PDFgui user guide - Total Scattering at LANL
Contents
1. ff Lamno3 PsNm I Imo pbnm 550 1 O 5 55774633328 Imo pbnm 550 2 o 5 70892291739 550K gr mo pbnm 550 3 7 77228844079 SAE Imo pbnm 650 Ilmo pbnm 550 7 O 0 0104134874586 mo pbnm 550 8 0 00691474151902 fj Lamno3 PBNM Imo pbnm 550 9 0 0147912717386 Dies or Imo pbnm 550 10 J 0 0136551443527 Imo pbnm 550 21 O 0 00639050933948 Plot Control 0X Ilmo pbnm 550 22 O 0 0400505047777 E v Imo pbnm 550 23 L1 0 0689967371807 S Ilmo pbnm 550 24 0 487201044936 Ilmo pbnm 550 25 O 0 727486523424 2 Imo pbnm 550 26 o 0 301941369405 e Wille ema Ss EE 7 Apply parameters es Kei El 7 12 9862 offset 3 Plot Reset Figure 3 4 An example of linked fits The output of a converged fit will be fed into the succeeding fit in the sequence as an input Additional fit parameters can be introduced when needed to the new fit If our Ni exam ple was used and copied in this exercise one can select Ni stru phase of Fit 1 copy and introduce parameter delta2 by inserting 5 in the appropriate box of the Constraints tab of that phase This is a quadratic atomic correlation factor a parameter related to the correlated motion of atoms and as such should help in sharpening up the nearest neighbor PDF peak in the model PDF profile Highlight the fits on the Fit Tree and run them in the same way as described earlier Only the highlighted fits will be execu2. E Figure 3 5 Appearance of the setup panel for specifying an incremental r series fit conditions The first row deals with the increment setup of the upper r of the refinements User should specify the first and the last fit maximum r value and corresponding step incre ment all in units of Angstroms In the second row information is needed to specify the lower r refinement limit Again the user sets the first and the last value and step This allows for a box car of either fixed or variable width to be defined If the second row is left blank the corresponding refinement series will be with incremental maximum r only and fixed lower limit For the purpose of this exercise lets perform incremental fitting of Ni data with 4 steps total and fixed lower limit To achieve this type 5 for the first upper limit 20 for the last upper limit and the step of 5 Angstroms Leave the second row blank Chapter 3 Examples and tutorials 24 Once this is done make sure that the Ni fit which in this situation serves as a template is highlighted and then click OK in the Current Action panel This will generate 4 new fits below the original fit and these four fits will constitute your series with desired incremental limits You select all four of them and execute the refinement Once the sequence is done you can review the results using Plot Control 3 3 3 Sequential fitting of temperature series More frequ
3. Figure 2 3 Adjusting data set related configuration Click on the Ni xcray gr in the Fit Tree In Figure 2 3 Data Set Configuration panel is shown At this stage we adjust the fitting range as well as other parameters that reflect the experimental conditions as appropriate Initial values for refined parameters can be set and Chapter 2 Quick start 10 reviewed when the fit is selected on the Fit Tree on the Parameters tab Since there is no physical information in the region of r below the nearest neighbor PDF peak position and since this region is often affected by noise and experimental artifacts it is wise to exclude it from fitting We therefore set the value of the lower boundary of the fitting range to 1 7 In addition we set Qdamp parameter to a more realistic starting value of 0 08 This parameter is typically obtained through a conventional calibration process at each PDF experiment using a standard sample such as Ni or Si Next we select the Constraints tab and type into the Scale Factor edit box This will assign refinement parameter 1 to the data scale factor Note that this is the syntax used for assigning the refinement parameters in PDFfit2 engine Similarly assign parameter 2 to Qdamp by inserting 02 into the appropriate edit box This is illustrated in Figure Figure 2 4 v PDFgui ex File Edit View Fits Phases Data Calculations Help BEUS al FitTee x f
4. diffpy VERSION exe file launch the executable and follow the prompts That s all PDFgui and PDFfit2 should be now ready for use If you wish to have structure plot ting capabilities download and install AtomEye as directed on the AtomEye web page http 164 107 79 177 Archive Graphics A Once PDFzgui is up and running enter the location of the AtomEye executable under Edit gt Preferences Building from Subversion repository The latest development sources of DiffPy are available in a public Subversion code reposi tory To obtain the latest code run svn checkout svn svn danse us diffraction diffraction diffpy You need to have svn a subversion client installed on your computer In addition a GNU documentation system Texinfo http www gnu org software texinfo is required to compile users manual Chapter 1 Introduction 5 Otherwise the installation procedure is the same as for Unix like operating systems Change to the diffpy directory and execute python setup py install The checked out diffpy directory can be kept around for future updates To bring it up to date with the latest sources one just needs to execute svn update inside this directory 1 5 Community There are several Google groups for support and development of PDF gui and other DiffPy software Visit the links below for message archives or instructions on subscription and posting diffpy users http groups google com group diffpy users He
5. Shift and A keys simultaneously This will select all the phases at once On the Plot Control choose the temperature for x axis and select the Uiso of O2 for example atom 20 Clicking on Plot button a plot will be displayed featuring Uiso vs T Chapter 3 Examples and tutorials 26 v Imo template ddp tutorial Imo template ddp PDFgui DIR File Edit View Fits Phases Data Calculations Help E Q 9 e u FET eee Configure constraints Plot 5 u33 20 TREES Hi 300K Ka E Imo pbnm 550 TREES Ei 550K gr u33 20 NE EZ Imo pbnm 650 Ix temperature pY u33 17 u33 18 0 00 u33 19 d 300 400 500 600 700 800 900 1000 1100 1200 temperature ZOO a X x 720 0 y 0 0117582417582 x 1 x 2 sour oes eT offset 3 Plot Reset V Figure 3 7 Displaying the refinement results as a function of external parameter T series refinement of LaMnO3 example of isotropic ADP of oxygen atom on general position in Pbnm setting Notable are the offsets just above 700 K Jahn Teller transition and at around 1000 K when sample converts from orthorhombic to rhombohedral symmetry Despite quite high temperatures an onset of the static offset above the transition tem perature is clearly marked by this parameter as apparent in Figure 3 7 Curious user could repeat the same T series refinement restricting the refinement range upper limi
6. 0 068554 3 3 531606 4 0 005127 chisq 29951 1 red chisq 16 3936 Figure 2 7 While the refinement is running the refinement progress is displayed in the PDFfit2 Output panel After the fitting is completed the fit summary is provided in the Results tab of the Current Action panel when Fit 1 is selected on the Fit Tree Similarly if Results tab is displayed when Mi stra or Ni xray gr are selected values of all corresponding refined parameters for the converged model are displayed If the fit results are acceptable one or more refined values could be copied to become new initial parameters for possible further refinement where appropriate This can be done when Fit 1 is selected on the Parameters tab By highlighting refined parameters to be copied and right clicking on mouse a drop down menu is invoked Selecting Copy Refined To Initial will perform the desired initial parameter update as illustrated in Figure 2 8 Chapter 2 Quick start 14 ni example ddp tutorial ni example ddp PDFgui File Edit View Fits Phases Data Calculations Help S Qse qa SES TE Ni stru Ni xray gr Rename Parameters Apply parameters Itt ttt tite tt teeter eee ee e P P eee tte PDFFIT Version 2 0 971 2007 02 02 Figure 2 8 Updating the set of initial values of refined parameters The fit can be displayed graphicall
7. 3m and hit enter You can also type Fm 3m or 225 the space group number This will expand the unit cell accordingly showing 4 Ni sites Chapter 3 Examples and tutorials 19 v PDFgui ex File Edit View Fits Phases Data Calculations Help EUIS e u iTee ne Configure Constraints Results vV Ni from scratch S Phase Constraints d d d alpha beta gamma Space Group Constraints 4 atoms selected Space Group i v Origin Offset 0 0 0 0 Plot Control x x constrain positions step E 7 constrain temperature factors offset 3 Plot Reset Figure 3 2 Setting up symmetry constraints to be used in a refinement In order to set the symmetry constraints for the refinement select Constraints tab highlight all the atoms and right click to invoke a menu Note that hitting Control and A simlutaneously will select all the atoms if the grid is active If the Fit Tree is active it will select all tree items Click on Symmetry constraints and a dialog box will appear asking for the space group to be used and whether you want the positions and or the thermal parameters to be constrained as shown in Figure 3 2 The default is to use the space group used for expansion and to constrain everything according to the symmetry Since all the positions are speci
