forked from lijiext/lammps
2589 lines
124 KiB
C
2589 lines
124 KiB
C
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/* Generated by Cython 0.9.8.1.1 on Thu Oct 1 16:33:24 2009 */
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#define PY_SSIZE_T_CLEAN
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#include "Python.h"
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#include "structmember.h"
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#ifndef PY_LONG_LONG
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#define PY_LONG_LONG LONG_LONG
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#endif
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#ifndef DL_EXPORT
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#define DL_EXPORT(t) t
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#endif
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#if PY_VERSION_HEX < 0x02040000
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#define METH_COEXIST 0
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#endif
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#if PY_VERSION_HEX < 0x02050000
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typedef int Py_ssize_t;
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#define PY_SSIZE_T_MAX INT_MAX
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#define PY_SSIZE_T_MIN INT_MIN
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#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
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#define PyInt_AsSsize_t(o) PyInt_AsLong(o)
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#define PyNumber_Index(o) PyNumber_Int(o)
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#define PyIndex_Check(o) PyNumber_Check(o)
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#if PY_VERSION_HEX < 0x02060000
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#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
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#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
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#define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
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#define PyVarObject_HEAD_INIT(type, size) \
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PyObject_HEAD_INIT(type) size,
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#define PyType_Modified(t)
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typedef struct {
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void *buf;
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Py_ssize_t len;
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int readonly;
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const char *format;
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int ndim;
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Py_ssize_t *shape;
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Py_ssize_t *strides;
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Py_ssize_t *suboffsets;
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Py_ssize_t itemsize;
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void *internal;
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} Py_buffer;
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#define PyBUF_SIMPLE 0
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#define PyBUF_WRITABLE 0x0001
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#define PyBUF_LOCK 0x0002
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#define PyBUF_FORMAT 0x0004
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#define PyBUF_ND 0x0008
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#define PyBUF_STRIDES (0x0010 | PyBUF_ND)
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#define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
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#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
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#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
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#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
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#endif
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#if PY_MAJOR_VERSION < 3
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#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
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#else
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#define __Pyx_BUILTIN_MODULE_NAME "builtins"
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#endif
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#if PY_MAJOR_VERSION >= 3
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#define Py_TPFLAGS_CHECKTYPES 0
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#define Py_TPFLAGS_HAVE_INDEX 0
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#endif
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#if PY_MAJOR_VERSION >= 3
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#define PyBaseString_Type PyUnicode_Type
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#define PyString_Type PyBytes_Type
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#define PyInt_Type PyLong_Type
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#define PyInt_Check(op) PyLong_Check(op)
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#define PyInt_CheckExact(op) PyLong_CheckExact(op)
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#define PyInt_FromString PyLong_FromString
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#define PyInt_FromUnicode PyLong_FromUnicode
