Changeset 4309
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 Feb 16, 2020 12:08:16 PM (3 years ago)
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trunk/GSASIIobj.py
r4308 r4309 114 114 key subkey explanation 115 115 ============= =============== ==================================================== 116 newCellDict \ dict withlattice parameters computed by117 :func:`GSASIIstrMath.GetNewCellParms` (dict)116 newCellDict \ (dict) lattice parameters computed by 117 :func:`GSASIIstrMath.GetNewCellParms` 118 118 title \ Name of gpx file(?) (str) 119 119 variables \ Values for all N refined variables … … 155 155 .. tabularcolumns:: llp{4in} 156 156 157 ========== =============== ==================================================== 157 ========== =============== ===================================================================================================== 158 158 key subkey explanation 159 ========== =============== ==================================================== 159 ========== =============== ===================================================================================================== 160 160 General \ Overall information for the phase (dict) 161 161 \ 3Dproj projections for 3D pole distribution plots … … 169 169 interatomic distances (list of floats) 170 170 \ Cell List with 8 items: cell refinement flag (bool) 171 a, b, c, (:math:`\\unicode{x212B}`, float)171 a, b, c, (:math:`\\unicode{x212B}`, float) 172 172 alpha, beta & gamma (degrees, float) 173 volume (:math:`\\unicode{x212B}^3`, float)173 volume (:math:`\\unicode{x212B}^3`, float) 174 174 \ Color Colors for atoms (list of (r,b,g) triplets) 175 175 \ Compare dict of polygon comparison parameters … … 205 205 \ Pawley neg wt Restraint value for negative Pawley intensities 206 206 (float) 207 \ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>` 207 \ SGData Space group details as a 208 :ref:`space group (SGData) object <SGData_table>` 208 209 as defined in :func:`GSASIIspc.SpcGroup`. 209 210 \ SH Texture dict of spherical harmonic preferred orientation … … 237 238 \ bondRadius Size of binds in A (float) 238 239 \ cameraPos Viewing position in A for plot (float) 239 \ contourLevel map contour level in :math:`e/\\unicode{x212B}^3` (float)240 \ contourLevel map contour level in :math:`e/\\unicode{x212B}^3` (float) 240 241 \ contourMax float map contour maximum 241 242 \ depthFog True if use depthFog on plot  set currently as False (bool) … … 284 285 \ LeBail Flag for LeBail extraction (bool) 285 286 \ Mustrain List of microstrain parameters, in order: 286 287 0. Type, one of u'isotropic', u'uniaxial', u'generalized' 288 1. Isotropic/uniaxial parameters  list of 3 floats 289 2. Refinement flags  list of 3 bools 290 3. Microstrain axis  list of 3 ints, [h, k, l] 291 4. Generalized mustrain parameters  list of 26 292 floats, depending on space group 293 5. Generalized refinement flags  list of bools, 294 corresponding to the parameters of (4) 295 \ Pref.Ori. Preferred Orientation. List of eight parameters. 296 Items marked SH are only used for Spherical Harmonics. 297 298 0. Type, 'MD' for MarchDollase or 'SH' for Spherical Harmonics 299 1. Value, float 300 2. Refinement flag, bool 301 3. Preferred direction, list of ints, [h, k, l] 302 4. SH  number of terms, int 303 5. SH  dict 304 6. SH  list 305 7. SH  float 287 0. Type, one of u'isotropic', u'uniaxial', u'generalized' 288 1. Isotropic/uniaxial parameters  list of 3 floats 289 2. Refinement flags  list of 3 bools 290 3. Microstrain axis  list of 3 ints, [h, k, l] 291 4. Generalized mustrain parameters  list of 26 floats, depending on space group 292 5. Generalized refinement flags  list of bools, corresponding to the parameters of (4) 293 \ Pref.Ori. Preferred Orientation (8 parameters in list, Items marked SH are used only for Spherical Harmonics). 294 0. Type, 'MD' for MarchDollase or 'SH' for Spherical Harmonics 295 1. Value, float 296 2. Refinement flag, bool 297 3. Preferred direction, list of ints, [h, k, l] 298 4. SH  number of terms, int 299 5. SH  dict 300 6. SH  list 301 7. SH  float 306 302 \ Scale Phase fraction, list of [float, bool]. 