Crystal Menus
Crystal Unit Cell & Spacegroup
Crystal Scattering Powers (atom types)
To import such a matrix, you must first create an empty ZScatterer,
then use the ZScatterer 'File'->'Import Fenske-Hall Z-Matrix'.
The easiest way to generate this file is to use babel or openbabel, to convert another format (pdb) to this Fenske-Hall Z-matrix. For example, use "babel -ipdb cime.pdb -ofhz cime.fhz -d" to convert the 'cime.pdb' file to 'cime.fhz', while removing all hydrogens.
Note1: that you do not need to declare the ScatteringPowers first, they will be automatically added if necessary.
Note2: after importing, all parameters are set with tight limits, so that the molecule is almost rigid.
Single Crystal Diffraction DataPowder Menus Radiation
- "Data" allows to import several types of data. If you wish to add another format, send an email to me with an example data, and saying why you think it is important that this format is supported. You can also save the calculated and observed spectra, and use the 'simulation mode', which will use a dummy observed pattern (I=1. in all points).
- "Parameters" allows you to fix all parameters. Note that only preferred orientation parameters and the global temperature factor are refinable anyway.
- "Components" is the menu to describe your powder pattern in terms of the sum of components, which can be one interpolated background, and any number of crystalline phases.
- "Radiation" allows you to choose the radiation for your experiment. It is also possible to use the radiation interface just below the menus, but to choose an X-Ray tube it is easier that way (unless you know by heart the delta-lambda !). Do not forget to input the correct polarization rate (0.95 typically for a synchrotron experiment).
- "Pattern" allows you to open the graph window with the observed and calculated patterns, and to fit the scale factor. It is also possible to add "excluded 2-theta zones" which will be ignored during global optimization: you will be prompted for the minimum and maximum 2theta values of the region to ignore (to remove thos region, you have to edit the xml file).
Here you can describe the radiation corresponding to your experiment (neutron, X-Ray, tube,...). The wavelength is in Angstroem as usual. Set the polarization rate between 0.95 and 1 for synchrotron experiments, and 0 for an X-Ray tube (actually if you use a monochromator it should be above 0, but a precise value is not critical for a global optimization).2theta correction parameters
These parameters allow to correct for experimental errors in the 2theta positions of reflections, due to a wrong zero, or a misplacement of the sample holder or its transparency. Practically, using the 2theta zero is sufficient (note that it does not necessary correspond to the convention used by other programs, you may have to change the sign and/or to multiply by 2 the value). After each change, you can right-click on the powder pattern graph to update it.Maximum sin(theta)/lambda
Use this field to limit the extent of the calculations on the powder pattern. It is usually a very good idea to do that, since for a global optimization, high-angle data is useless. A good value is 0.25 Angstroem-1 (corresponding to a resolution of 2 Angstroems), although you can go higher to 0.4 A-1 if you feel there are not enough reflections...Powder Pattern Background
So far the background can only modelized using linear interpolation between at user-chosen 2theta values. To input the (2theta, intensity) points you must create a text file with a list of "2theta intensity" on each line (2theta in degrees), and load it using the menu. See the tutorials for examples.If you want to change the points, just change the values in the text file, and reload it from the menu.
There is currently no limit to the number of points, but even for complex backgrounds 10 should be enough.
PowderPatternDiffraction
This allows to describe the contribution of a crystalline phase to the powder pattern.
It is possible to save the calculated structure factors using the menu (note that structure factors above the chosen sin(theta)/lambda limit are not calculated).Profile parameters
These are the usual profile parameters:Crystal choice
- U V W defining the width using Caglioti's law (W is the constant width, which is generally sufficient if you are using integrated Rfactors as recommended)
- A pull-down menu allows you to xhoose between Gaussian, Lorentzian and pseudo-Voigt.
- Eta0 (constant) and Eta1 (theta-dependant) define the mixing parameter for a pseudo-Voigt profile.
You are asked to choose a crystal structure upon creation of the PowderPatternDiffraction object. You can change it afterwards by clicking on the crystal name.
Global Biso
This can be used as a global temperature factor for this crystalline phase (affects all atoms). This is refinable, although it slows the optimization without helping a lot.
Texture (Preferred Orientation) using the March-Dollase Model
FOX supports optimization of Preferred orientation, usign the March-Dollase model. To add one phase, use the "Phases" local menu. You can then enter the fraction, March coefficient (>1 for needles, <1 for plate-like crystallites), and HKL coordinates for the preferred orientation.Note: it is very important to use this only as a last resort, or if you know for sure that you have preferred orientation. Taking one more day to prepare carefully a non-textured sample is definitely worth it, since even if a solution is found, it will be much slower - preferred orientation reduces the information available in some direction of the crystal.
If you finally decide to search for preferred orientation parameters, it is recommended to input as much information as possible. For example, you should be able to know what kind of preferred orientation to expect (plates or needles), so that you can restrict the March coefficient to be either >1 or <1 (e.g. use limits [.1;1] or [1;10] - never go below .1 or above 10, that would just slow things). If you know what the preferred orientation vector is, that's even better.
Note that it is possible to use several preferred orientations, but I strongly discourage to do this for a global optimization.
MenusGlobal Optimization Algorithms
You can use the menus to load data from a text file (either four columns H K L Iobs, or five columns H K L Iobs sigma). If you do not have data, you can also use the "simulation mode" and generate a full list of H K L up to a given 2theta value.
Finally, you can export the structure factors in a text file.Twinning option
This is a "hack" to have a very basic handling of twinned single crystal data. If selected, comparison between observed and calculated intensities will not be made on individual reflections, but on the sum of intensities of reflections with approximately identical 2theta angle (i.e. not only equivalent reflections).
This allows to search for a crystal structure without any knowledge on the type of twinning, effectively handling the data as "powder data", but without any computing penalty.Radiation
Same as for powder pattern...
Crystal
You can click on the crystal name to change the crystal structure associated to this data.
Maximum sin(theta)/lambda
Same as for powder pattern...
Algorithm
You can choose between Parallel Tempering (highly recommended) and
Simulated Annealing (use this only if you know how... you'd have to carefully
choose the number of trials). Normally, the default choice (Parallel Tempering)
should not be changed.
Temperature
These are the minimum and maximum temperatures to ensure that the algorithm
will search all possible configurations, while insisting on the best configurations.
It is highly recommended not to change the default choices, with a "smart"
temperature schedule which will be tuned by the algorithm.
Displacement amplitude
These are used to define the amplitude of displacements of all parameters
during random moves. Again, you should not change the default parameters
which should be fine for any optimization, with an exponential schedule.
Autosave
This allows you to save regularly the "best" configuration reached
by Fox. Note that the saved xml files will always be in the working directory
(i.e. the one from which you launched FOX, or the directory of the FOX
application).
Trials
Put here the total number of trials that you want to make. For Parallel
tempering, you can put a large number (100 000 000), and then stop manually
the algorithm when it seems to have converged (the algorithm has the advantage
of being invariant with the number of trials). (for simulated annealing,
you need to more carefully evaluate the number of trials for your specific
configuration...).
Objects
This is the list of the objects optimized, which have een added through
the menu.
Cost function(s)
Here is displayed the cost function name and the associated value,
and the weight associated to it. The overall cost function is the weighted
sum of all cost functions. Note if you are using an antibump cost function,
you may have to reduce its weight so that it does not make the Rw cost
function negligeable.
A cost function which as a weight equal to 0 is only computed for each
new best configuration, and does not affect the algorithm speed.