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1、晶体学结构的解析X-ray粉末衍射法Topas软件,李国宝北京大学化学学院2006,晶体学结构,晶体学结构,一种描述简单原则 三斜合理原则,讨论内容,基本处理(结构解析(一)结构解析(二)结构精修一般性问题,结构解析(一):基本处理,样品的准备和数据的采集数据的处理(衍射图),一般步骤,数据的读入寻峰(峰形拟合)指标化空间群的判断结构解析,数据的读入,布鲁克衍射仪的数据(*.raw)理学衍射仪的数据中子衍射的数据,程序的启用,可读入数据的格式,布鲁克衍射仪的数据(*.raw) Bruker AXS binaries (DIFFRAC AT and DIFFRACplus)*.DAT Sever
2、al ASCII file formats including LHPM/RIET7/CSRIET, GSAS (std - const, alt -ralf) and FullProf. *.XDD / *.CAL ASCII file format. *.XY, *XYE ASCII file formats. Can be used for non-equidistant x-axis steps.,岛津衍射仪的ASCII数据,* Group : YSH* Data : Ti-c1* File Name : Ti-c1.RAW* Comment : 10.0000 0.02000 120
3、.00202 200 238 188 236 210 210 208 220 198 218 224 198 192 210 190 210 222 192 218 196 186 196 216 186,* Group : YSH* Data : Ti-c1* File Name : Ti-c1.RAW* Comment : *5501 10.0000 0.02000202 200 238 188 236 210 210 208 220 198 218 224 198 192 210 190 210 222 192 218,理学衍射仪的ASCII数据,GSAS数据格式,5.000 0.020
4、 120.000 050104 7.3.2006 BANK 1 5751 575 CONST 500 2 0 0 STD 1374 1294 1388 1368 1342 1366 1350 1364 1400 1360 1360 1410 1372 1338 1330 1308 1318 1372 1374 1314 1414 1346 1340 1348 1342 1318 1290 1314 1384 1348 1294 1316 1358 1280 1336 1294 1378 1268 1324 1374 1276 1356 1320 1280 1388 1300 1396 1386
5、 1282 1306 1332 1336 1282 1328 1298 1374 1392 1350 1262 1310,*.XY格式,050104 Original Data 5751 5 1372 5.02 1384 5.04 1370 5.06 1388 5.08 1384 5.1 1334 5.12 1378 5.14 1352 5.16 1372 5.18 1368 5.2 1378,5 1372 5.02 1384 5.04 1370 5.06 1388 5.08 1384 5.1 1334 5.12 1378,界面简介（user interface）, MenubarContai
6、ns the names of submenus, which provide lists of all commands available together with their shortcuts respectively toolbar icons, if existing. ToolbarDisplays the most important commands in form of icons for fast access. Working AreaContains all elements needed for profile fitting such as observed a
7、nd calculateddata, fit parameters, and fit results, which are displayed in separated views. Status BarDisplays some context sensitive help information and the x- and y-coordinates of the data cursor in the active Scan Window, which is described in section 2.2.,数据的处理,数据的组成,背底 峰位置 峰形,Global item(全域项),
8、Background (section 2.3.2.4)Instrument (section 2.3.2.5)Corrections (section 2.3.2.6)Miscellaneous (section 2.3.2.7)Display All Peaks (section 2.3.2.8)All Structures / hkl Phases (section 2.3.2.11),Background,Two background functions are provided1. a Chebychev polynomial of any order2. a 1/X functio
9、n. The Chebychev Coefficients page contains the coefficients of the polynomial.,Emission profile(光源的信息),Gives the ability to add and delete emission lines which form the emissionprofile of the X-ray source.The Options page contains the following options:Option: Remarks: Ymin on Ymax Determines the x
10、-axis extent to which peak tails are calculated (cut off) No Th dependence Defines an emission profile that is 2 independent. Allows the use of non-X-ray data or fitting to negative 2 values. For LAM cursor Switches the mouse cursor to a multi-line cursor representing the different emission lines of
