Changeset 5f3c534 in sasmodels

Ignore:
Timestamp:
Mar 27, 2019 12:11:45 PM (11 months ago)
Branches:
master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
9947865
Parents:
055ec4f
Message:

Tweaks to docs for all S(q) models as described in #1187

Location:
sasmodels/models
Files:
4 edited

Unmodified
Removed
• sasmodels/models/hardsphere.py

 r0507e09 # Note: model title and parameter table are inserted automatically r"""Calculate the interparticle structure factor for monodisperse r""" Calculates the interparticle structure factor for monodisperse spherical particles interacting through hard sphere (excluded volume) interactions. May be a reasonable approximation for other shapes of particles that freely rotate, and for moderately polydisperse systems. Though strictly the maths needs to be modified (no \Beta(Q) correction yet in sasview). interactions. This $S(q)$ may also be a reasonable approximation for other particle shapes that freely rotate (but see the note below), and for moderately polydisperse systems. .. note:: This routine is intended for uncharged particles! For charged particles try using the :ref:hayter-msa $S(q)$ instead. .. note:: Earlier versions of SasView did not incorporate the so-called $\beta(q)$ ("beta") correction [1] for polydispersity and non-sphericity. This is only available in SasView versions 4.2.2 and higher. radius_effective is the effective hard sphere radius. volfraction is the volume fraction occupied by the spheres. In sasview the effective radius may be calculated from the parameters In SasView the effective radius may be calculated from the parameters used in the form factor $P(q)$ that this $S(q)$ is combined with. For numerical stability the computation uses a Taylor series expansion at very small $qR$, there may be a very minor glitch at the transition point in some circumstances. at very small $qR$, but there may be a very minor glitch at the transition point in some circumstances. The S(Q) uses the Percus-Yevick closure where the interparticle potential is This S(q) uses the Percus-Yevick closure relationship [2] where the interparticle potential $U(r)$ is .. math:: \end{cases} where $r$ is the distance from the center of the sphere of a radius $R$. where $r$ is the distance from the center of a sphere of a radius $R$. For a 2D plot, the wave transfer is defined as References ---------- .. [#] M Kotlarchyk & S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 .. [#] J K Percus, J Yevick, *J. Phys. Rev.*, 110, (1958) 1 [Hard sphere structure factor, with Percus-Yevick closure] Interparticle S(Q) for random, non-interacting spheres. May be a reasonable approximation for other shapes of particles that freely rotate, and for moderately polydisperse systems. Though strictly the maths needs to be modified - which sasview does not do yet. May be a reasonable approximation for other particle shapes that freely rotate, and for moderately polydisperse systems . The "beta(q)" correction is available in versions 4.2.2 and higher. radius_effective is the hard sphere radius volfraction is the volume fraction occupied by the spheres.
• sasmodels/models/hayter_msa.py

 r0507e09 # Note: model title and parameter table are inserted automatically r""" This calculates the structure factor (the Fourier transform of the pair correlation function $g(r)$) for a system of charged, spheroidal objects in a dielectric medium. When combined with an appropriate form factor (such as sphere, core+shell, ellipsoid, etc), this allows for inclusion of the interparticle interference effects due to screened coulomb repulsion between charged particles. Calculates the interparticle structure factor for a system of charged, spheroidal, objects in a dielectric medium [1,2]. When combined with an appropriate form factor $P(q)$, this allows for inclusion of the interparticle interference effects due to screened Coulombic repulsion between the charged particles. **This routine only works for charged particles**. If the charge is set to zero the routine may self-destruct! For non-charged particles use a hard sphere potential. .. note:: This routine only works for charged particles! If the charge is set to zero the routine may self-destruct! For uncharged particles use the :ref:hardsphere $S(q)$ instead. .. note:: Earlier versions of SasView did not incorporate the so-called $\beta(q)$ ("beta") correction [3] for polydispersity and non-sphericity. This is only available in SasView versions 4.2.2 and higher. The salt concentration is used to compute the ionic strength of the solution which in turn is used to compute the Debye screening length. At present there is no provision for entering the ionic strength directly nor for use of any multivalent salts, though it should be possible to simulate the effect of this by increasing the salt concentration. The counterions are also assumed to be monovalent. which in turn is used to compute the Debye screening length. There is no provision for entering the ionic strength directly. **At present the counterions are assumed to be monovalent**, though it should be possible to simulate the effect of multivalent counterions by increasing the salt concentration. In sasview the effective radius may be calculated from the parameters Over the range 0 - 100 C the dielectric constant $\kappa$ of water may be approximated with a maximum deviation of 0.01 units by the empirical formula [4] .. math:: \kappa = 87.740 - 0.40008 T + 9.398x10^{-4} T^2 - 1.410x10^{-6} T^3 where $T$ is the temperature in celsius. In SasView the effective radius may be calculated from the parameters used in the form factor $P(q)$ that this $S(q)$ is combined with. .. [#] J B Hayter and J Penfold, *Molecular Physics*, 42 (1981) 109-118 .. [#] J P Hansen and J B Hayter, *Molecular Physics*, 46 (1982) 651-656 .. [#] M Kotlarchyk and S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 .. [#] C G Malmberg and A A Maryott, *J. Res. Nat. Bureau Standards*, 56 (1956) 2641 Source * **Author:** * **Last Modified by:** * **Last Reviewed by:** * **Last Reviewed by:** Steve King **Date:** March 27, 2019 * **Source added by :** Steve King **Date:** March 25, 2019 """ name = "hayter_msa" title = "Hayter-Penfold rescaled MSA, charged sphere, interparticle S(Q) structure factor" title = "Hayter-Penfold Rescaled Mean Spherical Approximation (RMSA) structure factor for charged spheres" description = """\ [Hayter-Penfold RMSA charged sphere interparticle S(Q) structure factor] Interparticle structure factor S(Q)for a charged hard spheres. Routine takes absolute value of charge, use HardSphere if charge goes to zero. In sasview the effective radius and volume fraction may be calculated from the parameters used in P(Q). Interparticle structure factor S(Q) for charged hard spheres. This routine only works for charged particles! For uncharged particles use the hardsphere S(q) instead. The "beta(q)" correction is available in versions 4.2.2 and higher. """ ["temperature",   "K",  318.16,   [0, 450],    "", "temperature, in Kelvin, for Debye length calculation"], ["concentration_salt",      "M",    0.0,    [0, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"], ["dielectconst",  "None",    71.08,   [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, default water, for Debye length"] ["dielectconst",  "None",    71.08,   [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, kappa, default water, for Debye length"] ] # pylint: enable=bad-whitespace, line-too-long
• sasmodels/models/squarewell.py

