TOPAS-Academic V4.1

by Coelho Software

Brisbane, Australia

July, 2007

Australian Business Number

70 827 688 789

Introduction
What's new
What is TOPAS-Academic
Who is it for
Input to TOPAS-Academic
TOPAS-Academic/TOPAS comparison
Pricing
Support
Purchasing
Acknowledgements

Introduction

    Version 4.1 of TOPAS-Academic is now available to degree-granting institutions comprising universities, university run institutes, laboratories and schools. TOPAS-Academic comprises all the functionality of BRUKER-AXS TOPAS operating in Launch mode including all graphics and OpenGL structure editor and viewer. Launch mode is where the full functionality of TOPAS is realized.

What's new

    Charge-flipping (Oszlányi, G. & Süto A. 2005. Acta Cryst. A61, 147-152) implemented with a number of enhancements, these include:

    • Works with powder or single crystal data.

    • Tangent formula can be used in each CF iteration.

    • For powder data the A matrix from a Pawley refinement can be used to attribute intensities to E-values each CF iteration.

    • A new electron density atom picking routine that is both fast and independent of atom size.

    • Can operate in any space group and not just P1.

    • Space group symmetry restraints can be applied to the electron density each CF iteration.

    • Further options include Histogram Matching, Low Density Elimination and the Random Omitting and Insertion of atoms.

    • Real time OpenGL display of electron density with atom picking.

    • Computer algebra control for up to 30 CF parameters.

    Fourier maps

    • For x-ray or neutron single crystal or powder data.

    • Calculated from standard TOPAS INP files with an OpenGL display showing the electron density cloud, structure and picked atoms.

    • Allows for enlargement of the Ewald sphere with Fobs set to Fcalc.

    • Inserts missing reflections within the Ewald sphere with Fobs set to Fcalc

    • Comprises a computer algebra equation that can be a function of Fobs, Fcalc and D_spacing, for example:

      • fourier_map_formula = 2 Fobs - Fcalc;

    For single crystal refinement

    • Implementation of the Flack parameter.

    • Ouput of more single crystal details with phase symmetry considered.

    Improvements

    • Bootstrap errors for fractional coordinates that are a function of a rigid body.

    • Enhanced computer algebra routines whereby 10s of thousands of equations can be loaded and simplified without difficulty. Each node of an equation requires on average 10 bytes of memory.

    • INP files are more rigorously validated, for example, parameter input such as 1/3 are now disallowed; instead an equation such as =1/3; is necessary. In addition parameters that cannot be a function of multivalued parameters are now checked. For example, an x coordinate written in terms of H, K, L etc... will throw an exception. Validation is also performed regarding the type of multivalued parameters used in equations. For example, the fourier_map_formula can only be a function of its multivalued parameters of Fobs, Fcalc and D_spacing.

What is TOPAS-Academic

    TOPAS-Academic is a Windows XP based (or later) general non-linear least squares system driven by a scripting language. Its main focus is in crystallography, solid state chemistry and optimization. At the core of TA is its superb minimization routines wrapped by a computer algebra system; it is this foundation that makes subject dependent modules such as Rietveld refinement shine. The main features include:

    • Computer algebra system for function minimization and for the application of linear/non-linear constraints.

    • A fully functional Rietveld program for laboratory x-ray diffraction, synchrotron, single crystal and neutron fixed wavelength and TOF data.

    • A simulated annealing algorithm for all systems including structure solution in real space from powder, neutron, neutron TOF and single crystal data.

    • An indexing algorithm.

    • A command line program called TC.EXE which comprises the Kernel of TA; used for batch processing.

    Tutorials describing the functionality of TOPAS-Academic, courtesy of John Evans, can be found here.

Who is it for

    TOPAS-Academic is for scientists and PhD students working in the fields of crystallography, solid state chemistry, optimization and function minimization in general. Requests for TA without crystallographic modules or as a teaching aid should be made to the author.

Input to TOPAS-Academic - Writing INP scripts

    Power users of BRUKER-AXS TOPAS use Launch mode where data input is through an editor for writing the input script known as INP format. Equipped with a good editor and help system the writing of INP scripts is straight forward.

    Editors are a personal choice and it would be unwise to expect all users to settle for any particular one. However in an effort to standardize the editing of INP files and to encourage the use of a good editor and the sharing of editor macors the open source editor jEdit (licensed under GNU General Public License, GNU GPL) is recommended.

TOPAS-Academic/TOPAS comparison

    There’s no difference between the kernel of TA and Bruker-AXS TOPAS for the same version number. TA will always comprise the latest kernel.

    There are no differences in regards to single crystal refinement, structure solution, neutron TOF and non-standard Rietveld refinement.

    There are some differences in how data input is handled for peak fitting as seen in the tutorials here.

    For standard Rietveld refinement then TOPAS offers the use of Windows dialogs.

    Indexing is different but on the whole similar - again see the tutorials here.

Pricing

    TOPAS-Academic

    • 700 Euros for a single computer/user license.
    • 400 Euros each for the next 3 additional licenses to the same department.
    • 300 Euros each for the next 3 additional licenses to the same department.
    • 100 Euros each for further additional licenses to the same department.

    Each license will run one instance of the program on a specific computer. More than one person can of course use that computer but not at the same time. Note TA.EXE and TC.EXE can both be run at the same time.

    Previous version 4 customers will receive V4.1 at no charge.

    Previous version 3 customers will receive a 20% discount on a license by license basic.

    VAT is charged for Australian customers only. Universities requiring the filling out of vendor forms, government forms, import/export forms or forms of any type will be charged *** 100 *** Euros per form. Pre-filled forms are not charged for.

Support

    Support regarding suggested techniques and porgram operation is generously given via e-mail. However the whole sale solving of problems requiring sometimes days of work is not support; it is consulting and customers will be charged accordingly.

Purchasing

    Send an e-mail to AlanCoelho@bigpond. Include a university web address displaying your e-mail address. PhD students should supply their supervisor or department's head web and e-mail address. Additional suggestions for verifying your academic status are considered.

Acknowledgements

    BRUKER-AXS for recognisng the needs of the scientifc community and granting permanent use of TOPAS code in TOPAS-Academic.

    John Evans for continuous support, testing and guidance in the development of TA's functionality.


History - V4, October 2006


If you have queries then e-mail AlanCoelho@bigpond.com

please do not download

V3 Skeleton - please do not download

V4.1 Skeleton - please do not download