Backport updates to amalgamated pyne in DAGMC

docs/conf.py

@@ -49,7 +49,7 @@
 
 # General information about the project.
 project = u'PyNE'
-copyright = u'2011-2017, The PyNE Development Team'
+copyright = u'2011-2019, The PyNE Development Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/install/linux_source.rst

@@ -22,7 +22,7 @@ PyNE has the following dependencies:
    #. `BLAS <http://www.netlib.org/blas/>`_
 
 Optional Depenendencies:
-   #. `MOAB <http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB>`_
+   #. `MOAB <https://press3.mcs.anl.gov/sigma/moab-library>`_
    #. `PyTAPS <https://pythonhosted.org/PyTAPS/index.html>`_
 
 Most of the dependencies are readily available through package managers.  Once

license.txt

@@ -1,4 +1,4 @@
-Copyright 2011-2017, the PyNE Development Team. All rights reserved.
+Copyright 2011-2019, the PyNE Development Team. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are
 permitted provided that the following conditions are met:
@@ -31,7 +31,7 @@ Copyright 2004 Sandia Corporation.  Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Coroporation, the U.S. Government
 retains certain rights in this software.
 
-http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB
+https://press3.mcs.anl.gov/sigma/moab-library
 
 -------------------------------------------------------------------------------
 The files in fortranformat/ are covered by: 

readme.rst

@@ -40,7 +40,7 @@ PyNE has the following dependencies:
    #. `Jinja2 <http://jinja.pocoo.org/>`_
 
 Optional Depenendencies:
-   #. `MOAB <http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB>`_
+   #. `MOAB <https://press3.mcs.anl.gov/sigma/moab-library>`_
    #. `PyTAPS <https://pythonhosted.org/PyTAPS/index.html>`_
 
 Additionally, building the documentation requires the following:

src/particle.cpp

@@ -167,14 +167,14 @@ void * pyne::particle::_fill_maps() {
   altnames["Gamma"] = name_id["Photon"];
   altnames["X-Ray"] = name_id["Photon"];
 
-  part_to_mcnp["Neutron"]="N";
-  part_to_mcnp["Photon"]="P";
-  part_to_mcnp["Electron"]="E";
+  part_to_mcnp["Neutron"]="n";
+  part_to_mcnp["Photon"]="p";
+  part_to_mcnp["Electron"]="e";
 
-  part_to_mcnp6["Neutron"]="N";
-  part_to_mcnp6["Photon"]="P";
-  part_to_mcnp6["Electron"]="E";
-  part_to_mcnp6["Proton"]="H";
+  part_to_mcnp6["Neutron"]="n";
+  part_to_mcnp6["Photon"]="p";
+  part_to_mcnp6["Electron"]="e";
+  part_to_mcnp6["Proton"]="h";
 
   part_to_fluka["Electron"]="ELECTRON";
   part_to_fluka["Positron"]="POSITRON";
@@ -183,7 +183,7 @@ void * pyne::particle::_fill_maps() {
   part_to_fluka["Muon"]="MUON+";
   part_to_fluka["AntiMuon"]="MUON-";
   part_to_fluka["MuonNeutrino"]="NEUTRIM";
-  part_to_fluka["MuonAntiNeutrino"]="ANEUTRIM",
+  part_to_fluka["MuonAntiNeutrino"]="ANEUTRIM";
   part_to_fluka["Tauon"]="TAU+";
   part_to_fluka["Anti Tauon"]="TAU-";
   part_to_fluka["TauNeutrino"]="NEUTRIT";
@@ -221,7 +221,7 @@ void * pyne::particle::_fill_maps() {
   part_to_geant4["Muon"]="mu+";
   part_to_geant4["AntiMuon"]="mu-";
   part_to_geant4["MuonNeutrino"]="nu_mu";
-  part_to_geant4["MuonAntiNeutrino"]="anti_nu_mu",
+  part_to_geant4["MuonAntiNeutrino"]="anti_nu_mu";
   part_to_geant4["Tauon"]="tau+";
   part_to_geant4["Anti Tauon"]="tau-";
   part_to_geant4["TauNeutrino"]="nu_tau";

src/state_map.cpp

@@ -1022,7 +1022,8 @@ int map_nuc_ids [TOTAL_STATE_MAPS] = {110240001,
 1102700001,
 1102710001,
 1082770001,
-};int map_metastable [TOTAL_STATE_MAPS] = {1,
+};
+int map_metastable [TOTAL_STATE_MAPS] = {1,
 1,
 1,
 1,
@@ -2041,4 +2042,4 @@ int map_nuc_ids [TOTAL_STATE_MAPS] = {110240001,
 };
 }
 }
-#endif
+#endif

src/state_map.py

@@ -30,7 +30,7 @@ def generate_state_id_map(nuc_data):
             if item['metastable'] > 0 and item['nuc_id'] != lastnuc:
                 lastnuc = item['nuc_id']
                 sm.write(str(item['nuc_id']) + ",\n")
-        sm.write('};')
+        sm.write('};\n')
         sm.write('int map_metastable [TOTAL_STATE_MAPS] = {')
         for item in f.root.decay.level_list:
             if item['metastable'] > 0 and item['nuc_id'] != lastnuc:

tutorial/07-mesh-basics.ipynb

@@ -14,7 +14,7 @@
      "source": [
       "The PyNE ```mesh``` module provides generic mesh creation and manipulation capabilities. Both Cartesian and tetrahedral mesh are supported. PyNE meshes can be tagged with scalar and vector quantities and also PyNE `Material` objects. Tagged data can all be easily accessed with a common syntax.\n",
       "\n",
-      "Under the hood, the PyNE `Mesh` class is a wrapper around a [MOAB](https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB) mesh.\n",
+      "Under the hood, the PyNE `Mesh` class is a wrapper around a [MOAB](https://press3.mcs.anl.gov/sigma/moab-library) mesh.\n",
       "A `Mesh` object stores a MOAB iMesh instance, and additionally a PyNE `MaterialLibrary` object (to map PyNE `Material`s to mesh volume elements).\n",
       "\n",
       "The notebook will provide some basic examples of PyNE mesh usage. First let's import the necessary components of PyNE and a few other things that will be explained in this notebook:\n"
@@ -645,4 +645,4 @@
    "metadata": {}
   }
  ]
-}
+}