uniform options for CifParser, and pymatgen imports

xraypy · Aug 15, 2023 · 325cb6c · 325cb6c
1 parent 28ba79b
commit 325cb6c
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Showing 3 changed files with 27 additions and 28 deletions.
diff --git a/larch/xrd/amcsd_utils.py b/larch/xrd/amcsd_utils.py
@@ -9,10 +9,21 @@
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy.pool import SingletonThreadPool
 
+try:
+    from pymatgen.io.cif import CifParser
+    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    from pymatgen.core import Molecule, IMolecule, IStructure
+except:
+    CifParser = SpacegroupAnalyzer = None
+    Molecule = IMolecule = IStructure = None
+
 from larch.utils.physical_constants import ATOM_SYMS, ATOM_NAMES
 
 __version__ = '1'
 
+PMG_CIF_OPTS = dict(occupancy_tolerance=10, site_tolerance=5e-3)
+
+
 def make_engine(dbname):
     "create engine for sqlite connection"
     return create_engine('sqlite:///%s' % (dbname),

diff --git a/larch/xrd/cif2feff.py b/larch/xrd/cif2feff.py
@@ -2,18 +2,12 @@
 import random
 from io import StringIO
 
-HAS_PYMATGEN = False
-try:
-    from pymatgen.io.cif import CifParser
-    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    from pymatgen.core import Molecule
-    HAS_PYMATGEN = True
-except:
-    HAS_PYMATGEN = False
 
 from xraydb import atomic_symbol, atomic_number, xray_edge
 from larch.utils import fix_varname, strict_ascii, gformat
 
+from .amcsd_utils import PMG_CIF_OPTS, CifParser, Molecule, SpacegroupAnalyzer
+
 def get_atom_map(structure):
     """generalization of pymatgen atom map
     Returns:
@@ -43,10 +37,10 @@ def read_cif_structure(ciftext):
     -------
       pymatgen Structure object
     """
-    if not HAS_PYMATGEN:
-        raise ImportError('pymatgen required')
+    if CifParser is None:
+        raise ValueError("CifParser from pymatgen not available. Try 'pip install pymatgen'.")
     try:
-        cifstructs = CifParser(StringIO(ciftext), site_tolerance=5.e-4)
+        cifstructs = CifParser(StringIO(ciftext), **PMG_CIF_OPTS)
         parse_ok = True
         file_found = True
     except:
@@ -55,7 +49,7 @@ def read_cif_structure(ciftext):
         if os.path.exists(ciftext):
             file_found = True
             try:
-                cifstructs = CifParser(ciftext, site_tolerance=5.e-4)
+                cifstructs = CifParser(ciftext, **PMG_CIF_OPTS)
                 parse_ok = True
             except:
                 parse_ok = False

diff --git a/larch/xrd/structure2feff.py b/larch/xrd/structure2feff.py
@@ -1,13 +1,7 @@
 import os
 import random
 
-HAS_PYMATGEN = False
-try:
-    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-    from pymatgen.core import Molecule, IMolecule, IStructure
-    HAS_PYMATGEN = True
-except:
-    HAS_PYMATGEN = False
+from .amcsd_utils import (SpacegroupAnalyzer, Molecule, IMolecule, IStructure)
 
 from xraydb import atomic_symbol, atomic_number, xray_edge
 from larch.utils.strutils import fix_varname, strict_ascii
@@ -43,16 +37,16 @@ def read_structure(structure_text, fmt="cif"):
     -------
       pymatgen Structure object or Molecule object
     """
-    if not HAS_PYMATGEN:
-        raise ImportError('pymatgen required')
+    if Molecule is None:
+        raise ImportError("pymatgen required. Try 'pip install pymatgen'.")
     try:
         if fmt.lower() in ('cif', 'poscar', 'contcar', 'chgcar', 'locpot', 'cssr', 'vasprun.xml'):
             struct = IStructure.from_str(structure_text, fmt, merge_tol=5.e-4)
         else:
             struct = IMolecule.from_str(structure_text, fmt)
         parse_ok = True
         file_found = True
-        
+
     except:
         parse_ok = False
         file_found = False
@@ -100,9 +94,9 @@ def parse_structure(structure_text, fmt='cif', fname="default.filename"):
         struct = read_structure(structure_text, fmt=fmt)
     except ValueError:
         return '# could not read structure file'
-    
+
     return {'formula': struct.composition.reduced_formula, 'sites': struct.sites, 'structure_text': structure_text, 'fmt': fmt, 'fname': fname}
-    
+
 
 def structure2feffinp(structure_text, absorber, edge=None, cluster_size=8.0, absorber_site=1,
                       site_index=None, extra_titles=None, with_h=False, version8=True, fmt='cif'):
@@ -146,16 +140,16 @@ def structure2feffinp(structure_text, absorber, edge=None, cluster_size=8.0, abs
         struct = read_structure(structure_text, fmt=fmt)
     except ValueError:
         return '# could not read structure file'
-  
+
     is_molecule = False
-  
+
     if isinstance(struct, IStructure):
         sgroup = SpacegroupAnalyzer(struct).get_symmetry_dataset()
         space_group = sgroup["international"]
     else:
         space_group = 'Molecule'
         is_molecule = True
-        
+
 
     if isinstance(absorber, int):
         absorber   = atomic_symbol(absorber_z)
@@ -236,7 +230,7 @@ def structure2feffinp(structure_text, absorber, edge=None, cluster_size=8.0, abs
     out_text.append(f'*     using absorber at site {1+absorber_index:d} in the list below')
     out_text.append(f'*     selected as absorber="{absorber:s}", absorber_site={absorber_site:d}')
     out_text.append('* index   X        Y        Z      species')
-    
+
     for i, site in enumerate(struct):
         # The method of obtaining the cooridanates depends on whether the structure is a molecule or not
         if is_molecule: