mirror of
https://github.com/NehZio/Crystal-MEC
synced 2024-12-22 04:14:30 +01:00
NehZio
parent
66a2871086
commit
3de31e2123
@ -31,7 +31,7 @@ if __name__=='__main__':
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inputFile = sys.argv[1]
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# Reads all the parameters from the input file
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rB , rPP, center, X, Y, Z, xOy, yOz, xOz, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translation = read_input(inputFile)
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rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translation = read_input(inputFile)
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if verbose > 0:
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out_input_param(rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translation)
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@ -79,59 +79,25 @@ if __name__=='__main__':
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# Orienting the big cell
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if xOy != []:
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a = find_center(xOy[0], coordinates)
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b = a
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w = [a]
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while np.absolute ( np.absolute( np.dot( a / np.linalg.norm(a) , b / np.linalg.norm(a) ) ) - 1 ) <= 1e-6:
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b = find_center(xOy[1], coordinates, without=w)
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w.append(b)
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c = np.cross(a, b)
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k = [0,0,1]
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M = rotation_matrix(c, k)
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coordinates = rotate(M, coordinates)
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if xOz != []:
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a = find_center(xOz[0], coordinates)
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b = a
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w = [a]
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while np.absolute ( np.absolute( np.dot( a / np.linalg.norm(a) , b / np.linalg.norm(a) ) ) - 1 ) <= 1e-6:
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b = find_center(xOz[1], coordinates, without=w)
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w.append(b)
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c = np.cross(a, b)
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k = [0,1,0]
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M = rotation_matrix(c, k)
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coordinates = rotate(M, coordinates)
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if yOz != []:
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a = find_center(yOz[0], coordinates)
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b = a
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w = [a]
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while np.absolute ( np.absolute( np.dot( a / np.linalg.norm(a) , b / np.linalg.norm(a) ) ) - 1 ) <= 1e-6:
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b = find_center(yOz[1], coordinates, without=w)
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w.append(b)
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c = np.cross(a, b)
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k = [1,0,0]
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M = rotation_matrix(c, k)
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coordinates = rotate(M, coordinates)
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if X != []:
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k = [1,0,0]
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xVec = find_center(X,coordinates)
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M = rotation_matrix(xVec, k)
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M = rotation_matrix(k,xVec)
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coordinates = rotate(M, coordinates)
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if Y != []:
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k = [0,1,0]
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yVec = find_center(Y,coordinates)
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M = rotation_matrix(yVec, k)
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M = rotation_matrix(k,yVec)
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coordinates = rotate(M, coordinates)
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if Z != []:
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k = [0,0,1]
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zVec = find_center(Z,coordinates)
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M = rotation_matrix(zVec, k)
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M = rotation_matrix(k,zVec)
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coordinates = rotate(M, coordinates)
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@ -9,9 +9,6 @@ def read_input(inputFile):
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X = []
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Y = []
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Z = []
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xOy = []
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xOz = []
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yOz = []
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symmetry = []
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outputFile = ""
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pattern = []
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@ -70,27 +67,6 @@ def read_input(inputFile):
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elif ls[0].casefold() == 'z_axis':
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ls.pop(0)
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Z = [i for i in ls]
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elif ls[0].casefold() == "xoy":
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line = f.readline()
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ls = line.split()
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xOy.append(ls)
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line = f.readline()
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ls = line.split()
