Changeset 1896dff in sasmodels

Timestamp:

Feb 28, 2017 7:31:56 AM (7 years ago)

Author:

wojciech

Branches:

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

Children:

ae32bb8

Parents:

faf83f2 (diff), a3002be (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.

Message:

Merge branch 'master' of ​https://github.com/SasView/sasmodels

Files:

• sasmodels/models/ellipsoid.c (modified) (4 diffs)
• sasmodels/models/hayter_msa.c (modified) (1 diff)
• sasmodels/sasview_model.py (modified) (8 diffs)
• doc/ref/gpu/gpu_computations.rst (modified) (2 diffs)

sasmodels/models/ellipsoid.c

@@ -4 +4 @@
     double radius_polar, double radius_equatorial, double theta, double phi);
 
-double _ellipsoid_kernel(double q, double radius_polar, double radius_equatorial, double sin_alpha);
-double _ellipsoid_kernel(double q, double radius_polar, double radius_equatorial, double sin_alpha)
+static double
+_ellipsoid_kernel(double q, double radius_polar, double radius_equatorial, double cos_alpha)
 {
     double ratio = radius_polar/radius_equatorial;
-    // Given the following under the radical:
-    //     1 + sin^2(T) (v^2 - 1)
-    // we can expand to match the form given in Guinier (1955)
-    //     = (1 - sin^2(T)) + v^2 sin^2(T) = cos^2(T) + sin^2(T)
+    // Using ratio v = Rp/Re, we can expand the following to match the
+    // form given in Guinier (1955)
+    //     r = Re * sqrt(1 + cos^2(T) (v^2 - 1))
+    //       = Re * sqrt( (1 - cos^2(T)) + v^2 cos^2(T) )
+    //       = Re * sqrt( sin^2(T) + v^2 cos^2(T) )
+    //       = sqrt( Re^2 sin^2(T) + Rp^2 cos^2(T) )
+    //
     // Instead of using pythagoras we could pass in sin and cos; this may be
     // slightly better for 2D which has already computed it, but it introduces
@@ -17 +20 @@
     // leave it as is.
     const double r = radius_equatorial
-                     * sqrt(1.0 + sin_alpha*sin_alpha*(ratio*ratio - 1.0));
+                     * sqrt(1.0 + cos_alpha*cos_alpha*(ratio*ratio - 1.0));
     const double f = sas_3j1x_x(q*r);
 
@@ -39 +42 @@
     double total = 0.0;
     for (int i=0;i<76;i++) {
-        //const double sin_alpha = (Gauss76Z[i]*(upper-lower) + upper + lower)/2;
-        const double sin_alpha = Gauss76Z[i]*zm + zb;
-        total += Gauss76Wt[i] * _ellipsoid_kernel(q, radius_polar, radius_equatorial, sin_alpha);
+        //const double cos_alpha = (Gauss76Z[i]*(upper-lower) + upper + lower)/2;
+        const double cos_alpha = Gauss76Z[i]*zm + zb;
+        total += Gauss76Wt[i] * _ellipsoid_kernel(q, radius_polar, radius_equatorial, cos_alpha);
     }
     // translate dx in [-1,1] to dx in [lower,upper]
@@ -59 +62 @@
     double q, sin_alpha, cos_alpha;
     ORIENT_SYMMETRIC(qx, qy, theta, phi, q, sin_alpha, cos_alpha);
-    const double form = _ellipsoid_kernel(q, radius_polar, radius_equatorial, sin_alpha);
+    const double form = _ellipsoid_kernel(q, radius_polar, radius_equatorial, cos_alpha);
     const double s = (sld - sld_solvent) * form_volume(radius_polar, radius_equatorial);
 

sasmodels/models/hayter_msa.c

@@ -70 +70 @@
                 SofQ=sqhcal(Qdiam, gMSAWave);
         }else{
-        //SofQ=NaN;
-                SofQ=-1.0;
+        SofQ=NAN;
                 //      print "Error Level = ",ierr
                 //      print "Please report HPMSA problem with above error code"

sasmodels/sasview_model.py

@@ -16 +16 @@
 import logging
 from os.path import basename, splitext
+import thread
 
 import numpy as np  # type: ignore
@@ -38 +39 @@
 except ImportError:
     pass
+
+calculation_lock = thread.allocate_lock()
 
 SUPPORT_OLD_STYLE_PLUGINS = True
@@ -605 +608 @@
         to the card for each evaluation.
         """
+        ## uncomment the following when trying to debug the uncoordinated calls
+        ## to calculate_Iq
+        #if calculation_lock.locked():
+        #    logging.info("calculation waiting for another thread to complete")
+        #    logging.info("\n".join(traceback.format_stack()))
+
+        with calculation_lock:
+            return self._calculate_Iq(qx, qy)
+
+    def _calculate_Iq(self, qx, qy=None):
         #core.HAVE_OPENCL = False
         if self._model is None:
@@ -721 +734 @@
             return [self.params[par.name]], [1.0]
 
-def test_model():
+def test_cylinder():
     # type: () -> float
     """
-    Test that a sasview model (cylinder) can be run.
+    Test that the cylinder model runs, returning the value at [0.1,0.1].
     """
     Cylinder = _make_standard_model('cylinder')
@@ -733 +746 @@
     # type: () -> float
     """
-    Test that a sasview model (cylinder) can be run.
+    Test that 2-D hardsphere model runs and doesn't produce NaN.
     """
     Model = _make_standard_model('hardsphere')
@@ -744 +757 @@
     # type: () -> float
     """
-    Test that a sasview model (cylinder) can be run.
+    Test that the 2-D RPA model runs
     """
     RPA = _make_standard_model('rpa')
@@ -750 +763 @@
     return rpa.evalDistribution([0.1, 0.1])
 
+def test_empty_distribution():
+    # type: () -> None
+    """
+    Make sure that sasmodels returns NaN when there are no polydispersity points
+    """
+    Cylinder = _make_standard_model('cylinder')
+    cylinder = Cylinder()
+    cylinder.setParam('radius', -1.0)
+    cylinder.setParam('background', 0.)
+    Iq = cylinder.evalDistribution(np.asarray([0.1]))
+    assert np.isnan(Iq[0]), "empty distribution fails"
 
 def test_model_list():
     # type: () -> None
     """
-    Make sure that all models build as sasview models.
+    Make sure that all models build as sasview models
     """
     from .exception import annotate_exception
@@ -781 +805 @@
 
 if __name__ == "__main__":
-    print("cylinder(0.1,0.1)=%g"%test_model())
+    print("cylinder(0.1,0.1)=%g"%test_cylinder())
+    #test_empty_distribution()

doc/ref/gpu/gpu_computations.rst

@@ -31 +31 @@
 from available OpenCL platforms.
 
+OpenCL devices can be set from OpenCL options dialog in Fitting menu or as
+enviromental variables.
+
+**If you don't want to use OpenCL, you can select "No OpenCL" option from**
+**GUI dialog or set *SAS_OPENCL=None* in your environment settings**
+**This will only use normal programs.**
+
 SasView prefers AMD or NVIDIA drivers for GPU, and prefers Intel or
 Apple drivers for CPU. Both GPU and CPU are included on the assumption that CPU 
@@ -39 +46 @@
 chose to run the model.
 
-**If you don't want to use OpenCL, you can set** *SAS_OPENCL=None*
-**in your environment settings, and it will only use normal programs.**
-
-If you want to use one of the other devices, you can run the following
-from the python console in SasView::
+If you want to use one of the other devices, you can select it from OpenCL
+options dialog (accessible from Fitting menu) or run the following from
+the python console in SasView::
 
     import pyopencl as cl