Changeset a34b811 in sasmodels


Ignore:
Timestamp:
Mar 28, 2019 5:02:53 PM (6 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, ticket-1257-vesicle-product, ticket_1156, ticket_822_more_unit_tests
Children:
db1d9d5
Parents:
e5cb3df
Message:

use radius_effective/radius_effective_mode/radius_effective_modes consistently throughout the code

Files:
73 edited

Legend:

Unmodified
Added
Removed

  • explore/beta/sasfit_compare.py

    r119073a ra34b811  
    408408        #radius_effective=12.59921049894873, 
    409409        ) 
    410     target = sasmodels_theory(q, model, effective_radius_mode=0, structure_factor_mode=1, **pars) 
     410    target = sasmodels_theory(q, model, radius_effective_mode=0, structure_factor_mode=1, **pars) 
    411411    actual = ellipsoid_pe(q, norm='sasview', **pars) 
    412412    title = " ".join(("sasmodels", model, pd_type)) 

  • explore/beta/sasfit_compare_new.py

    r0b8a1fc ra34b811  
    360360#polydispersity for hollow_cylinder 
    361361def hollow_cylinder_pe(q,radius=20, thickness=10, length=80, sld=4, sld_solvent=1, volfraction=0.15, 
    362         radius_pd=0.1, thickness_pd=0.2, length_pd=0.05, radius_pd_type="gaussian", length_pd_type="gaussian",  
     362        radius_pd=0.1, thickness_pd=0.2, length_pd=0.05, radius_pd_type="gaussian", length_pd_type="gaussian", 
    363363        thickness_pd_type="gaussian", radius_effective=None, background=0, scale=1, 
    364364                 norm='sasview'): 
    … …  
    595595#       this one is only used locally for "actual" 
    596596        ) 
    597     target = sasmodels_theory(q, model, effective_radius_type=0, structure_factor_mode=1, **pars) 
     597    target = sasmodels_theory(q, model, radius_effective_mode=0, structure_factor_mode=1, **pars) 
    598598    actual = sphere_r(q, norm='sasview', **pars) 
    599599    title = " ".join(("sasmodels", model, pd_type)) 
    … …  
    612612        background=0, 
    613613        radius_pd=0.01, thickness_pd=0.01, radius_pd_type=pd_type, thickness_pd_type=pd_type, 
    614         radius_effective=30. )  
     614        radius_effective=30. ) 
    615615        # equivalent average sphere radius for local "actual" to match what sasview uses, use None to compute average outer radius here, 
    616616 
    617     target = sasmodels_theory(q, model, effective_radius_type=0, structure_factor_mode=1, **pars) 
     617    target = sasmodels_theory(q, model, radius_effective_mode=0, structure_factor_mode=1, **pars) 
    618618    actual = vesicle_pe(q, norm='sasview', **pars) 
    619619    title = " ".join(("sasmodels", model, pd_type)) 
    … …  
    633633        background=0, 
    634634        radius_pd=0.1, thickness_pd=0.0, length_pd=0.0, radius_pd_type=pd_type, thickness_pd_type=pd_type, length_pd_type=pd_type, 
    635         radius_effective=40.687)   
     635        radius_effective=40.687) 
    636636        # equivalent average sphere radius for local "actual" to match what sasview uses 
    637     target = sasmodels_theory(q, model, effective_radius_type=0, structure_factor_mode=1, **pars) 
     637    target = sasmodels_theory(q, model, radius_effective_mode=0, structure_factor_mode=1, **pars) 
    638638    actual = hollow_cylinder_pe(q, norm='sasview', **pars) 
    639639# RKH monodisp was OK,    actual = hollow_cylinder_theta(q,radius=20, thickness=10, length=80, sld=4, sld_solvent=1 ) 
    … …  
    656656# if change radius_effective to some other value, the S(Q) from sasview does not agree 
    657657        ) 
    658     target = sasmodels_theory(q, model, effective_radius_type=0, structure_factor_mode=1, **pars) 
     658    target = sasmodels_theory(q, model, radius_effective_mode=0, structure_factor_mode=1, **pars) 
    659659    actual = ellipsoid_pe(q, norm='sasview', **pars) 
    660660# RKH test       actual = ellipsoid_theta(q, radius_polar=20, radius_equatorial=400, sld=4, sld_solvent=1, volfraction=0.15, radius_effective=270.) 

  • sasmodels/direct_model.py

    rd8e81f7 ra34b811  
    7171    For solid objects V_shell is equal to V_form and the volume ratio is 1. 
    7272 
    73     Use parameter *effective_radius_type* to select the effective radius THIS MIGHT NEED CHECKING radius_effective_mode or effecive_radius_type??? 
    74     calculation. 
     73    Use parameter *radius_effective_mode* to select the effective radius 
     74    calculation to use amongst the *radius_effective_modes* list given in the 
     75    model. 
    7576    """ 
    7677    R_eff_type = int(pars.pop(RADIUS_MODE_ID, 1.0)) 