8. 880K gr 980K gr 1050K gr 1100K gr and 1150K gr We will establish a T series fit sequence Select Macros from the Fit menu on the menu bar and choose Temperature Series The Current Action panel will reflect the selection A tool is provided that allows for data sets to be added Click on Add button Using Shift and mouse select operation you should select all the data sets mentioned in the above list except the 300 K one as this is already in the template fit and then press Open button All the data sets will be loaded Since the files contain meta data as mentioned earlier the gui is going to pick up temperature information from the files User should verify that the information is correct The data can be ordered by temperature by clicking the Temperature header Chapter 3 Examples and tutorials 25 Imo template ddp tutorial Imo template ddp PDFgui File Edit View Fits Phases Data Calculations Help 9 Q9 e u Select a fit from the tree on the left then add datasets and assign D temperatues below If you have not set up a fit to be the template E for the series hit cancel and rerun this macro once a fit has been created TH LaMno3 PBNM Temperature Data Set Ei 300k 550 0 550K gr e 650 0 650K gr 700 0 700K gr 720 0 720K gr 730 0 730K gr 4 740 0 7
9. Angstroms in contrast to 32 inverse Angstroms in previous example Since different instrument was used the value of Qdamp is different than in previous example Icmo template ddp tutorial examples Icmo template ddp PDFgui File Edit View Fits Phases Data Calculations Help 9E Qd ou _ Select a fit from the tree on the left then add datasets and assign 7 Elicmo pbnm doping elements and values below If you have not set up a fit to be DI Lamno3 PBNM x000t010q35 gr the template for the series hit cancel and rerun this macro once a fit has been created Base element La Dopant Ca Doping Data set 0 04 _ 04t010q35 ar 16 0 16t010q35 ar 20 0 20t010q35 gr 24 0 24t010q35 gr 28 0 28t010q35 gr oo to sort by doping Ki Delete e OK 3 Cancel offset 5 Plot Reset Figure 3 8 After loading of the Ca doping data series of LaMnO3 system proper doping assignment needs to be carried out as the doping levels introspected from the file names in this example incorrectly reflect the scientific situation Note that dopant atom has to be present in the template seed used to generate the linked sequence of fits In the same directory data corresponding to various Ca contents exist collected at 10 K temperature in particular 2004t010q35 gr 2012t010q35 gr z016t010q35 gr 2020t010q
10. E Configure Constraints Results Y Fit 1 T Nistru Data Set Constraints Scale Factor 1 Qdamp 2 Qbroad Spdiameter PlotControl o x E r v IY Gdiff Gobs Gtrunc dGcalc offset 5 B Figure 2 4 Setting up the refinement parameters and constraints Further we set constraints related to the structural model by selecting the Ni stru on the Fit Tree adjusting the initial parameter values if necessary not done here and proceeding to the Constraints tab We assign the refinement parameter 3 to all three lattice constants a b and c reflecting the fact that the structure is cubic Isotropic ADPs are assigned to all Ni atoms in the refined cell as refinement parameter 4 This can conveniently be done by highlighting all the appropriate boxes together and type only once 04 The outcome is shown in Figure Figure 2 5 Chapter 2 Quick start 11 vy PDEgui File Edit View Fits Phases Data Calculations Help 9 20 eo Hl Configure Constraints Results v Elit lw stru Phase Constraints El Nav er DES pe ee alpha beta gamma Scale Factor deltal delta2 sratio rcut Included Pairs all all elem x y z ull w22 u33 nz s as oce 1 Ni ba 4 4 4 4 2 Ni 4 4 3 Ni 4 04 Y 4 Ni Q4 4 4 offset 5 Plot Reset Figure 2 5 Setting u
11. for graphically displaying the fits as well as various fit related parameters The content of the Current Action panel changes as the refinement is being set up It is a functional panel through which the user configures the fit attributes sets the fit constraints reviews the fit settings displays fitting results and also carries out other setup steps The progress of the PDFfit2 program is displayed in the PDFfit2 output panel All panels except the Current Action panel are dockable windows that can be dragged across the screen resized and arranged to accommodate the individual visual needs of the user The window layout can also be controlled via the View drop down menu on the menu bar An important part of the PDFgui operativity is also conveniently available through mouse operations such as select and right click 2 2 Creating a simple fit using a preexisting structure file The purpose of this example is to familiarize the novice user with the PDFgui basics The goal is to create a simple fit of Ni PDF from a preexisting structure file associate a dataset with the refinement configure and execute a refinement and display the result Files to be used in this exercise are Ni stru and Ni xray gr To start invoke PDFgui First a new fit needs to be established In the Fit Tree pane right click the mouse button and select New Fit This will generate a new fit called Fit 1 in the Fit Tree The Current Action panel will change accordingly wi
12. is displayed which can be adjusted rotated and zoomed in and out through the mouse functionality The size of the displayed atoms can be controlled via Page Up and Page Down keys For advanced AtomEye usage please consult corresponding AtomEye user documentation An example Ni structure visualization is shown in Figure 4 2 v ni example ddp tutorial ni example ddp PDFgui ERR File Edit View Fits Phases Data Calculations Help DEES olm Fere Configure Constraints Results v Erfti Sm Phase Configuration EU Ni xray or structure Ni FCC lat 2 lat 3 ull l ull 2 s Plot Reset Figure 4 2 Using AtomEye functionality if installed on your system for 3D visualiza tion of the initial and refined PDF structures example of Ni structure 4 3 Advanced usage and special needs The PDFgui is designed to accommodate most common modeling situations However it is not encapsulating all the capabilities available within the modeling engine such as calculation of differential PDFs handling atoms with special scattering properties etc Advanced usage of PDFfit2 engine to resolve any such special modeling need that user may have is available through usage of Python scripts in the expert command line mode similar to that featured in the PDFFIT program where various special situations could be accounted for Handling these situ
13. nano ddp This project contains two fits the first one is a bulk CdSe reference and the other pertains to the CdSe nanoparticle For consistency the PDFs of both bulk and nano samples were obtained using Qmaz of 14 inverse Angstroms although the bulk material PDF could have been processed using a higher value Synchrotron x ray radiation was used to obtain the data at 300 K based on an experiment carried out at 6 ID D at the Advanced Photon Source at Argonne National Laboratory The structure used for both data sets is wurtzite space group P63mc From calibrations on Ni standard Qdamp value of 0 0486 was obtained and is used here We first carry out a refinement on the bulk reference This is carried out over a range from 1 7 to 19 8 Angstroms using 7 parameters lattice parameters a and c 07 and 02 respectively selenium z fractional coordinate 011 isotropic ADPs for Cd and Se 021 and 023 respectively the data scale factor 0100 and finally correlated motion related quadratic term coefficient delta2 0200 The converged fit results in parameter values that can be further used for reference when modeling the nanoparticle data We note that while the fit is reasonable the values of the isotropic ADPs are enlarged The fit can be further improved if anisotropic ADPs are introduced although the z direciton related components Chapter 3 Examples and tutorials 31 will remain enlarged due to the stacking disorder present in the structure Th
14. of the fatures of this PDF modeling suite is a capability of modeling the effect of the finite nanoparticle size using a spherical form factor Relevant PDF parameter is Spdiameter which is the diameter of the nanoparticle The PDF nalysis is rather difficult as this parameter is highly correlated with various other parameters one would like to refine such as anisotropic ADPs scale factors correlated motion parameters and so on The refinement procedure is therefore rather delicate and the solutions are not as robust as we are used to in cases of crystalline materials Chapter 3 Examples and tutorials 30 v CdSe nano ddp tutorial examples CdSe nano ddp PDFgui DIN File Edit View Fits Phases Data Calculations Help E u eo u Parameters Results v E cdse bulk ficis murze stru itil xed Refined E cdse bulk gr S C 4 302215896 E 2 701 D 7 00611078346 0 373083000599 Plot 38 CdSe 3nm gr G CdSe 3nm gr G e X x 35 3005 y 0 246248 red cmisq 3818 15 KW U 3282460 offset 5 Plot Figure 3 10 Fitting the structure of a nanoparticle 3nm CdSe nanoparticle example To illustrate the program capabilities we present a case of CdSe nanoparticle approx imately 3nm in size It useful to have PDF data for a crystalline reference where avail able applicable In this exercise we start from a prepared project file CdSe
15. results in an exponential dampening of the PDF peaks which is modeled using the parameter qdamp Index Index A acknowledgements 000s seen eee 2 advanced USAGES isis oe eet PERRO 33 availability i2 bre eee deena des RARE 3 B building structure from scratch 17 C calculating PDF ege genee ebe EE eda es 20 COMMUNIGY iu epepERPewee lv wed pP RR 5 copyright zcenierl cd dere eeweepEuid Mb RI 2 D displaying the structure 33 doping TEEN 26 E le WEE ER 35 I installation secsi resce 294 29 P464 re inpr 3 introduction uellsLIeBRbRSPQQ4dev enr didlos 1 Ee Ce THE 17 L list Of variables o Ae ELiS CER s 35 M dn ES uc be E ea EA 5 multistage TEE 21 38 N nanoparticle diameter ee 29 Nanoparticle size ic beech EE sede ee 8 nanoparticle structure 29 P PDF plotting oth EDS der 32 SE 42er ger ERE A ERI 1 PDF fit variables vo yere p ena 35 PID Egi 222122 4 ReRtips EE 2 PD oui layout id rx EEN ie 6 PDF gui reference beet 35 PDFgui shortcut kens 35 Quick Start dE Reokeermll3ei dE dek D R IcSOIlOB Saws AOL LPTPNRIDaN D Gens da tee 23 reference sheets cus asp Ive Rp p ORAE Up 35 refinement ee dE prede Ged eeu een 6 12 sequential fitting 21 23 24 26 Seet pM PER 35 simple f t s2nlclseelec9ebie le 4e B EAM 6 Sp cial eege ic icon bee ER PURSE wd vanos 33 symmetry expansion sees Ir T temperature serien 2
