Changeset 4308
- Timestamp:
- Feb 16, 2020 6:44:12 AM (5 years ago)
- File:
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- 1 edited
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trunk/GSASIIobj.py (modified) (11 diffs)
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TabularUnified trunk/GSASIIobj.py ¶
r4307 r4308 155 155 .. tabularcolumns:: |l|l|p{4in}| 156 156 157 ========== =============== ====================================================158 key sub-key explanation159 ========== =============== ====================================================160 General \ Overall information for the phase (dict)161 \ 3Dproj projections for 3D pole distribution plots162 \ AngleRadii Default radius for each atom used to compute163 interatomic angles (list of floats)164 \ AtomMass List of masses for atoms165 \ AtomPtrs list of four locations (cx,ct,cs & cu) to use to pull info166 from the atom records (list)167 \ AtomTypes List of atom types168 \ BondRadii Default radius for each atom used to compute169 interatomic distances (list of floats)170 \ Cell List with 8 items: cell refinement flag (bool)157 ========== =============== ==================================================== 158 key sub-key explanation 159 ========== =============== ==================================================== 160 General \ Overall information for the phase (dict) 161 \ 3Dproj projections for 3D pole distribution plots 162 \ AngleRadii Default radius for each atom used to compute 163 interatomic angles (list of floats) 164 \ AtomMass List of masses for atoms 165 \ AtomPtrs list of four locations (cx,ct,cs & cu) to use to pull info 166 from the atom records (list) 167 \ AtomTypes List of atom types 168 \ BondRadii Default radius for each atom used to compute 169 interatomic distances (list of floats) 170 \ Cell List with 8 items: cell refinement flag (bool) 171 171 a, b, c, (:math:`\\unicode{x212B}`, float) 172 alpha, beta & gamma (degrees, float)172 alpha, beta & gamma (degrees, float) 173 173 volume (:math:`\\unicode{x212B}^3`, float) 174 \ Color Colors for atoms (list of (r,b,g) triplets)175 \ Compare dict of polygon comparison parameters176 \ Data plot type data plot type ('Mustrain', 'Size' or177 'Preferred orientation') for powder data (str)178 \ DisAglCtls Dict with distance/angle search controls,179 which has keys 'Name', 'AtomTypes',180 'BondRadii', 'AngleRadii' which are as above181 except are possibly edited. Also contains182 'Factors', which is a 2 element list with183 a multiplier for bond and angle search range184 [typically (0.85,0.85)].185 \ F000X x-ray F(000) intensity (float)186 \ F000N neutron F(000) intensity (float)187 \ Flip dict of Charge flip controls188 \ HydIds dict geometrically generated hydrogen atoms189 \ Isotope dict of isotopes for each atom type190 \ Isotopes dict of scattering lengths for each isotope191 combination for each element in phase192 \ MCSA controls Monte Carlo-Simulated Annealing controls (dict)193 \ Map dict of map parameters194 \ Mass Mass of unit cell contents in g/mol195 \ Modulated bool True if phase modulated196 \ Mydir directory of current .gpx file (str)197 \ Name phase name (str)198 \ Type 'nuclear' or 'macromolecular' for now (str)199 \ NoAtoms Number of atoms per unit cell of each type (dict)200 \ POhkl March-Dollase preferred orientation direction201 \ Pawley dmin maximum Q (as d-space) to use for Pawley202 extraction (float)203 \ Pawley dmax minimum Q (as d-space) to use for Pawley204 extraction (float)205 \ Pawley neg wt Restraint value for negative Pawley intensities206 (float)207 \ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>`208 as defined in :func:`GSASIIspc.SpcGroup`.209 \ SH Texture dict of spherical harmonic preferred orientation210 parameters211 \ Super int dimension of super group (0,1 only)212 \ Type str phase type (e.g. 