Http://aimpro.ncl.ac.ukMMG Skills Lecture Series Introductory concepts: Diagram preparation Jon Goss

http://aimpro.ncl.ac.uk MMG Skills Lecture Series

Introductory concepts:Diagram preparation

Jon Goss

MMG Skills Lecture Series2

Outline

For the purposes of this session, the term diagram refers to any pictorial or graphical representation of data.What is the purpose behind making a diagram?

1. To show something to yourself2. To communicate information to a colleague3. To illustrate a report or paper4. To include in a poster or talk


Diagrams: for diagnosis for diagnosis

The classic types of diagram for diagnosis are where we want to understand something about a run. For example:

minimol FORCESETOTHomer


Diagrams: for diagnosis for diagnosis


Diagrams: for internal consumption for internal consumption

The second class of diagrams are those used to show something to a colleague

On paperElectronically

For example, a bandstructure plot, DoS, …These are typically non-trivial to construct (i.e. not via a single command).However, they are quick and dirty in comparison to something that we’d publish!Nevertheless, the basic skills required are very similar……familiarity with the software!


Diagrams: for written reports for written reports

We’ll now look at five types of diagrams typical of AIMPRO papers:

Basic atomistic structures (xbs)Kohn-Sham functions and charge densities (AIMVIEW)Hyperfine tensors (POV-Ray)Band structures (gnuplot)Formation energies (gnuplot)

Each of you should invest some time to learn how to use at least AIMVIEW and gnuplot!Before beginning, you check the following:

Keep all images in a report stylistically similar, so related structures should be viewed from the same direction, and at the same distance.For publications, there may be publisher-defined constraints (e.g. how units are included in graph – in parentheses “(eV)”, or as a division “/eV”).


Diagrams: for written reports - xbs for written reports - xbs

“xbs” is a very simple structure plotting package that has the capacity for producing slightly better images than, say, minimol.

(We’ll also look at much more lick-able structures with AIMVIEW and POV-Ray.)

xbs is available on snufkin.It takes as input a relatively simple format which describes the atom species and how they bond, plus a structure (of course).This can be generated automatically from an “xyz” file using “x2bs” (~njpg/bin).The GUI is invoked as “xbs file”…

atom X 0.86294 0.86294 0.81914atom C 2.75763934061345 2.75763934061345 2.75240668935108atom C -0.881961575033624 -0.881961575033624 2.51027987788644atom C -1.0145315223104 2.5906159091129 -0.99306990425811atom C 2.5906159091129 -1.0145315223104 -0.99306990425811atom C 3.63561359381117 3.63561359381117 0.101720170513226atom C 4.53509481848491 4.53509481848491 2.17033706980097atom C 7.58079831961937 7.58079831961937 0.873266945760172atom C 9.23574664110324 9.23574664110324 2.4968004624099atom C 9.13529069727637 5.83342350003411 -0.821401526277635atom C -0.848286657917147 2.50071030548027 5.81240407786314atom C 7.6783648724097 4.20453261020676 4.32568105360856atom C 9.26537565487816 5.86036910290525 5.9141034613905atom C 5.83342350003411 9.13529069727637 -0.821401526277635atom C 4.20453261020676 7.6783648724097 4.32568105360856atom C 5.86036910290525 9.26537565487816 5.9141034613905atom C 2.50071030548027 -0.848286657917147 5.81240407786314atom C 5.77922804840765 2.31987864618118 -1.07273697248462atom C 2.31987864618118 5.77922804840765 -1.07273697248462atom C 6.20109425754999 6.20109425754999 2.88765815780565atom C 4.20916999778273 0.792760839194733 4.20898102518387atom C 5.88873955917179 2.48169777230918 5.89192752691452atom C 0.792760839194733 4.20916999778273 4.20898102518387atom C 2.48169777230918 5.88873955917179 5.89192752691452

spec N 0.750 0.8spec C 0.825 0spec X 0.825 1

bonds N N 0.000 3.000 0.300 0.5bonds N C 0.000 3.180 0.300 0.5bonds C C 0.000 3.80 0.300 0.5bonds C X 0.000 3.80 0.100 1bonds X X 0.000 3.80 0.300 0.5

tmat -0.707 -0.707 0.000 0.000 0.000 1.000 -0.707 0.707 0.000dist 25.000inc 5.000scale 25.000rfac 0.60bfac 0.60pos 10.000 0.000pos 0.000 0.000switches 1 0 1 0 0 1 1 2 1





