def test_get_pattern(self):
s = self.get_structure("CsCl")
c = XRDCalculator()
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertTrue(xrd.to_json()) # Test MSONAble property
# Check the first two peaks
self.assertAlmostEqual(xrd.x[0], 21.107738329639844)
self.assertAlmostEqual(xrd.y[0], 36.483184003748946)
self.assertEqual(xrd.hkls[0], [{'hkl': (1, 0, 0), 'multiplicity': 6}])
self.assertAlmostEqual(xrd.d_hkls[0], 4.2089999999999996)
self.assertAlmostEqual(xrd.x[1], 30.024695921112777)
self.assertAlmostEqual(xrd.y[1], 100)
self.assertEqual(xrd.hkls[1], [{"hkl": (1, 1, 0), "multiplicity": 12}])
self.assertAlmostEqual(xrd.d_hkls[1], 2.976212442014178)
s = self.get_structure("LiFePO4")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 17.03504233621785)
self.assertAlmostEqual(xrd.y[1], 50.400928948337075)
s = self.get_structure("Li10GeP2S12")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 14.058274883353876)
self.assertAlmostEqual(xrd.y[1], 4.4111123641667671)
# Test a hexagonal structure.
s = self.get_structure("Graphite")
xrd = c.get_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[0], 26.21057350859598)
self.assertAlmostEqual(xrd.y[0], 100)
self.assertAlmostEqual(len(xrd.hkls[0][0]["hkl"]), 4)
# Add test case with different lengths of coefficients.
# Also test d_hkl.
coords = [[0.25, 0.25, 0.173], [0.75, 0.75, 0.827], [0.75, 0.25, 0],
[0.25, 0.75, 0], [0.25, 0.25, 0.676], [0.75, 0.75, 0.324]]
sp = ["Si", "Si", "Ru", "Ru", "Pr", "Pr"]
s = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
xrd = c.get_pattern(s)
self.assertAlmostEqual(xrd.x[0], 12.86727341476735)
self.assertAlmostEqual(xrd.y[0], 31.448239816769796)
self.assertAlmostEqual(xrd.d_hkls[0], 6.88)
self.assertEqual(len(xrd), 42)
xrd = c.get_pattern(s, two_theta_range=[0, 60])
self.assertEqual(len(xrd), 18)
# Test with and without Debye-Waller factor
tungsten = Structure(Lattice.cubic(3.1653), ["W"] * 2,
[[0, 0, 0], [0.5, 0.5, 0.5]])
xrd = c.get_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2414237.5633093244)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c = XRDCalculator(debye_waller_factors={"W": 0.1526})
xrd = c.get_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2377745.2296686019)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c.get_plot(tungsten).show()
def get_xrd_plot(args):
"""
Plot XRD
Args:
args (dict): Args from argparse
"""
s = Structure.from_file(args.xrd_structure_file)
c = XRDCalculator()
return c.get_plot(s)
def get_xrd():
struct = readstructure()
xrd = XRDCalculator()
# xrd_data=xrd.get_xrd_pattern(struct)
xrd_data = xrd.get_pattern(struct)
jxrd_data = jsanitize(xrd_data.as_dict())
fname = 'XRD.json'
proc_str = "Saving data to " + fname + " File ..."
procs(proc_str, 1, sp='-->>')
json_store(jxrd_data, fname)
data = np.vstack((xrd_data.x, xrd_data.y)).T
margin = 10.
ds = xrd_data.x[0] - margin
de = xrd_data.x[-1] + margin
tmp_data = [ds] + xrd_data.x.tolist() + [de]
tmp_data1 = np.diff(tmp_data).tolist()
tmp_data2 = np.array([0] + np.cumsum(tmp_data1).tolist())
tmp_data3 = tmp_data2 / tmp_data2[-1]
x_data = np.linspace(ds, de, 10000)
y_data = np.zeros((len(x_data)))
for i in range(1, len(tmp_data3) - 1):
index = int(tmp_data3[i] * 10000)
y_data[index] = xrd_data.y[i - 1]
data = np.vstack((x_data, y_data))
data = (smear(data, sigma=0.1)).T
head_line = "#%(key1)+12s %(key2)+12s" % {
'key1': '2theta',
'key2': 'Intensity'
}
fname = 'XRD.dat'
proc_str = "Saving data to " + fname + " File ..."
procs(proc_str, 2, sp='-->>')
write_col_data(fname, data, head_line)
check_matplotlib()
fname = 'XRD.png'
proc_str = "Saving plot to " + fname + " File ..."
procs(proc_str, 3, sp='-->>')
plt = xrd.get_plot(struct)
plt.savefig(fname, format='png')
from IPython.display import Image, display
from matplotlib import pyplot
# Create CsCl structure
a = 4.209 #Angstrom(埃:一个长度单位，用来表示原子尺寸、键长和电磁波波长。)
latt = Lattice.cubic(a)
#latt:点阵一个长度为a的立方体
#species：物质，这里是["Cs", "Cl"]
#坐标：三位数组的列表，表示物质的坐标
structure = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
c = XRDCalculator()
#get_plot返回的结果就是一个pyplot类型的图片
image = c.get_plot(structure, two_theta_range=(0, 90), annotate_peaks=True, ax=None, with_labels=True, fontsize=16)
#image.show()
image.savefig("alpha CsCl.jpg")
#display(Image(filename=('./PDF - alpha CsCl.png')))
a = 6.923 #Angstrom
latt = Lattice.cubic(a)
structure = Structure(latt, ["Cs", "Cs", "Cs", "Cs", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5],
[0.5, 0.5, 0.5], [0, 0, 0.5], [0, 0.5, 0], [0.5, 0, 0]])
image = c.get_plot(structure, two_theta_range=(0, 90), annotate_peaks=True, ax=None, with_labels=True, fontsize=16)
#display(Image(filename=('./PDF - beta CsCl.png')))这段代码display我还没有弄明白，帮我看看哪里出问题了
#image.show()
image.savefig("beta CsCl.jpg")
def get_xrd_plot(args):
s = Structure.from_file(args.xrd_structure_file)
c = XRDCalculator()
return c.get_plot(s)
# This initializes the REST adaptor. Put your own API key in.
from pymatgen import MPRester, Element
from pymatgen.analysis.diffraction.xrd import XRDCalculator
a = MPRester("")
# Entries are the basic unit for thermodynamic and other analyses in pymatgen.
# This gets all entries belonging to the MnO2 material.
entry = a.get_entry_by_material_id(
"mp-18759",
inc_structure=True,
property_data=["material_id", "energy", "energy_per_atom", "volume"])
#print(entry)
xrdc = XRDCalculator()
xrdc.get_plot(entry.structure).show()
def get_xrd_plot(args):
s = Structure.from_file(args.xrd_structure_file)
c = XRDCalculator()
return c.get_plot(s)
