Computing for Science

The Computing for Science (CS) group supports ILL scientists, students and visitors in a number of activities including data analysis, instrument simulation and sample simulation.

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4. Special Display Interfaces

The DISPLAY FUNCTIONS list on the right of the classical LAMP interface and the TOOLS list in the Menu-bar contain buttons to select the following interfaces :-

1. SuperPlot

This interface provides a window for plotting several individual spectra. The current workspace number used in Lamp is automatically used as the default workspace. You can change it with the workspace slider. The cut axis and the cutting value can also be easily choosen using X or Y button and cutting value slider.

The SuperPlot window diplaying five spectra from 1 workspace
The SuperPlot window diplaying five spectra from 1 workspace

1.1. Overplotting

Select the desired cutting value and cutting axis of the workspace, the requested plot will appear. You can keep this plot by pressing the Keep as button, at the top of one of the six local buffer control panels. By selecting another cutting value or cutting axis or reselecting a workspace, you create another plot. To get rid of it, just select an empty workspace.

1.2. Cut applied to ...

There are two exclusive buttons :Current workspace and All workspaces.
In current workspace mode, the cut is only applied to the current workspace, in All workspaces mode cut is applied to every buffer, subsequent plot is made only if possible (Only if the cut value and axis exist in workspace)

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1.3. Scaling and Zooming

By default SuperPlot will autoscale to suit all spectra in the window.
All spectra are scaled by default because the scale button is set for each workspace. The scale toggle button allows you to specify wether or not a plot can be scaled.
The two bottom sliders allow you to perform an x range zoom by setting minimum and maximum values to be plotted on the X axis.

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1.4. Plot Style and Printing

The Linestyle for plotting depends on which buffer is choosen. Until a plot is stored in a buffer, the current workspace plot has a thickness of 2. If the coloured mode is set, the lines are in color except the current workspace plot, which is still black, but with a thickness of 1. plots can be printed using the PRINT button if the printer is set in Plotting preferences, otherwise just a postscript file is generated. If you want to print an annotated plot, use the annotate print option.

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1.5. Tips

If you change from a cut applied to the current workspace mode to the All workspace mode, the buffered workspaces are preserved. For example, plot W1 at x0, W2 at x3 and W3 at y5. Then change to "All W" mode, you get W1, W2 and W3 cut at the current cutting value and axis, which can be changed. Go back to current workspace mode, you will have back your W1 at x0, W2 at x3 and W3 at y5 plots (nice, isn't it !)


Also in the DISPLAY FUNCTIONS area on the right of the main LAMP interface are buttons to select a Radial Integration programs, a curve function fitting program (GK_Fit), SCAN for more elaborate image manipulation, and Load new Colours.

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2. RADIAL INTEGRATIONS

This interface provides a window for radial and azimutal integrations using user defined sectors.

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3. UNROLLING RINGS

This interface provides a window for unrolling large images.The analyse becomes easier since integrations are simple projections.

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4. CURVE FITTING with Str_Fit

Originally developed for analysing strain scanning aquisitions in which a Bragg peak is measured as a function of the position in the sample. The diffraction peak in each pattern is fitted with a given theorical lineshape (e.g. pseudo-Voigt), including convolution with a resolution function.
The fitted data, residuals and parameters can be viewed in different ways.
Today the program aims to give users a general fitting interface in which we can:

  • Construct a model by entering own formulae and using predefined functions.
  • Constraint and tie parameters for independent spectra or 2D spectra (simultaneous fitting).
  • Fit parameters in one go using previous spectra results.
  • Choose a resolution as a function or numerical input spectra.
  • Save models and results. Call "Str_fit" from a macro without using the interface.

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5. CURVE FITTING with GK_Fit

From one to six Gaussian & Lorenzian functions can be fitted from this interface.

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6. CURVE FITTING with Qens_Fit

Used to analyse quasi-elastic spectra. Inelastic excitations can also be treated. The input for "Qens_fit" consists of two workspaces, one containing the data as a function of Q(or temperature,pressure etc), the other containing the corresponding set of resolution functions, and a fitting model(typically a delta function for the elastic peak and lorentzians and gaussians for the quasi/inelastic features).
Once one spectrum has been fitted the remaining spectra can be fitted in one go and parameters can be fixed for all spectra. Instead of fitting independently each spectrum, a physical model can be imposed, for example for diffusion on a sphere. Models are added when needed.

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7. TOMOGRAPHY

A straightforward interface for reconstruction.

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8. MAGNETIC STRUCTURE

An editor for magnetic strutures representations with the possibility to add planes and do animations. MAGDRAW reads the nuclear and magnetic structures following Rietvelt refinement in standard programs like "FULLPROF". The structure is displayed as a 3D object that can be easily rotated.

DyMn6Ge6 incommensurate magnetic structure in MAGDRAW. The magnetic structure is characterized by two propagation vectors K1=(0,0,0) and K2=(0,0,.16). the first one provides a ferro-magetic component to the helical part described in K2.

Cu4O3 commensurate magnetic structure in MAGDRAW

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9. MILLER PLANES, ISOSURFACE OF ELECTRON OR SPIN DENSITY

Miller planes can be shown in the crystallographic cell to help visualise local structure. Standard representations of atoms and structural units(balls,sticks,polyhedra etc) are available. High quality images and animations can be saved for publications or presentations.
Atomistic representations are also being explored for visualising the results of solid state, first principles calculations on materials. Computational codes like VASP based on density functional theory (DFT), allow electron and spin density to be calculated and these can be displayed with the crystal structure.

3D isosurface and 2D contour plot representations of electron density, calculated by VASP for LiFePO4.

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10. MOLECULES/DISPLACEMENTS

The animation capabilities in LAMP can be used to visualise molecular dynamics simulations and calculated phonons and molecular vibrations.

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10.1. Scroll Spectra

This provides a window for scrolling through the individual spectra within a workspace. At start-up only triangles are displayed until an input workspace is selected using Load W#.

The Scroll Spectra window diplaying just two spectra from a workspac
The Scroll Spectra window diplaying just two spectra from a workspac

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10.2. Scrolling

Select the number of spectra to view in one window with the Number of plots bar. To scroll through the spectra use the scroll bar, scroll one at a time by selecting the scroll bar (click on it) then use the keyboard up and down keys. The Animate button allows you to scroll continuously (select either Slow, Normal, Fast or Stop to halt the animation).

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10.3. Scaling and Zooming

By default LAMP will autoscale to suit the spectra in the window. If an individual spectrum is zoomed (by dragging with the left mouse-button) all the spectra in the window will zoom. The zoom rectangle can be moved (using the middle mouse-button) to view any area of the spectra with the same scale. N.B. To zoom in the Y direction No Autoscale must be selected. To unzoom use the right mouse-button or the Full range button.

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10.4. Plot Style and Printing

The Plot symbol button can be used to plot individual points and the Draw lines button to join up the points. The displayed plots can be printed using the To PS file.. button if the printer is set in Plotting preferences, otherwise just a postscript file is made.

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10.5. Tips

Spectra in different workspaces can be compared by opening further windows with the Scroll Spectra button in the main LAMP interface. The SuperPlot interface is nevertheless more adapted to do this.
Scroll spectra can be used to visually select spectra that are usefull and you can then extract spectra from the workspace using the formula-entry window. N.B. You must subtract 1 from the Spectrum # to form the true spectrum number because spectra are numbered from 0 not 1 as they are in Scroll Spectra. (Mask & Group can also be used to select spectra)

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