11、 the current emission profile (Fig. 2-14) Lam for Bragg angle Only for expert users, refer to the Technical Reference manual Calculate Lam Only for expert users, refer to the Technical Reference manual,*.lam文件的内容,普通衍射仪：lam ymin_on_ymax 0.0001 la 0.653817 lo 1.540596 lh 0.501844 la 0.346183 lo 1.5444
12、93 lh 0.626579,布鲁克的D8 Advance： lam ymin_on_ymax 0.0001 la 1 lo 1.540596 lh 0.401844,Instrument（仪器参数）,Bragg-Brentano geometryAdditional Convolutions,Bragg-Brentano geometry,Corrections,Miscellaneous,Fit method Constraints and keywords 1)SPF: Single peak fittingNo constraints by default. Optionally al
13、l profile parameters can beconstrained (e.g. same shape, same width, relative intensity, .)Keywords: xo_I, d_IWPPF: Whole Powder pattern fitting. No constraints by default. Optionally all profile parameters can be constrained (e.g. same shape, same width, relative intensity, .) Profile parameters co
14、nstrained to be smoothly varying functions of 2Keywords: xo_I, d_IWPPD: Whole powder pattern decompositionPawley and LeBail methodNumber of peaks and their positions constrained by crystal system /spacegroup plus lattice parametersKeyword: hkl_IRietveld: Rietveld structure refinement, ab-initio stru
15、cture determinationPeak intensities constrained by the crystal structureKeyword: str1) For details refer to the Technical Reference manual,寻峰,单谱线拟合,步骤,峰形函数,Topas Users Manual.pdf,TOPAS提供的两类峰形拟合方法,1. Analytical Profile Fitting: analytical peak shape functions (PSF) Gaussian, Lorentzian, sums of Gauss
16、ians or Lorentzians, Voigt, pseudo-Voigt and Pearson VII functions2. Direct Convolution Approach: Y(2) = W F1(2) F2(2) . Fi(2) . Fn(2) Y(2) is the observed line profile shape, W is the source emission profile, and denotes the convolution process.,Source emission profiles（衍射源谱线的描述）,单色器对峰形的影响,Direct c
17、onvolution approachEmpirical parameterisation（直接卷积法：实验参数法）,经验函数,Direct convolution approach: Fundamental parameters（基本参数法）,Diffractometer configurations and their geometrical aberrations,Divergent Beam Laboratory DiffractometersParallel Beam Diffractometers,Divergent Beam Laboratory Diffractometers,
18、Position sensitive detectors (PSDs),Parallel Beam Diffractometers,Position sensitive detectors (PSDs),Treatment of satellite peaks and tube tails,全谱拟合,如何指标化,LSI LP-Search,Advances inIndexing of Powder Diffraction Patterns:Iterative Use of Least Squares(LSI) and Monte-Carlo Based Whole Powder Pattern
19、 Decomposition,Arnt Kern,TOPAS V3TOtal Pattern Analysis Solutions,Intensity ExtractionLeBail, PawleyStructure Determination using F2(obs)Structure Refinement using yi(obs),ProfilingLeBail, PawleyStructure Determination AND Refinementusing yi(obs),TOPAS ApproachCoelho (2000),New,TOPAS V3LSI and LP-Se
20、arch,LSIIterative use of least squaresOperates on d-values extracted from reasonable quality powder diffraction dataLP-SearchMonte-Carlo Based Whole Powder Pattern DecompositionIndependent of d-spacing extraction and line profile shape and therefore suited for indexing of poor quality powder data,!