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xOy.append(ls)
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elif ls[0].casefold() == "xoz":
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line = f.readline()
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ls = line.split()
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xOz.append(ls)
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line = f.readline()
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ls = line.split()
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xOz.append(ls)
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elif ls[0].casefold() == "yoz":
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line = f.readline()
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ls = line.split()
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yOz.append(ls)
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line = f.readline()
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ls = line.split()
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yOz.append(ls)
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elif ls[0].casefold() == 'symmetry':
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ls.pop(0)
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symmetry = [i for i in ls]
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@ -216,4 +192,4 @@ def read_input(inputFile):
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print("Bad input : missing the keyword -- %s --"%t)
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sys.exit()
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return rB , rPP, center, X, Y, Z, xOy, yOz, xOz, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translate
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return rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translate
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@ -1,196 +0,0 @@
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import sys
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# Parses the input file
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def read_input(inputFile):
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rB = 0.0
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rPP = 0.0
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center = []
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X = []
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Y = []
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Z = []
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symmetry = []
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outputFile = ""
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pattern = []
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npattern = []
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atoms = []
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dist = []
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a = 0.0
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b = 0.0
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c = 0.0
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alpha = 90.0
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beta = 90.0
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gamma = 90.0
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showBath = False
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evjen = False
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showFrag = False
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notInPseudo = []
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notInFrag = []
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symGenerator = []
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generator = []
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translate = [0.0,0.0,0.0]
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checkInput = {'bath':False,'pseudo':False,'output':False,'pattern':False,'npattern':False,'a':False,'b':False,'c':False,'atoms':False,'symmetry_generator':False,'generator':False}
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f = open(inputFile,'r')
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line = 'x'
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while line.casefold() != 'end_of_input':
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line = f.readline().strip()
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ls = line.split()
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print(ls)
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if ls == []:
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continue
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if ls[0].casefold() in checkInput:
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checkInput[ls[0].casefold()] = True
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if ls[0].casefold() == 'bath':
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try:
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rB = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : %s is not a valid bath radius value"%(ls[1]))
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sys.exit()
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elif ls[0].casefold() == 'pseudo':
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try:
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rPP = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : %s is not a valid pseudopotential radius value"%(ls[1]))
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sys.exit()
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elif ls[0].casefold() == 'center':
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ls.pop(0)
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center = [i for i in ls]
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elif ls[0].casefold() == 'x_axis':
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ls.pop(0)
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X = [i for i in ls]
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elif ls[0].casefold() == 'y_axis':
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ls.pop(0)
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Y = [i for i in ls]
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elif ls[0].casefold() == 'z_axis':
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ls.pop(0)
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Z = [i for i in ls]
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elif ls[0].casefold() == 'symmetry':
