Changeset 5ed76f8 in sasview for src/sas/sasgui/perspectives/calculator
- Timestamp:
- Apr 7, 2017 3:11:41 AM (8 years ago)
- Branches:
- master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- fca1f50
- Parents:
- 727c05f
- Location:
- src/sas/sasgui/perspectives/calculator/media
- Files:
-
- 1 deleted
- 5 edited
-
kiessig_calculator_help.rst (modified) (2 diffs)
-
resolution_calculator_help.rst (modified) (5 diffs)
-
sas_calculator_help.rst (modified) (8 diffs)
-
sld_calculator_help.rst (modified) (3 diffs)
-
slit_calculator_help.rst (modified) (2 diffs)
-
v_j.png (deleted)
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst
r7805458 r5ed76f8 10 10 ----------- 11 11 12 This tool is approximately estimates the thickness of a layer or the diameter13 of particles from the position of the Kiessig fringe/Bragg peak in NR/SAS data 14 usingthe relation12 This tool estimates real space dimensions from the position or spacing of 13 features in recipricol space. In particular a particle of size $d$ will 14 give rise to Bragg peaks with spacing $\Delta q$ according to the relation 15 15 16 (thickness *or* size) = 2 * |pi| / (fringe_width *or* peak position) 17 16 .. math:: 17 18 d = 2\pi / \Delta q 19 20 Similarly, the spacing between the peaks in Kiessig fringes in reflectometry 21 data arise from layers of thickness $d$. 22 18 23 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 19 24 … … 21 26 -------------- 22 27 23 To get a rough thickness or particle size, simply type the fringe or peak 28 To get a rough thickness or particle size, simply type the fringe or peak 24 29 position (in units of 1/|Ang|\) and click on the *Compute* button. 25 30 26 31 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 27 32 28 .. note:: This help document was last changed by Steve King, 01May2015 29 33 .. note:: This help document was last changed by Paul Kienzle, 05Apr2017 -
src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst
r6aad2e8 r5ed76f8 10 10 ----------- 11 11 12 This tool is approximately estimates the resolution of Q from SAS instrumental13 parameter values assuming that the detector is flat and normal to the 12 This tool is approximately estimates the resolution of $Q$ from SAS instrumental 13 parameter values assuming that the detector is flat and normal to the 14 14 incident beam. 15 15 … … 23 23 2) Select the source (Neutron or Photon) and source type (Monochromatic or TOF). 24 24 25 *NOTE! The computational difference between the sources is only the 25 *NOTE! The computational difference between the sources is only the 26 26 gravitational contribution due to the mass of the particles.* 27 27 28 3) Change the default values of the instrumental parameters as required. Be 28 3) Change the default values of the instrumental parameters as required. Be 29 29 careful to note that distances are specified in cm! 30 30 31 4) Enter values for the source wavelength(s), |lambda|\ , and its spread (= FWHM/|lambda|\).32 33 For monochromatic sources, the inputs are just one value. For TOF sources, 34 the minimum and maximum values should be separated by a '-' to specify a 31 4) Enter values for the source wavelength(s), $\lambda$, and its spread (= $\text{FWHM}/\lambda$). 32 33 For monochromatic sources, the inputs are just one value. For TOF sources, 34 the minimum and maximum values should be separated by a '-' to specify a 35 35 range. 36 37 Optionally, the wavelength (BUT NOT of the wavelength spread) can be extended 38 by adding '; nn' where the 'nn' specifies the number of the bins for the 39 numerical integration. The default value is nn = 10. The same number of bins 36 37 Optionally, the wavelength (BUT NOT of the wavelength spread) can be extended 38 by adding '; nn' where the 'nn' specifies the number of the bins for the 39 numerical integration. The default value is nn = 10. The same number of bins 40 40 will be used for the corresponding wavelength spread. 