晶体学结构的解析 X-ray粉末衍射法Topas软件

null晶体学结构的解析 X-ray粉末衍射法 Topas软件晶体学结构的解析 X-ray粉末衍射法 Topas软件李国宝 北京大学化学学院 2006null晶体学结构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程序的启用nullnullnull可读入数据的格式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 Several 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. null岛津衍射仪的ASCII数据岛津衍射仪的ASCII数据* Group : YSH * Data : Ti-c1 * File Name : Ti-c1.RAW * Comment : 10.0000 0.02000 120.00 202 200 238 188 236 210 210 208 220 198 218 224 198 192 210 190 210 222 192 218 196 186 196 216 186 * Group : YSH * Data : Ti-c1 * File Name : Ti-c1.RAW * Comment : * 5501 10.0000 0.02000 202 200 238 188 236 210 210 208 220 198 218 224 198 192 210 190 210 222 192 218 理学衍射仪的ASCII数据GSAS数据格式GSAS数据格式 5.000 0.020 120.000 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 1282 1306 1332 1336 1282 1328 1298 1374 1392 1350 1262 1310nullnull*.XY格式*.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 null界面简介（user interface）界面简介（user interface）• Menubar Contains the names of submenus, which provide lists of all commands available together with their shortcuts respectively toolbar icons, if existing. • Toolbar Displays the most important commands in form of icons for fast access. • Working Area Contains all elements needed for profile fitting such as observed and calculated data, fit parameters, and fit results, which are displayed in separated views. • Status Bar Displays 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. nullnull数据的处理数据的组成数据的组成背底 峰位置 峰形 Global item(全域项) Global item(全域项)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)BackgroundBackgroundTwo background functions are provided 1. a Chebychev polynomial of any order 2. a 1/X function. The Chebychev Coefficients page contains the coefficients of the polynomial. nullEmission profile (光源的信息)Emission profile (光源的信息)Gives the ability to add and delete emission lines which form the emission profile of the X-ray source. The Options page contains the following options: Option: Remarks: • Ymin on Ymax Determines the x-axis extent to which peak tails are calculated (cut off) • No Th dependence Defines an emission profile that is 2θ independent. Allows the use of non-X-ray data or fitting to negative 2θ values. • For LAM cursor Switches the mouse cursor to a multi-line cursor representing the different emission lines of 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 nullnull*.lam文件的内容*.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 1.544493 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）Instrument （仪器参数）Bragg-Brentano geometry Additional Convolutions nullBragg-Brentano geometryBragg-Brentano geometrynullnullnullnullCorrectionsCorrectionsnullMiscellaneousMiscellaneousnull寻峰Fit method Constraints and keywords 1) SPF: Single peak fitting No constraints by default. Optionally all profile parameters can be constrained (e.g. same shape, same width, relative intensity, ...) Keywords: "xo_I", "d_I" WPPF: 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 constrained to be smoothly varying functions of 2θ Keywords: "xo_I", "d_I" WPPD: Whole powder pattern decomposition Pawley and LeBail method Number of peaks and their positions constrained by crystal system / spacegroup plus lattice parameters Keyword: "hkl_I" Rietveld: Rietveld structure refinement, ab-initio structure determination Peak intensities constrained by the crystal structure Keyword: "str" 1) For details refer to the Technical Reference manual寻峰单谱线拟合单谱线拟合步骤步骤nullnullnull峰形函数峰形函数Topas Users Manual.pdfTOPAS提供的两类峰形拟合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 Gaussians or Lorentzians, Voigt, pseudo-Voigt and Pearson VII functions 2. Direct Convolution Approach: Y(2θ) = W ⊗ F1(2θ) ⊗ F2(2θ) ⊗ ... ⊗ Fi(2θ) ⊗ ... ⊗ Fn(2θ) Y(2θ) 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）Source emission profiles （衍射源谱线的描述）null单色器对峰形的影响单色器对峰形的影响nullnullnullDirect convolution approach Empirical parameterisation （直接卷积法：实验参数法）Direct convolution approach Empirical parameterisation （直接卷积法：实验参数法）nullnullnullnull经验函数经验函数Direct convolution approach: Fundamental parameters （基本参数法）Direct convolution approach: Fundamental parameters （基本参数法）Diffractometer configurations and their geometrical aberrationsDiffractometer configurations and their geometrical aberrationsDivergent Beam Laboratory Diffractometers Parallel Beam Diffractometers nullDivergent Beam Laboratory DiffractometersPosition sensitive detectors (PSDs)Parallel Beam DiffractometersParallel Beam DiffractometersPosition sensitive detectors (PSDs)nullnullTreatment of satellite peaks and tube tailsTreatment of satellite peaks and tube tailsnullnull全谱拟合全谱拟合nullnullnullnull如何指标化如何指标化LSI LP-SearchAdvances in Indexing of Powder Diffraction Patterns: Iterative Use of Least Squares(LSI) and Monte-Carlo Based Whole Powder Pattern DecompositionAdvances in Indexing of Powder Diffraction Patterns: Iterative Use of Least Squares(LSI) and Monte-Carlo Based Whole Powder Pattern Decomposition Arnt Kern TOPAS V3 TOtal Pattern Analysis Solutions TOPAS V3 TOtal Pattern Analysis SolutionsIntensity Extraction LeBail, Pawley Structure Determination using F2(obs) Structure Refinement using yi(obs)"Profiling" LeBail, Pawley Structure Determination AND Refinement using yi(obs)TOPAS Approach Coelho (2000)NewTOPAS V3 LSI and LP-Search TOPAS V3 LSI and LP-Search LSI Iterative use of least squares Operates on d-values extracted from reasonable quality powder diffraction data LP-Search Monte-Carlo Based Whole Powder Pattern Decomposition Independent of d-spacing extraction and line profile shape and therefore suited for indexing of poor quality powder data ! No d-values required !TOPAS V3 LSITOPAS V3 LSIMethod 1. LSI Iterative Process hkls assigned using present (random) lattice parameters Reciprocal lattice relationship solved using least squares for all hkl 2. Monte-Carlo approach to searching parameter space Randomize lattice parameters Execution of the LSI iterative process until convergenceTOPAS V3 LSITOPAS V3 LSIReciprocal 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 automaticallyTOPAS V3 LSITOPAS V3 LSILSI is applied consecutively with hkls corresponding 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 lattices. On present personal computers LSI searches all crystals systems down to the triclinic lattice in less than three minutes.TOPAS V3 LSITOPAS V3 LSIMost important features: Seamless integration into TOPAS V3 Zero-point error consideration Automatic determination of possible spacegroups Highly tolerant to impurity 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 problems Weighting of reflections using observed peak intensities or user-defined weights Fully automated Pawley or Le Bail fitting of all or user-selected solutions Goodness-of-fit versus volume plotsTOPAS V3 LSI TOPAS V3 LSI Powder pattern overlaid with both observed (blue) and calculated (red) peak positions Detailed indexing results for all solutionsTOPAS V3 LSI TOPAS V3 LSI Goodness-of-fit versus volume display Easy identification of fractional and multiple volumes Fully automatic Pawley or Le Bail fitting of all or user selected solutionsTOPAS V3 LSI ReferenceTOPAS V3 LSI ReferenceIndexing of powder diffraction patterns by iterative use of singular value decomposition A. A. Coelho J. Appl. Cryst. (2003), 36, 86–95TOPAS V3 LP-SearchTOPAS V3 LP-SearchLP-Search is a Monte-Carlo based Whole Powder Pattern Decomposition approach It 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 positions 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 linesTOPAS V3 LP-SearchTOPAS V3 LP-SearchPoor solution, high R-valueGood solution, low R-valueGenerate sets of lattice