I. Standard information exchange formalisms: pdCIF and the messy world of real data
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Toby, Brian H.
Powder diffraction may well be the impoverished cousin of single crystal diffraction, but for many materials and measurements there is no other choice; structural analyses have been performed from powders for materials ranging from simple salts to proteins. Many other types of material characterizations can be performed with powder diffraction. Excellent instruments are available that measure powder diffraction in different ways, depending on the needs of the study and the type of illumination source. Successful modeling requires that data be kept in a form close to the original measurement, which creates complexity for a powder CIF dictionary (pdCIF). It has been nearly 15 years since the initial pdCIF dictionary was completed and the successes and failures of pdCIF will be considered.
 I can't start this talk without mentioning all the people who funded this work, perhaps inadvertently over the period that I've been involved in it. And as I was going back through it, I realized that it actually included my first employer, post-graduate school, Union Carbide Corporation. I've modified the title that Brian suggested to me, but I like it very much. And I will start by explaining a little bit about powder diffraction and indeed why it perhaps is messy from the perspective of, in comparison to single crystal measurements. I would like to point out that I love being a powder diffraction crystallographer because, in fact, it's still a sport. The material still has a potential for defeating the crystallographer in terms of the process of determining structures. For those of you who have not thought about powder diffraction since freshman physics or perhaps even before that, I'll remind you that if you have an incident beam on a crystal, if the crystal is oriented properly, it diffracts. If it's not oriented properly, you don't get diffraction. If you have a large number of crystals in the X-ray beam and they are randomly oriented, then you will get diffraction at where those crystals are able to do that. One might think that, in fact, when you have an infinite or a near infinite number of crystals in the beam, you will get diffraction in all angles and you'll get no signal out that you care about. But in fact, you'll only get diffraction at specified rings corresponding to the Bragg angles. So if we take a detector and we sweep it along an angle like so, here's our detector moving, you will see intensity at specific Bragg angles. And popping up over here, this is a relatively simple diffractometer that does that. This is a then Siemens D500 diffractometer and that works by moving this detector up along that angle and here's the X-ray tube right there. If that were all that we needed to worry about, my job would have been a lot simpler and would have been forgotten about a long time ago. But the problem is that powder diffraction, as I'll explain to you, is collected in a variety of ways. And one of the problems is that we spend a lot of time fighting with that. So we very early on realized that, actually long before I was even involved in this, it's important to have a universal format for powder diffraction. Why? One reason is that, as I'll show you towards the end of the talk, that graphical examination of the results of the analysis is key to establishing quality. We do not have any metric that can replace the human eye in terms of the analysis. Every instrument has its own format and we waste tremendous amount of time. I would be actually a very rich man if I had been paid for every time I got an email message saying how do I convert data from format X to be used in software Y. And I think that we are scientists. The process of archive and reproduction of previous work is vital to our field. So back in the late 1980s, I volunteered to head up a committee through the International Center for Diffraction Data, which despite its spelling is in Newtown, Pennsylvania. And that's where I started on this. Very quickly, what did we want to think about being able to do? Well, we wanted to store powder diffraction data, but we realized that powder diffraction data by itself is meaningless. You need to also keep track of all sorts of metadata. Very often the data are not used exactly as collected, more often than not. You have to do some sort of reduction. You need to calibrate and so on. If you have a material that's at that point unidentified, probably the first thing you will do is reduce it to a table of diffraction peaks so you can work with it more simply. You will impose, if you can, a structural model, for example, if you're doing Reedfeld analysis. And unlike in single crystal work, the structure factor tables flow from the structural model, not the other way around. So the structure factor tables are actually subjective. The challenge is that there are lots of different ways that powder diffraction are recorded, and I'd like to take you through that a little bit to give you an appreciation of the problem. So let me start by showing you something that's near and dear to my heart. This is the powder diffractometer, high resolution powder diffractometer at the APS. And this is a mechanical engineer's conception of what the diffractometer looks like, large hubric circle on its side, robot, and a detection system which consists of 12 analyzer crystals, perfect analyzer crystals, each with its own scintillator data collection. I point out that this is coming from a mechanical engineer because of two things, one of which is that my older son has finished a year of mechanical engineering study and plans on making that his career. Also because I want to point out that mechanical engineers don't think about wires, here's what the instrument actually looks like. So this