41 41 42 5) For TOF, the default wavelength spectrum is flat. A custom spectral 43 distribution file (2-column text: wavelength (|Ang|\) vs Intensity) can also 42 5) For TOF, the default wavelength spectrum is flat. A custom spectral 43 distribution file (2-column text: wavelength (|Ang|\) vs Intensity) can also 44 44 be loaded by selecting *Add new* in the combo box. 45 45 46 6) When ready, click the *Compute* button. Depending on the computation the 46 6) When ready, click the *Compute* button. Depending on the computation the 47 47 calculation time will vary. 48 48 49 7) 1D and 2D dQ values will be displayed at the bottom of the panel, and a 2D50 resolution weight distribution (a 2D elliptical Gaussian function) will also 51 be displayed in the plot panel even if the Q inputs are outside of the49 7) 1D and 2D $dQ$ values will be displayed at the bottom of the panel, and a 2D 50 resolution weight distribution (a 2D elliptical Gaussian function) will also 51 be displayed in the plot panel even if the $Q$ inputs are outside of the 52 52 detector limit (the red lines indicate the limits of the detector). 53 54 TOF only: green lines indicate the limits of the maximum Q range accessible53 54 TOF only: green lines indicate the limits of the maximum $Q$ range accessible 55 55 for the longest wavelength due to the size of the detector. 56 57 Note that the effect from the beam block/stop is ignored, so in the small Q58 region near the beam block/stop59 56 60 [ie., Q < 2. |pi|\ .(beam block diameter) / (sample-to-detector distance) / |lambda|\_min] 57 Note that the effect from the beam block/stop is ignored, so in the small $Q$ 58 region near the beam block/stop 59 60 [i.e., $Q < (2 \pi \cdot \text{beam block diameter}) / (\text{sample-to-detector distance} \cdot \lambda_\text{min})$] 61 61 62 62 the variance is slightly under estimated. 63 63 64 8) A summary of the calculation is written to the SasView *Console* at the 64 8) A summary of the calculation is written to the SasView *Console* at the 65 65 bottom of the main SasView window. 66 66 … … 76 76 .. image:: q.png 77 77 78 In the small-angle limit, the variance of Q is to a first-order78 In the small-angle limit, the variance of $Q$ is to a first-order 79 79 approximation 80 80 … … 85 85 .. image:: sigma_table.png 86 86 87 Finally, a Gaussian function is used to describe the 2D weighting distribution 88 of the uncertainty in Q.87 Finally, a Gaussian function is used to describe the 2D weighting distribution 88 of the uncertainty in $Q$. 89 89 90 90 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ … … 93 93 ---------- 94 94 95 D.F.R. Mildner and J.M. Carpenter 95 D.F.R. Mildner and J.M. Carpenter 96 96 *J. Appl. Cryst.* 17 (1984) 249-256 97 97 98 D.F.R. Mildner, J.M. Carpenter and D.L. Worcester 98 D.F.R. Mildner, J.M. Carpenter and D.L. Worcester 99 99 *J. Appl. Cryst.* 19 (1986) 311-319 100 100 -
src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst
r6aad2e8 r5ed76f8 19 19 ------ 20 20 21 In general, a particle with a volume *V* can be described by an ensemble22 containing *N* 3-dimensional rectangular pixels where each pixel is much23 smaller than *V*.21 In general, a particle with a volume $V$ can be described by an ensemble 22 containing $N$ 3-dimensional rectangular pixels where each pixel is much 23 smaller than $V$. 24 24 25 Assuming that all the pixel sizes are the same, the elastic scattering 25 Assuming that all the pixel sizes are the same, the elastic scattering 26 26 intensity from the particle is 27 27 … … 30 30 Equation 1. 31 31 32 where |beta|\ :sub:`j` and *r*\ :sub:`j` are the scattering length density and33 the position of the j'thpixel respectively.32 where $\beta_j$ and $r_j$ are the scattering length density and 33 the position of the $j^\text{th}$ pixel respectively. 34 34 35 The total volume *V*35 The total volume $V$ 36 36 37 .. image:: v_j.png37 .. math:: 38 38 39 for |beta|\ :sub:`j` |noteql|\0 where *v*\ :sub:`j` is the volume of the j'th 40 pixel (or the j'th natural atomic volume (= atomic mass / (natural molar 39 V = \sum_j^N v_j 40 41 for $\beta_j \ne 0$ where $v_j$ is the volume of the $j^\text{th}$ 42 pixel (or the $j^\text{th}$ natural atomic volume (= atomic mass / (natural molar 41 43 density * Avogadro number) for the atomic structures). 42 44 43 *V* can be corrected by users. This correction is useful especially for an 44 atomic structure (such as taken from a PDB file) to get the right normalization. 45 $V$ can be corrected by users. This correction is useful especially for an 46 atomic structure (such as taken from a PDB file) to get the right normalization. 45 47 46 *NOTE! * |beta|\ :sub:`j` *displayed in the GUI may be incorrect but this will not48 *NOTE! $\beta_j$ displayed in the GUI may be incorrect but this will not 47 49 affect the scattering computation if the correction of the total volume V is made.