FAQ
Frequently
Asked Questions
This chapter will answer to
Frequently
Asked Questions
with
Q&A style
Dynamical Scattering Calculation(MultiGUI)
Q001:
How to use Atom Parameter Editor?
Q002:
How to use "Occupancy"?
Q003:
I saw the example, where an angle of lattice parameter is zero (o)...
Q004:
How many phase gratings can we use?
Q005:
How many slices can we divide a unit cell (or a supercell) into?
Q006:
How is a phase grating (transmission function) evaluated?
Q007:
How to specify the range of scattered waves to be included in the multislice
calculation?
Q008:
What is a slice thickness for [011] or [111] incidence?
Q009:
How to specify an incident beam direction?
Q010:
Why is the incident beam direction with c=0 not allowed?
Q011:
How to treat an incident beam direction with c=0?
Q012:
How is an atom scattering factor for electrons calculated?
Q013:
Can we use scatter factor for ions?
Q014:
How to specify a thermal factor (thermal vibration effect)?
Q015:
How does thermal factor affect an atomic scattering factor?
Q016:
How do we use "Unitary test"?
Q017:
What kind of propagation function is used in calculation?
Q018:
What is threedimensional effect?
Q019:
How to include threedimensional effect in multislice calculation?
Q020:
How to specify model symmetry (symmetry operations)?
Q021:
I can't read atom parameters from a text file.
Q022:
How to create an atom parameter file (text data)?
Q023:
What is a format of atom parameter file (test data)?
Q024:
How does an atomic potential contribute to a projected potential?
Image Calculation(ImageGUI)
Q101:
My image does not show any contrast.
Q102:
Let me know the differences between Simulation Modes.
Q103:
When I select "First Order (Envelope)" from Simulation Mode, I can get a
correct image, but not with "Second order (TCC)".
Dynamical Scattering Amplitude Output(DFOutGUI)
Q201:
Why is a reflection specified using only two indexes? How can we relate these
indexes to a normal threeindex system?
Q202:
How is the phase displayed?
CBED Extension
Q301:
High angle area is not displayed.
Q302:
Does HOLZ lines appear under the projection approximation?
Q303:
Can we calculate a Largeangle CBED (LACBED, Tanaka pattern)?
Q304:
How can we improve HOLZ line accuracy?
STEM Extension
Q401:
An output from STEM image does not seem to represent a model structure.
Q402:
How to select a supercell size?
Q403:
Computation becomes extremely slow, when a model size becomes large.
Q404:
What is a range to be included for scattering calculation? Does this range
depend on the model size?
Q405:
What is a strategy to shorten computation time?
Dynamical Scattering Calculation(MultiGUI)
Q001

How to use
Atom Parameter Editor?



A

1.
Click "Edit" button from Atom
Parameters pane. Then, the following "Atom Parameter Editor" window will
appear. In this example, the parameters for two atoms are already registered.
2.
Input the following parameters for each
atom in separate row.
l
"Name": Atom identifier including an
element name. You can add figure(s) before or after the element name to
identify each atom.
l
"x", "y" and "z": Atom positions in
terms of a unit cell length.
l
"Occupancy": Average probability of
occupying the site (normally one).
l
"Thermal": Thermal parameter, namely
DebyeWaller factor. If this parameter is zero (0), "Overall Thermal Factor"
will be used.
3.
When you finish entering the parameters
for all the atoms, click "OK" to save the data and close the window. You can
click "Cancel" to abort an input at any time.
NOTE You can save atom parameters as a text file by clicking "Export." Then,
you can edit its content easily using your favorite text editor. You can
import atom parameters in a text file using "Import" in the "Atom Parameters"
pane of MultiGUI. Please check also Q023.
Go Back

Q002

How to use
"Occupancy"?



A

"Occupancy" is a probability, with
which the element occupy the site as an average over many unit cells. Since each
element cannot occupy the site in fraction, occupancy is normally one (1).
However, in a disordered structure, for example, a specific site will be
occupied more than one element, and an occupancy of each element becomes less
than one,
For a special atom position, the
symmetry operation generates an atom at the original atom position.
"Multiplicity" (the total number of symmetrygenerated atoms at the same
position) is automatically taken into account by xHREM, so you may not
necessary to set "Occupancy" to 1/"Multiplicity" as sometime required by
other software.
Go Back

Q003

I saw the
example, where an angle of lattice parameter is zero (o)...



