correct superstructure scale

Fix for issue #30

classes_crystal.py
 - updated scale parameter of Superstructure() so it doesn't give zero.

classes_plotting.py
 - updates to plotting of superstructure intensity cuts

functions_crystallography.py
 - change calc_vol to always give positive volume

Author: DanPorter

Dans_Diffraction/__init__.py

@@ -31,8 +31,8 @@
 Diamond
 2017-2025
 
-Version 3.3.3
-Last updated: 06/02/2025
+Version 3.3.4
+Last updated: 12/04/2025
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -84,6 +84,7 @@
 06/11/24 3.3.1  Fixed incorrect cell basis for triclinic cells. Added functions_lattice.py and tests. Thanks LeeRichter!
 20/11/24 3.3.2  Added alternate option for neutron scattering lengths
 06/02/25 3.3.3  Added scattering options for polarised neutron and x-ray scattering. Thanks dragonyanglong!
+12/04/25 3.3.4  Improved superstructure calculations by fixing scale parameter
 
 Acknoledgements:
     2018        Thanks to Hepesu for help with Python3 support and ideas about breaking up calculations
@@ -113,7 +114,7 @@
     Dec 2024    Thanks to dragonyanglong for pointing out the error with magnetic neutron scattering
 
 -----------------------------------------------------------------------------
-   Copyright 2024 Diamond Light Source Ltd.
+   Copyright 2018-2025 Diamond Light Source Ltd.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

Dans_Diffraction/classes_crystal.py

@@ -24,8 +24,8 @@
 Diamond
 2017
 
-Version 3.3.0
-Last updated: 06/02/25
+Version 3.3.1
+Last updated: 06/04/25
 
 Version History:
 27/07/17 1.0    Version History started.
@@ -49,7 +49,8 @@
 15/11/21 3.2.2  Added Cell.orientation, updated Cell.UV()
 12/01/21 3.2.3  Added Symmetry.axial_vector
 22/05/23 3.2.4  Added Symmetry.wyckoff_label(), Symmetry.spacegroup_dict
-06/05/25 3.3.0  Symmetry.from_cif now loads operations from find_spacegroup if not already loaded
+06/05/24 3.3.0  Symmetry.from_cif now loads operations from find_spacegroup if not already loaded
+06/04/25 3.3.1  scale parameter of superlattice improved
 
 @author: DGPorter
 """
@@ -68,7 +69,7 @@
 from .classes_multicrystal import MultiCrystal
 from .classes_plotting import Plotting, PlottingSuperstructure
 
-__version__ = '3.3.0'
+__version__ = '3.3.1'
 
 
 class Crystal:
@@ -2386,7 +2387,7 @@ def __init__(self, Parent, P):
         self.Parent = Parent
         newUV = Parent.Cell.calculateR(P)
         self.new_cell(fl.basis2latpar(newUV))
-        parent_cells_in_supercell = np.prod(np.sqrt(np.sum(np.square(P), axis=1)))
+        parent_cells_in_supercell = fc.calc_vol(P)
         self.scale = Parent.scale * parent_cells_in_supercell
 
         # Add exta functions

Dans_Diffraction/functions_crystallography.py

@@ -72,6 +72,7 @@
 PENGFILE = os.path.join(datadir, 'peng.dat')
 NSLFILE = os.path.join(datadir, 'neutron_isotope_scattering_lengths.dat')
 NSLFILE_SEARS = os.path.join(datadir, 'neutron_isotope_scattering_lengths_sears.dat')
+ASFFILE = os.path.join(datadir, 'atomic_scattering_factors.npy')
 
 # List of Elements in order sorted by length of name
 ELEMENT_LIST = [
@@ -1236,8 +1237,7 @@ def atomic_scattering_factor(element, energy_kev=None):
     :param energy_kev: float or list energy in keV (None to return original, uninterpolated list)
     :return: f1, f2, shape dependent on shapes of element and energy_kev:  float, or [ene] or [ele, ene]
     """
-    asf_file = os.path.join(datadir, 'atomic_scattering_factors.npy')
-    asf = np.load(asf_file, allow_pickle=True)
+    asf = np.load(ASFFILE, allow_pickle=True)
     asf = asf.item()
 
     element = np.asarray(element, dtype=str).reshape(-1)
@@ -1295,8 +1295,7 @@ def xray_dispersion_corrections(elements, energy_kev=None):
     :param energy_kev: float or list energy in keV (None to return original, uninterpolated list)
     :return: f', f" with shape (len(energy), len(elements))
     """
-    asf_file = os.path.join(datadir, 'atomic_scattering_factors.npy')
-    asf = np.load(asf_file, allow_pickle=True)
+    asf = np.load(ASFFILE, allow_pickle=True)
     asf = asf.item()
 
     energy_kev = np.asarray(energy_kev, dtype=float).reshape(-1)
@@ -3446,7 +3445,7 @@ def group_intensities(q_values, intensity, min_overlap=0.01):
 def calc_vol(UV):
     """Calculate volume in Angstrom^3 from unit vectors"""
     a, b, c = UV
-    return np.dot(a, np.cross(b, c))
+    return np.abs(np.dot(a, np.cross(b, c)))
 
 
 def cif2table(cif):

Examples/example_supercell.py

@@ -3,11 +3,11 @@
 Build a supercell from multiple unit cells and simulate the diffraction pattern
 """
 
-import sys,os
+import sys, os
 import numpy as np
-import matplotlib.pyplot as plt # Plotting
+import matplotlib.pyplot as plt  # Plotting
 cf = os.path.dirname(__file__)
-sys.path.insert(0,os.path.join(cf,'..'))
+sys.path.insert(0, os.path.join(cf, '..'))
 import Dans_Diffraction as dif
 
 
@@ -23,8 +23,8 @@
 #sup = xtl.generate_superstructure(P)
 
 # Set discrete occupancies for average structure
-xtl.Atoms.occupancy[2]=0
-xtl.Atoms.occupancy[3]=1
+xtl.Atoms.occupancy[2] = 0
+xtl.Atoms.occupancy[3] = 1
 xtl.generate_structure()
 
 # Generate the superstructure, repeating the parent/average structure to fill the supercell