parameters and calculate d-values For each solution, for each calculated d-value define pattern segments sum the absolute values of (step intensities * distance to the d-value) Refine the best solution ReiterateTOPAS V3 LP-SearchTOPAS V3 LP-SearchMost important features: Seamless integration into TOPAS V3 Independent of 2q or d-spacing extraction Independent of line profile shape Zero-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 d-spacing extraction is difficult or even impossibleTOPAS V3 LP-SearchTOPAS V3 LP-SearchDirect Pawley or Le Bail fitting of random lattice parameters to the powder pattern ! No d-values required !TOPAS V3 LP-Search: LT-ZrMo2O8TOPAS V3 LP-Search: LT-ZrMo2O8Particulary suited for indexing of poor quality powder data: How many peaks are there?Peak overlap?2+ phases?Anisotropic line broadening?TOPAS V3 LP-Search: LT-ZrMo2O8TOPAS V3 LP-Search: LT-ZrMo2O8Data are easily indexed with LP-Search LP-Search profile fit reveals strong anisotropic line broadeningLT-ZrMo2O8 a = 5.879 Ǻ b = 7.329 Ǻ c = 9.130 Ǻ D8 ADVANCE, Ka1 Allen et al. (2003)TOPAS V3 LP-Search: LT-ZrMo2O8TOPAS V3 LP-Search: LT-ZrMo2O8Final Pawley fit taking anisotropic line broadening into account Spherical harmonics function used to model excess broadeningLT-ZrMo2O8 a = 5.879 Ǻ b = 7.329 Ǻ c = 9.130 Ǻ D8 ADVANCE, Ka1 Allen et al. (2003)具体操作具体操作存储峰位置文件存储峰位置文件null16.90666, 17.46451 23.95561, 134.764 27.24924, 4.839198Copy the Data to ClipboardnullnullnullnullnullLP-Search方法LP-Search方法nullnull其他方法其他方法Powder-X 中国科学院物理研究所 董成研究员nullnullnullnullnullnull如何确定空间群如何确定空间群消光规律 简单尝试nullIm-3nullP23使用Sir97程序使用Sir97程序nullnullnull结构解析结构解析GUI模式 Lauch模式添加Structure项添加Structure项设定相关参数设定相关参数nullnullnullnullnullnull*.cif格式的变换*.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 411.5907 loop_ _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-3 loop_ _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 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 411.5907 nullnullGUI and LaunchGUI and Launch一般特点一般特点nullnullnullnullFeatures available in GUI and Launch ModeFeatures available in GUI and Launch ModenullnullFile types and formatsFile types and formatsnullnullnullnullnullnullnullnullThe Scan WindowThe Scan WindownullnullnullnullnullChart Options DialogChart Options DialogPeak Search DialogPeak Search DialogPeak Details DialogPeak Details DialogOptions DialogOptions DialognullFit WindownullnullnullnullThe Parameters WindowThe Parameters WindowGlobal item Range item(s) Peak Phase hkl Phase Structure Structures / hkl PhasesGlobal itemGlobal 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) • Display Additionally the following items may be displayed as well: • All Peaks (section 2.3.2.8) • All Structures / hkl Phases (section 2.3.2.11) nullnullRange item(s)Range item(s)nullnullEmission profileEmission profilenullnullnullnullnullnullnullnullnullnullnullnullnullPeak PhasePeak Phasenullhkl Phasehkl PhasenullStructureStructurenullnullnullnullnullStructures / hkl PhasesStructures / hkl PhasesnullPrinting and reportingPrinting and reportingnullOperation in GUI and Launch ModeOperation in GUI and Launch ModeLauch模式Lauch模式Set INP file*.inp的来源*.inp的来源GUI模式的输出文件 已有的模版null 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_Durbin_Watson 1.333 gof 1.336 iters 1000 chi2_convergence_criteria 0.001 xdd D:\北京青少年科技后备人才培养计划\杜乔羽\CaTaTi\d11\d11s.dat 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_Durbin_Watson 1.333 gof 1.336 bkg @ 1215.64401 208.701692 -188.17575 298.679653 -151.780171 59.956008 -87.3989484 39.2693905 16.2762255 One_on_X(@, 6118.28199) Zero_Error(@, -0.20911) Specimen_Displacement(@, -0.00575) LP_Factor( 26.4) Rp 217.5 Rs 217.5 Cylindrical_2Th_Correction(@, 0.63346) Absorption(@, 31.40650) Specimen_Tilt(@, 0.37208)null lam ymin_on_ymax 0.001 la 0.653817 lo 1.540596 lh 0.501844 la 