Changeset 4306
 Timestamp:
 Feb 15, 2020 10:04:50 AM (3 years ago)
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trunk/GSASIIobj.py
r4303 r4306 158 158 ========== =============== ==================================================== 159 159 General \ Overall information for the phase (dict) 160 \ AtomPtrs list of four locations to use to pull info 160 \ 3Dproj projections for 3D pole distribution plots 161 \ AngleRadii Default radius for each atom used to compute 162 interatomic angles (list of floats) 163 \ AtomMass List of masses for atoms 164 \ AtomPtrs list of four locations (cx,ct,cs & cu) to use to pull info 161 165 from the atom records (list) 162 \ F000X xray F(000) intensity (float) 163 \ F000N neutron F(000) intensity (float) 164 \ Mydir directory of current .gpx file (str) 165 \ MCSA controls Monte CarloSimulated Annealing controls (dict) 166 \ AtomTypes List of atom types 167 \ BondRadii Default radius for each atom used to compute 168 interatomic distances (list of floats) 166 169 \ Cell List with 8 items: cell refinement flag (bool) 167 170 a, b, c, (Angstrom, float) 168 171 alpha, beta & gamma (degrees, float) 169 172 volume (A^3, float) 170 \ Type 'nuclear' or 'macromolecular' for now (str) 171 \ Map dict of map parameters 172 \ SH Texture dict of spherical harmonic preferred orientation 173 parameters 174 \ Isotope dict of isotopes for each atom type 175 \ Isotopes dict of scattering lengths for each isotope 176 combination for each element in phase 177 \ Name phase name (str) 178 \ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>` 179 as defined in :func:`GSASIIspc.SpcGroup`. 180 \ Pawley neg wt Restraint value for negative Pawley intensities 181 (float) 182 \ Flip dict of Charge flip controls 173 \ Color Colors for atoms (list of (r,b,g) triplets) 174 \ Compare dict of polygon comparison parameters 183 175 \ Data plot type data plot type ('Mustrain', 'Size' or 184 176 'Preferred orientation') for powder data (str) 185 \ Mass Mass of unit cell contents in g/mol186 \ POhkl MarchDollase preferred orientation direction187 \ Z dict of atomic numbers for each atom type188 \ vdWRadii dict of van der Waals radii for each atom type189 \ Color Colors for atoms (list of (r,b,g) triplets)190 \ AtomTypes List of atom types191 \ AtomMass List of masses for atoms192 \ doPawley Flag for Pawley intensity extraction (bool)193 \ NoAtoms Number of atoms per unit cell of each type (dict)194 \ Pawley dmin maximum Q (as dspace) to use for Pawley195 extraction (float)196 \ BondRadii Default radius for each atom used to compute197 interatomic distances (list of floats)198 \ AngleRadii Default radius for each atom used to compute199 interatomic angles (list of floats)200 177 \ DisAglCtls Dict with distance/angle search controls, 201 178 which has keys 'Name', 'AtomTypes', … … 205 182 a multiplier for bond and angle search range 206 183 [typically (0.85,0.85)]. 184 \ F000X xray F(000) intensity (float) 185 \ F000N neutron F(000) intensity (float) 186 \ Flip dict of Charge flip controls 187 \ HydIds dict geometrically generated hydrogen atoms 188 \ Isotope dict of isotopes for each atom type 189 \ Isotopes dict of scattering lengths for each isotope 190 combination for each element in phase 191 \ MCSA controls Monte CarloSimulated Annealing controls (dict) 192 \ Map dict of map parameters 193 \ Mass Mass of unit cell contents in g/mol 194 \ Modulated bool True if phase modulated 195 \ Mydir directory of current .gpx file (str) 196 \ Name phase name (str) 197 \ Type 'nuclear' or 'macromolecular' for now (str) 198 \ NoAtoms Number of atoms per unit cell of each type (dict) 199 \ POhkl MarchDollase preferred orientation direction 200 \ Pawley dmin maximum Q (as dspace) to use for Pawley 201 extraction (float) 202 \ Pawley dmax minimum Q (as dspace) to use for Pawley 203 extraction (float) 204 \ Pawley neg wt Restraint value for negative Pawley intensities 205 (float) 206 \ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>` 207 as defined in :func:`GSASIIspc.SpcGroup`. 208 \ SH Texture dict of spherical harmonic preferred orientation 209 parameters 210 \ Super int dimension of super group (0,1 only) 211 \ Type str phase type (e.g. 