16. this exercise is Ni zray gr To start invoke PDF gui To begin a new fit again needs to be established by right clicking the mouse button on the Fit Tree pane and selecting New Fit This will generate a new fit called Fit 1 as in the previous example The next step in populating the fitting tree is to introduce a structural model This time a new phase will be added and the model built up from scratch Select the fit icon in the Fit Tree pane Then right click the mouse invoking a drop down menu Select Insert Phase which will modify the current action panel The same action could be performed from the Phases drop down menu on the menu bar by selecting New Phase In the current action panel options are offered to load a structure from a file or to generate it from scratch Select New to build up structure from scratch The Fit Tree will be populated with a new item New Phase Rename this phase to Ni fcc The Current Action panel now displays default phase configuration with dummy values and no atoms Edit the lattice parameters and set them to reflect the symmetry in this case set the lengths to 3 52 Angstroms and all the angles to 90 degrees The Tab keyboard shortcut feature can be used for moving quickly from one form field to the next To introduce new atoms right click with your mouse onto elem tab in the Current Action panel and select desired number of atoms in the asymmetric unit via the dialog box that po
17. 0 5 0 0 0 5 0 0025 0 0025 0 0025 0 0 0 0 0 0 1 0 Iv 0 5 0 5 0 0 0 0025 0 0025 0 0025 0 0 0 0 0 0 1 0 offset 5 Plot Reset Figure 2 1 PDFgui window with Fit Tree and Plot Control panels to the left and Current Action panel to the right The Fit Tree panel features the current fit and the loaded Ni structure which is selected The current action panel displays phase configuration within the Configure tab Figure 2 1 shows the PDFgui appearance at this stage of the exercise The Current Ac tion panel has three tabs Configure Constraints and Results that could be selected using mouse These will be returned to later The Configure panel displays configuration information from the structure file The top portion contains lattice parameters phase scale factor and a set of parameters intended to be used to account for correlated atomic motion effects that typically sharpen the nearest neighbor PDF peak These are delta1 delta2 sratio and rcut Their usage is explained later The bottom part of the panel con tains standard unit cell content related information such as atomic species their fractional coordinates anisotropic ADPs and site occupancies The next step is to load an experimental data set to be fit To achieve this Fit 1 is selected on a Fit Tree and a drop down window is invoked by a right click of a mouse From the menu Insert Data Set is chosen The same action could be
18. 35 gr 024t010q35 gr and x028t010q35 gr It should be noted at this point that the data files do not contain any relevant meta data in the file headers However the doping level is somehow encrypted into the file names We will establish a doping series fit sequence Select Macros from the Fit menu on the menu bar and choose Doping Series The Current Action panel will reflect the selection Base element and dopant need to be specified A tool is provided that allows for data sets to be added Click on Add button Using Shift and mouse select operation you should select all the data sets mentioned in the above list and then press Open button All the data sets will be loaded The gui will introspect both the file names and files themselves in attempt to obtain the doping or in previous example temperature information Since the files do not contain meta data as mentioned Chapter 3 Examples and tutorials 28 earlier the gui is going to pick up doping information from the file names User should verify that the information is correct In this particular case the doping information will not be correctly picked up as for example 004 from the name is meant to be 0 04 doping and the gui would try to interpret it as 4 0 doping Similarly 028 would be interpreted as 28 0 while it was intended to mean 0 28 doping These values should be edited and fixed manually by clicking on the corresponding values and simply typing i
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20. 40K gr v 750 0 750K gr EE Plot Contral X 800 0 800K gr x 880 0 880K gr step v 980 0 980K gr Y 4 z J 4 Add Delete Plot Reset Figure 3 6 Setting up a T series sequential refinement for LaMnO3 Ordering by tem perature will ensure that the fits are linked correctly Order the data by temperature Figure 3 6 as otherwise the series of fits that is to be automatically generated in the next step will be linked in an arbitrary way in which the data were loaded rather than to reflect the scientific logic There should be 13 data sets Next ensure that the template fit is selected on the Fit Tree If this is the case the OK button becomes clickable Clicking on the OK button will generate a sequence of linked fits in the Fit Tree in the order of the temperature increase These fits are linked which can be verified by inspecting the initial values on the Parameters tab of each fit Highlight all the fits in the Fit Tree to start the sequential refinement of the T series The results can then be displayed in Fit Control such that various converged fit parameters are plotted versus temperature In terms of the science behind the LaMnO3 example it is interesting to plot isotropic ADP of the oxygen at general position Select all the phases on the Fit Tree by selecting one and then clicking on Control
21. HEN ud Petes beds ddp duse d 1 1 2 IPD FSU ccs eie ten oe On eoe Pe EAR CDU aenea 2 1 2 1 Design principles 2 12 2 Capabilities 4 ceci eret Kee Rr eR EE EUR 2 1 3 Availabilty otic exin ni rre aud ab ea vado ees edd vai edd 3 l4 Installation 2c e btt en SE E Raps ded 3 Unix Linux MAC uoa doccia sarees aes Cro xa d CERE dug ox 3 WindOWS 22 eben da EUER E IA UO or e eda Pa ont eds 4 Building from Subversion repository ss eese eee e eee 4 L5 Community asis aata mna e ertt a tt eR Re RAT ch 5 2 QUICK Stall ases e3epevkseet e dawekxe wx ipe 6 2 1 PDEsu layout nt i eR CLER ee SER beards 6 2 2 Creating a simple fit using a preexisting structure file 6 3 Examples and tutorials eh 17 3 1 Building structure model using crystal symmetry 17 3 2 Calculating PDF from a structure 19 3 3 Sequential tts 21 3 94 1 Multistage fitting selon debe kd poe RR d 21 3 3 2 Sequential fitting of incremental r series 22 3 3 3 Sequential fitting of temperature series 24 3 3 4 Sequential fitting of doping serien 26 3 4 Nanoparticle structure 29 do BRIS oes coe eh AE Rp xve des vg ue ex AE 32 4 1 PDF plotting 2 044 523 mm e teh pee ERR 32 4 2 Displaying the structure 33 4 9 Advanced usage and special need 33 5 PDFgui reference sheets 35 5 1 PDE guishortcut kee cess eee ead ete rte regan eed 35 5 2 List of PDFfit2 vanables 0 0 22 35 New Vari
22. PDF gui user guide 1 0 Beta release 06 July 2007 C L Farrow P Juhas J W Liu D Bryndin E S Bozin J Bloch Th Proffen and S J L Billinge Acknowledgements PDFgui was developed as part of the Distributed Analysis of Neutron Scattering Data DANSE project which is funded by NSF under DMR 0520547 The PDFfit2 development was funded by NSF under contract DMR 0304391 The program is part of the DiffPy and DANSE open source projects at Michigan State University and is available subject to the conditions and terms laid out below Several of the examples in the tutorial part were made possible and benefited from samples synthesized by J F Mitchell and from data collected and processed by M Schmidt P G Radaelli and X Qiu If you use this program to do productive scientific research that leads to publication we ask that you acknowledge use of the program by citing the following paper in your publication 1 C L Farrow P Juh s J W Liu D Bryndin E S Bozin J Bloch Th Proffen and S J L Billinge PDFfit2 and PDFgui computer programs for studying nanostructure in crystals J Phys Condens Matter 19 335219 2007 Copyright 2006 2007 trustees of Michigan State University all rights reserved For more information please visit http www diffpy org or contact Prof Simon Billinge at billinge pa msu edu Preface Using PDFGui and PDFfit2 Redistribution and use in source and binary forms wi
23. ables 0 0 00 ce cece eee eect hh 35 Renamed Variables 0 0 0 cece eect teens 36 Preserved Variables 2 5442 odo s crc duane ine teed d tee 37 PDF Peak Width 0 0 cece pihit paR EEE EE EE ei 37 Chapter 1 Introduction 1 1 Introduction PDF gui is a graphical interface built on the PDFfit2 engine which is a program as well as library for real space refinement of crystal structures based on the atomic pair distri bution function PDF method PDF gui organizes fits and simplifies many data analysis tasks such as configuring and plotting multiple fits PDF fit2 is capable of fitting a theoret ical three dimensional structure to atomic pair distribution function data and is ideal for nanoscale investigations The fit system accounts for lattice constants atomic positions and anisotropic atomic displacement parameters correlated atomic motion and experimental factors that may affect the data The atomic positions and thermal coefficients can be con strained to follow symmetry requirements of an arbitrary space group The PDF fit2 engine is written in C and accessible via Python allowing it to inter operate with other Python programs 1 1 PDFfit2 PDFfit2 is a major upgrade to PDFfit and inherits many of its features PDF fit is capable of fitting a theoretical three dimensional structure to an experimentally determined PDF It can simultaneously fit multiple structures accounting for different structural phases in a m
