Total time: 358.778 s
File: ./md_003.py
Function: properties at line 159
Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
   159                                           @profile
   160                                           def properties(p_num, d_num, pos, vel, mass):
   161
   162        50        164.0      3.3      0.0      import numpy as np
   163
   164
   165                                               # compute force, potential, kinetic
   166        50        351.0      7.0      0.0      force = np.zeros([ d_num, p_num ])
   167        50        153.0      3.1      0.0      rij = np.zeros(d_num)
   168
   169        50         30.0      0.6      0.0      potential = 0.0
   170
   171     25050      14447.0      0.6      0.0      for i in range(0, p_num):
   172
   173                                                   #  Compute the potential energy and forces
   174  12525000    7036459.0      0.6      2.0          for j in range(0, p_num):
   175  12500000    7730669.0      0.6      2.2              if (i != j):
   176                                                           #  Compute RIJ, the displacement vector
   177  49900000   33530834.0      0.7      9.3                  for k in range(0, d_num):
   178  37425000   39827594.0      1.1     11.1                      rij[k] = pos[k,i] - pos[k,j]
   179                                                           # end for
   180
   181                                                           #  Compute D and D2, a distance and a truncated distance
   182  12475000    7182783.0      0.6      2.0                  d = 0.0
   183  49900000   33037923.0      0.7      9.2                  for k in range(0, d_num):
   184  37425000   39131501.0      1.0     10.9                      d = d + rij[k] ** 2
   185                                                           # end for
   186  12475000   25236413.0      2.0      7.0                  d = np.sqrt(d)
   187  12475000   13375864.0      1.1      3.7                  d2 = min(d, np.pi / 2.0)
   188
   189                                                           #  Attribute half of the total potential energy to particle J
   190  12475000   31104186.0      2.5      8.7                  potential = potential + 0.5 * np.sin(d2) * np.sin(d2)
   191
   192                                                           #  Add particle J's contribution to the force on particle I.
   193  49900000   34782251.0      0.7      9.7                  for k in range(0, d_num):
   194  37425000   86664317.0      2.3     24.2                      force[k,i] = force[k,i] - rij[k] * np.sin(2.0 * d2) / d
   195                                                           # end for
   196                                                       # end if
   197
   198                                                   # end for
   199                                               # end for
   200
   201                                               #  Compute the kinetic energy
   202        50         33.0      0.7      0.0      kinetic = 0.0
   203       200        147.0      0.7      0.0      for k in range(0, d_num):
   204     75150      44048.0      0.6      0.0          for j in range(0, p_num):
   205     75000      78144.0      1.0      0.0              kinetic = kinetic + vel[k,j] ** 2
   206                                                   # end for
   207                                                # end for
   208
   209        50         47.0      0.9      0.0      kinetic = 0.5 * mass * kinetic
   210
   211        50         37.0      0.7      0.0      return force, kinetic, potential