A

You can specify an angle in terms of
cosine. Thus, zero means 90 degree. However, you should not mix a degree and
cosine, so a mixed set of three angles, say 0, 0, 120 are not acceptable.
TIPS Cosine of
the angle is used inside the program.
Go Back

Q004

How many
phase gratings can we use?



A

You can use up to 1000 different phase
gratings. The sequence of the phase grating to be used in calculation will be
easily is specified by using "PG Sequence Editor".
Go Back

Q005

How many
slices can we divide a unit cell (or a supercell) into?



A

Since the maximum different phase
grating is 1000, you can divide the unit cell (your model structure) into
1000 slices.
Go Back

Q006

How is a
phase grating (transmission function) evaluated?



A

A phase grating is directly evaluated
by assigning a projected potential of the slice to a complex exponential
function. Here, the direction of potential projection is not perpendicular to
the slice, but along the incident beam direction.
Go Back

Q007

How to
specify the range of scattered waves to be included in the multislice
calculation?



A

The range of scattered waves included
in the multislice iteration is specified by "Range" parameter of "Dynamical
Calculation" pane of the Preferences window.
Go Back

Q008

What is a
slice thickness for [011] or [111] incidence?



A

Normally, the slice thickness is
measured perpendicular to the slice (this is a physical thickness of the
slice). However, the length of a slice measured along the incident beam direction
is more important from electron scattering point of view.
For example, the scattering conditions
are different even for the same incident beam direction of [011], when the
incident surfaces is (001) or (011). xHREM can handle such differences.
xHREM uses the slice that is always
parallel to the entrance surface, but projects the potential along the
incident beam direction.
If you are interested in knowing more details, please
consult the paper:
K. Ishizuka, Acta Cryst. A38 (1982) 773779.
Go Back

Q009

How to
specify an incident beam direction?



A

An incident beam direction t
is specified by three unit cell vectors in the real space as follows:
For example, the incident beam
direction parallel to caxis is defined as [0, 0, 1]. If the incident beam
direction is not specified by a simple sum of three unit cell vectors, it is
not a good condition to take an EM image.
NOTE In an experiment of electron
diffraction, the incident beam direction may be specified by the Laue point,
which corresponds to the Ewald sphere center projected on the observation
diffraction plane.
TIPS Given the incident beam directions
specified in real and reciprocal unit cell
each
coefficient can be easily evaluated as follows:
Go Back

Q010

Why is the
incident beam direction with c=0 not allowed?



A

xHREM assumes that an incident surface
is the (001) plane (the cplane of an input unit cell). Thus, the incident
beam direction with c=0 means that the electron beam is parallel to an
entrance surface, which is not occurred in practice.
TIPS You can specify an incident surface
of the specimen, on which an electron beam impinges. Therefore, using xHREM
it may become possible to treat a surface effect that is usually neglected by
other programs.
Go Back

Q011

How to treat
an incident beam direction with c=0?



A

An incident beam direction with c=0 in
terms of an input unit cell is not accepted (see Q010). To handle this
problem, you can transform the coordinate system from "Preferences" dialog
under Edit menu, and make the entrance surface include the caxis.
MultiGUI takes care of all the
necessary transformations, such as atomic coordinates, symmetry operations,
an incident beam direction and so on, and creates a correct data set for
calculation.
Go Back

Q012

How is an
atom scattering factor for electrons calculated?



A

Atom scattering factor (ASF) can be
chosen from the following two types in the "Atom Scattering Factor" pane of
"Preferences".
DoyleTurner: ASF for electrons is calculated from xray ASF using the
following Mott's formula:
Here, xray ASF is approximated by a
sum of Gaussians, whose coefficients are tabulated in International Tables for xray Crystallography, Vol. IV. It
should be noted that DoyleTurner ASF is valid only up to s=2.0.
WeikenmeierKohl: This form factor is valid also for highangle scattering
beyond s=2.0. Thus, this form factor can be used to estimate absorption
potential due to thermal diffuse scattering (TDS).
Go Back

Q013

Can we use
scatter factor for ions?



