added filetype attribute as 'wmp' and included a nuclide name

Author: liangjg

README.md

@@ -67,13 +67,21 @@ Detailed specifications can be found in
 
 ## Download
 
-[Git LFS] is used to store the binary HDF5 files.
-To download the real WMP library, you need to firstly install [Git LFS] and then
-clone this repository.
+- download the compressed library from the latest releases: https://github.com/mit-crpg/WMP_Library/releases
 
-``` bash
-$ git clone https://github.com/mit-crpg/WMP_Library.git
-```
+  ``` bash
+  $ wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.0.1/WMP_Library_v1.0.1.tar.gz
+  ```
+
+- clone from git repository 
+
+  [Git LFS] is used to store the binary HDF5 files.
+  To download the real WMP library, you need to firstly install [Git LFS] and
+  then clone this repository.
+
+  ``` bash
+  $ git clone https://github.com/mit-crpg/WMP_Library.git
+  ```
 
 ## Usage
 
@@ -84,7 +92,7 @@ absorption, and fission.
 
 An excellent reference is [OpenMC], which implements WMP in both the transport
 solver and the [OpenMC Python API]. You can also check the scripts `scripts/WMP.py`
-for an Python implementation, which illustrates how to read, evaluate and export
+for a Python implementation, which illustrates how to read, evaluate and export
 an windowed multipole format library.
 For example, the following script demonstrates how to utilize WMP library using
 the nuclear data interface [WindowedMultipole].

scripts/WMP.py

@@ -24,29 +24,6 @@
 _FIT_A = 1       # Absorption
 _FIT_F = 2       # Fission
 
-ATOMIC_SYMBOL = {0: 'n', 1: 'H', 2: 'He', 3: 'Li', 4: 'Be', 5: 'B', 6: 'C',
-                 7: 'N', 8: 'O', 9: 'F', 10: 'Ne', 11: 'Na', 12: 'Mg', 13: 'Al',
-                 14: 'Si', 15: 'P', 16: 'S', 17: 'Cl', 18: 'Ar', 19: 'K',
-                 20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V', 24: 'Cr', 25: 'Mn',
-                 26: 'Fe', 27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga',
-                 32: 'Ge', 33: 'As', 34: 'Se', 35: 'Br', 36: 'Kr', 37: 'Rb',
-                 38: 'Sr', 39: 'Y', 40: 'Zr', 41: 'Nb', 42: 'Mo', 43: 'Tc',
-                 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In',
-                 50: 'Sn', 51: 'Sb', 52: 'Te', 53: 'I', 54: 'Xe', 55: 'Cs',
-                 56: 'Ba', 57: 'La', 58: 'Ce', 59: 'Pr', 60: 'Nd', 61: 'Pm',
-                 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy', 67: 'Ho',
-                 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta',
-                 74: 'W', 75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au',
-                 80: 'Hg', 81: 'Tl', 82: 'Pb', 83: 'Bi', 84: 'Po', 85: 'At',
-                 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th', 91: 'Pa',
-                 92: 'U', 93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk',
-                 98: 'Cf', 99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No',
-                 103: 'Lr', 104: 'Rf', 105: 'Db', 106: 'Sg', 107: 'Bh',
-                 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn',
-                 113: 'Nh', 114: 'Fl', 115: 'Mc', 116: 'Lv', 117: 'Ts',
-                 118: 'Og'}
-ATOMIC_NUMBER = {value: key for key, value in ATOMIC_SYMBOL.items()}
-
 def check_type(name, value, expected_type):
     r"""Ensure that an object is of an expected type.
 
@@ -263,7 +240,8 @@ class WindowedMultipole(object):
         a/E + b/sqrt(E) + c + d sqrt(E) + ...
 