 r0507e09 # Note: model title and parameter table are inserted automatically r""" This calculates the interparticle structure factor for a square well fluid spherical particles. The mean spherical approximation (MSA) closure was used for this calculation, and is not the most appropriate closure for an attractive interparticle potential. This solution has been compared to Monte Carlo simulations for a square well fluid, showing this calculation to be limited in applicability to well depths $\epsilon < 1.5$ kT and volume fractions $\phi < 0.08$. Calculates the interparticle structure factor for a hard sphere fluid with a narrow, attractive, square well potential. **The Mean Spherical Approximation (MSA) closure relationship is used, but it is not the most appropriate closure for an attractive interparticle potential.** However, the solution has been compared to Monte Carlo simulations for a square well fluid and these show the MSA calculation to be limited to well depths $\epsilon < 1.5$ kT and volume fractions $\phi < 0.08$. Positive well depths correspond to an attractive potential well. Negative well depths correspond to a potential "shoulder", which may or may not be physically reasonable. The stickyhardsphere model may be a better choice in some circumstances. Computed values may behave badly at extremely small $qR$. physically reasonable. The :ref:stickyhardsphere model may be a better choice in some circumstances. Computed values may behave badly at extremely small $qR$. .. note:: Earlier versions of SasView did not incorporate the so-called $\beta(q)$ ("beta") correction [2] for polydispersity and non-sphericity. This is only available in SasView versions 4.2.2 and higher. The well width $(\lambda)$ is defined as multiples of the particle diameter The interaction potential is: .. image:: img/squarewell.png .. math:: \end{cases} where $r$ is the distance from the center of the sphere of a radius $R$. where $r$ is the distance from the center of a sphere of a radius $R$. In sasview the effective radius may be calculated from the parameters In SasView the effective radius may be calculated from the parameters used in the form factor $P(q)$ that this $S(q)$ is combined with. .. [#] R V Sharma, K C Sharma, *Physica*, 89A (1977) 213 .. [#] M Kotlarchyk and S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 Source ------ * **Author:** * **Last Modified by:** * **Last Reviewed by:** * **Last Reviewed by:** Steve King **Date:** March 27, 2019 * **Source added by :** Steve King **Date:** March 25, 2019 """ name = "squarewell" title = "Square well structure factor, with MSA closure" title = "Square well structure factor with Mean Spherical Approximation closure" description = """\ [Square well structure factor, with MSA closure] Interparticle structure factor S(Q)for a hard sphere fluid with a narrow attractive well. Fits are prone to deliver non-physical parameters, use with care and read the references in the full manual. In sasview the effective radius will be calculated from the parameters used in P(Q). Interparticle structure factor S(Q) for a hard sphere fluid with a narrow attractive well. Fits are prone to deliver non- physical parameters; use with care and read the references in the model documentation.The "beta(q)" correction is available in versions 4.2.2 and higher. """ category = "structure-factor"
• sasmodels/models/stickyhardsphere.py