A

In principle, the answer is YES.
However, the current GUI does not support such cases, and you have to modify
manually the data (.DA1) created by MultuGUI. Please contact our user support
for detailed steps.
Go Back

Q014

How to
specify a thermal factor (thermal vibration effect)?



A

Effect of thermal vibration is taken
into account by using a DebyeWaller thermal factor.
l When
you want to use a different thermal factor to each atom, you can specify each
thermal factor at "Thermal" column of atom parameters.
l When
"Thermal" parameter of individual atom is zero, the thermal factor specified
at "Overall Thermal Factor" will be applied to that atom,
TIPS For simplicity, you may want to
use the same thermal factor for all the atoms in the model. In this case,
specify the thermal factor in "Overall Thermal Factor" and leave blank (or
set to zero) at "Thermal" column of each atom.
Go Back

Q015

How does
thermal factor affect an atomic scattering factor?



A

An
atomic scattering factor (ASF) is attenuated by a DebyeWaller thermal factor
B as a function of a scattering angle :
You may note that highangle scattering
is more affected by thermal vibration than lowangle scattering.
Go Back

Q016

How do we
use "Unitary test"?



A

Without absorption there is no decrease
of electrons. Thus, the total sum of electron density distribution or
electron diffraction distribution is always constant. However, if an enough
scattering area is not included in scattering calculation, some electrons
tends to scatter outside of the scattering area, and the total sum of
diffracted electrons will decrease with a sample thickness. Therefore,
Australian group introduced the Unitary Test to check calculation conditions
for their reciprocalspace multislice formula.
However, xHREM uses the multislice
formula (in mixedspace) based on Fast Fourier Transform (FFT), and thus the
total sums of both electron density distribution and electron diffraction
distribution are identical, and always equal to unity. Therefore, a usual
way of Unitary Test has no meaning.
The Unitary Test of xHREM calculates
the total sum of electron diffraction distribution excluding intensities at
the outermost pixels. Therefore, if an enough scattering area is not included
in scattering calculation, the total sum of scattering distribution will decrease
with a sample thickness. However, since this attenuation is mild, the Limit
of Unitary Test should be very close to one to make the test effective.
NOTE When you include absorption due to thermal
diffuse scattering (TDS) using WeikenmeierKohl atomic scattering factors, a
number of electrons will actually decrease due to absorption. Thus, if you
don't set the Unitary Test limit sufficiently low, a computation will stop in
the middle of multislice iteration (scattering calculation) owing to the
Unitary Test.
Go Back

Q017

What kind of
propagation function is used in calculation?



A

xHREM uses the propagation function that corresponds to a
spherical wave, not a propagation function with parabola approximation. If
you are interested in knowing more details, please consult the paper: K.
Ishizuka, Acta Cryst. A38 (1982)
773779.
Go Back

Q018

What is
threedimensional effect?



A

Threedimensional effect is such that
relative atom positions along the incident direction of an electron beam
affect scattering intensity distribution.
Go Back

Q019

How to
include threedimensional effect in multislice calculation?



A

Threedimensional effect may be
included in multislice calculation, when relative atom positions along the
incident direction of an electron beam are taken into account by dividing a
unit cell (model structure) into a multiple slices.
NOTE How accurate the multislice
formulation can take into account a threedimensional effect is still an open
question.
Go Back

Q020

How to
specify model symmetry (symmetry operations)?

A

The way to specify symmetry operations
follows the rule used in International
Tables for Crystallography.
l yxz
components of symmetry operation will be separated by a comma (,).
l each
symmetry operation will be separated by a semicolon (;).
l end
of all the symmetry operation is a period (.).
Example:
x, y, z; y, x, z+1/2.
Go Back

Q021

I can't read
atom parameters from a text file.



A

Please make sure that you are
specifying parameter entries in a correct order.
Go Back

Q022

How to
create an atom parameter file (text data)?