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ls.pop(0)
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symmetry = [i for i in ls]
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elif ls[0].casefold() == 'output':
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outputFile = ls[1]
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elif ls[0].casefold() == 'pattern':
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line = f.readline()
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while line.strip().casefold() != 'end':
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pattern.append([])
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ls = line.split()
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for i in range(len(ls)):
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if i%2 == 0:
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pattern[-1].append(int(ls[i]))
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else:
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pattern[-1].append(ls[i])
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line = f.readline()
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elif ls[0].casefold() == 'npattern':
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ls.pop(0)
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try:
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npattern = [int(i) for i in ls]
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except ValueError:
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print("Error while parsing the input file : the number of patterns is not valid %s"%(line))
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sys.exit()
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elif ls[0].casefold() == 'lattice':
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line = f.readline()
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while line.strip().casefold() != 'end':
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ls = line.split()
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if ls[0].casefold() in checkInput:
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checkInput[ls[0].casefold()] = True
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if ls[0].casefold() == 'a':
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try:
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a = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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elif ls[0].casefold() == 'b':
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try:
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b = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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elif ls[0].casefold() == 'c':
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try:
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c = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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elif ls[0].casefold() == 'alpha':
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try:
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alpha = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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elif ls[0].casefold() == 'beta':
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try:
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beta = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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elif ls[0].casefold() == 'gamma':
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try:
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gamma = float(ls[1])
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except ValueError:
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print("Error while parsing the input file : bad value for the lattice parameter %s"%ls[1])
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sys.exit()
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line = f.readline()
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elif ls[0].casefold() == 'atoms':
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line = f.readline()
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while line.strip().casefold() != 'end':
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ls = line.split()
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if(len(ls)) != 4:
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print("Error while parsing the input file : not enough values given for the atom in line %s"%line)
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sys.exit()
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try:
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atoms.append([ls[0], float(ls[1]), int(ls[2]), float(ls[3])])
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except ValueError:
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print("Error while parsing the input file : bad value for the atom %s"%line)
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line = f.readline()
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elif ls[0].casefold() == 'show_bath':
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showBath = True
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elif ls[0].casefold() == 'translate':
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ls.pop(0)
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try:
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translate = [float(ls[0]),float(ls[1]),float(ls[2])]
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except ValueError:
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print("Error while parsing the input file : the translation vector is not valid %s"%line)
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sys.exit()
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elif ls[0].casefold() == 'not_in_pseudo':
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ls.pop(0)
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notInPseudo = [i for i in ls]
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elif ls[0].casefold() == 'show_frag':
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showFrag = True
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elif ls[0].casefold() == 'evjen':
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evjen = True
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elif ls[0].casefold() == 'symmetry_generator':
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line = f.readline().replace("'","")
