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: cython_gaussian_entanglement.c

+01: '''Cython implementation of the G' computation'''
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 02: cimport cython
 03: 
 04: @cython.boundscheck(False)  # Deactivate bounds checking
 05: @cython.wraparound(False)   # Deactivate negative indexing.
+06: cdef void cross(
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 07:     double[:] x,
 08:     double[:] a,
 09:     double[:] b):
 10:     '''Computes the cross product'''
+11:     x[0] = a[1]*b[2] - a[2]*b[1]
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+12:     x[1] = a[2]*b[0] - a[0]*b[2]
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 14: 
 15: @cython.boundscheck(False)  # Deactivate bounds checking
 16: @cython.wraparound(False)   # Deactivate negative indexing.
+17: cdef double dot(
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 18:     double[:] a,
 19:     double[:] b):
 20:     '''Compute dot product'''
+21:     return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
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 22: 
 23: @cython.boundscheck(False)  # Deactivate bounds checking
 24: @cython.wraparound(False)   # Deactivate negative indexing.
+25: def cython_gaussian_entanglement(
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 27:     Py_ssize_t i2,
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 30:     double[:, :] R,
 31:     double[:, :] deltaR):
 32:     '''Returns G' for loop starting from residue i1 to i2 and
 33:     thread starting from residue j1 to j2'''
 34: 
 35:     cdef Py_ssize_t i, j, k
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        *((double *) ( /* dim=0 */ (__pyx_v_dR.data + __pyx_t_16 * __pyx_v_dR.strides[0]) )) = ((*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_R.data + __pyx_t_12 * __pyx_v_R.strides[0]) ) + __pyx_t_13 * __pyx_v_R.strides[1]) ))) - (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_R.data + __pyx_t_14 * __pyx_v_R.strides[0]) ) + __pyx_t_15 * __pyx_v_R.strides[1]) ))));
      }
 49: 
+50:             cross(ddR, deltaR[i], deltaR[j])
      __pyx_t_4.data = __pyx_v_deltaR.data;
      __pyx_t_4.memview = __pyx_v_deltaR.memview;
      __PYX_INC_MEMVIEW(&__pyx_t_4, 0);
      {
    Py_ssize_t __pyx_tmp_idx = __pyx_v_i;
    Py_ssize_t __pyx_tmp_stride = __pyx_v_deltaR.strides[0];
        __pyx_t_4.data += __pyx_tmp_idx * __pyx_tmp_stride;
}

__pyx_t_4.shape[0] = __pyx_v_deltaR.shape[1];
__pyx_t_4.strides[0] = __pyx_v_deltaR.strides[1];
    __pyx_t_4.suboffsets[0] = -1;

__pyx_t_17.data = __pyx_v_deltaR.data;
      __pyx_t_17.memview = __pyx_v_deltaR.memview;
      __PYX_INC_MEMVIEW(&__pyx_t_17, 0);
      {
    Py_ssize_t __pyx_tmp_idx = __pyx_v_j;
    Py_ssize_t __pyx_tmp_stride = __pyx_v_deltaR.strides[0];
        __pyx_t_17.data += __pyx_tmp_idx * __pyx_tmp_stride;
}

__pyx_t_17.shape[0] = __pyx_v_deltaR.shape[1];
__pyx_t_17.strides[0] = __pyx_v_deltaR.strides[1];
    __pyx_t_17.suboffsets[0] = -1;

__pyx_f_4pyge_9cythonlib_28cython_gaussian_entanglement_cross(__pyx_v_ddR, __pyx_t_4, __pyx_t_17);
      __PYX_XDEC_MEMVIEW(&__pyx_t_4, 1);
      __pyx_t_4.memview = NULL;
      __pyx_t_4.data = NULL;
      __PYX_XDEC_MEMVIEW(&__pyx_t_17, 1);
      __pyx_t_17.memview = NULL;
      __pyx_t_17.data = NULL;
+51:             ge += dot(dR, ddR)/(dot(dR, dR)**(3/2))
      __pyx_t_18 = __pyx_f_4pyge_9cythonlib_28cython_gaussian_entanglement_dot(__pyx_v_dR, __pyx_v_ddR);
      __pyx_t_19 = pow(__pyx_f_4pyge_9cythonlib_28cython_gaussian_entanglement_dot(__pyx_v_dR, __pyx_v_dR), (3.0 / 2.0));
      if (unlikely(__pyx_t_19 == 0)) {
        PyErr_SetString(PyExc_ZeroDivisionError, "float division");
        __PYX_ERR(0, 51, __pyx_L1_error)
      }
      __pyx_v_ge = (__pyx_v_ge + (__pyx_t_18 / __pyx_t_19));
    }
  }
 52: 
+53:     return ge/(4*PI)
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_19 = (4.0 * __pyx_v_PI);
  if (unlikely(__pyx_t_19 == 0)) {
    PyErr_SetString(PyExc_ZeroDivisionError, "float division");
    __PYX_ERR(0, 53, __pyx_L1_error)
  }
  __pyx_t_2 = PyFloat_FromDouble((__pyx_v_ge / __pyx_t_19)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 53, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;