diffpy.structure 3.2.0__py3-none-any.whl

diffpy/structure/expansion/shapeutils.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.structure  by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2008 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Chris Farrow
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+
+"""Utilities for making shapes."""
+
+
+def findCenter(S):
+    """Find the approximate center `Atom` of a `Structure`.
+
+    The center of the `Structure` is the `Atom` closest to ``(0.5, 0.5, 0.5)``.
+
+    Parameters
+    ----------
+    S : Structure
+        A `Structure` instance.
+
+    Returns
+    -------
+    int
+        The index of the center `Atom`.
+    """
+    best = -1
+    bestd = len(S)
+    center = [0.5, 0.5, 0.5]  # the cannonical center
+
+    for i in range(len(S)):
+        d = S.lattice.dist(S[i].xyz, center)
+        if d < bestd:
+            bestd = d
+            best = i
+
+    return best

diffpy/structure/expansion/supercell_mod.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.structure  by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2008 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Chris Farrow, Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+
+"""This module contains functions for simple `Structure` manipulation.
+"""
+
+import numpy
+
+from diffpy.structure import Atom, Structure
+
+
+def supercell(S, mno):
+    """
+    Perform supercell expansion for a `Structure`.
+
+    New `lattice` parameters are multiplied and fractional coordinates
+    divided by corresponding multiplier. New `Atoms` are grouped with
+    their source in the original cell.
+
+    Parameters
+    ----------
+    S : Structure
+        An instance of `Structure` from `diffpy.structure`.
+    mno : array_like
+        Sequence of 3 integers for cell multipliers along
+        the `a`, `b` and `c` axes.
+
+    Returns
+    -------
+    Structure
+        A new `Structure` instance representing the expanded supercell.
+
+    Raises
+    ------
+    TypeError
+        `S` is not a `Structure` instance.
+    ValueError
+        Invalid `mno` argument.
+    """
+    # check arguments
+    if len(mno) != 3:
+        emsg = "Argument mno must contain 3 numbers."
+        raise ValueError(emsg)
+    elif min(mno) < 1:
+        emsg = "Multipliers must be greater or equal 1"
+        raise ValueError(emsg)
+    if not isinstance(S, Structure):
+        emsg = "The first argument must be a Structure instance."
+        raise TypeError(emsg)
+
+    # convert mno to a tuple of integers so it can be used as range limit.
+    mno = (int(mno[0]), int(mno[1]), int(mno[2]))
+
+    # create return instance
+    newS = Structure(S)
+    if mno == (1, 1, 1):
+        return newS
+
+    # back to business
+    ijklist = [(i, j, k) for i in range(mno[0]) for j in range(mno[1]) for k in range(mno[2])]
+    # numpy.floor returns float array
+    mnofloats = numpy.array(mno, dtype=float)
+
+    # build a list of new atoms
+    newAtoms = []
+    for a in S:
+        for ijk in ijklist:
+            adup = Atom(a)
+            adup.xyz = (a.xyz + ijk) / mnofloats
+            newAtoms.append(adup)
+    # newS can own references in newAtoms, no need to make copies
+    newS.__setitem__(slice(None), newAtoms, copy=False)
+
+    # take care of lattice parameters
+    newS.lattice.setLatPar(a=mno[0] * S.lattice.a, b=mno[1] * S.lattice.b, c=mno[2] * S.lattice.c)
+    return newS
+
+
+# End of supercell