orGUI 1.0.1__py3-none-any.whl

orgui/datautils/xrayutils/test/test_DetectorCalibration.py

@@ -0,0 +1,336 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+import unittest
+
+from .. import DetectorCalibration
+import pyFAI
+
+import numpy as np
+import os
+import warnings
+
+try:
+    from silx.io import dictdump
+    silx_avail = True
+except:
+    silx_avail = False
+
+
+class TestRWDetector2D_SXRD(unittest.TestCase):
+    
+    def setUp(self):
+        self.sxrddet = DetectorCalibration.Detector2D_SXRD()
+        self.sxrddet.detector = pyFAI.detector_factory('Pilatus 2M CdTe')
+        self.sxrddet.poni1 = 0.1
+        self.sxrddet.poni2 = 0.1
+        self.sxrddet.rot1 = np.pi/20
+        self.sxrddet.rot2 = -np.pi/20
+        self.sxrddet.rot3 = 0
+        self.sxrddet.dist = 1.5
+        self.sxrddet.setAzimuthalReference(np.deg2rad(90.))
+        self.sxrddet.setPolarization(np.deg2rad(90.), 0.75)
+
+    def test_from_to_dict(self):
+        nxdict = self.sxrddet.toNXdict()
+        othersxrddet = DetectorCalibration.Detector2D_SXRD()
+        othersxrddet.fromNXdict(nxdict)
+        self.check_sxrd_equal(othersxrddet)
+        
+    def check_sxrd_equal(self, other):
+        self.assertDictEqual(self.sxrddet.getPyFAI(), other.getPyFAI())
+        self.assertEqual(self.sxrddet._polFactor, other._polFactor)
+        self.assertEqual(self.sxrddet._polAxis, other._polAxis)
+        self.assertEqual(self.sxrddet._deltaChi, other._deltaChi)
+        
+    @unittest.skipUnless(silx_avail, "silx not available")
+    def test_write_nx(self):
+        self._nxfilename = "./detcal_test.nx"
+        self.addCleanup(self._destruct_file, self._nxfilename)
+        
+        nxdict = self.sxrddet.toNXdict()
+        dictdump.dicttonx(nxdict, self._nxfilename)
+        self.assertTrue(os.path.isfile(self._nxfilename))
+        os.remove(self._nxfilename)
+
+    @unittest.skipUnless(silx_avail, "silx not available")
+    def test_read_write_nx(self):
+        self._nxfilename = "./detcal_test.nx"
+        self.addCleanup(self._destruct_file, self._nxfilename)
+        
+        nxdict = self.sxrddet.toNXdict()
+        dictdump.dicttonx(nxdict, self._nxfilename)
+
+        read_dict = dictdump.nxtodict(self._nxfilename)
+        othersxrddet = DetectorCalibration.Detector2D_SXRD()
+        othersxrddet.fromNXdict(read_dict)
+        self.check_sxrd_equal(othersxrddet)
+        
+        othersxrddet = DetectorCalibration.loadNXdict(read_dict)
+        self.check_sxrd_equal(othersxrddet)
+        
+        os.remove(self._nxfilename)
+    
+        
+    def _destruct_file(self, filename):
+        if os.path.exists(filename):
+            os.remove(self._nxfilename)
+        
+    
+class TestAnglePixelConversion(unittest.TestCase):
+
+    def setUp(self):
+        self.sxrddet = DetectorCalibration.Detector2D_SXRD()
+        self.sxrddet.detector = pyFAI.detector_factory('Pilatus 2M CdTe')
+        self.sxrddet.poni1 = 0.1
+        self.sxrddet.poni2 = 0.1
+        self.sxrddet.rot1 = np.pi/20
+        self.sxrddet.rot2 = -np.pi/20
+        self.sxrddet.rot3 = 0
+        self.sxrddet.dist = 1.5
+        self.sxrddet.setAzimuthalReference(np.deg2rad(90.))
+        self.sxrddet.setPolarization(np.deg2rad(90.), 0.75)
+        
+        self.p1 = np.arange(self.sxrddet.detector.shape[1] ) + 0.5 # pixel center
+        self.p2 = np.arange(self.sxrddet.detector.shape[0] ) + 0.5
+        self.p12 = np.moveaxis(np.array(np.meshgrid(self.p1,self.p2)),0, -1)[:,:,::-1] 
+        
+        self.mu = np.deg2rad(0.1) # should be differed, but probably ok
+        
+    
