Moved write_xyz to conversion module

appveyor.yml

@@ -13,6 +13,7 @@ environment:
                         # of 32 bit and 64 bit builds are needed, move this
                         # to the matrix section.
       TEST_CMD: "python -m unittest discover --verbose"
+      FORMAT_CMD: "black .\crystals"
       NUMPY_VERSION: "stable"
       CONDA_CHANNELS: "conda-forge"
       # ase and biopython are only required for tests
@@ -58,6 +59,7 @@ build: false
 
 test_script:
   - "%CMD_IN_ENV% %TEST_CMD%"
-  - black .\crystals --check
+  # We also check formatting
+  - "%CMD_IN_ENV% %FORMAT_CMD%"
 
 on_success:

crystals/__init__.py

@@ -20,6 +20,7 @@
 from .base import AtomicStructure
 from .base import Base
 from .conversion import ase_atoms
+from .conversion import write_xyz
 from .crystal import Crystal
 from .crystal import symmetry_expansion
 from .lattice import Lattice

crystals/conversion.py

@@ -15,6 +15,40 @@
 else:
     WITH_ASE = True
 
+# TODO: test against known XYZ file
+def write_xyz(crystal, fname, comment=None):
+    """
+    Generate an atomic coordinates .xyz file from a crystal structure.
+
+    Parameters
+    ----------
+    crystal : crystals.Crystal
+        Crystal to be converted.
+    fname : path-like
+        The XYZ file will be written to this file. If the file already exists,
+        it will be overwritten.
+    comment : str or None, optional
+        Comment to include at the second line of ``fname``.
+    """
+    # Format is specified here:
+    #   http://openbabel.org/wiki/XYZ_%28format%29
+    comment = comment or ""
+    atom_format_str = "  {:<2}       {:10.5f}       {:10.5f}       {:10.5f}"
+
+    with open(fname, "wt", encoding="ascii") as file:
+        # First two lines are:
+        #   1. Number of atoms described in the file
+        #   2. Optional comment
+        file.write(str(len(crystal)) + "\n")
+        file.write(comment + "\n")
+
+        # Write atomic data row-by-row
+        # For easier human readability, atoms are sorted
+        # by element
+        for atom in crystal.itersorted():
+            row = atom_format_str.format(atom.element, *atom.coords_cartesian)
+            file.write(row + "\n")
+
 
 def ase_atoms(crystal, **kwargs):
     """ 

crystals/crystal.py

@@ -200,38 +200,6 @@ def from_ase(cls, atoms):
             lattice_vectors=lattice_vectors,
         )
 
-    # TODO: test against known XYZ file
-    def write_xyz(self, fname, comment=None):
-        """
-        Generate an atomic coordinates .xyz file from a crystal structure.
-
-        Parameters
-        ----------
-        fname : path-like
-            The XYZ file will be written to this file. If the file already exists,
-            it will be overwritten.
-        comment : str or None, optional
-            Comment to include at the second line of ``fname``.
-        """
-        # Format is specified here:
-        #   http://openbabel.org/wiki/XYZ_%28format%29
-        comment = comment or ""
-        atom_format_str = "  {:<2}       {:10.5f}       {:10.5f}       {:10.5f}"
-
-        with open(fname, "wt", encoding="ascii") as file:
-            # First two lines are:
-            #   1. Number of atoms described in the file
-            #   2. Optional comment
-            file.write(str(len(self)) + "\n")
-            file.write(comment + "\n")
-
-            # Write atomic data row-by-row
-            # For easier human readability, atoms are sorted
-            # by element
-            for atom in self.itersorted():
-                row = atom_format_str.format(atom.element, *atom.xyz(self))
-                file.write(row + "\n")
-
     def _spglib_cell(self):
         """ Returns an array in spglib's cell format. """
         arr = np.asarray(self)

docs/functions/crystals.write_xyz.rst

@@ -0,0 +1,6 @@
+crystals.write\_xyz
+===================
+
+.. currentmodule:: crystals
+
+.. autofunction:: write_xyz

docs/reference.rst

@@ -63,4 +63,5 @@ Conversion between ``Crystal`` and other packages
     :nosignatures:
 
     ase_atoms
-    Crystal.from_ase
+    Crystal.from_ase
+    write_xyz