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#define PyInt_FromLong PyLong_FromLong
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#define PyInt_FromSize_t PyLong_FromSize_t
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#define PyInt_FromSsize_t PyLong_FromSsize_t
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#define PyInt_AsLong PyLong_AsLong
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#define PyInt_AS_LONG PyLong_AS_LONG
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#define PyInt_AsSsize_t PyLong_AsSsize_t
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#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
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#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
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#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
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#else
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#define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
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#define PyBytes_Type PyString_Type
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#endif
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#if PY_MAJOR_VERSION >= 3
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#define PyMethod_New(func, self, klass) PyInstanceMethod_New(func)
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#endif
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#if !defined(WIN32) && !defined(MS_WINDOWS)
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#ifndef __stdcall
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#define __stdcall
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#endif
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#ifndef __cdecl
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#define __cdecl
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#endif
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#else
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#define _USE_MATH_DEFINES
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#endif
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#ifdef __cplusplus
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#define __PYX_EXTERN_C extern "C"
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#else
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#define __PYX_EXTERN_C extern
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#endif
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#include <math.h>
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#define __PYX_HAVE_API__lmp2radii
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#ifdef __GNUC__
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#define INLINE __inline__
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#elif _WIN32
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#define INLINE __inline
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#else
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#define INLINE
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#endif
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typedef struct {PyObject **p; char *s; long n; char is_unicode; char intern; char is_identifier;} __Pyx_StringTabEntry; /*proto*/
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static int __pyx_skip_dispatch = 0;
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/* Type Conversion Predeclarations */
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#if PY_MAJOR_VERSION < 3
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#define __Pyx_PyBytes_FromString PyString_FromString
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#define __Pyx_PyBytes_AsString PyString_AsString
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#else
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#define __Pyx_PyBytes_FromString PyBytes_FromString
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#define __Pyx_PyBytes_AsString PyBytes_AsString
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#endif
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#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
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static INLINE int __Pyx_PyObject_IsTrue(PyObject* x);
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static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x);
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static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x);
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static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b);
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#define __pyx_PyInt_AsLong(x) (PyInt_CheckExact(x) ? PyInt_AS_LONG(x) : PyInt_AsLong(x))
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#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
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static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x);
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static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x);
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static INLINE char __pyx_PyInt_char(PyObject* x);
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static INLINE short __pyx_PyInt_short(PyObject* x);
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static INLINE int __pyx_PyInt_int(PyObject* x);
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static INLINE long __pyx_PyInt_long(PyObject* x);
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static INLINE signed char __pyx_PyInt_signed_char(PyObject* x);
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static INLINE signed short __pyx_PyInt_signed_short(PyObject* x);
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static INLINE signed int __pyx_PyInt_signed_int(PyObject* x);
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static INLINE signed long __pyx_PyInt_signed_long(PyObject* x);
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static INLINE long double __pyx_PyInt_long_double(PyObject* x);
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#ifdef __GNUC__
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/* Test for GCC > 2.95 */
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#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
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#define likely(x) __builtin_expect(!!(x), 1)
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#define unlikely(x) __builtin_expect(!!(x), 0)
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#else /* __GNUC__ > 2 ... */
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#define likely(x) (x)
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#define unlikely(x) (x)
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#endif /* __GNUC__ > 2 ... */
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#else /* __GNUC__ */
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#define likely(x) (x)
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#define unlikely(x) (x)
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#endif /* __GNUC__ */
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static PyObject *__pyx_m;
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static PyObject *__pyx_b;
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static PyObject *__pyx_empty_tuple;
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static int __pyx_lineno;
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static int __pyx_clineno = 0;
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static const char * __pyx_cfilenm= __FILE__;
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static const char *__pyx_filename;
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static const char **__pyx_f;
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static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
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static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
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static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
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static int __Pyx_EndUnpack(PyObject *); /*proto*/
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static INLINE PyObject *__Pyx_GetItemInt(PyObject *o, Py_ssize_t i, int is_unsigned) {
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PyObject *r;
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if (PyList_CheckExact(o) && 0 <= i && i < PyList_GET_SIZE(o)) {
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r = PyList_GET_ITEM(o, i);
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Py_INCREF(r);
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}
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else if (PyTuple_CheckExact(o) && 0 <= i && i < PyTuple_GET_SIZE(o)) {
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r = PyTuple_GET_ITEM(o, i);
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Py_INCREF(r);
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}
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else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0) || !is_unsigned))
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r = PySequence_GetItem(o, i);
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else {
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PyObject *j = (likely(i >= 0) || !is_unsigned) ? PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i);
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if (!j)
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return 0;
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r = PyObject_GetItem(o, j);
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Py_DECREF(j);
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}
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return r;
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}
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static int __Pyx_Print(PyObject *, int); /*proto*/
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#if PY_MAJOR_VERSION >= 3
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static PyObject* __pyx_print = 0;
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static PyObject* __pyx_print_kwargs = 0;
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#endif
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static void __Pyx_AddTraceback(const char *funcname); /*proto*/
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static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
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/* Type declarations */
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/* Module declarations from lmp2radii */
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/* Implementation of lmp2radii */
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static char __pyx_k_1[] = "\nModule name: lmp2radii.py \n\nAuthor: (c) Andres Jaramillo-Botero\nCalifornia Institute of Technology\najaramil@wag.caltech.edu\nProject: pEFF\nVersion: August 2009\n\nExtracts the electron radii from a lammps trajectory dump of style custom:\n\ndump 1 all custom period dump_file id type x y z spin radius ...\n\nNOTE: The radius must be the 6th column per trajectory entry in the dump file\n\n";
