LCPQ/Crystal-MET
3
0
Fork 0
mirror of https://github.com/NehZio/Crystal-MEC synced 2024-09-27 12:01:01 +02:00
Code Issues Releases Wiki Activity

bug correction

Browse Source
This commit is contained in:
Léo Gaspard 2019-05-08 14:49:36 +02:00
parent e235125b39
commit bd414ac6ae
1 changed files with 16 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
crystal_met.py
View File

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