculation.
6.1 RCN program for RXES
The only difference with respect to the case of absorption calculation is that three congurations must
be specied. Take care that the order in which they must be specied is: Initial, Intermediate, Final.
This is all for this program.
6.2 RCN2 program for RXES
This program does not require any additional information to what given in the section devoted to ab-
sorption calculation.
6.3 RCG program for RXES
In RCG some more parameters must be given in the Congure... button: as anticipated, the Rearrange
tab plays a role here: the role of the declared congurations must be specied. In the given example
the ground state contains the rst conguration, the intermediate state is the third conguration, and
the nal state is the second conguration (in case of states with multiple, interacting congurations, the
panel allows to specify groups of congurations). The lower block (the one starting with Note: this section
6.4 RACER program for RXES 15
Figure 18: Racer Operators tab in the HTML button.
refers to TFluor calculations only) gives the right format to the RCG input in view of an RXES calculation:
in fact in the input le for RCG, the parameters for the intermediate conguration must appear only
once. in order to obtain this, Omit energy parameters for |i must be checked. Finally, the RME tab: this
works exactly like for the absorption measurements, since the parities in the calculation are only two.
6.4 RACER program for RXES
The input for RACER in the case of an emission calculation is longer than in the case of an absorption
calculation since it includes the parameters for the two steps of the process. Several standard input les
are specied for different symmetries. A good strategy is to set to 1.0 the strength of all operators, and
to 3.286335345 the strength of the crystal eld operator, so that the numbers specied at the next step
(TFLUOR program for RXES) will be the energy (in eV) of each of them.
6.5 TFLUOR program for RXES
This is the nal step of the program, where all parameters for the calculation based on the Kramers-
Heisenberg formula are specied. If you checked the Generated by RGAss box (see Fig. 19) then the input
le is generated by the program based on the information contained in the Parameters and Photons tab
in the Congure button. Otherwise (if you checked Custom) you can write yourself the input le. A
good option is also to have the program generate it, and then click on the Custom tab and do further
modications.
The meaning of all the numbers appearing in the Input File is here specied and can be at least partly
retrieved from the tabs.
7. Data postprocessing 16
First line: NCONF species the number of electronic congurations present in the initial, nal and
intermediate state respectively. In our case it is always 1 because we are not considering any interacting
congurations. The meaning of the string N2 1 is unknown also to us, so do not change it.
Second line: XHAM species the number of operators used for the rst, i.e. the initial conguration,
and their values: in the present case 3 means that three operators were specied for the initial con-
guration, which are the Hamiltonian operator, the Crystal Field operator and the Spin operator (this
depends on which operators were specied in Racer). The other values (1.0, 1.1 and 0.15 in the example)
are the numbers that multiply the values already specied in Racer. For instance in the present case the
Hamiltonian will have the nal value of 1 eV (1.0 multiplied by 1.0), the Crystal Field operator the nal
value of 1.1 eV (since, as said before, the number 3.286335345 specied in Racer is the one that converts
the CF parameter into electronVolts), and the Spin operator has a value of 0.225 (0.15 in Racer multiplied
by 0.15 here - of course another option is to set the value to 1.0 in Racer and specify in TFluor the actual
strength.
Third and fourth line: the same as the line before but for the nal and intermediate state respectively.
Fifth line: the numbers coming after FLUOR allow to specify the numbers of congurations present
in the initial, intermediate and nal state. In the case of simple congurations please just do not modify
it.
Sixth and seventh lines: Mean life of intermediate and nal conguration states (can be selected
from the Photons tab).
Eigth line: Number of incoming and outgoing energy values at which the spectra are calculated,
and energy step (can be selected from the Photons tab).
Ninth line: First incident energy value and rst outgoing energy value (can be selected from the
Photons tab).
Tenth and eleventh lines: the polarization of the photons and the azimuthal and polar angle are
specied both for the incoming and outgoing beam (can be selected from the Photons tab).
Twelvth line: Here you specify the absolute temperature of the system (can be selected from the
Parameters tab).
Thirteenth line: INTERFERENCE indicates that all the states that fall within the lifetime specied in
the denominator of the Kramers-Heisenberg formula interfere with each other (can be selected from the
Parameters tab).
Finally, by selecting Generated by RGAss you will see all the Triads (not shown in the gure): these are
all the possible combinations of initial, intermediate and nal states of your system, and depending on
your requirements you will select only those that are of interesting to you (e.g. only those that have the
ground state as the initial state.
