Electron Direct Methods
EDM 3.2
L. D. Marks
Northwestern University
Acknowledgements
Roar Kilaas, Chris Own, Kenji Tsuda, FuRong Chen, Bin Deng, Wharton Sinkler, Jim
Rondinelli, James Ciston
Concept
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A strength of x-ray diffraction is that all one has is
numbers, not images
– Makes computer analysis the obvious approach
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A weakness of TED/TEM is that images look
good, and there is a lack of widely available
software for analysis.
Codes, where available, are often expensive,
require strings of numbers to be input by hand,
and cannot talk to each other
EDM Philosophy
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Attempt to create software using the Open
Software (GNU) model
Code is free, but comes with no guarantees
Because this program is licensed free of charge, there is no warranty
for the program, to the extent permitted by applicable law. Except
when otherwise stated in writing the copyright holders and/or other
parties provide the program "as is" without warranty of any kind,
either expressed or implied, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose.
The entire risk as to the quality and performance of the program is
with you. Should the program prove defective, you assume the cost of
all necessary servicing, repair or correction.
http://www.numis.northwestern.edu
CVSROOT=":ext:XXX@129.105.122.84:/home/cvsroot
Philosophy & Strategy
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Code should run on all systems
– Unix base; cygwin for windows
– Xwindows interface
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Code should be simple to install
– autoconf/automake structure
– g77, gcc base (autoconf handles messy details)
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Code should be maintainable by the wider
community
– List server
– Cvs structure
Choice
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For code, g77 and gcc, g++ GNU base as close to a
standard as one can get (although g77 is close to being
retired)
For display, X-windows
For PC’s, cygwin (commonly used to create utilities)
For file/directories, forms library (included with edm)
For fft’s, fftw library, included with edm since it keeps
changing (needs to be updated)
For Help, file browser (netscape/firefox/wordpad or
whatever) – let the OS handle this
GNU Automake/Autoconfig
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Long term maintenance/portability is a 99%
solved problem
– Autoconf: finds parameters, file locations etc
for the user’s computer
– Automake: creates “Makefile” which is
customized to a given computer
Initial Framework
GUI
NCEM Code
Direct Methods
fs98
EDM 1.0
Intensity Measurement
(Semper)
MaxEnt Image
Restoration (beta)
EDM 3.2
Direct Methods
Structure
Completion
(Kinematical)
Intensity
Measurement
NCEMSS
Multislice
EDM 3.0
CBED
(MBFIT)
NUMIS
Multislice
Dynamical
Refinement
(beta)
MaxEnt Image
Restoration (beta)
Towards a unified platform
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Inverse Analysis
Image Processing Fourier
Averaging
– Wiener, Parametric filters
Phase Recovery
– Linear: Shiske, Wiener
– Non-linear, e.g. Wavefront
Direct Methods Chemical
Composition
– EDX, EELS
Symmetry
– CBED (beta), Precession
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Forward Analysis
Simulation
– Multislice (NUMIS/NCEMSS)
– Bloch Wave (Mbfit)
– Non-linear Imaging
– CBED (Mbfit)
– Precession (NUMIS)
Fitting
– Dynamical Refinement (present
but unfriendly)
DFT
– Wien2K (hkl input to NUMIS)
Contributors
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Original Code
– LDM + Roar Kilaas
Documentation (Chris Own, Jim Rondinelli)
Cell generalization + 3D phases (Wharton Sinkler)
CBED (Kenji Tsuda + Bin Deng)
Wien2k DFT input (Bin Deng)
NUMIS port (Jim Ciston)
C++ fix for NCEMSS (Volunteer needed)
Substantive Changes (2011)
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More accurate intensity measurement code
More user friendly with better unix integration
Can be used to do all steps of a structure analysis
(in 2D, 3D framework exists)
Can be used to do a dynamical refinement (beta,
needs some help from someone)
Can simulate CBED patterns
Better direct methods algorithm (same as fs2002)
Maintenance Structure
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cvs (tracks changes) at one central location, see
http://www.numis.northwestern.edu/Software
Anyone can download a version, compile under
windows (cygwin) or unix.
Users can submit patches by email.
Maintainers can make changes to the main
distribution.
Example
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Kenji Tsuda (Tohoku, Japan) makes a change in
the output for CBED, debugs it, commits it to the
cvs.
Bin Deng (Northwestern) updates the
documentation to reflect this and commits this to
the cvs.
Computer automatically creates updated files (cvs
& cron).
Thomas White (Cambridge) and Mohandas
Eladath (IGCAR, India) download and install the
latest version.
Recently Added
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Numis 2.0 code
– Calculates precession diffraction intensities
– Interfaced to Wien2k all-electron DFT code so
charge density effects can be completely
included
– Can do CBED with charge density, also
imaging
Extensions ?
Diffractive Imaging (Russell Luke)
 Integrate other image types (e.g. gif, DM)
 Integrate HOLZ or similar measurements
 Documentation
 Other Direct Methods Approaches
 Two-beam codes & Bloch Wave methods
 Charge Density Analysis
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A very brief introduction…