  • sasmodels/generate.py

    rb297ba9 ra34b811  
    2727    which are hollow. 
    2828 
    29     *effective_radius(mode, p1, p2, ...)* returns the effective radius of 
     29    *radius_effective(mode, p1, p2, ...)* returns the effective radius of 
    3030    the form with particular dimensions.  Mode determines the type of 
    3131    effective radius returned, with mode=1 for equivalent volume. 
    … …  
    820820                              for p in partable.kernel_parameters)) 
    821821    # Define the function calls 
    822     call_effective_radius = "#define CALL_EFFECTIVE_RADIUS(_mode, _v) 0.0" 
     822    call_radius_effective = "#define CALL_RADIUS_EFFECTIVE(_mode, _v) 0.0" 
    823823    if partable.form_volume_parameters: 
    824824        refs = _call_pars("_v.", partable.form_volume_parameters) 
    … …  
    833833                "do { _form = _shell = form_volume(%s); } " 
    834834                "while (0)") % (",".join(refs)) 
    835         if model_info.effective_radius_type: 
    836             call_effective_radius = ( 
    837                 "#define CALL_EFFECTIVE_RADIUS(_mode, _v) " 
    838                 "effective_radius(_mode, %s)") % (",".join(refs)) 
     835        if model_info.radius_effective_modes: 
     836            call_radius_effective = ( 
     837                "#define CALL_RADIUS_EFFECTIVE(_mode, _v) " 
     838                "radius_effective(_mode, %s)") % (",".join(refs)) 
    839839    else: 
    840840        # Model doesn't have volume.  We could make the kernel run a little 
    … …  
    845845            "do { _form = _shell = 1.0; } while (0)") 
    846846    source.append(call_volume) 
    847     source.append(call_effective_radius) 
     847    source.append(call_radius_effective) 
    848848    model_refs = _call_pars("_v.", partable.iq_parameters) 
    849849 

  • sasmodels/kernel.py

    rb297ba9 ra34b811  
    7878        """ 
    7979        _, F2, _, shell_volume, _ = self.Fq(call_details, values, cutoff, 
    80                                             magnetic, effective_radius_type=0) 
     80                                            magnetic, radius_effective_mode=0) 
    8181        combined_scale = values[0]/shell_volume 
    8282        background = values[1] 
    … …  
    8585 
    8686    def Fq(self, call_details, values, cutoff, magnetic, 
    87            effective_radius_type=0): 
     87           radius_effective_mode=0): 
    8888        # type: (CallDetails, np.ndarray, np.ndarray, float, bool, int) -> np.ndarray 
    8989        r""" 
    … …  
    143143        volume fraction of the particles.  The model can have several 
    144144        different ways to compute effective radius, with the 
    145         *effective_radius_type* parameter used to select amongst them.  The 
     145        *radius_effective_mode* parameter used to select amongst them.  The 
    146146        volume fraction of particles should be determined from the total 
    147147        volume fraction of the form, not just the shell volume fraction. 
    … …  
    153153        """ 
    154154        self._call_kernel(call_details, values, cutoff, magnetic, 
    155                           effective_radius_type) 
     155                          radius_effective_mode) 
    156156        #print("returned",self.q_input.q, self.result) 
    157157        nout = 2 if self.info.have_Fq and self.dim == '1d' else 1 
    … …  
    165165        form_volume = self.result[nout*self.q_input.nq + 1]/total_weight 
    166166        shell_volume = self.result[nout*self.q_input.nq + 2]/total_weight 
    167         effective_radius = self.result[nout*self.q_input.nq + 3]/total_weight 
     167        radius_effective = self.result[nout*self.q_input.nq + 3]/total_weight 
    168168        if shell_volume == 0.: 
    169169            shell_volume = 1. 
    … …  
    171171              if nout == 2 else None) 
    172172        F2 = self.result[0:nout*self.q_input.nq:nout]/total_weight 
    173         return F1, F2, effective_radius, shell_volume, form_volume/shell_volume 
     173        return F1, F2, radius_effective, shell_volume, form_volume/shell_volume 
    174174 
    175175    def release(self): 
    … …  
    181181 
    182182    def _call_kernel(self, call_details, values, cutoff, magnetic, 
    183                      effective_radius_type): 
     183                     radius_effective_mode): 
    184184        # type: (CallDetails, np.ndarray, np.ndarray, float, bool, int) -> np.ndarray 
    185185        """ 

  • sasmodels/kernel_iq.c

    r12f4c19 ra34b811  
    2727//      parameters in the parameter table. 
    2828//  CALL_VOLUME(form, shell, table) : assign form and shell values 
    29 //  CALL_EFFECTIVE_RADIUS(type, table) : call the R_eff function 
     29//  CALL_RADIUS_EFFECTIVE(mode, table) : call the R_eff function 
    3030//  CALL_IQ(q, table) : call the Iq function for 1D calcs. 
    3131//  CALL_IQ_A(q, table) : call the Iq function with |q| for 2D data. 
    … …  
    285285    pglobal double *result,       // nq+1 return values, again with padding 
    286286    const double cutoff,          // cutoff in the dispersity weight product 
    287     int32_t effective_radius_type // which effective radius to compute 
     287    int32_t radius_effective_mode // which effective radius to compute 
    288288    ) 
    289289{ 
    … …  
    703703      weighted_form += weight * form; 
    704704      weighted_shell += weight * shell; 
    705       if (effective_radius_type != 0) { 
    706         weighted_radius += weight * CALL_EFFECTIVE_RADIUS(effective_radius_type, local_values.table); 
     705      if (radius_effective_mode != 0) { 
     706        weighted_radius += weight * CALL_RADIUS_EFFECTIVE(radius_effective_mode, local_values.table); 
    707707      } 
    708708      BUILD_ROTATION(); 

  • sasmodels/kernelcl.py

    r069743a ra34b811  
    577577 
    578578    def _call_kernel(self, call_details, values, cutoff, magnetic, 
    579                      effective_radius_type): 
     579                     radius_effective_mode): 
    580580        # type: (CallDetails, np.ndarray, float, bool, int) -> np.ndarray 
    581581        env = environment() 
    … …  
    601601            self._result_b,   # Result storage. 
    602602            self._as_dtype(cutoff),  # Probability cutoff. 
    603             np.uint32(effective_radius_type),  # R_eff mode. 
     603            np.uint32(radius_effective_mode),  # R_eff mode. 
    604604        ] 
    605605 

  • sasmodels/kernelcuda.py

    rb297ba9 ra34b811  
    473473 
    474474    def _call_kernel(self, call_details, values, cutoff, magnetic, 
    475                      effective_radius_type): 
     475                     radius_effective_mode): 
    476476        # type: (CallDetails, np.ndarray, float, bool, int) -> np.ndarray 
    477477 
    … …  
    492492            self._result_b,   # Result storage. 
    493493            self._as_dtype(cutoff),  # Probability cutoff. 
    494             np.uint32(effective_radius_type),  # R_eff mode. 
     494            np.uint32(radius_effective_mode),  # R_eff mode. 
    495495        ] 
    496496        grid = partition(self.q_input.nq) 