     """
-    def __init__(self):
+    def __init__(self, name):
+        self.name = name
         self.spacing = None
         self.sqrtAWR = None
         self.E_min = None
@@ -273,6 +251,10 @@ def __init__(self):
         self.broaden_poly = None
         self.curvefit = None
 
+    @property
+    def name(self):
+        return self._name
+
     @property
     def fit_order(self):
         return self.curvefit.shape[1] - 1
@@ -313,6 +295,11 @@ def broaden_poly(self):
     def curvefit(self):
         return self._curvefit
 
+    @name.setter
+    def name(self, name):
+        check_type('name', name, str)
+        self._name = name
+
     @spacing.setter
     def spacing(self, spacing):
         if spacing is not None:
@@ -422,9 +409,10 @@ def from_hdf5(cls, group_or_filename):
                 raise ValueError('The given WMP data uses version '
                     + version + ' whereas your installation of the OpenMC '
                     'Python API expects version ' + WMP_VERSION)
-            group = h5file['nuclide']
+            group = list(h5file.values())[0]
 
-        out = cls()
+        name = group.name[1:]
+        out = cls(name)
 
         # Read scalars.
 
@@ -570,26 +558,29 @@ def __call__(self, E, T):
         fun = np.vectorize(lambda x: self._evaluate(x, T))
         return fun(E)
 
-    def export_to_hdf5(self, path, libver='earliest'):
+    def export_to_hdf5(self, path, mode='a', libver='earliest'):
         """Export windowed multipole data to an HDF5 file.
 
         Parameters
         ----------
         path : str
             Path to write HDF5 file to
+        mode : {'r', r+', 'w', 'x', 'a'}
+            Mode that is used to open the HDF5 file. This is the second argument
+            to the :class:`h5py.File` constructor.
         libver : {'earliest', 'latest'}
             Compatibility mode for the HDF5 file. 'latest' will produce files
             that are less backwards compatible but have performance benefits.
 
         """
 
         # Open file and write version.
-        with h5py.File(path, 'w', libver=libver) as f:
+        with h5py.File(path, mode, libver=libver) as f:
+            f.attrs['filetype'] = np.string_('data_wmp')
             f.create_dataset('version', (1, ), dtype='S10')
             f['version'][:] = WMP_VERSION.encode('ASCII')
 
-            # Make a nuclide group.
-            g = f.create_group('nuclide')
+            g = f.create_group(self.name)
 
             # Write scalars.
             g.create_dataset('spacing', data=np.array(self.spacing))

scripts/parse_wmp_info.py

@@ -23,13 +23,8 @@
 for i, wmp_library in enumerate(wmp_files):
   result = []
   nuc_wmp = WMP.WindowedMultipole.from_hdf5(wmp_library)
-
+  nuc_name = nuc_wmp.name
   wmp_name = os.path.basename(wmp_library)
-  atomic_number = int(wmp_name[0:3])
-  mass_number = int(wmp_name[3:6])
-  nuc_name = WMP.ATOMIC_SYMBOL[atomic_number] + str(mass_number)
-  if wmp_name[6:-3] is not '':
-    nuc_name += '_{}'.format(wmp_name[6:-3])
 
   result.append(nuc_name)
   result.append(wmp_name)

scripts/validation.py

@@ -57,14 +57,9 @@
 
 print("Start validating {} nuclides - {}".format(len(wmp_files), time.ctime()))
 for i, wmp_library in enumerate(wmp_files):
-  wmp_name = os.path.basename(wmp_library)
-  nuc_Z = int(wmp_name[0:3])
-  nuc_A = int(wmp_name[3:6])
-  nuc_m = wmp_name[6:-3]
-  nuc_name = WMP.ATOMIC_SYMBOL[nuc_Z]
-  nuc_name += '{}'.format(nuc_A)
-  if nuc_m is not '':
-    nuc_name += '_{}'.format(nuc_m)
+  # load wmp data
+  nuc_wmp = WMP.WindowedMultipole.from_hdf5(wmp_library)
+  nuc_name = nuc_wmp.name
 
   print("{:>3}/{:<3} Processing {} {} - {} ".format(
           i+1, len(wmp_files), nuc_name, wmp_library, time.ctime()))
@@ -76,11 +71,6 @@
   logfile = os.path.join(out_dir, logfile_name);
   f = open(logfile, 'w');
 
-  # load wmp data
-  nuc_wmp = WMP.WindowedMultipole.from_hdf5(wmp_library)
-  f.write("Load wmp library: {}".format(wmp_library))
-  f.write("\n")
-
   # write info
   f.write("Energy range: {} {}".format(nuc_wmp.E_min, nuc_wmp.E_max))
   f.write("\n")