instrument is producing a series of 12 overlapping diffraction patterns which are collected with these detectors actually sluying to collect the data. I should mention that this is now the highest publishing instrument in the physical sciences at the advanced photon source despite being on a bending magnet which is sort of considered the third rate source at our facility. So that's one type of instrument. A similar type of instrument despite being at a completely different source and Brian carefully pointed out laboratory and synchrotron sources in the interests of speaking to the other side. This is from a nuclear reactor. Nuclear reactors over here somewhere sending a neutron beam which is diffracted by monochromators in this housing. Sample sits over here. We have 32 detectors sitting around the sample. This whole big banana shape thing in banana shape color moves over a 10 degree range and you collect your data. So data collected over the period of sort of an hour to 12 hours typically and you now have 32 overlapping scans that you need to deal with. Going to another type of detector. This is I think the PSI. The dectris detector is a very popular position sensitive detector. This gives you data in one dimension because these detectors will have gaps. You typically if you want to get a complete diffraction pattern need to collect the data by moving this to whole detector set up to more than one setting. Another way that's commonly used for collecting diffraction data is with area detection. So here is a sample, this picture which you can't really see the detail of. This is a sample of a I believe a silicate glass former which is just below its crystallization temperature which is why it's glowing red hot. And behind here is an area detector and if we zoom in on the area detector you can see that it's a grainy sample. These are diffraction from individual crystallites showing up as individual spots. But if you integrate around these rings you get a fairly good powder diffraction pattern. This is a way that we can currently collect data. Typical diffraction pattern is collected in a tenth of a second and the resolution is nowhere near the high resolution instruments that I showed you in the beginning either in neutron or X-ray. But the ability to collect a diffraction pattern as you modify your sample in some process you can collect tremendous amounts of data on the fly. So this is yet another way that we can collect powder diffraction data. And last and probably most complicated is to use a time of flight neutron source. In this source periodically on tenths of hertz type timescale you'll send protons into a heavy metal target produces a cascade of neutrons which are slowed down by a moderator. So you can imagine we have neutrons coming out of this source of various colors in bursts. By the de Broglie equation for neutrons energy turns into speed. So by the time the neutrons get down to here at where a sample is they've separated out in time. So we have the most energetic neutrons arriving first and the least energetic neutrons arriving somewhat later. If we look at a fixed detector angle we will see that some of these neutrons will have the right energy to diffract. If we look at another place we'll see diffraction of different neutrons. So in this experiment you tile as much of 4 pi steradians as you can afford and you collect these neutrons in a as a function of both angle and time. So these days we have older instruments that collect discrete time of flight patterns but we're heading towards instruments which are highly pixelated and in some of these instruments we actually don't collect the intensity versus pixelation we actually just collect events. So every event that comes in we record where it occurred, where it was detected and what the time stamps for it are. So going back to thinking about what the data requirements are to capture this kind of raw data in the simplest case we'll have counts or intensity. I'm not going to spend too much time thinking about the difference between that but of course intensities we can't take the Poisson statistics or square root to understand the uncertainties versus angle. But we may have either fixed wavelength or variable wavelength in the time of flight case. We may have counts versus time of flight at fixed angle. We may have counts versus or intensity versus pixel. We may have intensity, pixel versus time of flight. And we may have so we may have 2D data sets or three dimensional data sets. We don't typically work with things as complicated as that. We reduce the data. We apply corrections for various effects and we may have we usually will end up with one dimensional Q versus intensity versus Q in some fashion but we may be collecting data versus some other variables such as temperature, pressure, azimuth, maybe even a combination of these things. I'd also like to remind you particularly speaking to this audience that the purpose of doing all this is not only to study crystal structure but we do this in some cases to identify materials or quantify what phases are present. Then one software package I've been involved with for quite a few years, GSAS implemented nine being able to quantify nine phases in a material. My assumption was that was easily good for a century. We're finding problems with people who are studying cement clinker would like to go up to perhaps 20 or 30 components in their materials and quantify it. And with the synchrotron data collection we can easily quantify materials at the level of a tenth of a percent without doing anything terribly heroic. Texture is the orientation of the crystallites. That's what gives the Coca-Cola can the strength to stand up to one of my children shaking it without exploding. Full stress or applied stress is something that's very important for those of us who would prefer that airplane wings don't crack and