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static char __pyx_k_5[] = "-h";
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static PyObject *__pyx_int_1;
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static PyObject *__pyx_int_7;
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static PyObject *__pyx_int_0;
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static PyObject *__pyx_int_9;
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static PyObject *__pyx_int_3;
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static char __pyx_k_Info[] = "Info";
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static PyObject *__pyx_kp_Info;
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static char __pyx_k_sys[] = "sys";
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static PyObject *__pyx_kp_sys;
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static char __pyx_k_os[] = "os";
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static PyObject *__pyx_kp_os;
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static char __pyx_k_math[] = "math";
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static PyObject *__pyx_kp_math;
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static char __pyx_k_2[] = "log10";
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static PyObject *__pyx_kp_2;
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static char __pyx_k_shutil[] = "shutil";
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static PyObject *__pyx_kp_shutil;
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static char __pyx_k_rmtree[] = "rmtree";
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static PyObject *__pyx_kp_rmtree;
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static char __pyx_k_getopt[] = "getopt";
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static PyObject *__pyx_kp_getopt;
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static char __pyx_k_gnu_getopt[] = "gnu_getopt";
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static PyObject *__pyx_kp_gnu_getopt;
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static char __pyx_k_numpy[] = "numpy";
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static PyObject *__pyx_kp_numpy;
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static char __pyx_k___name__[] = "__name__";
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static PyObject *__pyx_kp___name__;
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static char __pyx_k_3[] = "__main__";
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static PyObject *__pyx_kp_3;
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static char __pyx_k_argv[] = "argv";
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static PyObject *__pyx_kp_argv;
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static char __pyx_k_4[] = "h";
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|||
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static PyObject *__pyx_kp_4;
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static char __pyx_k_opts[] = "opts";
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|||
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static PyObject *__pyx_kp_opts;
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|||
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static char __pyx_k_printHelp[] = "printHelp";
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|||
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static PyObject *__pyx_kp_printHelp;
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|||
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static char __pyx_k_exit[] = "exit";
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|||
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static PyObject *__pyx_kp_exit;
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|||
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static char __pyx_k_infile[] = "infile";
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|||
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static PyObject *__pyx_kp_infile;
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static char __pyx_k_opt[] = "opt";
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|||
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static PyObject *__pyx_kp_opt;
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|||
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static char __pyx_k_arg[] = "arg";
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|||
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static PyObject *__pyx_kp_arg;
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|||
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static char __pyx_k_makeradii[] = "makeradii";
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|||
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static PyObject *__pyx_kp_makeradii;
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static char __pyx_k_open[] = "open";
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static PyObject *__pyx_kp_open;
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static char __pyx_k_8[] = "r";
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static PyObject *__pyx_kp_8;
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static char __pyx_k_xreadlines[] = "xreadlines";
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static PyObject *__pyx_kp_xreadlines;
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static char __pyx_k_system[] = "system";
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static PyObject *__pyx_kp_system;
