Changes in / [dd4f5ed:9644b5a] in sasmodels


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  • deploy.sh

    r2ba5ba5 r9d1e3e4  
    1 if [ "$encrypted_cb04388797b6_iv" ] 
     1if [[ $encrypted_cb04388797b6_iv ]] 
    22then 
    33    eval "$(ssh-agent -s)" 

  • sasmodels/models/fractal_core_shell.py

    rca04add r8f04da4  
    2222    \frac{\sin(qr_c)-qr_c\cos(qr_c)}{(qr_c)^3}+ 
    2323    3V_s(\rho_s-\rho_{solv}) 
    24     \frac{\sin(qr_s)-qr_s\cos(qr_s)}{(qr_s)^3}\right]^2 \\ 
     24    \frac{\sin(qr_s)-qr_s\cos(qr_s)}{(qr_s)^3}\right]^2 
     25 
    2526    S(q) &= 1 + \frac{D_f\ \Gamma\!(D_f-1)}{[1+1/(q\xi)^2]^{(D_f-1)/2}} 
    2627    \frac{\sin[(D_f-1)\tan^{-1}(q\xi)]}{(qr_s)^{D_f}} 

  • sasmodels/models/mass_surface_fractal.py

    rca04add r232bb12  
    2222.. math:: 
    2323 
    24     I(q) = scale \times P(q) + background \\ 
     24    I(q) = scale \times P(q) + background 
     25 
    2526    P(q) = \left\{ \left[ 1+(q^2a)\right]^{D_m/2} \times 
    2627                   \left[ 1+(q^2b)\right]^{(6-D_s-D_m)/2} 
    27            \right\}^{-1} \\ 
    28     a = R_{g}^2/(3D_m/2) \\ 
    29     b = r_{g}^2/[-3(D_s+D_m-6)/2] \\ 
     28           \right\}^{-1} 
     29 
     30    a = R_{g}^2/(3D_m/2) 
     31 
     32    b = r_{g}^2/[-3(D_s+D_m-6)/2] 
     33 
    3034    scale = scale\_factor \times NV^2 (\rho_{particle} - \rho_{solvent})^2 
    3135 

  • sasmodels/models/mono_gauss_coil.py

    rca04add r404ebbd  
    2424 
    2525     I_0 &= \phi_\text{poly} \cdot V 
    26             \cdot (\rho_\text{poly} - \rho_\text{solv})^2 \\ 
    27      P(q) &= 2 [\exp(-Z) + Z - 1] / Z^2 \\ 
    28      Z &= (q R_g)^2 \\ 
     26            \cdot (\rho_\text{poly} - \rho_\text{solv})^2 
     27 
     28     P(q) &= 2 [\exp(-Z) + Z - 1] / Z^2 
     29 
     30     Z &= (q R_g)^2 
     31 
    2932     V &= M / (N_A \delta) 
    3033 

  • sasmodels/models/onion.py

    rca04add rbccb40f  
    8181        \left[ B\exp 
    8282            \left(A (r - r_{\text{shell}-1}) / \Delta t_\text{shell} \right) + C 
    83         \right] \frac{\sin(qr)}{qr}\,r^2\,\mathrm{d}r \\ 
     83        \right] \frac{\sin(qr)}{qr}\,r^2\,\mathrm{d}r 
     84 
    8485    &= 3BV(r_\text{shell}) e^A h(\alpha_\text{out},\beta_\text{out}) 
    8586        - 3BV(r_{\text{shell}-1}) h(\alpha_\text{in},\beta_\text{in}) 
    … …  
    9495    \begin{align*} 
    9596    B&=\frac{\rho_\text{out} - \rho_\text{in}}{e^A-1} 
    96          & C &= \frac{\rho_\text{in}e^A - \rho_\text{out}}{e^A-1} \\ 
     97         &C &= \frac{\rho_\text{in}e^A - \rho_\text{out}}{e^A-1} \\ 
    9798    \alpha_\text{in} &= A\frac{r_{\text{shell}-1}}{\Delta t_\text{shell}} 
    98          & \alpha_\text{out} &= A\frac{r_\text{shell}}{\Delta t_\text{shell}} \\ 
     99         &\alpha_\text{out} &= A\frac{r_\text{shell}}{\Delta t_\text{shell}} \\ 
    99100    \beta_\text{in} &= qr_{\text{shell}-1} 
    100         & \beta_\text{out} &= qr_\text{shell} \\ 
     101        &\beta_\text{out} &= qr_\text{shell} \\ 
    101102    \end{align*} 
    102103 