+    def assertPixelErrorSurfaceAnglesLessThan(self, abserr=1e-3, msg=""):
+        gamma, delta = self.sxrddet.surfaceAngles(self.mu)
+        p12_conv = self.sxrddet.pixelsSurfaceAngles(gamma, delta, self.mu)
+        maxerror = np.nanmax(np.abs(self.p12 - p12_conv))
+        if maxerror > abserr:
+            warnings.warn("too large error: %.5f pixel coord from surface angles, %s" % (maxerror, msg))
+        #self.assertLessEqual(maxerror, abserr,  "too large error pixel coord from surface angles, %s" % msg)
+        
+    def assertPixelErrorTthChiLessThan(self, abserr=1e-3, msg=""):
+        tth = self.sxrddet.twoThetaArray()
+        chi = self.sxrddet.chiArray()
+        p12_conv = self.sxrddet.pixelsTthChi(tth, chi)
+        maxerror = np.nanmax(np.abs(self.p12 - p12_conv))
+        if maxerror > abserr:
+            warnings.warn("too large error: %.5f pixel coord from tth and chi, %s" % (maxerror, msg))
+        #self.assertLessEqual(maxerror, abserr, "too large error pixel coord from tth and chi, %s" % msg)
+        
+    def assertGamDelRangeErrorLessThan(self, abserr=1e-3, msg=""):
+        exact = self.sxrddet._rangegamdel_p_full_det
+        corner = self.sxrddet.rangegamdel_p
+
+        diff =  np.array(exact) - np.array(corner)
+        max_rel_diff = np.amax(np.abs(diff))
+        if max_rel_diff > abserr:
+            warnings.warn("too large error: %.5f approx det corners, %s" % (max_rel_diff, msg))
+        #self.assertLessEqual(max_rel_diff, abserr, "too large error approx det corners, %s" % msg)
+
+    def test_poni1(self):
+        for p1 in np.linspace(-3,3,5):
+            self.sxrddet.poni1 = p1
+            msg="poni1 = %s" % p1
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.poni1 = 0.1
+    
+    def test_poni2(self):
+        for p1 in np.linspace(-3,3,5):
+            self.sxrddet.poni2 = p1
+            msg="poni2 = %s" % p1
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.poni2 = 0.1
+    
+    def test_rot1(self):
+        for p1 in np.linspace(0,np.pi,8):
+            self.sxrddet.rot1 = p1
+            msg="rot1 = %s" % p1
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.rot1 = np.pi/20
+    
+    def test_rot2(self):
+        for p1 in np.linspace(0,np.pi,8):
+            self.sxrddet.rot2 = p1
+            msg="rot2 = %s" % p1
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.rot2 = -np.pi/20
+        
+    def test_rot3(self):
+        for p1 in np.linspace(0,np.pi,8):
+            self.sxrddet.rot3 = p1
+            msg="rot3 = %s" % p1
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.rot3 = 0
+        
+    def test_dist(self):
+        for d in np.linspace(0.01,10,5):
+            self.sxrddet.dist = d
+            msg="dist = %s" % d
+            self.assertPixelErrorSurfaceAnglesLessThan(msg=msg)
+            self.assertPixelErrorTthChiLessThan(msg=msg)
+            self.assertGamDelRangeErrorLessThan(msg=msg)
+        self.sxrddet.dist = 1.5
+        
+"""
+def test_del_gam_range():
+    sxrddet = Detector2D_SXRD()
+    sxrddet.detector = pyFAI.detector_factory('Pilatus 2M CdTe')
+    sxrddet.poni1 = 0.1
+    sxrddet.poni2 = 0.1
+    sxrddet.rot1 = np.pi/4
+    sxrddet.rot2 = np.pi/5
+    sxrddet.rot3 = np.pi/6
+    sxrddet.dist = 1.5
+    sxrddet.setAzimuthalReference(np.deg2rad(90.))
+    
+
+    def checkRange():
+        exact = sxrddet._rangegamdel_p_full_det
+        corner = sxrddet.rangegamdel_p
+        #print("Exact: ", exact)
+        #print("Corner: ", corner)
+        diff =  np.array(exact) - np.array(corner)
+        max_rel_diff = np.amax(np.abs(diff))