'nuclear') 212 \ Z dict of atomic numbers for each atom type 213 \ doDysnomia bool flag for max ent map modification via Dysnomia 214 \ doPawley bool Flag for Pawley intensity extraction 215 \ vdWRadii dict of van der Waals radii for each atom type 207 216 ranId \ unique random number Id for phase (int) 208 217 pId \ Phase Id number for current project (int). … … 213 222 (list of lists) 214 223 Drawing \ Display parameters (dict) 215 \ ballScale Size of spheres in ballandstick display (float) 216 \ bondList dict with bonds 217 \ contourLevel map contour level in e/A^3 (float) 218 \ showABC Flag to show view point triplet (bool). True=show. 219 \ viewDir cartesian viewing direction (np.array with three 220 elements) 224 \ Atoms A list of lists with an entry for each atom 225 that is plotted. 226 \ Plane list Controls for contour density plane display 227 \ Quaternion Viewing quaternion (4 element np.array) 221 228 \ Zclip clipping distance in A (float) 229 \ Zstep Step to de/increase Zclip (float) 230 \ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list) 222 231 \ backColor background for plot as and R,G,B triplet 223 232 (default = [0, 0, 0], black). 224 233 (list with three atoms) 234 \ ballScale Size of spheres in ballandstick display (float) 235 \ bondList dict with bonds 236 \ bondRadius Size of binds in A (float) 237 \ cameraPos Viewing position in A for plot (float) 238 \ contourLevel map contour level in e/A^3 (float) 239 \ contourMax float map contour maximum 240 \ depthFog True if use depthFog on plot  set currently as False (bool) 241 \ ellipseProb Probability limit for display of thermal 242 ellipsoids in % (float). 243 \ magMult float multiplier for magnetic moment arrows 244 \ mapSize float x & y dimensions of contourmap (fixed internally) 245 \ modelView 4,4 array from openGL drawing transofmation matrix 246 \ oldxy previous view point (list with two floats) 247 \ radiusFactor Distance ratio for searching for bonds. ? Bonds 248 are located that are within r(Ra+Rb) and (Ra+Rb)/r 249 where Ra and Rb are the atomic radii. 225 250 \ selectedAtoms List of selected atoms (list of int values) 251 \ showABC Flag to show view point triplet (bool). True=show. 252 \ showHydrogen Flag to control plotting of H atoms. 226 253 \ showRigidBodies Flag to highlight rigid body placement 254 \ showSlice flag to show contour map 227 255 \ sizeH Size ratio for H atoms (float) 228 \ bondRadius Size of binds in A (float) 229 \ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list) 256 \ unitCellBox Flag to control display of the unit cell. 257 \ vdwScale Multiplier of van der Waals radius for 258 display of vdW spheres. 259 \ viewDir cartesian viewing direction (np.array with three 260 elements) 230 261 \ viewPoint list of lists. First item in list is [x,y,z] 231 262 in fractional coordinates for the center of 232 263 the plot. Second item list of previous & current 233 264 atom number viewed (may be [0,0]) 234 \ showHydrogen Flag to control plotting of H atoms.235 \ unitCellBox Flag to control display of the unit cell.236 \ ellipseProb Probability limit for display of thermal237 ellipsoids in % (float).238 \ vdwScale Multiplier of van der Waals radius for239 display of vdW spheres.240 \ Atoms A list of lists with an entry for each atom241 that is plotted.242 \ Zstep Step to de/increase Zclip (float)243 \ Quaternion Viewing quaternion (4 element np.array)244 \ radiusFactor Distance ratio for searching for bonds. ? Bonds245 are located that are within r(Ra+Rb) and (Ra+Rb)/r246 where Ra and Rb are the atomic radii.247 \ oldxy previous view point (list with two floats)248 \ cameraPos Viewing position in A for plot (float)249 \ depthFog True if use depthFog on plot  set currently as False (bool)250 265 RBModels \ Rigid body assignments (note Rigid body definitions 251 266 are stored in their own main toplevel tree entry.) 267 RMC \ dict RMCProfile & rmcfull controls 252 268 Pawley ref \ Pawley reflections 253 269 Histograms \ A dict of dicts. The key for the outer dict is … … 268 284 \ Mustrain List of microstrain parameters, in order: 269 285 270 0. Type, one of u'generalized', u'isotropic',271 u' uniaxial'286 0. Type, one of u'isotropic', u'uniaxial', 287 u'generalized' 272 288 1. Isotropic/uniaxial parameters  list of 3 floats 273 289 2. Refinement flags  list of 3 bools … … 291 307 \ Scale Phase fraction, list of [float, bool]. 