  • sasmodels/kerneldll.py

    rb297ba9 ra34b811  
    403403 
    404404    def _call_kernel(self, call_details, values, cutoff, magnetic, 
    405                      effective_radius_type): 
     405                     radius_effective_mode): 
    406406        # type: (CallDetails, np.ndarray, float, bool, int) -> np.ndarray 
    407407 
    … …  
    417417            self.result.ctypes.data,   # Result storage. 
    418418            self._as_dtype(cutoff),  # Probability cutoff. 
    419             effective_radius_type,  # R_eff mode. 
     419            radius_effective_mode,  # R_eff mode. 
    420420        ] 
    421421 

  • sasmodels/kernelpy.py

    rb297ba9 ra34b811  
    172172        volume = model_info.form_volume 
    173173        shell = model_info.shell_volume 
    174         radius = model_info.effective_radius 
     174        radius = model_info.radius_effective 
    175175        self._volume = ((lambda: (shell(*volume_args), volume(*volume_args))) if shell and volume 
    176176                        else (lambda: [volume(*volume_args)]*2) if volume 
    … …  
    180180                        else (lambda mode: 1.0)) 
    181181 
    182     def _call_kernel(self, call_details, values, cutoff, magnetic, effective_radius_type): 
     182    def _call_kernel(self, call_details, values, cutoff, magnetic, radius_effective_mode): 
    183183        # type: (CallDetails, np.ndarray, np.ndarray, float, bool) -> np.ndarray 
    184184        if magnetic: 
    … …  
    186186        #print("Calling python kernel") 
    187187        #call_details.show(values) 
    188         radius = ((lambda: 0.0) if effective_radius_type == 0 
    189                   else (lambda: self._radius(effective_radius_type))) 
     188        radius = ((lambda: 0.0) if radius_effective_mode == 0 
     189                  else (lambda: self._radius(radius_effective_mode))) 
    190190        self.result = _loops( 
    191191            self._parameter_vector, self._form, self._volume, radius, 

  • sasmodels/modelinfo.py

    rb297ba9 ra34b811  
    265265    other sld parameters. The volume parameters are used for calls 
    266266    to form_volume within the kernel (required for volume normalization), 
    267     to shell_volume (for hollow shapes), and to effective_radius (for 
     267    to shell_volume (for hollow shapes), and to radius_effective (for 
    268268    structure factor interactions) respectively. 
    269269 
    … …  
    841841    info.structure_factor = getattr(kernel_module, 'structure_factor', False) 
    842842    # TODO: find Fq by inspection 
    843     info.effective_radius_type = getattr(kernel_module, 'effective_radius_type', None) 
     843    info.radius_effective_modes = getattr(kernel_module, 'radius_effective_modes', None) 
    844844    info.have_Fq = getattr(kernel_module, 'have_Fq', False) 
    845845    info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y']) 
    … …  
    848848    info.source = getattr(kernel_module, 'source', []) 
    849849    info.c_code = getattr(kernel_module, 'c_code', None) 
    850     info.effective_radius = getattr(kernel_module, 'effective_radius', None) 
     850    info.radius_effective = getattr(kernel_module, 'radius_effective', None) 
    851851    # TODO: check the structure of the tests 
    852852    info.tests = getattr(kernel_module, 'tests', []) 
    … …  
    961961    #: List of options for computing the effective radius of the shape, 
    962962    #: or None if the model is not usable as a form factor model. 
    963     effective_radius_type = None   # type: List[str] 
     963    radius_effective_modes = None   # type: List[str] 
    964964    #: List of C source files used to define the model.  The source files 
    965965    #: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the 
    … …  
    989989    #: monodisperse approximation for non-dilute solutions, P@S.  The first 
    990990    #: argument is the integer effective radius mode, with default 0. 
    991     effective_radius = None  # type: Union[None, Callable[[int, np.ndarray], float]] 
     991    radius_effective = None  # type: Union[None, Callable[[int, np.ndarray], float]] 
    992992    #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined 
    993993    #: by the parameter table.  *Iq* can be defined as a python function, or 

  • sasmodels/models/_spherepy.py

    r0507e09 ra34b811  
    4848---------------------------- 
    4949 
    50 * **Author: P Kienzle**  
    51 * **Last Modified by:**  
     50* **Author: P Kienzle** 
     51* **Last Modified by:** 
    5252* **Last Reviewed by:** S King and P Parker **Date:** 2013/09/09 and 2014/01/06 
    5353* **Source added by :** Steve King **Date:** March 25, 2019 
    … …  
    8383    return 1.333333333333333 * pi * radius ** 3 
    8484 
    85 def effective_radius(mode, radius): 
     85def radius_effective(mode, radius): 
    8686    """Calculate R_eff for sphere""" 
    87     return radius 
     87    return radius if mode else 0. 
    8888 
    8989def Iq(q, sld, sld_solvent, radius): 

  • sasmodels/models/barbell.c

    r99658f6 ra34b811  
    8585 
    8686static double 
    87 effective_radius(int mode, double radius_bell, double radius, double length) 
     87radius_effective(int mode, double radius_bell, double radius, double length) 
    8888{ 
    8989    switch (mode) { 

  • sasmodels/models/barbell.py

    r0507e09 ra34b811  
    126126source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "barbell.c"] 
    127127have_Fq = True 
    128 effective_radius_type = [ 
     128radius_effective_modes = [ 
    129129    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    130130    "radius", "half length", "half total length", 

  • sasmodels/models/capped_cylinder.c

    r99658f6 ra34b811  
    107107 
    108108static double 
    109 effective_radius(int mode, double radius, double radius_cap, double length) 
     109radius_effective(int mode, double radius, double radius_cap, double length) 
    110110{ 
    111111    switch (mode) { 