There are some advantages in using this “primitive” software:

It produces simple images which may be much more clear than the shiny atoms we’ll see laterIt produces smaller files

Why is this important?The graphics are vector postscript and therefore scalable

Why is this useful?It is much faster to use (once you’ve got used to it)

But there are also disadvantages:Requires some linux expertise

You should be developing this anyway!

You may need to edit the postscript output

Never a bad thing Can absorb lots of time “fiddling about” if you’re not careful

This is a bad thing!

Goss et al Phys. Rev. B 76, 045203 (2007)


Diagrams: for written reports - AIMVIEW for written reports - AIMVIEW

This is not the place to learn how to use AIMVIEW – there is a whole manual provided by Jerry.Therefore, today I’ll assume that you’ll be able to read the manual, and/or collaborate with your peers to view your structure from an AIMVIEW dump file.However, we will look at some important factors in generating the image files.First some guiding principles:

What makes a good or bad illustration for a structure and wave function?



My answer (invert for bad)Important part is centralThere’s minimal additional material (the surroundings)There is a minimisation of anything in the foreground that may eclipse the actionThe sizes, colours and direction of view accentuate the key elements

Remember – you’ve been thinking about your system for weeks or months, but this is new to the reader of the report!



Now for the tricks in creating a high-quality image

1. When choosing the aspect, use a modest quality for the wave functions, atoms, bonds…

2. When you’ve hit on the final view, up the accuracies of these terms

3. Go to the save image 4. Up the resolution of the output5. Save as a “png” (portable network

graphics)6. Open the png file in gimp7. Save it as a jpeg (Joint

Photographic Experts Group)8. If you’re using the file in a power-

point poster or talk, you’re done9. If you’re using LaTeX, then you’ll

want an eps file.10. Use “sam2p” to convert from jpeg

to eps:sam2p -c:jpeg file.jpg EPS: file.eps






























































graphics)6. Open the png file in gimp7. “Save-as” it as a jpeg (Joint





























Do not generate the eps directly from gimp!Of course, you can make pictures of structures without wave functions in the same way (c.f. xbs).


Diagrams: for written reports - POV-Ray for written reports - POV-Ray

POV-Ray = Persistence of Vision Persistence of Vision ray-tracingray-tracingIt is not trivial, but most of the hard work for the HFI tensors has already been done1. By AIMPRO2. By HFI2POV

"Shorebirds" by Jim Charter (2000)

Wildlife inhabiting the boundary zone between land and sea.

www.POV-Ray.org



What is a hyperfine interaction?What is a tensor?



For some molecules, radical and crystal defects there are one or more unpaired electrons that interact with nuclear spins, so that in a magnetic field…The details of the interaction tensor take the form of three magnitudes and three directions (of course). The directions form an orthogonal set, and beyond any symmetry, the magnitudes may take any values.The question is how do you succinctly present this in a report?

A table?A structure?



I personally favour a combination of table for the numerical values of the tensor elements, but combine it with a figure to help show how the directions relate to the (say) relative positions of radical sites.HFI2POV takes AIMPRO output and generates POV-Ray input.



HFi2POV usage: HFi2POV <options> [AIMPRO HFi output FILE]Options: -h This information -o <x y z> The origin of the cutout -v <9 numbers> The three basis vectors for the cutout -l <a b c> The lengths of the cuboid in the directions of the basis vectors

To compile the image, you'll need to make sure that the orientationof the camera and object is correct. The povray compilation may besomething like

'povray +A -D +J +H800 +W800 +V -lPOV.pov'

to generate an 800x800 pixel rendered image (POV.png).

Internal to the POV.pov dile are the TYPE and SITE bolean flags toturn on/off the sets of equivilent sites, and individial atoms inthe hyperfine tensors.

