# Changeset 78f02c3 in sasview

Ignore:
Timestamp:
Feb 14, 2015 12:12:40 PM (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, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
Children:
898a8b9
Parents:
3e2ebbb
Message:

Level 1 sphinx-ready commit of remaining help files

Location:
src/sas
Files:
14 edited

Unmodified
Removed
• ## src/sas/calculator/media/density_calculator_help.rst

 r37bbd5f ..density_calculator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. Density/Volume Calculator Tool ============================== Placeholder for density calculator help Description ----------- This tool is to calculate the mass density from the molar volume or vice versa. To calculate the mass density, the chemical formula and molar volume should be provided. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How To ------ 1. Molecular Formula: The chemical formula of ONE molecule or ONE atom. For mixtures, the ratio of the each molecules should be used; for example, (H2O)0.5(D2O)0.5. 2. Select input (molar volume or mass density) from combobox. Then type in the input value. 3. Click the 'Calculate' button to perform the calculation. 4. Outputs also include the molar mass (weight) that depends only on the chemical formula .. image:: density_tutor.gif
• ## src/sas/calculator/media/kiessig_calculator_help.rst

 r37bbd5f ..kiessig_calculator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. Kiessig Thickness Calculator Tool ================================= Placeholder for Kiessig calculator help Description ----------- This tool is to approximately estimate the thickness of a layer or the diameter of particles from the Kiessig fringe in SAS/NR data, and using the Kiessig relation thickness = 2*Pi/fringe_width. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How To ------ To get a rough thickness or particle size, just type the Kiessig fringe width (in units of 1/Angstrom) and click on the 'Compute' button. Then the output value will be show up in the 'Thickness' text box.
• ## src/sas/calculator/media/resolution_calculator_help.rst

 r37bbd5f ..resolution_calculator_help.rst Resolution Calculator ===================== .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. Placeholder for resolution calculator help Q Resolution Estimator ====================== Description ----------- This tool is to approximately estimate the resolution of Q based on the SAS instrumental parameter values assuming that the detector is flat and vertical to the incident beam direction. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How To ------ 1. Select the source and source type (Monochromatic or TOF). Note that the computational difference between the sources is only the gravitational contribution due to the mass. 2. Change the default values of the instrumental parameters as desired. 3. The input formats of wavelength and its spread (=FWHM/wavelength) depend on the source type.For monochromatic wave, the inputs are just one values as shown with the defaults.For TOF, the min and max values should be separated by "-" to describe the wavelength band range. Optionally, the input of the wavelength (NOT of the wavelength spread) could be extended by adding "; --" where the -- is the number of the bins for the numerical integration. Otherwise, the default value "10" bins will be used. The same number of bins will be used for the corresponding wavelength spread in either cases. 4. For TOF, the default wavelength spectrum is flat. The custom spectrum file (with 2 column text: wavelength(A) vs. intensity) can also be loaded by selecting "Add new" in the combobox. 5. Once set all the input values, click the compute button. Depending on computation loads the calculation time will vary. 6. 1D and 2D dQ will be displayed in the text-box at the bottom of the panel. Two dimensional resolution weight distribution (2D elliptical Gaussian function) will also be displayed in the plot panel even if the Q inputs are outside of the detector limit. The red lines indicate the limits of the detector (if a green lines appear (for TOF), it indicates the limits of the maximum q range for the largest wavelength due to the size of the detector). Note that the effect from the beam block is ignored, so in the small q region near the beam block [ie., q<2*pi*(beam block diameter) / (sample to detector distance) / lamda_min] the variance is slightly under estimated. 7. The summary can be accessed by clicking the 'light-bulb' icon at the bottom of the SasView main window. .. image:: resolution_tutor.gif .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ Theory ------ The scattering wave transfer vector is by definition .. image:: q.gif In the limit of the small angle, the variance of q in the first order approximation is .. image:: sigma_q.gif In summary, the geometric and gravitational contributions depending on the shape of each factors can be expressed as shown the table. .. image:: sigma_table.gif Finally, we use a Gaussian function to describe the 2D weighting distribution of the uncertainty in q. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ References ---------- D.F.R. Mildner and J.M. Carpenter, J. Appl. Cryst. 17, 249-256 (1984) D.F.R. Mildner, J.M. Carpenter and D.L. Worcester, J. Appl. Cryst. 19, 311-319 (1986)
• ## src/sas/calculator/media/sas_calculator_help.rst

