Bug fixes for step3 many-body

[MohammadShakiba]

• A simple but important bug fix was made for step3. The TDDFT coefficient matrix was not considered for the (t+\delta t) in the matrix multiplication. old:

          for i in range(len(St_sds_cmatrix)):
              sd2ci = SD2CI[i]
              St_ci = np.linalg.multi_dot([sd2ci.T, St_sds[i].todense().real, sd2ci])

  new:

          for i in range(len(St_sds_cmatrix)-1):
              sd2ci_prev = SD2CI[i]
              sd2ci_curr = SD2CI[i+1]
              St_ci = np.linalg.multi_dot([sd2ci_prev.T, St_sds[i].todense().real, sd2ci_curr])

• Made code compatible with new changes in libra_py/packages/cp2k/methods.py
• Some working ML scripting for K-means but not perfectly polished