21、No d-values required !,TOPAS V3LSI,Method1. LSI Iterative Processhkls assigned using present (random) lattice parametersReciprocal lattice relationship solved using least squares for all hkl2. Monte-Carlo approach to searching parameter space Randomize lattice parametersExecution of the LSI iterativ
22、e process until convergence,TOPAS V3LSI,Reciprocal lattice relationship:Modified to include a zero error and a weighting function:Objective function:For large d-spacings as well as for high 2q errors weightings are increased automatically,TOPAS V3LSI,LSI is applied consecutively with hkls correspond
23、ing to minimum symmetry Bravais lattices from each crystal system and in decreasing order of symmetry. Monoclinic lattices are treated differently where a search is performed using the six unique sets of hkls corresponding to the space groups P2, P21, Pc, P21/c, C2, and Cc and not just the Bravais l
24、attices. On present personal computers LSI searches all crystals systems down to the triclinic lattice in less than three minutes.,TOPAS V3LSI,Most important features:Seamless integration into TOPAS V3Zero-point error considerationAutomatic determination of possible spacegroupsHighly tolerant to imp
25、urity peaks, missing high d-spacings, extreme lattice parameter ratios as well as large d-spacing and zero point errors ( 0.05 2q)Particularily strong in indexing of very large cells ( 100.000 A3) and dominant zone problemsWeighting of reflections using observed peak intensities or user-defined weig
26、htsFully automated Pawley or Le Bail fitting of all or user-selected solutionsGoodness-of-fit versus volume plots,TOPAS V3LSI,Powder pattern overlaid with both observed (blue) and calculated (red) peak positions,Detailed indexing resultsfor all solutions,TOPAS V3LSI,Goodness-of-fit versus volume dis
27、playEasy identification of fractional and multiple volumes,Fully automatic Pawley or Le Bail fitting of all or user selected solutions,TOPAS V3LSI Reference,Indexing of powder diffraction patterns by iterative use of singular value decompositionA. A. CoelhoJ. Appl. Cryst. (2003), 36, 8695,TOPAS V3LP
28、-Search,LP-Search is a Monte-Carlo based Whole Powder Pattern Decomposition approachIt minimizes on a new figure of merit function that gives a measure of correctness for a particular set of lattice parameters The figure of merit function assigns parts of the diffraction pattern to calculated peak p
29、ositions and then sums the absolute values of the products of the diffraction intensities multiplied by the distance to the calculated peak positions LP-Search avoids difficulties associated with extracting d-spacings from complex patterns comprising heavily overlapped lines,TOPAS V3LP-Search,Poor s
30、olution, high R-value,Good solution, low R-value,Generate sets of lattice parameters and calculate d-valuesFor each solution, for each calculated d-valuedefine pattern segmentssum the absolute values of (step intensities * distance to the d-value) Refine the best solutionReiterate,TOPAS V3LP-Search,
