Generated by Cython 0.29.32

Yellow lines hint at Python interaction.
Click on a line that starts with a "+" to see the C code that Cython generated for it.

Raw output: q_routines.c

+01: import numpy as np
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 02: 
 03: cimport cython
 04: from libc.math cimport sqrt
 05: 
+06: DTYPE = np.double
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 07: 
 08: @cython.boundscheck(False)  # Deactivate bounds checking
 09: @cython.wraparound(False)   # Deactivate negative indexing.
+10: cdef double distance(
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 11:     double[:, :] pos_ts,
 12:     Py_ssize_t atom1,
 13:     Py_ssize_t atom2):
 14: 
 15:     cdef double dx, dy, dz
 16: 
+17:     dx = pos_ts[atom1,0] - pos_ts[atom2,0]
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 21: 
 22: @cython.boundscheck(False)
 23: @cython.wraparound(False)
 24: @cython.cdivision(True) # avoide checking the 0 division
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        __pyx_v_k = __pyx_t_15;
+46:                 if distance(pos_ts, j, k) <= gamma*cm_mod[j,k]:
        __pyx_t_16 = __pyx_v_j;
        __pyx_t_17 = __pyx_v_k;
        __pyx_t_18 = ((__pyx_f_5utils_10q_routines_distance(__pyx_v_pos_ts, __pyx_v_j, __pyx_v_k) <= (__pyx_v_gamma * (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_cm_mod.data + __pyx_t_16 * __pyx_v_cm_mod.strides[0]) ) + __pyx_t_17 * __pyx_v_cm_mod.strides[1]) ))))) != 0);
        if (__pyx_t_18) {
/* … */
        }
      }
    }
+47:                     tot += 1
          __pyx_v_tot = (__pyx_v_tot + 1.0);
 48: 
+49:         q[i] = tot/total_contacts
    __pyx_t_17 = __pyx_v_i;
    *((double *) ( /* dim=0 */ (__pyx_v_q.data + __pyx_t_17 * __pyx_v_q.strides[0]) )) = (__pyx_v_tot / __pyx_v_total_contacts);
  }
 50: 
+51:     return q
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_5 = __pyx_memoryview_fromslice(__pyx_v_q, 1, (PyObject *(*)(char *)) __pyx_memview_get_double, (int (*)(char *, PyObject *)) __pyx_memview_set_double, 0);; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 51, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __pyx_r = __pyx_t_5;
  __pyx_t_5 = 0;
  goto __pyx_L0;