by Coelho Software
Australian Business Number
70 827 688 789
Version 5 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
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 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.
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
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)
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
For standard Rietveld refinement then TOPAS offers the use of Windows dialogs.
Indexing is different but on the whole similar - again see the tutorials
Pricing - Single computer/user licenses on a departmental basis
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;
TA.EXE and TC.EXE however can both be run at the same time. 10% VAT is charged for Australian customers only.
- 1250 Euros for first license
- 425 Euros for each additional license
Version 4.1 users upgrading to Version 5
- 700 Euros for first upgrade license
- 250 Euros for each additional upgrade license
A fee of 200 Euros is charged for license transfers for computer upgrade reasons after an initial 2 year period
- 1000 Euros for first license
- 400 Euros for each additional license
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.
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.
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 - V4.1, October 2007
History - V4, October 2006
Version 4 is a huge step forward in almost all areas, some of these include:
Overall speed has increased and refinement convergence improved. All refinements should converge
in a more robust and often quicker manner. This is due to an
automatic Marquardt constant determination and the calling of the very fast BCCG
routine twice to solve the normal equations were parameter limits violated.
A completely rewritten version of the BFGS method
for approximating the Hessian matrix. This Quasi-Newton method has been
modified to dampen changes in the system
in early iterations of a refinement. It converges better in cases where
the minima is far off. It's convergence in general on smaller structure refinement problems
is comparable in time to that of the fully calculated Hessian matrix.
Together with a reworking of the automatic parameter removal scheme
structure solution can now progress at a rapid pace. Version 4 solves structures that version 3 could not.
The BFGS method together with aggressive memory conservation techniques now allow
for refinements comprising tens of thousands of parameters. Refinements of this sort were
not possible with version 3.
The bootstrap method of error determination has been implemented; it can be used to
determine esds and in particular errors can be estimated for very large problems
where matrix inversion is impractical.
Reworked simulated annealing and automatic temperature regime algorithms
that in most cases finds the global minima far quicker than before. In many cases the
new version finds global minima missed by the previous version.
Faster and more accurate convolutions in most cases.
New convolutions for describing peak shapes resulting from the use of linear position sensitive detectors
and capillaries. Each of these convolutions corrects for peak shape, peak position and peak intensity.
The inclusion of torsion angle penalties to complement previous distance and angle restraints.
Improved convergence for phase penalties. Preliminary tests have shown that only
nine phase penalties are required to solve a centrosymmetric structure comprising 43 atoms in the
asymmetric unit in a period of minutes. Further tests indicate that phase penalties
can be used to determine phases from non-centrosymmetric structures.
The Cloud - an atomic position averaging techniques that allows for the visual display of atomic movements.
High density positions in the cloud can be searched and atomic positions extracted. Good for locating heavy elements
or tracking atomic movements in general.
A greatly improved Rigid Body Editor that can load and overlay rigid bodies, structures, clouds and INP files.
An improved indexing algorithm that is both faster and more likely to find the right solution.
If you have queries then e-mail AlanCoelho@bigpond.com
V5 Skeleton - please do not download
please do not download
V4.1 Skeleton - please do not download