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odestuff.c
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odestuff.c
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static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
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#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
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#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
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#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
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static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
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#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
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static int __Pyx_sys_getdefaultencoding_not_ascii;
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PyObject* default_encoding = NULL;
PyObject* ascii_chars_u = NULL;
PyObject* ascii_chars_b = NULL;
const char* default_encoding_c;
sys = PyImport_ImportModule("sys");
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default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
Py_DECREF(sys);
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PyErr_Format(
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goto bad;
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Py_DECREF(ascii_chars_u);
Py_DECREF(ascii_chars_b);
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Py_DECREF(default_encoding);
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Py_XDECREF(ascii_chars_b);
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#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
PyObject* sys;
PyObject* default_encoding = NULL;
char* default_encoding_c;
sys = PyImport_ImportModule("sys");
if (!sys) goto bad;
default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
Py_DECREF(sys);
if (!default_encoding) goto bad;
default_encoding_c = PyBytes_AsString(default_encoding);
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__PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
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strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
Py_DECREF(default_encoding);
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bad:
Py_XDECREF(default_encoding);
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/* Test for GCC > 2.95 */
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#define likely(x) __builtin_expect(!!(x), 1)
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#else /* !__GNUC__ or GCC < 2.95 */
#define likely(x) (x)
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static PyObject *__pyx_m;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
static PyObject *__pyx_empty_unicode;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
static const char *__pyx_f[] = {
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#define __Pyx_XINCREF(r) Py_XINCREF(r)
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#define __Pyx_XGOTREF(r)
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static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
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/* GetBuiltinName.proto */
static PyObject *__Pyx_GetBuiltinName(PyObject *name);
/* RaiseArgTupleInvalid.proto */
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
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/* RaiseDoubleKeywords.proto */
static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
/* ParseKeywords.proto */
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
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/* GetItemInt.proto */
#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
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__Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
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#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
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/* PySequenceContains.proto */
static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) {
int result = PySequence_Contains(seq, item);
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}
/* GetModuleGlobalName.proto */
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
/* PyObjectCall.proto */
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static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
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#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
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/* PyObjectCallMethO.proto */
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static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
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/* PyObjectCallOneArg.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
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static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
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/* pyobject_as_double.proto */
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#define __Pyx_PyObject_AsDouble(obj)\
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/* None.proto */
static CYTHON_INLINE int __Pyx_mod_int(int, int);
/* ListCompAppend.proto */
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static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
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Py_INCREF(x);
PyList_SET_ITEM(list, len, x);
Py_SIZE(list) = len+1;
return 0;
}
return PyList_Append(list, x);
}
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#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
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/* Import.proto */
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
/* ImportFrom.proto */
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
/* CodeObjectCache.proto */
typedef struct {
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int code_line;
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struct __Pyx_CodeObjectCache {
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static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
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static PyCodeObject *__pyx_find_code_object(int code_line);
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
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/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
/* CIntFromPy.proto */
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
/* CIntFromPy.proto */
static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *);
/* CIntFromPy.proto */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
/* CIntToPy.proto */
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/* CheckBinaryVersion.proto */
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/* InitStrings.proto */
