[ Identification | Description | Input parameters | Output parameters | Links ]

`Single_crystal`

Component-
**Author:**Kristian Nielsen -
**Origin:**Risoe -
**Date:**December 1999 -
**Version:**(Unknown) -
**Modification history:**- EF, 22nd Apr 2003 : now uses Read_Table library
- M. Schulz, March 2012 : allow to curve the crystal planes
- EF, PW, May 2014: code efficiency improvement when SPLIT is used
- EF, PW, 2015: powder/PG and texture mode
- PW, May 2017: Remove statement about being under validation
- PW, June 2017: Doc updates

Single crystal with mosaic. Delta-D/D option for finite-size effects. Rectangular geometry. Multiple scattering and secondary extinction included. The mosaic may EITHER be specified isotropic by setting the mosaic input parameter, OR anisotropic by setting the mosaic_a, mosaic_b, and mosaic_c parameters. The crystal lattice can be bent locally, keeping the external geometry unchanged. Curvature is spherical along vertical and horizontal axes.Speed/stat optimisation using SPLITIn order to dramatically improve the simulation efficiency, we recommend to use a SPLIT keyword on this component (or prior to it), as well as to disable the multiple scattering handling by setting order=1. This is especially powerful for large reflection lists such as with macromolecular proteins. When an incoming particle is identical to the preceeding, reciprocal space initialisation is skipped, and a Monte Carlo choice is done on available reflections from the last repciprocal space calculation! To assist the user in choosing a "relevant" value of the SPLIT, a rolling average of the number of available reflections is calculated and presented in the component output.Mosacitiy modes:The component features three independent ways of parametrising mosaicity: a) The original algorithm where mosaicity is implemented by extending each reflection by a Gaussian "cigar" in reciprocal space, characterised by the parameters mosaic and delta_d_d. (Also known as "isotropic mosaicity".) b) A similar mode where mosaicities can be non-isotropic and given as the parameters mosaic_a, mosaic_b and mosaic_c, around the unit cell axes. (Also known as "anisotropic mosaicity".) c) Given two "macroscopically"/experimentally measured width/mosaicities of two independent reflections, parametrised by the list mosaic_AB = {mos_a, mos_b, a_h, a_k, a_l, b_h, b_k, b_l}, a set of microscopic mosaicities as in b) are estimated (internally) and applied. (Also known as "phenomenological mosaicity".)Powder- and PG-modeWhen these two modes are used (powder=1 or PG=1), a randomised transformation of the particle direction is made before and after scattering, thereby letting the single crystal behave as a crystallite of either a powder (crystallite orientation fully randomised) or pyrolytic graphite (crystallite randomised around the c-axis).Curved crystal modeThe component features a method to curve the lattice planes slightly with respect to the outer geometry of the crystal. The method is implemented as a transformation on the particle direction vector, and should be used only in cases where a) The reflection lattice vector is ~ orthogonal to the crystal surface b) The modelled curvarture is "small" with respect to the crystal surfaceSample shape:Sample shape may be a cylinder, a sphere, a box or any other shape box/plate: xwidth x yheight x zdepth cylinder: radius x yheight sphere: radius (yheight=0) any shape: geometry=OFF file The complex geometry option handles any closed non-convex polyhedra. It computes the intersection points of the neutron ray with the object transparently, so that it can be used like a regular sample object. It supports the PLY, OFF and NOFF file format but not COFF (colored faces). Such files may be generated from XYZ data using: qhull < coordinates.xyz Qx Qv Tv o > geomview.off or powercrust coordinates.xyz and viewed with geomview or java -jar jroff.jar (see below). The default size of the object depends on the OFF file data, but its bounding box may be resized using xwidth,yheight and zdepth.Crystal definition file formatCrystal structure is specified with an ascii data file. Each line contains 4 or more numbers, separated by white spaces: h k l ... F2 The first three numbers are the (h,k,l) indices of the reciprocal lattice point, and the 7-th number is the value of the structure factor |F|**2, in barns. The rest of the numbers are not used; the file is in the format output by the Crystallographica program. The reflection list should be ordered by decreasing d-spacing values. Lines begining by '#' are read as comments (ignored). Most sample parameters may be defined from the data file header, following the same mechanism as PowderN. Current data file header keywords include, for data format specification: #column_h#column_k #column_l #column_F2 #column_F and for material specification: #sigma_abs #sigma_inc #Delta_d/d #lattice_a #lattice_b #lattice_c #lattice_aa #lattice_bb #lattice_cc See the Component Manual for more defails. Example: Single_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, mosaic = 5, reflections="YBaCuO.lau") A PG graphite crystal plate, cut for (002) reflections Single_crystal(xwidth = 0.002, yheight = 0.1, zdepth = 0.1, mosaic = 30, reflections = "C_graphite.lau", ax=0, ay=2.14, az=-1.24, bx = 0, by = 0, bz = 2.47, cx = 6.71, cy = 0, cz = 0) A leucine protein, without multiple scattering Single_crystal(xwidth=0.005, yheight=0.005, zdepth=0.005, mosaic = 5, reflections="leucine.lau", order=1) A Vanadium incoherent elastic scattering with multiple scattering Single_crystal(xwidth=0.01, yheight=0.01, zdepth=0.01, reflections="", sigma_abs=5.08, sigma_inc=4.935, ax=3.0282, by=3.0282, cz=3.0282/2) Also, always use a non-zero value of delta_d_d. %VALIDATION: This component has been validated.

