MEGACELL: A nanocrystal model construction software for HRTEM
multislice simulation
Daniel G. Stroppa*, Luciano A. Montoro, Ricardo D. Righetto, Antonio J. Ramirez
Brazilian Synchrotron Light Laboratory, 13083-970, Campinas, SP, Brazil
*dstroppa@lnls.br
Intro:
This document contains the support information for MEGACELL software. It includes the
disclaimer, the technical information and the user’s manual for MEGACELL 1.1. Please contact
the corresponding author if additional information is required. MEGACELL files are available at
http://megacell.lnls.br
1. Disclaimer
MEGACELL may be freely distributed and edited as open-source citation-ware
software, provided that no charge above the cost of distribution is levied, and that this
disclaimer text is always attached to it. Please contact the corresponding author for including
any substantial improvement made on MEGACELL code on the updated versions.
Please consider using the following citation if MEGACELL application provided relevant
support: “Stroppa, D. G.; Righetto, R. D.; Montoro, L. A.; Ramirez, A. J.; MEGACELL: A
nanocrystal model construction software for HRTEM multislice simulation, Ultramicroscopy,
2011, doi:10.1016/j.ultramic.2011.03.013.”
MEGACELL is provided as is without any guarantees or warranty. Although the authors
have attempted to find and correct any bugs in it, the authors are not responsible for any
damage or losses of any kind caused by the use or misuse of MEGACELL. The authors are under
no obligation to provide support, service, corrections, or upgrades to MEGACELL. For more
information, please send an email to the corresponding author.
MEGACELL development was related to D. G. Stroppa Ph.D. thesis work at State University
of Campinas. This project was funded by FAPESP and supported by LNLS.
2. Technical features
2.1 Programming Language
MEGACELL was fully developed in the MATLAB platform.
2.2 Compatibility
MEGACELL is available as a 32-bit standalone executable for the Microsoft Windows
2000/XP/Vista/7 platforms, in which it was tested and assured to run. This executable was
generated with the MATLAB Compiler toolbox. Also, the megacell.m file (as well as its auxiliary
functions) is available, which can be edited and executed in MATLAB, regarding the MEGACELL
disclaimers. Although MEGACELL is not readily compatible with GNU Octave, this compatibility
might be achieved with some minor changes in the code and relaying of the graphical user
interface.
2.3 Known Issues
MEGACELL may be incompatible with outdated MATLAB versions. The oldest MATLAB
version in which MEGACELL was tested is R2009a.
2.4 Release notes
Version 1.1:
- Inclusion of .xyz input file support.
- Inclusion of the bbox_factor on the parameter input file.
- Graphical user interface update
2.5 Install instructions
The executable (.exe) version of MEGACELL requires the MATLAB Compiler Runtime
Environment installation. This compiler is included on the self-extracting package
(megacell_pkg.exe).
2.5.1 MEGACELL standalone executable installation
1.
Copy the MEGACELL self-extracting package (megacell_pkg.exe) to the desired
path on your local machine;
2.
Execute it from there; All the files contained in the package will be extracted to
the current location;
3.
The installation of the MATLAB Compiler Runtime Environment will begin
automatically. Follow the instructions;
4.
MEGACELL is ready to run just by clicking megacell.exe!
2.5.2 MEGACELL source code installation
1.
Extract the megacell_source.zip file to the desired location;
2.
Open MATLAB;
3.
Point MATLAB path to the MEGACELL location;
4.
Type megacell in the MATLAB command line to run the program;
The MEGACELL source code can be edited from the MATLAB Editor or any other preferred
text editor;
3. Basic instructions
3.1 MEGACELL standalone executable
1.
Run MEGACELL.exe - the following interface will be loaded;
2.
Proceed to the software interface by clicking on I Agree - the following interface
will be loaded;
3.
Browse the input parameter file on the upper field;
4.
Select the supercell output format;
5.
Click “Generate File”;
The output files will be placed on the same folder as the input text file. A complete
description for the input text file is presented on Section 4.