24. aded The program automatically computes the analytical derivatives of the constraints that are required by the minimization routine This simplifies user input and reduces the possibility of errors In addition new fitting parameters for handling dynamic atomic correlations and experimental resolution have been introduced as well Instead of rewriting the PDF fit command interpreter which is used to define the fitting problem and to control and run the refinement its functions are carried out using the Python language http www python org Python is a powerful cross platform open source interpreted programming language i e it does not need to be compiled to run similar to scripting that emphasizes object oriented and modular design PDFfit2 scripts written in Python syntax take the place of PDF fit macros and the Python interpreter can handle everything that the old interpreter could and more Using Python as an interpreter Chapter 1 Introduction 2 allows PDF fit2 to be combined with and enhanced by other Python libraries We make use of this capability with PDF gui as described below 1 2 PDF gui The PDFfit2 engine can be used either directly from the Python command line or as part of larger and more complex software applications The first application built on PDFhft2 is PDF gui a graphical environment for PDF fitting 1 2 1 Design principles PDFgui has been designed to provide users with an easy to use yet powerful inter
25. al these will not be refinable by symmetry and the thermal parameters will be isotropic The program will assign parameters according to symmetry using default names that can be renamed and or reassigned by the user To be consistent with the naming from the first example one could assign the lattice parameters as 3 and the isotropic ADPs as 4 Note that parameters can be quickly renamed or consolidated in the Parameters panel of the Fit node using the right click menu It is important to note that the table reflecting constraints is the only place that program refers to for the symmetry What is written there will be used and if the table is tampered with then the original symmetry obtained using symmetry expansion feature will not be preserved Therefore the expansion tool represents a convenience tool and nothing more than that The remaining steps of this example are identical to these described in Section 2 2 Simple fit page 6 Chapter 3 Examples and tutorials 20 3 2 Calculating PDF from a structure There is often a need for obtaining a calculated PDF profile for a given structure instead of performing a fit In order to carry out a calculation an underlying structure needs to be specified This can either be loaded from a file or generated from scratch Suppose that we have a Ni structure populating a Fit Tree using steps described in either Section 2 2 Simple fit page 6 or in Section 3 1 Symmetry expansion page 17 and t
26. anage multiple fits at once Each fit can have multiple experimental data sets and structure models Fits in a sequence can call upon other fits for their starting parameters and configured fits can be queued to run while the user is away All the initial final and intermediate data are stored in a platform independent project file that can be loaded on any computer All management tasks such as fit creation configuration modification and visualization can be done through the graphical interface PDF gui can be configured to run fits on a remote computer This uses the secure shell protocol ssh2 so that the connections are stable and secure In this distributed mode the core fitting computation does not compete for system resources with the graphical functions which speeds up the fit over fast network connections and gives faster user response at the console PDFgui supports space group operations Users can define an asymmetric unit and let PDF gui expand it to a full cell with all symmetry related positions PDFgui can also gener ate symmetry constraints for atom positions and atomic ADPs Users just need to specify the space group and the program will identify equivalent sites and generate constraint equations for their coordinates and temperature factors to keep the structure consistent Chapter 1 Introduction 3 with the symmetry requirements This can be done either for all atoms in the structure or for an arbitrary subset for exa
27. are provided hoping that the usage is sufficiently simple for users to master individually with ease An example plot of Rw vs refinement step is shown in Figure 4 1 for Ni example v ni example ddp tutorial ni example ddp PDFgui 5 x File Edit View Fits Phases Data Calculations Help DEUSE Re r reme nena Vv EAS i TE Ni stru EU Ni xray g Fit 1 rw Fee Plot 0 Fit 1 rw meters 3 4 TCENEEEEN Ge x 2 95053763441 y 0 15054945054 OOF G 2a x offset 3 Plot Reset Figure 4 1 Plotting window featuring Rw vs refinement step for Ni example The basic functionality for manipulating the plot is provided through icons on the tool bar of the plotting window Chapter 4 Extras 33 4 2 Displaying the structure For those users having AtomEye structural visualizer available in their system configuration PDFzgui allows for initial or refined structures to be visualized by passing required struc tural information to AtomEye that is invoked and corresponding 3D structure displayed on screen This is achieved by highlighting a desired phase on the Fit Tree and then selecting Plot Initial Structure or Plot Refined Structure from the Phases drop down menu The quickplot button will also invoke AtomEye with the refined struture or initial structure if the refined structure does not yet exist Corresponding structure visualization
28. ase float A or degrees i 1 2 6 Lattice parameters a b c alpha beta gamma of the current phase Can be also used as lat a etc x n y n zOD Phase float unitless Fractional coordinates for atom n rcut Phase float A default 0 A Radius cutoff for applying sratio sharpening factor PDF Peak Width The PDF peak width contains contributions from thermal and zero point displacements as well as static disorder For large distances r the motion of the two contributing atoms is uncorrelated for small distances however the motion can be strongly correlated leading to a sharpening of the first peak s in the observed PDF The program PDFfit2 provides three different correction terms for the PDF peak width The final width is given by A A Tij af ES CS E road T3 Here the primed sigma is the peak width without correlation given by the structural model The first two terms correct for the effects of correlated motion Within the scope of the users guide we just mention that the term delta2 r describes the low temperature behavior and term deltal r describes the high temperature case Since the two parameters are highly correlated one will in practice choose which one to refine The last term in the equation models the PDF peak broadening as a result of the Q resolution of the diffractometer In many cases this term will only be significant for refinements over wider r ranges Note that the Q resolution also
29. aterial PDF fit has a constraint system that allows expressing structure variables as sim ple functions of fitted parameters PDF fit structure variables include lattice constants data and phase scale factors atomic site occupation anisotropic atomic displacement parameters ADPs and atomic vibrational correlations PDF fit has a built in FORTRAN style com mand language that understands simple FOR loops and some built in arithmetic functions The original PDF fit was written in FORTRAN 77 which imposes some limitations on the program For example it uses fixed size arrays for internal storage This precludes the analysis of structures with large cells without modifying the code Though the constraint system is powerful it requires that a constraint equation be accompanied by its first deriva tive This places the burden of determining the derivatives on the user which can introduce errors that lead to instability in the convergence Furthermore the code is monolithic not easily extensible and hard to integrate with external programs The primary focus of PDFfit2 development was to remedy the limitations of PDF fit while extending its functionality The old PDFfit engine has been completely rewritten in C and many bugs have been fixed The new engine uses dynamic memory allocation so that the size of the structure or extent of the fit range of the PDF is limited only by the physical memory available The constraint system has also been upgr
30. ations requires detailed knowledge of the PDFfit2 Chapter 4 Extras 34 syntax based on Python which is beyond the scope of this user guide and will be described elsewhere Chapter 5 PDFgui reference sheets 35 5 PDF gui reference sheets 5 1 PDF gui shortcut keys Fit Tree Ctr1 A Select all items in the Fit Tree Ctrl Shift A Once an object is selected on the Fit Tree using this shortcut key will sellect all the objects on the tree that are of the same type For example if a single data set is selected on the tree hitting this hot key will make all the data sets belonging to all the fits in the tree to become selected This is particularly useful for simultaneously plotting various fit results across the Fit Tree Ctrl C Copy selected item Ctrl X Delete selected item Note that this does not place a copy of the item in the clipboard Delete Same as Ctrl X Ctrl V Paste previously copied item Note that this will only paste the item to a legal position in the tree For example a phase node cannot be pasted into an empty tree Phase configuration grid Ctri A Delete Ctrl Ctrl Select all items Delete row This will delete any wholly selected row Add an atom to the grid Same as Delete Phase constraints grid Ctrl A Delete Select all items Delete contents of selected cells 5 2 List of PDFfit2 variables The following is the list of PDFfit2 variables including their default values in pare
