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Performance + bugfix with not_in_frag keyword

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This commit is contained in:
Léo Gaspard 2021-06-01 09:10:06 +02:00
parent 19a92fb431
commit eef1cf3d03
4 changed files with 18 additions and 6 deletions
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8
crystal_mec.py
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@ -84,21 +84,21 @@ if __name__=='__main__':
xVec = find_center(X,coordinates) xVec = find_center(X,coordinates)
M = rotation_matrix(k,xVec) M = rotation_matrix(k,xVec)
rotate(M, coordinates) coordinates = rotate(M, coordinates)
if Y != []: if Y != []:
k = [0,1,0] k = [0,1,0]
yVec = find_center(Y,coordinates) yVec = find_center(Y,coordinates)
M = rotation_matrix(k,yVec) M = rotation_matrix(k,yVec)
rotate(M, coordinates) coordinates = rotate(M, coordinates)
if Z != []: if Z != []:
k = [0,0,1] k = [0,0,1]
zVec = find_center(Z,coordinates) zVec = find_center(Z,coordinates)
M = rotation_matrix(k,zVec) M = rotation_matrix(k,zVec)
rotate(M, coordinates) coordinates = rotate(M, coordinates)
if verbose > 2: if verbose > 2:
print("The big cell contains %5i atoms and will be printed in the file big_cell.xyz\n"%len(coordinates)) print("The big cell contains %5i atoms and will be printed in the file big_cell.xyz\n"%len(coordinates))
@ -113,6 +113,8 @@ if __name__=='__main__':
# Finding the fragment # Finding the fragment
coordinates = sorted(coordinates, key=lambda x:distance(x,[0,0,0]))
nAt, coordinates = find_fragment(coordinates,pattern,npattern,notInFrag) nAt, coordinates = find_fragment(coordinates,pattern,npattern,notInFrag)
if verbose > 2 or showFrag: if verbose > 2 or showFrag:

2
src/out.py
View File

@ -70,7 +70,7 @@ def out_input_param(rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, np
if len(notInFrag) > 0: if len(notInFrag) > 0:
print("The following %5s will be excluded from the fragment :"%('atom'+'s'*(len(notInFrag)>1))) print("The following %5s will be excluded from the fragment :"%('atom'+'s'*(len(notInFrag)>1)))
for i in notInFrag: for i in notInFrag:
print(" %2s % 8.6f % 8.6f % 8.6f"%(i[0],i[1],i[2],i[3])) print(" % 8.6f % 8.6f % 8.6f"%(i[0],i[1],i[2]))
print() print()
# Write the coordinates to a file using the string # Write the coordinates to a file using the string

2
src/read_input.py
View File

@ -181,7 +181,7 @@ def read_input(inputFile):
while line.strip().casefold() != 'end': while line.strip().casefold() != 'end':
ls = line.split() ls = line.split()
try: try:
notInFrag.append([ls[0],float(ls[1]),float(ls[2]),float(ls[3])]) notInFrag.append([float(ls[0]),float(ls[1]),float(ls[2])])
except ValueError: except ValueError:
print("Error while parsing the input file : bad value for the atom %s"%line) print("Error while parsing the input file : bad value for the atom %s"%line)
sys.exit() sys.exit()

12
src/utils.py
View File

@ -204,6 +204,8 @@ def find_fragment(coordinates, patterns, npatterns,notInFrag):
for at in coordinates: for at in coordinates:
if at[3] == pattern[1]: if at[3] == pattern[1]:
d = distance([0,0,0],at) d = distance([0,0,0],at)
if d > 10:
break
if d < dc : if d < dc :
accept = True accept = True
for exc in notInFrag: for exc in notInFrag:
@ -222,12 +224,20 @@ def find_fragment(coordinates, patterns, npatterns,notInFrag):
atIn.append([100,100,100,d]) atIn.append([100,100,100,d])
for at in coordinates: for at in coordinates:
if distance(at,[0,0,0]) > 10:
break
if at[3] == pattern[j+1]: if at[3] == pattern[j+1]:
atIn = sorted(atIn,key=operator.itemgetter(3)) atIn = sorted(atIn,key=operator.itemgetter(3))
d = distance(at,c) d = distance(at,c)
trial = [at[0],at[1],at[2],d,coordinates.index(at)] trial = [at[0],at[1],at[2],d,coordinates.index(at)]
if d < atIn[-1][3] and trial not in atIn: if d < atIn[-1][3] and trial not in atIn:
atIn[-1] = trial accept = True
for exc in notInFrag:
d = distance(exc,trial)
if d < 1e-5:
accept = False
if accept:
atIn[-1] = trial
for at in atIn: for at in atIn:
inPattern.append(at[4]) inPattern.append(at[4])