  • sasmodels/models/parallelepiped.py

    rca04add r30b60d2  
    6262        \left\{S\left[\frac{\mu}{2}\cos\left(\frac{\pi}{2}u\right)\right] 
    6363               S\left[\frac{\mu a}{2}\sin\left(\frac{\pi}{2}u\right)\right] 
    64                \right\}^2 du \\ 
    65     S(x) &= \frac{\sin x}{x} \\ 
     64               \right\}^2 du 
     65 
     66    S(x) &= \frac{\sin x}{x} 
     67 
    6668    \mu &= qB 
    6769 
    … …  
    131133.. math:: 
    132134 
    133     \cos\alpha &= \hat A \cdot \hat q, \\ 
    134     \cos\beta  &= \hat B \cdot \hat q, \\ 
     135    \cos\alpha &= \hat A \cdot \hat q, 
     136 
     137    \cos\beta  &= \hat B \cdot \hat q, 
     138 
    135139    \cos\gamma &= \hat C \cdot \hat q 
    136140 

  • sasmodels/models/poly_gauss_coil.py

    rca04add r404ebbd  
    2121.. math:: 
    2222 
    23      I_0 &= \phi_\text{poly} \cdot V \cdot (\rho_\text{poly}-\rho_\text{solv})^2 \\ 
    24      P(q) &= 2 [(1 + UZ)^{-1/U} + Z - 1] / [(1 + U) Z^2] \\ 
    25      Z &= [(q R_g)^2] / (1 + 2U) \\ 
    26      U &= (Mw / Mn) - 1 = \text{polydispersity ratio} - 1 \\ 
     23     I_0 &= \phi_\text{poly} \cdot V \cdot (\rho_\text{poly}-\rho_\text{solv})^2 
     24 
     25     P(q) &= 2 [(1 + UZ)^{-1/U} + Z - 1] / [(1 + U) Z^2] 
     26 
     27     Z &= [(q R_g)^2] / (1 + 2U) 
     28 
     29     U &= (Mw / Mn) - 1 = \text{polydispersity ratio} - 1 
     30 
    2731     V &= M / (N_A \delta) 
    2832 

  • sasmodels/models/polymer_micelle.py

    rca04add r404ebbd  
    2626 
    2727.. math:: 
    28     P(q) = N^2\beta^2_s\Phi(qR)^2+N\beta^2_cP_c(q)+2N^2\beta_s\beta_cS_{sc}s_c(q)+N(N-1)\beta_c^2S_{cc}(q) \\ 
    29     \beta_s = v\_core(sld\_core - sld\_solvent) \\ 
     28    P(q) = N^2\beta^2_s\Phi(qR)^2+N\beta^2_cP_c(q)+2N^2\beta_s\beta_cS_{sc}s_c(q)+N(N-1)\beta_c^2S_{cc}(q) 
     29 
     30    \beta_s = v\_core(sld\_core - sld\_solvent) 
     31 
    3032    \beta_c = v\_corona(sld\_corona - sld\_solvent) 
    3133 
    … …  
    3941.. math:: 
    4042 
    41    P_c(q) &= 2 [\exp(-Z) + Z - 1] / Z^2 \\ 
     43   P_c(q) &= 2 [\exp(-Z) + Z - 1] / Z^2 
     44 
    4245   Z &= (q R_g)^2 
    4346 
    … …  
    4750.. math:: 
    4851 
    49    S_{sc}(q)=\Phi(qR)\psi(Z)\frac{sin(q(R+d.R_g))}{q(R+d.R_g)} \\ 
    50    S_{cc}(q)=\psi(Z)^2\left[\frac{sin(q(R+d.R_g))}{q(R+d.R_g)} \right ]^2 \\ 
     52   S_{sc}(q)=\Phi(qR)\psi(Z)\frac{sin(q(R+d.R_g))}{q(R+d.R_g)} 
     53 
     54   S_{cc}(q)=\psi(Z)^2\left[\frac{sin(q(R+d.R_g))}{q(R+d.R_g)} \right ]^2 
     55 
    5156   \psi(Z)=\frac{[1-exp^{-Z}]}{Z} 
    5257 

