- Timestamp:
- Feb 15, 2020 1:28:57 PM (5 years ago)
- Location:
- trunk
- Files:
-
- 2 edited
-
GSASIIobj.py (modified) (17 diffs)
-
GSASIIscriptable.py (modified) (1 diff)
Legend:
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TabularUnified trunk/GSASIIobj.py ¶
r4306 r4307 131 131 \ Nobs Number of observed data points (int) 132 132 \ Rwp overall weighted profile R-factor (%, float) 133 \ chisq sum[w*(Iobs-Icalc)**2] for all data 134 note this is not the reduced chi squared (float) 133 \ chisq :math:`\sum w*(I_{obs}-I_{calc})^2` 134 for all data. 135 Note: this is not the reduced :math:`\chi^2`. (float) 135 136 \ lamMax Marquardt value applied to Hessian diagonal 136 137 (float) … … 168 169 interatomic distances (list of floats) 169 170 \ Cell List with 8 items: cell refinement flag (bool) 170 a, b, c, ( Angstrom, float)171 a, b, c, (:math:`\\unicode{x212B}`, float) 171 172 alpha, beta & gamma (degrees, float) 172 volume ( A^3, float)173 volume (:math:`\\unicode{x212B}^3`, float) 173 174 \ Color Colors for atoms (list of (r,b,g) triplets) 174 175 \ Compare dict of polygon comparison parameters … … 236 237 \ bondRadius Size of binds in A (float) 237 238 \ cameraPos Viewing position in A for plot (float) 238 \ contourLevel map contour level in e/A^3(float)239 \ contourLevel map contour level in :math:`e/\\unicode{x212B}^3` (float) 239 240 \ contourMax float map contour maximum 240 241 \ depthFog True if use depthFog on plot - set currently as False (bool) … … 387 388 .. tabularcolumns:: |l|p{4.5in}| 388 389 389 ========== ==================================================== 390 ========== ======================================================================================== 390 391 key explanation 391 ========== ==================================================== 392 ========== ======================================================================================== 392 393 BNSlattsym mag - BNS magnetic space group symbol and centering vector 393 394 GenFlg mag - list of symmetry generators indices … … 398 399 OprNames mag - names for each space group operation 399 400 SGCen Symmetry cell centering vectors. A (n,3) np.array 400 of centers. Will always have at least one row: 401 ``np.array([[0, 0, 0]])`` 402 SGFixed bool only True if phase mported from a magnetic cif file 401 of centers. Will always have at least one row: ``np.array([[0, 0, 0]])`` 402 SGFixed bool, only True if phase mported from a magnetic cif file 403 403 then the space group can not be changed by the user because 404 404 operator set from cif may be nonstandard … … 408 408 SGLatt Lattice centering type. Will be one of 409 409 P, A, B, C, I, F, R (str) 410 SGLaue 411 -1, 2/m, mmm, 4/m, 4/mmm, 3R,412 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)410 SGLaue str, one of the following 14 Laue classes: 411 -1, 2/m, mmm, 4/m, 4/mmm, 3R, 412 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m 413 413 SGOps symmetry operations as a list of form 414 414 ``[[M1,T1], [M2,T2],...]`` … … 435 435 SpGrp space group symbol (str) 436 436 SpnFlp mag - list of magnetic spin flips for every magnetic space group operator 437 438 ========== ==================================================== 437 ========== ======================================================================================== 439 438 440 439 .. _SSGData_table: … … 519 518 .. tabularcolumns:: |l|p{4.5in}| 520 519 521 ============== ==================================================== 520 ============== =================================================================================== 522 521 location explanation 523 ============== ==================================================== 522 ============== =================================================================================== 524 523 ct-4 mm - residue number (str) 525 524 ct-3 mm - residue name (e.g. ALA) (str) … … 537 536 cs+5...cs+11 U11, U22, U33, U12, U13, U23 (6 floats) 538 537 ci unique atom identifier; matches source atom Id in Atom Records (int) 539 ============== ==================================================== 538 ============== =================================================================================== 540 539 541 540 .. _Powder_table: … … 560 559 .. tabularcolumns:: |p{1in}|p{1in}|p{4in}| 561 560 562 ====================== =============== ==================================================== 561 ====================== =============== =========================================================== 563 562 key sub-key explanation 564 ====================== =============== ==================================================== 563 ====================== =============== =========================================================== 565 564 Comments \ Text strings extracted from the original powder 566 565 data header. These cannot be changed by the user; … … 576 575 the :ref:`Powder Reflections <PowderRefl_table>` 577 576 description. 