Example #1
0
    oline = src.readlines()
    #Here, we prepend the string we want to on first line
    oline.insert(0, fline)
    src.close()

    #We again open the file in WRITE mode
    src = open(f"30-{a}.xyz", "w")
    src.writelines(oline)
    src.close()

    print(src)

    atoms = ase.io.read(f'30-{a}.xyz')

    cm = CoulombMatrix(n_atoms_max=55, permutation="sorted_l2").create(atoms)
    cm1 = cm.reshape(55, 55)
    print(cm1)
    df2 = pd.DataFrame(cm1)
    df2.to_csv(open(f'30-cm-{a}.csv', 'w'), index=False, header=False)

    m1 = np.array(cm1)
    w, v = np.linalg.eig(m1)

    df3 = pd.DataFrame(w)
    df3_tr = df3.transpose()
    df3_tr.to_csv(open(f'30-e.val{a}.csv', 'w'), index=False)

    df4 = pd.DataFrame(v)
    df4.to_csv(open(f'30-e.vec{a}.csv', 'w'), index=False, header=False)
print(cm1.shape)
Example #2
0
    oline = src.readlines()
    #Here, we prepend the string we want to on first line
    oline.insert(0, fline)
    src.close()

    #We again open the file in WRITE mode
    src = open(f"cl-{a}.xyz", "w")
    src.writelines(oline)
    src.close()

    #    print(src)

    atoms = ase.io.read(f'cl-{a}.xyz')

    cm = CoulombMatrix(n_atoms_max=50, permutation="sorted_l2").create(atoms)
    cm1 = cm.reshape(50, 50)
    #    print(cm1)
    df2 = pd.DataFrame(cm1)
    df2.to_csv(open(f'cl-cm-{a}.csv', 'w'), index=False, header=False)

    m1 = np.array(cm1)
    w, v = np.linalg.eig(m1)

    df3 = pd.DataFrame(w)
    df3_tr = df3.transpose()
    df3_tr.to_csv(open(f'cl-e.val{a}.csv', 'w'), index=False)

    df4 = pd.DataFrame(v)
    df4.to_csv(open(f'cl-e.vec{a}.csv', 'w'), index=False, header=False)
#    print(cm1.shape)