  • sasmodels/models/spherical_sld.py

    rca04add r2ad5d30  
    5151    3 \rho_\text{core} V(r_\text{core}) 
    5252    \Big[ \frac{\sin(qr_\text{core}) - qr_\text{core} \cos(qr_\text{core})} 
    53     {qr_\text{core}^3} \Big] \\ 
     53    {qr_\text{core}^3} \Big] 
     54 
    5455    f_{\text{inter}_i} &= 4 \pi \int_{\Delta t_{ \text{inter}_i } } 
    55     \rho_{ \text{inter}_i } \frac{\sin(qr)} {qr} r^2 dr \\ 
     56    \rho_{ \text{inter}_i } \frac{\sin(qr)} {qr} r^2 dr 
     57 
    5658    f_{\text{shell}_i} &= 4 \pi \int_{\Delta t_{ \text{inter}_i } } 
    5759    \rho_{ \text{flat}_i } \frac{\sin(qr)} {qr} r^2 dr = 
    … …  
    6466    -3 \rho_{ \text{flat}_i } V(r_{ \text{inter}_i }) 
    6567    \Big[ \frac{\sin(qr_{\text{inter}_i}) - qr_{\text{flat}_i} 
    66     \cos(qr_{\text{inter}_i}) } {qr_{\text{inter}_i}^3} \Big] \\ 
     68    \cos(qr_{\text{inter}_i}) } {qr_{\text{inter}_i}^3} \Big] 
     69 
    6770    f_\text{solvent} &= 4 \pi \int_{r_N}^{\infty} \rho_\text{solvent} 
    6871    \frac{\sin(qr)} {qr} r^2 dr = 
    … …  
    119122    4 \pi \sum_{j=1}^{n_\text{steps}} 
    120123    \int_{r_j}^{r_{j+1}} \rho_{ \text{inter}_i } (r_j) 
    121     \frac{\sin(qr)} {qr} r^2 dr \\ 
    122     \approx 4 \pi \sum_{j=1}^{n_\text{steps}} \Big[ 
     124    \frac{\sin(qr)} {qr} r^2 dr 
     125 
     126    &\approx 4 \pi \sum_{j=1}^{n_\text{steps}} \Big[ 
    123127    3 ( \rho_{ \text{inter}_i } ( r_{j+1} ) - \rho_{ \text{inter}_i } 
    124128    ( r_{j} ) V (r_j) 
    125129    \Big[ \frac {r_j^2 \beta_\text{out}^2 \sin(\beta_\text{out}) 
    126130    - (\beta_\text{out}^2-2) \cos(\beta_\text{out}) } 
    127     {\beta_\text{out}^4 } \Big] \\ 
    128     {} - 3 ( \rho_{ \text{inter}_i } ( r_{j+1} ) - \rho_{ \text{inter}_i } 
     131    {\beta_\text{out}^4 } \Big] 
     132 
     133    &{} - 3 ( \rho_{ \text{inter}_i } ( r_{j+1} ) - \rho_{ \text{inter}_i } 
    129134    ( r_{j} ) V ( r_{j-1} ) 
    130135    \Big[ \frac {r_{j-1}^2 \sin(\beta_\text{in}) 
    131136    - (\beta_\text{in}^2-2) \cos(\beta_\text{in}) } 
    132     {\beta_\text{in}^4 } \Big] \\ 
    133     {} + 3 \rho_{ \text{inter}_i } ( r_{j+1} )  V ( r_j ) 
     137    {\beta_\text{in}^4 } \Big] 
     138 
     139    &{} + 3 \rho_{ \text{inter}_i } ( r_{j+1} )  V ( r_j ) 
    134140    \Big[ \frac {\sin(\beta_\text{out}) - \cos(\beta_\text{out}) } 
    135141    {\beta_\text{out}^4 } \Big] 
    … …  
    146152    \begin{align*} 
    147153    V(a) &= \frac {4\pi}{3}a^3 && \\ 
    148     a_\text{in} \sim \frac{r_j}{r_{j+1} -r_j} \text{, } & a_\text{out} 
    149     \sim \frac{r_{j+1}}{r_{j+1} -r_j} \\ 
    150     \beta_\text{in} &= qr_j \text{, } & \beta_\text{out} &= qr_{j+1} 
     154    a_\text{in} &\sim \frac{r_j}{r_{j+1} -r_j} \text{, } &a_\text{out} 
     155    &\sim \frac{r_{j+1}}{r_{j+1} -r_j} \\ 
     156    \beta_\text{in} &= qr_j \text{, } &\beta_\text{out} &= qr_{j+1} 
    151157    \end{align*} 
    152158 

  • sasmodels/models/star_polymer.py

    r5da1ac8 r30b60d2  
    3636   Star polymers in solutions tend to have strong interparticle and osmotic 
    3737   effects. Thus the Benoit equation may not work well for many real cases. 
    38    A newer model for star polymer incorporating excluded volume has been 
    39    developed by Li et al in arXiv:1404.6269 [physics.chem-ph].  Also, at small 
    40    $q$ the scattering, i.e. the Guinier term, is not sensitive to the number of 
    41    arms, and hence 'scale' here is simply $I(q=0)$ as described for the 
    42    :ref:`mono-gauss-coil` model, using volume fraction $\phi$ and volume V 
    43    for the whole star polymer. 
     38   At small $q$ the Guinier term and hence $I(q=0)$ is the same as for $f$ arms 
     39   of radius of gyration $R_g$, as described for the :ref:`mono-gauss-coil` 
     40   model. A newer model for star polymer incorporating excluded volume has been 
     41   developed by Li et al in arXiv:1404.6269 [physics.chem-ph]. 
    4442 
    4543References 
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