578 Instrument Parameters (CW) \ A list containing two dicts for constant wavelength 579 data where the possible keys in each dict are listed 580 below. The value for each item is a list containing 581 three values: the initial value, the current value 582 and a refinement flag which can have a value of 583 True, False or 0 where 0 indicates a value that 584 cannot be refined. The first and second 585 values are floats unless otherwise noted. 586 Items in the first dict are noted as [1] 587 \ Type Histogram type (str) [1]: 588 * 'PXC' for constant wavelength x-ray 589 * 'PNC' for constant wavelength neutron 590 \ Bank Data set number in a multidata file (usually 1) 591 \ Lam Specifies a wavelength in Angstroms [1] 592 \ Lam1 Specifies the primary wavelength in 593 Angstrom, when an alpha1, alpha2 594 source is used [1] 595 \ Lam2 Specifies the secondary wavelength in 596 Angstrom, when an alpha1, alpha2 597 source is used [1] 598 I(L2)/I(L1) Ratio of Lam2 to Lam1 [1] 599 \ Zero Two-theta zero correction in *degrees* [1] 600 \ Azimuth Azimuthal setting angle for data recorded 601 with differing setting angles [1] 602 \ U, V, W Cagliotti profile coefficients 603 for Gaussian instrumental broadening, where the 604 FWHM goes as 605 :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1] 606 \ X, Y, Z Cauchy (Lorentzian) instrumental broadening 607 coefficients [1] 608 \ SH/L Variant of the Finger-Cox-Jephcoat asymmetric 609 peak broadening ratio. Note that this is the 610 sum of S/L and H/L where S is 611 sample height, H is the slit height and 612 L is the goniometer diameter. [1] 613 \ Polariz. Polarization coefficient. [1] 614 Instrument Parameters (TOF) \ A list containing two dicts for neutron time-of-flight 615 (TOF) data where the possible keys in each dict are listed 616 below. The value for each item is a list containing 617 three values: the initial value, the current value 618 and a refinement flag which can have a value of 619 True, False or 0 where 0 indicates a value that 620 cannot be refined. The first and second 621 values are floats unless otherwise noted. 622 Items in the first dict are noted as [1] 623 \ Type Histogram type (str) [1]: 624 * 'PNT' for time of flight neutron 625 \ Bank Data set number in a multidata file 626 \ 2-theta Nominal scattering angle for the detector 627 \ fltPath Total flight path source-sample-detector 628 \ Azimuth Azimuth angle for detector righ hand rotation 629 from horizontal away from source 630 \ difC,difA,difB Diffractometer constants for conversion of d-spacing to TOF 631 in microseconds 632 \ Zero Zero point offset (microseconds) 633 \ alpha Exponential rise profile coefficients 634 \ beta-0 Exponential decay profile coefficients 635 beta-1 636 beta-q 637 \ sig-0 Gaussian profile coefficients 638 sig-1 639 sig-2 640 sig-q 641 \ X,Y,Z Lorentzian profile coefficients 577 Instrument Parameters \ The instrument parameters uses different dicts 578 for the constant wavelength (CW) and time-of-flight (TOF) 579 cases. See below for the descriptions of each. 642 580 wtFactor \ A weighting factor to increase or decrease 643 581 the leverage of data in the histogram (float). … … 699 637 4. the background values 700 638 5. Yobs-Ycalc 701 ====================== =============== ==================================================== 639 ====================== =============== =========================================================== 640 641 642 ----------------------------- 643 CW Instrument Parameters 644 ----------------------------- 645 646 Instrument Parameters are placed in a list of two dicts, 647 where the keys in each dict listed below. Note that the dict contents are different for 648 constant wavelength (CW) vs. time-of-flight (TOF) histograms. 649 The value for each item is a list containing three values: the initial value, the current value 650 and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that 651 cannot be refined. The first and second values are floats unless otherwise noted. 652 Items in the first dict are noted as [1] 653 654 .. tabularcolumns:: |p{1in}|p{1in}|p{4in}| 655 656 ====================== =============== =========================================================== 657 key sub-key explanation 658 ====================== =============== =========================================================== 659 Instrument Parameters Type [1] Histogram type (str): 660 * 'PXC' for constant wavelength x-ray 661 * 'PNC' for constant wavelength neutron 662 \ Bank Data set number in a multidata file (usually 1) 663 \ Lam [1] Specifies a wavelength in :math:`\\unicode{x212B}` 664 \ Lam1 [1] Specifies the primary wavelength in 665 :math:`\\unicode{x212B}`, used in place of Lam 666 when an :math:`\\alpha_1, \\alpha_2` 667 source is used. 668 \ Lam2 [1] Specifies the secondary wavelength in 669 :math:`\\unicode{x212B}`, used with Lam1 670 \ I(L2)/I(L1) Ratio of Lam2 to Lam1, 671 [1] used with Lam1 672 \ Zero [1] Two-theta zero correction in *degrees* 673 \ Azimuth Azimuthal setting angle for data recorded 674 [1] with differing setting angles 675 \ U, V, W Cagliotti profile coefficients 676 [1] for Gaussian instrumental broadening, where the 677 FWHM goes as 678 :math:`U \\tan^2\\theta + V \\tan\\theta + W` 679 \ X, Y, Z Cauchy (Lorentzian) instrumental broadening 680 [1] coefficients 681 \ SH/L Variant of the Finger-Cox-Jephcoat asymmetric 682 [1] peak broadening ratio. Note that this is the 683 sum of S/L and H/L where S is 684 sample height, H is the slit height and 685 L is the goniometer diameter. 