Nexus: Refactor periodic_table.py

nexus/nexus/basisset.py

@@ -5,7 +5,7 @@
 
 import os
 import numpy as np
-from .periodic_table import is_element
+from .periodic_table import Elements
 from .developer import DevBase, obj, error, to_str, unavailable
 from .fileio import TextFile
 
@@ -110,11 +110,11 @@ def __init__(self,filepath=None):
             self.filename = os.path.basename(filepath)
             self.location = os.path.abspath(filepath)
             elem_label = self.filename.split('.')[0]
-            is_elem,symbol = is_element(elem_label,symbol=True)
+            is_elem, elem = Elements.is_element(elem_label, return_element=True)
             if not is_elem:
                 self.error('cannot determine element for basis file: {0}\nbasis file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(filepath))
             #end if
-            self.element = symbol
+            self.element = elem.symbol
             self.element_label = elem_label
         #end if
     #end def __init__

nexus/nexus/fileio.py

@@ -27,7 +27,7 @@
 import numpy as np
 from numpy.linalg import det, norm
 from .developer import DevBase, obj, error, to_str
-from .periodic_table import is_element, pt as ptable
+from .periodic_table import Elements
 from .unit_converter import convert
 from . import numpy_extensions as npe
 
@@ -826,9 +826,9 @@ def incorporate_structure(self,structure):
         s.recenter()
         elem = []
         for e in s.elem:
-            is_elem,e = is_element(e,symbol=True)
+            is_elem, element = Elements.is_element(e, return_element=True)
             if is_elem:
-                elem.append(ptable.elements[e].atomic_number)
+                elem.append(element.atomic_number)
             else:
                 elem.append(0)
             #end if
@@ -1127,9 +1127,9 @@ def validity_checks(self):
                 msgs.append('elem must be an array of text')
             else:
                 for e in self.elem:
-                    iselem,symbol = is_element(e,symbol=True)
+                    iselem, element = Elements.is_element(e, return_element=True)
                     if not iselem:
-                        msgs.append('elem entry "{0}" is not an element'.format(e))
+                        msgs.append('elem entry "{0}" is not an element'.format(element))
                     #end if
                 #end for
             #end for
@@ -1193,9 +1193,9 @@ def write_text(self):
         #end for
         if self.elem is not None:
             for e in self.elem:
-                iselem,symbol = is_element(e,symbol=True)
+                iselem, element = Elements.is_element(e, return_element=True)
                 if not iselem:
-                    self.error('{0} is not an element'.format(e))
+                    self.error('{0} is not an element'.format(element))
                 #end if
                 text += e+' '
             #end for
@@ -1269,7 +1269,7 @@ def incorporate_xsf(self,xsf):
         species_ind = species
         species = []
         for i in species_ind:
-            species.append(ptable.simple_elements[i].symbol)
+            species.append(Elements(i).symbol)
         #end for
 
         self.scale      = 1.0

nexus/nexus/gamess_input.py

@@ -32,7 +32,7 @@
 
 
 import numpy as np
-from .periodic_table import pt
+from .periodic_table import Elements
 from .developer import DevBase, obj, error, warn
 from .nexus_base import nexus_noncore
 from .simulation import SimulationInput
@@ -1116,7 +1116,7 @@ def generate_any_gamess_input(**kwargs):
             #end if
             for i in range(len(elem)):
                 a = elem[i]
-                Z = pt[a].atomic_number
+                Z = Elements(a).atomic_number
                 data+='{0} {1:3.2f} {2:16.8f} {3:16.8f} {4:16.8f}\n'.format(a,Z,*pos[i])
                 if a in bss:
                     data+=bss[a].text+'\n\n'
@@ -1129,7 +1129,7 @@ def generate_any_gamess_input(**kwargs):
                 )
             pps = nexus_noncore.pseudopotentials.pseudos_by_atom(*pskw.pseudos)
             for i,a in enumerate(elem):
-                Z = pt[a].atomic_number
+                Z = Elements(a).atomic_number
                 data+='{0} {1} {2:16.8f} {3:16.8f} {4:16.8f}\n'.format(a,Z,*pos[i])
                 if a in pps:
                     data += pps[a].basis_text+'\n\n'

nexus/nexus/numerics.py

@@ -88,7 +88,7 @@
 from numpy.linalg import norm
 from .developer import obj, unavailable, error
 from .unit_converter import convert
-from .periodic_table import pt as ptable
+from .periodic_table import Elements
 
 try:
     from scipy.special import betainc
@@ -146,13 +146,14 @@ def morse_params(re, a, De, E_inf): return re, 1./a, De, E_inf
 # morse_reduced_mass gives the reduced mass in Hartree units
 #   m1 and m2 are masses or atomic symbols
 def morse_reduced_mass(m1,m2=None):
+    amu_me = convert(1., "amu", "me")
     if isinstance(m1,str):
-        m1 = ptable[m1].atomic_weight.me
+        m1 = Elements(m1).atomic_weight * amu_me
     #end if
     if m2 is None:
         m2 = m1
     elif isinstance(m2,str):
-        m2 = ptable[m2].atomic_weight.me
+        m2 = Elements(m2).atomic_weight * amu_me
     #end if
     m = 1./(1./m1+1./m2) # reduced mass
     return m