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static char __pyx_k_12[] = "frames";
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static PyObject *__pyx_kp_12;
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static char __pyx_k_13[] = "r";
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static PyObject *__pyx_kp_13;
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static char __pyx_k_readline[] = "readline";
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static PyObject *__pyx_kp_readline;
|
|||
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static char __pyx_k_split[] = "split";
|
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static PyObject *__pyx_kp_split;
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|||
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static char __pyx_k_close[] = "close";
|
|||
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static PyObject *__pyx_kp_close;
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static char __pyx_k_14[] = "atoms";
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|||
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static PyObject *__pyx_kp_14;
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|||
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static char __pyx_k_15[] = "r";
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|||
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static PyObject *__pyx_kp_15;
|
|||
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static char __pyx_k_readlines[] = "readlines";
|
|||
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static PyObject *__pyx_kp_readlines;
|
|||
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static char __pyx_k_zeros[] = "zeros";
|
|||
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static PyObject *__pyx_kp_zeros;
|
|||
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|
static char __pyx_k_dtype[] = "dtype";
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|||
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|
static PyObject *__pyx_kp_dtype;
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|||
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static char __pyx_k_enumerate[] = "enumerate";
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|||
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static PyObject *__pyx_kp_enumerate;
|
|||
|
|
static char __pyx_k_stdout[] = "stdout";
|
|||
|
|
static PyObject *__pyx_kp_stdout;
|
|||
|
|
static char __pyx_k_write[] = "write";
|
|||
|
|
static PyObject *__pyx_kp_write;
|
|||
|
|
static char __pyx_k_flush[] = "flush";
|
|||
|
|
static PyObject *__pyx_kp_flush;
|
|||
|
|
static char __pyx_k_23[] = "w";
|
|||
|
|
static PyObject *__pyx_kp_23;
|
|||
|
|
static char __pyx_k_range[] = "range";
|
|||
|
|
static PyObject *__pyx_kp_range;
|
|||
|
|
static char __pyx_k_writelines[] = "writelines";
|
|||
|
|
static PyObject *__pyx_kp_writelines;
|
|||
|
|
static PyObject *__pyx_kp_1;
|
|||
|
|
static PyObject *__pyx_kp_5;
|
|||
|
|
static PyObject *__pyx_builtin___name__;
|
|||
|
|
static PyObject *__pyx_builtin_open;
|
|||
|
|
static PyObject *__pyx_builtin_enumerate;
|
|||
|
|
static PyObject *__pyx_builtin_range;
|
|||
|
|
static PyObject *__pyx_kp_6;
|
|||
|
|
static char __pyx_k_6[] = "Usage: python lmp2radii.pyx test.lammpstrj\n";
|
|||
|
|
static PyObject *__pyx_kp_7;
|
|||
|
|
static PyObject *__pyx_kp_9;
|
|||
|
|
static PyObject *__pyx_kp_10;
|
|||
|
|
static PyObject *__pyx_kp_11;
|
|||
|
|
static PyObject *__pyx_kp_16;
|
|||
|
|
static PyObject *__pyx_kp_17;
|
|||
|
|
static PyObject *__pyx_kp_19;
|
|||
|
|
static PyObject *__pyx_kp_18;
|
|||
|
|
static PyObject *__pyx_kp_21;
|
|||
|
|
static PyObject *__pyx_kp_20;
|
|||
|
|
static PyObject *__pyx_kp_22;
|
|||
|
|
static PyObject *__pyx_kp_24;
|
|||
|
|
static PyObject *__pyx_kp_25;
|
|||
|
|
static PyObject *__pyx_kp_27;
|
|||
|
|
static PyObject *__pyx_kp_26;
|
|||
|
|
static PyObject *__pyx_kp_28;
|
|||
|
|
static PyObject *__pyx_kp_29;
|
|||
|
|
static PyObject *__pyx_kp_30;
|
|||
|
|
static PyObject *__pyx_kp_31;
|
|||
|
|
static char __pyx_k_7[] = "Reading %s ... [WAIT]";
|
|||
|
|
static char __pyx_k_9[] = "";
|
|||
|
|
static char __pyx_k_10[] = "[DONE]";
|
|||
|
|
static char __pyx_k_11[] = "grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms";
|
|||
|
|
static char __pyx_k_16[] = "rm -rf frames atoms";
|
|||
|
|
static char __pyx_k_17[] = "Extracting electron radii per frame from %s ... ";
|
|||
|
|
static char __pyx_k_18[] = "%d/%d%s";
|
|||
|
|
static char __pyx_k_19[] = "";
|
|||
|
|
static char __pyx_k_20[] = "Writing radii/frame table to %s ... ";
|
|||
|
|
static char __pyx_k_21[] = ".out";
|
|||
|
|
static char __pyx_k_22[] = ".out";
|
|||
|
|
static char __pyx_k_24[] = "\tF";
|
|||
|
|
static char __pyx_k_25[] = "\n";
|
|||
|
|
static char __pyx_k_26[] = "%d/%d%s";
|
|||
|
|
static char __pyx_k_27[] = "";
|
|||
|
|
static char __pyx_k_28[] = "%d\t";
|
|||
|
|
static char __pyx_k_29[] = "%f\t";
|
|||
|
|
static char __pyx_k_30[] = "\n";
|
|||
|
|
static char __pyx_k_31[] = "DONE .... GOODBYE !!";
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":27
|
|||
|
|
* import numpy
|
|||
|
|
*
|
|||
|
|
* def printHelp(): # <<<<<<<<<<<<<<
|
|||
|
|
* print Info
|
|||
|
|
* print "Usage: python lmp2radii.pyx test.lammpstrj\n"
|
|||
|
|
*/
|
|||
|
|
|
|||
|
|
static PyObject *__pyx_pf_9lmp2radii_printHelp(PyObject *__pyx_self, PyObject *unused); /*proto*/
|
|||
|
|
static PyObject *__pyx_pf_9lmp2radii_printHelp(PyObject *__pyx_self, PyObject *unused) {
|
|||
|
|
PyObject *__pyx_r;
|
|||
|
|
PyObject *__pyx_1 = 0;
|
|||
|
|
PyObject *__pyx_2 = 0;
|
|||
|
|
__pyx_self = __pyx_self;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":28
|
|||
|
|
*
|
|||
|
|
* def printHelp():
|
|||
|
|
* print Info # <<<<<<<<<<<<<<
|
|||
|
|
* print "Usage: python lmp2radii.pyx test.lammpstrj\n"
|
|||
|
|
* return
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = __Pyx_GetName(__pyx_m, __pyx_kp_Info); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_1);
|
|||
|
|
__pyx_1 = 0;
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_2), 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":29
|
|||
|
|
* def printHelp():
|
|||
|
|
* print Info
|
|||
|
|
* print "Usage: python lmp2radii.pyx test.lammpstrj\n" # <<<<<<<<<<<<<<
|
|||
|
|
* return
|
|||
|
|
*
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_kp_6);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_kp_6);
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_1), 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":30
|
|||
|
|
* print Info
|
|||
|
|
* print "Usage: python lmp2radii.pyx test.lammpstrj\n"
|
|||
|
|
* return # <<<<<<<<<<<<<<
|
|||
|
|
*
|
|||
|
|
* def makeradii(infile):
|
|||
|
|
*/
|
|||
|
|
__pyx_r = Py_None; Py_INCREF(Py_None);
|
|||
|
|
goto __pyx_L0;
|
|||
|
|
|
|||
|
|
__pyx_r = Py_None; Py_INCREF(Py_None);
|
|||
|
|
goto __pyx_L0;
|
|||
|
|
__pyx_L1_error:;
|
|||
|
|
Py_XDECREF(__pyx_1);
|
|||
|
|
Py_XDECREF(__pyx_2);
|
|||
|
|
__Pyx_AddTraceback("lmp2radii.printHelp");
|
|||
|
|
__pyx_r = NULL;
|
|||
|
|
__pyx_L0:;
|
|||
|
|
return __pyx_r;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":32
|
|||
|
|
* return
|
|||
|
|
*
|
|||
|
|
* def makeradii(infile): # <<<<<<<<<<<<<<
|
|||
|
|
*
|
|||
|
|
* print "Reading %s ... [WAIT]"%infile,
|
|||
|
|
*/
|
|||
|
|
|
|||
|
|
static PyObject *__pyx_pf_9lmp2radii_makeradii(PyObject *__pyx_self, PyObject *__pyx_v_infile); /*proto*/
|
|||
|
|
static PyObject *__pyx_pf_9lmp2radii_makeradii(PyObject *__pyx_self, PyObject *__pyx_v_infile) {
|
|||
|
|
PyObject *__pyx_v_fin;
|
|||
|
|
PyObject *__pyx_v_lines;
|
|||
|
|
PyObject *__pyx_v_frame;
|
|||
|
|
PyObject *__pyx_v_radii;
|
|||
|
|
PyObject *__pyx_v_tmp;
|
|||
|
|
PyObject *__pyx_v_frames;
|
|||
|
|
PyObject *__pyx_v_atoms;
|
|||
|
|
PyObject *__pyx_v_arry;
|
|||
|
|
PyObject *__pyx_v_framecnt;
|
|||
|
|
PyObject *__pyx_v_header;
|
|||
|
|
PyObject *__pyx_v_ecount;
|
|||
|
|
PyObject *__pyx_v_i;
|
|||
|
|
PyObject *__pyx_v_line;
|
|||
|
|
PyObject *__pyx_v_lo;
|
|||
|
|
PyObject *__pyx_v_hi;
|
|||
|
|
PyObject *__pyx_v_lparse;
|
|||
|
|
PyObject *__pyx_v_id;
|
|||
|
|
PyObject *__pyx_v_r;
|
|||
|
|
PyObject *__pyx_v_fout;
|
|||
|
|
PyObject *__pyx_v_e;
|
|||
|
|
PyObject *__pyx_v_a;
|
|||
|
|
PyObject *__pyx_v_f;
|
|||
|
|
PyObject *__pyx_r;
|
|||
|
|
PyObject *__pyx_1 = 0;
|
|||
|
|
PyObject *__pyx_2 = 0;
|
|||
|
|
PyObject *__pyx_3 = 0;
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|||
|
|
PyObject *__pyx_4 = 0;
|
|||
|
|
Py_ssize_t __pyx_5 = 0;
|
|||
|
|
int __pyx_6;
|
|||
|
|
PyObject *__pyx_7 = 0;
|
|||
|
|
PyObject *__pyx_8 = 0;
|
|||
|
|
PyObject *__pyx_9 = 0;
|
|||
|
|
Py_ssize_t __pyx_10 = 0;
|
|||
|
|
__pyx_self = __pyx_self;
|
|||
|
|
__pyx_v_fin = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_lines = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_frame = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_radii = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_tmp = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_frames = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_atoms = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_arry = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_framecnt = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_header = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_ecount = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_i = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_line = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_lo = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_hi = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_lparse = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_id = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_r = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_fout = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_e = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_a = Py_None; Py_INCREF(Py_None);
|
|||
|
|
__pyx_v_f = Py_None; Py_INCREF(Py_None);
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":34
|
|||
|
|
* def makeradii(infile):
|
|||
|
|
*
|
|||
|
|
* print "Reading %s ... [WAIT]"%infile, # <<<<<<<<<<<<<<
|
|||
|
|
* fin = open(infile,'r')
|
|||
|
|
* lines = fin.xreadlines()
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyNumber_Remainder(__pyx_kp_7, __pyx_v_infile); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_1);
|
|||
|
|
__pyx_1 = 0;
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_2), 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":35
|
|||
|
|
*
|
|||
|
|
* print "Reading %s ... [WAIT]"%infile,
|
|||
|
|
* fin = open(infile,'r') # <<<<<<<<<<<<<<
|
|||
|
|
* lines = fin.xreadlines()
|
|||
|
|
* print 7*"\b"+"[DONE]"
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyTuple_New(2); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_infile);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_v_infile);
|
|||
|
|
Py_INCREF(__pyx_kp_8);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 1, __pyx_kp_8);
|
|||
|
|
__pyx_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_1), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_fin);
|
|||
|
|
__pyx_v_fin = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":36
|
|||
|
|
* print "Reading %s ... [WAIT]"%infile,
|
|||
|
|
* fin = open(infile,'r')
|
|||
|