 r37bbd5f ..sas_calculator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. .. |beta| unicode:: U+03B2 .. |gamma| unicode:: U+03B3 .. |theta| unicode:: U+03B8 .. |mu| unicode:: U+03BC .. |sigma| unicode:: U+03C3 .. |phi| unicode:: U+03C6 .. |equiv| unicode:: U+2261 .. |noteql| unicode:: U+2260 Generic Scattering Calculator Tool ================================== Placeholder for generic SAS calculator help Polarization and Magnetic Scattering Theory_ GUI_ PDB_Data_ .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ .. _Theory: Theory ------ In general, a particle with a volume V can be described by an ensemble containing N 3-dimensional rectangular pixels where each pixels are much smaller than V. Assuming that all the pixel sizes are same, the elastic scattering intensity by the particle .. image:: gen_i.gif where /beta/jand rj are the scattering length density and the position of the j'th pixel respectively. And the total volume .. image:: v_j.gif for /beta/j/noteql/0 where vj is the volume of the j'th pixel (or the j'th natural atomic volume (= atomic mass/natural molar density/Avogadro number) for the atomic structures). The total volume V can be corrected by users. This correction is useful especially for an atomic structure (taken from a pdb file) to get the right normalization. Note that the /beta/j displayed in GUI may be incorrect but will not affect the scattering computation if the correction of the total volume is made. The scattering length density (SLD) of each pixel where the SLD is uniform, is a combination of the nuclear and magnetic SLDs and depends on the spin states of the neutrons as follows:For magnetic scattering, only the magnetization component, *M*perp, perpendicular to the scattering vector *Q* contributes to the the magnetic scattering length. (Figure below). .. image:: mag_vector.bmp The magnetic scattering length density is then .. image:: dm_eq.gif where /gamma/= -1.913 the gyromagnetic ratio, /mu/B is the Bohr magneton, r0 is the classical radius of electron, and */sigma/* is the Pauli spin. For polarized neutron, the magnetic scattering is depending on the spin states. Let's consider that the incident neutrons are polarised parallel (+)/ anti-parallel (-) to the x' axis (See both Figures above). The possible out-coming states then are + and - states for both incident states, where - Non-spin flips: (+ +) and (- -) - Spin flips:     (+ -) and (- +) .. image:: gen_mag_pic.bmp Now, let's assume that the angles of the *Q*  vector and the spin-axis (x') from x-axis are /phi/ and /theta/up respectively (See Figure above). Then, depending upon the polarization (spin) state of neutrons, the scattering length densities, including the nuclear scattering length density (/beta/N) are given as, for non-spin-flips .. image:: sld1.gif and for spin-flips .. image:: sld2.gif where .. image:: mxp.gif .. image:: myp.gif .. image:: mzp.gif .. image:: mqx.gif .. image:: mqy.gif Here, the M0x, M0yand M0zare the x, y and z components of the magnetisation vector given in the xyz lab frame. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ .. _GUI: GUI --- .. image:: gen_gui_help.bmp After the computation, the result will be listed in the 'Theory' box in the data explorer panel on the main window.The 'Up_frac_in' and 'Up_frac_out' are the ratio, (spin up) /(spin up + spin down) neutrons before the sample and at the analyzer, respectively. *Note I: The values of 'Up_frac_in' and 'Up_frac_out' must be in the range between 0 and 1. For example, both values are 0.5 for unpolarized neutrons.* *Note II: This computation is totally based on the pixel (or atomic) data fixed in the xyz coordinates. Thus no angular orientational averaging is considered.* *Note III: For the nuclear scattering length density, only the real component is taken account.* .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ .. _PDB_Data: PDB Data -------- This Generic scattering calculator also supports some pdb files without considering polarized/magnetic scattering so that the related parameters such as Up_*** will be ignored (see the Picture below). The calculation for fixed orientation uses (the first) Equation above resulting in a 2D output, whileas the scattering calculation averaged over all the orientations uses the Debye equation providing a 1D output .. image:: gen_debye_eq.gif where vj /beta/j /equiv/ bj the scattering length of the j'th atom. The resultant outputs will be displayed in the DataExplorer for further uses. .. image:: pdb_combo.jpg
• ## src/sas/calculator/media/sld_calculator_help.rst