31. ch can be found under the View menu and represents a convenient way for generating storing and using for further refer ence of project related notes as illustrated in Figure 2 11 These notes can be exported as a text file or saved along with the entire project v ni example ddp tutorial ni example ddp PDFgui DIN File Edit View Fits Phases Data Calculations Help Project Journal bi EAS Fantastic fit of Ni data has been obtained using TE Ni stru EU Ni xray ar Apply parameters offset 3 Export Plot Reset Figure 2 11 Using Journal feature can be a convenient way for taking notes The project can be saved at any stage in its present configuration through choice of Save Project as or Save Project as appropriate from the File drop down menu The PDFgui project file has ddp extension In addition to saving a project various parts of the project both structure related and data related can be exported to external files by making an appropriate selection from the Phases and Data drop down menus The phases starting or converged are saved as standard PDFFIT stru files The model PDF profile can be exported through Data menu and will be saved as a five column fgr file The first four columns are r G r dr and dG r and the fifth column is the d
32. e PDFFIT Version 2 0 971 2007 02 02 Figure 2 6 Reviewing the fit parameters and conditions 12 The setup for the present example is now completed By selecting Fit 1 on the Fit Tree the Current Action window shows Parameters tab which displays the used refinement parameters for review Figure 2 6 It shows the initial values and allows for updates and for refinement parameters to be released or fixed depending on whether the corresponding Fixed box is unchecked or checked respectively The Refined column which is currently empty will be populated with the refined values of the parameters If the initial parameter values are to be changed using Apply parameters button will update the values of the parameters on all relevant setup tabs The refinement is executed by clicking the gear icon on the tool bar The refinement could be stopped by clicking on the stop icon on the tool bar During the refinement the refinement progress will be directly reported in the PDFhfit2 Output panel This is illustrated in Figure 2 7 Chapter 2 Quick start 13 ni example ddp tutorial ni example ddp PDFgui File Edit View Fits Phases Data Calculations Help BERUSET Parameters E Parameters Resus TE Ni stru Ni xray gr f 0 759662217159 0 0685537741738 3 5316062748 0 00512703158962 Apply parameters Refinement parameters 1 0 759662 2
33. e referent value of 5 69 for delta2 will be used as a starting value for the nanoparticle fit In the nanoparticle refinement we will use the same starting values for all the parameters except for delta2 and the nanoparticle diameter The former is set to 5 69 and the later to 25 Angstroms In other cases an approximate value of the spherical nanoparticle size is usually known and it is the best to start from a reasonably good guess Refining the nanoparticle data reveals nanoparticle diameter of approximately 30 Angstroms as further illustrated in Figure 3 10 Enlarged values of isotropic ADPs are again observed and the fit is reasonably good Further improvements can be obtained by introducing anisotropic ADPs where again values related to the z direction will remain abnormally large most probably due to the stacking related disorder The fitting protocol is not very robust as mentioned earlier Enthusiastic user is encouraged to play around with the refinement conditions and witness the difficulties Going into the greater details of the structural properties of nanosized CdSe is beyond the scope of this tutorial The successful fitting scenario depends on particular details of a structural problem one is determined to solve The problem of determining the structure of a nanopartcle remains difficult The PDFgui suite is not intended to necessarily provide the solution it is rather a helpful tool in the process of determining new details and expl
34. ent modeling scenario is handling a large number of data sets originating from a single sample collected at various temperatures One of the common modeling schemes in such cases is to perform sequential fitting of such data series which is known to yield well behaved modeling parameters PDFgui has a pre written macro that allows for this modeling situation to be accommodated We will describe the procedure using an example of a temperature series of data col lected on LaMnO3 at various temperatures from 300 K to 1150 K at NPDF instrument at LANSCE at Los Alamos National Laboratory This material exhibits Jahn Teller J T order disorder phase transition just above 700 K where the long range orbital order is lost at high temperature but the local JT distortion survives The formal space group does not change at this transition To begin from the File menu use Open Project selection to open Imo template dpp project from the tutorial directory This project consists of a fit called mo pbmm which will serve as a template and which contains Pbnm phase of LaMnO3 and a 300 K data set The fit refinement is set up to cover 1 7 19 5 Angstroms range and all the parameter values are set to their converged values for this temperature The fit setup uses isotropic ADPs for all atomic sites In the same directory data corre sponding to various temperatures exist in particular 300K gr 550K gr 650K gr 700K gr 720K gr 730K gr 740K gr 750K gr 800K gr
35. face for fitting structure models to PDF data It makes use of an object oriented component based architecture which makes it highly extensible and maintainable This allows for powerful usability features such as real time plotting and remote execution of the fitting program whilst visualizing the results locally PDFgui has been designed with multitasking in mind It is multi threaded so that the work being done by the PDFfit2 engine does not interfere with the tasks of the user interface PDF gui is written in the Python programming language Python features a relaxed and friendly syntax supports write once run anywhere portability and has extensive libraries and modules for virtually every task Software codes written in a variety of programming languages can be bound into Python which allows them to be used together Python is becoming a popular choice in the scientific computation community PDFgui s interface is built using wxPython http www wxPython org the Python package for wxWidgets a mature cross platform GUI library Graphical applications writ ten in wxPython provide a look and feel native to the platform on which they are run PDFzgui is designed to run on Windows Mac OS Linux and all major Unix systems 1 2 2 Capabilities PDF gui contains all of the functionality of PDFfit2 along with additional enhancements for usability Mundane tasks are handled by the program and difficult tasks are made simple PDFgui can m
36. g sl delta2 lat 1 lat 3 ull l ull 2 ull 3 ull 4 ull 5 EET offset 5 Plot Reset Figure 3 9 Sequence of refined parameters such as lattice constants can be plotted vs doping using PDFgui plotting facilities Figure features lattice parameter b in Pbnm space group setting for series of Ca doped LaMnO3 samples for doping concentrations between 0 and 0 28 at 10 K temperature Chapter 3 Examples and tutorials 29 After the convergence is achieved for all the fits in the Fit Tree the results can be displayed in Fit Control such that various converged fit parameters are plotted versus Ca content An example is provided in Figure Figure 3 9 featuring one of the lattice parameters 3 4 Nanoparticle structure Determining the structure of a nanoparticle is notoriously difficult Diffraction experiments on nanoparticle samples yield broad diffraction patterns that are hard to analyze using conventional crystallographic approach One of the options that remain is to approach the problem through the PDF analysis The PDF of a nanoparticle features sharp peaks conveying structural information The PDF signal gets damped at higher distances due to the convolution caused by the finite nanoparticle size For certain simpler cases when nanoparticles can be assumed to have spherical shape characteristic parameters such as nanoparticle diameter can be obtained One
37. gin create a fit as explained earlier The next step is to copy the fit This is achieved by right clicking on the existing fit name Fit 1 in the the Fit Tree and selecting Copy option from the pop up menu Once this is done a paste fit operation is done by right clicking at the empty space on the Fit Tree and selecting Paste Fit option from the pop up menu This will create Fit 1_copy a copy of Fit 1 in the Fit Tree The next step is to link the fits Select Fit 1 copy on the Fit Tree In the Parameters panel select the entire Initial column Type Fit 1 and then press Enter The Initial values of the parameters should now read Fit 1 n where n is the index of the parameter This brings us to the linking syntax which is name index Here name is the name of another fit to which the link is made and index is the index of a parameter in that fit If index is omitted it will default to the index of the parameter one is linking from A linked parameter uses the refined value of the link as its initial value This is useful when one runs several related fits An example of this is shown in Figure 3 4 Chapter 3 Examples and tutorials 22 Imo template ddp tutorial Imo template ddp PDFgui File Edit View Fits Phases Data Calculations Help S Qs e qa p Parameters Results v mo pbnm 550 a x H a Refined
