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Journal self-archiving policies

One of the most-viewed pages here (it’s all relative; still not very many hits really) is the list of dodgy publishers. It’s a drop in the ocean, but it gets a few hits. Something else I’d like to bring all into one place, even though it’s been done elsewhere, is to summarise self-archiving polices. I’ll focus on the journals I’ve published in, preparatory to putting together a web archive of all my papers that I am allowed to self-archive (on my website and maybe on ResearchGate). It’s really just a resource for me, but I might as well make it public.

Some journals are open access; you don’t need to self-archive those, but usually you can.

Some allow you to archive a proper reprint, processed and edited by the journal — like the IUCr, as shown below.

Some suggest you archive the ‘author’s final version’ but don’t want you to put up anything with the journal’s imprimatur.

Some say ‘mine mine mine’ and don’t let you host it at all. I hope to make this clear.

The page lives at https://darrengoossens.wordpress.com/journal-self-archiving-policies, and so far has exactly one (1) entry, the good old IUCr, which has a very enlightened policy. They allow self-archiving as long as you use the official e-reprint, rather than just the downloaded PDF, and they request that you provide a link to the journal. Seems very reasonable. The official e-reprint is easy to recognise; it has a distinctive front page with some official words on it, something like this (colours may vary):

Front page of IUCr reprint, showing it is dfferent from download from journal.

Note the box with the notice near the bottom of the page.

 

I think their policy is very reasonable because the IUCr has a very professional publication and editorial team who need to be paid and ought to be paid. Subscriptions are part of the mix, yet they allow authors to house their own work and to distribute copies to colleagues freely. It seems a very sensible mix.

More updates as they come to hand.

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My Appendix: Chains of molecules, planes of scattering

In a very recent post, I mentioned an appendix to an article I wrote. I rather like it. The appendix grew out of a little document I put together. That document is longer, vaguer and a little different from the published appendix, and so I am putting it here. Now, the article was written in LaTeX, and this is a website, so I tried running htlatex on the file. It was very complicated:

$ htlatex planes
$ firefox planes.html

And it worked. Next thing is to get it into WordPress… Easy enough to cut and paste the HTML code into the window here, but what about all the graphics that were turned into png files?Ah well…bit of manual fiddling. Equations and symbols seem to sit high, and some of the inline equations have been broken into a mix of graphics and characters… still, not too bad. The PDF version is available here.


Planes perpendicular to vectors

Say you have a vector in real space, expressed say in direct lattice terms, for

example  planes0x= paplanes1x + pbplanes2x + pcplanes3x where planes1x is the a lattice parameter, which is a vector.

You may want the reciprocal plane(s) perpendicular to this vector.

Why?

Because correlations in a crystal collapse the scattering into features perpendicular to the direction of the correlation. In a normal, fully ordered three dimensions (3D) crystal, this collapsing happens in all three directions, so the scattered intensity coming off the atoms gets concentrated at points, the reciprocal lattice points, usually denoted hkl.

If you have only two dimensional ordering, the scattering is collapsed down in two directions but not the third, giving rise to rods or lines of scattering in reciprocal space (that is, in diffraction space). If there are only one dimensional correlations, the scattering collapses into sheets, that is, it is delocalised in two dimensions and only localised in one dimension (because there are only correlations in one dimension).

In diffuse scattering the crystal is typically long-range ordered in three dimensions, and the diffraction pattern shows nice Bragg peaks (hkl reflections). However, there can also be disorder, for example in the motions of the molecules or the chemical; substitution of one species of atom or molecule for another.

In a molecular crystal, one can sometimes identify a chain of molecules running through the crystal, and interactions within these chains are likely to be much stronger than those within. That tends to mean that the motions of the molecules along the direction of the chain (call that ‘longitudinal’ motion) is highly correlated, while it is not well correlated laterally.

In such a situation, the single crystal diffuse scattering will show ‘sheets’ of scattering perpendicular to the length of the chain.

Let’s say the chain of molecules extends along an arbitrary real-space direction, which we’ll define by the vectorplanes0x as above.

Now, a plane perpendicular to planes0x can be specified by giving two (nor more) non-collinear vectors that lie in it. Let’s look at two vectors and we’ll call them planes7x and planes8x, for no good reason.

