Documentaiton and cleanup.

cpp/measure.cpp

@@ -25,7 +25,7 @@
 
 #include <math.h>
 
-#include "measure.hpp"
+#include "measure.h"
 
 class CartVect {
   private:

cpp/source_sampling.cpp

@@ -91,15 +91,15 @@ void Sampler::get_mesh_geom_data(MBRange ves, vect_d &volumes) {
       MBCartVect x(coords[3], coords[4], coords[5]);
       MBCartVect y(coords[9], coords[10], coords[11]);
       MBCartVect z(coords[12], coords[13], coords[14]);
-      edge_vects ev = {o, x-o, y-o, z-o};
-      _all_edge_vects.push_back(ev);
+      edge_points ep = {o, x-o, y-o, z-o};
+      _all_edge_points.push_back(ep);
     } else if (_ve_type == MBTET) {
       MBCartVect o(coords[0], coords[1], coords[2]);
       MBCartVect x(coords[3], coords[4], coords[5]);
       MBCartVect y(coords[6], coords[7], coords[8]);
       MBCartVect z(coords[9], coords[10], coords[11]);
-      edge_vects ev = {o, x-o, y-o, z-o};
-      _all_edge_vects.push_back(ev);
+      edge_points ep = {o, x-o, y-o, z-o};
+      _all_edge_points.push_back(ep);
     }
   }
 }
@@ -112,7 +112,7 @@ void Sampler::get_mesh_tag_data(MBRange ves, const vect_d volumes) {
                               MB_TYPE_DOUBLE, 
                               src_tag);
   // THIS rval FAILS because we do not know number of energy groups a priori.
-
+  // That's okay. That's what the next line is all about:
   _num_e_groups = get_num_groups(src_tag);
   vect_d pdf(_num_ves*_num_e_groups); 
   rval = _mesh->tag_get_data(src_tag, ves, &pdf[0]);
@@ -226,10 +226,10 @@ MBCartVect Sampler::get_xyz(int ve_idx, vect_d rands) {
     }
   }
 
- return s*_all_edge_vects[ve_idx].x_vec + \
-        t*_all_edge_vects[ve_idx].y_vec + \
-        u*_all_edge_vects[ve_idx].z_vec + \
-          _all_edge_vects[ve_idx].o_point;
+ return s*_all_edge_points[ve_idx].x_vec + \
+        t*_all_edge_points[ve_idx].y_vec + \
+        u*_all_edge_points[ve_idx].z_vec + \
+          _all_edge_points[ve_idx].o_point;
 }
 
 double Sampler::get_e(int e_idx, double rand) {

cpp/source_sampling.h

@@ -1,12 +1,26 @@
-#ifndef PYNE_6OR6BJURKJHHTOFWXO2VMQM5EY
-#define PYNE_6OR6BJURKJHHTOFWXO2VMQM5EY
 /// \file source_sampling.h
 /// \author Elliott Biondo (biondo\@wisc.edu)
 ///
-/// \brief The tally class and helper functions
+/// \brief Mesh-based Monte Carlo source sampling.
 /// 
-/// The tally class is in essesence a structure containing attributes
-/// related to tallies
+/// The Sampler class is used for Monte Carlo source sampling from mesh-based
+/// sources.  The source density distribution and optional biased source density
+/// distribution are defined on a MOAB mesh. Upon instantiation, a Sampler  
+/// object reads this mesh and creates an alias table for randomly sampling
+/// particle birth parameters. The particle_birth member function is supplied 
+/// with 6 pseudo-random numbers and returns the position, energy, and weight 
+/// of a particle upon birth.  There are three sampling modes: analog, uniform, 
+/// and user. In analog sampling, no source biasing is used and birth weights
+/// are all 1. In uniform sampling, all phase space is sampled evenly and weights
+/// are adjusted accordingly. In user mode, a user-supplied biased source
+/// density distribution is used for sampling and particle weights are adjusted
+/// accordingly. The biased source density distribution must have the same number 
+/// of energy groups as the unbiased distribution. Alternatively, it may have 
+/// exactly 1 energy group, in which case this value is used for all energies
+/// within a particular mesh volume element.
+
+#ifndef PYNE_6OR6BJURKJHHTOFWXO2VMQM5EY
+#define PYNE_6OR6BJURKJHHTOFWXO2VMQM5EY
 
