Command line: md_002.py
Total duration: 1662.48s
File: md_002.py
File duration: 1661.74s (99.96%)
Line #|      Hits|         Time| Time per hit|      %|Source code
------+----------+-------------+-------------+-------+-----------
     1|         0|            0|            0|  0.00%|# md test code
     2|         0|            0|            0|  0.00%|
     3|         2|  3.50475e-05|  1.75238e-05|  0.00%|import platform
     4|         1|  2.19345e-05|  2.19345e-05|  0.00%|from time import clock
(call)|         1|  2.67029e-05|  2.67029e-05|  0.00%|# :1009 _handle_fromlist
     5|         1|  2.55108e-05|  2.55108e-05|  0.00%|import numpy as np
(call)|         1|     0.745732|     0.745732|  0.04%|# :978 _find_and_load
     6|         1|  2.57492e-05|  2.57492e-05|  0.00%|from sys import exit
(call)|         1|   1.7643e-05|   1.7643e-05|  0.00%|# :1009 _handle_fromlist
     7|         1|  7.86781e-06|  7.86781e-06|  0.00%|import time
...
   234|         0|            0|            0|  0.00%|        #  Compute the potential energy and forces
   235|  12525000|      51.0831|  4.07849e-06|  3.07%|        for j in range(0, p_num):
   236|  12500000|      51.6473|  4.13179e-06|  3.11%|            if (i != j):
   237|         0|            0|            0|  0.00%|                #  Compute RIJ, the displacement vector
   238|  49900000|      210.704|  4.22253e-06| 12.67%|                for k in range(0, d_num):
   239|  37425000|      177.055|  4.73093e-06| 10.65%|                    rij[k] = pos[k,i] - pos[k,j]
   240|         0|            0|            0|  0.00%|                # end for
   241|         0|            0|            0|  0.00%|
   242|         0|            0|            0|  0.00%|                #  Compute D and D2, a distance and a truncated distance
   243|  12475000|      50.5158|  4.04936e-06|  3.04%|                d = 0.0
   244|  49900000|      209.465|   4.1977e-06| 12.60%|                for k in range(0, d_num):
   245|  37425000|      175.823|  4.69801e-06| 10.58%|                    d = d + rij[k] ** 2
   246|         0|            0|            0|  0.00%|                # end for
   247|  12475000|      78.9422|  6.32803e-06|  4.75%|                d = np.sqrt(d)
   248|  12475000|      64.7463|  5.19008e-06|  3.89%|                d2 = min(d, np.pi / 2.0)
   249|         0|            0|            0|  0.00%|
   250|         0|            0|            0|  0.00%|                #  Attribute half of the total potential energy to particle J
   251|  12475000|      84.7846|  6.79636e-06|  5.10%|                potential = potential + 0.5 * np.sin(d2) * np.sin(d2)
   252|         0|            0|            0|  0.00%|
   253|         0|            0|            0|  0.00%|                #  Add particle J's contribution to the force on particle I.
   254|  49900000|       227.88|  4.56674e-06| 13.71%|                for k in range(0, d_num):
   255|  37425000|      244.374|  6.52971e-06| 14.70%|                    force[k,i] = force[k,i] - rij[k] * np.sin(2.0 * d2) / d
   256|         0|            0|            0|  0.00%|                # end for
   257|         0|            0|            0|  0.00%|            # end if
   258|         0|            0|            0|  0.00%|
   259|         0|            0|            0|  0.00%|        # end for
...