Then we can say that

planes9x (1)

but note that we are not assuming planes7xplanes8x = 0, since right angles within the plane are not that important — especially as for generality I am not assuming orthogonal axes.

Now, planes7x exists in reciprocal space, so it is a linear combination of the reciprocal lattice vectors, planes13x, planes14x and planes15x like this

planes16x (2)

and these reciprocal vectors are defined in terms of the direct space vectors like this

planes17x (3)

and similarly for the other reciprocal vectors. The important thing for us to note is that this means planes13x is perpendicular to planes3x and planes2x . This is important when we go to take dot products later on. The bottom line here is basically the volume of the unit cell, and 2π is just a scalar, so from the point of view of defining the plane that we want, these are not important.

Ignoring the scalar parts, substituting eq. 3 into eq. 2 gives

planes21x (4)

and since we have more variables than we need if we are to satisfy eq. 1, we can arbitrarily set qc = 0.

Now, considering the dot product of planes7x and planes0x , in full it is

planes24x (5)

and this is useful because, to take the last term on the first line as an example, planes1x is perpendicular to (planes3x × planes1x) by the very nature of the cross product. This means that any terms with a repeated vector go to zero. Further, in the remaining terms the vector part is just of the form planes1x planes29x which is the unit cell volume and a constant, which we can also factor out to be left with

planes30x (6)

which is nice and simple. This is not a surprise but still…

The next step is to find another vector in that plane. This is just planes8x, and if we use the same logic but, to make planes8x non-collinear with planes0x , we choose rb to be zero, we get an equation analogous to eq. 6. These can be summed up as

planes34x (7)

where planes35x is a fairly straightforward extension.

Now, in terephthalic acid (TPA), triclinic polymorph of form II, each molecule has a -COOH group at each end. These H-bond strongly with the groups on neighbouring molecules and you get strongly correlated chains of molecules running along the [-111] (direct space) direction. This then suggests that the planes of scattering perpendicular to these chains will extend in the directions

planes36x (8)

or

planes37x (9)

Now, does this work? Figure 1 is some data from TPA, diffuse scattering data measured on a synchrotron. It also shows the reciprocal axes and the white, two-ended arrows show the directions of the diffuse planes and by
counting Bragg spots it can be seen that these agree with the calculation above.


planes38x

Figure 1: Observed data, measured at the Advanced Photon Source, showing what looks like multiple crystallites with similar orientations.


This means that we can ascribe these features to correlations in the displacements of the TPA molecules linked by the -COOH groups.

Before, before. Stop living in the past.

A Paper! Good God, a Paper: ‘Synchrotron X-ray diffuse scattering from a stable polymorphic material: terephthalic acid, C8H6O4’

I’ve been doing science for a long time, and while I’m in a bit of a career transition at the moment (see here for example), I’ve still got a few fingers in a few pies, and a few pieces of work slowly wending their ways through the system. Most recently, Eric Chan and I put out ‘Synchrotron X-ray diffuse scattering from a stable polymorphic material: terephthalic acid, C8H6O4‘. It’s a paper about the fuzzy, diffuse scattering from two polymorphs of the title compound.

It’s out in Acta Crystallographica Section B: STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS, a highly reputable but not open access journal, although they do allow authors to self-archive. At the moment, what that means is if you want a copy send me a message and I’ll punt one back to you.

Terephthalic acid molecule, drawn in Mercury.

Terephthalic acid molecule, drawn in Mercury.

What is terephthalic acid (TPA)? Well, it is a chemical used a lot in industry (plastics and such) and at room temperature it can crystallise out of solution in two forms, called (wait for it) form I and form II. (Well, actually the word ‘form’ is poorly defined in this context, technically, and it’s better to just say ‘polymorph I’ and ‘polymorph II’). In this context, a molecule is polymorphic if it can form more than one crystal structure and these structures can co-exist. Many materials change structure as you heat them up or squash them, but in a polymorphic system separate crystals of the structures can sit there side by side, under the same conditions. In most case, those conditions are room temperature and one atmosphere of pressure.