4. Construction stages
The nanocrystal model construction by MEGACELL is performed according to the
parameters informed by the user on the input text file, which is thoroughly discussed in this
chapter subsections. The input file parameters description is divided among the MEGACELL
construction steps, which are depicted on software workflow in Figure 1.
Figure 1: MEGACELL simplified workflow. The operation blocks are highlighted on bold boxes.
4.1 Unit Cell definition
The Unit Cell operation block retrieves the unit cell information and stores it for the
subsequent steps. Firstly, the unit cell general information is retrieved from the [Unit Cell]
subsection as depicted in Table 1.
Table 1: Unit Cell general information input in the [Unit Cell] subsection
General layout
Example
Comments
name = sample
name = Si_x
sample is the project name and the generated files prefix
n_atoms = N
n_atoms = 18
N is the number of atoms within the unit cell
a=A
a = 0.5431
A is the a lattice parameter in nanometers
b=B
b = 0.5431
B is the b lattice parameter in nanometers
c=C
c = 0.5431
C is the c lattice parameter in nanometers
alpha = D
alpha = 90
D is the alpha lattice angle in degrees
beta = E
beta = 90
E is the beta lattice angle in degrees
gamma = F
gamma = 90
F is the gamma lattice angle in degrees
Secondly, the atoms relative coordinates within the unit cell are retrieved from the input
text file subsection named [Atoms Coordinates]. Each atom coordinates are informed
relatively to the lattice parameters and range from 0 to 1 for each axis, as exemplified on Table
2.
Table 2: Atoms relative coordinates input in the [Atoms Coordinates] subsection
General layout
Example
Comments
tn = Z
t1 = Si
n are integers ranging from 1 to N; Z is the atom type
xn = x0
x1 = 0
x0 is the relative coordinate of the atom n in the a axis
yn = y0
y1 = 0
y0 is the relative coordinate of the atom n in the b axis
zn = z0
z1 = 0
z0 is the relative coordinate of the atom n in the c axis
4.2 Supercell
The Supercell operation block generates a supercell structure, which is a combination of
unit cells replications along the space and cuts steps. Note that all the operations in this
section are performed on the points space, which is equivalent to consider the lattice
parameters equal to 1 and the lattice angles equal to 90. The application of lattice parameters
and angles is only performed on the Real space operation block.
4.2.1 Block Building
The Block Building operation generates block with dimensions l x m x n (unit cells) by
replicating the unit cell along the Cartesian directions (x; y; z) according to the [Supercell]
subsection, as exemplified in Table 3. The constructed block is centered at the (0,0,0) position
and each atomic position is checked in order to prevent duplicated atoms.
Table 3: Input for the [Supercell] subsection
General layout
Example
Comments
bulkx = l
bulkx = 8
l is the block dimension in unit cells along the x axis
bulky = m
bulky = 8
m is the block dimension in unit cells along the y axis
bulkz = n
bulkz = 8
n is the block dimension in unit cells along the z axis
bbox_factor = bb
bbox_factor = 0.8
bb is the final supercell fraction occupied by the model
4.2.2 Symmetric Cuts
The Symmetric Cuts operation crops the atomic positions which are beyond the cutting
planes specified by the user on the input text file section named [Symmetric Cuts]. As this
operation performs cuts in the first octant (x ≥ 0; y ≥ 0; z ≥ 0) and automatically executes
mirrored cuts for the other octants, this routine should only be used when the desired cuts can
be described with a 4m symmetry. The Asymmetric cuts operation is indicated for any other
cutting operation.
The input information for the Symmetric cuts routine defines the cutting planes using the
crystalline plane notation and the distance from the origin. An example for the input
information is shown in Table 4 and the geometric relationships for a {110] cut is depicted in
Figure 2.
Table 5: Symmetric cuts input in the [Symmetric Cuts] subsection
General layout
Example
Comments
cuts = h
cuts = 1
h is the number of cuts in the first octant
wxh = xs
wx1 = 1
xs is the a Miller index for the specified cut plane
wyh = ys
wy1 = 1
ys is the b Miller index for the specified cut plane
wzh = zs
wz1 = 0
zs is the c Miller index for the specified cut plane
wdh = ds
wd1 = 4.5
ds is the specified cut distance from the origin in unit cells units
Figure 2: Dimetric view (left) and top-view (center) from a symmetric cut plane designation
example. It was considered an 8 x 8 x 8 unit cells building block, a (110) cut plane and a cut
distance equal to 4.5 unit cells units. The cut result is shown after the 4m symmetry operations
(right).