Also, the arrows showing the principal direcationare defined by the parameters:

#declare HFIscale = 1; #declare ArrowPoint = 0.7; #declare ArrowCone = 3;

Have fun with variying these paramters and everything else to getpublication quality images.

Copyright JPG Sept 2008

For an AIMPRO output file containing HFI tensors called out, you execute:

HFi2POV out(perhaps with other flags)

and get three files:POV.povPOV.xyzUSED.dat

You compile the image:povray +A -D +J +H800 +W800 +V -lPOV.povThe resolution is dictated by the 800’s in this case.

You get a new file:POV.png…



This is the default orientation in the POV.pov fileWe need to do a bit of manipulation to get it rightTherefore we need to know a (very) little POV-RayIn the POV.pov file there are two places you need to update.The first is to add some rotations:

The z-axis is out of the screen (always), the x-axis is horizontal and the y is vertical…



Look for this in the file:

After it you can add terms like “rotate -45*z” to rotate anti-clockwise by 45°.

/********************************************************************//* End of union: put transformations here... ************************//********************************************************************/



Now we rotate about the x-axis by 90°



We can see that the centring is important, so we can translate using “translate <1,1,1>”, or whatever displacement suits…



And to zoom in, we change something else.Look for “direction” in the camera definition: increasing the value of z effectively moves the camera toward the object…



But we can’t really see what’s going on here, so we rotate it about y by a small angle…But it’s still pretty difficult to see what’s going on

We don’t need all the arrows,and we can shave off a few atoms in the foreground



We can either work out which atoms we want to remove, or go back and chop out a different volume using HFi2POV



The HFi arrows can be turned on and off using parameters set in the POV.pov file:

The species are listed in types and sites: equivalent sites are of the same type

We’ll keep one of each type…



We can reverse any of the vector directions without affecting the physics

We do this by finding the vector we want in POV.pov and change the sign of the vector



The HFi arrows can be turned on and off using parameters set in the POV.pov file:

The species are listed in types and sites: equivalent sites are of the same type

We’ll keep one of each type…



Finally, you may need to annote the figure, in the example to distinguish between the carbon site.This can be done most simply using xfig…


Diagrams: for written reports - xfig for written reports - xfig



This is a pretty basic drawing packageYou can plot basic shapes, lines and curves, or add text or import graphics files…



For each of these items, there are user definable qualities such as line thickness, colour, style and so on.The “depth” value allows you to define which elements lie in front or behind others.



You can edit you figure using a range of tools familiar to most of you…

MoveCopyRotateScale…

Others may be more obscure

you can group and ungroup as in Power pointedit brings up a dialogue box to change settings



The “File” menu allows you to export your figure to eps or some other image-file type.



Beware: the text you add to a figure on the screen does not match that produced in an eps file.This may relate to both size and position.For papers, xfig text annotation interfaces well with LaTeX using the “psfrag” package.


Diagrams: for written reports - for written reports - psfragpsfrag

The text in the eps file is discarded, and replaced with LaTeX text.This maintains consistency with fonts and font sizesIt means you don’t have to worry about complex notation in xfig.You may have to play around with the location of the text to get the desired finished product.


Diagrams: for written reports - for written reports - gnuplotgnuplot

We’ll now look at two examples of using gnuplot to produce publication quality graphs.

A band structureA formation energy

What information are we hoping to show in a band structure plot?



Typically we’ll have several data sets to plot on the same graph:

Maybe two spin statesA context, such as the bulk bands as a reference

We need to ensure that they’re all mutually consistent (i.e. basis, sampling, lattice constant etc).I tend to plot the bulk as solid lines, and the analysis for a defect as points

Goss et al Phys. Rev. B 76, 075204 (2007)



However, the defaultdefault appearance of a gnuplot graph is pretty poor.Let’s go through some steps to getting a polished image for incorporation in a paper.What’s wrong with the graph shown in the figure?

gnuplot of “sin(x)”



The formatting of the numbers:

set format y “%.1f”



The lack of labels on the axes:

set xlabel “x”



Choose a y-range set yrange [-1.1:1.1]



Remove the legend:unset key



But these are just screen-shots – we want images (e.g. jpeg, eps, …) When you run gnuplot interactively you are using a “x11” terminal, but we want something else now.