|
* lines = fin.xreadlines() # <<<<<<<<<<<<<<
|
|||
|
|
* print 7*"\b"+"[DONE]"
|
|||
|
|
* frame=0
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyObject_GetAttr(__pyx_v_fin, __pyx_kp_xreadlines); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_Call(__pyx_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_lines);
|
|||
|
|
__pyx_v_lines = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":37
|
|||
|
|
* fin = open(infile,'r')
|
|||
|
|
* lines = fin.xreadlines()
|
|||
|
|
* print 7*"\b"+"[DONE]" # <<<<<<<<<<<<<<
|
|||
|
|
* frame=0
|
|||
|
|
* radii=[]
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyNumber_Multiply(__pyx_int_7, __pyx_kp_9); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyNumber_Add(__pyx_1, __pyx_kp_10); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_2);
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_1), 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":38
|
|||
|
|
* lines = fin.xreadlines()
|
|||
|
|
* print 7*"\b"+"[DONE]"
|
|||
|
|
* frame=0 # <<<<<<<<<<<<<<
|
|||
|
|
* radii=[]
|
|||
|
|
* # grep the number of frames and atoms/frame
|
|||
|
|
*/
|
|||
|
|
Py_INCREF(__pyx_int_0);
|
|||
|
|
Py_DECREF(__pyx_v_frame);
|
|||
|
|
__pyx_v_frame = __pyx_int_0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":39
|
|||
|
|
* print 7*"\b"+"[DONE]"
|
|||
|
|
* frame=0
|
|||
|
|
* radii=[] # <<<<<<<<<<<<<<
|
|||
|
|
* # grep the number of frames and atoms/frame
|
|||
|
|
* os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile))
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyList_New(0); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_radii);
|
|||
|
|
__pyx_v_radii = ((PyObject *)__pyx_2);
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":41
|
|||
|
|
* radii=[]
|
|||
|
|
* # grep the number of frames and atoms/frame
|
|||
|
|
* os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile)) # <<<<<<<<<<<<<<
|
|||
|
|
* tmp=open("frames",'r')
|
|||
|
|
* frames=int(tmp.readline().split()[0])
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = __Pyx_GetName(__pyx_m, __pyx_kp_os); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_1, __pyx_kp_system); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(2); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_infile);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_v_infile);
|
|||
|
|
Py_INCREF(__pyx_v_infile);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 1, __pyx_v_infile);
|
|||
|
|
__pyx_3 = PyNumber_Remainder(__pyx_kp_11, ((PyObject *)__pyx_1)); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_3);
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_1), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":42
|
|||
|
|
* # grep the number of frames and atoms/frame
|
|||
|
|
* os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile))
|
|||
|
|
* tmp=open("frames",'r') # <<<<<<<<<<<<<<
|
|||
|
|
* frames=int(tmp.readline().split()[0])
|
|||
|
|
* tmp.close()
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyTuple_New(2); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_kp_12);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_kp_12);
|
|||
|
|
Py_INCREF(__pyx_kp_13);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 1, __pyx_kp_13);
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_2), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_tmp);
|
|||
|
|
__pyx_v_tmp = __pyx_1;
|
|||
|
|
__pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":43
|
|||
|
|
* os.system("grep TIMESTEP %s | wc -l > frames; grep -m 1 -A 1 ATOMS %s > atoms"%(infile,infile))
|
|||
|
|
* tmp=open("frames",'r')
|
|||
|
|
* frames=int(tmp.readline().split()[0]) # <<<<<<<<<<<<<<
|
|||
|
|
* tmp.close()
|
|||
|
|
* tmp=open("atoms",'r')
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyObject_GetAttr(__pyx_v_tmp, __pyx_kp_readline); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_Call(__pyx_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_1 = PyObject_GetAttr(__pyx_2, __pyx_kp_split); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
__pyx_2 = __Pyx_GetItemInt(__pyx_3, 0, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_2);
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_1), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_frames);
|
|||
|
|
__pyx_v_frames = __pyx_3;
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":44
|
|||
|
|
* tmp=open("frames",'r')
|
|||
|
|
* frames=int(tmp.readline().split()[0])
|
|||
|
|
* tmp.close() # <<<<<<<<<<<<<<
|
|||
|
|
* tmp=open("atoms",'r')
|
|||
|
|
* atoms=int(tmp.readlines()[1].split()[0])
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_v_tmp, __pyx_kp_close); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":45
|
|||
|
|
* frames=int(tmp.readline().split()[0])
|
|||
|
|
* tmp.close()
|
|||
|
|
* tmp=open("atoms",'r') # <<<<<<<<<<<<<<
|
|||
|
|
* atoms=int(tmp.readlines()[1].split()[0])
|
|||
|
|
* tmp.close()
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyTuple_New(2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_kp_14);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_kp_14);
|
|||
|
|
Py_INCREF(__pyx_kp_15);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 1, __pyx_kp_15);
|
|||
|
|
__pyx_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_3), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_tmp);
|
|||
|
|
__pyx_v_tmp = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":46
|
|||
|
|
* tmp.close()
|
|||
|
|
* tmp=open("atoms",'r')
|
|||
|
|
* atoms=int(tmp.readlines()[1].split()[0]) # <<<<<<<<<<<<<<
|
|||
|
|
* tmp.close()
|
|||
|
|
* os.system("rm -rf frames atoms")
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyObject_GetAttr(__pyx_v_tmp, __pyx_kp_readlines); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