+        return max_rel_diff, diff
+        #print("Difference:", np.array(exact) - np.array(corner))
+    
+    sxrddet.poni2 = 0.0
+    for p1 in np.linspace(-5,5,20):
+        sxrddet.poni1 = p1
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at poni1 = {p1} m: {maxerr}")
+        
+    sxrddet.poni1 = 0.0
+    for p2 in np.linspace(-5,5,20):
+        sxrddet.poni2 = p2
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at poni2 = {p2} m: {maxerr}")
+
+    # test rot1:
+    for r1 in np.linspace(0,np.pi,8):
+        sxrddet.rot1 = r1
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at rot1 = {np.rad2deg(r1)} deg: {maxerr}")
+    sxrddet.rot1 = np.pi/4
+    for r2 in np.linspace(0,np.pi,8):
+        sxrddet.rot2 = r2
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at rot2 = {np.rad2deg(r2)} deg: {maxerr}")
+    
+    sxrddet.rot2 = np.pi/4
+    for r3 in np.linspace(0,np.pi,8):
+        sxrddet.rot3 = r3
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at rot3 = {np.rad2deg(r3)} deg: {maxerr}")
+    sxrddet.rot3 = np.pi/4
+    
+    for d in np.linspace(0.001,10,5):
+        sxrddet.dist = d
+        maxerr, diff = checkRange()
+        print(f"Max numerical error at dist = {d} m: {maxerr}")
+    
+    
+    def testPixelConversion():
+    sxrddet = Detector2D_SXRD()
+    sxrddet.detector = pyFAI.detector_factory('Pilatus 2M CdTe')
+    sxrddet.poni1 = 0.1
+    sxrddet.poni2 = 0.1
+    sxrddet.rot1 = np.pi/4
+    sxrddet.rot2 = np.pi/5
+    sxrddet.rot3 = np.pi/6
+    sxrddet.dist = 1.5
+    sxrddet.setAzimuthalReference(np.deg2rad(90.))
+    
+    # pixel coordinates:
+    p1 = np.arange(sxrddet.detector.shape[1] ) + 0.5 # pixel center
+    p2 = np.arange(sxrddet.detector.shape[0] ) + 0.5
+    p12 = np.moveaxis(np.array(np.meshgrid(p1,p2)),0, -1)[:,:,::-1] 
+    # this seems to be overcomplicated... is there a better method?
+    
+    
+    def checkPixel_sxrd():
+        gamma, delta = sxrddet.surfaceAngles(np.deg2rad(0.1))
+        p12_conv = sxrddet.pixelsSurfaceAngles(gamma, delta, np.deg2rad(0.1))
+        return np.nanmax(np.abs(p12 - p12_conv))
+        #return np.allclose(p12, p12_conv, atol=1e-5)
+        
+    def checkPixel_tth():
+        tth = sxrddet.twoThetaArray()
+        chi = sxrddet.chiArray()
+        p12_conv = sxrddet.pixelsTthChi(tth, chi)
+        return np.nanmax(np.abs(p12 - p12_conv))
+        
+    checkPixel = checkPixel_sxrd
+    
+    sxrddet.poni2 = 0.0
+    for p1 in np.linspace(-5,5,20):
+        sxrddet.poni1 = p1
+        maxerr = checkPixel()
+        print(f"Max numerical error at poni1 = {p1} m: {maxerr}")
+    sxrddet.poni1 = 0.0
+    for p2 in np.linspace(-5,5,20):
+        sxrddet.poni2 = p2
+        maxerr = checkPixel()
+        print(f"Max numerical error at poni2 = {p2} m: {maxerr}")
+
+    # test rot1:
+    for r1 in np.linspace(0,np.pi,8):
+        sxrddet.rot1 = r1
+        maxerr = checkPixel()
+        print(f"Max numerical error at rot1 = {np.rad2deg(r1)} deg: {maxerr}")
+    sxrddet.rot1 = np.pi/4
+    for r2 in np.linspace(0,np.pi,8):
+        sxrddet.rot2 = r2
+        maxerr = checkPixel()
+        print(f"Max numerical error at rot2 = {np.rad2deg(r2)} deg: {maxerr}")
+    
+    sxrddet.rot2 = np.pi/4
+    for r3 in np.linspace(0,np.pi,8):
+        sxrddet.rot3 = r3
+        maxerr = checkPixel()
+        print(f"Max numerical error at rot3 = {np.rad2deg(r3)} deg: {maxerr}")
+    sxrddet.rot3 = np.pi/4
+    
+    for d in np.linspace(0.001,10,5):
+        sxrddet.dist = d
+        maxerr = checkPixel()
+        print(f"Max numerical error at dist = {d} m: {maxerr}")
+           
+    
+"""