686 \ Polariz. Polarization coefficient. 687 [1] 688 ====================== =============== =========================================================== 689 690 ----------------------------- 691 TOF Instrument Parameters 692 ----------------------------- 693 694 Instrument Parameters are also placed in a list of two dicts, 695 where the keys in each dict listed below, but here for 696 time-of-flight (TOF) histograms. 697 The value for each item is a list containing three values: the initial value, the current value 698 and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that 699 cannot be refined. The first and second values are floats unless otherwise noted. 700 Items in the first dict are noted as [1] 701 702 .. tabularcolumns:: |p{1in}|p{1in}|p{4in}| 703 704 ====================== =============== =========================================================== 705 key sub-key explanation 706 ====================== =============== =========================================================== 707 Instrument Parameters Type [1] Histogram type (str): 708 * 'PNT' for time of flight neutron 709 \ Bank Data set number in a multidata file 710 \ 2-theta Nominal scattering angle for the detector 711 \ fltPath Total flight path source-sample-detector 712 \ Azimuth Azimuth angle for detector right hand rotation 713 from horizontal away from source 714 \ difC,difA, Diffractometer constants for conversion of d-spacing to TOF 715 difB in microseconds 716 \ Zero Zero point offset (microseconds) 717 \ alpha Exponential rise profile coefficients 718 \ beta-0 Exponential decay profile coefficients 719 beta-1 720 beta-q 721 \ sig-0 Gaussian profile coefficients 722 sig-1 723 sig-2 724 sig-q 725 \ X,Y,Z Lorentzian profile coefficients 726 ====================== =============== =========================================================== 702 727 703 728 .. _PowderRefl_table: … … 719 744 0,1,2 h,k,l (float) 720 745 3 multiplicity 721 4 d-space, Angstrom746 4 d-space, :math:`\\unicode{x212B}` 722 747 5 pos, two-theta 723 748 6 sig, Gaussian width … … 770 795 The first and second 771 796 values are floats unless otherwise noted. 772 \ Lam Specifies a wavelength in Angstroms (two floats) 797 \ Lam Specifies a wavelength in :math:`\\unicode{x212B}` 798 (two floats) 773 799 \ Type Histogram type (two str values): 774 800 * 'SXC' for constant wavelength x-ray … … 809 835 0,1,2 h,k,l (float) 810 836 3 multiplicity 811 4 d-space, Angstrom837 4 d-space, :math:`\\unicode{x212B}` 812 838 5 :math:`F_{obs}^2` 813 839 6 :math:`\sigma(F_{obs}^2)` … … 914 940 \ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively. 915 941 \ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90. 916 \ wavelength (float) Th a radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).917 942 \ wavelength (float) The radiation wavelength (:math:`\\unicode{x212B}`) as entered by the user 943 (or someday obtained from the image header). 918 944 Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask 919 945 to be excluded from integration … … 2346 2372 2347 2373 * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``. 2348 * 'wavelength': wavelength in Angstoms.2374 * 'wavelength': wavelength in :math:`\\unicode{x212B}`. 2349 2375 * 'distance': distance of detector from sample in cm. 2350 2376 * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``. -
TabularUnified trunk/GSASIIscriptable.py ¶
r4305 r4307 4741 4741 :param str parmType: should be 'size' or 'microstrain' (can be abbreviated to 's' or 'm') 4742 4742 :param str mode: should be 'isotropic' or 'uniaxial' (can be abbreviated to 'i' or 'u') 4743 :param float val1: value for isotropic size (in microns) or 4744 microstrain (delta Q/Q x 10**6, unitless) or the equatorial value in the uniaxial case 4745 :param float val2: value for axial size (in microns) or 4746 microstrain (delta Q/Q x 10**6, unitless) in uniaxial case; not used for isotropic 4743 :param float val1: value for isotropic size (in :math:`\mu m`) or 4744 microstrain (unitless, :math:`\Delta Q/Q \\times 10^6`) or the equatorial value in the uniaxial case 4745 :param float val2: value for axial size (in :math:`\mu m`) or 4746 axial microstrain (unitless, :math:`\Delta Q/Q \\times 10^6`) 4747 in uniaxial case; not used for isotropic 4747 4748 :param list axis: tuple or list with three values indicating the preferred direction 4748 4749 for uniaxial broadening; not used for isotropic
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