Changeset 8632a35 in sasmodels

Timestamp:

Feb 19, 2015 10:53:28 AM (10 years ago)

Author:

jhbakker

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

16bc3fc, 33d38d5

Parents:

9c117a2 (diff), c9801b8 (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:

• .gitignore (modified) (1 diff)
• sasmodels/bumps_model.py (modified) (1 diff)
• sasmodels/direct_model.py (added)
• sasmodels/generate.py (modified) (2 diffs)
• sasmodels/kernelcl.py (modified) (1 diff)
• sasmodels/kerneldll.py (modified) (1 diff)
• sasmodels/models/bcc.py (modified) (1 diff)
• sasmodels/models/broad_peak.py (added)
• sasmodels/models/fcc.c (modified) (6 diffs)
• sasmodels/models/fcc.py (modified) (9 diffs)
• sasmodels/models/hardsphere.py (added)
• sasmodels/models/img/hardSphere_223.PNG (added)
• sasmodels/models/img/hardSphere_224.jpg (added)
• sasmodels/models/img/lamellarCailleHG_139.PNG (added)
• sasmodels/models/img/lamellarCailleHG_140.PNG (added)
• sasmodels/models/img/lamellarCailleHG_141.jpg (added)
• sasmodels/models/img/lamellarCailleHG_143.jpg (added)
• sasmodels/models/img/lamellarCaille_134.jpg (added)
• sasmodels/models/img/lamellarCaille_139.PNG (added)
• sasmodels/models/img/lamellarCaille_140.PNG (added)
• sasmodels/models/img/lamellarCaille_142 .jpg (added)
• sasmodels/models/img/lamellarFFHG_137.jpg (added)
• sasmodels/models/img/lamellarFFHG_138.jpg (added)
• sasmodels/models/img/lamellarPC_146.jpg (added)
• sasmodels/models/img/lamellarPC_147.jpg (added)
• sasmodels/models/img/lamellarPC_45.jpg (added)
• sasmodels/models/lamellarCaille.py (added)
• sasmodels/models/lamellarCailleHG.py (added)
• sasmodels/models/lamellarCailleHG_kernel.c (added)
• sasmodels/models/lamellarCaille_kernel.c (added)
• sasmodels/models/lamellarFFHG.py (added)
• sasmodels/models/lamellarPC.py (added)
• sasmodels/models/lamellarPC_kernel.c (added)
• setup.py (added)
• example/sesansfit.py (modified) (4 diffs)

.gitignore

@@ -1 +1 @@
 /build/
 /dist/
+/*.csv
 *.pyc
 *.cl

sasmodels/bumps_model.py

@@ -17 +17 @@
 try:
     from .kernelcl import load_model as _loader
-except ImportError,exc:
+except RuntimeError,exc:
     import warnings
     warnings.warn(str(exc))

sasmodels/generate.py

@@ -731 +731 @@
     info['limits'] = dict((p[0],p[3]) for p in info['parameters'])
     info['partype'] = categorize_parameters(info['parameters'])
+    info['defaults'] = dict((p[0],p[2]) for p in info['parameters'])
 
     source = make_model(info)
@@ -757 +758 @@
     print "time:",toc()
 
-def demo():
-    from .models import cylinder
-    source, info = make(cylinder)
-    #print doc(cylinder)
-    print source
+def main():
+    if len(sys.argv) <= 1:
+        print "usage: python -m sasmodels.generate modelname"
+    else:
+        name = sys.argv[1]
+        import sasmodels.models
+        __import__('sasmodels.models.'+name)
+        model = getattr(sasmodels.models, name)
+        source, info = make(model); print source
+        #print doc(model)
 
 if __name__ == "__main__":
-    demo()
+    main()

sasmodels/kernelcl.py

@@ -30 +30 @@
 try:
     import pyopencl as cl
-except RuntimeError,exc:
+except ImportError,exc:
     warnings.warn(str(exc))
     raise RuntimeError("OpenCL not available")
+
+try:
+    context = cl.create_some_context(interactive=False)
+    del context
+except cl.RuntimeError, exc:
+    warnings.warn(str(exc))
+    raise RuntimeError("OpenCl not available")
 
