Changeset 2ead7e2 in sasmodels for sasmodels

Timestamp:

Sep 5, 2017 10:08:03 AM (7 years ago)

Author:

GitHub <noreply@…>

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

142a8e2

Parents:

573ffab (diff), 133103b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Paul Butler <butlerpd@…> (09/05/17 10:08:03)

git-committer:

GitHub <noreply@…> (09/05/17 10:08:03)

Message:

Merge pull request #47 from rprospero/sesans_tof

Sesans tof

Location:

sasmodels

Files:

• sesans.py (modified) (3 diffs)
• alignment.py (modified) (1 diff)
• core.py (modified) (3 diffs)
• generate.py (modified) (2 diffs)
• model_test.py (modified) (4 diffs)
• models/multilayer_vesicle.py (modified) (1 diff)
• models/star_polymer.py (modified) (5 diffs)
• resolution.py (modified) (3 diffs)
• rst2html.py (modified) (4 diffs)

sasmodels/sesans.py

@@ -41 +41 @@
     _H0 = None # type: np.ndarray
 
-    def __init__(self, z, SElength, zaccept, Rmax):
+    def __init__(self, z, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         #import logging; logging.info("creating SESANS transform")
         self.q = z
-        self._set_hankel(SElength, zaccept, Rmax)
+        self._set_hankel(SElength, lam, zaccept, Rmax)
 
     def apply(self, Iq):
@@ -54 +54 @@
         return P
 
-    def _set_hankel(self, SElength, zaccept, Rmax):
+    def _set_hankel(self, SElength, lam, zaccept, Rmax):
         # type: (np.ndarray, float, float) -> None
         # Force float32 arrays, otherwise run into memory problems on some machines
@@ -71 +71 @@
         H = np.float32(dq/(2*pi)) * j0(repSE*repq) * repq
 
+        replam = np.tile(lam, (q.size, 1))
+        reptheta = np.arcsin(repq*replam/2*np.pi)
+        mask = reptheta > zaccept
+        H[mask] = 0
+
         self.q_calc = q
         self._H, self._H0 = H, H0

sasmodels/alignment.py

@@ -42 +42 @@
     view[:] = x
     return view
-

sasmodels/core.py

@@ -117 +117 @@
     Load model info and build model.
 
-    *model_name* is the name of the model as used by :func:`load_model_info`.
-    Additional keyword arguments are passed directly to :func:`build_model`.
+    *model_name* is the name of the model, or perhaps a model expression
+    such as sphere*hardsphere or sphere+cylinder.
+
+    *dtype* and *platform* are given by :func:`build_model`.
     """
     return build_model(load_model_info(model_name),
@@ -128 +130 @@
     """
     Load a model definition given the model name.
+
+    *model_name* is the name of the model, or perhaps a model expression
+    such as sphere*hardsphere or sphere+cylinder.
 
     This returns a handle to the module defining the model.  This can be
@@ -227 +232 @@
 
     Possible types include 'half', 'single', 'double' and 'quad'.  If the
-    type is 'fast', then this is equivalent to dtype 'single' with the
-    fast flag set to True.
+    type is 'fast', then this is equivalent to dtype 'single' but using
+    fast native functions rather than those with the precision level guaranteed
+    by the OpenCL standard.
+
+    Platform preference can be specfied ("ocl" vs "dll"), with the default
+    being OpenCL if it is availabe.  If the dtype name ends with '!' then
+    platform is forced to be DLL rather than OpenCL.
+
+    This routine ignores the preferences within the model definition.  This
+    is by design.  It allows us to test models in single precision even when
+    we have flagged them as requiring double precision so we can easily check
+    the performance on different platforms without having to change the model
+    definition.
     """
     # Assign default platform, overriding ocl with dll if OpenCL is unavailable

sasmodels/generate.py

@@ -210 +210 @@
 
 # Conversion from units defined in the parameter table for each model
-# to units displayed in the sphinx documentation.
+# to units displayed in the sphinx documentation. 
+# This section associates the unit with the macro to use to produce the LaTex
+# code.  The macro itself needs to be defined in sasmodels/doc/rst_prolog.
+#
+# NOTE: there is an RST_PROLOG at the end of this file which is NOT
+# used for the bundled documentation. Still as long as we are defining the macros
+# in two places any new addition should define the macro in both places. 
 RST_UNITS = {
     "Ang": "|Ang|",
@@ -216 +222 @@
     "1/Ang^2": "|Ang^-2|",
     "Ang^3": "|Ang^3|",
+    "Ang^2": "|Ang^2|",
     "1e15/cm^3": "|1e15cm^3|",
     "Ang^3/mol": "|Ang^3|/mol",

