Changes in / [aba7b40:96032b3] in sasview
- Location:
- src/sas/perspectives/calculator/media
- Files:
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- 3 edited
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resolution_calculator_help.rst (modified) (3 diffs)
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sas_calculator_help.rst (modified) (3 diffs)
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sld_calculator_help.rst (modified) (3 diffs)
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src/sas/perspectives/calculator/media/resolution_calculator_help.rst
r850c753 rbc9a0e1 23 23 ------ 24 24 25 1) Select *SAS Resolution Es timator* from the *Tool* menu on the SasView toolbar.25 1) Select *SAS Resolution Esimator* from the *Tool* menu on the SasView toolbar. 26 26 27 27 2) Select the source (Neutron or Photon) and source type (Monochromatic or TOF). … … 33 33 careful to note that distances are specified in cm! 34 34 35 4) Enter values for the source wavelength(s) , |lambda|\ , and its spread (= FWHM/|lambda|\).35 4) Enter values for the source wavelength(s) and its spread (= FWHM / wavelength). 36 36 37 37 For monochromatic sources, the inputs are just one value. For TOF sources, … … 62 62 region near the beam block/stop 63 63 64 [ie., Q < 2 . |pi|\ .(beam block diameter) / (sample-to-detector distance) / |lambda|\_min]64 [ie., Q < 2*|pi|\*(beam block diameter) / (sample-to-detector distance) / |lambda|\_min] 65 65 66 66 the variance is slightly under estimated. -
src/sas/perspectives/calculator/media/sas_calculator_help.rst
r850c753 rec392464 17 17 ================================== 18 18 19 Nuclear_Scattering_ 19 Polarization and Magnetic Scattering 20 20 21 Magnetic_Scattering_Polarisation_ 22 23 Using_the_SAS_Calculator_GUI_ 24 25 Using_PDB_Data_ 21 Theory_ 22 GUI_ 23 PDB_Data_ 26 24 27 25 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 28 26 29 .. _ Nuclear_Scattering:27 .. _Theory: 30 28 31 Nuclear Scattering 32 ------ ------------29 Theory 30 ------ 33 31 34 In general, a particle with a volume *V* can be described by an ensemble 35 containing *N* 3-dimensional rectangular pixels where each pixel is much 36 smaller than *V*. 37 38 Assuming that all the pixel sizes are the same, the elastic scattering 39 intensity from the particle is 32 In general, a particle with a volume V can be described by an ensemble 33 containing N 3-dimensional rectangular pixels where each pixels are much 34 smaller than V. Assuming that all the pixel sizes are same, the elastic 35 scattering intensity by the particle 40 36 41 37 .. image:: gen_i.gif 42 38 43 Equation 1. 44 45 where |beta|\ :sub:`j` and *r*\ :sub:`j` are the scattering length density and 46 the position of the j'th pixel respectively. 47 48 The total volume *V* 39 where /beta/jand rj are the scattering length density and the position of the 40 j'th pixel respectively. And the total volume 49 41 50 42 .. image:: v_j.gif 51 43 52 for |beta|\ :sub:`j` |noteql|\0 where *v*\ :sub:`j` is the volume of the j'th 53 pixel (or the j'th natural atomic volume (= atomic mass / (natural molar 54 density * Avogadro number) for the atomic structures). 55 56 *V* can be corrected by users. This correction is useful especially for an 57 atomic structure (such as taken from a PDB file) to get the right normalization. 58 59 *NOTE!* |beta|\ :sub:`j` *displayed in the GUI may be incorrect but this will not 60 affect the scattering computation if the correction of the total volume V is made.* 61 62 The scattering length density (SLD) of each pixel, where the SLD is uniform, is 63 a combination of the nuclear and magnetic SLDs and depends on the spin states 64 of the neutrons as follows. 65 66 .. _Magnetic_Scattering_Polarisation: 67 68 Magnetic Scattering & Polarisation 69 ---------------------------------- 70 71 For magnetic scattering, only the magnetization component, *M*\ :sub:`perp`\ , 72 perpendicular to the scattering vector *Q* contributes to the magnetic 73 scattering length. 44 for /beta/j/noteql/0 where vj is the volume of the j'th pixel (or the j'th 45 natural atomic volume (= atomic mass/natural molar density/Avogadro number) for 46 the atomic structures). The total volume V can be corrected by users. This 47 correction is useful especially for an atomic structure (taken from a pdb file) 48 to get the right normalization. Note that the /beta/j displayed in GUI may be 49 incorrect but will not affect the scattering computation if the correction of 50 the total volume is made. The scattering length density (SLD) of each pixel 51 where the SLD is uniform, is a combination of the nuclear and magnetic SLDs and 52 depends on the spin states of the neutrons as follows:For magnetic scattering, 53 only the magnetization component, *M*perp, perpendicular to the scattering 54 vector *Q* contributes to the the magnetic scattering length. (Figure below). 74 55 75 56 .. image:: mag_vector.bmp … … 79 60 .. image:: dm_eq.gif 80 61 81 where the gyromagnetic ratio |gamma| = -1.913, |mu|\ :sub:`B` is the Bohr 82 magneton, *r*\ :sub:`0` is the classical radius of electron, and |sigma| is the 83 Pauli spin. 62 where /gamma/= -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0 is 63 the classical radius of electron, and */sigma/* is the Pauli spin. 84 64 85 For apolarized neutron, the magnetic scattering is depending on the spin states.65 For polarized neutron, the magnetic scattering is depending on the spin states. 