The two room temperature polymorphs are both triclinic, so of low symmetry. The difference is in how the molecules are arranged relative to each other. In both cases the -COOH groups on the ends of the molecules connect strongly to those on neighbouring molecules, so long chains of molecules form. (In the picture here, the -COOH groups are those at the ends of the molecule consisting of two red (oxygen) atoms, one white (hydrogen) and the grey (carbon) atom attached to the two whites.) These chains are sort of like one dimensional crystals, and then they are stacked up (like logs or a pile of pipes), but you can stack them up with, say, the -COOH in neighbouring chains close together, or you might have the phenyl rings (that is, the hexagon of grey carbon atoms) in one chain adjacent to the -COOH in the next. So in that sort of way you can get different crystal structures depending on how you stack things up.

Anyway, the paper looks at these polymorphs and how they are similar and how they differ. It uses my old ZMC program, which you can download from here (it comes with an example simulation, though not this one I’m talking about now). (That link goes to a paper I wrote and published for an Open Access journal, which I chose specifically so that you could go and download ZMC and everything for free…)

So in doing this I think about the connectivity of the molecule — how do the atoms depend on each other and where does the molecule need to be able to flex and twist? That means I end up drawing diagrams like this one:

 

connectivity

That’s exciting, isn’t it? I start at the middle (X) and then each atom is positioned relative to the ones that went before. Here’s another picture (because I happen to have it handy)…. This shows how the atoms were numbered, and how by numbering them correctly and building the molecule up in the right order it is easy to let the -COOH groups spin around. mol_num

The X-ray diffuse scatting in the <i>h</i>0<i>l</i> layer of reciprocal space of TPA.

The X-ray diffuse scattering in the h0l layer of reciprocal space of TPA. Measured at the Advanced Photon Source.

Here I show typical data. You can see the little white spots — these are the sharp diffraction peaks, Bragg peaks, and they indicate where a lot of X-rays were reflected off the crystal. They are what is used to work out what is usually called the ‘crystal structure’ which consists of the unit cell (the repeating unit) that the crystal is made up from. But you can also see blobs and streaks and stuff, and these are wider (‘diffuse’) features, and these tell us about how the molecules interact and shuffle each other around, and stuff like that.

Anyway, the paper is online now. The DOI link is https://doi.org/10.1107/S2052520616018801. One thing I really like about it is it’s got a mathematical appendix. I always wanted to write an article with a mathematical appendix. I think I might post on that separately.

 

 

 

 

https://doi.org/10.1107/S2052520616018801

AANSS 2016 — it’s approximately that time of year again, again.

Get that neutron feeling.

Get that neutron feeling.

 

www.anbug.org

The AANSS is a great mix of formality and informality, quality science in a relaxed atmosphere. Anyone who has or might or ought to use neutron scattering in their work (and isn’t that all of us, really?) is invited. And here’s a trick: Registration is $50 cheaper for ANBUG members but ANBUG membership is free! So join up!

AINSE

 

Oldly.

Very simple-minded automation of gnuplot

I have lots of datafiles I want to plot. gnuplot is scriptable. Since I don’t need any fancy output yet — this is data investigation, not manufacture of publication-quality diagrams — I can get multiple plots out quickly by writing a simple (simplish) couple of scripts.

I am sure people who know bash and perl and stuff can do this much better, but this works for me.

I have a wrapper script that simply consists of multiple calls to an inner script. It is here that I select the files I want to plot:

$ cat make_lots_of_plots.sh
./script_auto.sh r_0001_o_xy_TPA_21_Biso4p8_reread.inp
./script_auto.sh r_0001_o_yz_TPA_21_Biso4p8_reread.inp
./script_auto.sh r_0001_o_zx_TPA_21_Biso4p8_reread.inp
.
.
etc
.
.
./script_auto.sh r_0050_o_yz_TPA_21_Biso4p8_reread.inp
./script_auto.sh r_0050_o_zx_TPA_21_Biso4p8_reread.inp

I know I could do this in a single script, but I like to be able to call the inner one directly if I just want to make one plot. The inner script, script_auto.sh looks like this:

$ cat script_auto.sh
epsname=`basename $1 .inp`.eps
echo $epsname
scriptname=`basename $1 .inp`.gp
echo $scriptname
echo "set term postscript eps solid enhanced font 'Times,24'" > $scriptname
echo $epsname > temp1111
echo 'set output "' > temp2222
echo '"' > temp3333
paste -d '' temp2222 temp1111 temp3333 >> $scriptname
echo "set angles degrees; set polar" >> $scriptname
echo "set size square" >> $scriptname
echo "set xrange [-0.8:0.8]" >> $scriptname
echo "set yrange [-0.8:0.8]" >> $scriptname
echo $1 > temp1111
echo 'plot "' > temp2222
echo '" w l lw 3' > temp3333
paste -d '' temp2222 temp1111 temp3333 >> $scriptname
echo "set output" >> $scriptname
echo "set terminal x11" >> $scriptname
echo "quit" >> $scriptname
cat $scriptname
rm temp1111 temp2222 temp3333
gnuplot $scriptname
ls -ltrh $epsname

What’s going on here?

epsname=`basename $1 .inp`.eps
echo $epsname
scriptname=`basename $1 .inp`.gp
echo $scriptname

The bit above just uses basename to create the two filenames I need, one for the encapsulated postscript output, and one for the gnuplot script. Then I basically assemble the lines I want to see go into the gnuplot script. Mostly I can just echo stuff into the file, but I have various quote marks within quote marks, and (for simple-minded me) the solution that I know works is to go via the paste command, and write stuff out to little text files. I am sure there are much tidier ways to do this, but this works for me.

The line:

paste -d '' temp2222 temp1111 temp3333 >> $scriptname

causes the contents of the temporary files to be pasted together and put into the script, where the delimiter (‘-d‘) is the thing between the single quotes — which is nothing since the quotes are adjacent. This pastes stuff together with no gaps. The things being echoed into the file are gnuplot commands of various kinds.

Then I cat the script to the screen so I can see what it is doing (if I direct the output from the plotting script into a file, this lets me capture the commands I used), then I remove the temporary files, run gnuplot, and list the newly made file.

Clunky, but simple and effective. Useful changes could include outputting to pdf or some other format, and adding a step at the end (perhaps using pdfjoin) to combine all the resulting files in a single file.

Here is a png of the result. The gnuplot formatting could be made much nicer (title is too big, etc), but the overall process can always be improved, so I’m not worried about that. And the fact that it is a script means I can replot quickly when I know what the final format should be. For now I just want to see what I’ve got.

A simple plot from a diffuse scattering simulation, made using gnuplot.

A simple plot from a diffuse scattering simulation, made using gnuplot.

Whatever suits.

Diffuse in HgBa2CuO4+δ

It has long been an intention of mine to take our techniques for exploring the way the atoms are arranged in complicated materials and apply them to superconductors. The crystal structures of the oxide (high-temperature) superconductors are similar to those found in ferroelectric materials, which we have looked at in some detail. The difference is that in ferroelectrics the positions of the atoms relate directly to the interesting properties, since the ferroelectricity arises from atomic displacements (that is, from atoms moving around), whereas in superconductors the useful property shows up in how the electrons behave, and while this must be enabled by the crystal structure, the link is less direct. Even so, it seems to me that if we want to have a good idea of how the properties arise from the structure, then we need to know what the structure is.

One of the high-temperature superconductors is HgBa2CuO4+δ, a classic ‘copper oxide layer’ superconductor, descended from the original high-TC materials discovered in the late 1980s. We found some data on it in the literature, and decided that while the modelling there was a useful place to start, the model that was developed did not really do a great job of mimicking the observed scattering. Hence, we decided to re-analyse their data.

The paper came out recently in IUCrJ, which is open access which means you can download it now, without a subscription…so here it is (or click on the image below).

iucrj_hgba

In summary, we find that when the extra oxygen atoms are added to the structure (that’s the ‘+δ’ in the chemical formula), they go into the structure as long strings of atoms, as correctly identified by the authors of the paper with the original data, which is behind a paywall. What we have done that is new is improve the agreement between model and data by adjusting the positions of the surrounding atoms; it makes sense that when you stuff new atoms into a structure, the ones already there have to adjust to accommodate them. Based on things like bond valence sums, we can get some idea of what these adjustments should be, and then create a model crystal in which the atoms are pushed around in sensible ways in response top the added oxygens. These new atomic positions will then influence the environments of other atoms, and of electrons moving through the structure. Here is an image to break up the text:

hgbapic

An image to break up the text. On the left we see a row of added (‘interstitial’) oxygen atoms [‘O(3)’], moving between rows of mercury (Hg) atoms, and dragging the barium (Ba) atoms along with them. On the right we see a diffuse scattering pattern calculated from our model; X, Y and Z indicate important features on the plots, discussed in the paper.