  • sasmodels/models/capped_cylinder.py

    r0507e09 ra34b811  
    146146source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "capped_cylinder.c"] 
    147147have_Fq = True 
    148 effective_radius_type = [ 
     148radius_effective_modes = [ 
    149149    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    150150    "radius", "half length", "half total length", 

  • sasmodels/models/core_multi_shell.c

    rd42dd4a ra34b811  
    2626 
    2727static double 
    28 effective_radius(int mode, double core_radius, double fp_n, double thickness[]) 
     28radius_effective(int mode, double core_radius, double fp_n, double thickness[]) 
    2929{ 
    3030  switch (mode) { 

  • sasmodels/models/core_multi_shell.py

    r0507e09 ra34b811  
    108108source = ["lib/sas_3j1x_x.c", "core_multi_shell.c"] 
    109109have_Fq = True 
    110 effective_radius_type = ["outer radius", "core radius"] 
     110radius_effective_modes = ["outer radius", "core radius"] 
    111111 
    112112def random(): 

  • sasmodels/models/core_shell_bicelle.c

    r99658f6 ra34b811  
    6060 
    6161static double 
    62 effective_radius(int mode, double radius, double thick_rim, double thick_face, double length) 
     62radius_effective(int mode, double radius, double thick_rim, double thick_face, double length) 
    6363{ 
    6464    switch (mode) { 

  • sasmodels/models/core_shell_bicelle.py

    r0507e09 ra34b811  
    165165          "core_shell_bicelle.c"] 
    166166have_Fq = True 
    167 effective_radius_type = [ 
     167radius_effective_modes = [ 
    168168    "excluded volume", "equivalent volume sphere", "outer rim radius", 
    169169    "half outer thickness", "half diagonal", 

  • sasmodels/models/core_shell_bicelle_elliptical.c

    r99658f6 ra34b811  
    3535 
    3636static double 
    37 effective_radius(int mode, double r_minor, double x_core, double thick_rim, double thick_face, double length) 
     37radius_effective(int mode, double r_minor, double x_core, double thick_rim, double thick_face, double length) 
    3838{ 
    3939    switch (mode) { 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r0507e09 ra34b811  
    155155          "core_shell_bicelle_elliptical.c"] 
    156156have_Fq = True 
    157 effective_radius_type = [ 
     157radius_effective_modes = [ 
    158158    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    159159    "outer rim average radius", "outer rim min radius", 

  • sasmodels/models/core_shell_bicelle_elliptical_belt_rough.c

    r99658f6 ra34b811  
    3636 
    3737static double 
    38 effective_radius(int mode, double r_minor, double x_core, double thick_rim, double thick_face, double length) 
     38radius_effective(int mode, double r_minor, double x_core, double thick_rim, double thick_face, double length) 
    3939{ 
    4040    switch (mode) { 

  • sasmodels/models/core_shell_bicelle_elliptical_belt_rough.py

    r0507e09 ra34b811  
    168168          "core_shell_bicelle_elliptical_belt_rough.c"] 
    169169have_Fq = True 
    170 effective_radius_type = [ 
     170radius_effective_modes = [ 
    171171    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    172172    "outer rim average radius", "outer rim min radius", 

  • sasmodels/models/core_shell_cylinder.c

    r99658f6 ra34b811  
    3737 
    3838static double 
    39 effective_radius(int mode, double radius, double thickness, double length) 
     39radius_effective(int mode, double radius, double thickness, double length) 
    4040{ 
    4141    switch (mode) { 

  • sasmodels/models/core_shell_cylinder.py

    r0507e09 ra34b811  
    141141source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "core_shell_cylinder.c"] 
    142142have_Fq = True 
    143 effective_radius_type = [ 
     143radius_effective_modes = [ 
    144144    "excluded volume", "equivalent volume sphere", "outer radius", "half outer length", 
    145145    "half min outer dimension", "half max outer dimension", "half outer diagonal", 

  • sasmodels/models/core_shell_ellipsoid.c

    r99658f6 ra34b811  
    6868 
    6969static double 
    70 effective_radius(int mode, double radius_equat_core, double x_core, double thick_shell, double x_polar_shell) 
     70radius_effective(int mode, double radius_equat_core, double x_core, double thick_shell, double x_polar_shell) 
    7171{ 
    7272    const double radius_equat_tot = radius_equat_core + thick_shell; 

  • sasmodels/models/core_shell_ellipsoid.py

    r0507e09 ra34b811  
    155155source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "core_shell_ellipsoid.c"] 
    156156have_Fq = True 
    157 effective_radius_type = [ 
     157radius_effective_modes = [ 
    158158    "average outer curvature", "equivalent volume sphere", 
    159159    "min outer radius", "max outer radius", 

  • sasmodels/models/core_shell_parallelepiped.c

    r99658f6 ra34b811  
    7575 
    7676static double 
    77 effective_radius(int mode, double length_a, double length_b, double length_c, 
     77radius_effective(int mode, double length_a, double length_b, double length_c, 
    7878                 double thick_rim_a, double thick_rim_b, double thick_rim_c) 
    7979{ 

  • sasmodels/models/core_shell_parallelepiped.py

    r0507e09 ra34b811  
    236236source = ["lib/gauss76.c", "core_shell_parallelepiped.c"] 
    237237have_Fq = True 
    238 effective_radius_type = [ 
     238radius_effective_modes = [ 
    239239    "equivalent cylinder excluded volume", 
    240240    "equivalent volume sphere", 

  • sasmodels/models/core_shell_sphere.c

    rd42dd4a ra34b811  
    66 
    77static double 
    8 effective_radius(int mode, double radius, double thickness) 
     8radius_effective(int mode, double radius, double thickness) 
    99{ 
    1010    switch (mode) { 