sasmodels/model_test.py

@@ -47 +47 @@
 import sys
 import unittest
+
+try:
+    from StringIO import StringIO
+except ImportError:
+    # StringIO.StringIO renamed to io.StringIO in Python 3
+    # Note: io.StringIO exists in python 2, but using unicode instead of str
+    from io import StringIO
 
 import numpy as np  # type: ignore
@@ -337 +344 @@
 
 def run_one(model):
-    # type: (str) -> None
+    # type: (str) -> str
     """
     Run the tests for a single model, printing the results to stdout.
@@ -350 +357 @@
 
     # Build a object to capture and print the test results
-    stream = _WritelnDecorator(sys.stdout)  # Add writeln() method to stream
+    stream = _WritelnDecorator(StringIO())  # Add writeln() method to stream
     verbosity = 2
     descriptions = True
@@ -388 +395 @@
     else:
         stream.writeln("Note: no test suite created --- this should never happen")
+
+    output = stream.getvalue()
+    stream.close()
+    return output
 
 

sasmodels/models/multilayer_vesicle.py

@@ -71 +71 @@
   sufficiently fine grained in certain cases. Please report any such occurences
   to the SasView team. Generally, for the best possible experience:
- * Start with the best possible guess
- * Using a priori knowledge, hold as many parameters fixed as possible
- * if N=1, tw (water thickness) must by definition be zero. Both N and tw should
+
+ - Start with the best possible guess
+ - Using a priori knowledge, hold as many parameters fixed as possible
+ - if N=1, tw (water thickness) must by definition be zero. Both N and tw should
    be fixed during fitting.
- * If N>1, use constraints to keep N > 1
- * Because N only really moves in integer steps, it may get "stuck" if the
+ - If N>1, use constraints to keep N > 1
+ - Because N only really moves in integer steps, it may get "stuck" if the
    optimizer step size is too small so care should be taken
    If you experience problems with this please contact the SasView team and let

sasmodels/models/star_polymer.py

@@ -1 +1 @@
 r"""
-The Benoit model for a simple star polymer, with Gaussian coils arms from
-a common point.
-
 Definition
 ----------
+
+Calcuates the scattering from a simple star polymer with f equal Gaussian coil
+arms. A star being defined as a branched polymer with all the branches
+emanating from a common central (in the case of this model) point.  It is
+derived as a special case of on the Benoit model for general branched
+polymers\ [#CITBenoit]_ as also used by Richter ''et. al.''\ [#CITRichter]_
 
 For a star with $f$ arms the scattering intensity $I(q)$ is calculated as
@@ -15 +18 @@
 where
 
-.. math:: v=\frac{u^2f}{(3f-2)}
+.. math:: v=\frac{uf}{(3f-2)}
 
 and
@@ -21 +24 @@
 .. math:: u = \left\langle R_{g}^2\right\rangle q^2
 
-contains the square of the ensemble average radius-of-gyration of an arm.
+contains the square of the ensemble average radius-of-gyration of the full
+polymer while v contains the radius of gyration of a single arm $R_{arm}$.
+The two are related as:
+
+.. math:: R_{arm}^2 = \frac{f}{3f-2} R_{g}^2
+
 Note that when there is only one arm, $f = 1$, the Debye Gaussian coil
-equation is recovered. Star polymers in solutions tend to have strong
-interparticle and osmotic effects, so the Benoit equation may not work well.
-At small $q$ the Guinier term and hence $I(q=0)$ is the same as for $f$ arms
-of radius of gyration $R_g$, as described for the :ref:`mono-gauss-coil` model.
+equation is recovered.
+
+.. note::
+   Star polymers in solutions tend to have strong interparticle and osmotic
+   effects. Thus the Benoit equation may not work well for many real cases.
+   At small $q$ the Guinier term and hence $I(q=0)$ is the same as for $f$ arms
+   of radius of gyration $R_g$, as described for the :ref:`mono-gauss-coil`
+   model. A newer model for star polymer incorporating excluded volume has been
+   developed by Li et al in arXiv:1404.6269 [physics.chem-ph].
 