fall off. We're also very interested particularly in these days of nano materials and things like what are the crystallite sizes. So these are all kinds of studies that people are interested in performing with powder diffraction and we want to capture in a file. So let me tell you quickly about the progress or lack thereof with powder diffraction SIF. As I mentioned initially we started with an effort from the International Center for Diffraction Data and we went looking at a spectroscopic format called J-Camp DX. We completed a J-Camp DX format when Sid Hall came and spoke to me and presented to me this brand new SIF format and suggested that I drop everything that I'd already done and start again. Sid is very persuasive. I'll leave it at that. But he was right. So stage zero was negative progress. Stage one was to create a data dictionary and it took quite a few years to get the ICDD actually to follow and with adopting this dictionary. We advanced from useless to write only which may be another way of saying useless with a prototype export program. And during that period I'm pleased to say that in 1995 as best as I can tell the first powder diffraction dataset was sent in to a journal. I have no idea what happened to that. Might be actually on the web for all I know. Describing a crystal structure. A little bit later on we developed a, I should say I, developed a first reading program that would actually take the data out. At this point we do have some software that reads powder diffraction SIFs. But I think that we're really reaching a stage where we can look forward to PD SIF finally after two decades starting to see routine use. So the ICDD has released a data deposition application that people can put onto their own computers to prepare data files for their deposition process. And that actually assembles if even if you don't have it, a PD SIF and sends it off to them for analysis. I wish I remembered the name that they released this program on but I love the name that it was used for development which was called the data quacker. And I think that, and I'll spend some time talking about what I consider to be a really brilliant move forward that's coming from the IC, the IUCR journals by integrating the PD SIF into the publication process. Okay, so what are some of the reasons that PD SIF is complicated? Well for one thing we often have to deal with the issue as I mentioned that there are multiple crystallographic phases in a single diffraction data set. Something less common but still important is that people often will collect different diffraction data sets to study a single problem. Perhaps multiple temperatures, also quite possibly collecting both an X-ray data set and a neutron data set, sometimes even a X-ray single crystal data set and a neutron powder data set. So SIF or SIF 1 does not allow multiple definitions of core items. So for example if you want to specify two lattice sets of lattice constants because you have two different unit cells you need to put that in different blocks. If you have the simplest case, one data set, one phase, you can do it all in one SIF block but if the number of data sets or the number of phases is greater than one then you're going to have to have more than one SIF block and I won't talk about this but my opinion is that it's best to have one more than the number of data sets plus the number of phases. But these things are interrelated so PD SIF uses block pointers to explain to the reading individual or software how the data sets are interrelated because data can go into this format in a number of different ways. We have a lot of different data items that one may have to read from in order to find the powder diffraction data in the file. So where are we now? Well the IUCR has developed something which I'll show you a little bit about. I'm not quite at 20 minutes according to my clock over here James. Let's see. The ICDD as I told you about has embraced this but I will have to say that as I've got up here the IUCR is finding that there's a lot of variable quality in the PD SIFs that are making it to Chester and that's a significant problem. I'm really very impressed. I would have liked to give you an online demo but I dare not. If you go to the current issue of the Journal of Applied Crystallography you'll see that there's a new button here, powder diffraction data. If you click on that button you will bring up in this case another page where you can see a plot button over there and if you click on that it transfers the diffraction data over to your computer where you can see a live plot of this data. You can zoom in on that. So here's where zooming in on it. This by zooming in exposes a problem with these data right here. That lack of intensity there is an issue. Another nice feature of this is that over here you will see that there's this little cryptic button there which allows you to download the pattern in a publication quality format. This is zooming in on that little corner there so I don't think too many journals will have problems publishing a figure of that quality. So I think that this will actually provide quite a bit of utility to the powder user and I'm hopeful that this is going to help bring us forward. With bringing some conclusions the community stands clearly to benefit from adoption of pdcif but it's not going to happen without the interests of the producer of the data To adopt any standard I feel that the standard needs to be well designed and it must fill in need. You must have good software to smooth the use of the software and the user must gain something from adoption of the standard. The user now will gain something particularly with this recent work from Chester. The standard I believe is well designed and fills in need and this is the real place where we need to work on improving the quality of the software. And that's what I have.