 from pyopencl import mem_flags as mf

sasmodels/kerneldll.py

@@ -24 +24 @@
     #COMPILE = "cl /nologo /Ox /MD /W3 /GS- /DNDEBUG /Tp%(source)s /link /DLL /INCREMENTAL:NO /MANIFEST /OUT:%(output)s"
     #COMPILE = "cl /nologo /Ox /MD /W3 /GS- /DNDEBUG /Tp%(source)s /openmp /link /DLL /INCREMENTAL:NO /MANIFEST /OUT:%(output)s"
-    COMPILE = "gcc -shared -fPIC -std=c99 -fopenmp -O2 -Wall %(source)s -o %(output)s -lm"
+    #COMPILE = "gcc -shared -fPIC -std=c99 -fopenmp -O2 -Wall %(source)s -o %(output)s -lm"
+    COMPILE = "gcc -shared -fPIC -std=c99 -O2 -Wall %(source)s -o %(output)s -lm"
 else:
     COMPILE = "cc -shared -fPIC -std=c99 -fopenmp -O2 -Wall %(source)s -o %(output)s -lm"

sasmodels/models/bcc.py

@@ -80 +80 @@
 from numpy import pi, inf
 
-name = "BCCparacrystal"
+name = "bcc_paracrystal"
 title = "Body-centred cubic lattic with paracrystalline distortion"
 description = """

sasmodels/models/fcc.c

@@ -5 +5 @@
     double theta, double phi, double psi);
 
-double _BCC_Integrand(double q, double dnn, double d_factor, double theta, double phi);
-double _BCCeval(double Theta, double Phi, double temp1, double temp3);
+double _FCC_Integrand(double q, double dnn, double d_factor, double theta, double phi);
+double _FCCeval(double Theta, double Phi, double temp1, double temp3);
 double _sphereform(double q, double radius, double sld, double solvent_sld);
 
 
-double _BCC_Integrand(double q, double dnn, double d_factor, double theta, double phi) {
+double _FCC_Integrand(double q, double dnn, double d_factor, double theta, double phi) {
 
         const double Da = d_factor*dnn;
@@ -16 +16 @@
         const double temp3 = q*dnn;
 
-        double retVal = _BCCeval(theta,phi,temp1,temp3)/(4.0*M_PI);
+        double retVal = _FCCeval(theta,phi,temp1,temp3)/(4.0*M_PI);
         return(retVal);
 }
 
-double _BCCeval(double Theta, double Phi, double temp1, double temp3) {
+double _FCCeval(double Theta, double Phi, double temp1, double temp3) {
 
         double temp6,temp7,temp8,temp9,temp10;
@@ -26 +26 @@
 
         temp6 = sin(Theta);
-        temp7 = sin(Theta)*cos(Phi)+sin(Theta)*sin(Phi)+cos(Theta);
-        temp8 = -1.0*sin(Theta)*cos(Phi)-sin(Theta)*sin(Phi)+cos(Theta);
-        temp9 = -1.0*sin(Theta)*cos(Phi)+sin(Theta)*sin(Phi)-cos(Theta);
+        temp7 = sin(Theta)*sin(Phi)+cos(Theta);
+        temp8 = -1.0*sin(Theta)*cos(Phi)+cos(Theta);
+        temp9 = -1.0*sin(Theta)*cos(Phi)+sin(Theta)*sin(Phi);
         temp10 = exp((-1.0/8.0)*temp1*((temp7*temp7)+(temp8*temp8)+(temp9*temp9)));
-        result = pow(1.0-(temp10*temp10),3)*temp6/((1.0-2.0*temp10*cos(0.5*temp3*(temp7))+(temp10*temp10))*(1.0-2.0*temp10*cos(0.5*temp3*(temp8))+(temp10*temp10))*(1.0-2.0*temp10*cos(0.5*temp3*(temp9))+(temp10*temp10)));
+        result = pow((1.0-(temp10*temp10)),3)*temp6/((1.0-2.0*temp10*cos(0.5*temp3*(temp7))+(temp10*temp10))*(1.0-2.0*temp10*cos(0.5*temp3*(temp8))+(temp10*temp10))*(1.0-2.0*temp10*cos(0.5*temp3*(temp9))+(temp10*temp10)));
 
         return (result);
@@ -54 +54 @@
 
         //Volume fraction calculated from lattice symmetry and sphere radius
-        const double s1 = dnn/sqrt(0.75);
-        const double latticescale = 2.0*(4.0/3.0)*M_PI*(radius*radius*radius)/(s1*s1*s1);
+        const double s1 = dnn*sqrt(2.0);
+        const double latticescale = 4.0*(4.0/3.0)*M_PI*(radius*radius*radius)/(s1*s1*s1);
 