307 303 \ Show bool 308 304 \ Size List of crystallite size parameters, in order: 309 310 0. Type, one of u'isotropic', u'uniaxial', u'ellipsoidal' 311 1. Isotropic/uniaxial parameters  list of 3 floats 312 2. Refinement flags  list of 3 bools 313 3. Size axis  list of 3 ints, [h, k, l] 314 4. Ellipsoidal size parameters  list of 6 floats 315 5. Ellipsoidal refinement flags  list of bools, 316 corresponding to the parameters of (4) 305 0. Type, one of u'isotropic', u'uniaxial', u'ellipsoidal' 306 1. Isotropic/uniaxial parameters  list of 3 floats 307 2. Refinement flags  list of 3 bools 308 3. Size axis  list of 3 ints, [h, k, l] 309 4. Ellipsoidal size parameters  list of 6 floats 310 5. Ellipsoidal refinement flags  list of bools, corresponding to the parameters of (4) 317 311 \ Use bool 318 312 \ newLeBail Whether to perform a new LeBail extraction 319 313 MCSA \ MonteCarlo simulated annealing parameters (dict) 320 \ 321 ========== =============== ==================================================== 314 ========== =============== ===================================================================================================== 322 315 323 316 .. _RBData_table: … … 346 339 \ rbXYZ Cartesian coordinates for Vector rigid body (list of 3 float) 347 340 \ rbRef 3 assigned reference atom nos. in rigid body for origin 348 341 definition, use center of atoms flag (list of 3 int & 1 bool) 349 342 \ VectRef refinement flags for VectMag values (list of bool) 350 343 \ rbTypes Atom types for each atom in rigid body (list of str) … … 387 380 key explanation 388 381 ========== ======================================================================================== 389 BNSlattsym mag  BNS magnetic space group symbol and centering vector390 GenFlg mag  list of symmetry generators indices391 GenSym mag  list of names for each generator392 MagMom mag  list of "time reversals" for each magnetic operator393 MagPtGp mag Magnetic point group symbol394 MagSpGrp mag  Magnetic space group symbol395 OprNames mag  names for each space group operation382 BNSlattsym BNS magnetic space group symbol and centering vector (mag) 383 GenFlg list of symmetry generators indices (mag) 384 GenSym list of names for each generator (mag) 385 MagMom list of "time reversals" for each magnetic operator (mag) 386 MagPtGp Magnetic point group symbol (mag) 387 MagSpGrp Magnetic space group symbol (mag) 388 OprNames names for each space group operation (mag) 396 389 SGCen Symmetry cell centering vectors. A (n,3) np.array 397 390 of centers. Will always have at least one row: ``np.array([[0, 0, 0]])`` … … 402 395 SGGray True if space group is a gray group (incommensurate magnetic structures) 403 396 SGInv True if centrosymmetric, False if not (bool) 404 SGLatt Lattice centering type. Will be one of 405 P, A, B, C, I, F, R (str) 406 SGLaue str, one of the following 14 Laue classes: 407 1, 2/m, mmm, 4/m, 4/mmm, 3R, 408 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m 409 SGOps symmetry operations as a list of form 410 ``[[M1,T1], [M2,T2],...]`` 411 where :math:`M_n` is a 3x3 np.array 412 and :math:`T_n` is a length 3 np.array. 397 SGLatt (str) Lattice centering type. Will be one of: 398 P, A, B, C, I, F, R 399 400 SGLaue (str) one of the following 14 Laue classes: 401 1, 2/m, mmm, 4/m, 4/mmm, 3R, 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m 402 403 SGOps symmetry operations as a list of form ``[[M1,T1], [M2,T2],...]`` 404 where :math:`M_n` is a 3x3 np.array and :math:`T_n` is a length 3 np.array. 413 405 Atom coordinates are transformed where the 414 406 Asymmetric unit coordinates [X is (x,y,z)] 415 are transformed using 416 :math:`X^\prime = M_n*X+T_n` 417 SGPolax Axes for space group polarity. Will be one of 418 '', 'x', 'y', 'x y', 'z', 'x z', 'y z', 419 'xyz'. In the case where axes are arbitrary 420 '111' is used (P 1, and ?). 407 are transformed using :math:`X^\prime = M_n*X+T_n` 408 SGPolax Axes for space group polarity. Will be one of: 409 '', 'x', 'y', 'x y', 'z', 'x z', 'y z','xyz'. 410 411 In the case where axes are arbitrary, '111' is used (P 1, and ?). 421 412 SGPtGrp Point group f the space group 422 413 SGUniq unique axis if monoclinic. Will be 423 414 a, b, or c for monoclinic space groups. 