A

Input a name, coordinates (x, y, z),
occupancy and thermal factor for each atom in a single line using an editor
or a word processor. A serial number can be added at the beginning
of each line. Each parameter will be separated by a comma (,) or any number
of spaces (blanks). Thus, you don't need to align the column position of each
parameter.
Example
Name  X 
Y  Z  Occupancy  Thermal 
Sn1  0  0  0  1.0  0 
O1  0.307  0.307  0  1.0  0 
NOTE Name should include an element name. You can
add a number to the element name to distinguish different atoms of the same
element.
Save a created data to a text file (samplename.atm).
Go Back

Q023

What is a
format of atom parameter file (test data)?



A

Atom parameter file is a text file,
each line of which contains a name, coordinates (x, y, z), occupancy and
thermal factor. A number can be added at the beginning of each line. Each
parameter will be separated by a comma (,) or any number of spaces (blanks).
Thus, you don't need to align the column position of each parameter.
The order of parameters in the text
file may be arbitrary, since the order of parameters can be specified as
shown below, when you read them.
When atom coordinates are defined in a
physical unit (nm or A), you can change the parameters in a lattice unit by
using "Convert Physical Scale to Fraction." This function is especially
useful, when you create a atomic model using a thirdparty model building application.
Go Back

Q024

How does an
atomic potential contribute to a projected potential?

A

When a whole unit cell is treated as a
single slice (projection approximation), a whole atomic potential will be
projected.
When a unit cell is divided into a
multiple slices, in principle, only the part of potential belongs to a slice
should be projected. However, xHREM will project the whole atomic potential
to the slice, which the center of atom (atom coordinate) belongs to. In this
way, we can use the projection theorem of Fourier transform to efficiently
project an atom potential.
Go Back

Image Calculation(ImageGUI)
Q101

My image
does not show any contrast.



A

Please check an aperture radius for
image calculation. The smallest fringe spacing that will contribute to image
formation depends on the unit (s or d*), which you can select from
"Preferences" window. (Note: 2s = d*)
The smallest fringe spacing = 1/2s = 1/d*
Especially, when you have forbidden
reflections, please check whether allowed reflections are included within the
aperture.
Go Back

Q102

Let me know
the differences between Simulation Modes.



A

Simulation Mode determines the way to
treat partial coherence.
Using xHREM you can choose a commonly
used technique using Envelope functions, or a more elaborate technique using
Transmission Crosscoefficient (TCC).
The technique using TCC, except a small
model, requires more computation time than the technique using Envelope
functions.
Go Back

Q103

When I select
"First Order (Envelope)" from Simulation Mode, I can get a correct image, but
not with "Second order (TCC)".



A

In the case of "Second order (TCC)" the
spatial frequencies of twice of the objective aperture radius will be
included in image calculation. This is because interference terms between
scattered waves that pass the objective aperture should be included in image
calculation.
Thus, "Second order (TCC)" calculation
requires the Fourier space that is twice of the aperture size, although "First
Order (Envelope)" calculation requires the Fourier space that corresponds to
the aperture size. Here, image calculation uses the same area (the same size
of Fourier space) used by scattering calculation.
When the Fourier space used for image
calculation is not enough, "Range" parameter of "Dynamical calculation" pane
should be increased from the "Preferences" window of MultiGUI, and scattering
calculation should be done again. The Fourier space used for image
calculation cannot be modified by changing "Range" from the "Preferences"
window of ImageGUI.
Note Except you don't specify an exceptionally
small "Range" for scattering calculation, this situation will not occur.
Go Back

Dynamical Scattering Amplitude Output(DFOutGUI)
Q201

Why is a reflection
specified using only two indexes? How can we relate these indexes to a normal
threeindex system?



A

Multislice calculation determines
scattering amplitudes using twodimensional slices (Phase Gratings). Thus, a
wave function calculated is twodimensional, and its Fourier transform is
also twodimensional. The two indexes specifies a reflection in 2D reciprocal
space.
This 2D index can be converted to a
normal 3D index by finding a relation between the 3D reciprocal lattice and
the 2D reciprocal lattice. The same technique can be used to find a relation
for Higher Order Laue Zone (HOLZ).
Go Back

Q202

How is the
phase displayed?