  • sasmodels/models/core_shell_sphere.py

    r0507e09 ra34b811  
    6060---------------------------- 
    6161 
    62 * **Author:**  
    63 * **Last Modified by:**  
    64 * **Last Reviewed by:**  
     62* **Author:** 
     63* **Last Modified by:** 
     64* **Last Reviewed by:** 
    6565* **Source added by :** Steve King **Date:** March 25, 2019 
    6666""" 
    … …  
    9292source = ["lib/sas_3j1x_x.c", "lib/core_shell.c", "core_shell_sphere.c"] 
    9393have_Fq = True 
    94 effective_radius_type = ["outer radius", "core radius"] 
     94radius_effective_modes = ["outer radius", "core radius"] 
    9595 
    9696demo = dict(scale=1, background=0, radius=60, thickness=10, 

  • sasmodels/models/cylinder.c

    r99658f6 ra34b811  
    3232 
    3333static double 
    34 effective_radius(int mode, double radius, double length) 
     34radius_effective(int mode, double radius, double length) 
    3535{ 
    3636    switch (mode) { 

  • sasmodels/models/cylinder.py

    r6652522 ra34b811  
    155155source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "cylinder.c"] 
    156156have_Fq = True 
    157 effective_radius_type = [ 
     157radius_effective_modes = [ 
    158158    "excluded volume", "equivalent volume sphere", "radius", 
    159159    "half length", "half min dimension", "half max dimension", "half diagonal", 

  • sasmodels/models/ellipsoid.c

    r99658f6 ra34b811  
    3232 
    3333static double 
    34 effective_radius(int mode, double radius_polar, double radius_equatorial) 
     34radius_effective(int mode, double radius_polar, double radius_equatorial) 
    3535{ 
    3636    switch (mode) { 

  • sasmodels/models/ellipsoid.py

    r0507e09 ra34b811  
    167167source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "ellipsoid.c"] 
    168168have_Fq = True 
    169 effective_radius_type = [ 
     169radius_effective_modes = [ 
    170170    "average curvature", "equivalent volume sphere", "min radius", "max radius", 
    171171    ] 

  • sasmodels/models/elliptical_cylinder.c

    r99658f6 ra34b811  
    4141 
    4242static double 
    43 effective_radius(int mode, double radius_minor, double r_ratio, double length) 
     43radius_effective(int mode, double radius_minor, double r_ratio, double length) 
    4444{ 
    4545    switch (mode) { 

  • sasmodels/models/elliptical_cylinder.py

    r0507e09 ra34b811  
    131131source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "elliptical_cylinder.c"] 
    132132have_Fq = True 
    133 effective_radius_type = [ 
     133radius_effective_modes = [ 
    134134    "equivalent cylinder excluded volume", 
    135135    "equivalent volume sphere", "average radius", "min radius", "max radius", 

  • sasmodels/models/fuzzy_sphere.c

    rd42dd4a ra34b811  
    55 
    66static double 
    7 effective_radius(int mode, double radius, double fuzziness) 
     7radius_effective(int mode, double radius, double fuzziness) 
    88{ 
    99    switch (mode) { 

  • sasmodels/models/fuzzy_sphere.py

    r0507e09 ra34b811  
    6363---------------------------- 
    6464 
    65 * **Author:**  
    66 * **Last Modified by:**  
    67 * **Last Reviewed by:**  
     65* **Author:** 
     66* **Last Modified by:** 
     67* **Last Reviewed by:** 
    6868* **Source added by :** Steve King **Date:** March 25, 2019 
    6969""" 
    … …  
    9898source = ["lib/sas_3j1x_x.c", "fuzzy_sphere.c"] 
    9999have_Fq = True 
    100 effective_radius_type = ["radius", "radius + fuzziness"] 
     100radius_effective_modes = ["radius", "radius + fuzziness"] 
    101101 
    102102def random(): 

  • sasmodels/models/hollow_cylinder.c

    r99658f6 ra34b811  
    3434 
    3535static double 
    36 effective_radius(int mode, double radius, double thickness, double length) 
     36radius_effective(int mode, double radius, double thickness, double length) 
    3737{ 
    3838    switch (mode) { 

  • sasmodels/models/hollow_cylinder.py

    r0507e09 ra34b811  
    110110source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "hollow_cylinder.c"] 
    111111have_Fq = True 
    112 effective_radius_type = [ 
     112radius_effective_modes = [ 
    113113    "excluded volume", "equivalent outer volume sphere", 
    114114    "outer radius", "half length", 

  • sasmodels/models/hollow_rectangular_prism.c

    r99658f6 ra34b811  
    3030 
    3131static double 
    32 effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio, double thickness) 
     32radius_effective(int mode, double length_a, double b2a_ratio, double c2a_ratio, double thickness) 
    3333// NOTE length_a is external dimension! 
    3434{ 

  • sasmodels/models/hollow_rectangular_prism.py

    r0507e09 ra34b811  
    157157source = ["lib/gauss76.c", "hollow_rectangular_prism.c"] 
    158158have_Fq = True 
    159 effective_radius_type = [ 
     159radius_effective_modes = [ 
    160160    "equivalent cylinder excluded volume", "equivalent outer volume sphere", 
    161161    "half length_a", "half length_b", "half length_c", 

  • sasmodels/models/hollow_rectangular_prism_thin_walls.c

    r99658f6 ra34b811  
    2626 
    2727static double 
    28 effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
     28radius_effective(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
    2929{ 
    3030    switch (mode) { 

  • sasmodels/models/hollow_rectangular_prism_thin_walls.py

    r0507e09 ra34b811  
    117117source = ["lib/gauss76.c", "hollow_rectangular_prism_thin_walls.c"] 
    118118have_Fq = True 
    119 effective_radius_type = [ 
     119radius_effective_modes = [ 
    120120    "equivalent cylinder excluded volume", "equivalent outer volume sphere", 
    121121    "half length_a", "half length_b", "half length_c", 

