Automatic printing of e_bounds file

docs/usersguide/r2s.rst

@@ -105,11 +105,13 @@ decay time. These files will be named like:
 
 source_1.h5m, source_2.h5m ... source_N.h5m
 
-These files can now be used as sources
-for photon transport within MCNP. Information on compiling a version of MCNP5
-that can utilize these sources is found in the PyNE user's guide entry on 
+An "e_bounds" file containing the photon lower and upper energy bounds will also be generated. 
+These source files, combined with the "e_bounds" file can now be used as sources
+for photon transport within MCNP. Information on compiling/using a version of MCNP5
+that can utilize these mesh-based sources is found in the PyNE user's guide entry on 
 `mesh-based source sampling <http://pyne.io/usersguide/source_sampling.html#source-sampling-in-mcnp5>`_.
-Note the each of these source files must be renamed to "source.h5m" for this purpose. By using these sources for photon transport, the shutdown dose rate can be obtained as a final answer.
+Note that each of these source files must be renamed to "source.h5m" for this purpose.
+By using these sources for photon transport, the shutdown dose rate can be obtained. Tally results will have to be normalized by the total photon source intentity. This information is found in the "total_photon_source_intensites.txt" file printed out by r2s.py step2.
 
 **********
 References

pyne/alara.py

@@ -534,6 +534,34 @@ def irradiation_blocks(material_lib, element_lib, data_library, cooling,
 
     return s
 
+def phtn_src_energy_bounds(input_file):
+    """Reads an ALARA input file and extracts the energy bounds from the 
+    photon_source block.
+
+    Parameters
+    ----------
+    input_file : str
+         The ALARA input file name, which must contain a photon_source block.
+    
+    Returns
+    -------
+    e_bounds : list of floats
+        The lower and upper energy bounds for the photon_source discretization.
+    """
+    phtn_src_lines = ""
+    with open(input_file, 'r') as f:
+        line = f.readline()
+        while not (' photon_source ' in line and line.strip()[0] != "#"):
+            line = f.readline()
+        num_groups = float(line.split()[3])
+        upper_bounds = [float(x) for x in line.split()[4:]]
+        while len(upper_bounds) < num_groups:
+            line = f.readline()
+            upper_bounds += [float(x) for x in line.split("#")[0].split('end')[0].split()]
+    e_bounds = [0.] + upper_bounds
+    return e_bounds
+
+
 def _build_matrix(N):
     """ This function  builds burnup matrix, A. Decay only.
     """

scripts/r2s.py

@@ -5,8 +5,10 @@
 
 from pyne.mesh import Mesh
 from pyne.dagmc import cell_materials, load
-from pyne.r2s import irradiation_setup, photon_sampling_setup
-from pyne.alara import photon_source_to_hdf5, photon_source_hdf5_to_mesh
+from pyne.r2s import irradiation_setup, photon_sampling_setup,\
+                       total_photon_source_intensity
+from pyne.alara import photon_source_to_hdf5, photon_source_hdf5_to_mesh,\
+                       phtn_src_energy_bounds
 from pyne.mcnp import Meshtal
 
 config_filename = 'config.ini'
@@ -69,6 +71,7 @@
 
 output zone
        integrate_energy
+       # Energy group upper bounds. The lower bound is always zero.
        photon_source  fendl3bin  phtn_src 24 1.00E4 2.00E4 5.00E4 1.00E5
        2.00E5 3.00E5 4.00E5 6.00E5 8.00E5 1.00E6 1.22E6 1.44E6 1.66E6
        2.00E6 2.50E6 3.00E6 4.00E6 5.00E6 6.50E6 8.00E6 1.00E7 1.20E7
@@ -158,12 +161,19 @@ def step2():
         tags = {('TOTAL', dc): tag_name}
         photon_source_hdf5_to_mesh(mesh, h5_file, tags)
         mesh.mesh.save('{0}_{1}.h5m'.format(output, i+1))
-        intensity = total_photon_source_intensity(m, tag_name)
-        intensities += "{0}: {1}".format(dc, intensity)
+        intensity = total_photon_source_intensity(mesh, tag_name)
+        intensities += "{0}: {1}\n".format(dc, intensity)
 
-    with open(tot_phtn_src_intensities, 'r') as f:
+    with open(tot_phtn_src_intensities, 'w') as f:
         f.write(intensities)
 
+    e_bounds = phtn_src_energy_bounds(alara_geom)
+    e_bounds_str = ""
+    for e in e_bounds:
+        e_bounds_str += "{0}\n".format(e)
+    with open("e_bounds", 'r') as f:
+        f.write(e_bounds_str)
+
     print('R2S step2 complete.')
 
 def main():

tests/test_alara.py

@@ -27,7 +27,7 @@
 from pyne.material import Material
 from pyne.alara import mesh_to_fluxin, photon_source_to_hdf5, \
     photon_source_hdf5_to_mesh, mesh_to_geom, num_density_to_mesh, \
-    irradiation_blocks, record_to_geom
+    irradiation_blocks, record_to_geom, phtn_src_energy_bounds
 
 thisdir = os.path.dirname(__file__)
 
@@ -429,3 +429,14 @@ def test_irradiation_blocks():
 
     assert_equal(act, exp)
 
+def test_phtn_src_energy_bounds():
+
+    input_file = os.path.join(thisdir, "files_test_alara", 
+                              "alara_other_blocks.txt")
+    e_bounds = phtn_src_energy_bounds(input_file)
+    expected_e_bounds = [0, 1.00E4, 2.00E4, 5.00E4, 1.00E5, 2.00E5, 3.00E5, 
+                         4.00E5, 6.00E5, 8.00E5, 1.00E6, 1.22E6, 1.44E6, 1.66E6, 
+                         2.00E6, 2.50E6, 3.00E6, 4.00E6, 5.00E6, 6.50E6, 8.00E6, 
+                         1.00E7, 1.20E7, 1.40E7, 2.00E7]
+
+    assert_array_equal(e_bounds, expected_e_bounds)