Since the paper is open access, I won’t go into massive detail here, but when it comes to modelling the streaks of scattering in the pattern the results are pretty solid. There are some other, subtle details we continue to work on, but so far I think we can conclude that the methods of Monte Carlo analysis of single crystal diffuse scattering promise to deepen our understanding of superconductors and maybe — maybe! — will help us design ones that work at ever-higher temperatures.

More of the similar.

Some (Sort of) Science: Monte Carlo Modelling of Single-Crystal Diffuse Scattering from Intermetallics

Well, I got an invitation to write a paper for a journal. The journal was Metals. The request was to write something for a special issue called “Metals Challenged by Neutron and Synchrotron Radiation”.

Some random screengrab.

Some random screengrab.

For a while I was convinced that I lacked anything suitable.  But I did some reading, and I was working a little bit on a relevant problem — diffuse scattering from CePdSb.  Unfortunately, the analysis of the data was not very far advanced.

However.

As I read around the topic I realised that the diffuse scattering methods I’ve been working on were not all that much discussed in the metals community.  Now, diffuse scattering and highly advanced methods in crystallography are common in metallurgy and the study of metals — no question there.  And, as I mention in the article, many of the most important works in the field of short-range order we done using metallic systems.  Metals have the wonderful advantage that it is often possible to grow fairly large crystals, and they are also a very important class of materials.

However, there was not much evidence that the particular methods I’ve worked on and developed over the years were being used on metallic systems, so I decided to use the model I had (part) developed for CePdSb to demonstrate (1) how one can model diffuse scattering from metallics and (2) what kinds of diffraction effects one sees in the patterns when short-range order of different kinds is present.

Hence I came up with a technique-focused article that was recently accepted.  Metals is also open access (which I did not have to pay for, being invited), so it is an opportunity to get the work out there and not behind a paywall.

Another screengrab, this time of the pdf of the paper.

Another screengrab, this time of the pdf of the paper.

 

Since the paper is open access, I won’t include any of the pictures or whatnot here, because anyone who is interested can go and have a look, and if you’d like to ask me any questions just drop me a line by email or on this blog or whatever.

Thanks to Klaus-Dieter Liss for the invitation and Matthias Gutmann for the CePdSb.

 

Related, but not too closely.

My new toy.

It’s here and on my desk… my new toy is a…number crunching computer for Monte Carlo modelling of materials.

Intel 6th-Gen i7 6700K SSD DDR4 4.0GHz CPU, 16GB DDR4 RAM, 2TB SATA III 6GB/s HDD,N600 Wireless Dual Band PCI-Express Network Adapter with 2 Antennae. (Just a cut and paste from the specs.)

It's just a box.

It’s just a box.

 

Ordered it from D&D Computer Technology Pty Ltd, and delivery was pretty quick. At my work the standard Linux ‘solution’ is RHEL, so it is running RHEL 6.7 (the IT guys here don’t like 7 — it uses the controversial systemd, for one thing…)

Wireless internet so I can put it wherever I want to.

Compared to our previous generation of boxen (4+ years old), it runs a fairly typical Monte Carlo simulation in 20m55s instead of 27m21s, which is a useful but not massive improvement, which is really the result of code that is really just a single, single-threaded process which results in it scaling more with the clock speed than anything else.

I’ve put LaTeX on the box, but I am going to manage it via TeXLive’s tlmgr rather than RHEL’s package management, so we’ll see how that works out…

 

At the other end of the spectrum.

Single Crystal Diffuse Scattering and Pair Distribution Function: Some Kind of Comparison

Here begins a technicalish, science-y post.

This post is all about a paper we recently published in IUCrJ, here is the link: http://dx.doi.org/10.1107/S2052252515018722.

