Electron Direct MethodsEDM 3.2L. D. Marks

Northwestern UniversityAcknowledgements

Roar Kilaas, Chris Own, Kenji Tsuda, Fu-Rong Chen, Bin Deng, Wharton Sinkler, Jim

Rondinelli, James Ciston

Concept

A strength of x-ray diffraction is that all one has is numbers, not images– Makes computer analysis the obvious approach

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

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

Code should run on all systems– Unix base; cygwin for windows– Xwindows interface

Code should be simple to install– autoconf/automake structure– g77, gcc base (autoconf handles messy details)

Code should be maintainable by the wider community– List server– Cvs structure

Choice

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

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

Direct Methodsfs98

GUINCEM Code

Intensity Measurement(Semper)

EDM 1.0

MaxEnt Image Restoration (beta)

EDM 3.2

Direct MethodsNUMIS

Multislice

Intensity Measurement

EDM 3.0Structure

Completion(Kinematical)

NCEMSSMultislice

DynamicalRefinement

(beta)

CBED(MBFIT)

MaxEnt Image Restoration (beta)

Towards a unified platform

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

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

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)

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

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

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

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

A very brief introduction…