Name | Unit | Description | Default |
---|---|---|---|

mosaic_AB | arc_minutes, arc_minutes,1, 1, 1, 1, 1, 1 | In Plane mosaic rotation and plane vectors (anisotropic), mosaic_A, mosaic_B, A_h,A_k,A_l, B_h,B_k,B_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic_A, mosaic_B, denotes the resp. mosaicities (gaussian RMS) with respect to the the two reflections chosen by A and B (Miller indices). | Mosaic_AB_Undefined |

reflections | string | File name containing structure factors of reflections. Use empty ("") or NULL for incoherent scattering only | 0 |

geometry | str | Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust | 0 |

xwidth | m | Width of crystal | 0 |

yheight | m | Height of crystal | 0 |

zdepth | no extinction simulated | [m] Depth of crystal | 0 |

radius | m | Outer radius of sample in (x,z) plane | 0 |

delta_d_d | 1 | Lattice spacing variance, gaussian RMS | 1e-4 |

mosaic | arc minutes | Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the isotropic mosaic model state, thus disregarding other mosaicity parameters. | -1 |

mosaic_a | arc minutes | Horizontal (rotation around lattice vector a) mosaic (anisotropic), gaussian RMS. Put the crystal in the anisotropic crystal vector state. I.e. model mosaicity through rotation around the crystal lattice vectors. Has precedence over in-plane mosaic model. | -1 |

mosaic_b | arc minutes | Vertical (rotation around lattice vector b) mosaic (anisotropic), gaussian RMS. | -1 |

mosaic_c | arc minutes | Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS | -1 |

recip_cell | 1 | Choice of direct/reciprocal (0/1) unit cell definition | 0 |

barns | 1 | Flag to indicate if |F|^2 from 'reflections' is in barns or fm^2. barns=1 for laz and isotropic constant elastic scattering (reflections=NULL), barns=0 for lau type files | 0 |

ax | AA or AA^-1 | Coordinates of first (direct/recip) unit cell vector | 0 |

ay | 0 | ||

az | 0 | ||

bx | AA or AA^-1 | Coordinates of second (direct/recip) unit cell vector | 0 |

by | 0 | ||

bz | 0 | ||

cx | AA or AA^-1 | Coordinates of third (direct/recip) unit cell vector | 0 |

cy | 0 | ||

cz | 0 | ||

p_transmit | 1 | Monte Carlo probability for neutrons to be transmitted without any scattering. Used to improve statistics from weak reflections | -1 |

sigma_abs | barns | Absorption cross-section per unit cell at 2200 m/s | 0 |

sigma_inc | barns | Incoherent scattering cross-section per unit cell Use -1 to unactivate | 0 |

aa | deg | Unit cell angles alpha, beta and gamma. Then uses norms of vectors a,b and c as lattice parameters | 0 |

bb | deg | Beta angle | 0 |

cc | deg | Gamma angle | 0 |

order | 0: all, 1: first, 2: second, ... | [1] Limit multiple scattering up to given order | 0 |

RX | m | Radius of horizontal along X lattice curvature. flat for 0 | 0 |

RY | m | Radius of vertical lattice curvature. flat for 0 | 0 |

RZ | m | Radius of horizontal along Z lattice curvature. flat for 0 | 0 |

powder | 1 | Flag to indicate powder mode, for simulation of Debye-Scherrer cones via random crystallite orientation. A powder texture can be approximated with 0 | 0 |

PG | 1 | Flag to indicate "Pyrolytic Graphite" mode, only meaningful with choice of Graphite.lau, models PG crystal. A powder texture can be approximated with 0 | 0 |

Name | Unit | Description | Default |
---|---|---|---|

hkl_info |
- | .l: | |

offdata |

- Source code for
`Single_crystal.comp`

. - See ICSD Inorganic Crystal Structure Database
- Cross sections for single elements
- Web Elements
- Fullprof powder refinement
- Crystallographica software
- Geomview and Object File Format (OFF)
- Java version of Geomview (display only) jroff.jar
- qhull
- powercrust

[ Identification | Description | Input parameters | Output parameters | Links ]

Generated automatically by McDoc, Peter Willendrup <peter.willendrup@risoe.dk> / Tue Nov 6 13:46:39 2018