diff --git a/main.py b/main.py deleted file mode 100644 index f833494..0000000 --- a/main.py +++ /dev/null @@ -1,163 +0,0 @@ -import sys -import numpy as np - -from src.read_input import * -from src.out import * -from src.utils import * - -if __name__=='__main__': - - verbose = 2 - - if len(sys.argv) == 1: - print("Please provide the input file") - sys.exit() - elif len(sys.argv) == 3 : - if sys.argv[2] == 's': - verbose = 0 - elif sys.argv[2] == 'v': - verbose = 1 - elif sys.argv[2] == 'vv': - verbose = 2 - elif sys.argv[2] == 'vvv': - verbose = 3 - else: - print("Unknown argument -%s-"%sys.argv[3]) - elif len(sys.argv) > 3: - print("Too much arguments, please provide an input file and a verbose level (v, vv, vvv)") - sys.exit() - - inputFile = sys.argv[1] - - # Reads all the parameters from the input file - 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) - - if verbose > 0: - 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) - - # Converting the angles to radian - alpha = alpha * np.pi / 180.0 - beta = beta * np.pi / 180.0 - gamma = gamma * np.pi / 180.0 - - - # Computing the number of replications needed in each directions using the interreticular distance - # for the planes 100, 010 and 001. - # - # The condition is : d_{hkl} >= 2*bath_radius + |translation_vector| - - 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)) - - nA = int(np.ceil(np.sin(alpha)*(2*rB+np.linalg.norm(translation))/(a*fac)))+1 - nB = int(np.ceil(np.sin(beta)*(2*rB+np.linalg.norm(translation))/(b*fac)))+1 - nC = int(np.ceil(np.sin(gamma)*(2*rB+np.linalg.norm(translation))/(c*fac)))+1 - - if verbose > 1: - print("The big cell will be of dimensions %2ix%2ix%2i\n"%(nA,nB,nC)) - - coordinates = big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC) - - # Computing the translation vector by addition of the user translation vector and a translation - # vector that puts the origin at the center of the big cell - t = [-0.5,-0.5,-0.5] - M = get_cell_matrix(nA*a,nB*b,nC*c,alpha,beta,gamma) - t = np.matmul(M,t) - t = [t[0]+translation[0],t[1]+translation[1],t[2]+translation[2]] - - # Translating the coordinates - coordinates = translate(t, coordinates) - - # Finding the center and translating the coordinates - # If this vector creates a displacment bigger than a, b or c - # in any of the abc directions, this might result in an incomplete - # sphere later, the user should provide a translation vector - # to correct this - if center != []: - c = find_center(center,coordinates) - coordinates = translate(-c,coordinates) - - - # Orienting the big cell - if X != []: - k = [1,0,0] - - xVec = find_center(X,coordinates) - M = rotation_matrix(k,xVec) - - rotate(M, coordinates) - if Y != []: - k = [0,1,0] - - yVec = find_center(Y,coordinates) - M = rotation_matrix(k,yVec) - - rotate(M, coordinates) - if Z != []: - k = [0,0,1] - - zVec = find_center(Z,coordinates) - M = rotation_matrix(k,zVec) - - rotate(M, coordinates) - - if verbose > 2: - print("The big cell contains %5i atoms and will be printed in the file big_cell.xyz\n"%len(coordinates)) - write_coordinates(coordinates,'big_cell.xyz',3) - - # Cutting the sphere in the big cell - coordinates = cut_sphere(coordinates,rB) - - if verbose > 2: - print("The sphere contains %5i atoms and will be printed in the file sphere.xyz\n"%len(coordinates)) - write_coordinates(coordinates,'sphere.xyz',3) - - # Finding the fragment - - nAt, coordinates = find_fragment(coordinates,pattern,npattern,notInFrag) - - if verbose > 2 or showFrag: - print("The fragment contains %3i atoms and will be printed in the file fragment.xyz\n"%nAt) - write_coordinates(coordinates,'fragment.xyz',4,'O') - - coordinates = find_pseudo(coordinates,rPP,notInPseudo) - - if verbose > 2 or showBath: - print("The bath will be printed in the file bath.xyz\n") - write_coordinates(coordinates,'bath.xyz',3) - print("The bath sorted with the fragment/pseudo/charge will be printed in the file bath_coloured.xyz\n") - write_coordinates(coordinates,'bath_coloured.xyz',3,color='yes') - - if evjen: - charges = evjen_charges(coordinates,atoms) - else: - charges = [] - for i in range(len(coordinates)): - li = coordinates[i][3] - ii = np.where(atoms=li)[0] - charges.append(atoms[ii+1]) - - if verbose > 1: - print("The total charge fragment+pseudopotential+bath is : % 8.6f\n"%np.sum(charges)) - - if symmetry != []: - nuc1 = nuclear_repulsion(coordinates,charges) - if verbose > 1: - print("Nuclear repulsion before the symmetry : % 8.6f\n"%nuc1) - - coordinates,charges,indexList = compute_symmetry(coordinates,charges,symmetry) - - nuc2 = nuclear_repulsion(coordinates,charges) - if verbose > 1: - print("Nuclear repulsion after the symmetry : % 8.6f\n"%nuc2) - print("The total charge fragment+pseudopotential+bath after symmetry is : % 8.6f\n"%np.sum(charges)) - if verbose > 2: - print("The symmetrized coordinates contain %5i atoms \n"%len(indexList)) - - else: - indexList = [i for i in range(len(coordinates))] - - write_output(outputFile,coordinates,charges,indexList) - if verbose > 2: - print("The output has been written to %s \n"%outputFile) - out_interatomic_distances(coordinates) -