* 48 50 49 The scattering length density (SLD) of each pixel, where the SLD is uniform, is 50 a combination of the nuclear and magnetic SLDs and depends on the spin states 51 The scattering length density (SLD) of each pixel, where the SLD is uniform, is 52 a combination of the nuclear and magnetic SLDs and depends on the spin states 51 53 of the neutrons as follows. 52 54 … … 54 56 ^^^^^^^^^^^^^^^^^^^ 55 57 56 For magnetic scattering, only the magnetization component, *M*\ :sub:`perp`\ ,57 perpendicular to the scattering vector *Q* contributes to the magnetic58 For magnetic scattering, only the magnetization component, $M_\perp$, 59 perpendicular to the scattering vector $Q$ contributes to the magnetic 58 60 scattering length. 59 61 … … 64 66 .. image:: dm_eq.png 65 67 66 where the gyromagnetic ratio |gamma| = -1.913, |mu|\ :sub:`B` is the Bohr67 magneton, *r*\ :sub:`0` is the classical radius of electron, and |sigma| is the68 where the gyromagnetic ratio is $\gamma = -1.913$, $\mu_B$ is the Bohr 69 magneton, $r_0$ is the classical radius of electron, and $\sigma$ is the 68 70 Pauli spin. 69 71 70 72 For a polarized neutron, the magnetic scattering is depending on the spin states. 71 73 72 Let us consider that the incident neutrons are polarised both parallel (+) and 73 anti-parallel (-) to the x' axis (see below). The possible states after 74 scattering from the sample are then 74 Let us consider that the incident neutrons are polarised both parallel (+) and 75 anti-parallel (-) to the x' axis (see below). The possible states after 76 scattering from the sample are then 75 77 76 78 * Non-spin flips: (+ +) and (- -) … … 79 81 .. image:: gen_mag_pic.png 80 82 81 Now let us assume that the angles of the *Q* vector and the spin-axis (x') 82 to the x-axis are |phi| and |theta|\ :sub:`up` respectively (see above). Then,83 depending upon the polarization (spin) state of neutrons, the scattering 84 length densities, including the nuclear scattering length density ( |beta|\ :sub:`N`\ )83 Now let us assume that the angles of the *Q* vector and the spin-axis (x') 84 to the x-axis are $\phi$ and $\theta_\text{up}$ respectively (see above). Then, 85 depending upon the polarization (spin) state of neutrons, the scattering 86 length densities, including the nuclear scattering length density ($\beta_N$) 85 87 are given as 86 88 … … 105 107 .. image:: mqy.png 106 108 107 Here the *M0*\ :sub:`x`\ , *M0*\ :sub:`y` and *M0*\ :sub:`z` are the x, y and z108 components of the magnetisation vector in the laboratory xyz frame.109 Here the $M0_x$, $M0_y$ and $M0_z$ are the $x$, $y$ and $z$ 110 components of the magnetisation vector in the laboratory $xyz$ frame. 109 111 110 112 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ … … 115 117 .. image:: gen_gui_help.png 116 118 117 After computation the result will appear in the *Theory* box in the SasView 119 After computation the result will appear in the *Theory* box in the SasView 118 120 *Data Explorer* panel. 119 121 120 *Up_frac_in* and *Up_frac_out* are the ratio 122 *Up_frac_in* and *Up_frac_out* are the ratio 121 123 122 124 (spin up) / (spin up + spin down) 123 125 124 126 of neutrons before the sample and at the analyzer, respectively. 125 127 126 *NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range 128 *NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range 127 129 0.0 to 1.0. Both values are 0.5 for unpolarized neutrons.* 128 130 129 *NOTE 2. This computation is totally based on the pixel (or atomic) data fixed 131 *NOTE 2. This computation is totally based on the pixel (or atomic) data fixed 130 132 in xyz coordinates. No angular orientational averaging is considered.* 131 133 132 *NOTE 3. For the nuclear scattering length density, only the real component 134 *NOTE 3. For the nuclear scattering length density, only the real component 133 135 is taken account.* 134 136 … … 139 141 140 142 The SANS Calculator tool can read some PDB, OMF or SLD files but ignores 141 polarized/magnetic scattering when doing so, thus related parameters such as 143 polarized/magnetic scattering when doing so, thus related parameters such as 142 144 *Up_frac_in*, etc, will be ignored. 143 145 144 The calculation for fixed orientation uses Equation 1 above resulting in a 2D 145 output, whereas the scattering calculation averaged over all the orientations 146 The calculation for fixed orientation uses Equation 1 above resulting in a 2D 147 output, whereas the scattering calculation averaged over all the orientations 146 148 uses the Debye equation below providing a 1D output 147 149 148 150 .. image:: gen_debye_eq.png 149 151 150 where *v*\ :sub:`j` |beta|\ :sub:`j` |equiv| *b*\ :sub:`j` is the scattering151 length of the j'th atom. The calculation output is passed to the *Data Explorer*152 where $v_j \beta_j \equiv b_j$ is the scattering 153 length of the $j^\text{th}$ atom. The calculation output is passed to the *Data Explorer* 152 154 for further use. 153 155 -
