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Corrected a bug in the generation of the big cell

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This commit is contained in:
Léo Gaspard 2021-03-10 09:32:15 +01:00
parent ca0318c37b
commit 9b68ebdc52
1 changed files with 6 additions and 1 deletions
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7
src/utils.py
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@ -60,15 +60,19 @@ def big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC):
r1 = np.array(coords[i][:3]) r1 = np.array(coords[i][:3])
r2 = np.array(coords[j][:3]) r2 = np.array(coords[j][:3])
r12 = r1-r2 r12 = r1-r2
da = np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
r12 = r12 - np.round(r12) r12 = r12 - np.round(r12)
db = da - np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
r12 = np.matmul(fracToCart,r12) r12 = np.matmul(fracToCart,r12)
d = np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2) d = np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
if(d<1e-5): if(d<1e-2):
# We check if we don't already want to delete this atom # We check if we don't already want to delete this atom
if j not in toDel: if j not in toDel:
toDel.append(j) toDel.append(j)
toDel = sorted(toDel)
# We delete the atoms in the list # We delete the atoms in the list
for i in range(len(toDel)): for i in range(len(toDel)):
coords.pop(toDel[i]-i) coords.pop(toDel[i]-i)
@ -101,6 +105,7 @@ def big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC):
rxyz = np.matmul(fracToCart,r) rxyz = np.matmul(fracToCart,r)
coords.append([rxyz[0],rxyz[1],rxyz[2],at[3],'C']) coords.append([rxyz[0],rxyz[1],rxyz[2],at[3],'C'])
# Returns the list of the atoms [x,y,z,label,second_label] # Returns the list of the atoms [x,y,z,label,second_label]
return coords return coords