292 308 \ Show bool 309 \ Size List of crystallite size parameters, in order: 310 311 0. Type, one of u'isotropic', u'uniaxial', 312 u'ellipsoidal' 313 1. Isotropic/uniaxial parameters  list of 3 floats 314 2. Refinement flags  list of 3 bools 315 3. Size axis  list of 3 ints, [h, k, l] 316 4. Ellipsoidal size parameters  list of 6 317 floats 318 5. Ellipsoidal refinement flags  list of bools, 319 corresponding to the parameters of (4) 293 320 \ Use bool 294 321 \ newLeBail Whether to perform a new LeBail extraction … … 356 383 Space groups are interpreted by :func:`GSASIIspc.SpcGroup` 357 384 and the information is placed in a SGdata object 358 which is a dict with these keys :385 which is a dict with these keys. Magnetic ones are marked "mag" 359 386 360 387 .. tabularcolumns:: lp{4.5in} … … 363 390 key explanation 364 391 ========== ==================================================== 365 SpGrp space group symbol (str) 366 Laue one of the following 14 Laue classes: 367 1, 2/m, mmm, 4/m, 4/mmm, 3R, 368 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str) 392 BNSlattsym mag  BNS magnetic space group symbol and centering vector 393 GenFlg mag  list of symmetry generators indices 394 GenSym mag  list of names for each generator 395 MagMom mag  list of "time reversals" for each magnetic operator 396 MagPtGp mag Magnetic point group symbol 397 MagSpGrp mag  Magnetic space group symbol 398 OprNames mag  names for each space group operation 399 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 403 then the space group can not be changed by the user because 404 operator set from cif may be nonstandard 405 SGGen list of generators 406 SGGray True if space group is a gray group (incommensurate magnetic structures) 369 407 SGInv True if centrosymmetric, False if not (bool) 370 408 SGLatt Lattice centering type. Will be one of 371 409 P, A, B, C, I, F, R (str) 372 SGUniq unique axis if monoclinic. Will be 373 a, b, or c for monoclinic space groups. 374 Will be blank for nonmonoclinic. (str) 375 SGCen Symmetry cell centering vectors. A (n,3) np.array 376 of centers. Will always have at least one row: 377 ``np.array([[0, 0, 0]])`` 410 SGLaue 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 (str) 378 413 SGOps symmetry operations as a list of form 379 414 ``[[M1,T1], [M2,T2],...]`` … … 384 419 are transformed using 385 420 :math:`X^\prime = M_n*X+T_n` 421 SGPolax Axes for space group polarity. Will be one of 422 '', 'x', 'y', 'x y', 'z', 'x z', 'y z', 423 'xyz'. In the case where axes are arbitrary 424 '111' is used (P 1, and ?). 425 SGPtGrp Point group f the space group 426 SGUniq unique axis if monoclinic. Will be 427 a, b, or c for monoclinic space groups. 428 Will be blank for nonmonoclinic. (str) 429 SGSpin mag  list of spin flip operatiors (+1 or 1) for the space group operations 386 430 SGSys symmetry unit cell: type one of 387 431 'triclinic', 'monoclinic', 'orthorhombic', 388 432 'tetragonal', 'rhombohedral', 'trigonal', 389 433 'hexagonal', 'cubic' (str) 390 S GPolax Axes for space group polarity. Will be one of391 '', 'x', 'y', 'x y', 'z', 'x z', 'y z', 392 'xyz'. In the case where axes are arbitrary 393 '111' is used (P 1, and ?).434 SSGK1 list of superspace multipliers 435 SpGrp space group symbol (str) 436 SpnFlp mag  list of magnetic spin flips for every magnetic space group operator 437 394 438 ========== ==================================================== 395 439 … … 430 474 are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``, 431 475 which define locations in the atom record, as shown below. Items shown are 432 always present; additional ones for macromolecular phases are marked 'mm' 476 always present; additional ones for macromolecular phases are marked 'mm', 477 and those for magnetic structures are marked 'mg' 433 478 434 479 .. tabularcolumns:: lp{4.5in} … … 442 487 ct1 atom label (str) 443 488 ct atom type (str) 444 ct+1 refinement flags; combination of 'F', 'X', 'U' (str)489 ct+1 refinement flags; combination of 'F', 'X', 'U', 'M' (str) 445 490 cx,cx+1,cx+2 the x,y and z coordinates (3 floats) 446 491 cx+3 site occupancy (float) 492 cx+4,5,6 mg  