When X-rays or neutrons scatter off a sample of crystalline powder, the result is a powder diffraction pattern.  Usually the intensity of the scatting is measured as a function of the angle of scattering for radiation of a fixed wavelength. The angle can be converted to the more universal ‘scattering vector’:

Simulated powder diffraction pattern of the average structure of PZN for both X-rays and neutrons with the reflections labelled. The intensity is an arbitrary scale where relative height and widths of the peaks are important. A large Gaussian broadening parameter is used in the simulation to allow easier comparison of X-ray and neutron peaks.

Simulated powder diffraction pattern of the average structure of PZN for both X-rays and neutrons with the reflections labelled. The intensity is an arbitrary scale where relative height and widths of the peaks are important. A large Gaussian  broadening parameter is used in the simulation to allow easier comparison of X-ray and neutron peaks.

 

Now, when analysing  a pattern like this, the most common method is Rietveld refinement, in which a possible unit cell is posited, and its diffraction pattern calculated and compared to the observed.

Now, this is very useful indeed, but there are a couple of issues.  The first is that this sort of analysis only uses the strong Bragg reflections in the pattern — the big sharp peaks.  Mathematically, this means it finds the single body average which is to say that it can show what is going on on each atomic site but not how one site relates to another.  For example, it might say that a site has a 50% chance of having an atom of type A on it and 50% of type B, but it can’t say how this influences a neighbouring site.  Do A atoms cluster?  Do they like to stay apart?  This information, if we can get it, tells of the short-range order (SRO) in a crystalline material, where the Bragg peaks tell of the long-range order.  SRO is important, interesting, and rather difficult to get a handle on.

Now, the flat, broad (‘diffuse‘) scattering between the Bragg peaks — stuff that looks rather like background, and is often mixed up with background — contains two body information.  If the non-sample scattering is carefully removed, then what is left is all the scattering from the sample, and only scattering from the sample.  This is called the Total Scattering.  This can then be analysed to try to understand what it going on.  The most common way of doing that is to calculate the pair distribution function (PDF) from the TS.  This essentially shows the probabilities of finding scatterers at different separations — a two-body probability, which helps us ‘get inside’ the average structure that we get from Bragg peak (Rietveld) analysis.

Simulated PDF, using PDFgui, of the average structure of PZN for both X-rays and neutrons with the four nearest neighbour distances labelled. The a label is the unit cell length and corresponds to a number of different atom pairs. B is the B-site atom and is either Zn or Nb.

Simulated PDF, using PDFgui, of the average structure of PZN for both X-rays and neutrons with the four nearest neighbour distances labelled. The a label is the unit cell length and corresponds to a number of different atom pairs. B is the B-site atom and is either Zn or Nb.

Now, this is all talking about powders.  The main issue is that a powder is a collection of randomly oriented crystallites/grains which means the pattern is averaged.  Ideally, it would be nice to have a single crystal, to measure the total scattering in a way that is not averaged by random orientation.  This is Single Crystal Diffuse Scattering, SCDS.  It is (in my opinion) rather a gold standard in structural studies, but is pretty tricky to do…

A comparison of the hk0 plane for 100K X-ray (left) and 160K neutron (right).

A comparison of the hk0 plane for 100K X-ray (left) and 160K neutron (right).  This is SCDS data, shown in all its false-colour glory.  The features do not overlap and  are clearly separated.

What the paper we have just published in IUCrJ does is to take a system we have studied using SCDS, and then study it using PDF to show what things the PDF can reasonably be expected to reveal and what features are hidden from it (but apparent in the SCDS).  We did this because we felt that PDF, powerful as it is, was perhaps being over-interpreted, and treated as more definitive than it is, and in many cases it is the only viable technique, so it is hard to gauge when it is being over-interpreted.  Hence we look at in for a case when it is not the only available method.

What we found was that PDF is very good for showing the magnitudes of the spacings between atoms, and for showing the population of the spacings between atoms, but is not good for showing how these spacings might be correlated (ie, are the closely spaced atoms clustering together?).  Similarly, it was not good at showing up the ordering of atoms (…ABABA… vs …AAABBBB… for example).

The hk0 SCDS plane calculated from two different models fitted to the 300K neutron data. (a) is a model of size 10×10×10 unit cells refined over the range 1.75 < r < 20Angstrom, while (b) is a model of size 20×20×20 unit cells refined over the range 1.75 < r < Angstrom.