 I can't start this talk without mentioning all the people who funded this work, perhaps  inadvertently over the period that I've been involved in it.  And as I was going back through it, I realized that it actually included my first employer,  post-graduate school, Union Carbide Corporation.  I've modified the title that Brian suggested to me, but I like it very much.  And I will start by explaining a little bit about powder diffraction and indeed why it  perhaps is messy from the perspective of, in comparison to single crystal measurements.  I would like to point out that I love being a powder diffraction crystallographer because,  in fact, it's still a sport.  The material still has a potential for defeating the crystallographer in terms of the process  of determining structures.  For those of you who have not thought about powder diffraction since freshman physics  or perhaps even before that, I'll remind you that if you have an incident beam on a crystal,  if the crystal is oriented properly, it diffracts.  If it's not oriented properly, you don't get diffraction.  If you have a large number of crystals in the X-ray beam and they are randomly oriented,  then you will get diffraction at where those crystals are able to do that.  One might think that, in fact, when you have an infinite or a near infinite number of crystals  in the beam, you will get diffraction in all angles and you'll get no signal out that you  care about.  But in fact, you'll only get diffraction at specified rings corresponding to the Bragg  angles.  So if we take a detector and we sweep it along an angle like so, here's our detector moving,  you will see intensity at specific Bragg angles.  And popping up over here, this is a relatively simple diffractometer that does that.  This is a then Siemens D500 diffractometer and that works by moving this detector up  along that angle and here's the X-ray tube right there.  If that were all that we needed to worry about, my job would have been a lot simpler and would  have been forgotten about a long time ago.  But the problem is that powder diffraction, as I'll explain to you, is collected in a  variety of ways.  And one of the problems is that we spend a lot of time fighting with that.  So we very early on realized that, actually long before I was even involved in this, it's  important to have a universal format for powder diffraction.  Why?  One reason is that, as I'll show you towards the end of the talk, that graphical examination  of the results of the analysis is key to establishing quality.  We do not have any metric that can replace the human eye in terms of the analysis.  Every instrument has its own format and we waste tremendous amount of time.  I would be actually a very rich man if I had been paid for every time I got an email message  saying how do I convert data from format X to be used in software Y.  And I think that we are scientists.  The process of archive and reproduction of previous work is vital to our field.  So back in the late 1980s, I volunteered to head up a committee through the International  Center for Diffraction Data, which despite its spelling is in Newtown, Pennsylvania.  And that's where I started on this.  Very quickly, what did we want to think about being able to do?  Well, we wanted to store powder diffraction data, but we realized that powder diffraction  data by itself is meaningless.  You need to also keep track of all sorts of metadata.  Very often the data are not used exactly as collected, more often than not.  You have to do some sort of reduction.  You need to calibrate and so on.  If you have a material that's at that point unidentified, probably the first thing you  will do is reduce it to a table of diffraction peaks so you can work with it more simply.  You will impose, if you can, a structural model, for example, if you're doing Reedfeld  analysis.  And unlike in single crystal work, the structure factor tables flow from the structural model,  not the other way around.  So the structure factor tables are actually subjective.  The challenge is that there are lots of different ways that powder diffraction are recorded,  and I'd like to take you through that a little bit to give you an appreciation of the problem.  So let me start by showing you something that's near and dear to my heart.  This is the powder diffractometer, high resolution powder diffractometer at the APS.  And this is a mechanical engineer's conception of what the diffractometer looks like, large  hubric circle on its side, robot, and a detection system which consists of 12 analyzer crystals,  perfect analyzer crystals, each with its own scintillator data collection.  I point out that this is coming from a mechanical engineer because of two things, one of which  is that my older son has finished a year of mechanical engineering study and plans on  making that his career.  Also because I want to point out that mechanical engineers don't think about wires, here's what  the instrument actually looks like.  So this instrument is producing a series of 12 overlapping diffraction patterns which are  collected with these detectors actually sluying to collect the data.  I should mention that this is now the highest publishing instrument in the physical sciences  at the advanced photon source despite being on a bending magnet which is sort of considered  the third rate source at our facility.  So that's one type of instrument.  A similar type of instrument despite being at a completely different source and Brian  carefully pointed out laboratory and synchrotron sources in the interests of speaking to the  other side.  This is from a nuclear reactor.  