Generated by Cython 0.29.32
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" 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
__Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_double); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_2) < 0) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
07:
08: @cython.boundscheck(False) # Deactivate bounds checking
09: @cython.wraparound(False) # Deactivate negative indexing.
+10: cdef double distance(
static double __pyx_f_5utils_10q_routines_distance(__Pyx_memviewslice __pyx_v_pos_ts, Py_ssize_t __pyx_v_atom1, Py_ssize_t __pyx_v_atom2) { double __pyx_v_dx; double __pyx_v_dy; double __pyx_v_dz; double __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("distance", 0); /* … */ /* function exit code */ __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; }
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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+18: dy = pos_ts[atom1,1] - pos_ts[atom2,1]
__pyx_t_4 = __pyx_v_atom1; __pyx_t_3 = 1; __pyx_t_2 = __pyx_v_atom2; __pyx_t_1 = 1; __pyx_v_dy = ((*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_ts.data + __pyx_t_4 * __pyx_v_pos_ts.strides[0]) ) + __pyx_t_3 * __pyx_v_pos_ts.strides[1]) ))) - (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_ts.data + __pyx_t_2 * __pyx_v_pos_ts.strides[0]) ) + __pyx_t_1 * __pyx_v_pos_ts.strides[1]) ))));
+19: dz = pos_ts[atom1,2] - pos_ts[atom2,2]
__pyx_t_1 = __pyx_v_atom1; __pyx_t_2 = 2; __pyx_t_3 = __pyx_v_atom2; __pyx_t_4 = 2; __pyx_v_dz = ((*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_ts.data + __pyx_t_1 * __pyx_v_pos_ts.strides[0]) ) + __pyx_t_2 * __pyx_v_pos_ts.strides[1]) ))) - (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_ts.data + __pyx_t_3 * __pyx_v_pos_ts.strides[0]) ) + __pyx_t_4 * __pyx_v_pos_ts.strides[1]) ))));
+20: return sqrt(dx*dx + dy*dy + dz*dz)
__pyx_r = sqrt((((__pyx_v_dx * __pyx_v_dx) + (__pyx_v_dy * __pyx_v_dy)) + (__pyx_v_dz * __pyx_v_dz))); goto __pyx_L0;
21:
22: @cython.boundscheck(False)
23: @cython.wraparound(False)
24: @cython.cdivision(True) # avoide checking the 0 division
+25: def q_time_series(
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26: u,
27: double total_contacts,
28: double[:, :] cm_mod,
29: double gamma):
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35: cdef double[:,:] pos_ts
36:
37: cdef Py_ssize_t i, j, k
38: cdef double tot
39:
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42:
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+47: tot += 1
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48:
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50:
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