424 415 Will be blank for nonmonoclinic. (str) 425 SGSpin mag  list of spin flip operatiors (+1 or 1) for the space group operations426 SGSys symmetry unit cell: type one of427 'triclinic', 'monoclinic', 'orthorhombic',428 'tetragonal', 'rhombohedral', 'trigonal',429 'hexagonal', 'cubic' (str)416 SGSpin list of spin flip operatiors (+1 or 1) for the space group operations (mag) 417 SGSys (str) symmetry unit cell: type one of: 418 'triclinic', 'monoclinic', 'orthorhombic', 419 'tetragonal', 'rhombohedral', 'trigonal', 420 'hexagonal', 'cubic' 430 421 SSGK1 list of superspace multipliers 431 SpGrp space group symbol (str)432 SpnFlp mag  list of magnetic spin flips for every magnetic space group operator422 SpGrp (str) space group symbol 423 SpnFlp list of magnetic spin flips for every magnetic space group operator (mag) 433 424 ========== ======================================================================================== 434 425 … … 571 562 the :ref:`Powder Reflections <PowderRefl_table>` 572 563 description. 573 Instrument Parameters \ The instrument parameters uses different dicts 574 for the constant wavelength (CW) and timeofflight (TOF) 575 cases. See below for the descriptions of each. 564 Instrument Parameters \ The instrument parameters contains a list of two dicts. 565 The contents of the first dict differs between 566 the :ref:`constant wavelength (CW) <CWPowder_table>` 567 and the :ref:`timeofflight (TOF) <TOFPowder_table>` 568 cases. See below for the descriptions of 569 the :ref:`CW <CWPowder_table>` 570 and :ref:`TOF <TOFPowder_table>` contents. 576 571 wtFactor \ A weighting factor to increase or decrease 577 572 the leverage of data in the histogram (float). … … 586 581 specifies if the value is refined, otherwise 587 582 the value is a float unless otherwise noted. 588 \ ScaleThe histogram scale factor (refinable)589 \ AbsorptionThe sample absorption coefficient as583 \ Scale The histogram scale factor (refinable) 584 \ Absorption The sample absorption coefficient as 590 585 :math:`\\mu r` where r is the radius 591 586 (refinable). Only valid for DebyeScherrer geometry. 592 \ SurfaceRoughA Surface roughness parameter A as defined by 593 Surotti,J. Appl. Cryst, 5,325331, 1972.(refinable  587 \ SurfaceRoughA Surface roughness parameter A as defined by 588 Surotti, *J. Appl. Cryst*, **5**, 325331, 1972. 589 (refinable  only valid for BraggBrentano geometry) 590 \ SurfaceRoughB Surface roughness parameter B (refinable  594 591 only valid for BraggBrentano geometry) 595 \ SurfaceRoughB Surface roughness parameter B (refinable  596 only valid for BraggBrentano geometry) 597 \ DisplaceX, Sample displacement from goniometer center 598 DisplaceY where Y is along the beam direction and 592 \ DisplaceX, Sample displacement from goniometer center 593 DisplaceY where Y is along the beam direction and 599 594 X is perpendicular. Units are :math:`\\mu m` 600 595 (refinable). 601 \ Phi, Chi,Goniometer sample setting angles, in degrees.602 603 \ Gonio. radiusRadius of the diffractometer in mm604 \ InstrNameA name for the instrument, used in preparing596 \ Phi, Chi, Goniometer sample setting angles, in degrees. 597 Omega 598 \ Gonio. radius Radius of the diffractometer in mm 599 \ InstrName A name for the instrument, used in preparing 605 600 a CIF (str). 606 \ Force,Variables that describe how the measurement607 Temperature,was performed. Not used directly in608 Humidity,any computations.609 610 611 \ ranIdThe randomnumber Id for the histogram601 \ Force, Variables that describe how the measurement 602 Temperature, was performed. Not used directly in 603 Humidity, any computations. 604 Pressure, 605 Voltage 606 \ ranId The randomnumber Id for the histogram 612 607 (same value as where toplevel key is ranId) 613 \ TypeType of diffraction data, may be 'DebyeScherrer'608 \ Type Type of diffraction data, may be 'DebyeScherrer' 614 609 or 'BraggBrentano' (str). 