0.346183 lo 1.544493 lh 0.626579 str CS_L(@, 120.54707) PVII_Peak_Type(@, 0.03757,@, 0.00372,@, 0.12792,@, 0.00010,@, 1.56236,@, 0.39528) r_bragg 0.490306945 phase_name Structure MVW( 1680.577, 411.7866, 100.000) scale @ 0.0001260772 space_group "I_m_-3" Phase_LAC_1_on_cm( 725.41115) Phase_Density_g_on_cm3( 6.77697) Cubic(@ 7.43973) site Cu1 num_posns 6 occ Cu+2 1 beq 1 x 0 y 0.5 z 0.5 site O2 num_posns 24 occ O-2 1 beq 1 x 0 y @ 0.29392 z @ 0.22710 site Ti1 num_posns 8 occ Ti+4 0.5 beq 1 x 0.25 y 0.25 z 0.25 site ta2 num_posns 8 occ Ta+5 0.5 beq 1 x 0.25 y 0.25 z 0.25 xo_Is xo @ 16.9550599 I @ 13.078614 CS_L(@, 216.24903) peak_type fpnull"keywords" and "macros" "keywords" and "macros" null*.inp*.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 1.336 iters 1000 chi2_convergence_criteria 0.001精修的参数nullnullnullnullnullnull*.inp*.inpxdd D:\北\杜\CaTaTi\d11\d11s.dat 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 1.336 bkg @ 1215.64267 208.70024 -188.175586 298.679649 -151.780757 59.9557014 -87.3990974 39.2693852 16.2758868 One_on_X(@, 6118.28036)数据文件名及背底函数nullnullnullBackground functions using fit_objectsBackground functions using fit_objects*.inp*.inp Zero_Error(@, -0.20911) Specimen_Displacement(@, -0.00575) LP_Factor( 26.4) Rp 217.5 Rs 217.5 Specimen_Tilt(@, 0.37208) Cylindrical_2Th_Correction(@, 0.63346) Absorption(@, 31.40664) lam ymin_on_ymax 0.001 la 0.653817 lo 1.540596 lh 0.501844 la 0.346183 lo 1.544493 lh 0.626579nullnullnullnullnullnullnulllam ymin_on_ymax 0.001 la 0.653817 lo 1.540596 lh 0.501844 la 0.346183 lo 1.544493 lh 0.626579nullnullCuKa5(0.001)*.inp*.inp str CS_L(@, 120.54619) PVII_Peak_Type(@, 0.03757,@, 0.00372,@, 0.12792,@, 0.00010,@, 1.56236,@, 0.39524) r_bragg 0.489677278 phase_name Structure MVW( 1680.577, 411.7860, 100.000) scale @ 0.0001260781 space_group "I_m_-3"nullnullSample convolutionsSample convolutionsnullnullnullnullnullnullnullnullQuantitative analysisQuantitative analysisnullnullnull*.inp*.inp Phase_LAC_1_on_cm( 725.41213) Phase_Density_g_on_cm3( 6.77698) Cubic(@ 7.43973) site Cu1 num_posns 6 occ Cu+2 1 beq 1 x 0 y 0.5 z 0.5 site O2 num_posns 24 occ O-2 1 beq 1 x 0 y @ 0.29393 z @ 0.22710 site Ti1 num_posns 8 occ Ti+4 0.5 beq 1 x 0.25 y 0.25 z 0.25 site ta2 num_posns 8 occ Ta+5 0.5 beq 1 x 0.25 y 0.25 z 0.25 xo_Is xo @ 16.9550654 I @ 13.0775354 CS_L(@, 216.31479)nullnullnullnullnullnull关于单晶数据关于单晶数据nullnullShelxl, Shelxs nullsite O1 num_posns 2 occ O-2 1 beq 1 x 0.0000 y 0.000 z 0.000Rigid bodies and bond length restraintsRigid bodies and bond length restraintsnullnullnullnullPenalties used in structure determinationPenalties used in structure determinationnullnullnullnull拟合因子null结构精修 两相的精修结构精修 两相的精修nullnull物相鉴定物相鉴定 寻峰 数据库的使用结构解析(二)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Ba1-xLaxTi1-xCrxO3 的相关系示意图0 x1 x2 x3 x4 x5 x6 1T, 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的结构参数四方固熔体Ba1-xLaxTi1-xCrxO3的结构参数0≤x≤0.029P4mm立方固熔体Ba1-xLaxTi1-xCrxO3的结构参数立方固熔体Ba1-xLaxTi1-xCrxO3的结构参数0.0365≤x≤0.600Rwp<5.0%Rp<4.5%三方固熔体Ba1-xLaxTi1-xCrxO3的结构参数三方固熔体Ba1-xLaxTi1-xCrxO3的结构参数0.700≤x≤0.873Rwp<2.5%, Rp<2.2%正交固熔体Ba1-xLaxTi1-xCrxO3的结构参数正交固熔体Ba1-xLaxTi1-xCrxO3的结构参数0.956≤x≤1PnmaRwp<2.4%Rp<2.1%利用发光特性确定对称中心的存在 Ba6-xEuxTi2+xTa8-xO30的结构问题 （对称性和占位问题）利用发光特性确定对称中心的存在 Ba6-xEuxTi2+xTa8-xO30的结构问题 （对称性和占位问题）对称性和占位问题对称性和占位问题P4/mbm Eu占据2a位置P4bm Eu占据2a位置P4/mbm Eu占据2a位置 Eu占据4g位置P4bm Eu占据2a位置 Eu占据4g位置解决解决方案解决方案解决方案解决方案解决方案结论：Ba6-xEuxTi2+xTa8-xO30的结构结论：Ba6-xEuxTi2+xTa8-xO30的结构空间群: P4/mbm Eu占据2a位置 X最大值为2.0nullBa(Fe1/2Ta1/2)O3 的结构与问题 (汇聚束)电子衍射a=4.065ÅBa, (0, 0, 0); Ta(Fe), (0.5, 0.5, 0.5);O, (0.5, 0.5, 0)Ba(Fe1/2Ta1/2)O3 的可能结构Ba(Fe1/2Ta1/2)O3 的可能结构汇聚束电子衍射[CBED] 汇聚束电子衍射[CBED] R3m P3m1null电子衍射电子衍射nullBa(Fe1/2Ta1/2)O3 的结构最终结论Ba(Fe1/2Ta1/2)O3 的结构最终结论nullLa4Cu3-xZnxMoO12nullPmnm, P21/mnull一般性问题一般性问题单一相的确定 杂相峰、超结构峰、非公度峰 杂相峰杂相峰超结构峰超结构峰nullnull非公度峰非公度峰Jana2000nul