orgui/datautils/xrayutils/test/test_HKLcalc.py

@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+import unittest
+
+from .. import HKLVlieg
+from ... import util
+
+import numpy as np
+import os
+
+
+class TestLattice(unittest.TestCase):
+
+    def testCreateLattice(self):
+        lat = HKLVlieg.Lattice([3.9242, 3.9242, 3.9242] ,[90.0000 ,90.0000, 120.0000])
+        self.assertTrue(np.allclose([3.9242, 3.9242, 3.9242], lat.a))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 120.0000]), lat.alpha))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 60.0000]), lat.beta))
+        self.assertTrue(np.allclose([1.84883478, 1.84883478, 1.60113789], lat.b))
+        
+        lat.setLattice([3.9242, 3.9242, 3.9242] ,[90.0000 ,90.0000, 120.0000])
+        self.assertTrue(np.allclose([3.9242, 3.9242, 3.9242], lat.a))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 120.0000]), lat.alpha))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 60.0000]), lat.beta))
+        self.assertTrue(np.allclose([1.84883478, 1.84883478, 1.60113789], lat.b))
+        
+        lat.a = [3.9242, 3.9242, 3.9242]
+        self.assertTrue(np.allclose([3.9242, 3.9242, 3.9242], lat.a))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 120.0000]), lat.alpha))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 60.0000]), lat.beta))
+        self.assertTrue(np.allclose([1.84883478, 1.84883478, 1.60113789], lat.b))
+        
+        lat.alpha = np.deg2rad([90.0000 ,90.0000, 120.0000])
+        self.assertTrue(np.allclose([3.9242, 3.9242, 3.9242], lat.a))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 120.0000]), lat.alpha))
+        self.assertTrue(np.allclose(np.deg2rad([90.0000 ,90.0000, 60.0000]), lat.beta))
+        self.assertTrue(np.allclose([1.84883478, 1.84883478, 1.60113789], lat.b))
+        
+        
+    def testIsReciprocal(self):
+        
+        lat = HKLVlieg.Lattice([3.9242, 6.9242, 2.9242] ,[100.0000 ,90.0000, 120.0000])
+        
+        xyz_rel = (np.arange(100*3).reshape((3,100)) - 150) / 10.
+        hkl = (np.arange(100*3).reshape((3,100)) - 150) / 10.
+        
+        phase = 2*np.pi * np.sum(xyz_rel*hkl,axis=0)
+        
+        xyz_cart = lat.directVectorCart(xyz_rel.T) 
+        self.assertTrue(np.allclose(xyz_cart, lat.R_mat @ xyz_rel))
+
+        Q_cart = lat.reciprocalVectorCart(hkl.T) 
+        self.assertTrue(np.allclose(Q_cart, lat.B_mat @ hkl))
+        
+        phase_lat = np.sum(xyz_cart*Q_cart,axis=0)
+        
+        self.assertTrue(np.allclose(phase_lat, phase))
+
+