 #include <assert.h>
 #include <iostream>
@@ -20,7 +34,7 @@
 
 #include "moab/Range.hpp"
 #include "MBCore.hpp"
-#include "measure.hpp"
+#include "measure.h"
 #include "MBCartVect.hpp"
 
 #ifdef __cplusplus
@@ -31,13 +45,7 @@ void get_e_bounds_data(std::string e_bounds_file);
 typedef std::vector<double> vect_d;
 typedef std::string str;
 
-struct Sample {
-  vect_d xyz; /// \param type
-  double e;
-  double w;
-};
-
-struct edge_vects {
+struct edge_points {
   MBCartVect o_point;
   MBCartVect x_vec;
   MBCartVect y_vec;
@@ -66,9 +74,9 @@ class Sampler
   Sampler(str filename, str src_tag_name, vect_d e_bounds, bool uniform);
   Sampler(str filename, str src_tag_name, vect_d e_bounds, str bias_tag_name);
   ~Sampler() {
-     delete _mesh;
-     delete _at;
-     };
+    delete _mesh;
+    delete _at;
+  };
   vect_d particle_birth(vect_d rands);
 
 private:
@@ -84,7 +92,7 @@ class Sampler
   int _num_ves;
   MBEntityType _ve_type;
   int _verts_per_ve;
-  std::vector<edge_vects> _all_edge_vects;
+  std::vector<edge_points> _all_edge_points;
   AliasTable* _at;
   std::vector<double> _biased_weights;
 

docs/theorymanual/source_sampling.rst

@@ -0,0 +1,52 @@
+.. _source_sampling:
+
+=============================
+Source Sampling
+=============================
+
+.. currentmodule:: pyne.source_sampling
+
+This page presents a detailed explanation of how :py:mod:`Source Sampling` works, including
+underlying theory, any assocaited assumptions, and information about correct and
+appropriate use of this physics. 
+
+
+*****************************
+Descriptive Heading of Method
+*****************************
+
+Mathematical Details, some example math syntax:
+
+You can use LaTeX format in rst. To do inline expressions (what $expression$ would
+do in LaTeX) :math:`A\vec{x} = \vec{b}`.
+
+To have blocks of mathematical content, do this
+
+.. math::
+    
+    A\vec{x} = \vec{b}
+
+Support is limited to a subset of LaTeX math by the conversion required for many output formats.
+
+***********
+Assumptions
+***********
+
+Any assumptions (explicit or implicit) about this method that would impact use, conclusions, validity, etc.
+
+
+
+**********************
+Additional Information
+**********************
+
+Details about impact of this theory on method use.
+
+**********
+References
+**********
+
+All of the justification for us listening to you.
+
+
+

pyne/cpp_source_sampling.pxd

@@ -51,22 +51,5 @@ cdef extern from "source_sampling.h" :
 
 
 
-cdef extern from "source_sampling.h" :
-
-    cdef cppclass Sample:
-        # constructors
-        Sample() except +
-
-        # attributes
-        double e
-        double w
-        cpp_vector[double] xyz
-
-        # methods
-
-        pass
-
-
-
 
 {'cpppxd_footer': '', 'pyx_header': '', 'pxd_header': '', 'pxd_footer': '', 'cpppxd_header': '', 'pyx_footer': ''}

pyne/source_sampling.pxd

@@ -8,9 +8,6 @@
 ################################################
 
 
-cimport dtypes
-cimport numpy as np
-from libcpp.vector cimport vector as cpp_vector
 from pyne cimport cpp_source_sampling
 
 
@@ -24,16 +21,6 @@ cdef class Sampler:
 
 
 
-cdef class Sample:
-    cdef void * _inst
-    cdef public bint _free_inst
-    cdef public np.ndarray _xyz
-    pass
-
-
-
-
-
 cdef class AliasTable:
     cdef void * _inst
     cdef public bint _free_inst