'nuclear')213 \ Z dict of atomic numbers for each atom type214 \ doDysnomia bool flag for max ent map modification via Dysnomia215 \ doPawley bool Flag for Pawley intensity extraction216 \ vdWRadii dict of van der Waals radii for each atom type217 ranId \ unique random number Id for phase (int)218 pId \ Phase Id number for current project (int).219 Atoms \ Atoms in phase as a list of lists. The outer list220 is for each atom, the inner list contains varying221 items depending on the type of phase, see222 the :ref:`Atom Records <Atoms_table>` description.223 (list of lists)224 Drawing \ Display parameters (dict)225 \ Atoms A list of lists with an entry for each atom226 that is plotted.227 \ Plane list Controls for contour density plane display228 \ Quaternion Viewing quaternion (4 element np.array)229 \ Zclip clipping distance in A (float)230 \ Zstep Step to de/increase Z-clip (float)231 \ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list)232 \ backColor background for plot as and R,G,B triplet233 (default = [0, 0, 0], black).234 (list with three atoms)235 \ ballScale Size of spheres in ball-and-stick display (float)236 \ bondList dict with bonds237 \ bondRadius Size of binds in A (float)238 \ cameraPos Viewing position in A for plot (float)174 \ Color Colors for atoms (list of (r,b,g) triplets) 175 \ Compare dict of polygon comparison parameters 176 \ Data plot type data plot type ('Mustrain', 'Size' or 177 'Preferred orientation') for powder data (str) 178 \ DisAglCtls Dict with distance/angle search controls, 179 which has keys 'Name', 'AtomTypes', 180 'BondRadii', 'AngleRadii' which are as above 181 except are possibly edited. Also contains 182 'Factors', which is a 2 element list with 183 a multiplier for bond and angle search range 184 [typically (0.85,0.85)]. 185 \ F000X x-ray F(000) intensity (float) 186 \ F000N neutron F(000) intensity (float) 187 \ Flip dict of Charge flip controls 188 \ HydIds dict geometrically generated hydrogen atoms 189 \ Isotope dict of isotopes for each atom type 190 \ Isotopes dict of scattering lengths for each isotope 191 combination for each element in phase 192 \ MCSA controls Monte Carlo-Simulated Annealing controls (dict) 193 \ Map dict of map parameters 194 \ Mass Mass of unit cell contents in g/mol 195 \ Modulated bool True if phase modulated 196 \ Mydir directory of current .gpx file (str) 197 \ Name phase name (str) 198 \ Type 'nuclear' or 'macromolecular' for now (str) 199 \ NoAtoms Number of atoms per unit cell of each type (dict) 200 \ POhkl March-Dollase preferred orientation direction 201 \ Pawley dmin maximum Q (as d-space) to use for Pawley 202 extraction (float) 203 \ Pawley dmax minimum Q (as d-space) to use for Pawley 204 extraction (float) 205 \ Pawley neg wt Restraint value for negative Pawley intensities 206 (float) 207 \ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>` 208 as defined in :func:`GSASIIspc.SpcGroup`. 209 \ SH Texture dict of spherical harmonic preferred orientation 210 parameters 211 \ Super int dimension of super group (0,1 only) 212 \ Type str phase type (e.g. 'nuclear') 213 \ Z dict of atomic numbers for each atom type 214 \ doDysnomia bool flag for max ent map modification via Dysnomia 215 \ doPawley bool Flag for Pawley intensity extraction 216 \ vdWRadii dict of van der Waals radii for each atom type 217 ranId \ unique random number Id for phase (int) 218 pId \ Phase Id number for current project (int). 219 Atoms \ Atoms in phase as a list of lists. The outer list 220 is for each atom, the inner list contains varying 221 items depending on the type of phase, see 222 the :ref:`Atom Records <Atoms_table>` description. 223 (list of lists) 224 Drawing \ Display parameters (dict) 225 \ Atoms A list of lists with an entry for each atom 226 that is plotted. 227 \ Plane list Controls for contour density plane display 228 \ Quaternion Viewing quaternion (4 element np.array) 229 \ Zclip clipping distance in A (float) 230 \ Zstep Step to de/increase Z-clip (float) 231 \ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list) 232 \ backColor background for plot as and R,G,B triplet 233 (default = [0, 0, 0], black). 234 (list with three atoms) 235 \ ballScale Size of spheres in ball-and-stick display (float) 236 \ bondList dict with bonds 237 \ bondRadius Size of binds in A (float) 238 \ cameraPos Viewing position in A for plot (float) 239 239 \ contourLevel map contour level in :math:`e/\\unicode{x212B}^3` (float) 240 \ contourMax float map contour maximum 241 \ depthFog True if use depthFog on plot - set currently as False (bool) 242 \ ellipseProb Probability limit for display of thermal 243 ellipsoids in % (float). 244 \ magMult float multiplier for magnetic moment arrows 245 \ mapSize float x & y dimensions of contourmap (fixed internally) 246 \ modelView 4,4 array from openGL drawing transofmation matrix 247 \ oldxy previous view point (list with two floats) 248 \ radiusFactor Distance ratio for searching for bonds. ? Bonds 249 are located that are within r(Ra+Rb) and (Ra+Rb)/r 250 where Ra and Rb are the atomic radii. 251 \ selectedAtoms List of selected atoms (list of int values) 252 \ showABC Flag to show view point triplet (bool). True=show. 253 \ showHydrogen Flag to control plotting of H atoms. 