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https://github.com/NehZio/Crystal-MEC
synced 2024-10-19 22:41:50 +02:00
bug correction
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e235125b39
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@ -67,6 +67,12 @@ def big_cell(na,nb,nc):
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i[0] *= a
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i[1] *= b
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i[2] *= c
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if i[0] > a:
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i[0] -= a
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if i[1] > b:
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i[1] -= b
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if i[2] > c:
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i[2] -= c
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if i[0] < 0:
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i[0] += a
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if i[1] < 0:
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@ -659,6 +665,15 @@ def main():
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nC = int(np.floor(2*rBath/(c*np.sin(np.radians(beta))))+3)
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coords = big_cell(nA,nB,nC)
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f = open('test.xyz','w')
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f.write(str(len(coords)))
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f.write('\n\n')
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for i in coords:
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f.write('%s % 6.3f % 6.3f % 6.3f \n'%(i[3],i[0],i[1],i[2]))
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f.close()
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coords = translation([nA*a/2,nB*b/2,nC*c/2],coords) #Putting the origin at the center of the cell
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@ -708,7 +723,7 @@ def main():
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for i in coords:
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nAxiss = sorted(nAxiss,key=operator.itemgetter(3))
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if i[3] in nAxis:
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if i[3] in nAxis and dist_zero(i) > da:
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if distance(i,[0,0,0]) <= nAxiss[-1][3]:
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nAxiss[-1] = [i[0],i[1],i[2],distance(i,[0,0,0])]
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newN = np.mean(np.array(nAxiss),axis=0)
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@ -728,7 +743,6 @@ def main():
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#We now have one big cell oriented and centered as we want
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coords = sorted(coords,key=dist_zero)
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coords = cut_bath(rBath,coords)
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coords = find_frag(pattern, npattern ,coords)
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coords = sorted(coords,key=operator.itemgetter(4))
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