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Merge some minor changes to code from laptop with main branch
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Hamish Brown authored and Hamish Brown committed May 6, 2024
2 parents 8ecde71 + 0e59644 commit 8743f21
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Showing 13 changed files with 1,166 additions and 62 deletions.
802 changes: 802 additions & 0 deletions Demos/4D_STEM_workshop.ipynb
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4 changes: 2 additions & 2 deletions Demos/EFTEM.ipynb
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4 changes: 2 additions & 2 deletions Demos/Multislice_fundamentals.ipynb
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],
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"name": "python",
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"version": "3.7.3"
"version": "3.9.7"
}
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4 changes: 2 additions & 2 deletions Demos/STEM.ipynb
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],
"metadata": {
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"display_name": "Python 3",
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"language": "python",
"name": "python3"
},
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"name": "python",
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"version": "3.7.3"
"version": "3.9.7"
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194 changes: 194 additions & 0 deletions Demos/Structures/Bournonite_DW.xyz
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57 changes: 52 additions & 5 deletions Test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,11 +37,11 @@ def clean_temp_structure():
os.remove(scratch_cell_name)


def Single_atom(Z=79, r=[0.5, 0.5, 0.5], R=[10.0, 10.0, 10.0]):
def Single_atom(Z=79, r=[0.5, 0.5, 0.5], R=[10.0, 10.0, 10.0],dwf = 0.0):
"""Single atom structure for testing."""
atoms = np.asarray(
[
[*r, Z, 1.0, 0.0],
[*r, Z, 1.0, dwf],
]
)
return pyms.structure(R, atoms[:, :4], dwf=atoms[:, 5])
Expand Down Expand Up @@ -493,6 +493,53 @@ def test_make_potential(self):
)
self.assertTrue(within_spec)

def test_atom_placement(self):
"""Test that the code places atoms in the correct location with correct
mean square vibration"""
nT = 128
gridshape = [128,128]
# Make single Silver atom
R = 10
dwf = 0.02
r = [0.25,0.25,0.25]
cell = Single_atom(r=r, Z=2, R=[R, R, 2],dwf=dwf)

pot = np.zeros([nT]+gridshape)
for i in range(nT):
pot[i] = cell.make_potential(gridshape).cpu().numpy()

# Calculate COM in fraction of unit cell
M = np.sum(pot,axis=(-2,-1))
COMx = np.sum(pot*np.arange(gridshape[-1])/gridshape[-1],axis=(-2,-1))/M
COMy = np.sum(pot*np.arange(gridshape[-2]).reshape([gridshape[-2],1])/gridshape[-2],axis=(-2,-1))/M
COM = np.stack([COMy,COMx],axis=0)
# fig,ax=plt.subplots(ncols=2)
# ax[0].imshow(np.sum(pot,axis=0),origin='lower')
# ax[1].plot(COMx,COMy,'bo')
# plt.show(block=True)

moving_average = np.cumsum(COM,axis=1)/(np.arange(nT)+1)
moving_ms = np.cumsum(COMx**2+COMy**2)/(np.arange(nT)+1)/2 - np.average(moving_average**2,axis=0)
moving_ms*= R**2

# fig,ax = plt.subplots(ncols=2)
# ax[0].plot(COMx,COMy,'bo')
# ax[1].plot(moving_ms)
# from matplotlib.patches import Circle
# ax[0].add_patch(Circle(r[:2],radius=np.sqrt(dwf)/R))
# plt.show(block=True)

meanCOM = np.sum(COM,axis=1)/nT
# 5 Sigma test, ie. 1/3.5 million probability of failing assuming correct functioning
fiveSigma = dwf/nT*5**2
sigmaofvariance = dwf*np.sqrt(2/(nT-1))
muwithinspec = np.sum((meanCOM-r[0])**2) < fiveSigma
sigmawithinspec = np.abs(moving_ms[-1]-dwf) < 5*sigmaofvariance

withinspec = sigmawithinspec and muwithinspec
self.assertTrue(withinspec)


def test_resize(self):
"""Test the structure resize routine for cropping and padding with vaccuum."""
unitcell = [5.0, 5.0, 5.0]
Expand Down Expand Up @@ -1324,7 +1371,7 @@ def test_DPC(self):
# plt.show(block=True)
# print(sumsqr_diff(convolved_phase, reconstructed_phase,norm=True) )
self.assertTrue(
sumsqr_diff(convolved_phase, reconstructed_phase,norm=True)
sumsqr_diff(convolved_phase, reconstructed_phase,norm=True)
< 1e-1
)

Expand Down Expand Up @@ -1983,7 +2030,7 @@ def test_amplitude(self):
if __name__ == "__main__":
# test = Test_util_Methods()
# test.test_crop_tobandwidthlimit()

# test = Test_py_multislice_Methods()
# test.test_DPC()
# import sys; sys.exit()
Expand All @@ -2002,7 +2049,7 @@ def test_amplitude(self):
# suite.run()
# test.run()
# test = Test_Structure_Methods()
# test.test_multilayer_objects()
# test.test_atom_placement()

# test.test_electron_scattering_factor()
# test.test_make_potential()
Expand Down
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