615 \ Diffusenot in use?610 \ Diffuse not in use? 616 611 hId \ The number assigned to the histogram when 617 612 the project is loaded or edited (can change) … … 627 622 containing in order: 628 623 629 0. the xpostions (twotheta in degrees),630 1. the intensity values (Yobs),631 2. the weights for each Yobs value632 3. the computed intensity values (Ycalc)633 4. the background values634 5. YobsYcalc624 0. the xpostions (twotheta in degrees), 625 1. the intensity values (Yobs), 626 2. the weights for each Yobs value 627 3. the computed intensity values (Ycalc) 628 4. the background values 629 5. YobsYcalc 635 630 ====================== =============== =========================================================== 636 631 632 .. _CWPowder_table: 633 634 .. index:: 635 single: Powder data CW Instrument Parameters 637 636 638 637  … … 641 640 642 641 Instrument Parameters are placed in a list of two dicts, 643 where the keys in each dictlisted below. Note that the dict contents are different for642 where the keys in the first dict are listed below. Note that the dict contents are different for 644 643 constant wavelength (CW) vs. timeofflight (TOF) histograms. 645 644 The value for each item is a list containing three values: the initial value, the current value 646 645 and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that 647 646 cannot be refined. The first and second values are floats unless otherwise noted. 648 Items in the first dict are noted as [1] 649 650 .. tabularcolumns:: p{1in}p{1in}p{4in} 651 652 ====================== =============== =========================================================== 653 key subkey explanation 654 ====================== =============== =========================================================== 655 Instrument Parameters Type [1] Histogram type (str): 656 * 'PXC' for constant wavelength xray 657 * 'PNC' for constant wavelength neutron 658 \ Bank Data set number in a multidata file (usually 1) 659 \ Lam [1] Specifies a wavelength in :math:`\\unicode{x212B}` 660 \ Lam1 [1] Specifies the primary wavelength in 661 :math:`\\unicode{x212B}`, used in place of Lam 662 when an :math:`\\alpha_1, \\alpha_2` 663 source is used. 664 \ Lam2 [1] Specifies the secondary wavelength in 665 :math:`\\unicode{x212B}`, used with Lam1 666 \ I(L2)/I(L1) Ratio of Lam2 to Lam1, 667 [1] used with Lam1 668 \ Zero [1] Twotheta zero correction in *degrees* 669 \ Azimuth Azimuthal setting angle for data recorded 670 [1] with differing setting angles 671 \ U, V, W Cagliotti profile coefficients 672 [1] for Gaussian instrumental broadening, where the 673 FWHM goes as 674 :math:`U \\tan^2\\theta + V \\tan\\theta + W` 675 \ X, Y, Z Cauchy (Lorentzian) instrumental broadening 676 [1] coefficients 677 \ SH/L Variant of the FingerCoxJephcoat asymmetric 678 [1] peak broadening ratio. Note that this is the 679 sum of S/L and H/L where S is 680 sample height, H is the slit height and 681 L is the goniometer diameter. 682 \ Polariz. Polarization coefficient. 683 [1] 684 ====================== =============== =========================================================== 647 648 .. tabularcolumns:: p{1in}p{4in} 649 650 ====================== =========================================================== 651 key explanation 652 ====================== =========================================================== 653 Type Histogram type (str): 654 * 'PXC' for constant wavelength xray 655 * 'PNC' for constant wavelength neutron 656 Bank Data set number in a multidata file (usually 1) 657 Lam Specifies a wavelength in :math:`\\unicode{x212B}` 658 Lam1 Specifies the primary wavelength in 659 :math:`\\unicode{x212B}`, used in place of Lam 660 when an :math:`\\alpha_1, \\alpha_2` 661 source is used. 662 Lam2 Specifies the secondary wavelength in 663 :math:`\\unicode{x212B}`, used with Lam1 664 I(L2)/I(L1) Ratio of Lam2 to Lam1, used with Lam1 665 Zero Twotheta zero correction in *degrees* 666 Azimuth Azimuthal setting angle for data recorded 667 with differing setting angles 668 U, V, W Cagliotti profile coefficients 669 for Gaussian instrumental broadening, where the 670 FWHM goes as 671 :math:`U \\tan^2\\theta + V \\tan\\theta + W` 672 X, Y, Z Cauchy (Lorentzian) instrumental broadening 673 coefficients 674 SH/L Variant of the FingerCoxJephcoat asymmetric 675 peak broadening ratio. Note that this is the 676 sum of S/L and H/L where S is 677 sample height, H is the slit height and 678 L is the goniometer diameter. 