Command line: ./md_001.py
Total duration: 1510.79s
File: ./md_001.py
File duration: 1510.04s (99.95%)
Line #|      Hits|         Time| Time per hit|      %|Source code
------+----------+-------------+-------------+-------+-----------
...
   141|     25551|    0.0946999|  3.70631e-06|  0.01%|    for i in range(0, p_num):
   142|         0|            0|            0|  0.00%|
   143|         0|            0|            0|  0.00%|        #  Compute the potential energy and forces.
   144|  12775500|      47.1989|  3.69449e-06|  3.12%|        for j in range(0, p_num):
   145|  12750000|      47.4793|  3.72387e-06|  3.14%|            if (i != j):
   146|         0|            0|            0|  0.00%|
   147|         0|            0|            0|  0.00%|                #  Compute RIJ, the displacement vector.
   148|  50898000|      194.963|  3.83046e-06| 12.90%|                for k in range(0, d_num):
   149|  38173500|      166.983|  4.37432e-06| 11.05%|                    rij[k] = pos[k,i] - pos[k,j]
   150|         0|            0|            0|  0.00%|                # end for
   151|         0|            0|            0|  0.00%|
   152|         0|            0|            0|  0.00%|                #  Compute D and D2, a distance and a truncated distance.
   153|         0|            0|            0|  0.00%|
   154|  12724500|      46.7333|   3.6727e-06|  3.09%|                d = 0.0
   155|  50898000|      195.426|  3.83956e-06| 12.94%|                for k in range(0, d_num):
   156|  38173500|      165.494|  4.33531e-06| 10.95%|                    d = d + rij[k] ** 2
   157|         0|            0|            0|  0.00%|                # end for
   158|  12724500|      72.0723|  5.66406e-06|  4.77%|                d = np.sqrt(d)
   159|  12724500|      59.0492|  4.64059e-06|  3.91%|                d2 = min(d, np.pi / 2.0)
   160|         0|            0|            0|  0.00%|
   161|         0|            0|            0|  0.00%|                #  Attribute half of the total potential energy to particle J.
   162|  12724500|      76.7099|  6.02852e-06|  5.08%|                potential = potential + 0.5 * np.sin(d2) * np.sin(d2)
   163|         0|            0|            0|  0.00%|
   164|         0|            0|            0|  0.00%|                #  Add particle J's contribution to the force on particle I.
   165|  50898000|      207.158|  4.07005e-06| 13.71%|                for k in range(0, d_num):
   166|  38173500|      228.123|  5.97595e-06| 15.10%|                    force[k,i] = force[k,i] - rij[k] * np.sin(2.0 * d2) / d
   167|         0|            0|            0|  0.00%|                # end for
   168|         0|            0|            0|  0.00%|            # end if
   169|         0|            0|            0|  0.00%|
   170|         0|            0|            0|  0.00%|        # end for
   171|         0|            0|            0|  0.00%|    # end for
   172|         0|            0|            0|  0.00%|
...