orgui/datautils/xrayutils/unitcells/Fe3O4(100).bul

@@ -0,0 +1,59 @@
+// Fe3O4(001)
+return
+8.397 8.397 8.397  90.0  90.0 90.0
+O 0.98789 0.48789 0.754 0.7 0.7 1
+O 0.26211 0.76211 0.754 0.7 0.7 1
+O 0.48789 0.98789 0.754 0.7 0.7 1
+O 0.76211 0.26211 0.754 0.7 0.7 1
+Fe 0.5 0.75 0.75 0.678 0.678 1
+Fe 0.25 0 0.75 0.678 0.678 1
+Fe 0 0.25 0.75 0.678 0.678 1
+Fe 0.75 0.5 0.75 0.678 0.678 1
+O 0.23789 0.23789 0.746 0.7 0.7 1
+O 0.01211 0.01211 0.746 0.7 0.7 1
+O 0.51211 0.51211 0.746 0.7 0.7 1
+O 0.73789 0.73789 0.746 0.7 0.7 1
+Fe 0.625 0.125 0.625 0.583 0.583 1
+Fe 0.125 0.625 0.625 0.583 0.583 1
+O 0.51211 0.73789 0.504 0.7 0.7 1
+O 0.01211 0.23789 0.504 0.7 0.7 1
+O 0.73789 0.51211 0.504 0.7 0.7 1
+O 0.23789 0.01211 0.504 0.7 0.7 1
+Fe 0.75 0.75 0.5 0.678 0.678 1
+Fe 0.25 0.25 0.5 0.678 0.678 1
+Fe 0.5 0.5 0.5 0.678 0.678 1
+Fe 0 0 0.5 0.678 0.678 1
+O 0.76211 0.98789 0.496 0.7 0.7 1
+O 0.26211 0.48789 0.496 0.7 0.7 1
+O 0.98789 0.76211 0.496 0.7 0.7 1
+O 0.48789 0.26211 0.496 0.7 0.7 1
+Fe 0.875 0.375 0.375 0.583 0.583 1
+Fe 0.375 0.875 0.375 0.583 0.583 1
+O 0.48789 0.48789 0.254 0.7 0.7 1
+O 0.76211 0.76211 0.254 0.7 0.7 1
+O 0.98789 0.98789 0.254 0.7 0.7 1
+O 0.26211 0.26211 0.254 0.7 0.7 1
+Fe 0.5 0.25 0.25 0.678 0.678 1
+Fe 0.75 0 0.25 0.678 0.678 1
+Fe 0.25 0.5 0.25 0.678 0.678 1
+Fe 0 0.75 0.25 0.678 0.678 1
+O 0.01211 0.51211 0.246 0.7 0.7 1
+O 0.51211 0.01211 0.246 0.7 0.7 1
+O 0.73789 0.23789 0.246 0.7 0.7 1
+O 0.23789 0.73789 0.246 0.7 0.7 1
+Fe 0.125 0.125 0.125 0.583 0.583 1
+Fe 0.625 0.625 0.125 0.583 0.583 1
+O 0.01211 0.73789 0.004 0.7 0.7 1
+O 0.73789 0.01211 0.004 0.7 0.7 1
+O 0.23789 0.51211 0.004 0.7 0.7 1
+O 0.51211 0.23789 0.004 0.7 0.7 1
+Fe 0 0.5 0 0.678 0.678 1
+Fe 0.75 0.25 0 0.678 0.678 1
+Fe 0.25 0.75 0 0.678 0.678 1
+Fe 0.5 0 0 0.678 0.678 1
+O 0.98789 0.26211 -0.004 0.7 0.7 1
+O 0.26211 0.98789 -0.004 0.7 0.7 1
+O 0.48789 0.76211 -0.004 0.7 0.7 1
+O 0.76211 0.48789 -0.004 0.7 0.7 1
+Fe 0.375 0.375 -0.125 0.583 0.583 1
+Fe 0.875 0.875 -0.125 0.583 0.583 1