Nuclear reactors over here somewhere sending a neutron beam which is diffracted by monochromators  in this housing.  Sample sits over here.  We have 32 detectors sitting around the sample.  This whole big banana shape thing in banana shape color moves over a 10 degree range and  you collect your data.  So data collected over the period of sort of an hour to 12 hours typically and you now  have 32 overlapping scans that you need to deal with.  Going to another type of detector.  This is I think the PSI.  The dectris detector is a very popular position sensitive detector.  This gives you data in one dimension because these detectors will have gaps.  You typically if you want to get a complete diffraction pattern need to collect the data  by moving this to whole detector set up to more than one setting.  Another way that's commonly used for collecting diffraction data is with area detection.  So here is a sample, this picture which you can't really see the detail of.  This is a sample of a I believe a silicate glass former which is just below its crystallization  temperature which is why it's glowing red hot.  And behind here is an area detector and if we zoom in on the area detector you can see  that it's a grainy sample.  These are diffraction from individual crystallites showing up as individual spots.  But if you integrate around these rings you get a fairly good powder diffraction pattern.  This is a way that we can currently collect data.  Typical diffraction pattern is collected in a tenth of a second and the resolution is  nowhere near the high resolution instruments that I showed you in the beginning either  in neutron or X-ray.  But the ability to collect a diffraction pattern as you modify your sample in some process  you can collect tremendous amounts of data on the fly.  So this is yet another way that we can collect powder diffraction data.  And last and probably most complicated is to use a time of flight neutron source.  In this source periodically on tenths of hertz type timescale you'll send protons into  a heavy metal target produces a cascade of neutrons which are slowed down by a moderator.  So you can imagine we have neutrons coming out of this source of various colors in bursts.  By the de Broglie equation for neutrons energy turns into speed.  So by the time the neutrons get down to here at where a sample is they've separated out  in time.  So we have the most energetic neutrons arriving first and the least energetic neutrons arriving  somewhat later.  If we look at a fixed detector angle we will see that some of these neutrons will have  the right energy to diffract.  If we look at another place we'll see diffraction of different neutrons.  So in this experiment you tile as much of 4 pi steradians as you can afford and you  collect these neutrons in a as a function of both angle and time.  So these days we have older instruments that collect discrete time of flight patterns but  we're heading towards instruments which are highly pixelated and in some of these instruments  we actually don't collect the intensity versus pixelation we actually just collect events.  So every event that comes in we record where it occurred, where it was detected and what  the time stamps for it are.  So going back to thinking about what the data requirements are to capture this kind of raw  data in the simplest case we'll have counts or intensity.  I'm not going to spend too much time thinking about the difference between that but of course  intensities we can't take the Poisson statistics or square root to understand the uncertainties  versus angle.  But we may have either fixed wavelength or variable wavelength in the time of flight  case.  We may have counts versus time of flight at fixed angle.  We may have counts versus or intensity versus pixel.  We may have intensity, pixel versus time of flight.  And we may have so we may have 2D data sets or three dimensional data sets.  We don't typically work with things as complicated as that.  We reduce the data.  We apply corrections for various effects and we may have we usually will end up with one  dimensional Q versus intensity versus Q in some fashion but we may be collecting data  versus some other variables such as temperature, pressure, azimuth, maybe even a combination  of these things.  I'd also like to remind you particularly speaking to this audience that the purpose of doing  all this is not only to study crystal structure but we do this in some cases to identify materials  or quantify what phases are present.  Then one software package I've been involved with for quite a few years, GSAS implemented  nine being able to quantify nine phases in a material.  My assumption was that was easily good for a century.  We're finding problems with people who are studying cement clinker would like to go up  to perhaps 20 or 30 components in their materials and quantify it.  And with the synchrotron data collection we can easily quantify materials at the level  of a tenth of a percent without doing anything terribly heroic.  Texture is the orientation of the crystallites.  That's what gives the Coca-Cola can the strength to stand up to one of my children shaking  it without exploding.  Full stress or applied stress is something that's very important for those of us who  would prefer that airplane wings don't crack and fall off.  We're also very interested particularly in these days of nano materials and things like  what are the crystallite sizes.  So these are all kinds of studies that people are interested in performing with powder diffraction  and we want to capture in a file.  So let me tell you quickly about the progress or lack thereof with powder diffraction SIF.  