254 \ showRigidBodies Flag to highlight rigid body placement 255 \ showSlice flag to show contour map 256 \ sizeH Size ratio for H atoms (float) 257 \ unitCellBox Flag to control display of the unit cell. 258 \ vdwScale Multiplier of van der Waals radius for 259 display of vdW spheres. 260 \ viewDir cartesian viewing direction (np.array with three 261 elements) 262 \ viewPoint list of lists. First item in list is [x,y,z] 263 in fractional coordinates for the center of 264 the plot. Second item list of previous & current 265 atom number viewed (may be [0,0]) 266 RBModels \ Rigid body assignments (note Rigid body definitions 267 are stored in their own main top-level tree entry.) 268 RMC \ dict RMCProfile & rmcfull controls 269 Pawley ref \ Pawley reflections 270 Histograms \ A dict of dicts. The key for the outer dict is 271 the histograms tied to this phase. The inner 272 dict contains the combined phase/histogram 273 parameters for items such as scale factors, 274 size and strain parameters. The following are the 275 keys to the inner dict. (dict) 276 \ Babinet For protein crystallography. Dictionary with two 277 entries, 'BabA', 'BabU' 278 \ Extinction Extinction parameter (list of float, bool) 279 \ HStrain Hydrostatic strain. List of two lists. The first is 280 a list of the HStrain parameters (1, 2, 3, 4, or 6 281 depending on unit cell), the second is a list of boolean 282 refinement parameters (same length) 283 \ Histogram The name of the associated histogram (str) 284 \ LeBail Flag for LeBail extraction (bool) 285 \ Mustrain List of microstrain parameters, in order: 286 287 0. Type, one of u'isotropic', u'uniaxial', 288 u'generalized' 289 1. Isotropic/uniaxial parameters - list of 3 floats 290 2. Refinement flags - list of 3 bools 291 3. Microstrain axis - list of 3 ints, [h, k, l] 292 4. Generalized mustrain parameters - list of 2-6 240 \ contourMax float map contour maximum 241 \ depthFog True if use depthFog on plot - set currently as False (bool) 242 \ ellipseProb Probability limit for display of thermal 243 ellipsoids in % (float). 244 \ magMult float multiplier for magnetic moment arrows 245 \ mapSize float x & y dimensions of contourmap (fixed internally) 246 \ modelView 4,4 array from openGL drawing transofmation matrix 247 \ oldxy previous view point (list with two floats) 248 \ radiusFactor Distance ratio for searching for bonds. ? Bonds 249 are located that are within r(Ra+Rb) and (Ra+Rb)/r 250 where Ra and Rb are the atomic radii. 251 \ selectedAtoms List of selected atoms (list of int values) 252 \ showABC Flag to show view point triplet (bool). True=show. 253 \ showHydrogen Flag to control plotting of H atoms. 254 \ showRigidBodies Flag to highlight rigid body placement 255 \ showSlice flag to show contour map 256 \ sizeH Size ratio for H atoms (float) 257 \ unitCellBox Flag to control display of the unit cell. 258 \ vdwScale Multiplier of van der Waals radius for 259 display of vdW spheres. 260 \ viewDir cartesian viewing direction (np.array with three 261 elements) 262 \ viewPoint list of lists. First item in list is [x,y,z] 263 in fractional coordinates for the center of 264 the plot. Second item list of previous & current 265 atom number viewed (may be [0,0]) 266 RBModels \ Rigid body assignments (note Rigid body definitions 267 are stored in their own main top-level tree entry.) 268 RMC \ dict RMCProfile & rmcfull controls 269 Pawley ref \ Pawley reflections 270 Histograms \ A dict of dicts. The key for the outer dict is 271 the histograms tied to this phase. The inner 272 dict contains the combined phase/histogram 273 parameters for items such as scale factors, 274 size and strain parameters. The following are the 275 keys to the inner dict. (dict) 276 \ Babinet For protein crystallography. Dictionary with two 277 entries, 'BabA', 'BabU' 278 \ Extinction Extinction parameter (list of float, bool) 279 \ HStrain Hydrostatic strain. List of two lists. The first is 280 a list of the HStrain parameters (1, 2, 3, 4, or 6 281 depending on unit cell), the second is a list of boolean 282 refinement parameters (same length) 283 \ Histogram The name of the associated histogram (str) 284 \ LeBail Flag for LeBail extraction (bool) 285 \ 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 2-6 293 292 floats, depending on space group 294 5. Generalized refinement flags - list of bools,293 5. Generalized refinement flags - list of bools, 295 294 corresponding to the parameters of (4) 296 \ Pref.Ori. Preferred Orientation. List of eight parameters. 