  • sasmodels/models/mono_gauss_coil.c

    r153f8f6 ra34b811  
    66 
    77static double 
    8 effective_radius(int mode, double rg) 
     8radius_effective(int mode, double rg) 
    99{ 
    1010    switch (mode) { 

  • sasmodels/models/mono_gauss_coil.py

    r0507e09 ra34b811  
    5959---------------------------- 
    6060 
    61 * **Author:**  
    62 * **Last Modified by:**  
    63 * **Last Reviewed by:**  
     61* **Author:** 
     62* **Last Modified by:** 
     63* **Last Reviewed by:** 
    6464* **Source added by :** Steve King **Date:** March 25, 2019""" 
    6565 
    … …  
    8686source = ["mono_gauss_coil.c"] 
    8787have_Fq = False 
    88 effective_radius_type = ["R_g", "2R_g", "3R_g", "sqrt(5/3)*R_g"] 
     88radius_effective_modes = ["R_g", "2R_g", "3R_g", "sqrt(5/3)*R_g"] 
    8989 
    9090 

  • sasmodels/models/multilayer_vesicle.c

    ree60aa7 ra34b811  
    4848 
    4949static double 
    50 effective_radius(int mode, double radius, double thick_shell, double thick_solvent, double fp_n_shells) 
     50radius_effective(int mode, double radius, double thick_shell, double thick_solvent, double fp_n_shells) 
    5151{ 
    5252    // case 1: outer radius 

  • sasmodels/models/multilayer_vesicle.py

    r0507e09 ra34b811  
    154154source = ["lib/sas_3j1x_x.c", "multilayer_vesicle.c"] 
    155155have_Fq = True 
    156 effective_radius_type = ["outer radius"] 
     156radius_effective_modes = ["outer radius"] 
    157157 
    158158def random(): 

  • sasmodels/models/onion.c

    ree60aa7 ra34b811  
    4747 
    4848static double 
    49 effective_radius(int mode, double radius_core, double n_shells, double thickness[]) 
     49radius_effective(int mode, double radius_core, double n_shells, double thickness[]) 
    5050{ 
    5151  // case 1: outer radius 

  • sasmodels/models/onion.py

    r0507e09 ra34b811  
    182182---------------------------- 
    183183 
    184 * **Author:**  
    185 * **Last Modified by:**  
    186 * **Last Reviewed by:**  
     184* **Author:** 
     185* **Last Modified by:** 
     186* **Last Reviewed by:** 
    187187* **Source added by :** Steve King **Date:** March 25, 2019 
    188188""" 
    … …  
    329329single = False 
    330330have_Fq = True 
    331 effective_radius_type = ["outer radius"] 
     331radius_effective_modes = ["outer radius"] 
    332332 
    333333profile_axes = ['Radius (A)', 'SLD (1e-6/A^2)'] 

  • sasmodels/models/parallelepiped.c

    r99658f6 ra34b811  
    3737 
    3838static double 
    39 effective_radius(int mode, double length_a, double length_b, double length_c) 
     39radius_effective(int mode, double length_a, double length_b, double length_c) 
    4040{ 
    4141    switch (mode) { 

  • sasmodels/models/parallelepiped.py

    r0507e09 ra34b811  
    240240source = ["lib/gauss76.c", "parallelepiped.c"] 
    241241have_Fq = True 
    242 effective_radius_type = [ 
     242radius_effective_modes = [ 
    243243    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    244244    "half length_a", "half length_b", "half length_c", 

  • sasmodels/models/pearl_necklace.c

    r9b5fd42 ra34b811  
    8686 
    8787static double 
    88 effective_radius(int mode, double radius, double edge_sep, double thick_string, double fp_num_pearls) 
     88radius_effective(int mode, double radius, double edge_sep, double thick_string, double fp_num_pearls) 
    8989{ 
    9090    switch (mode) { 

  • sasmodels/models/pearl_necklace.py

    r0507e09 ra34b811  
    6565---------------------------- 
    6666 
    67 * **Author:**  
    68 * **Last Modified by:**  
    69 * **Last Reviewed by:**  
     67* **Author:** 
     68* **Last Modified by:** 
     69* **Last Reviewed by:** 
    7070* **Source added by :** Steve King **Date:** March 25, 2019 
    7171""" 
    … …  
    111111source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"] 
    112112single = False  # use double precision unless told otherwise 
    113 effective_radius_type = ["equivalent volume sphere"] 
     113radius_effective_modes = ["equivalent volume sphere"] 
    114114 
    115115def random(): 

  • sasmodels/models/poly_gauss_coil.py

    r0507e09 ra34b811  
    5858---------------------------- 
    5959 
    60 * **Author:**  
    61 * **Last Modified by:**  
    62 * **Last Reviewed by:**  
     60* **Author:** 
     61* **Last Modified by:** 
     62* **Last Reviewed by:** 
    6363* **Source added by :** Steve King **Date:** March 25, 2019 
    6464""" 

  • sasmodels/models/pringle.c

    r99658f6 ra34b811  
    111111 
    112112static double 
    113 effective_radius(int mode, double radius, double thickness, double alpha, double beta) 
     113radius_effective(int mode, double radius, double thickness, double alpha, double beta) 
    114114{ 
    115115    switch (mode) { 

  • sasmodels/models/pringle.py

    r0507e09 ra34b811  
    8585source = ["lib/polevl.c", "lib/sas_J0.c", "lib/sas_J1.c", 
    8686          "lib/sas_JN.c", "lib/gauss76.c", "pringle.c"] 
    87 effective_radius_type = [ 
     87radius_effective_modes = [ 
    8888    "equivalent cylinder excluded volume", 
    8989    "equivalent volume sphere", 

  • sasmodels/models/raspberry.c

    rd42dd4a ra34b811  
    1515 
    1616static double 
    17 effective_radius(int mode, double radius_lg, double radius_sm, double penetration) 
     17radius_effective(int mode, double radius_lg, double radius_sm, double penetration) 
    1818{ 
    1919    switch (mode) { 