A

All
the phases are shifted by ,
and thus the phase of scattered wave from a thin sample corresponds to the
phase of crystallographic structure factor (the phase of the incident wave is
displayed as ).
In
crystallography the phase of structure factor is zero or for the
structure that has a center of symmetry (Namely, the structure factor is
real, and will be positive or negative value). xHREM makes the phase of
scattered wave from a thin sample correspond to the phase of crystallographic
structure factor.
Go Back

CBED Extension
Q301

High angle
area is not displayed.



A

The output range of CBED pattern is
specified by "Range" of "Dynamical Structure Factor" in "Output Control"
pane. Please check the unit (s ot d*) and the specified output value.
Go Back

Q302

Does HOLZ
lines appear under the projection approximation?



A

Yes,
HOLZ lines will appear close to the correct positions even under the
projection approximation. However, their intensities may not be accurate. Go Back

Q303

Can we
calculate a Largeangle CBED (LACBED, Tanaka pattern)?



A

In
LACBED experiment, a sample is placed off the electron beam focus point.
Then, only the transmitted beam selected by an aperture is recorded.
Since
xHREM calculates a CBED pattern by creating the focused probe at the specimen
entrance surface, LACBED cannot be obtained.
Go Back

Q304

How can we
improve HOLZ line accuracy?



A

In
order to get a fine HOLZ line, use a higher "Resolution" of "Calculation
Control" of the CBED dialog. Please consult the CBED Manual for a calculation
step for each resolution setting.
In
order to obtain a CBED pattern with an accurate position and intensity of
HOLZ lines, the 3D effect (see Q019) should be properly included. Thus, a
unit cell should be divided into a multiple slices.
Go Back

STEM Extension
Q401

An output
from STEM image does not seem to represent a model structure.



A

At first, check a projected model
structure using Model Viewer (Model View of MultiGUI). If the projected model
is displayed correctly, then check a scan step. If the scan step is larger
than 0.3 A, you may not get a smoothed atomic structure.
NOTE: If a displayed projected model structure is
not correct, even when input atom parameters and a selected space group are right,
then the symmetry operations of the selected space group may be wrong. If you
find such an error, please report your finding to our support.
Go Back

Q402

How to
select a supercell size?



A

The
size of a supercell determines a sampling interval of Fourier space (an inverse
of supercell size corresponds to a calculation step of scattering
distribution). Therefore, a supercell size of larger than 5 nm (scattering
calculation step of less than 0.2 /nm) should be employed for a good
simulation.
1.
Crystal model
If
a unit cell of the model is less than 5 nm, select "Standard" from
"Supercell size." Then, the input unit cell will be automatically repeated
to create an approximately 5nm supercell. If a unit cell of the model is
larger than 5 nm, select a size of supercell larger than the unit cell.
2.
Interface or a defect model
Select
an appropriate size of supercell that is larger than the longer edge of the
structure model. Other short direction will be automatically repeated to fill
the selected supercell.
3.
Model with no periodicity, such as a
nanoparticle
Select
an appropriate size of supercell that can accommodate the whole model.
Go Back

Q403

Computation
becomes extremely slow, when a model size becomes large.



A

STEM
calculation requires all the phase gratings at each scan point. Therefore,
even when a part of phase gratings cannot be loaded into the mail memory
(RAM), all the phase gratings should be read from an external memory for each
scan points in the case of a large model. Since computation speed of a
contemporary PC is astonishingly fast, a total computation time will be
extremely deteriorated due to this data access.
To
avoid this defect you have to install more RAM. If the total size of phase
gratings becomes more than about 2GM, you may have to use the 64bit version
(STEM Extension Pro) that
supports a 64bit OS to handle more memory.
Go Back

Q404

What is a
range to be included for scattering calculation? Does this range depend on
the model size?



A

In
order to evaluate probe propagation under elastic scattering, calculation
including s=2.5/A (d*=5.0/A) is normally sufficient. This range does not
depend on the model size.
Go Back

Q405

What is a
strategy to shorten computation time?



A

Since
STEM simulation requires scattering calculation at each scan point, a total
computation time tends to become very long. The current version of STEM
Extension supports MultiCPU (core). Thus, if you use a PC with a multiCPU,
you can reduce a total computation time by a factor that is approximately a
number of CPU (Core).
A
further reduction of computation time will be obtained, if you use a cluster
version (STEM Extension Cluster)
that uses multiple computers simultaneously.
Go Back