     const double va = 0.0;
@@ -71 +71 @@
                         //20 gauss points for the inner integral
                         double ztheta = ( Gauss150Z[j]*(vbj-vaj) + vaj + vbj )/2.0;             //the inner dummy is theta
-                        double yyy = Gauss150Wt[j] * _BCC_Integrand(q,dnn,d_factor,ztheta,zphi);
+                        double yyy = Gauss150Wt[j] * _FCC_Integrand(q,dnn,d_factor,ztheta,zphi);
                         summj += yyy;
                 }
@@ -140 +140 @@
     // The following test should always pass
     if (fabs(cos_val_b3)>1.0) {
-      //printf("bcc_ana_2D: Unexpected error: cos()>1\n");
+      //printf("FCC_ana_2D: Unexpected error: cos()>1\n");
       cos_val_b3 = 1.0;
     }
     if (fabs(cos_val_b2)>1.0) {
-      //printf("bcc_ana_2D: Unexpected error: cos()>1\n");
+      //printf("FCC_ana_2D: Unexpected error: cos()>1\n");
       cos_val_b2 = 1.0;
     }
     if (fabs(cos_val_b1)>1.0) {
-      //printf("bcc_ana_2D: Unexpected error: cos()>1\n");
+      //printf("FCC_ana_2D: Unexpected error: cos()>1\n");
       cos_val_b1 = 1.0;
     }

sasmodels/models/fcc.py

@@ -1 @@
-#bcc paracrystal model
+#fcc paracrystal model
 #note model title and parameter table are automatically inserted
 #note - calculation requires double precision
-"""
-Calculates the scattering from a **body-centered cubic lattice** with paracrystalline distortion. Thermal vibrations
+r"""
+Calculates the scattering from a **face-centered cubic lattice** with paracrystalline distortion. Thermal vibrations
 are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is
 assumed to be isotropic and characterized by a Gaussian distribution.
@@ -14 +14 @@
 The scattering intensity *I(q)* is calculated as
 
-.. image:: img/image167.jpg
+.. image:: img/image158.jpg
 
 where *scale* is the volume fraction of spheres, *Vp* is the volume of the primary particle, *V(lattice)* is a volume
 correction for the crystal structure, *P(q)* is the form factor of the sphere (normalized), and *Z(q)* is the
-paracrystalline structure factor for a body-centered cubic structure.
+paracrystalline structure factor for a face-centered cubic structure.
 
-Equation (1) of the 1990 reference is used to calculate *Z(q)*, using equations (29)-(31) from the 1987 paper for
+Equation (1) of the 1990 reference is used to calculate *Z(q)*, using equations (23)-(25) from the 1987 paper for
 *Z1*\ , *Z2*\ , and *Z3*\ .
 
-The lattice correction (the occupied volume of the lattice) for a body-centered cubic structure of particles of radius
+The lattice correction (the occupied volume of the lattice) for a face-centered cubic structure of particles of radius
 *R* and nearest neighbor separation *D* is
 
@@ -34 +34 @@
 where *g* is a fractional distortion based on the nearest neighbor distance.
 
-The body-centered cubic lattice is
+The face-centered cubic lattice is
 
-.. image:: img/image168.jpg
+.. image:: img/image161.jpg
 
 For a crystal, diffraction peaks appear at reduced q-values given by
@@ -42 +42 @@
 .. image:: img/image162.jpg
 
-where for a body-centered cubic lattice, only reflections where (\ *h* + *k* + *l*\ ) = even are allowed and
-reflections where (\ *h* + *k* + *l*\ ) = odd are forbidden. Thus the peak positions correspond to (just the first 5)
+where for a face-centered cubic lattice *h*\ , *k*\ , *l* all odd or all even are allowed and reflections where
+*h*\ , *k*\ , *l* are mixed odd/even are forbidden. Thus the peak positions correspond to (just the first 5)
 
-.. image:: img/image169.jpg
+.. image:: img/image163.jpg
 
 **NB: The calculation of** *Z(q)* **is a double numerical integral that must be carried out with a high density of**
@@ -52 +52 @@
 makes a triple integral. Very, very slow. Go get lunch!
 