  • sasmodels/models/raspberry.py

    r0507e09 ra34b811  
    161161 
    162162source = ["lib/sas_3j1x_x.c", "raspberry.c"] 
    163 effective_radius_type = ["radius_large", "radius_outer"] 
     163radius_effective_modes = ["radius_large", "radius_outer"] 
    164164 
    165165def random(): 

  • sasmodels/models/rectangular_prism.c

    r99658f6 ra34b811  
    1414 
    1515static double 
    16 effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
     16radius_effective(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
    1717{ 
    1818    switch (mode) { 

  • sasmodels/models/rectangular_prism.py

    r0507e09 ra34b811  
    110110---------------------------- 
    111111 
    112 * **Author:**  
    113 * **Last Modified by:**  
    114 * **Last Reviewed by:**  
     112* **Author:** 
     113* **Last Modified by:** 
     114* **Last Reviewed by:** 
    115115* **Source added by :** Steve King **Date:** March 25, 2019 
    116116""" 
    … …  
    151151source = ["lib/gauss76.c", "rectangular_prism.c"] 
    152152have_Fq = True 
    153 effective_radius_type = [ 
     153radius_effective_modes = [ 
    154154    "equivalent cylinder excluded volume", "equivalent volume sphere", 
    155155    "half length_a", "half length_b", "half length_c", 

  • sasmodels/models/sphere.c

    ree60aa7 ra34b811  
    55 
    66static double 
    7 effective_radius(int mode, double radius) 
     7radius_effective(int mode, double radius) 
    88{ 
    99    // case 1: radius 

  • sasmodels/models/sphere.py

    r6140894 ra34b811  
    8181source = ["lib/sas_3j1x_x.c", "sphere.c"] 
    8282have_Fq = True 
    83 effective_radius_type = ["radius"] 
     83radius_effective_modes = ["radius"] 
    8484 
    8585def random(): 
    … …  
    9999      0.2, 792.0646662454202, 1166737.0473152, 120.0, 7246723.820358589, 1.0], # the longer list here checks  F1, F2, R_eff, volume, volume_ratio = call_Fq(kernel, pars) 
    100100   #  But note P(Q) = F2/volume 
    101    #  F and F^2 are "unscaled", with for  n <F F*>S(q) or for beta approx I(q) = n [<F F*> + <F><F*> (S(q) - 1)]  
    102    #  for n the number density and <.> the orientation average, and F = integral rho(r) exp(i q . r) dr.   
    103    #  The number density is volume fraction divided by particle volume.   
     101   #  F and F^2 are "unscaled", with for  n <F F*>S(q) or for beta approx I(q) = n [<F F*> + <F><F*> (S(q) - 1)] 
     102   #  for n the number density and <.> the orientation average, and F = integral rho(r) exp(i q . r) dr. 
     103   #  The number density is volume fraction divided by particle volume. 
    104104   #  Effectively, this leaves F = V drho form, where form is the usual 3 j1(qr)/(qr) or whatever depending on the shape. 
    105105   # [{"@S": "hardsphere"}, 
    … …  
    124124     "structure_factor_mode": 1,  # 0 = normal decoupling approximation, 1 = beta(Q) approx 
    125125     "radius_effective_mode": 0   # this used r_eff =0 or default 50? 
    126      }, 0.01, 1324.7375636587356 ],    
     126     }, 0.01, 1324.7375636587356 ], 
    127127    [{"@S": "hardsphere", 
    128128     "radius": 120., "radius_pd": 0.2, "radius_pd_n":45, 
    … …  
    131131     "structure_factor_mode": 1,  # 0 = normal decoupling approximation, 1 = beta(Q) approx 
    132132     "radius_effective_mode": 1   # this used 120 ??? 
    133      }, 0.01, 1579.2858949296565 ]    
     133     }, 0.01, 1579.2858949296565 ] 
    134134] 
    135135# putting None for expected result will pass the test if there are no errors from the routine, but without any check on the value of the result 

  • sasmodels/models/spherical_sld.c

    ree60aa7 ra34b811  
    1919 
    2020static double 
    21 effective_radius(int mode, double fp_n_shells, double thickness[], double interface[]) 
     21radius_effective(int mode, double fp_n_shells, double thickness[], double interface[]) 
    2222{ 
    2323    // case 1: outer radius 

  • sasmodels/models/spherical_sld.py

    r0507e09 ra34b811  
    232232single = False  # TODO: fix low q behaviour 
    233233have_Fq = True 
    234 effective_radius_type = ["outer radius"] 
     234radius_effective_modes = ["outer radius"] 
    235235 
    236236profile_axes = ['Radius (A)', 'SLD (1e-6/A^2)'] 

  • sasmodels/models/triaxial_ellipsoid.c

    r99658f6 ra34b811  
    7676 
    7777static double 
    78 effective_radius(int mode, double radius_equat_minor, double radius_equat_major, double radius_polar) 
     78radius_effective(int mode, double radius_equat_minor, double radius_equat_major, double radius_polar) 
    7979{ 
    8080    switch (mode) { 

  • sasmodels/models/triaxial_ellipsoid.py

    r0507e09 ra34b811  
    164164source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "triaxial_ellipsoid.c"] 
    165165have_Fq = True 
    166 effective_radius_type = [ 
     166radius_effective_modes = [ 
    167167    "equivalent biaxial ellipsoid average curvature", 
    168168    "equivalent volume sphere", "min radius", "max radius", 

  • sasmodels/models/vesicle.c

    r12f4c19 ra34b811  
    1313 
    1414static double 
    15 effective_radius(int mode, double radius, double thickness) 
     15radius_effective(int mode, double radius, double thickness) 
    1616{ 
    1717    // case 1: outer radius 