 References
 ----------
 
-H Benoit *J. Polymer Science*, 11, 596-599 (1953)
+.. [#CITBenoit] H Benoit *J. Polymer Science*, 11, 507-510 (1953)
+.. [#CITRichter] D Richter, B. Farago, J. S. Huang, L. J. Fetters,
+   B Ewen *Macromolecules*, 22, 468-472 (1989)
+
+Authorship and Verification
+----------------------------
+
+* **Author:** Kieran Campbell **Date:** July 24, 2012
+* **Last Modified by:** Paul Butler **Date:** Auguts 26, 2017
+* **Last Reviewed by:** Ziang Li and Richard Heenan **Date:** May 17, 2017
 """
 
@@ -45 +67 @@
         - v = u^2f/(3f-2)
         - u = <R_g^2>q^2, where <R_g^2> is the ensemble average radius of
-        gyration squared of an arm
+        gyration squared of the entire polymer
         - f is the number of arms on the star
+        - the radius of gyration of an arm is given b
+        Rg_arm^2 = R_g^2 * f/(3f-2)
         """
 category = "shape-independent"
@@ -52 +76 @@
 # pylint: disable=bad-whitespace, line-too-long
 #             ["name", "units", default, [lower, upper], "type","description"],
-parameters = [["rg_squared", "Ang^2", 100.0, [0.0, inf], "", "Ensemble radius of gyration SQUARED of an arm"],
+parameters = [["rg_squared", "Ang^2", 100.0, [0.0, inf], "", "Ensemble radius of gyration SQUARED of the full polymer"],
               ["arms",    "",      3,   [1.0, 6.0], "", "Number of arms in the model"],
              ]

sasmodels/resolution.py

@@ -437 +437 @@
     .. math::
 
-         \log \Delta q = (\log q_n - log q_1) / (n - 1)
+         \log \Delta q = (\log q_n - \log q_1) / (n - 1)
 
     From this we can compute the number of steps required to extend $q$
@@ -451 +451 @@
 
          n_\text{extend} = (n-1) (\log q_\text{max} - \log q_n)
-            / (\log q_n - log q_1)
+            / (\log q_n - \log q_1)
     """
     q = np.sort(q)
@@ -459 +459 @@
         log_delta_q = log(10.) / points_per_decade
     if q_min < q[0]:
-        if q_min < 0: q_min = q[0]*MINIMUM_ABSOLUTE_Q
+        if q_min < 0:
+            q_min = q[0]*MINIMUM_ABSOLUTE_Q
         n_low = log_delta_q * (log(q[0])-log(q_min))
         q_low = np.logspace(log10(q_min), log10(q[0]), np.ceil(n_low)+1)[:-1]

sasmodels/rst2html.py

@@ -38 +38 @@
     - mathml
     - mathjax
-    See `http://docutils.sourceforge.net/docs/user/config.html#math-output`_
+    See `<http://docutils.sourceforge.net/docs/user/config.html#math-output>`_
     for details.
 
@@ -176 +176 @@
         from PyQt5.QtCore import QUrl
     except ImportError:
-        from PyQt4.QtWebkit import QWebView
+        from PyQt4.QtWebKit import QWebView
         from PyQt4.QtCore import QUrl
     helpView = QWebView()
@@ -204 +204 @@
         from PyQt5.QtCore import QUrl
     except ImportError:
-        from PyQt4.QtWebkit import QWebView
+        from PyQt4.QtWebKit import QWebView
         from PyQt4.QtCore import QUrl
     frame = QWebView()
@@ -211 +211 @@
     sys.exit(app.exec_())
 
+def can_use_qt():
+    """
+    Return True if QWebView exists.
+
+    Checks first in PyQt5 then in PyQt4
+    """
+    try:
+        from PyQt5.QtWebKitWidgets import QWebView
+        return True
+    except ImportError:
+        try:
+            from PyQt4.QtWebKit import QWebView
+            return True
+        except ImportError:
+            return False
+
 def view_help(filename, qt=False):
     import os
-    url="file:///"+os.path.abspath(filename).replace("\\","/")
+
+    if qt:
+        qt = can_use_qt()
+
+    url = "file:///"+os.path.abspath(filename).replace("\\", "/")
     if filename.endswith('.rst'):
         html = load_rst_as_html(filename)