Prsentation PowerPoint

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McMaille Sous le Capot(Under the Bonnet)

• Le BailUniversité du MaineLaboratoire des
  Oxydes et FluoruresCNRS UMR 6010FRANCEalb_at_cr
  istal.orghttp//cristal.org/

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Content Overview of functionality of the
McMaille (pronounce Mac My)(what does it
do?) Features that differentiate the program
(why/when should I use it?) Summary of
implementation (language, platform, gui/cmd line
- how/where can I use/get it?) Description of
2-3 favorite algorithm/implementation tricks
(what is under the bonnet?)
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No way to escape theindexing bottleneck in the
SDPD maze (figure extracted from the IUCr
monograph 13) SDPD Structure Determination by
Powder Diffractometry
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What does it do ?
Indexing powder diffraction patterns. Using not
only peak positions, also intensities. Applying
the Monte Carlo method in order to generate
randomly cell parameters tested against an
idealized powder profile.
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The columnar peak shapes used by McMaille v3
The width in the automated mode is calculated as
0.3 x ? / 1.54056it depends on the user in
manual mode
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 Simplicity  of the Monte Carlo algorithm in
McMaille
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Features that differentiate the program
(why/when should I use it?)
Good for providing near-complete lists of
 solutions  ordered by R factor (FoM)Cell
volumeMost frequently found cellsLargest number
of peak indexed
But slow Up to 1-15 mn in  black box
mode .Up to 1-15 hours in manual
mode.(depending if monoclinic and triclinic are
examined) To be used if TREOR, DICVOL (etc) fail,
or if you have time or if you love it
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Summary of implementation
Language old good FORTRAN 77Compilers
Compaq Visual Fortran, Intel Visual Fortran,
G77 Platforms Windows (XP, etc), Linuxwill
benefit of dual-core and future multi-core
processors(once the code will be paralellized
project by using the Intel Visual Fortran
compiler) Gui/CMD line CMD line
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Typical  DOS box  with CMD line You just
give the filenameand can stop by typingK
(capital letter),saving all results.
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Where can I get it ? Program download (GNU
Public Licence) http//www.cristal.org/McMaille/
Everything is there(executable, Fortran code,
manual, examples)
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How can I use it ?
The first recommended approach with McMaille is
to use the quite simple automated  black box 
mode. Peak positions and intensities can be
extracted by using the WinPlotr program which is
able to build the McMaille entry data file
directly for the automated mode.
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If the peak positions are extracted by WinPLOTR,
an entry file is directly prepared for McMaille
for an automated run.
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Y2O3! Wavelength, zeropoint and NGRID (NGRID3
black box mode)1.540560 0.000 3! List of
2theta positions, intensity (min.20)
20.50481 1411.71155 29.15784
11198.95700 33.79123 2632.66553
35.91046 531.02966 37.92135
135.21042 39.84880 606.23480
41.70092 118.49068 43.48877
881.15845 46.88918 271.40564
48.52835 4213.47021 50.12016
230.08562 51.68559 66.62399
53.20726 506.43854 54.69715
117.27492 56.16987 404.76215
57.61465 2603.39868 59.03540
563.80334 60.43375 471.21359
61.81146 194.23712 Etc
Typical file created by WinPLOTRforMcMaille
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Description of 2-3 favorite algorithm/implementati
on tricks (what is under the bonnet?)
Simplicity of use in black box mode (contains an
internal expert system presenting ordered lists
of possibilities according to several
criteria) Is a kind of Swiss knife for indexing
You may look deeply at selected possibilities
by using the alternative grid search mode (if
ambiguity on one parameter, etc). You can try
multi-pattern indexing.
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Final plot produced by McMaille, displayed by
WinPLOTR
with Gaussian peak shapes and width / 2.
Other software compatible with McMaille outputs
CHEKCELL, CRYSFIRE
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Compatibility with Chekcell
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Relative insensitivity to impurity
The user decides by two control parameters in
manual mode N number of unindexed lines ( 3
in automated mode). R2 consider only proposals
with R lt R2. Fixing it at 15 means that cell
proposals explaining at least 85 of the peaks
total intensity will be listed. An impurity
should not concern more than 15 of the total
intensity, right ? But the number of (small)
peaks belonging to the impurity can be high
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Indexing a 2-phases powder pattern with McMaille
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Preliminary conclusions about two-phases indexing
with McMaille Provided at least 30 lines are
examined with 13-17 lines belonging to each
phases, and 40-60 of the total intensity
distributed to each phase, then McMaille
appears to be able to produce solutions in
reasonable times (lt1 hour) for combinations of
two phases either cubic or hexagonal or
tetragonal or orthorhombic. Monoclinic and
triclinic not examined (too long).
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Example of 2-phases indexing (20 minutes) One
mixture of a tetragonal with an orthorhombic
phaseMcMaille combines the cell proposals by
couples and detects the best combinations
indexing the largest number of peaks
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Last publication from Robin Shirley et al.
 Renewed interest in powder diffraction data
indexing , J. Bergmann, A. Le Bail, R. Shirley
and V. Zlokazov, Z. Kristallogr. 219 (2004)
783-790.
From the indexing benchmarks Do not limit
yourself to only one indexing software
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• Conclusions about McMaille
• - Promising (?) method (please verify)
• Already quite efficient if you have time and a
  fast computer.
• Needs some skills in manual mode, but nothing to
  do in black box   mode (except finding the
  zeropoint).
• Improve it if you have some ideas (GNU Public
  Licence).
• Completely free access.
• Use cautiously the 2-phases mode