mirror of https://github.com/NehZio/Crystal-MEC
216 lines
8.1 KiB
Python
216 lines
8.1 KiB
Python
import sys
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import numpy as np
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from src.read_input import *
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from src.out import *
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from src.utils import *
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if __name__=='__main__':
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verbose = 2
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if len(sys.argv) == 1:
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print("Please provide the input file")
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sys.exit()
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elif len(sys.argv) == 3 :
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if sys.argv[2] == 's':
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verbose = 0
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elif sys.argv[2] == 'v':
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verbose = 1
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elif sys.argv[2] == 'vv':
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verbose = 2
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elif sys.argv[2] == 'vvv':
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verbose = 3
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else:
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print("Unknown argument -%s-"%sys.argv[2])
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sys.exit()
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elif len(sys.argv) > 3:
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print("Too much arguments, please provide an input file and a verbose level (v, vv, vvv)")
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sys.exit()
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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, xOy, xOz, yOz, 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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# Converting the angles to radian
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alpha = alpha * np.pi / 180.0
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beta = beta * np.pi / 180.0
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gamma = gamma * np.pi / 180.0
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# Computing the number of replications needed in each directions using the interreticular distance
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# for the planes 100, 010 and 001.
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#
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# The condition is : d_{hkl} >= 2*bath_radius + |translation_vector|
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fac = 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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nA = int(np.ceil(np.sin(alpha)*(2*rB+np.linalg.norm(translation))/(a*fac)))+1
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nB = int(np.ceil(np.sin(beta)*(2*rB+np.linalg.norm(translation))/(b*fac)))+1
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nC = int(np.ceil(np.sin(gamma)*(2*rB+np.linalg.norm(translation))/(c*fac)))+1
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if verbose > 1:
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print("The big cell will be of dimensions %2ix%2ix%2i\n"%(nA,nB,nC))
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coordinates = big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC)
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# Computing the translation vector by addition of the user translation vector and a translation
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# vector that puts the origin at the center of the big cell
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t = [-0.5,-0.5,-0.5]
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M = get_cell_matrix(nA*a,nB*b,nC*c,alpha,beta,gamma)
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t = np.matmul(M,t)
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t = [t[0]+translation[0],t[1]+translation[1],t[2]+translation[2]]
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# Translating the coordinates
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coordinates = translate(t, coordinates)
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# Finding the center and translating the coordinates
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# If this vector creates a displacment bigger than a, b or c
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# in any of the abc directions, this might result in an incomplete
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# sphere later, the user should provide a translation vector
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# to correct this
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if center != []:
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c = find_center(center,coordinates)
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coordinates = translate(-c,coordinates)
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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(b)))-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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M = rotation_matrix(c, [0,0,1])
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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(b)))-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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M = rotation_matrix(c, [0,1,0])
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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(b)))-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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M = rotation_matrix(c, [1,0,0])
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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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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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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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coordinates = rotate(M, coordinates)
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if verbose > 2:
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print("The big cell contains %5i atoms and will be printed in the file big_cell.xyz\n"%len(coordinates))
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write_coordinates(coordinates,'big_cell.xyz',3)
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# Cutting the sphere in the big cell
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coordinates = cut_sphere(coordinates,rB)
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if verbose > 2:
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print("The sphere contains %5i atoms and will be printed in the file sphere.xyz\n"%len(coordinates))
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write_coordinates(coordinates,'sphere.xyz',3)
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# Finding the fragment
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coordinates = sorted(coordinates, key=lambda x:distance(x,[0,0,0]))
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nAt, coordinates = find_fragment(coordinates,pattern,npattern,notInFrag)
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if verbose > 2 or showFrag:
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print("The fragment contains %3i atoms and will be printed in the file fragment.xyz\n"%nAt)
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write_coordinates(coordinates,'fragment.xyz',4,'O')
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coordinates = find_pseudo(coordinates,rPP,notInPseudo)
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if verbose > 2 or showBath:
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print("The bath will be printed in the file bath.xyz\n")
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write_coordinates(coordinates,'bath.xyz',3)
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print("The bath sorted with the fragment/pseudo/charge will be printed in the file bath_coloured.xyz\n")
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write_coordinates(coordinates,'bath_coloured.xyz',3,color='yes')
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if evjen:
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charges = evjen_charges(coordinates,atoms)
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else:
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charges = []
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atoms = np.array(atoms).flatten()
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for i in range(len(coordinates)):
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li = coordinates[i][3]
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ii = np.where(atoms==li)[0]
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charges.append(float(atoms[ii+1]))
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if verbose > 1:
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print("The total charge fragment+pseudopotential+bath is : % 8.6f\n"%np.sum(charges))
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if symmetry != []:
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nuc1 = nuclear_repulsion(coordinates,charges)
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if verbose > 1:
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print("Nuclear repulsion before the symmetry : % 8.6f\n"%nuc1)
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coordinates,charges,indexList = compute_symmetry(coordinates,charges,symmetry)
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nuc2 = nuclear_repulsion(coordinates,charges)
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if verbose > 1:
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print("Nuclear repulsion after the symmetry : % 8.6f\n"%nuc2)
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print("The total charge fragment+pseudopotential+bath after symmetry is : % 8.6f\n"%np.sum(charges))
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if verbose > 2:
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print("The symmetrized coordinates contain %5i atoms \n"%len(indexList))
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else:
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indexList = [i for i in range(len(coordinates))]
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write_output(outputFile,coordinates,charges,indexList)
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if verbose > 2:
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print("The output has been written to %s \n"%outputFile)
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out_interatomic_distances(coordinates)
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with open("output.tcl",'w') as f:
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tp = [atoms[i] for i in range(0, len(atoms), 4)]
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f.write("mol new fragment.xyz\nmol delrep 0 0\nmol representation CPK\n")
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for i in tp:
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if i in ["Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
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"Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd",
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"La", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hg"]:
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f.write('mol selection "type {:s}"\nmol color ColorID 3\nmol addrep 0\n'.format(i))
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elif i in ["F", "Cl", "Br", "I"]:
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f.write('mol selection "type {:s}"\nmol color ColorID 7\nmol addrep 0\n'.format(i))
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else:
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f.write('mol selection "type {:s}"\nmol color Name\nmol addrep 0\n'.format(i))
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f.write("mol new bath_coloured.xyz\nmol delrep 0 1\nmol representation Points\n")
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f.write('mol selection "type Cl"\nmol color colorID 17\nmol addrep 1\n')
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f.write('mol selection "type C"\nmol color colorID 0\nmol addrep 1\n')
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