As I mentioned initially we started with an effort from the International Center for Diffraction  Data and we went looking at a spectroscopic format called J-Camp DX.  We completed a J-Camp DX format when Sid Hall came and spoke to me and presented to me this  brand new SIF format and suggested that I drop everything that I'd already done and start  again.  Sid is very persuasive.  I'll leave it at that.  But he was right.  So stage zero was negative progress.  Stage one was to create a data dictionary and it took quite a few years to get the ICDD  actually to follow and with adopting this dictionary.  We advanced from useless to write only which may be another way of saying useless with  a prototype export program.  And during that period I'm pleased to say that in 1995 as best as I can tell the first  powder diffraction dataset was sent in to a journal.  I have no idea what happened to that.  Might be actually on the web for all I know.  Describing a crystal structure.  A little bit later on we developed a, I should say I, developed a first reading program that  would actually take the data out.  At this point we do have some software that reads powder diffraction SIFs.  But I think that we're really reaching a stage where we can look forward to PD SIF finally  after two decades starting to see routine use.  So the ICDD has released a data deposition application that people can put onto their  own computers to prepare data files for their deposition process.  And that actually assembles if even if you don't have it, a PD SIF and sends it off to  them for analysis.  I wish I remembered the name that they released this program on but I love the name that it  was used for development which was called the data quacker.  And I think that, and I'll spend some time talking about what I consider to be a really  brilliant move forward that's coming from the IC, the IUCR journals by integrating the  PD SIF into the publication process.  Okay, so what are some of the reasons that PD SIF is complicated?  Well for one thing we often have to deal with the issue as I mentioned that there are multiple  crystallographic phases in a single diffraction data set.  Something less common but still important is that people often will collect different  diffraction data sets to study a single problem.  Perhaps multiple temperatures, also quite possibly collecting both an X-ray data set  and a neutron data set, sometimes even a X-ray single crystal data set and a neutron powder  data set.  So SIF or SIF 1 does not allow multiple definitions of core items.  So for example if you want to specify two lattice sets of lattice constants because you  have two different unit cells you need to put that in different blocks.  If you have the simplest case, one data set, one phase, you can do it all in one SIF block  but if the number of data sets or the number of phases is greater than one then you're  going to have to have more than one SIF block and I won't talk about this but my opinion  is that it's best to have one more than the number of data sets plus the number of phases.  But these things are interrelated so PD SIF uses block pointers to explain to the reading  individual or software how the data sets are interrelated because data can go into this  format in a number of different ways.  We have a lot of different data items that one may have to read from in order to find  the powder diffraction data in the file.  So where are we now?  Well the IUCR has developed something which I'll show you a little bit about.  I'm not quite at 20 minutes according to my clock over here James.  Let's see.  The ICDD as I told you about has embraced this but I will have to say that as I've  got up here the IUCR is finding that there's a lot of variable quality in the PD SIFs that  are making it to Chester and that's a significant problem.  I'm really very impressed.  I would have liked to give you an online demo but I dare not.  If you go to the current issue of the Journal of Applied Crystallography you'll see that  there's a new button here, powder diffraction data.  If you click on that button you will bring up in this case another page where you can  see a plot button over there and if you click on that it transfers the diffraction data over  to your computer where you can see a live plot of this data.  You can zoom in on that.  So here's where zooming in on it.  This by zooming in exposes a problem with these data right here.  That lack of intensity there is an issue.  Another nice feature of this is that over here you will see that there's this little  cryptic button there which allows you to download the pattern in a publication quality  format.  This is zooming in on that little corner there so I don't think too many journals will have  problems publishing a figure of that quality.  So I think that this will actually provide quite a bit of utility to the powder user  and I'm hopeful that this is going to help bring us forward.  With bringing some conclusions the community stands clearly to benefit from adoption of  pdcif but it's not going to happen without the interests of the producer of the data  To adopt any standard I feel that the standard needs to be well designed and it must fill  in need.  You must have good software to smooth the use of the software and the user must gain  something from adoption of the standard.  The user now will gain something particularly with this recent work from Chester.  The standard I believe is well designed and fills in need and this is the real place where  we need to work on improving the quality of the software.  And that's what I have.
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