38. hat we would like to calculate Ni PDF using neutron radiation Highlight the Ni structure on Fit Tree On menu bar select New Calculation from Calculation drop down menu Current activity panel will display information very similar to that when a data set is loaded as shown in Figure 3 3 iv PDEgui Ie ix File Edit View Fits Phases Data Calculations Help ale qa FtTee x 5 gt DEIN from scratch Calculation Configuration T Ni fcc Scatterer Type Neutron X ray Range 0 01 to 50 0 spacing 0 01 Qmax 25 0 Qdamp 0 08 Qbroad 0 0 Spdiameter 0 0 Plot Reset offset 5 Figure 3 3 An example of the calculation configuration panel User has to specify conditions to be used for the calculation such as radiation type calculation range and corresponding r grid size as well as instrument resolution and max imum momentum transfer parameters For the later two the default values of parameters could be used or values could be specified that closely mimic the experimental conditions on some particular instrument of interest After the conditions are set the gear icon on the tool bar can be used to execute the calculation or alternatively select Run Selected Calculation from the Calculations menu For our exercise select neutrons for radiation The defaults for the range and other parameters would work just fine To get an experiment data lookal
39. i appearance at this stage of the exercise The Current Ac tion panel has three tabs Configure Constraints and Results that could be selected using mouse These will be returned to later The Configure panel displays configuration information from the data file It should be noted that depending on the software used to prepare the experimental PDF from the raw data the file may or may not contain meta data reflecting the experimental conditions and configuration For example software PDFgetX2 and PDFgetN used to prepare PDFs from x ray and neutron total scattering ex periments respectively are supplying meta data in the header of the data file The PDFgui is picking up this information and filling the appropriate fields in the Current Action panel for data set configuration Caution should be exercised by the user to verify that these data indeed correspond to the experimental conditions In the present example x ray radiation is used and so the x ray selection is turned on for the scatterer type The data range fit range data scale factor maximum Q value used in Fourier transform to obtain the ex Chapter 2 Quick start 9 perimental PDF spherical form factor diameter used for nanoparticle samples to account for the PDF signal dampening due to the finite particle size and the experiment specific parameters are displayed These comprise parameters describing experimental resolution effects Qdamp and Qbroad and e
40. ibuted under a BSD license They run on Windows Mac OS Linux and all major Unix systems The source code is freely available For more information please contact Professor Simon Billinge billinge pa msu edu or consult the web page http www diffpy org News of updates and releases will be posted at this website and on the diffpy users group at http groups google com group diffpy users 1 4 Installation PDF gui is included as a part of DiffPy a Python library for structure analysis from diffrac tion data The latest version of DiffPy can be obtained from http www diffpy org Refer to the section corresponding to your operating system for specific installation instruc tions Unix Linux MAC For unix like operating systems DiffPy is provided as a source archive which needs to be built and installed A successful build of DiffPy requires several libraries and applications Before proceeding any further make sure the packages below are installed All of these packages should be available as RPM files for recent Linux systems and it is then best to install them using the respective package manager such as apt get or yum In case an RPM package is not available refer to the corresponding project page for other installation options Required packages python http www python org Python interpreter minimum version 2 3 Chapter 1 Introduction 4 python dev http www python org development files for Python gsl deve
41. ifference curve between the data and the model Note that the model PDF and the difference are only calculated within the user specified fitting range PDF gui allows for PDFfit2 scripts written to operate refinements in the expert mode to be imported into the gui This option along with the option of exporting gui generated scripts and exporting the refinement results is available through the Fits menu on the menu bar Chapter 3 Examples and tutorials 17 3 Examples and tutorials In this chapter we present series of examples and tutorials aimed at users already comfort able with the gui to provide training in advanced gui features designed for most common modeling situations such as building the structure from scratch calculating the PDF based on a given structure linking two fits and creating and executing a series of fits on a sequence of data sets 3 1 Building structure model using crystal symmetry The purpose of this example is to demonstrate to the user the symmetry expansion capa bilities of PDFgui The goal is again to create a simple fit of Ni PDF but this time from scratch rather than from a preexisting structure file Further goal is to associate a dataset with the refinement configure and execute a refinement and display the result The focus will be on the symmetry expansion features only and the steps that are described earlier in Section 2 2 Simple fit page 6 are left for the user to recreate File to be used in
42. ike calculation select for example 0 01 for the r grid size and use 0 08 and 25 0 Chapter 3 Examples and tutorials 21 for resolution and maximum momentum transfer parameters respectively Execute the cal culation Observe the result by clicking on the quick plot icon on the tool bar To export the calculated PDF use the Export Selected Calculation choice on the Calculations menu after highlighting the performed calculation in question on the Fit Tree 3 3 Sequential fitting In many practical situations there is a need to set a series of refinements that are linked in a sequence Whether motivated by following certain fitting protocol on a single data set or such that numeric fluctuations of refined parameters are avoided in a temperature series data or any other similar situation sequential fitting capability is of clear importance and is supported in PDFgui In what follows we will describe multi stage fitting capabilities of PDF gui followed by description of three pre made macros that implement sequential fitting fitting of series on a single data set temperature series on a set of data corresponding to various temperatures and a doping series on a set of data corresponding to samples whose chemical content changes in some systematic way These macros can be accessed from the menu bar Fits menu Macros selection on the drop down menu 3 3 1 Multistage fitting Here we describe how to string together several fits To be
43. l http www gnu org software gsl GNU Scientific Library numpy http numpy scipy org Numerical Python minimum version 0 9 8 wxPython http wxpython org GUI toolkit for Python minimum version 2 6 recom mended 2 8 python matplotlib http matplotlib sourceforge net plotting library for Python minimum version 0 90 Optional packages AtomEye http 164 107 79 177 Archive Graphics A structure viewer Once all of these are in place and working download the latest tgz archive of the DiffPy sources from http www diffpy org The version number is embedded as part of the file name Unpack the sources using the command gzip d c diffpy VERSION tgz tar xf where you need to change VERSION to match the name of the archive file This will create a new diffpy VERSION directory Change to this directory and execute as a root python setup py install This installs DiffPy to a default location in python site packages directory and ex ecutable scripts pdfgui and pdffit2 to python prefix bin If you don t have root access you can install DiffPy to other locations by adding suitable options to setup py script For a list of available options see python setup py help or python setup py install help Once PDF gui is up and running enter the location of the AtomEye executable under Edit gt Preferences Windows DiffPy is provided as self installing archive for Windows systems Download the latest
44. lp on usage of PDFgui PDF fit2 and other DiffPy packages This group should become a knowledge base of PDF gui user tips tricks and troubleshoot ing Feel free to ask your question here diffpy dev http groups google com group diffpy dev For discussions about development and changes of PDF gui PDF fit2 and DiffPy library in general Chapter 2 Quick start 6 2 Quick start In this chapter the PDF gui layout is briefly described followed by a simple tutorial example spanning the gui functionality and aimed at novice users Users familiar with the basics can proceed to Chapter 3 Examples and tutorials page 17 or use Chapter 5 PDF gui reference sheets page 35 All the files used in examples are available in the tutorial subdirectory relative to this document 2 1 PDFgui layout Once PDF gui is invoked a PDFgui window comes up Its layout consists of a menu bar a tool bar and a set of four panes The menu bar contains drop down menus that provide various aspects of PDFgui functionality The tool bar features icons for commonly used operations starting a new project or opening an existing one saving a project executing a refinement or calculation stopping a refinement or calculation and making a quick plot of a refinement The four panes consist of fitting plotting current action and PDFfit2 output The fitting pane is home for Fit Tree and is used in setting up a fit protocol The Plot Control panel serves the user s needs