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/* Module declarations from 'libc.string' */
/* Module declarations from 'libc.stdlib' */
/* Module declarations from 'libc.math' */
/* Module declarations from 'odestuff' */
static void __pyx_f_8odestuff_dzdt(double, int, double, double *, int *, double *, double *); /*proto*/
static void __pyx_f_8odestuff_rk4(double *, double *, int, int, double, double, double, double *, int *, double *); /*proto*/
#define __Pyx_MODULE_NAME "odestuff"
int __pyx_module_is_main_odestuff = 0;
/* Implementation of 'odestuff' */
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_sum;
static const char __pyx_k_[] = " ";
static const char __pyx_k_C[] = "C";
static const char __pyx_k_N[] = "N";
static const char __pyx_k_a[] = "a";
static const char __pyx_k_f[] = "f";
static const char __pyx_k_i[] = "i";
static const char __pyx_k_j[] = "j";
static const char __pyx_k_o[] = "o";
static const char __pyx_k_p[] = "p";
static const char __pyx_k_r[] = "r";
static const char __pyx_k_t[] = "t";
static const char __pyx_k_w[] = "w";
static const char __pyx_k_x[] = "x";
static const char __pyx_k_y[] = "y";
static const char __pyx_k_z[] = "z";
static const char __pyx_k__3[] = "\n";
static const char __pyx_k_a2[] = "a2";
static const char __pyx_k_dt[] = "dt";
static const char __pyx_k_dz[] = "dz";
static const char __pyx_k_it[] = "it";
static const char __pyx_k_pC[] = "pC";
static const char __pyx_k_r2[] = "r2";
static const char __pyx_k_64e[] = "%.64e ";
static const char __pyx_k_eit[] = "eit";
static const char __pyx_k_pdt[] = "pdt";
static const char __pyx_k_r_k[] = "r_k";
static const char __pyx_k_run[] = "run";
static const char __pyx_k_sum[] = "sum";
static const char __pyx_k_avgx[] = "avgx";
static const char __pyx_k_avgy[] = "avgy";
static const char __pyx_k_line[] = "line";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_open[] = "open";
static const char __pyx_k_pall[] = "pall";
static const char __pyx_k_pavg[] = "pavg";
static const char __pyx_k_peit[] = "peit";
static const char __pyx_k_sumr[] = "sumr";
static const char __pyx_k_tequ[] = "tequ";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_tmax[] = "tmax";
static const char __pyx_k_zout[] = "zout";
static const char __pyx_k_close[] = "close";
static const char __pyx_k_gamma[] = "gamma";
static const char __pyx_k_npars[] = "npars";
static const char __pyx_k_nvars[] = "nvars";
static const char __pyx_k_omega[] = "omega";
static const char __pyx_k_ptequ[] = "ptequ";
static const char __pyx_k_ptmax[] = "ptmax";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_sline[] = "sline";
static const char __pyx_k_split[] = "split";
static const char __pyx_k_sumr2[] = "sumr2";
static const char __pyx_k_write[] = "write";
static const char __pyx_k_exists[] = "exists";
static const char __pyx_k_finitc[] = "finitc";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_lnghbr[] = "lnghbr";
static const char __pyx_k_sumrkx[] = "sumrkx";
static const char __pyx_k_sumrky[] = "sumrky";
static const char __pyx_k_xrange[] = "xrange";
static const char __pyx_k_os_path[] = "os.path";
static const char __pyx_k_odestuff[] = "odestuff";
static const char __pyx_k_readline[] = "readline";
static const char __pyx_k_fname_output[] = "fname_output";
static const char __pyx_k_fname_initialcond[] = "fname_initialcond";
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static PyObject *__pyx_kp_s_;
static PyObject *__pyx_kp_s_64e;
static PyObject *__pyx_n_s_C;
static PyObject *__pyx_n_s_N;
static PyObject *__pyx_kp_s_Users_nihil_phd_code_runx_odest;
static PyObject *__pyx_kp_s__3;
static PyObject *__pyx_n_s_a;
static PyObject *__pyx_n_s_a2;
static PyObject *__pyx_n_s_avgx;
static PyObject *__pyx_n_s_avgy;
static PyObject *__pyx_n_s_close;
static PyObject *__pyx_n_s_dt;
static PyObject *__pyx_n_s_dz;
static PyObject *__pyx_n_s_eit;
static PyObject *__pyx_n_s_exists;
static PyObject *__pyx_n_s_f;
static PyObject *__pyx_n_s_finitc;
static PyObject *__pyx_n_s_fname_initialcond;
static PyObject *__pyx_n_s_fname_output;
static PyObject *__pyx_n_s_gamma;
static PyObject *__pyx_n_s_i;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_it;
static PyObject *__pyx_n_s_j;
static PyObject *__pyx_n_s_line;
static PyObject *__pyx_n_s_lnghbr;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_npars;
static PyObject *__pyx_n_s_nvars;
static PyObject *__pyx_n_s_o;
static PyObject *__pyx_n_s_odestuff;
static PyObject *__pyx_n_s_omega;
static PyObject *__pyx_n_s_open;
static PyObject *__pyx_n_s_os_path;
static PyObject *__pyx_n_s_p;
static PyObject *__pyx_n_s_pC;
static PyObject *__pyx_n_s_pall;
static PyObject *__pyx_n_s_pavg;
static PyObject *__pyx_n_s_pdt;
static PyObject *__pyx_n_s_peit;
static PyObject *__pyx_n_s_ptequ;
static PyObject *__pyx_n_s_ptmax;
static PyObject *__pyx_n_s_r;
static PyObject *__pyx_n_s_r2;
static PyObject *__pyx_n_s_r_k;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_readline;
static PyObject *__pyx_n_s_run;
static PyObject *__pyx_n_s_sline;
static PyObject *__pyx_n_s_split;
static PyObject *__pyx_n_s_sum;
static PyObject *__pyx_n_s_sumr;
static PyObject *__pyx_n_s_sumr2;
static PyObject *__pyx_n_s_sumrkx;
static PyObject *__pyx_n_s_sumrky;
static PyObject *__pyx_n_s_t;
static PyObject *__pyx_n_s_tequ;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_tmax;
static PyObject *__pyx_n_s_w;
static PyObject *__pyx_n_s_write;
static PyObject *__pyx_n_s_x;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_n_s_y;
static PyObject *__pyx_n_s_z;
static PyObject *__pyx_n_s_zout;
static PyObject *__pyx_pf_8odestuff_run(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_N, PyObject *__pyx_v_o, PyObject *__pyx_v_lnghbr, PyObject *__pyx_v_pC, PyObject *__pyx_v_ptequ, PyObject *__pyx_v_ptmax, PyObject *__pyx_v_pdt, PyObject *__pyx_v_peit, PyObject *__pyx_v_fname_output, PyObject *__pyx_v_fname_initialcond, PyObject *__pyx_v_pall, PyObject *__pyx_v_pavg); /* proto */
static PyObject *__pyx_int_2;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__5;
static PyObject *__pyx_codeobj__6;
/* "odestuff.pyx":5
* from os.path import exists
*
* cdef void dzdt(double t, int N, double C, double p[], int a[], double z[], double dz[]): # <<<<<<<<<<<<<<
* cdef double x
* cdef double y
*/
static void __pyx_f_8odestuff_dzdt(CYTHON_UNUSED double __pyx_v_t, int __pyx_v_N, double __pyx_v_C, double *__pyx_v_p, int *__pyx_v_a, double *__pyx_v_z, double *__pyx_v_dz) {
double __pyx_v_x;
double __pyx_v_y;
double __pyx_v_r2;
double __pyx_v_omega;
double __pyx_v_c[2];
int __pyx_v_i;
int __pyx_v_j;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
long __pyx_t_4;
__Pyx_RefNannySetupContext("dzdt", 0);
/* "odestuff.pyx":13
* cdef int i
* cdef int j
* for i from 0<=i<N: # <<<<<<<<<<<<<<
* x=z[2*i+0]
* y=z[2*i+1]
*/
__pyx_t_1 = __pyx_v_N;
for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
/* "odestuff.pyx":14
* cdef int j
* for i from 0<=i<N:
* x=z[2*i+0] # <<<<<<<<<<<<<<
* y=z[2*i+1]
* c[0]=0.
