晶体学结构的解析-X-ray粉末衍射法Topas软件.ppt

单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,*,Folie.,*,2001 Bruker AXS All Rights Reserved,Arial 28 pt,Arial 16-24 pt,Arial 16-24 pt,Arial 16-24 pt,Arial 16-24 pt,Arial 16-24 pt,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,2006,1,晶体学结构,2,晶体学结构,一种描述,简单原则,三斜,合理原则,3,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,4,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),5,一般步骤,数据的读入,寻峰(峰形拟合),指标化,空间群的判断,结构解析,6,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,7,程序的启用,8,9,10,11,可读入数据的格式,布鲁克衍射仪的数据(*.raw),Bruker AXS binaries(DIFFRAC AT and DIFFRAC,plus,),*.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.,12,13,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,14,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 1310,15,16,17,*.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 1378,18,19,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.,20,21,数据的处理,22,数据的组成,背底,峰位置,峰形,23,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),24,Background,Two 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.,25,26,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 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 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,27,28,29,*.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 0.401844,30,Instrument,（仪器参数）,Bragg-Brentano geometry,Additional Convolutions,31,32,Bragg-Brentano geometry,33,34,35,36,37,Corrections,38,39,Miscellaneous,40,41,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 2,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,42,单谱线拟合,43,步骤,44,45,46,47,峰形函数,Topas Users Manual.pdf,48,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(2,)=W F,1,(2)F,2,(2).F,i,(2).F,n,(2),Y(2)is the observed line profile shape,W is the source emission profile,and denotes the convolution process,.,49,Source emission profiles,（衍射源谱线的描述）,50,51,单色器对峰形的影响52,53,54,55,Direct convolution approach,Empirical parameterisation（直接卷积法：实验参数法）,56,57,58,59,60,经验函数,61,Direct convolution approach:Fundamental parameters,（基本参数法）,62,Diffractometer configurations and their geometrical aberrations,Divergent Beam Laboratory Diffractometers,Parallel Beam Diffractometers,63,Divergent Beam Laboratory Diffractometers,Position sensitive detectors(PSDs),64,Parallel Beam Diffractometers,Position sensitive detectors(PSDs),65,66,67,Treatment of satellite peaks and tube tails,68,69,70,全谱拟合,71,72,73,74,75,如何指标化,LSI,LP-Search,76,Advances inIndexing of Powder Diffraction Patterns:,Iterative Use of Least Squares(LSI),and,Monte-Carlo Based Whole Powder Pattern Decomposition,Arnt Kern,TOPAS V3TO,tal,P,attern,A,nalysis,S,olutions,Intensity Extraction,LeBail,Pawley,Structure Determination using F,2,(obs),Structure Refinement using y,i,(obs),Profiling,LeBail,Pawley,Structure Determination AND Refinementusing y,i,(obs),Peak Finding,Indexing,TOPAS Approach,Coelho(2000),Quantitative Rietveld Analysis,New,TOPAS V3LSI,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,LSI,Method,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 convergence,TOPAS V3,LSI,Reciprocal lattice relationship,:,Modified to include a zero error and a weighting function:,Objective function:,For large d-spacings as well as for high 2,q,errors weightings are increased automatically,TOPAS V3,LSI,LSI 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,LSI,Most 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 2,q,),Particularily strong in indexing of very large cells(100.000 A,3,)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 plots,TOPAS V3,LSI,Powder pattern overlaid with both observed(blue)and calculated(red)peak positions,Detailed indexing resultsfor all solutions,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 solutions,TOPAS V3,LSI Reference,Indexing of powder diffraction patterns by iterative use of singular value decomposition,A.A.Coelho,J.Appl.Cryst.(2003),36,8695,TOPAS V3,LP-Search,LP-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 lines,TOPAS V3,LP-Search,Poor solution,high R-value,Good solution,low R-value,Generate 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,Reiterate,TOPAS V3,LP-Search,Most important features:,Seamless integration into,TOPAS V3,Independent of 2,q,or d-spacing extraction,Independent of line profile shape,Zero-point error consideration,highly tolerant to large zero point errors(0.05 2,q,),Particulary suited for indexing of poor quality powder data,where reliable 2,q,or d-spacing extraction is difficult or even impossible,TOPAS V3,LP-Search,Direct Pawley or Le Bail fitting of random lattice parameters to the powder pattern,!No d-values required!,TOPAS V3,LP-Search:,LT-ZrMo,2,O,8,Particulary 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-ZrMo,2,O,8,Data are easily indexed with LP-Search,LP-Search profile fit reveals strong anisotropic line broadening,LT-ZrMo,2,O,8,a=5.879,b=7.329,c=9.130,D8 ADVANCE,K,a,1,Allen et al.(2003),Final Pawley fit taking anisotropic line broadening into account,Spherical harmonics function used to model excess broadening,LT-ZrMo,2,O,8,a=5.879,b=7.329,c=9.130,D8 ADVANCE,K,a,1,Allen et al.(2003),TOPAS V3,LP-Search:,LT-ZrMo,2,O,8,具体操作,94,存储峰位置文件,95,Type,Use,Position,Area,Cry Size L(nm),Cry Size G(nm),Strain L,Strain G,SPVII,1,16.90666,17.46451,200.0,200.0,0.1,0.1,SPVII,1,23.95561,134.764,200.0,200.0,0.1,0.1,SPVII,1,27.24924,4.839198,200.0,200.0,0.1,0.1,16.90666,17.46451,23.95561,134.764,27.24924,4.839198,Copy the Data to Clipboard,96,97,98,99,100,101,LP-Search方法,102,103,104,其他方法,Powder-X,中国科学院物理研究所,董成研究员,105,106,107,108,109,110,111,如何确定空间群,消光规律,简单尝试,112,Im-3,113,P23,114,使用Sir97程序,115,116,117,118,结构解析,GUI模式,Lauch模式,119,添加Structure项,120,设定相关参数,121,122,123,124,125,126,127,*.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 411.5907,128,129,130,GUI and Launch,131,一般特点,132,133,134,135,136,Features available in GUI and Launch Mode,137,138,139,File types and formats,140,141,142,143,144,145,146,147,148,The Scan Window,149,150,151,152,153,154,Chart Options Dialog,155,Peak Search Dialog,156,Peak Details Dialog,157,Options Dialog,158,Fit Window,159,160,161,162,163,The Parameters Window,Global item,Range item(s),Peak Phase,hkl Phase,Structure,Structures/hkl Phases,164,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),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),165,166,167,Range item(s),168,169,170,Emission profile,171,172,173,174,175,176,177,178,179,180,181,182,183,184,Peak Phase,185,186,hkl Phase,187,188,Structure,189,190,191,192,193,194,Structures/hkl Phases,195,196,Printing and reporting,197,198,Operation in GUI and Launch Mode,199,Lauch模式,Set INP file,200,*.inp的来源,GUI模式的输出文件,已有的模版,201,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CaTaTid11d11s.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),202,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 fp,203,204,keywords and macros,205,206,*.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,207,208,209,210,211,212,213,*.inp,xdd,D:北杜CaTaTid11d11s.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 1333 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,214,215,216,217,Background functions using fit_objects,218,*.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 0.626579,219,220,221,222,223,224,225,lam,ymin_on_ymax 0.001,la 0.653817 lo 1.540596 lh 0.501844,la 0.346183 lo 1.544493 lh 0.