 r0507e09 # Note: model title and parameter table are inserted automatically r""" This calculates the interparticle structure factor for a hard sphere fluid with a narrow attractive well. A perturbative solution of the Percus-Yevick closure is used. The strength of the attractive well is described in terms of "stickiness" as defined below. The perturb (perturbation parameter), $\epsilon$, should be held between 0.01 and 0.1. It is best to hold the perturbation parameter fixed and let the "stickiness" vary to adjust the interaction strength. The stickiness, $\tau$, is defined in the equation below and is a function of both the perturbation parameter and the interaction strength. $\tau$ and $\epsilon$ are defined in terms of the hard sphere diameter $(\sigma = 2 R)$, the width of the square well, $\Delta$ (same units as $R$\ ), and the depth of the well, $U_o$, in units of $kT$. From the definition, it is clear that smaller $\tau$ means stronger attraction. Calculates the interparticle structure factor for a hard sphere fluid with a narrow, attractive, potential well. Unlike the :ref:squarewell model, here a perturbative solution of the Percus-Yevick closure relationship is used. The strength of the attractive well is described in terms of "stickiness" as defined below. The perturbation parameter (perturb), $\tau$, should be fixed between 0.01 and 0.1 and the "stickiness", $\epsilon$, allowed to vary to adjust the interaction strength. The "stickiness" is defined in the equation below and is a function of both the perturbation parameter and the interaction strength. $\epsilon$ and $\tau$ are defined in terms of the hard sphere diameter $(\sigma = 2 R)$, the width of the square well, $\Delta$ (having the same units as $R$\ ), and the depth of the well, $U_o$, in units of $kT$. From the definition, it is clear that smaller $\epsilon$ means a stronger attraction. .. math:: \tau     &= \frac{1}{12\epsilon} \exp(u_o / kT) \\ \epsilon &= \Delta / (\sigma + \Delta) \epsilon     &= \frac{1}{12\tau} \exp(u_o / kT) \\ \tau &= \Delta / (\sigma + \Delta) where the interaction potential is \end{cases} The Percus-Yevick (PY) closure was used for this calculation, and is an adequate closure for an attractive interparticle potential. This solution The Percus-Yevick (PY) closure is used for this calculation, and is an adequate closure for an attractive interparticle potential. The solution has been compared to Monte Carlo simulations for a square well fluid, with good agreement. The true particle volume fraction, $\phi$, is not equal to $h$, which appears in most of the reference. The two are related in equation (24) of the reference. The reference also describes the relationship between this perturbation solution and the original sticky hard sphere (or adhesive sphere) model by Baxter. **NB**: The calculation can go haywire for certain combinations of the input parameters, producing unphysical solutions - in this case errors are reported to the command window and the $S(q)$ is set to -1 (so it will disappear on a log-log plot). Use tight bounds to keep the parameters to values that you know are physical (test them) and keep nudging them until the optimization does not hit the constraints. In sasview the effective radius may be calculated from the parameters The true particle volume fraction, $\phi$, is not equal to $h$ which appears in most of reference [1]. The two are related in equation (24). Reference [1] also describes the relationship between this perturbative solution and the original sticky hard sphere (or "adhesive sphere") model of Baxter [2]. .. note:: The calculation can go haywire for certain combinations of the input parameters, producing unphysical solutions. In this case errors are reported to the command window and $S(q)$ is set to -1 (so it will disappear on a log-log plot!). Use tight bounds to keep the parameters to values that you know are physical (test them), and keep nudging them until the optimization does not hit the constraints. .. note:: Earlier versions of SasView did not incorporate the so-called $\beta(q)$ ("beta") correction [3] for polydispersity and non-sphericity. This is only available in SasView versions 4.2.2 and higher. In SasView the effective radius may be calculated from the parameters used in the form factor $P(q)$ that this $S(q)$ is combined with. .. [#] S V G Menon, C Manohar, and K S Rao, *J. Chem. Phys.*, 95(12) (1991) 9186-9190 .. [#] R J Baxter, *J. Chem. Phys.*, 49 (1968), 2770-2774 .. [#] M Kotlarchyk and S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 Source ------ * **Author:** * **Last Modified by:** * **Last Reviewed by:** * **Last Reviewed by:** Steve King **Date:** March 27, 2019 * **Source added by :** Steve King **Date:** March 25, 2019 """ name = "stickyhardsphere" title = "Sticky hard sphere structure factor, with Percus-Yevick closure" title = "'Sticky' hard sphere structure factor with Percus-Yevick closure" description = """\ [Sticky hard sphere structure factor, with Percus-Yevick closure] Interparticle structure factor S(Q)for a hard sphere fluid with a narrow attractive well. Fits are prone to deliver non-physical parameters, use with care and read the references in the full manual. In sasview the effective radius will be calculated from the parameters used in P(Q). Interparticle structure factor S(Q) for a hard sphere fluid with a narrow attractive well. Fits are prone to deliver non- physical parameters; use with care and read the references in the model documentation.The "beta(q)" correction is available in versions 4.2.2 and higher. """ category = "structure-factor" "volume fraction of hard spheres"], ["perturb", "", 0.05, [0.01, 0.1], "", "perturbation parameter, epsilon"], "perturbation parameter, tau"], ["stickiness", "", 0.20, [-inf, inf], "", "stickiness, tau"], "stickiness, epsilon"], ]
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