45. mple when it is known that only a certain species show a local distortion The code for space group definitions was provided by the Python Macro molecular Library mmLib http pymmlib sourceforge net PDFgui also supports supercell expansion of a normal unit cell PDF gui uses the matplotlib http matplotlib sourceforge net Python package for 2D plotting of data and results Matplotlib has a friendly interface so the user can quickly and easily view the results of a fitting PDFgui lets users plot data from a series of fits and plot it against selected meta data temperature doping etc plot the results of several fits in the same window plot the PDF in real time as the fitting is running plot the parameters or variables in real time as the refinement evolves and save plots in common image formats or export the data to a text file PDFgui uses AtomEye http 164 107 79 177 Archive Graphics A for 3D visualization The modular nature of PDFgui allows for other alternatives in the future such as PyMOL http pymol sourceforge net PDF gui supports built in macros for advanced fits For example for a set of experimental data from one system at different temperatures or doping levels PDFgui can expand a template fit to a series of related fits Another PDFgui macro makes it easy to set up boxcar fits where the same model is fit over different r ranges of the PDF data 1 3 Availability PDFfit2 and PDFgui are open source and distr
46. n equal zero See definition of PDF Peak Width page 37 for detailed explanation uij n Phase float A ij 11 22 33 12 13 23 u i n in PDFFIT Elements of anisotropic displacement tensor of atom n occ n Phase float unitless ofn in PDFFIT Occupancy of site n pscale Phase float unitless csca p in PDFFIT Scale factor of the current phase deltat Phase float A default 0 A gamm in PDFFIT Coefficient for 1 r contribution to the peak sharpening See definition of PDF Peak Width page 37 for detailed explanation delta2 Phase float A default 0 A delt in PDFFIT Coefficient for 1 r contribution to the peak sharpening See definition of PDF Peak Width page 37 for detailed explanation Chapter 5 PDFgui reference sheets 37 sratio Phase float unitless default 1 srat in PDFFIT Sigma ratio for bonded atoms Reduction factor for PDF peak width accounting for correlated motion of bonded atoms Preserved Variables qmax Dataset float default 0 A qmax cutoff is an experimental parameter having fixed value determined during the PDF data processing in the Fourier transform step Finite data range used in the Fourier transform is a source of termination ripples Termination ripples are not applied in PDF calculation when qmax is set to zero The effect is calculated using the following equation SP 8 d G r Gisele r sin E ast f F 2 dr r r rr lat i Ph
47. n the correct values Figure Figure 3 8 The data can be ordered by doping by clicking the header After you are done with editing order the data by doping as otherwise the series of fits that is to be automatically generated in the next step will be linked in an arbitrary way in which the data were loaded rather than to reflect the scientific logic There should be 6 data sets with the initial x 0 0 data set there will be 7 chained fits total after this setup is done Next ensure that the template fit is selected on the Fit Tree If this is the case the OK button becomes clickable Clicking on the OK button will generate a sequence of linked fits in the Fit Tree in the order of the Ca content increase These fits are linked which can be verified by inspecting the initial values on the Parameters tab of each fit Highlight all the fits in the Fit Tree to start the sequential refinement of the doping series v Icmo template ddp tutorial examples Icmo template ddp PDFgui DIR File Edit View Fits Phases Data Calculations Help BEUS Configure Constraints Results SEMEEo S lij xoo0t010935 0r Phase Constraints E lcmo pbnm 0 040 SESE H x004t010q35 a v EA lcmo pbnm 0 14 bil H xo12t010835 v E lemo pbnm 0 1 SENET EU xo16t010q35 v E lcmo pbnm 0 24 LS WM a 1 b 2 c 3 alpha beta gamma Plot 44 lat 2 x a dopin
48. nged incrementally or when a fixed width r window is to be defined for a box car fitting approach An example of this would be a situation when details of crossover from local to average structure are examined PDFgui has a pre written macro that allows for this modeling situation to be accommodated We will illustrate these capabilities through a simple Ni example Generate a complete fit including a phase and a dataset as explained in Section 2 2 Simple fit page 6 Select the fit from the Fit Tree From the Fits menu select Macros and choose r Series option The Current Action panel will display simple setting requirements arranged in two rows of three dialog boxes each that need to be filled with values to be specified by the user An example of this is shown in Figure Figure 3 5 ni example ddp tutorial ni example ddp PDFgui File Edit View Fits Phases Data Calculations Help H o Select a fit from the tree on the left and set the first value last value SS and the step size of the maximum and or minimum of the fit range H below If you have not set up a fit to be the template for the series hit cancel and rerun this macro once a fit has been created TH Ni stru fit maximum EU Ni xray or first 5 last 20 step 5 fit minimum a 5 first last step s OK Cancel Bet Com NM X step Ka Ly Y C offset 3 Plot Reset
49. ntheses and a brief description and a note where appropriate Note that some of the variables used in PDFFIT are renamed in PDFfit2 The reference of these changes is provided for the convenience and orientation of those users that are used to the old naming scheme New Variables spdiameter Dataset float A default 0 A spdiameter is a particle diameter for PDF shape damping function Shape damping is not applied when spdiameter equals zero Chapter 5 PDFgui reference sheets 36 anisotropy n Phase anisotropy n bool inferred from uij n values Flag for anisotropic thermal displacements of atom n Setting of anisotropy n up dates the uij n or uisoequiv n values uisoequiv n Phase float calculated from uij n values Isotropic thermal displacement of atom n or equivalent displacement for anisotropic atom For anisotropic sites the setting of uisoequiv n scales values of the uij n elements uisoequiv n can be constrained only for isotropic atoms Renamed Variables dscale Dataset float unitless dsca s in PDFFIT Scale factor for the selected dataset qdamp Dataset float default 0 qsig in PDFFIT PDF Gaussian dampening envelope due to limited Q resolution Not applied when equal zero The Gaussian envelope is of the form rQdaamp 2 Br e qbroad Dataset float default 0 qalp in PDFFIT PDF peak broadening from increased intensity noise at high Q Not applied whe
50. oring the space of possible solution candidates yielding success in some instances Chapter 4 Extras 32 4 Extras 4 1 PDF plotting Plotting capabilities of PDF gui are provided through the Plot Control panel and the quick plot icon on the tool bar The Plot Control allows for selection of x and y coordinates for plotting The actual quantities that could be assigned to the coordinates is determined by selection of either Fit or Phase or Data on the Fit Tree The choices for r and y coordinates varies depending on what is selected on the Fit Tree Special options like index temperature and doping are available as choices for x in cases of plotting multiple fit results from sequential fitting protocols The plot window provides essential functionality such as zoom pan cursor coordinate tracking and shifts Features such as saving exporting and printing are also available The principal intent of the plotting functionality is to allow quick access to the fitting results to enhance the scientific process If data is selected on the Fit Tree the user can plot various aspects of the PDF function such as data model and difference PDF profiles as a function of inter atomic distance r If the fit or the phase are selected then various parameters both structural and internal can be plotted instead Since several formal plotting examples were given through the tutorial exercise and having simplicity of usage in mind no other plotting examples
51. p the refinement parameters and constraints It should be noted that as a part of the PDFfit2 syntax a refined variable can also be defined as a math expression f n1 0n2 0Nn3 where n1 stands for fitted parameter and nl n2 are arbitrary positive integers enumerating the parameters This allows simple linking of related variables For example since cell lengths a b and c are all expressed as 03 the refined structure will remain cubic Also note that the enumeration of the parameters can be arbitrary enumeration does not have to follow any particular order The quantities within a fit that are enumeratued with the same number will be assigned the same parameter hence caution should be exercised to avoid unintentional assignment of the same parameter to physically different quantities The automatic parameter assignment is done in such a way as to disallow for such situations to happen If assignment is done in part manually in particular for complex setups it is recommended to verify that the parameter assignment is done correctly Chapter 2 Quick start E 2 9 e File Edit View Fits Phases Data Calculations Help D eee e PDF gui Bee eg TH Ni stru Ni xray gr offset 3 Plot Reset npe Jo 2 Apply parameters ee fede e Pee e Pe Tee e Pee e Pe Tee Pe Pe eee Pe Tee Pe Pee ee Pe e Pe Pee e Pe De e e Pe P e Pe De De Se Pe e De Se De ete ten