297 Items marked SH are only used for Spherical Harmonics. 298 299 0. Type, 'MD' for March-Dollase or 'SH' for 300 Spherical Harmonics 301 1. Value, float 302 2. Refinement flag, bool 303 3. Preferred direction, list of ints, [h, k, l] 304 4. SH - number of terms, int 305 5. SH - dict 306 6. SH - list 307 7. SH - float 308 \ Scale Phase fraction, list of [float, bool]. 309 \ Show bool 310 \ Size List of crystallite size parameters, in order: 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 March-Dollase 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 306 \ Scale Phase fraction, list of [float, bool]. 307 \ Show bool 308 \ Size List of crystallite size parameters, in order: 311 309 312 0. Type, one of u'isotropic', u'uniaxial', 313 u'ellipsoidal' 314 1. Isotropic/uniaxial parameters - list of 3 floats 315 2. Refinement flags - list of 3 bools 316 3. Size axis - list of 3 ints, [h, k, l] 317 4. Ellipsoidal size parameters - list of 6 318 floats 319 5. Ellipsoidal refinement flags - list of bools, 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, 320 316 corresponding to the parameters of (4) 321 \ Use bool322 \ newLeBail Whether to perform a new LeBail extraction323 MCSA \ Monte-Carlo simulated annealing parameters (dict)317 \ Use bool 318 \ newLeBail Whether to perform a new LeBail extraction 319 MCSA \ Monte-Carlo simulated annealing parameters (dict) 324 320 \ 325 ========== =============== ====================================================321 ========== =============== ==================================================== 326 322 327 323 .. _RBData_table: … … 341 337 .. tabularcolumns:: |l|l|p{4in}| 342 338 343 ========== =============== ====================================================344 key sub-key explanation345 ========== =============== ====================================================346 Vector RBId vector rigid bodies (dict of dict)347 \ AtInfo Drad, Color: atom drawing radius & color for each atom type (dict)348 \ RBname Name assigned by user to rigid body (str)349 \ VectMag vector magnitudes in A (list)350 \ rbXYZ Cartesian coordinates for Vector rigid body (list of 3 float)351 \ rbRef 3 assigned reference atom nos. in rigid body for origin352 definition, use center of atoms flag (list of 3 int & 1 bool)353 \ VectRef refinement flags for VectMag values (list of bool)354 \ rbTypes Atom types for each atom in rigid body (list of str)355 \ rbVect Cartesian vectors for each translation used to build rigid body (list of lists)356 \ useCount Number of times rigid body is used in any structure (int)357 Residue RBId residue rigid bodies (dict of dict)358 \ AtInfo Drad, Color: atom drawing radius & color for each atom type(dict)359 \ RBname Name assigned by user to rigid body (str)360 \ rbXYZ Cartesian coordinates for Residue rigid body (list of 3 float)361 \ rbTypes Atom types for each atom in rigid body (list of str)362 \ atNames Names of each atom in rigid body (e.g. C1,N2...) (list of str)363 \ rbRef 3 assigned reference atom nos. in rigid body for origin364 definition, use center of atoms flag (list of 3 int & 1 bool)365 \ rbSeq Orig,Piv,angle,Riding (list): definition of internal rigid body366 torsion; origin atom (int), pivot atom (int), torsion angle (float),367 riding atoms (list of int)368 \ SelSeq [int,int] used by SeqSizer to identify objects369 \ useCount Number of times rigid body is used in any structure (int)370 RBIds \ unique Ids generated upon creation of each rigid body (dict)371 \ Vector Ids for each Vector rigid body (list)372 \ Residue Ids for each Residue rigid body (list)373 ========== =============== ====================================================339 ========== =============== ==================================================== 340 key sub-key explanation 341 ========== =============== ==================================================== 342 Vector RBId vector rigid bodies (dict of dict) 343 \ AtInfo Drad, Color: atom drawing radius & color for each atom type (dict) 344 \ RBname Name assigned by user to rigid body (str) 345 \ VectMag vector magnitudes in A (list) 346 \ rbXYZ Cartesian coordinates for Vector rigid body (list of 3 float) 347 \ rbRef 3 assigned reference atom nos. in rigid body for origin 348 definition, use center of atoms flag (list of 3 int & 1 bool) 349 \ VectRef refinement flags for VectMag values (list of bool) 350 \ rbTypes Atom types for each atom in rigid body (list of str) 351 \ rbVect Cartesian vectors for each translation used to build rigid body (list of lists) 352 \ useCount Number of times rigid body is used in any structure (int) 353 Residue RBId residue rigid bodies (dict of dict) 354 \ AtInfo Drad, Color: atom drawing radius & color for each atom type(dict) 355 \ RBname Name assigned by user to rigid body (str) 356 \ rbXYZ Cartesian coordinates for Residue rigid body (list of 3 float) 357 \ rbTypes Atom types for each atom in rigid body (list of str) 358 \ atNames Names of each atom in rigid body (e.g. C1,N2...) (list of str) 359 \ rbRef 3 assigned reference atom nos. in rigid body for origin 360 definition, use center of atoms flag (list of 3 int & 1 bool) 361 \ rbSeq Orig,Piv,angle,Riding (list): definition of internal rigid body 362 torsion; origin atom (int), pivot atom (int), torsion angle (float), 363 riding atoms (list of int) 364 \ SelSeq [int,int] used by SeqSizer to identify objects 365 \ useCount Number of times rigid body is used in any structure (int) 366 RBIds \ unique Ids generated upon creation of each rigid body (dict) 367 \ Vector Ids for each Vector rigid body (list) 368 \ Residue Ids for each Residue rigid body (list) 369 ========== =============== ==================================================== 374 370 375 371 .. _SGData_table: … … 409 405 P, A, B, C, I, F, R (str) 410 406 SGLaue str, one of the following 14 Laue classes: 411 407 -1, 2/m, mmm, 4/m, 4/mmm, 3R, 412 408 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m 413 409 SGOps symmetry operations as a list of form … … 478 474 .. tabularcolumns:: |l|p{4.5in}| 479 475 480 ============== ====================================================481 location explanation482 ============== ====================================================483 ct-4 mm - residue number (str)484 ct-3 mm - residue name (e.g. ALA) (str)485 ct-2 mm - chain label (str)486 ct-1 atom label (str)487 ct atom type (str)488 ct+1 refinement flags; combination of 'F', 'X', 'U', 'M' (str)489 cx,cx+1,cx+2 the x,y and z coordinates (3 floats)490 cx+3 site occupancy (float)491 cx+4,5,6 mg - atom magnetic moment along a,b,c in Bohr magnetons492 cs site symmetry (str)493 cs+1 site multiplicity (int)494 cia ADP flag: Isotropic ('I') or Anisotropic ('A')495 cia+1 Uiso (float)496 cia+2...cia+7 U11, U22, U33, U12, U13, U23 (6 floats)497 atom[cia+8] unique atom identifier (int)498 499 ============== ====================================================476 ============== ==================================================== 477 location explanation 478 ============== ==================================================== 479 ct-4 mm - residue number (str) 480 ct-3 mm - residue name (e.g. ALA) (str) 481 ct-2 mm - chain label (str) 482 ct-1 atom label (str) 483 ct atom type (str) 484 ct+1 refinement flags; combination of 'F', 'X', 'U', 'M' (str) 485 cx,cx+1,cx+2 the x,y and z coordinates (3 floats) 486 cx+3 site occupancy (float) 487 cx+4,5,6 mg - atom magnetic moment along a,b,c in Bohr magnetons 488 cs site symmetry (str) 489 cs+1 site multiplicity (int) 490 cia ADP flag: Isotropic ('I') or Anisotropic ('A') 491 cia+1 Uiso (float) 492 cia+2...cia+7 U11, U22, U33, U12, U13, U23 (6 floats) 493 atom[cia+8] unique atom identifier (int) 494 495 ============== ==================================================== 500 496 501 497 .. _Drawing_atoms_table: … … 519 515 520 516 ============== =================================================================================== 521 location explanation517 location explanation 522 518 ============== =================================================================================== 523 ct-4 mm - residue number (str)524 ct-3 mm - residue name (e.g. ALA) (str)525 ct-2 mm - chain label (str)526 ct-1 atom label (str)527 ct atom type (str)528 cx,cx+1,cx+2 the x,y and z coordinates (3 floats)529 cx+3,4,5 mg - atom magnetic moment along a,b,c in Bohr magnetons530 cs-1 Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)531 cs atom drawing style; e.g. 'balls & sticks' (str)532 cs+1 atom label style (e.g. 'name') (str)533 cs+2 atom color (RBG triplet) (int)534 cs+3 ADP flag: Isotropic ('I') or Anisotropic ('A')535 cs+4 Uiso (float)536 cs+5...cs+11 U11, U22, U33, U12, U13, U23 (6 floats)537 ci unique atom identifier; matches source atom Id in Atom Records (int)519 ct-4 mm - residue number (str) 520 ct-3 mm - residue name (e.g. ALA) (str) 521 ct-2 mm - chain label (str) 522 ct-1 atom label (str) 523 ct atom type (str) 524 cx,cx+1,cx+2 the x,y and z coordinates (3 floats) 525 cx+3,4,5 mg - atom magnetic moment along a,b,c in Bohr magnetons 526 cs-1 Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str) 527 cs atom drawing style; e.g. 