-This example dataset is produced using 200 data points, *qmin* = 0.001 |Ang^-1|, *qmax* = 0.1 |Ang^-1| and the above
+This example dataset is produced using 200 data points, *qmin* = 0.01 |Ang^-1|, *qmax* = 0.1 |Ang^-1| and the above
 default values.
 
-.. image:: img/image170.jpg
+.. image:: img/image164.jpg
 
 *Figure. 1D plot in the linear scale using the default values (w/200 data point).*
@@ -65 +65 @@
 .. image:: img/image165.gif
 
-.. image:: img/image171.jpg
+.. image:: img/image166.jpg
 
 *Figure. 2D plot using the default values (w/200X200 pixels).*
@@ -80 +80 @@
 from numpy import pi, inf
 
-name = "BCCparacrystal"
-title = "Body-centred cubic lattic with paracrystalline distortion"
+name = "fcc_paracrystal"
+title = "Face-centred cubic lattic with paracrystalline distortion"
 description = """
-    Calculates the scattering from a **body-centered cubic lattice** with paracrystalline distortion. Thermal vibrations
+    Calculates the scattering from a **face-centered cubic lattice** with paracrystalline distortion. Thermal vibrations
     are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is
     assumed to be isotropic and characterized by a Gaussian distribution.
@@ -100 +100 @@
     ]
 
-source = [ "lib/J1.c", "lib/gauss150.c", "bcc.c" ]
+source = [ "lib/J1.c", "lib/gauss150.c", "fcc.c" ]
 
 def ER(radius, length):
@@ -119 +119 @@
 # For testing against the old sasview models, include the converted parameter
 # names and the target sasview model name.
-oldname='BCCrystalModel'
+oldname='FCCrystalModel'
 oldpars=dict(sld='sldSph',
              solvent_sld='sldSolv')

example/sesansfit.py

@@ -4 +4 @@
 from sasmodels import bumps_model as sas
 kernel = sas.load_model('sphere', dtype='single')
+#kernel = sas.load_model('triaxial_ellipsoid', dtype='single')
 
 
@@ -11 +12 @@
     loader=Loader()
     data=loader.load('testsasview1.ses')
+    data.x /=10
     
 #    data = load_sesans('mydatfile.pz')
@@ -20 +22 @@
     err_data = np.ones_like(SElength)*0.03
 
+    class Sample:
+        zacceptance = 0.1 # [A^-1]
+        thickness = 0.2 # [cm]
+        
     class SESANSData1D:
         #q_zmax = 0.23 # [A^-1]
-        zacceptance = 0.1 # [A^-1]
-        lam = 2e-10 # [m]
-        thickness = 0.2 # [cm]
+        lam = 0.2 # [nm]
         x = SElength
         y = data
         dy = err_data
-    data = SesansData()
-print dir(data)
+        sample = Sample()
+    data = SESANSData1D()
 
 radius = 1000
 data.Rmax = 3*radius # [A]
 
+##  Sphere parameters
+
 phi = Parameter(0.1, name="phi")
 model = sas.BumpsModel(data, kernel,
     scale=phi*(1-phi), sld=7.0, solvent_sld=1.0, radius=radius)
-phi.pmp(10)
-model.radius.pmp(40)
-model.sld.pm(2)
-model.background.range(0,5)
-
+phi.range(0.001,0.90)
+#model.radius.pmp(40)
+model.radius.range(100,10000)
+#model.sld.pmp(5)
+#model.background
+#model.radius_pd=0
+#model.radius_pd_n=0
 
 if False: # have sans data
@@ -49 +57 @@
     problem = FitProblem(model)
 
+
+### Tri-Axial Ellipsoid
+#
+#phi = Parameter(0.1, name='phi')
+#model = sas.BumpsModel(data, kernel,
+#    scale=phi*(1-phi), sld=7.0, solvent_sld=1.0, radius=radius)
+#phi.range(0.001,0.90)
+##model.radius.pmp(40)
+#model.radius.range(100,10000)
+##model.sld.pmp(5)
+##model.background
+##model.radius_pd=0
+##model.radius_pd_n=0
+#
+#if False: # have sans data
+#    sansmodel = sas.BumpsModel(sans_data, kernel, **model.parameters())
+#    problem = FitProblem([model, sansmodel])
+#else:
+#    problem = FitProblem(model)