  • sasmodels/models/vesicle.py

    r0507e09 ra34b811  
    107107source = ["lib/sas_3j1x_x.c", "vesicle.c"] 
    108108have_Fq = True 
    109 effective_radius_type = ["outer radius"] 
     109radius_effective_modes = ["outer radius"] 
    110110 
    111111def random(): 

  • sasmodels/product.py

    rd8e81f7 ra34b811  
    3131# pylint: enable=unused-import 
    3232 
    33 # TODO: make estimates available to constraints 
     33# TODO: make shape averages available to constraints 
    3434#ESTIMATED_PARAMETERS = [ 
    35 #    ["est_radius_effective", "A", 0.0, [0, np.inf], "", "Estimated effective radius"], 
    36 #    ["est_volume_ratio", "", 1.0, [0, np.inf], "", "Estimated volume ratio"], 
     35#    ["mean_radius_effective", "A", 0.0, [0, np.inf], "", "mean effective radius"], 
     36#    ["mean_volume", "A", 0.0, [0, np.inf], "", "mean volume"], 
     37#    ["mean_volume_ratio", "", 1.0, [0, np.inf], "", "mean form: mean shell volume ratio"], 
    3738#] 
    38 # NOTE there are radius_effective_mode, effective_radius_type, but only structure_factor_mode 
    3939STRUCTURE_MODE_ID = "structure_factor_mode" 
    4040RADIUS_MODE_ID = "radius_effective_mode" 
    … …  
    4444    # type: (ModelInfo) -> List[Parameter] 
    4545    """ 
    46     Create parameters for structure_factor_type and radius_effective_type. 
     46    Create parameters for structure factor and effective radius modes. 
    4747    """ 
    4848    pars = [] 
    … …  
    5656            "Structure factor calculation") 
    5757        pars.append(par) 
    58     if p_info.effective_radius_type is not None: 
     58    if p_info.radius_effective_modes is not None: 
    5959        par = parse_parameter( 
    6060            RADIUS_MODE_ID, 
    6161            "", 
    6262            1, 
    63             [["unconstrained"] + p_info.effective_radius_type], 
     63            [["unconstrained"] + p_info.radius_effective_modes], 
    6464            "", 
    6565            "Effective radius calculation") 
    … …  
    177177        S,                # type: np.ndarray 
    178178        scale,            # type: float 
    179         effective_radius, # type: float 
     179        radius_effective, # type: float 
    180180        beta_mode,        # type: bool 
    181181    ): 
    … …  
    193193            ("beta(Q)", F1**2 / F2), 
    194194            ("S_eff(Q)", 1 + (F1**2 / F2)*(S-1)), 
    195             ("effective_radius", effective_radius), 
     195            ("effective_radius", radius_effective), 
    196196            # ("I(Q)", scale*(F2 + (F1**2)*(S-1)) + bg), 
    197197        )) 
    … …  
    200200            ("P(Q)", scale*F2), 
    201201            ("S(Q)", S), 
    202             ("effective_radius", effective_radius), 
     202            ("effective_radius", radius_effective), 
    203203        )) 
    204204    return parts 
    … …  
    281281        # R_eff type parameter is the second parameter after P and S parameters 
    282282        # unless the model doesn't support beta mode, in which case it is first 
    283         have_radius_type = p_info.effective_radius_type is not None 
     283        have_radius_type = p_info.radius_effective_modes is not None 
    284284        #print(p_npars,s_npars) 
    285285        radius_type_offset = 2+p_npars+s_npars + (1 if have_beta_mode else 0) 
    … …  
    333333        # Call the form factor kernel to compute <F> and <F^2>. 
    334334        # If the model doesn't support Fq the returned <F> will be None. 
    335         F1, F2, effective_radius, shell_volume, volume_ratio = self.p_kernel.Fq( 
     335        F1, F2, radius_effective, shell_volume, volume_ratio = self.p_kernel.Fq( 
    336336            p_details, p_values, cutoff, magnetic, radius_type) 
    337337 
    … …  
    343343        # implementation details in kernel_iq.c. 
    344344        print("R_eff=%d:%g, volfrac=%g, volume ratio=%g" 
    345               % (radius_type, effective_radius, volfrac, volume_ratio)) 
     345              % (radius_type, radius_effective, volfrac, volume_ratio)) 
    346346        if radius_type > 0: 
    347347            # set the value to the model R_eff and set the weight to 1 
    348             s_values[2] = s_values[2+s_npars+s_offset[0]] = effective_radius 
     348            s_values[2] = s_values[2+s_npars+s_offset[0]] = radius_effective 
    349349            s_values[2+s_npars+s_offset[0]+nweights] = 1.0 
    350350        s_values[3] = s_values[2+s_npars+s_offset[1]] = volfrac*volume_ratio 
    … …  
    372372        # the results directly rather than through a lazy evaluator. 
    373373        self.results = lambda: _intermediates( 
    374             F1, F2, S, combined_scale, effective_radius, beta_mode) 
     374            F1, F2, S, combined_scale, radius_effective, beta_mode) 
    375375 
    376376        return final_result 

  • sasmodels/sasview_model.py

    rb297ba9 ra34b811  
    299299    attrs['category'] = model_info.category 
    300300    attrs['is_structure_factor'] = model_info.structure_factor 
    301     attrs['is_form_factor'] = model_info.effective_radius_type is not None 
     301    attrs['is_form_factor'] = model_info.radius_effective_modes is not None 
    302302    attrs['is_multiplicity_model'] = variants[0] > 1 
    303303    attrs['multiplicity_info'] = variants 
    … …  
    763763        #    if er_mode > 0: 
    764764        #        res = calculator.Fq(call_details, values, cutoff=self.cutoff, 
    765         #                            magnetic=False, effective_radius_type=mode) 
     765        #                            magnetic=False, radius_effective_mode=mode) 
    766766        #        R_eff, form_shell_ratio = res[2], res[4] 
    767767        #        return R_eff, form_shell_ratio 
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