'balls & sticks' (str) 528 cs+1 atom label style (e.g. 'name') (str) 529 cs+2 atom color (RBG triplet) (int) 530 cs+3 ADP flag: Isotropic ('I') or Anisotropic ('A') 531 cs+4 Uiso (float) 532 cs+5...cs+11 U11, U22, U33, U12, U13, U23 (6 floats) 533 ci unique atom identifier; matches source atom Id in Atom Records (int) 538 534 ============== =================================================================================== 539 535 … … 560 556 561 557 ====================== =============== =========================================================== 562 key sub-key explanation558 key sub-key explanation 563 559 ====================== =============== =========================================================== 564 Comments \Text strings extracted from the original powder565 data header. These cannot be changed by the user;566 it may be empty.567 Limits \A list of two two element lists, as [[Ld,Hd],[L,H]]568 where L and Ld are the current and default lowest569 two-theta value to be used and570 where H and Hd are the current and default highest571 two-theta value to be used.572 Reflection Lists \A dict with an entry for each phase in the573 histogram. The contents of each dict item574 is a dict containing reflections, as described in575 the :ref:`Powder Reflections <PowderRefl_table>`576 description.560 Comments \ Text strings extracted from the original powder 561 data header. These cannot be changed by the user; 562 it may be empty. 563 Limits \ A list of two two element lists, as [[Ld,Hd],[L,H]] 564 where L and Ld are the current and default lowest 565 two-theta value to be used and 566 where H and Hd are the current and default highest 567 two-theta value to be used. 568 Reflection Lists \ A dict with an entry for each phase in the 569 histogram. The contents of each dict item 570 is a dict containing reflections, as described in 571 the :ref:`Powder Reflections <PowderRefl_table>` 572 description. 577 573 Instrument Parameters \ The instrument parameters uses different dicts 578 574 for the constant wavelength (CW) and time-of-flight (TOF) 579 575 cases. See below for the descriptions of each. 580 wtFactor \A weighting factor to increase or decrease581 the leverage of data in the histogram (float).582 A value of 1.0 weights the data with their583 standard uncertainties and a larger value584 increases the weighting of the data (equivalent585 to decreasing the uncertainties).586 Sample Parameters \Specifies a dict with parameters that describe how587 the data were collected, as listed588 below. Refinable parameters are a list containing589 a float and a bool, where the second value590 specifies if the value is refined, otherwise591 the value is a float unless otherwise noted.592 \ Scale The histogram scale factor (refinable)593 \ Absorption The sample absorption coefficient as594 :math:`\\mu r` where r is the radius595 (refinable). Only valid for Debye-Scherrer geometry.596 \ SurfaceRoughA Surface roughness parameter A as defined by597 Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -598 only valid for Bragg-Brentano geometry)599 \ SurfaceRoughB Surface roughness parameter B (refinable -600 only valid for Bragg-Brentano geometry)601 \ DisplaceX, Sample displacement from goniometer center602 DisplaceY where Y is along the beam direction and603 X is perpendicular. Units are :math:`\\mu m`604 (refinable).605 \ Phi, Chi, Goniometer sample setting angles, in degrees.606 Omega607 \ Gonio. radius Radius of the diffractometer in mm608 \ InstrName A name for the instrument, used in preparing609 a CIF (str).610 \ Force, Variables that describe how the measurement611 Temperature, was performed. Not used directly in612 Humidity, any computations.613 Pressure,614 Voltage615 \ ranId The random-number Id for the histogram616 (same value as where top-level key is ranId)617 \ Type Type of diffraction data, may be 'Debye-Scherrer'618 or 'Bragg-Brentano' (str).619 \ Diffuse not in use?620 hId \The number assigned to the histogram when621 the project is loaded or edited (can change)622 ranId \A random number id for the histogram623 that does not change624 Background \The background is stored as a list with where625 the first item in the list is list and the second626 item is a dict. The list contains the background627 function and its coefficients; the dict contains628 Debye diffuse terms and background peaks.629 (TODO: this needs to be expanded.)630 Data \The data consist of a list of 6 np.arrays631 containing in order:632 633 0. the x-postions (two-theta in degrees),634 1. the intensity values (Yobs),635 2. the weights for each Yobs value636 3. the computed intensity values (Ycalc)637 4. the background values638 5. Yobs-Ycalc576 wtFactor \ A weighting factor to increase or decrease 577 the leverage of data in the histogram (float). 