4.2.3 Asymmetric Cuts
The Asymmetric Cuts operation crops the atomic positions which are beyond the cutting
planes specified by the user on the input text file section named [Asymmetric Cuts]. As this
operation perform cuts using a planes defined by sets of three points in the space, any convex
polyhedral shape can be obtained. The only restriction this operation presents is that (0, 0, 0)
cannot be used as a reference point for the cut planes.
An example for the input information is shown in Table 5 and a cut example is depicted in
Figure 3.
Table 6: Asymmetric cuts input in the [Asymmetric Cuts] subsection
General layout
Example
Comments
cuts = j
cuts = 1
h is the number of asymmetric cuts
x1j = x1
x1j = 5.0
x1 is the x coordinate for the first point used to define the cut plane
y1j = y1
y1j = 5.0
y1 is the y coordinate for the first point used to define the cut plane
z1j = z1
z1j = 3.0
z1 is the z coordinate for the first point used to define the cut plane
x2j = x2
x2j = 4.0
x2 is the x coordinate for the second point used to define the cut plane
y2j = y2
y2j = -1.0
y2 is the y coordinate for the second point used to define the cut plane
z2j = z2
z2j = 5.5
z2 is the z coordinate for the second point used to define the cut plane
x3j = x3
x3j = -5.0
x3 is the x coordinate for the third point used to define the cut plane
y3j = y3
y3j = 2.0
y3 is the y coordinate for the third point used to define the cut plane
z3j = z3
z3j = -1.5
z3 is the z coordinate for the third point used to define the cut plane
Figure 3: Dimetric view from an asymmetric cut plane designation example. It was considered
an 8 x 8 x 8 unit cells building block and the cut coordinates exemplified in Table 6.
4.3 Real Space
The Real Space operation converts the system coordinates from the point space to the
real space, considering the lattice parameters and angles informed on [Unit Cell] section on
the text input file. This process is a linear operation that can be described by four matrix
operations. The first one is the lattice expansion and is represented by matrix A on Figure 4.
The three next operations are related to the lattice angles consideration, which is evaluated as
rotation operations separately for each axis and are depicted by Matrices α, β, γ on Figure 4.
Figure 4: Matrices used to describe the point space to real space linear transformation. a, b, c
are the lattice parameters and α, β, γ are the lattice angles from the unit cell.
4.3.1 Zone Axis
The Zone Axis operation performs a rotation operation for each atomic coordinate
relative to the supercell center in order to orientate the construction according to the zone
axis informed by the user on the input file subsection named [Zone Axis]. The chosen zone axis
is aligned to the original Cartesian z axis on the point space.
An example for the zone axis input information is shown in Table 7 and some orientation
examples are depicted in Figure 5.
Table 7: Zone Axis input in the [Zone Axis] subsection
General layout
Example
Comments
zax = zx
zax = 0
zx is the a Miller index related to zone axis orientation
zay = zy
zay = 0
zy is the a Miller index related to zone axis orientation
zaz = zz
zaz = 1
zz is the a Miller index related to zone axis orientation
Figure 5: Examples of different zone axis orientations for a given supercell geometry.
4.4 Normalization
The Normalization operation rewrites the atomic position as a function of the supercell
total dimensions after the orientation step. This operation is necessary for generating the EMS
supercell input file, as well as a consideration that avoids atomic positions on the edges of the
structure in the relative coordinates. No changes on the input text file are required as this
operation is automatically performed as a function of the supercell dimensions.
4.5 Multislice
The Multislice operation segments the supercell file in m slices along the zone axis
direction according to the specification given by the user on the input file section named
[Multislice]. The slices thickness is given by the dimension of the supercell along the zone axis
direction divided by the number of slices. An additional normalization step is performed in
order to avoid the existence of atomic positions at the slices’ edges.