In the end you will be able to run the calculation and export it (for the export see the next sections).
7 Data postprocessing
When all the calls involved in a calculation are executed, the user can access a postprocessing phase
via the button Export as HTML (Fig. 22). This generates a sort of workspace documentation containing
a summary of all input parameters and data, all the output generated by the called applications and a
number of plots of physical quantities of interest such as wavefunctions and spectra.
To exemplify the procedure we choose the workspace generated in the NiO XAS example of section 5
(Fig. 22). Once the Export as HTML button is pressed, a dialog window asks the user for the lename
(with extension .html) of the main documentation le. In this context we choose the name NiOXAS.html:
Missing will then create an index le called NiOXAS.html and a folder called NiOXAS les containing
all the indexed les. As soon as the data are stored, the documentation tree is also opened in the default
HTML viewer of the system (Fig. 23).
The documentation window is organized in two tiled frames: the left frame contains an index of all the
workspace calls and links to corresponding data les while the right one contains workspace general
informations (this latter document is replaced by the desired data document when the user clicks on a
link on the right).
Items corresponding to each call include three xed data les (namely Input, Screen and Tape) and other
application-specic ones:
7. Data postprocessing 17
Figure 19: TFluor input le.
Figure 20: TFluor Parameters tab in the Congure button.
Input: contains all the parameters and the data provided by the user, together with the formatted
input le generated.
Screen: shows the messages printed on the screen during program execution.
Tape: contains all the human-readable genrated tapes
8. Software generalities 18
Figure 21: TFluor Photons tab in the Congure button.
Results (where applicable): links to all the post-processed data such as wavefunctions and spectra.
In our case we are interested to the absorption spectra in C
4H
symmetry (which in turn was generated by
the call to Racer labelled (03)). To that aim we click on the Results link under the section (03) RACER
of the left frame, obtaining the view in Fig. 24. A brief description of the resulting page follows:
A frame in the top section tells the symmetry of interest (C
4H
in the example) and the transforma-
tion chain used to reach it (O
3
O
H
D
4H
C
4H
)
Under the label Triads a list of the transition matrices parsed can be found
In the Spectra frame the user can access the spectral data of interest. In particular:
1. Near the words Lines selected the number of spectral lines selected on the base of user-provided
parameters can be found. The word selected points to a text-based le with a list of all such
lines.
2. The statement Spectra plots and tables introduces the available plots. The word plots points to
a high-quality PDF le containing all the generated plots in a print-ready fashion. Each plot
can also be retrieved in a text-based data le using the following links.
8 Software generalities
Missing 1.1
Copyright 2001-2004 Riccardo Gusmeroli.
All rights reserved.
9. Contact informations 19
Figure 22: Workspace at the end of a run command. The red circle highlights the Export as HTML button.
The software is a user-friendly PC interface to the Atomic Multiplet Code written by R.D.Cowan
(LANL) with extensions by B.T.Thole and others. Porting from the original code to the PC-compatible
version is intrinsically prone to the arising of bugs. Many of them have been found and removed by
the author but others might still be present. In case of results that are suspicious because undoubtedly
contrasting physical expectations, please contact the author enclosing the indicted workspace (see 9 for
contact informations).
The right to use the software free of charge is granted to scientic institution provided a reference to
the code and its author is included in any publication it contributes to. Any commercial use is instead
prohibited without explicit authorization by the author.
The software is provided as is, without warranty of any kind, express or implied, including but not
limited to the warranties of merchantability, tness for a particular purpose and noninfringement. In
no event shall the author be liable for any claim, damages or other liability, whether in an action of con-
tract, tort or otherwise, arising from, out of or in connection with Missing or the use or other dealings in
Missing.
9 Contact informations
Comments, suggestions and bug-reports can be sent to:
Prof. Claudia Dallera
Dipartimento di Fisica
Politecnico di Milano
Piazza L. Da Vinci, 32
REFERENCES 20
Figure 23: Index le of the documentation tree opened in the default HTML viewer.
20133 Milano (MI)
Email: claudia.dallera@si.polimi.it
References
[1] R. D. Cowan, The Theory of Atomic Structure and Spectra. University of California Press, 1981.
[2] P. H. Butler, Point Group Symmetry and Applications - Methods and Tables. Plenum Press, 1981.
REFERENCES 21
Figure 24: Postprocessed results of the Racer C
4H
calculation.