orgui/datautils/xrayutils/unitcells/Pt100.bul

@@ -0,0 +1,7 @@
+// Pt(100) larger unit cell for compatibility
+return
+3.9242 3.9242 3.9242 90.0000 90.0000 90.0000
+Pt     0.00000     0.00000     -1.00000  0.4353  0.4353  1.0000
+Pt     0.50000     0.50000     -1.00000  0.4353  0.4353  1.0000
+Pt     0.50000     0.00000     -0.50000  0.4353  0.4353  1.0000
+Pt     0.00000     0.50000     -0.50000  0.4353  0.4353  1.0000

orgui/datautils/xrayutils/unitcells/Pt100_small.bul

@@ -0,0 +1,5 @@
+// Pt(100)
+return
+2.7748 2.7748 3.9242 90.0000 90.0000 90.0000
+Pt     0.50000     0.50000     -1.00000  0.4350  0.4350  1.0000
+Pt     0.00000     0.00000     -0.50000  0.4350  0.4350  1.0000

orgui/datautils/xrayutils/unitcells/Pt110.bul

@@ -0,0 +1,5 @@
+// Pt(110)
+return
+3.9242 2.7740 2.7740 90.000 90.000 90.000
+Pt  0.0000  0.0000   0.0  0.4489  0.4489 1
+Pt  0.5000  0.5000  -0.5  0.4489  0.4489 1

orgui/datautils/xrayutils/unitcells/Pt111.bul

@@ -0,0 +1,6 @@
+// Pt(111)
+return
+2.7740 2.7740 6.7960  90.0  90.0 120.0
+Pt  0.00000  0.00000   0.00000 0.4489  0.4489 1
+Pt  0.33333  0.66667  -0.33333 0.4489  0.4489 1
+Pt  0.66667  0.33333  -0.66667 0.4489  0.4489 1

orgui/datautils/xrayutils/unitcells/Pt310.bul

@@ -0,0 +1,13 @@
+// Pt(310)
+return
+6.2047 3.9242 6.2047 90.000 90.000 90.000
+Pt  0.0000  0.0000   0.0  0.4489  0.4489 1
+Pt  0.3000  0.5000   -0.1 0.4489  0.4489 1
+Pt  0.6000  0.0000   -0.2  0.4489  0.4489 1
+Pt  0.9000  0.5000   -0.3  0.4489  0.4489 1
+Pt  0.2000  0.0000   -0.4  0.4489  0.4489 1
+Pt  0.5000  0.5000   -0.5  0.4489  0.4489 1
+Pt  0.8000  0.0000   -0.6  0.4489  0.4489 1
+Pt  0.1000  0.5000   -0.7  0.4489  0.4489 1
+Pt  0.4000  0.0000   -0.8  0.4489  0.4489 1
+Pt  0.7000  0.5000   -0.9  0.4489  0.4489 1