86 66 87 Let us consider that the incident neutrons are polarised both parallel (+) and88 anti-parallel (-) to the x' axis ( see below). The possible states after89 scattering from the sample are then67 Let's consider that the incident neutrons are polarised parallel (+)/ 68 anti-parallel (-) to the x' axis (See both Figures above). The possible 69 out-coming states then are + and - states for both incident states, where 90 70 91 *Non-spin flips: (+ +) and (- -)92 *Spin flips: (+ -) and (- +)71 - Non-spin flips: (+ +) and (- -) 72 - Spin flips: (+ -) and (- +) 93 73 94 74 .. image:: gen_mag_pic.bmp 95 75 96 Now let us assume that the angles of the *Q*vector and the spin-axis (x')97 to the x-axis are |phi| and |theta|\ :sub:`up` respectively (see above). Then,76 Now, let's assume that the angles of the *Q* vector and the spin-axis (x') 77 from x-axis are /phi/ and /theta/up respectively (See Figure above). Then, 98 78 depending upon the polarization (spin) state of neutrons, the scattering 99 length densities, including the nuclear scattering length density ( |beta|\ :sub:`N`\)100 are given as 79 length densities, including the nuclear scattering length density (/beta/N) 80 are given as, for non-spin-flips 101 81 102 * for non-spin-flips 82 .. image:: sld1.gif 103 83 104 .. image:: sld1.gif 84 and for spin-flips 105 85 106 * for spin-flips 107 108 .. image:: sld2.gif 86 .. image:: sld2.gif 109 87 110 88 where … … 120 98 .. image:: mqy.gif 121 99 122 Here the *M0*\ :sub:`x`\ , *M0*\ :sub:`y` and *M0*\ :sub:`z` are the x, y and z123 components of the magnetisation vector in the laboratory xyzframe.100 Here, the M0x, M0yand M0zare the x, y and z components of the magnetisation 101 vector given in the xyz lab frame. 124 102 125 103 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 126 104 127 .. _ Using_the_SAS_Calculator_GUI:105 .. _GUI: 128 106 129 Using the SAS CalculatorGUI130 --- -------------------------107 GUI 108 --- 131 109 132 110 .. image:: gen_gui_help.bmp 133 111 134 After computation the result will appear in the *Theory* box in the SasView 135 *Data Explorer* panel. 112 After the computation, the result will be listed in the 'Theory' box in the 113 data explorer panel on the main window.The 'Up_frac_in' and 'Up_frac_out' are 114 the ratio, (spin up) /(spin up + spin down) neutrons before the sample and at 115 the analyzer, respectively. 136 116 137 *Up_frac_in* and *Up_frac_out* are the ratio 117 *Note I: The values of 'Up_frac_in' and 'Up_frac_out' must be in the range 118 between 0 and 1. For example, both values are 0.5 for unpolarized neutrons.* 138 119 139 (spin up) / (spin up + spin down) 140 141 of neutrons before the sample and at the analyzer, respectively. 120 *Note II: This computation is totally based on the pixel (or atomic) data 121 fixed in the xyz coordinates. Thus no angular orientational averaging is 122 considered.* 142 123 143 *NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range 144 0.0 to 1.0. Both values are 0.5 for unpolarized neutrons.* 145 146 *NOTE 2. This computation is totally based on the pixel (or atomic) data fixed 147 in xyz coordinates. No angular orientational averaging is considered.* 148 149 *NOTE 3. For the nuclear scattering length density, only the real component 124 *Note III: For the nuclear scattering length density, only the real component 150 125 is taken account.* 151 126 152 127 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 153 128 154 .. _ Using_PDB_Data:129 .. _PDB_Data: 155 130 156 UsingPDB Data157 -------- ------131 PDB Data 132 -------- 158 133 159 The SAS Calculator tool can read some PDB, OMF or SLD files but ignores 160 polarized/magnetic scattering when doing so, thus related parameters such as 161 *Up_frac_in*, etc, will be ignored. 162 163 The calculation for fixed orientation uses Equation 1 above resulting in a 2D 164 output, whereas the scattering calculation averaged over all the orientations 165 uses the Debye equation below providing a 1D output 134 This Generic scattering calculator also supports some pdb files without 135 considering polarized/magnetic scattering so that the related parameters 136 such as Up_*** will be ignored (see the Picture below). The calculation for 137 fixed orientation uses (the first) Equation above resulting in a 2D output, 138 whileas the scattering calculation averaged over all the orientations uses 139 the Debye equation providing a 1D output 166 140 167 141 .. image:: gen_debye_eq.gif 168 142 169 where *v*\ :sub:`j` |beta|\ :sub:`j` |equiv| *b*\ :sub:`j` is the scattering 170 length of the j'th atom. The calculation output is passed to the *Data Explorer* 171 for further use. 143 where vj /beta/j /equiv/ bj the scattering length of the j'th atom. The resultant outputs 144 will be displayed in the DataExplorer for further uses. 172 145 173 146 .. image:: pdb_combo.jpg 174 175 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ176 177 .. note:: This help document was last changed by Steve King, 19Feb2015 -
src/sas/perspectives/calculator/media/sld_calculator_help.rst
r850c753 rec392464 14 14 The neutron scattering length density is defined as 15 15 16 16 SLD = (b_c1 + b_c2 + ... + b_cn) / Vm 17 17 18 18 where … … 31 31 Entering a wavelength value is optional (a default value of 6.0 |Ang| will 32 32 be used). 33 34 TIPS!35 33 36 34 * Formula strings consist of atoms and the number of them, such as "CaCO3+6H2O". … … 54 52 * Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 55 53 deuterium atoms, and 6 Oxygen-18 atoms). 56 57 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ58 59 .. note:: This help document was last changed by Steve King, 19Feb201560
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