31、Most important features:Seamless integration into TOPAS V3Independent of 2q or d-spacing extraction Independent of line profile shapeZero-point error consideration, highly tolerant to large zero point errors ( 0.05 2q)Particulary suited for indexing of poor quality powder data, where reliable 2q or
32、d-spacing extraction is difficult or even impossible,TOPAS V3LP-Search,Direct Pawley or Le Bail fitting of random lattice parameters to the powder pattern,! No d-values required !,TOPAS V3LP-Search: LT-ZrMo2O8,Particulary suited for indexing of poor quality powder data: How many peaks are there?,Pea
33、k overlap?,2+ phases?,Anisotropic line broadening?,TOPAS V3LP-Search: LT-ZrMo2O8,Data are easily indexed with LP-SearchLP-Search profile fit reveals strong anisotropic line broadening,LT-ZrMo2O8a = 5.879 b = 7.329 c = 9.130 D8 ADVANCE, Ka1 Allen et al. (2003),Final Pawley fit taking anisotropic line
34、 broadening into accountSpherical harmonics function used to model excess broadening,LT-ZrMo2O8a = 5.879 b = 7.329 c = 9.130 D8 ADVANCE, Ka1 Allen et al. (2003),TOPAS V3LP-Search: LT-ZrMo2O8,具体操作,存储峰位置文件,16.90666, 17.4645123.95561, 134.76427.24924, 4.839198,Copy the Data to Clipboard,LP-Search方法,其他方
35、法,Powder-X 中国科学院物理研究所 董成研究员,如何确定空间群,消光规律简单尝试,Im-3,P23,使用Sir97程序,结构解析,GUI模式Lauch模式,添加Structure项,设定相关参数,*.cif格式的变换,data_chemical_name_mineral Structure_cell_length_a 7.438554_cell_length_b 7.438554_cell_length_c 7.438554_cell_angle_alpha 90_cell_angle_beta 90_cell_angle_gamma 90_cell_volume 411.5907lo
36、op_symmetry_equiv_pos_as_xyz-x, -y, -z-x, -y, z-x, y, -z-x, y, z-y, -z, -x,data_chemical_name_mineral Structure_symmetry_cell_setting ?_symmetry_space_group_name_H-M Im-3loop_symmetry_equiv_pos_as_xyz-x, -y, -z_cell_length_a 7.438554_cell_length_b 7.438554_cell_length_c 7.438554_cell_angle_alpha 90_
37、cell_angle_beta 90_cell_angle_gamma 90_cell_volume 411.5907,GUI and Launch,一般特点,Features available in GUI and Launch Mode,File types and formats,The Scan Window,Chart Options Dialog,Peak Search Dialog,Peak Details Dialog,Options Dialog,Fit Window,The Parameters Window,Global itemRange item(s)Peak Ph
38、asehkl PhaseStructureStructures / hkl Phases,Global item, Background (section 2.3.2.4) Instrument (section 2.3.2.5) Corrections (section 2.3.2.6) Miscellaneous (section 2.3.2.7) DisplayAdditionally the following items may be displayed as well: All Peaks (section 2.3.2.8) All Structures / hkl Phases
39、(section 2.3.2.11),Range item(s),Emission profile,Peak Phase,hkl Phase,Structure,Structures / hkl Phases,Printing and reporting,Operation in GUI and Launch Mode,Lauch模式,Set INP file,*.inp的来源,GUI模式的输出文件已有的模版,r_exp 2.186 r_exp_dash 4.660 r_wp 2.922 r_wp_dash 6.227 r_p 2.275 r_p_dash 6.184 weighted_Dur
40、bin_Watson 1.333 gof 1.336iters 1000chi2_convergence_criteria 0.001xdd D:北京青少年科技后备人才培养计划杜乔羽CaTaTid11d11s.datr_exp 2.186 r_exp_dash 4.660 r_wp 2.922 r_wp_dash 6.227 r_p 2.275 r_p_dash 6.184 weighted_Durbin_Watson 1.333 gof 1.336bkg 1215.64401 208.701692 -188.17575 298.679653 -151.780171 59.956008 -87