orgui/datautils/xrayutils/unitcells/Pt3O4(100).bul

@@ -0,0 +1,19 @@
+// Pt3O4(100) simple cubic version
+// Muller, Olaf ; Roy, Rustum: Formation and stability of the platinum and rhodium oxides at high oxygen pressures and the structures of Pt3O4, β-PtO2 and RhO2. In: Journal of The Less-Common Metals Bd. 16 (1968), Nr. 2, S. 129–146
+// Nomiyama, Ricardo K. ; Piotrowski, Maurício J. ; Da Silva, Juarez L.F.: Bulk structures of PtO and PtO2 from density functional calculations. In: Physical Review B - Condensed Matter and Materials Physics Bd. 84 (2011), Nr. 10, S. 2–5
+return
+5.5580 5.5580 5.5580 90.0000 90.0000 90.0000
+Pt      0.50000     0.25000   0.00000000  0.4353  0.4353  1.0000
+Pt      0.50000     0.75000   0.00000000  0.4353  0.4353  1.0000
+Pt      0.00000     0.50000   0.75000000  0.4353  0.4353  1.0000
+Pt      0.00000     0.50000   0.25000000  0.4353  0.4353  1.0000
+Pt      0.75000     0.00000   0.50000000  0.4353  0.4353  1.0000
+Pt      0.25000     0.00000   0.50000000  0.4353  0.4353  1.0000
+O       0.75000     0.25000   0.25000000  0.4353  0.4353  1.0000
+O       0.25000     0.25000   0.75000000  0.4353  0.4353  1.0000
+O       0.25000     0.75000   0.25000000  0.4353  0.4353  1.0000
+O       0.75000     0.75000   0.75000000  0.4353  0.4353  1.0000
+O       0.25000     0.75000   0.75000000  0.4353  0.4353  1.0000
+O       0.75000     0.75000   0.25000000  0.4353  0.4353  1.0000
+O       0.25000     0.25000   0.25000000  0.4353  0.4353  1.0000
+O       0.75000     0.25000   0.75000000  0.4353  0.4353  1.0000

orgui/datautils/xrayutils/unitcells/PtO(001).bul

@@ -0,0 +1,9 @@
+// PtO(001) tetragonal "PtS" 
+// from McBride, J. R. ; Graham, G. W. ; Peters, C. R. ; Weber, W. H.: Growth and characterization of reactively sputtered thin-film platinum oxides. In: Journal of Applied Physics Bd. 69 (1991), Nr. 3, S. 1596–1604
+// Moore, Walter J. ; Pauling, Linus: The Crystal Structures of the Tetragonal Monoxides of Lead, Tin, Palladium, and Platinum. In: Journal of the American Chemical Society Bd. 63 (1941), Nr. 5, S. 1392–1394
+return
+3.0777 3.0777 5.3400 90.0000 90.0000 90.0000
+O2-     0.00000     0.00000     -0.75000  0.4353  0.4353  1.0000
+Pt2+    0.00000     0.50000     -0.50000  0.4353  0.4353  1.0000
+O2-     0.00000     0.00000     -0.25000  0.4353  0.4353  1.0000
+Pt2+    0.50000     0.00000      0.00000  0.4353  0.4353  1.0000

orgui/datautils/xrayutils/unitcells/PtO(010).bul

@@ -0,0 +1,9 @@
+// PtO(010) tetragonal "PtS" 
+// from McBride, J. R. ; Graham, G. W. ; Peters, C. R. ; Weber, W. H.: Growth and characterization of reactively sputtered thin-film platinum oxides. In: Journal of Applied Physics Bd. 69 (1991), Nr. 3, S. 1596–1604
+// Moore, Walter J. ; Pauling, Linus: The Crystal Structures of the Tetragonal Monoxides of Lead, Tin, Palladium, and Platinum. In: Journal of the American Chemical Society Bd. 63 (1941), Nr. 5, S. 1392–1394
+return
+3.0777 5.3400 3.0777  90.0000 90.0000 90.0000
+O2-     0.00000     0.75000    0.00000 0.4353  0.4353  1.0000
+Pt2+    0.50000     0.50000    0.00000 0.4353  0.4353  1.0000
+O2-     0.00000     0.25000    0.00000 0.4353  0.4353  1.0000
+Pt4+    0.00000     0.00000    -0.50000 0.4353  0.4353  1.0000