atom magnetic moment along a,b,c in Bohr magnetons 447 493 cs site symmetry (str) 448 494 cs+1 site multiplicity (int) … … 468 514 are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``, 469 515 which define locations in the atom record, as shown below. Items shown are 470 always present; additional ones for macromolecular phases are marked 'mm' 516 always present; additional ones for macromolecular phases are marked 'mm', 517 and those for magnetic structures are marked 'mg' 471 518 472 519 .. tabularcolumns:: lp{4.5in} … … 481 528 ct atom type (str) 482 529 cx,cx+1,cx+2 the x,y and z coordinates (3 floats) 530 cx+3,4,5 mg  atom magnetic moment along a,b,c in Bohr magnetons 483 531 cs1 Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,1') (str) 484 532 cs atom drawing style; e.g. 'balls & sticks' (str) … … 528 576 the :ref:`Powder Reflections <PowderRefl_table>` 529 577 description. 530 Instrument Parameters \ A list containing two dicts where the possible531 keys in each dict are listed below. The value532 for each item is a list containing three values:533 th e initial value, the current value and a534 refinement flag which can have a value of578 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 535 583 True, False or 0 where 0 indicates a value that 536 584 cannot be refined. The first and second 537 585 values are floats unless otherwise noted. 538 586 Items in the first dict are noted as [1] 587 \ Type Histogram type (str) [1]: 588 * 'PXC' for constant wavelength xray 589 * 'PNC' for constant wavelength neutron 590 \ Bank Data set number in a multidata file (usually 1) 539 591 \ Lam Specifies a wavelength in Angstroms [1] 540 592 \ Lam1 Specifies the primary wavelength in … … 545 597 source is used [1] 546 598 I(L2)/I(L1) Ratio of Lam2 to Lam1 [1] 547 \ Type Histogram type (str) [1]:548 * 'PXC' for constant wavelength xray549 * 'PNC' for constant wavelength neutron550 * 'PNT' for time of flight neutron551 599 \ Zero Twotheta zero correction in *degrees* [1] 552 600 \ Azimuth Azimuthal setting angle for data recorded … … 556 604 FWHM goes as 557 605 :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1] 558 \ X, Y 606 \ X, Y, Z Cauchy (Lorentzian) instrumental broadening 559 607 coefficients [1] 560 608 \ SH/L Variant of the FingerCoxJephcoat asymmetric 561 609 peak broadening ratio. Note that this is the 562 average betweenS/L and H/L where S is610 sum of S/L and H/L where S is 563 611 sample height, H is the slit height and 564 612 L is the goniometer diameter. [1] 565 613 \ Polariz. Polarization coefficient. [1] 614 Instrument Parameters (TOF) \ A list containing two dicts for neutron timeofflight 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 \ 2theta Nominal scattering angle for the detector 627 \ fltPath Total flight path sourcesampledetector 628 \ Azimuth Azimuth angle for detector righ hand rotation 629 from horizontal away from source 630 \ difC,difA,difB Diffractometer constants for conversion of dspacing to TOF 631 in microseconds 632 \ Zero Zero point offset (microseconds) 633 \ alpha Exponential rise profile coefficients 634 \ beta0 Exponential decay profile coefficients 635 beta1 636 betaq 637 \ sig0 Gaussian profile coefficients 638 sig1 639 sig2 640 sigq 641 \ X,Y,Z Lorentzian profile coefficients 566 642 wtFactor \ A weighting factor to increase or decrease 567 643 the leverage of data in the histogram (float). … … 652 728 11 intensity correction for reflection, this times 653 729 :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc 654 12 Pr fo655 13 Trans 656 14 Ext P730 12 Preferred orientation correction 731 13 Transmission (absorption correction) 732 14 Extinction correction 657 733 ========== ==================================================== 658 734 … … 852 928 \ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included 853 929 in integrsation. The tuple is the image intensity limits and the list are those set by the user. 930 \ SpotMask dict: 'esdMul'(int) number of standard deviations above mean ring intensity to mask 931 'spotMask' (bool array) the spot mask for every pixel in image 854 932 855 933 Stress/Strain Sample phi (float) Sample rotation about vertical axis.
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