578 A value of 1.0 weights the data with their 579 standard uncertainties and a larger value 580 increases the weighting of the data (equivalent 581 to decreasing the uncertainties). 582 Sample Parameters \ Specifies a dict with parameters that describe how 583 the data were collected, as listed 584 below. Refinable parameters are a list containing 585 a float and a bool, where the second value 586 specifies if the value is refined, otherwise 587 the value is a float unless otherwise noted. 588 \ Scale The histogram scale factor (refinable) 589 \ Absorption The sample absorption coefficient as 590 :math:`\\mu r` where r is the radius 591 (refinable). Only valid for Debye-Scherrer geometry. 592 \ SurfaceRoughA Surface roughness parameter A as defined by 593 Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable - 594 only valid for Bragg-Brentano geometry) 595 \ SurfaceRoughB Surface roughness parameter B (refinable - 596 only valid for Bragg-Brentano geometry) 597 \ DisplaceX, Sample displacement from goniometer center 598 DisplaceY where Y is along the beam direction and 599 X is perpendicular. Units are :math:`\\mu m` 600 (refinable). 601 \ Phi, Chi, Goniometer sample setting angles, in degrees. 602 Omega 603 \ Gonio. radius Radius of the diffractometer in mm 604 \ InstrName A name for the instrument, used in preparing 605 a CIF (str). 606 \ Force, Variables that describe how the measurement 607 Temperature, was performed. Not used directly in 608 Humidity, any computations. 609 Pressure, 610 Voltage 611 \ ranId The random-number Id for the histogram 612 (same value as where top-level key is ranId) 613 \ Type Type of diffraction data, may be 'Debye-Scherrer' 614 or 'Bragg-Brentano' (str). 615 \ Diffuse not in use? 616 hId \ The number assigned to the histogram when 617 the project is loaded or edited (can change) 618 ranId \ A random number id for the histogram 619 that does not change 620 Background \ The background is stored as a list with where 621 the first item in the list is list and the second 622 item is a dict. The list contains the background 623 function and its coefficients; the dict contains 624 Debye diffuse terms and background peaks. 625 (TODO: this needs to be expanded.) 626 Data \ The data consist of a list of 6 np.arrays 627 containing in order: 628 629 0. the x-postions (two-theta in degrees), 630 1. the intensity values (Yobs), 631 2. the weights for each Yobs value 632 3. the computed intensity values (Ycalc) 633 4. the background values 634 5. Yobs-Ycalc 639 635 ====================== =============== =========================================================== 640 636 … … 742 738 index explanation 743 739 ========== ==================================================== 744 0,1,2 h,k,l (float)745 3 multiplicity740 0,1,2 h,k,l (float) 741 3 multiplicity 746 742 4 d-space, :math:`\\unicode{x212B}` 747 5 pos, two-theta748 6 sig, Gaussian width749 7 gam, Lorenzian width750 8 :math:`F_{obs}^2`751 9 :math:`F_{calc}^2`752 10 reflection phase, in degrees753 11 intensity correction for reflection, this times754 :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc755 12 Preferred orientation correction756 13 Transmission (absorption correction)757 14 Extinction correction743 5 pos, two-theta 744 6 sig, Gaussian width 745 7 gam, Lorenzian width 746 8 :math:`F_{obs}^2` 747 9 :math:`F_{calc}^2` 748 10 reflection phase, in degrees 749 11 intensity correction for reflection, this times 750 :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc 751 12 Preferred orientation correction 752 13 Transmission (absorption correction) 753 14 Extinction correction 758 754 ========== ==================================================== 759 755 … … 779 775 .. tabularcolumns:: |l|l|p{4in}| 780 776 781 ====================== =============== ====================================================782 key sub-key explanation783 ====================== =============== ====================================================784 Data \A dict that contains the785 reflection table,786 as described in the787 :ref:`Single