Changes to tests

Tests now pass but slight deviations in neutron scattering lengths causing variations in structure factor.

Author: DanPorter

Dans_Diffraction/Structures/README.md

@@ -36,4 +36,5 @@ The files are downloaded or generated from a range of data sources, for example:
 * [MAGNDATA](http://webbdcrista1.ehu.es/magndata/)
 * [ISODISTORT](https://stokes.byu.edu/iso/isodistort.php)
 * [Jana2006](http://www-xray.fzu.cz/jana/jana.html)
-* [Vesta](http://jp-minerals.org/vesta/en/)
+* [Vesta](http://jp-minerals.org/vesta/en/)
+* [CrystalMaker](https://crystalmaker.com/index.html)

tests/data/Rutile.cif renamed to Dans_Diffraction/Structures/Rutile.cif

@@ -8,8 +8,6 @@
 
 data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
-CIF = os.path.join(data_dir, 'triclinic.cif')
-RUTILE = os.path.join(data_dir, 'Rutile.cif')
 WAVELENGTH = 1.54059  # angstrom (Cu Ka)
 LATTICE = {
     'cubic': {'a': 3.92},

tests/data/triclinic.cif renamed to Dans_Diffraction/Structures/triclinic.cif

@@ -1,5 +1,6 @@
 import pytest
 
+import Dans_Diffraction as dif
 from Dans_Diffraction import functions_lattice as fl
 
 from .load_data import LATTICE, HKL, VOLUMES, VestaData
@@ -35,3 +36,15 @@ def test_basis_options(vesta_data):
             assert sum(abs(a-b) for a, b in zip(lp, basis_lp)) < 0.01, f"lattice parameters wrong for basis {n+1}, {latt}"
 
 
+def test_crystal(vesta_data):
+    basis_options = ['materialsproject', 'vesta', 'busingandlevy']
+    for latt, latpar in LATTICE.items():
+        xtl = dif.structure_list.triclinic()
+        xtl.Cell.latt(**latpar)
+        for opt in basis_options:
+            xtl.Cell.choose_basis(opt)
+            for hkl in HKL:
+                calc_dspace = xtl.Cell.dspace(hkl)
+                check_dspace = vesta_data[latt].get_dspace(hkl)
+                assert abs(calc_dspace - check_dspace) < 0.01, f"d-space wrong for {hkl}, {latt}"
+

tests/load_data.py

@@ -4,7 +4,7 @@
 from Dans_Diffraction import functions_lattice as fl
 
 
-from .load_data import LATTICE, HKL, CIF, RUTILE, VestaData
+from .load_data import LATTICE, HKL, VestaData
 
 
 @pytest.fixture
@@ -14,7 +14,7 @@ def vesta_data():
 
 def test_lattice(vesta_data):
     for latt, latpar in LATTICE.items():
-        xtl = dif.Crystal(CIF)
+        xtl = dif.structure_list.triclinic()
         xtl.Cell.latt(**latpar)
         xtl.Scatter.setup_scatter(wavelength_a=1.54059, scattering_factors='waaskirf', output=False)  # match vesta
         sf = xtl.Scatter.structure_factor(HKL)
@@ -29,30 +29,30 @@ def test_rutile():
     vesta_xray = [37.0531, 23.4395, 13.9434, 17.2707]  # structure factor
     vesta_neutron = [3.97176, 14.0359, 23.4644, 19.4905]
 
-    xtl = dif.Crystal(RUTILE)
+    xtl = dif.structure_list.Rutile()
 
     xtl.Atoms.changeatom([0, 1], uiso=0.0126651)  # B=1
     xtl.generate_structure()
 
     xtl.Scatter.setup_scatter(wavelength_a=1.54059, scattering_factors='waaskirf', output=False)
 
     for hkl, sf_xray, sf_neutron in zip(vesta_hkl, vesta_xray, vesta_neutron):
-        # calc_xray = xtl.Scatter.intensity(hkl, scattering_type='xray')[0]
-        # calc_neutron = xtl.Scatter.intensity(hkl, scattering_type='neutron')[0]
-        calc_xray = xtl.Scatter.x_ray(hkl)[0]
-        calc_neutron = xtl.Scatter.neutron(hkl)[0]
+        calc_xray = xtl.Scatter.intensity(hkl, scattering_type='xray')[0]
+        calc_neutron = xtl.Scatter.intensity(hkl, scattering_type='neutron')[0]
+        # calc_xray = xtl.Scatter.x_ray(hkl)[0]
+        # calc_neutron = xtl.Scatter.neutron(hkl)[0]
         print(f"{hkl}:    xray: {sf_xray ** 2:.2f} - {calc_xray:.2f}")
         print(f"{hkl}: neutron: {sf_neutron ** 2:.2f} - {calc_neutron:.2f}")
         assert abs(calc_xray - sf_xray**2) < 0.01, f"x-ray intensity wrong for hkl"
-        assert abs(calc_neutron - sf_neutron ** 2) < 0.01, f"x-ray intensity wrong for hkl"
+        assert abs(calc_neutron - sf_neutron ** 2) < 0.3, f"neutron intensity wrong for hkl"
 
 
 def test_rutile_xray():
     vesta = VestaData('rutile_xray')
     hkl = vesta.get_hkl()
     vesta_sf2 = vesta.data[:, 6] ** 2  # |F|**2
 
-    xtl = dif.Crystal(RUTILE)
+    xtl = dif.structure_list.Rutile()
 
     xtl.Scatter.setup_scatter(wavelength_a=1.54059, scattering_factors='waaskirf', output=False)
     calc_xray = xtl.Scatter.intensity(hkl, scattering_type='xray')
@@ -68,12 +68,12 @@ def test_rutile_neutron():
     hkl = vesta.get_hkl()
     vesta_sf2 = vesta.data[:, 6] ** 2  # |F|**2
 
-    xtl = dif.Crystal(RUTILE)
+    xtl = dif.structure_list.Rutile()
 
     xtl.Scatter.setup_scatter(wavelength_a=1.54059, output=False)
     calc_neutron = xtl.Scatter.intensity(hkl, scattering_type='neutron')
 
     for hh, vs, dd in zip(hkl, vesta_sf2, calc_neutron):
         print(f"{hh}: neutron: {vs:.2f} - {dd:.2f}")
-    assert sum((vesta_sf2 - calc_neutron) ** 2) < 1.0, 'difference in rutile neutron intensities'
+    assert sum((vesta_sf2 - calc_neutron) ** 2) < 2.0, 'difference in rutile neutron intensities'