Changeset 78f02c3 in sasview for src/sas/calculator/media

Timestamp:

Feb 14, 2015 10:12:40 AM (9 years ago)

Author:

smk78

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/calculator/media

Files:

• density_calculator_help.rst (modified) (1 diff)
• kiessig_calculator_help.rst (modified) (1 diff)
• resolution_calculator_help.rst (modified) (1 diff)
• sas_calculator_help.rst (modified) (1 diff)
• sld_calculator_help.rst (modified) (1 diff)
• slit_calculator_help.rst (modified) (1 diff)

src/sas/calculator/media/density_calculator_help.rst

@@ -1 +1 @@
 ..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

@@ -1 +1 @@
 ..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

@@ -1 +1 @@
 ..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

@@ -1 +1 @@
 ..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

@@ -1 +1 @@
 ..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

@@ -1 +1 @@
 ..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.