Crystal Reflections788 <XtalRefl_table>`789 description.790 791 Instrument Parameters \A list containing two dicts where the possible792 keys in each dict are listed below. The value793 for most items is a list containing two values:794 the initial value, the current value.795 The first and second796 values are floats unless otherwise noted.777 ====================== =============== ==================================================== 778 key sub-key explanation 779 ====================== =============== ==================================================== 780 Data \ A dict that contains the 781 reflection table, 782 as described in the 783 :ref:`Single Crystal Reflections 784 <XtalRefl_table>` 785 description. 786 787 Instrument Parameters \ A list containing two dicts where the possible 788 keys in each dict are listed below. The value 789 for most items is a list containing two values: 790 the initial value, the current value. 791 The first and second 792 values are floats unless otherwise noted. 797 793 \ Lam Specifies a wavelength in :math:`\\unicode{x212B}` 798 794 (two floats) 799 \ Type Histogram type (two str values):800 * 'SXC' for constant wavelength x-ray801 * 'SNC' for constant wavelength neutron802 * 'SNT' for time of flight neutron803 \ InstrName A name for the instrument, used in preparing804 a CIF (str).805 806 wtFactor \A weighting factor to increase or decrease807 the leverage of data in the histogram (float).808 A value of 1.0 weights the data with their809 standard uncertainties and a larger value810 increases the weighting of the data (equivalent811 to decreasing the uncertainties).812 813 hId \The number assigned to the histogram when814 the project is loaded or edited (can change)815 ranId \A random number id for the histogram816 that does not change817 ====================== =============== ====================================================795 \ Type Histogram type (two str values): 796 * 'SXC' for constant wavelength x-ray 797 * 'SNC' for constant wavelength neutron 798 * 'SNT' for time of flight neutron 799 \ InstrName A name for the instrument, used in preparing 800 a CIF (str). 801 802 wtFactor \ A weighting factor to increase or decrease 803 the leverage of data in the histogram (float). 804 A value of 1.0 weights the data with their 805 standard uncertainties and a larger value 806 increases the weighting of the data (equivalent 807 to decreasing the uncertainties). 808 809 hId \ The number assigned to the histogram when 810 the project is loaded or edited (can change) 811 ranId \ A random number id for the histogram 812 that does not change 813 ====================== =============== ==================================================== 818 814 819 815 .. _XtalRefl_table: … … 833 829 index explanation 834 830 ========== ==================================================== 835 0,1,2 h,k,l (float)836 3 multiplicity831 0,1,2 h,k,l (float) 832 3 multiplicity 837 833 4 d-space, :math:`\\unicode{x212B}` 838 5 :math:`F_{obs}^2`839 6 :math:`\sigma(F_{obs}^2)`840 7 :math:`F_{calc}^2`841 8 :math:`F_{obs}^2T`842 9 :math:`F_{calc}^2T`843 10 reflection phase, in degrees844 11 intensity correction for reflection, this times845 :math:`F_{obs}^2` or :math:`F_{calc}^2`846 gives Iobs or Icalc834 5 :math:`F_{obs}^2` 835 6 :math:`\sigma(F_{obs}^2)` 836 7 :math:`F_{calc}^2` 837 8 :math:`F_{obs}^2T` 838 9 :math:`F_{calc}^2T` 839 10 reflection phase, in degrees 840 11 intensity correction for reflection, this times 841 :math:`F_{obs}^2` or :math:`F_{calc}^2` 842 gives Iobs or Icalc 847 843 ========== ==================================================== 848 844 … … 870 866 key sub-key explanation 871 867 ====================== ====================== ==================================================== 872 Comments \Text strings extracted from the original image data868 Comments \ Text strings extracted from the original image data 873 869 header or a metafile. These cannot be changed by 874 870 the user; it may be empty. … … 954 950 \ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included 955 951 in integrsation. The tuple is the image intensity limits and the list are those set by the user. 956 \ SpotMask dict: 'esdMul'(int) number of standard deviations above mean ring intensity to mask 952 \ SpotMask (dict: int & array) 953 'esdMul'(int) number of standard deviations above mean ring intensity to mask 957 954 'spotMask' (bool array) the spot mask for every pixel in image 958 955
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