 r2dee849 ..sld_calculator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. SLD Calculator Tool =================== Placeholder for SLD calculator help Description ----------- The neutron scattering length density is defined as SLD = (b_c1 +b_c2+...+b_cn )/Vm where b_ci is the bound coherent scattering length of ith of n atoms in a molecule with the molecular volume Vm .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How to Format the Compound Name ------------------------------- To calculate scattering length densities enter a compound and a mass density and click "Calculate". Entering a wavelength value is optional (a default value of 6.0 Angstroms will be used). * Formula strings consist of counts and atoms such as "CaCO3+6H2O". * Groups can be separated by *'+'* or *space*, so "CaCO3 6H2O" works as well. * Groups and be defined using parentheses, such as "CaCO3(H2O)6". * Parentheses can be nested, such as "(CaCO3(H2O)6)1". * Isotopes are represented by their index, e.g., "CaCO[18]3+6H2O", H[1], or H[2]. * Counts can be integer or decimal, e.g. "CaCO3+(3HO0.5)2". * Other compositions can be calculated as well, for example, for a 70-30 mixture of H2O/D2O write *H14O7+ D6O3* or more simply *H7D3O5* (i.e. this says 7 hydrogens, 3 deuteriums, and 5 oxygens) and the mass density calculated based on the percentages of H and D. * Type *C[13]6 H[2]12 O[18]6* for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 deuterium atoms, and 6 Oxygen-18 atoms)
• ## src/sas/calculator/media/slit_calculator_help.rst

 r37bbd5f ..slit_calculator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. Slit Size Calculator Tool ========================= Placeholder for slit calculator help Description ----------- This tool is for X-ray users to calculate the slit size (FWHM/2) for smearing based on their half beam profile data (SAXSess). .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How To ------- To calculate the slit size (FWHM/2), just load the beam profile data using the browse button. Once a data is loaded, the slit size will be computed and show up in the text box. Because the unit is not specified in the data file, we do not convert it into 1/Angstrom so  users are responsible for converting the units of their data. Note: This slit size calculator only works for beam profile data produced by 'SAXSess'. To see the file format, check the file, 'beam profile.DAT', in the 'test' folder of SasView.
• ## src/sas/data_util/media/data_operator_help.rst

 r37bbd5f ..data_operator_help.rst .. This is a port of the original SasView html help file to ReSTructured text .. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. Data Operations Tool ==================== Placeholder for data operator help Description ----------- This dialog panel provides arithmetic operations between two data sets (the last data set could be a number). When the data1 and data2 are selected, their x (or qx and qy for 2D) value(s) must match with each other. .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ How To ------ 1. Type the data name resulted from an operation. 2) Select a data/theory in the drop down menus. When data2 is set to number, type a number in the text control box. 3) Select an arithmetic operator symbol; + (for addition), - (for subtraction), * (for multiplication), / (for division), and | (for combination of two data sets). If two data sets do not match, the operation will fail and the background color of the combo box items will turn to red (WIN only). 4) If the operation is successful, hit the Apply button to make the new data. Then the data name will be shown up in the data box in the data explorer. Note: The errors and warnings will be displayed at the bottom of the SasView window. .. image:: data_oper_pic.png