Typically we want eps (encapsulated postscript).

set terminal postscript eps

set output “file.eps”

What’s happened?What’s wrong now? Eps file



The font-sizeThe font-typeThe line-thicknessEverything is black and whiteIt also may be that the sampling of the function is not particularly great…



Fonts:set terminal postscript eps “Times-Roman” 24

Line thickness:Either in the plot:

plot sin(x) lw 2

Or in the terminalset terminal postscript eps lw 2 “Times-Roman” 24

Black and white to colour:set terminal postscript eps color lw 2 “Times-Roman” 24





Sampling:When plotting a function, it is “sampled”.The sampling density is defined by the variable “sample”.set sample x, y

“x” is the number of points calculated in our plot.“y” is for surface plots.(See “help sample”.)



sample 30



sample 80



Still in error:The “x” and “y” are maths objects (should be in itallics).Individual terms can be modified in “enhanced” eps:set terminal postscript enhanced eps color lw 2 “Times-Roman” 24

Thenset xlabel “{/Times-Roman-Itallic x} (radians)”set ylabel “{/Times-Roman-Itallic y}”





The band-structure can be plotted from the bandst.plt.This is a two (or three) column format that gnuplot understands as

X Y (Z)

A quick plot can be generated “ plot ‘file’ ”, (postscript) which generates the basic plot…What’s wrong with this image?





1. There is too much dataDo all the valence bands need to be included?

2. Which are filled?…and which are empty?

3. Are enough empty bands plotted?What is the test?

4. Should we use symbols or lines?5. Colour?6. Fonts and key?7. What are the x-axis labels?8. This is a spin polarised system – is that evident?



Some elements are corrected in these plots, but not all

Set the x and y axis labelsAdd colourChange fontZoom in on important energy range

In making some improvements we also expose problems

Spin polarised data leads to some bands being obscuredWhat is the zero of energy? What’s diamond and what’s defect?

…and some remainThe filled/empty distinctionThe x-axis tick-marksThe number of empty bands



We need to do something which engages our brains a bit more

We need to reformat the data – note there is note there is not just one way to do this!not just one way to do this!We need to consider what information we are trying to communicate……and what achieves this in clearest way.We need to consider the data in context of the physical system.



Let’s assume we will persist with the bandst.plt data file.The three columns are “k”, “Energy, spin up”, “Energy, spin down”.Each “band” is separated (for plotting by gnuplot) by a blank line.



Let’s assume we will persist with the bandst.plt data file.The three columns are “k”, “Energy, spin up”, “Energy, spin down”.Each “band” is separated (for plotting by gnuplot) by a blank line…This signifies a break in the data and if the points are joined with lines, this step is missed out.If there were two blank lines, this would tell gnuplot that you’ve got a new set of data: these are numbered using the “index” variable.



We can use indexes to separate occupied and empty bands.In the example, we know there are 433 occupied up-bands & 432 occupied down-bands.We find the 433rd blank line and double it – we have reformatted the data.Then we use the plot command shownThis only includes spin up: can you see why?



We want to show both spin up and spin down, so we need to do something more elaborate.Again, starting with the “bandst.plt” file, we need to treat the up and down separately.

This can be done using indexing, with a two column formatThis can be done using ~njpg/bin/SplitPLT

Up and occupied

Up and empty

Down and occupied

Down and empty





This is still completely inappropriate for a paper…Lets change the symbols, add more empty bands and set the energy zero at the valence band top…





We might make life easier by using a “butterfly plot along the x-axis.



Now, to place further into context, lets add the bands from the bulk cell of the same basic composition as the defect cell…





A bit of finesse…Fewer points, larger font…Dividing line…


Diagrams: Summary Summary

Making clear diagrams can be very quick…Run-time diagnosticsQuick data analysis

…or very time-consumingPublication quality diagrams

In preparing your thesis, a lot of time is likely to me consumed in the making of diagrams, so adopting a style for consistency and efficiency is very helpful early onearly on.

Documents

Http://aimpro.ncl.ac.ukMMG Skills Lecture Series Introductory concepts: Diagram preparation Jon Goss