679 Polariz Polarization coefficient. 680 ====================== =========================================================== 681 682 .. _TOFPowder_table: 683 684 .. index:: 685 single: Powder data TOF Instrument Parameters 685 686 686 687  … … 694 695 and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that 695 696 cannot be refined. The first and second values are floats unless otherwise noted. 696 Items in the first dict are noted as [1] 697 698 .. tabularcolumns:: p{1in}p{1in}p{4in} 699 700 ====================== =============== =========================================================== 701 key subkey explanation 702 ====================== =============== =========================================================== 703 Instrument Parameters Type [1] Histogram type (str): 704 * 'PNT' for time of flight neutron 705 \ Bank Data set number in a multidata file 706 \ 2theta Nominal scattering angle for the detector 707 \ fltPath Total flight path sourcesampledetector 708 \ Azimuth Azimuth angle for detector right hand rotation 709 from horizontal away from source 710 \ difC,difA, Diffractometer constants for conversion of dspacing to TOF 711 difB in microseconds 712 \ Zero Zero point offset (microseconds) 713 \ alpha Exponential rise profile coefficients 714 \ beta0 Exponential decay profile coefficients 715 beta1 716 betaq 717 \ sig0 Gaussian profile coefficients 718 sig1 719 sig2 720 sigq 721 \ X,Y,Z Lorentzian profile coefficients 722 ====================== =============== =========================================================== 697 698 .. tabularcolumns:: p{1.5in}p{4in} 699 700 ========================= =========================================================== 701 key explanation 702 ========================= =========================================================== 703 Type (str) Histogram type: 704 * 'PNT' for time of flight neutron 705 Bank (int) Data set number in a multidata file 706 2theta Nominal scattering angle for the detector 707 fltPath Total flight path sourcesampledetector 708 Azimuth Azimuth angle for detector right hand rotation 709 from horizontal away from source 710 difC,difA,difB Diffractometer constants for conversion of dspacing to TOF 711 in microseconds 712 Zero Zero point offset (microseconds) 713 alpha Exponential rise profile coefficients 714 beta0,beta1,betaq Exponential decay profile coefficients 715 sig0,sig1,sig2,sigq Gaussian profile coefficients 716 X,Y,Z Lorentzian profile coefficients 717 ========================= =========================================================== 723 718 724 719 .. _PowderRefl_table: … … 740 735 0,1,2 h,k,l (float) 741 736 3 multiplicity 742 4 dspace, :math:`\\unicode{x212B}`737 4 dspace, :math:`\\unicode{x212B}` 743 738 5 pos, twotheta 744 739 6 sig, Gaussian width … … 748 743 10 reflection phase, in degrees 749 744 11 intensity correction for reflection, this times 750 745 :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc 751 746 12 Preferred orientation correction 752 747 13 Transmission (absorption correction) … … 791 786 The first and second 792 787 values are floats unless otherwise noted. 793 \ Lam Specifies a wavelength in :math:`\\unicode{x212B}`794 (two floats)788 \ Lam Specifies a wavelength in :math:`\\unicode{x212B}` 789 (two floats) 795 790 \ Type Histogram type (two str values): 796 * 'SXC' for constant wavelength xray797 * 'SNC' for constant wavelength neutron798 * 'SNT' for time of flight neutron791 * 'SXC' for constant wavelength xray 792 * 'SNC' for constant wavelength neutron 793 * 'SNT' for time of flight neutron 799 794 \ InstrName A name for the instrument, used in preparing 800 795 a CIF (str). … … 831 826 0,1,2 h,k,l (float) 832 827 3 multiplicity 833 4 dspace, :math:`\\unicode{x212B}`828 4 dspace, :math:`\\unicode{x212B}` 834 829 5 :math:`F_{obs}^2` 835 830 6 :math:`\sigma(F_{obs}^2)` … … 839 834 10 reflection phase, in degrees 840 835 11 intensity correction for reflection, this times 841 842 836 :math:`F_{obs}^2` or :math:`F_{calc}^2` 837 gives Iobs or Icalc 843 838 ========== ==================================================== 844 839
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