An example for the multislice input information is shown in Table 8.
Table 8: Zone Axis input in the [Zone Axis] subsection
General layout
Example
Comments
n = mn
n = 32
mn is the number of slices to be generated on the Multislice operation
4.6 Export
4.6.1 Raw Data
The Raw Data export operation takes place just after the Zone Axis operation and
generates a text file with the Supercell atomic positions in the real space. The output file
format is .xyz, which is exemplified in Table 9. Table 10 presents a brief list of softwares that
can import .xyz files for the supercell visualization.
Table 9: Example of a Raw Data export file in the .xyz format
Line
General layout
Example
Comments
1
Ntot
500
Ntot is the total number of atoms on the supercell
Z is the atomic type and xr, yr, zr are the atoms
n
Z ; xr ; yr ; zr
Si ; 1.2 ; 3.1 ; 0.0
coordinates in nm. n goes from 2 to N+1
; is a tabulation character
Table 10: Softwares for .xyz files visualization
Name
Link
Comments
Vesta
http://www.geocities.jp/kmo_mma/crystal/en/vesta.html
Citation-ware
Avogadro
http://avogadro.openmolecules.net/
Freeware, Open source
CrystalMaker
http://www.crystalmaker.com
Proprietary software,
demo freely availabe
4.6.2 EMS
The EMS export operation takes place after the Normalization operation for
generating a text file with the Supercell atomic positions in the real space, and after the
Multislice operation for generating the multislice files. The output file format is .txt with an
adequate header and atomic positions description for EMS HRTEM simulation software.
Additional information about the atomic species may be informed on the [Atom Type]
subsection on the input file according to the example shown in Table 11. Appendix 1 contains
an example file depicting the EMS header and atom input example.
Table 11: Atoms information input in the [Atom Info] subsection
General layout
Example
Comments
num_types = Na
num_types = 2
Na is the number of different atomic species in the unit cell
atomtypena = Z
atomtype1 = Ce
Z is the atomic type
occ1 = o
occ1 = 1
o is the occupancy value for the given atomic specie
dw1 = w
dw1 = 0.004
w is the Debye-Waller factor for the given atomic specie
abs1 = s
abs1 = 0.004
s is the absorbance for the given atomic specie
4.7 Raw files (.xyz) import
The construction of complex models from the combination of simpler ones is partially
supported by MEGACELL. A function the .xyz file path allows the user to load models and to
generate supercells according to EMS or Dr. Probe standards. This feature allows the user to
edit the simpler models to a complex structure and then load it again into MEGACELL. The
basic steps are:
1. Initial models construction; export .xyz format;
2. Edition and combination of the .xyz files using a text editor or custom script;
3. Browse a modified parameter input file including all the atomic species ([Atom Info]
section) contained on the final .xyz file;
4. Browse the final .xyz file;
5. Select the supercell output format;
6. Click “Generate File”;
Appendix 1: EMS format example
file|G:\HAP_TESTE.txt
name|HAP_TEST
creator|dstroppa
date|Tue Dec 07 11:02:50 BRST 2010
system|triclinic
superCell|false
HMSymbol|1|1|0|0|0| P 0
rps|0|x , y , z
lattice|0|8.6458
lattice|1|5.4362
lattice|2|2.2905
lattice|3|90.0
lattice|4|90.0
lattice|5|90.0
atom|0|Ca,_,0.390902,0.300178,0.200,0.005,1.000,0.041,Def,2
atom|1|Ca,_,0.336355,0.450437,0.200,0.005,1.000,0.041,Def,2
atom|2|Ca,_,0.281809,0.600696,0.200,0.005,1.000,0.041,Def,2
atom|3|Ca,_,0.227262,0.750955,0.200,0.005,1.000,0.041,Def,2
atom|4|Ca,_,0.499995,0.300178,0.200,0.005,1.000,0.041,Def,2
atom|5|Ca,_,0.445448,0.450437,0.200,0.005,1.000,0.041,Def,2
atom|6|Ca,_,0.390902,0.600696,0.200,0.005,1.000,0.041,Def,2
...
atom|n|Z,_,x,y,z,s,o ,w,Def,2