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while line.strip().casefold() != 'end':
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symGenerator.append(line.split(','))
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line = f.readline().replace("'","")
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elif ls[0].casefold() == 'generator':
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line = f.readline()
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while line.strip().casefold() != 'end':
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ls = line.split()
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try:
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generator.append([ls[0],float(ls[1]),float(ls[2]),float(ls[3])])
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except ValueError:
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print("Error while parsing the input file : bad value for the generator atom %s"%line)
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sys.exit()
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line = f.readline()
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elif ls[0].casefold() == 'not_in_frag':
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line = f.readline()
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while line.strip().casefold() != 'end':
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ls = line.split()
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try:
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notInFrag.append([float(ls[0]),float(ls[1]),float(ls[2])])
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except ValueError:
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print("Error while parsing the input file : bad value for the atom %s"%line)
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sys.exit()
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line = f.readline()
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f.close()
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for t in checkInput:
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if checkInput[t] == False:
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print("Bad input : missing the keyword -- %s --"%t)
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sys.exit()
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return rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translate
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10
src/utils.py
10
src/utils.py
@ -119,7 +119,7 @@ def translate(v,coordinates):
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# Finds the point at the center of the given atoms that are the
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# closest to the origin
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def find_center(centerList, coordinates, without=[]):
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def find_center(centerList, coordinates):
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centers = []
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for i in range(len(centerList)):
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@ -129,14 +129,6 @@ def find_center(centerList, coordinates, without=[]):
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c.append(distance(c,[0,0,0])) # Computing the distance to the origin
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for at in coordinates:
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w = True
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for i in without:
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d = distance(at, i)
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if d < 1e-6:
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w = False
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break
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if not w:
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continue
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if at[3] in centerList:
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centers = sorted(centers, key=operator.itemgetter(3)) # Sorting the list with respect to the distance to the origin
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d = distance(at,[0,0,0])
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390
src/utils.py~
390
src/utils.py~
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import numpy as np
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import operator
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import sys
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def distance(a,b):
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# Returns the 3D distance between a and b where
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# a and b are array where x, y and z are at the
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# position 0, 1 and 2
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x = a[0]-b[0]
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y = a[1]-b[1]
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z = a[2]-b[2]
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return np.sqrt(x**2+y**2+z**2)
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def get_cell_matrix(a,b,c,alpha,beta,gamma):
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# Computing the volume of the primitive cell
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omega = a*b*c*np.sqrt(1-np.cos(alpha)**2-np.cos(beta)**2-np.cos(gamma)**2+2*np.cos(alpha)*np.cos(beta)*np.cos(gamma))
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# Computing the matrix
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M = [
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[a,b*np.cos(gamma),c*np.cos(beta)],
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[0,b*np.sin(gamma),c*(np.cos(alpha)-np.cos(beta)*np.cos(gamma))/(np.sin(gamma))],
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[0,0,omega/(a*b*np.sin(gamma))]
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]
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return M
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def big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC):
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coords = []
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# Computing the matrix converting fractional to cartesian
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fracToCart = get_cell_matrix(a,b,c,alpha,beta,gamma)
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for gen in generator:
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x = gen[1]
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y = gen[2]
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z = gen[3]
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for sym in symGenerator:
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u = eval(sym[0])
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v = eval(sym[1])
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w = eval(sym[2])
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# Making sure the value is within the range [0,1]
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u = u + 1*(u<0) - 1*(u>1)
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v = v + 1*(v<0) - 1*(v>1)
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w = w + 1*(w<0) - 1*(w>1)
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coords.append([u,v,w,gen[0]])
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# Deleting the redundant atoms
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toDel = []
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for i in range(len(coords)-1):
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for j in range(i+1,len(coords)):
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# Computing the distance using the minimum image convention
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# as described in Appendix B equation 9 of
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# "Statistical Mechanics : Theory and Molecular Simulations
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# Mark E. Tuckerman"
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r1 = np.array(coords[i][:3])
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r2 = np.array(coords[j][:3])
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r12 = r1-r2
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da = np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
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r12 = r12 - np.round(r12)
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db = da - np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
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r12 = np.matmul(fracToCart,r12)
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d = np.sqrt(r12[0]**2+r12[1]**2+r12[2]**2)
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if(d<1e-2):
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# We check if we don't already want to delete this atom
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if j not in toDel:
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toDel.append(j)
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toDel = sorted(toDel)
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# We delete the atoms in the list
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for i in range(len(toDel)):
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coords.pop(toDel[i]-i)
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newCoords = []
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# We replicate the cell nA, nB, nC times
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for at in coords:
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newCoords.append([at[0],at[1],at[2],at[3]])
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for a in range(1,nA):
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newCoords.append([at[0]+a,at[1],at[2],at[3]])
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for b in range(1,nB):
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newCoords.append([at[0]+a,at[1]+b,at[2],at[3]])
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for c in range(1,nC):
|
||||
newCoords.append([at[0]+a,at[1]+b,at[2]+c,at[3]])
|
||||
for c in range(1,nC):
|
||||
newCoords.append([at[0]+a,at[1],at[2]+c,at[3]])
|
||||
for b in range(1,nB):
|
||||
newCoords.append([at[0],at[1]+b,at[2],at[3]])
|
||||
for c in range(1,nC):
|
||||
newCoords.append([at[0],at[1]+b,at[2]+c,at[3]])
|
||||
for c in range(1,nC):
|
||||
newCoords.append([at[0],at[1],at[2]+c,at[3]])
|
||||
|
||||
# Now we convert the fractionnal coordinates to cartesian coordinates
|
||||
coords = []
|
||||
|
||||
for at in newCoords:
|
||||
r = [at[0],at[1],at[2]]
|
||||
rxyz = np.matmul(fracToCart,r)
|
||||
coords.append([rxyz[0],rxyz[1],rxyz[2],at[3],'C'])
|
||||
|
||||
|
||||
# Returns the list of the atoms [x,y,z,label,second_label]
|
||||
return coords
|
||||
|
||||
# Translates all the coordinates with the vector v
|
||||
def translate(v,coordinates):
|
||||
for c in coordinates:
|
||||
c[0] += v[0]
|
||||
c[1] += v[1]
|
||||
c[2] += v[2]
|
||||
return coordinates
|
||||
|
||||
# Finds the point at the center of the given atoms that are the
|
||||
# closest to the origin
|
||||
def find_center(centerList, coordinates):
|
||||
|
||||
centers = []
|
||||
for i in range(len(centerList)):
|
||||
centers.append([100,100,100]) # Setting a large value for each center
|
||||
|
||||
for c in centers:
|
||||
c.append(distance(c,[0,0,0])) # Computing the distance to the origin
|
||||
|
||||
for at in coordinates:
|
||||
if at[3] in centerList:
|
||||
centers = sorted(centers, key=operator.itemgetter(3)) # Sorting the list with respect to the distance to the origin
|
||||
d = distance(at,[0,0,0])
|
||||
if d <= centers[-1][-1] and d > 0.0:
|
||||
centers[-1] = [at[0],at[1],at[2],d]
|
||||
|
||||
center = np.mean(centers,axis=0)[:3] # Computing the barycenter
|
||||
|
||||
return center
|
||||
|
||||
# Defines a rotation matrix that will put r1 at the position r2
|
||||
def rotation_matrix(r1,r2):
|
||||
|
||||
r1 = np.array(r1)/np.linalg.norm(r1)
|
||||
r2 = np.array(r2)/np.linalg.norm(r2)
|
||||
|
||||
# Computing the cross product which is the vector around which
|
||||
# the rotation is done
|
||||
crossProduct = np.cross(r1,r2)
|
||||
crossProduct = crossProduct/np.linalg.norm(crossProduct)
|
||||
|
||||
# Computing the angle of the rotation
|
||||
a = np.arccos(np.dot(r1,r2))
|
||||
|
||||
c = np.cos(a)
|
||||
s = np.sin(a)
|
||||
x = crossProduct[0]
|
||||
y = crossProduct[1]
|
||||
z = crossProduct[2]
|
||||
|
||||
M = [
|
||||
[x**2*(1-c)+c,x*y*(1-c)-z*s,x*z*(1-c)+y*s],
|
||||
[x*y*(1-c)+z*s,y**2*(1-c)+c,y*z*(1-c)-x*s],
|
||||
[x*z*(1-c)-y*s,y*z*(1-c)+x*s,z**2*(1-c)+c]
|
||||
]
|
||||
|
||||
return M
|
||||
|
||||
# Rotates all the coordinates using the rotation matric M
|
||||
def rotate(M,coordinates):
|
||||
for i in range(len(coordinates)):
|
||||
r = [coordinates[i][0],coordinates[i][1],coordinates[i][2]]
|
||||
