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Pattern recognition amelioration

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This commit is contained in:
Leo gaspard 2019-05-09 08:19:00 +02:00
parent bd414ac6ae
commit 92a00d2e59
3 changed files with 25 additions and 15 deletions
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8
DOC.md
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@ -10,11 +10,13 @@ There is no obligation to put any order in the keywords
* OUTPUT output_file_name
* PATTERN nAtom1 labelAtom1 nAtom2 labelAtom2 ...
* PATTERN
nAtom1 labelAtom1 nAtom2 labelAtom2 ...
...
NRETTAP
Not that, if you have more than once the Atom1, you will have to place it again at the end (for example, 5 Ir 8 Sr 6 O 5 Ir)
* NPATTERN nPattern
* NPATTERN nPattern1 nPattern2 ...
* LATTICE

2
README.md
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@ -5,7 +5,7 @@
<a href="url"><img src="https://github.com/NehZio/Crystal-MET/blob/master/images/fig3.png" align="left" height="400" width="400" ></a>
Crystal MET (Crystal Maker Effective Tool) is a python3 programs that helps you building a system using only the informations taken from a CIF file.
Crystal MET (Crystal Maker Effective Tool) is a python3 programs, developped during an internship at the [LCPQ](www.lcpq.ups-tlse.fr) that helps you building a system using only the informations taken from a CIF file.
Use it with care, always check the output, it may work differently from what you expect.

28
crystal_met.py
View File

@ -28,8 +28,8 @@ yAxis = 'x'
zAxis = 'x'
sym = 'x'
output_file = 'x'
pattern = 'x'
npattern = 'x'
pattern = []
npattern = []
atoms = 'x'
dist = 'x'
lattice = 'x'
@ -194,13 +194,19 @@ def read_input(inputFile):
output_file = line[1]
elif line[0] == 'PATTERN':
pattern = []
for i in range(1,len(line)):
if i%2 == 1:
pattern.append(int(line[i]))
line = f.readline()
while line.strip() != 'NRETTAP':
pattern.append([])
line = line.split()
for i in range(len(line)):
if i%2 == 0:
pattern[-1].append(int(line[i]))
else:
pattern.append(line[i])
pattern[-1].append(line[i])
line = f.readline()
elif line[0] == 'NPATTERN':
npattern = int(line[1])
for i in range(1,len(line)):
npattern.append(int(line[i]))
elif line[0] == 'LATTICE':
a = float(f.readline().split()[1])
b = float(f.readline().split()[1])
@ -336,7 +342,7 @@ def set_pp(rPP,coords, notIn): #Select which atoms are in the first shell of pse
now = datetime.datetime.now()
printProgressBar(start,now,i+1,len(coords),prefix='Finding the first shell',length=50)
for j in range(len(coords)):
if coords[i][4] != 'O' or dist_zero(coords[j]) > 2*(max([atoms[k] for k in range(3,len(atoms),4)])*npattern+rPP):
if coords[i][4] != 'O' or dist_zero(coords[j]) > 2*(max([atoms[k] for k in range(3,len(atoms),4)])*sum(npattern)+rPP):
break
if coords[i][4] == 'O':
if coords[j][4] == 'C' and coords[j][3] not in notIn:
@ -351,6 +357,7 @@ def find_frag(pattern, n, coords):
#the fragment according to user input
inFrag = []
start = datetime.datetime.now()
inPattern = []
for k in range(n):
closest = [100,100,100]
now = datetime.datetime.now()
@ -359,7 +366,7 @@ def find_frag(pattern, n, coords):
if j[3] == pattern[1]:
if distance(j,[0,0,0]) < distance([0,0,0],closest) and [j[0],j[1],j[2],distance(j,j), coords.index(j)] not in inFrag:
closest = [j[0],j[1],j[2],distance(j,j), coords.index(j)]
for i in range(1,len(pattern)//2):
for i in range(len(pattern)//2):
inPattern = [closest]
for j in range(int(pattern[2*i])):
inPattern.append([100,100,100,distance([100,100,100],closest)])
@ -744,7 +751,8 @@ def main():
coords = sorted(coords,key=dist_zero)
coords = cut_bath(rBath,coords)
coords = find_frag(pattern, npattern ,coords)
for i in range(len(pattern)):
coords = find_frag(pattern[i], npattern[i],coords)
coords = sorted(coords,key=operator.itemgetter(4))
coords = set_pp(rPP,coords,notIn)
coords = sorted(coords,key=dist_zero,reverse=True)