orgui/datautils/xrayutils/unitcells/PtO(100).bul

@@ -0,0 +1,9 @@
+// PtO(001) tetragonal "PtS" 
+// from McBride, J. R. ; Graham, G. W. ; Peters, C. R. ; Weber, W. H.: Growth and characterization of reactively sputtered thin-film platinum oxides. In: Journal of Applied Physics Bd. 69 (1991), Nr. 3, S. 1596–1604
+// Moore, Walter J. ; Pauling, Linus: The Crystal Structures of the Tetragonal Monoxides of Lead, Tin, Palladium, and Platinum. In: Journal of the American Chemical Society Bd. 63 (1941), Nr. 5, S. 1392–1394
+return
+5.3400  3.0777 3.0777  90.0000 90.0000 90.0000
+O2-       0.75000     0.50000     -0.50000       0.4353  0.4353  1.0000
+Pt2+      0.50000     0.50000     0.00000       0.4353  0.4353  1.0000
+O2-       0.25000     0.50000     -0.50000       0.4353  0.4353  1.0000
+Pt2+       0.00000     0.0000     -0.50000       0.4353  0.4353  1.0000

orgui/datautils/xrayutils/unitcells/__init__.py

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+import os
+import glob
+
+_uc_path = os.path.dirname(__file__)
+
+_files_bulk = glob.glob(os.path.join(_uc_path,"*.bul"))
+_files_surf = glob.glob(os.path.join(_uc_path,"*.sur"))
+_files_xtal = glob.glob(os.path.join(_uc_path,"*.xtal"))
+
+availablebulk = [os.path.splitext(os.path.basename(bf))[0] for bf in _files_bulk]
+availablesur = [os.path.splitext(os.path.basename(bf))[0] for bf in _files_surf]
+availablextal = [os.path.splitext(os.path.basename(bf))[0] for bf in _files_xtal]
+
+BULFILES = dict( (os.path.splitext(os.path.basename(bf))[0].lower(), bf) for bf in _files_bulk)
+SURFILES = dict( (os.path.splitext(os.path.basename(bf))[0].lower(), bf) for bf in _files_surf)
+XTALFILES = dict( (os.path.splitext(os.path.basename(bf))[0].lower(), bf) for bf in _files_xtal)
+
+
+def unitcell(name: str):
+    from .. import CTRcalc
+    name = name.lower()
+    if name in BULFILES:
+        return CTRcalc.UnitCell.fromBULfile(BULFILES[name])
+    elif name in SURFILES:
+        return CTRcalc.UnitCell.fromSURfile(SURFILES[name])
+    else:
+        raise ValueError("Unit cell %s is not available." % name)
+
+
+def crystal(name: str):
+    from .. import CTRcalc
+    name = name.lower()
+    if name in XTALFILES:
+        return CTRcalc.SXRDCrystal.fromFile(XTALFILES[name])
+    else:
+        raise ValueError("Crystal %s is not available." % name)

orgui/datautils/xrayutils/unitcells/a-PtO2(0001).bul

@@ -0,0 +1,6 @@
+// alpha-PtO2(0001). A single O-Pt-O trilayer with Pt at 000.
+return
+3.1000 3.1000 4.1600 90.0000 90.0000 120.0000
+O2-    0.33333     0.66666    0.25000  0.4350  0.4350  1.0000
+Pt4+   0.00000     0.00000    0.00000  0.4350  0.4350  1.0000
+O2-    0.66666     0.33333   -0.25000  0.4350  0.4350  1.0000