The hk0 SCDS plane calculated from two different models fitted to the 300K neutron PDF data. (a) is a model of size 10×10×10 unit cells refined over the range 1.75 < r < 20Angstrom, while (b) is a model of size 20×20×20 unit cells refined over the range 1.75 < r < 8 Angstrom.

The PDF is in real space — it is a plot of probability against separation, separation is measured in metres, like distances are measured in the world we experience.  The SCDS and the TS exist in reciprocal space, where distances are measured in inverse metres (m-1).  Some atomic orderings give rise to features that are highly localised in reciprocal space, so are best explored in that space.  Also, if the ordering in question only affects a small section of reciprocal space, and that is getting smeared out by the powder averaging, then it won’t show up very well in TS or then in PDF.

For example, above is a cut of SCDS calculated from an analysis of the PDF, whereas below is our model for the SCDS.  Clearly the latter should be a lot better —  and it is.  No surprise.  Now this is not making the PDF fight with one hand tied behind its back, and not setting up a straw man, either.  The point it not to show that SCDS is a more definitive measurement, the point is to show what PDF can be expected to tell us, so that when we are studying the many systems that we cannot do with SCDS because we cannot get a single crystal, we know when we are stretching the data too far.

The hk0 plane calculated for when the model allows the atom displace- ments to be swapped between the different B–site atoms, Zn and Nb. The diffuse scattering is almost identical to when the different B-site were not allowed to swap atomic displacements.

The hk0 plane calculated for when the model allows the atom displacements to be swapped between the different B–site atoms, Zn and Nb. The diffuse scattering is almost identical to when the different B-site were not allowed to swap atomic displacements.

Mission accomplished.

 

Ad nauseum.

Some Science: A Publication in Advances in Condensed Matter Physics

Advances in Condensed Matter Physics is an open access journal.  I have published in OA journals before, but I am pretty selective about them.  For example IUCrJ is is published by the IUCr, and I strongly believe that their name is a ‘guarantee of quality’ as good as any.  The other open access paper was in ISRN Materials Science,  which was more of an unknown quantity for me, and being a publisher who seems to have expanded via the OA model, the idea of sending work there initially filled me with skepticism.  This rather abated when it turned out they wanted a commissioned article and they were even prepared to pay me for it.  I am quite happy with how it turned out.  The picture below is not that paper but the new one.

 

Front page of a recent article in <i>Advances in Condensed Matter Physics</i>.

Front page of a recent article in Advances in Condensed Matter Physics (http://dx.doi.org/10.1155/2015/878463).

 

 

One slice of calculated diffuse scattering data from monoclinic 9-Chloro-10-methylanthracene.

One slice of calculated diffuse scattering data from monoclinic 9-Chloro-10-methylanthracene.

Recently, I got an email from Advances in Condensed Matter Physics asking me for an article.  Now, I delete several of these sorts of emails a day, and was about to delete this one when I thought, well, perhaps I should give the publisher — Hindawi, publishers of ISRN Materials Science — a second look.  The fact that they were prepared to commission something from me showed (of course) remarkable good taste, and the fact that they were prepared to pay for it (and did) suggested that they have an intention of climbing out of the ruck and mall of crappy OA publishers.

So I reread the email.  It appeared that they were prepared to waive the fee.  Good start.  I then went to the ACMP website and searched for the names and work of some scientists that I respect.  And they had indeed published there.  The journal has a proper impact factor, even if not especially high, and is not just indexed on google scholar (ie, not really indexed at all) but in proper databases like Web of Science. Okay, so it seems like a real journal.

There was an article I wanted to write, one of a very specific kind.  I have been developing and using the ZMC software for modelling diffuse scattering from molecular crystals — looking at subtle orderings in materials to improve understanding of structure and function.  The process is non-trivial, and not easy for the novice to get a  grip on.  So what I wanted to do was create an example of a simulation of a crystal, write a paper about it, then upload a bundle of files (as ‘additional material’) that would let a  user recreate the simulation.

This seemed like an ideal opportunity, because the software would then be available and not hidden behind a paywall.  Indeed, that is how it has worked out — the simulation (‘supplementary material’) can be downloaded by anyone by going to this page.

So not all OA publishers are alike, but it is important that a prospective author does their research into the journal and makes sure they are credible.

 

Avec.