41、.3989484 39.2693905 16.2762255One_on_X(, 6118.28199)Zero_Error(, -0.20911)Specimen_Displacement(, -0.00575)LP_Factor( 26.4)Rp 217.5Rs 217.5Cylindrical_2Th_Correction(, 0.63346)Absorption(, 31.40650)Specimen_Tilt(, 0.37208),lamymin_on_ymax 0.001la 0.653817 lo 1.540596 lh 0.501844la 0.346183 lo 1.5444
42、93 lh 0.626579str CS_L(, 120.54707)PVII_Peak_Type(, 0.03757, 0.00372, 0.12792, 0.00010, 1.56236, 0.39528)r_bragg 0.490306945phase_name StructureMVW( 1680.577, 411.7866, 100.000)scale 0.0001260772space_group I_m_-3Phase_LAC_1_on_cm( 725.41115)Phase_Density_g_on_cm3( 6.77697)Cubic( 7.43973)site Cu1 nu
43、m_posns 6 occ Cu+2 1 beq 1 x 0 y 0.5 z 0.5site O2 num_posns 24 occ O-2 1 beq 1 x 0 y 0.29392 z 0.22710site Ti1 num_posns 8 occ Ti+4 0.5 beq 1 x 0.25 y 0.25 z 0.25site ta2 num_posns 8 occ Ta+5 0.5 beq 1 x 0.25 y 0.25 z 0.25xo_Is xo 16.9550599I 13.078614CS_L(, 216.24903)peak_type fp,keywords and macro
44、s,*.inp,r_exp 2.186 r_exp_dash 4.660 r_wp 2.922 r_wp_dash 6.227 r_p 2.275 r_p_dash 6.185 weighted_Durbin_Watson 1.333 gof 1.336iters 1000chi2_convergence_criteria 0.001,精修的参数,*.inp,xdd D:北杜CaTaTid11d11s.datr_exp 2.186 r_exp_dash 4.660 r_wp 2.922 r_wp_dash 6.227 r_p 2.275 r_p_dash 6.185 weighted_Durb
45、in_Watson 1.333 gof 1.336bkg 1215.64267 208.70024 -188.175586 298.679649 -151.780757 59.9557014 -87.3990974 39.2693852 16.2758868One_on_X(, 6118.28036),数据文件名及背底函数,Background functions using fit_objects,*.inp,Zero_Error(, -0.20911)Specimen_Displacement(, -0.00575)LP_Factor( 26.4)Rp 217.5Rs 217.5Speci
46、men_Tilt(, 0.37208) Cylindrical_2Th_Correction(, 0.63346)Absorption(, 31.40664)lamymin_on_ymax 0.001la 0.653817 lo 1.540596 lh 0.501844la 0.346183 lo 1.544493 lh 0.626579,lamymin_on_ymax 0.001la 0.653817 lo 1.540596 lh 0.501844la 0.346183 lo 1.544493 lh 0.626579,CuKa5(0.001),*.inp,str CS_L(, 120.546
47、19)PVII_Peak_Type(, 0.03757, 0.00372, 0.12792, 0.00010, 1.56236, 0.39524)r_bragg 0.489677278phase_name StructureMVW( 1680.577, 411.7860, 100.000)scale 0.0001260781space_group I_m_-3,Sample convolutions,Quantitative analysis,*.inp,Phase_LAC_1_on_cm( 725.41213)Phase_Density_g_on_cm3( 6.77698)Cubic( 7.
48、43973)site Cu1 num_posns 6 occ Cu+2 1 beq 1 x 0 y 0.5 z 0.5site O2 num_posns 24 occ O-2 1 beq 1 x 0 y 0.29393 z 0.22710site Ti1 num_posns 8 occ Ti+4 0.5 beq 1 x 0.25 y 0.25 z 0.25site ta2 num_posns 8 occ Ta+5 0.5 beq 1 x 0.25 y 0.25 z 0.25xo_Is xo 16.9550654I 13.0775354CS_L(, 216.31479),关于单晶数据,Shelx
49、l, Shelxs,site O1 num_posns 2 occ O-2 1 beq 1 x 0.0000 y 0.000 z 0.000,Rigid bodies and bond length restraints,Penalties used in structure determination,拟合因子,结构精修两相的精修,物相鉴定,寻峰 数据库的使用,结构解析(二),真实结构与结构的可表征性有关物理性质与结构的相关性电子衍射等电镜技术中子衍射,有关物理性质与结构的相关性,对称中心二阶非线性光学系数铁电性压电系数发光,Ba1-xLaxTi1-xCrxO3 的相关系示意图,0 x1 x
50、2 x3 x4 x5 x6 1,T, Tetragonal; C, Cubic; R, Rhombohedral; O, Orthorhombic. X1=0.029, X2=0.0365, X3=0.600, X4=0.700, X5=0.873, X6=0.956.,利用铁电性确定对称中心的不存在,四方固熔体Ba1-xLaxTi1-xCrxO3的结构参数,0 x0.029,P4mm,立方固熔体Ba1-xLaxTi1-xCrxO3的结构参数,0.0365x0.600,Rwp5.0%Rp4.5%,三方固熔体Ba1-xLaxTi1-xCrxO3的结构参数,0.700 x0.873,Rwp2.5%