52. performed through a menu bar Data drop down menu and selecting New Data Set The Current Action panel changes accordingly giving an option for a data set to be loaded from a file In this exercise Ni PDF data obtained using synchrotron x ray radiation collected at 6 ID D at the Advanced Photon Source is used This is contained in a file Ni xray gr which is to be Chapter 2 Quick start 8 loaded Note that among the exercise files there is also a file Ni neutron gr obtained using neutron radiation at the GPPD diffractometer at the IPNS facility at the Argonne National Laboratory Both x ray and neutron datasets were collected at 300 K vj PDFaui BBE File Edit View Fits Phases Data Calculations Help BEUS al Cem n Configure Constraints Results v fiti SIE Data Set Configuration WNI xray EF Ni xray cr Scatterer Type Neutron X ray Fit Range 0 01 to 20 0 Scale Factor 1 0 Qmax 40 0 Qdamp 0 001 Qbroad 0 0 Spdiameter 0 0 Temperature 300 0 Doping 0 0 MECRO X r Iv IY ESP Gdiff Gobs Gtrunc dGcalc offset 5 Plot Reset r K Figure 2 2 Appearance of a PDFgui window after a PDF dataset is loaded The Fit Tree panel features the current fit loaded Ni structure and loaded Ni PDF dataset G r which is selected The Current Action panel displays data set configuration within the Configure tab Figure 2 2 shows the PDFgu
53. ps up In Ni case select one row only After action is invoked a new row will show up in the table This can also be performed by hitting Control Shift and simulataneously Type in Ni for the element name It is important that the element name is typed in correctly as this is further used to search a database for the scattering characteristics of that site Further highlight the three diagonal ADPs and type in the initial value 0 0025 To enter a specific isotope use the NucleonNumber Symbol syntax for example 12 C This does not apply for deuterium and tricium which have isotope symbols D and T Chapter 3 Examples and tutorials 18 PDFgui ox File Edit View Fits Phases Data Calculations Help Eueo u Configure Constraints Results U E Ni from scratch ama Phase Configuration a 3 52 b3 52 alpha 90 0 90 0 Scale Factor 1 0 Space Group Expansion Space Group Expansion 1 atom selected Expanding to 4 positions Space Group v Origin Offset 0 0 0 0 3 Cancel Figure 3 1 Expanding the unit cell using space group information Now right click with the mouse on the element name and select Expand space group option A dialog box will appear as shown in Figure 3 1 requesting space group information and the choice of origin Choose Fm
54. t to say 5 6 Angstroms and observe the outcome The refinement sequence execution should be very quick in this case 3 3 4 Sequential fitting of doping series Fitting a series of PDF data that correspond to a set of samples with related chemistry such as various doping series represents another important sequential modeling aspect that is supported in PDFgui PDFgui has a pre written macro that allows for this modeling situation to be accommodated We will describe the procedure using an example of a series of data collected on LaMnO3 and series of Ca doped LaMnO3 samples with various Ca content from 0 to 0 28 at GEM instrument at ISIS UK To begin from the File menu use Open Project selection to open Icmo template dpp project from the tutorial directory which has an initial setup for this exercise Note the letter c in the file name in contrast to the name used in the previous example This project consists of a fit called lemo pbnm which will serve as a template and which contains Pbnm phase of LaMnO3 and a 10 K data set 2000t010q35 gr The difference here with respect to the template used in the previous example is that Ca sites are introduced in the structure but are assigned zero occupancy However existence of the Chapter 3 Examples and tutorials 27 Ca dopant species in the structure of the template is essential for the macro to operate Also upper limit used in Fourier transform for obtaining this set of data is 35 inverse
55. ted The fitting will proceed in stages so the first fit is executed first and after it is converged the second one After the fitting of the sequence is over you may plot the results as described earlier This time hold down Control and select the data sets from both Fit 1 and Fit 1 copy You can change the offset in the plotting window to 0 if you would like to display the profiles on top of each other Notable is a sharper nearest neighbor PDF peak in the second fit improving the fit to the Ni data compared to the Fit 1 achievement We note here that there is also a linear atomic correlation factor deltal This one is appropriate to use in cases of high temperature while delta2 is more appropriate for the case of low temperatures Alternative way to include the correlated motion effects on PDF is to introduce sratio parameter that defines low r to high r PDF peak ratio and rcut limit needs to be specified that defines a cutoff distance The two approaches of accounting for correlated motion should not be used simultaneously Details of this and other issues related to the PDF method can be found elsewhere Chapter 3 Examples and tutorials 23 3 3 2 Sequential fitting of incremental r series In certain modeling situations user could benefit from fitting a data set through a series of refinements that differ one from another by the corresponding fitting ranges This could either be a case when upper r limit is to be cha
56. th generic appearance reflecting the fact that the fitting three is not populated with neither structure nor data Note that the same action could be achieved by selecting the New Fit option from the Fits drop down menu on the menu bar The next step in populating the fitting tree is to load structural model This is achieved through a simple sequence of actions first select the fit icon in the Fit Tree pane Then right click the mouse invoking a drop down menu Select Insert Phase which will modify the current action panel The same action could be performed from the Phases drop down menu on the menu bar by selecting New Phase In the current action panel options are offered to load a structure from a file or to generate it from scratch In this exercise a preexisting structure file Ni stru is to be loaded Chapter 2 Quick start 7 v IZ ex File Edit View Fits Phases Data Calculations Help 9 Emueo H FtTee x Configure Constraints Results v Eri e Elwen Phase Configuration a 3 52 b 3 52 DECH alpha 90 0 beta 90 0 gamma 90 0 Scale Factor 1 0 deltal 0 0 delta2 sratio 1 0 raut 0 Included Pairs ali all z ull u22 u33 az uis ues occ 0 0 0 0 0 0 0 0025 0 0025 0 0025 0 0 0 0 0 0 1 0 Plot Contrl Xx Ix d 0 0 0 5 0 5 0 0025 0 0025 0 0025 0 0 0 0 0 0 1 0 step v
57. th or without modification are per mitted provided that the following conditions are met Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer Redistributions in binary form must reproduce the above copyright notice this list of con ditions and the following disclaimer in the documentation and or other materials provided with the distribution Neither the name of MICHIGAN STATE UNIVERSITY nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission Disclaimer THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBU TORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAM AGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTER RUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE Table of Contents 1 Wntroduchions lt eg 6252650240968 Rech ER 1 1 17 P
58. xperimental conditions such as temperature and doping used for bookkeeping and for parametric plots If no meta data are present in a data file this information should be supplied by the user Note also that the changes occurred at this stage in the Plot Control panel allowing user to plot the data This is achieved by selecting an observed G r and clicking on a plot button that will invoke a plot Since no fitting has occurred so far an attempt to plot calculated PDF profile or a difference yields a blank plot Having specified the initial structure to be refined and the data set to be fit one proceeds to the refinement setup This is carried out through adjusting the initial parameters and variables as well as setting up the constraints The adjustments and constraint setup are done on both the experimental data and the refined structure levels toggling between the corresponding Configure and Constraints tabs In the present example the data related setup will be done first fv mI l el File Edit View Fits Phases Data Calculations Help BEUS o Hl Te x Configure Constraints Result v Eli A S SUE Data Set Configuration IM Ni xray DESS Scatterer Type O Neutron X ray Fit Range 1 7 to 20 0 Scale Factor 1 0 I Qmax 40 0 Qdamp 0 08 Qbroad 0 0 Spdiameter 0 0 Temperature 300 0 Doping 0 0 x r v M Gdiff Gobs Gtrunc dGcalc offset 5 Plot Reset
59. y by clicking at the quick plot icon on the tool bar Alternatively desired items to be displayed can be selected from the Plot Control and plotted on the screen Depending on whether the structure or the data are selected on the Fit Tree either refined structural parameters or the experiment related parameters and fit could be plotted An example of the fit display is shown in Figure 2 9 and a selected parameter plot vs iteration step in Figure 2 10 If the plotting window remains open while the fitting is in progress the content will be updated after each fit iteration Chapter 2 Quick start ni example ddp tutorial ni example ddp PDFgui File Edit View Fits Phases Data Calculations Help 9 E202 eo Hi v len 1 Ni stru GEES Plot 12 Ni xray gr Gcalc Gobs 2 0 971 2007 02 02 Figure 2 9 An example of PDFgui plotting capabilities displaying a fit s ni example ddp tutorial ni example ddp PDFgui ACIE Eile Edit View Fits Phases Data Calculations Help 9E Q906 HH v WE n EH Plot 1 Fit Low TH Ni stru EU Ni xray gr eee feed dede eee Fe Pe Fe PE fefe Fe Pe Be eee eee Pe Pe Pe fee Pe Pe Fe Pe Fe eee Pe Pe Pe Pe De eee fee t eee ete ee GH PDFFIT Version 2 0 971 2007 02 02 Figure 2 10 An example of PDF gui plotting capabilities displaying a parameter Chapter 2 Quick start 16 PDF eui is furnished with Journal capability whi
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