src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst
rf93b473f r5ed76f8 10 10 ----------- 11 11 12 The neutron scattering length density (SLD ) is defined as12 The neutron scattering length density (SLD, $\beta_N$) is defined as 13 13 14 SLD = (b_c1 + b_c2 + ... + b_cn) / Vm 14 .. math:: 15 15 16 where b_ci is the bound coherent scattering length of ith of n atoms in a molecule 17 with the molecular volume Vm 16 \beta_N = (b_{c1} + b_{c2} + ... + b_{cn}) / V_m 17 18 where $b_{ci}$ is the bound coherent scattering length of ith of n atoms in a molecule 19 with the molecular volume $V_m$. 18 20 19 21 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ … … 22 24 ---------------------------- 23 25 24 To calculate scattering length densities enter the empirical formula of a 26 To calculate scattering length densities enter the empirical formula of a 25 27 compound and its mass density and click "Calculate". 26 28 27 Entering a wavelength value is optional (a default value of 6.0 |Ang| will 29 Entering a wavelength value is optional (a default value of 6.0 |Ang| will 28 30 be used). 29 31 … … 38 40 * Parentheses can be nested, such as "(CaCO3(H2O)6)1". 39 41 40 * Isotopes are represented by their atomic number in *square brackets*, such 42 * Isotopes are represented by their atomic number in *square brackets*, such 41 43 as "CaCO[18]3+6H2O", H[1], or H[2]. 42 44 43 45 * Numbers of atoms can be integer or decimal, such as "CaCO3+(3HO0.5)2". 44 46 45 * The SLD of mixtures can be calculated as well. For example, for a 70-30 47 * The SLD of mixtures can be calculated as well. For example, for a 70-30 46 48 mixture of H2O/D2O write "H14O7+D6O3" or more simply "H7D3O5" (i.e. this says 47 49 7 hydrogens, 3 deuteriums, and 5 oxygens) and enter a mass density calculated 48 50 on the percentages of H2O and D2O. 49 51 50 * Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 52 * Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 51 53 deuterium atoms, and 6 Oxygen-18 atoms). 52 54 53 55 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 54 56 55 .. note:: This help document was last changed by Steve King, 01May201557 .. note:: This help document was last changed by Paul Kienzle, 05Apr2017 56 58 -
src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst
rf93b473f r5ed76f8 11 11 ----------- 12 12 13 This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing 13 This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing 14 14 based on their half beam profile data. 15 15 16 16 *NOTE! Whilst it may have some more generic applicability, the calculator has 17 only been tested with beam profile data from Anton-Paar SAXSess*\ |TM|\ 18 *software.* 17 only been tested with beam profile data from Anton-Paar SAXSess:sup:`TM` software.* 19 18 20 19 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ … … 27 26 2) Load a beam profile file in the *Data* field using the *Browse* button. 28 27 29 *NOTE! To see an example of the beam profile file format, visit the file 28 *NOTE! To see an example of the beam profile file format, visit the file 30 29 beam profile.DAT in your {installation_directory}/SasView/test folder.* 31 30 32 3) Once a data is loaded, the slit size is automatically computed and displayed 31 3) Once a data is loaded, the slit size is automatically computed and displayed 33 32 in the tool window. 34 33 35 *NOTE! The beam profile file does not carry any information about the units of 34 *NOTE! The beam profile file does not carry any information about the units of 36 35 the Q data. This calculator assumes the data has units of 1/\ |Ang|\ . If the 37 36 data is not in these units it must be manually converted beforehand.*
Note: See TracChangeset
for help on using the changeset viewer.