rV = np.matmul(M,r)
|
||||
coordinates[i][0] = rV[0]
|
||||
coordinates[i][1] = rV[1]
|
||||
coordinates[i][2] = rV[2]
|
||||
|
||||
return coordinates
|
||||
|
||||
# Cuts a sphere centered on the origin in the coordinates
|
||||
def cut_sphere(coordinates,r):
|
||||
sphere = []
|
||||
for i in range(len(coordinates)):
|
||||
if distance(coordinates[i],[0,0,0]) <= r:
|
||||
sphere.append(coordinates[i])
|
||||
|
||||
return sphere
|
||||
|
||||
# Finds the fragment in the coordinates
|
||||
def find_fragment(coordinates, patterns, npatterns,notInFrag):
|
||||
|
||||
inFrag = []
|
||||
|
||||
for n in range(len(patterns)):
|
||||
pattern = patterns[n]
|
||||
npattern = npatterns[n]
|
||||
for i in range(npattern):
|
||||
c = [100,100,100]
|
||||
dc = distance([0,0,0],c)
|
||||
|
||||
inPattern = []
|
||||
# Finding the closest atom of the first type in the pattern
|
||||
for at in coordinates:
|
||||
if at[3] == pattern[1]:
|
||||
d = distance([0,0,0],at)
|
||||
if d > 10:
|
||||
break
|
||||
if d < dc :
|
||||
accept = True
|
||||
for exc in notInFrag:
|
||||
d = distance(exc,at)
|
||||
if d < 1e-5:
|
||||
accept = False
|
||||
if accept and coordinates.index(at) not in inFrag:
|
||||
c = [at[0],at[1],at[2],0.0, coordinates.index(at)]
|
||||
dc = distance([0,0,0],c)
|
||||
# Finding the rest of the pattern around the atom previously found
|
||||
atIn = []
|
||||
for j in range(0,len(pattern),2):
|
||||
d = distance(c,[100,100,100])
|
||||
# Initializing the atoms
|
||||
for k in range(pattern[j]):
|
||||
atIn.append([100,100,100,d])
|
||||
|
||||
for at in coordinates:
|
||||
if distance(at,[0,0,0]) > 10:
|
||||
break
|
||||
if at[3] == pattern[j+1]:
|
||||
atIn = sorted(atIn,key=operator.itemgetter(3))
|
||||
d = distance(at,c)
|
||||
trial = [at[0],at[1],at[2],d,coordinates.index(at)]
|
||||
if d < atIn[-1][3] and trial not in atIn:
|
||||
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:
|
||||
inPattern.append(at[4])
|
||||
|
||||
for at in inPattern:
|
||||
if at not in inFrag:
|
||||
inFrag.append(at)
|
||||
|
||||
for at in inFrag:
|
||||
coordinates[at][4] = 'O'
|
||||
|
||||
return len(inFrag), coordinates
|
||||
|
||||
|
||||
# Finds the pseudopotential layer around
|
||||
# the fragment
|
||||
def find_pseudo(coordinates, rPP, notInPseudo):
|
||||
|
||||
for at in coordinates:
|
||||
if at[4] != 'O':
|
||||
continue
|
||||
for i in range(len(coordinates)):
|
||||
if coordinates[i][4] != 'C':
|
||||
continue
|
||||
d = distance(at,coordinates[i])
|
||||
if d < rPP:
|
||||
coordinates[i][4] = 'Cl'
|
||||
|
||||
return coordinates
|
||||
|
||||
# Creates lists containing the neighbours of each
|
||||
# atom
|
||||
def find_neighbours(coordinates, atoms):
|
||||
neighbourList = [[] for i in range(len(coordinates))]
|
||||
|
||||
atoms = np.array(atoms).flatten()
|
||||
|
||||
for i in range(len(coordinates)-1):
|
||||
for j in range(i+1,len(coordinates)):
|
||||
li = coordinates[i][3] # Label of the atom i
|
||||
lj = coordinates[j][3] # Label of the atom j
|
||||
|
||||
ii = np.where(atoms==li)[0]
|
||||
jj = np.where(atoms==lj)[0]
|
||||
|
||||
ci = float(atoms[ii+1]) # Charge of the atom i
|
||||
cj = float(atoms[jj+1]) # Charge of the atom j
|
||||
|
||||
if ci*cj < 0: # Checking if the charges have opposite signs
|
||||
d = distance(coordinates[i],coordinates[j])
|
||||
|
||||
if d < float(atoms[ii+3]) and d < float(atoms[jj+3]):
|
||||
neighbourList[i].append(j)
|
||||
neighbourList[j].append(i)
|
||||
return neighbourList
|
||||
|
||||
# For each atom, finds if it has the correct number of neighbours,
|
||||
# if not, modify its charge
|
||||
def evjen_charges(coordinates,atoms):
|
||||
neighbourList = find_neighbours(coordinates,atoms)
|
||||
|
||||
atoms = np.array(atoms).flatten()
|
||||
|
||||
charges = []
|
||||
|
||||
for i in range(len(coordinates)):
|
||||
li = coordinates[i][3]
|
||||
ii = np.where(atoms==li)[0]
|
||||
|
||||
nr = len(neighbourList[i])
|
||||
nt = int(atoms[ii+2])
|
||||
ci = float(atoms[ii+1])
|
||||
|
||||
if nr > nt:
|
||||
print("Error : too much neighbours for atom n°%i, count %i neighbours where it should have a maximum of %i"%(i,nr,nt))
|
||||
sys.exit()
|
||||
charges.append(ci*nr/nt)
|
||||
|
||||
return charges
|
||||
|
||||
# Computes the nuclear repulsion
|
||||
def nuclear_repulsion(coordinates,charges):
|
||||
|
||||
rep = 0.0
|
||||
|
||||
for i in range(len(coordinates)-1):
|
||||
for j in range(i+1,len(coordinates)):
|
||||
rij = distance(coordinates[i],coordinates[j])
|
||||
ci = charges[i]
|
||||
cj = charges[j]
|
||||
|
||||
if(rij < 1):
|
||||
print(i,j,"\n",coordinates[i],"\n",coordinates[j],"\n",rij)
|
||||
|
||||
rep += (ci*cj)/rij
|
||||
return rep
|
||||
|
||||
# Computes the symmetry in the whole system
|
||||
def compute_symmetry(coordinates,charges,symmetry):
|
||||
symmetrizedCoordinates = []
|
||||
symmetrizedCharges = []
|
||||
uniqueIndexList = [] # The list containing the indexes of the unique atoms
|
||||
|
||||
treated = [] # Will store the index of the atoms already treated
|
||||
|
||||
symOp = []
|
||||
|
||||
# Storing all the symmetry operations
|
||||
for s in symmetry:
|
||||
if s == 'C2x':
|
||||
symOp.append(np.array([1,-1,-1]))
|
||||
elif s == 'C2y':
|
||||
symOp.append(np.array([-1,1,-1]))
|
||||
elif s == 'C2z':
|
||||
symOp.append(np.array([-1,-1,1]))
|
||||
elif s == 'xOy':
|
||||
symOp.append(np.array([1,1,-1]))
|
||||
elif s == 'xOz':
|
||||
symOp.append(np.array([1,-1,1]))
|
||||
elif s == 'yOz':
|
||||
symOp.append(np.array([-1,1,1]))
|
||||
elif s == 'i':
|
||||
symOp.append(np.array([-1,-1,-1]))
|
||||
|
||||
for i in range(len(coordinates)):
|
||||
print(i)
|
||||
if i in treated:
|
||||
continue
|
||||
|
||||
treated.append(i)
|
||||
at1 = np.array(coordinates[i][:3])
|
||||
symmetrizedCoordinates.append(coordinates[i])
|
||||
symmetrizedCharges.append(charges[i])
|
||||
uniqueIndexList.append(len(symmetrizedCoordinates)-1)
|
||||
|
||||
for j in range(len(coordinates)):
|
||||
if j in treated or coordinates[i][3] != coordinates[j][3]:
|
||||
continue
|
||||
|
||||
at2 = np.array(coordinates[j][:3])
|
||||
|
||||
for s in symOp:
|
||||
if distance(at2, at1*s) < 5:
|
||||
if distance(at1,at1*s) > 1e-4 and distance(at2,at1*s) < 1e-4: # Checking if op.at1 != at1 and that op.at2 = at1
|
||||
p = at1*s
|
||||
treated.append(j)
|
||||
symmetrizedCoordinates.append([p[0],p[1],p[2],coordinates[i][3],coordinates[i][4]])
|
||||
symmetrizedCharges.append(charges[i])
|
||||
break
|
||||
|
||||
return symmetrizedCoordinates,symmetrizedCharges,uniqueIndexList
|
||||
Loading…
Reference in New Issue
Block a user