*/
__pyx_v_x = (__pyx_v_z[((2 * __pyx_v_i) + 0)]);
/* "odestuff.pyx":15
* for i from 0<=i<N:
* x=z[2*i+0]
* y=z[2*i+1] # <<<<<<<<<<<<<<
* c[0]=0.
* c[1]=0.
*/
__pyx_v_y = (__pyx_v_z[((2 * __pyx_v_i) + 1)]);
/* "odestuff.pyx":16
* x=z[2*i+0]
* y=z[2*i+1]
* c[0]=0. # <<<<<<<<<<<<<<
* c[1]=0.
* #for j in xrange(N):
*/
(__pyx_v_c[0]) = 0.;
/* "odestuff.pyx":17
* y=z[2*i+1]
* c[0]=0.
* c[1]=0. # <<<<<<<<<<<<<<
* #for j in xrange(N):
* for j from 0<=j<N:
*/
(__pyx_v_c[1]) = 0.;
/* "odestuff.pyx":19
* c[1]=0.
* #for j in xrange(N):
* for j from 0<=j<N: # <<<<<<<<<<<<<<
* if (a[i*N+j]==1):
* c[0]+=(z[2*j+0]-z[2*i+0])
*/
__pyx_t_2 = __pyx_v_N;
for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_2; __pyx_v_j++) {
/* "odestuff.pyx":20
* #for j in xrange(N):
* for j from 0<=j<N:
* if (a[i*N+j]==1): # <<<<<<<<<<<<<<
* c[0]+=(z[2*j+0]-z[2*i+0])
* c[1]+=(z[2*j+1]-z[2*i+1])
*/
__pyx_t_3 = (((__pyx_v_a[((__pyx_v_i * __pyx_v_N) + __pyx_v_j)]) == 1) != 0);
if (__pyx_t_3) {
/* "odestuff.pyx":21
* for j from 0<=j<N:
* if (a[i*N+j]==1):
* c[0]+=(z[2*j+0]-z[2*i+0]) # <<<<<<<<<<<<<<
* c[1]+=(z[2*j+1]-z[2*i+1])
* c[0]*=C
*/
__pyx_t_4 = 0;
(__pyx_v_c[__pyx_t_4]) = ((__pyx_v_c[__pyx_t_4]) + ((__pyx_v_z[((2 * __pyx_v_j) + 0)]) - (__pyx_v_z[((2 * __pyx_v_i) + 0)])));
/* "odestuff.pyx":22
* if (a[i*N+j]==1):
* c[0]+=(z[2*j+0]-z[2*i+0])
* c[1]+=(z[2*j+1]-z[2*i+1]) # <<<<<<<<<<<<<<
* c[0]*=C
* c[1]*=C
*/
__pyx_t_4 = 1;
(__pyx_v_c[__pyx_t_4]) = ((__pyx_v_c[__pyx_t_4]) + ((__pyx_v_z[((2 * __pyx_v_j) + 1)]) - (__pyx_v_z[((2 * __pyx_v_i) + 1)])));
/* "odestuff.pyx":20
* #for j in xrange(N):
* for j from 0<=j<N:
* if (a[i*N+j]==1): # <<<<<<<<<<<<<<
* c[0]+=(z[2*j+0]-z[2*i+0])
* c[1]+=(z[2*j+1]-z[2*i+1])
*/
}
}
/* "odestuff.pyx":23
* c[0]+=(z[2*j+0]-z[2*i+0])
* c[1]+=(z[2*j+1]-z[2*i+1])
* c[0]*=C # <<<<<<<<<<<<<<
* c[1]*=C
* r2=x*x+y*y
*/
__pyx_t_4 = 0;
(__pyx_v_c[__pyx_t_4]) = ((__pyx_v_c[__pyx_t_4]) * __pyx_v_C);
/* "odestuff.pyx":24
* c[1]+=(z[2*j+1]-z[2*i+1])
* c[0]*=C