__pyx_2 = __Pyx_GetItemInt(__pyx_3, 1, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_1 = PyObject_GetAttr(__pyx_2, __pyx_kp_split); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
__pyx_2 = __Pyx_GetItemInt(__pyx_3, 0, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_2);
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_1), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_atoms);
|
|||
|
|
__pyx_v_atoms = __pyx_3;
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":47
|
|||
|
|
* tmp=open("atoms",'r')
|
|||
|
|
* atoms=int(tmp.readlines()[1].split()[0])
|
|||
|
|
* tmp.close() # <<<<<<<<<<<<<<
|
|||
|
|
* os.system("rm -rf frames atoms")
|
|||
|
|
* arry=numpy.zeros((atoms,frames),dtype=float)
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_v_tmp, __pyx_kp_close); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":48
|
|||
|
|
* atoms=int(tmp.readlines()[1].split()[0])
|
|||
|
|
* tmp.close()
|
|||
|
|
* os.system("rm -rf frames atoms") # <<<<<<<<<<<<<<
|
|||
|
|
* arry=numpy.zeros((atoms,frames),dtype=float)
|
|||
|
|
* framecnt=0
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = __Pyx_GetName(__pyx_m, __pyx_kp_os); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_3, __pyx_kp_system); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_1 = PyTuple_New(1); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_kp_16);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_1, 0, __pyx_kp_16);
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_1), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_1)); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":49
|
|||
|
|
* tmp.close()
|
|||
|
|
* os.system("rm -rf frames atoms")
|
|||
|
|
* arry=numpy.zeros((atoms,frames),dtype=float) # <<<<<<<<<<<<<<
|
|||
|
|
* framecnt=0
|
|||
|
|
* header=9
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = __Pyx_GetName(__pyx_m, __pyx_kp_numpy); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_1 = PyObject_GetAttr(__pyx_2, __pyx_kp_zeros); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
__pyx_3 = PyTuple_New(2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_atoms);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_v_atoms);
|
|||
|
|
Py_INCREF(__pyx_v_frames);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 1, __pyx_v_frames);
|
|||
|
|
__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, ((PyObject *)__pyx_3));
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
__pyx_3 = PyDict_New(); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
if (PyDict_SetItem(__pyx_3, __pyx_kp_dtype, ((PyObject*)&PyFloat_Type)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyEval_CallObjectWithKeywords(__pyx_1, ((PyObject *)__pyx_2), ((PyObject *)__pyx_3)); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_arry);
|
|||
|
|
__pyx_v_arry = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":50
|
|||
|
|
* os.system("rm -rf frames atoms")
|
|||
|
|
* arry=numpy.zeros((atoms,frames),dtype=float)
|
|||
|
|
* framecnt=0 # <<<<<<<<<<<<<<
|
|||
|
|
* header=9
|
|||
|
|
* ecount=0
|
|||
|
|
*/
|
|||
|
|
Py_INCREF(__pyx_int_0);
|
|||
|
|
Py_DECREF(__pyx_v_framecnt);
|
|||
|
|
__pyx_v_framecnt = __pyx_int_0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":51
|
|||
|
|
* arry=numpy.zeros((atoms,frames),dtype=float)
|
|||
|
|
* framecnt=0
|
|||
|
|
* header=9 # <<<<<<<<<<<<<<
|
|||
|
|
* ecount=0
|
|||
|
|
* print "Extracting electron radii per frame from %s ... "%(infile),
|
|||
|
|
*/
|
|||
|
|
Py_INCREF(__pyx_int_9);
|
|||
|
|
Py_DECREF(__pyx_v_header);
|
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|
|
__pyx_v_header = __pyx_int_9;
|
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|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":52
|
|||
|
|
* framecnt=0
|
|||
|
|
* header=9
|
|||
|
|
* ecount=0 # <<<<<<<<<<<<<<
|
|||
|
|
* print "Extracting electron radii per frame from %s ... "%(infile),
|
|||
|
|
* for i,line in enumerate(lines):
|
|||
|
|
*/
|
|||
|
|
Py_INCREF(__pyx_int_0);
|
|||
|
|
Py_DECREF(__pyx_v_ecount);
|
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|
|
__pyx_v_ecount = __pyx_int_0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":53
|
|||
|
|
* header=9
|
|||
|
|
* ecount=0
|
|||
|
|
* print "Extracting electron radii per frame from %s ... "%(infile), # <<<<<<<<<<<<<<
|
|||
|
|
* for i,line in enumerate(lines):
|
|||
|
|
* lo=(atoms+header)*framecnt+header
|
|||
|
|
*/
|
|||
|
|
__pyx_1 = PyNumber_Remainder(__pyx_kp_17, __pyx_v_infile); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_1);
|
|||
|
|
__pyx_1 = 0;
|
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|
|
if (__Pyx_Print(((PyObject *)__pyx_2), 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":54
|
|||
|
|
* ecount=0
|
|||
|
|
* print "Extracting electron radii per frame from %s ... "%(infile),
|
|||
|
|
* for i,line in enumerate(lines): # <<<<<<<<<<<<<<
|
|||
|
|
* lo=(atoms+header)*framecnt+header
|
|||
|
|
* hi=lo+atoms
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyTuple_New(1); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_lines);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_v_lines);
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|||
|
|
__pyx_4 = PyObject_Call(__pyx_builtin_enumerate, ((PyObject *)__pyx_3), NULL); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
if (PyList_CheckExact(__pyx_4) || PyTuple_CheckExact(__pyx_4)) {
|
|||
|
|
__pyx_5 = 0; __pyx_1 = __pyx_4; Py_INCREF(__pyx_1);
|
|||
|
|
} else {
|
|||
|
|
__pyx_5 = -1; __pyx_1 = PyObject_GetIter(__pyx_4); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
for (;;) {
|
|||
|
|
if (likely(PyList_CheckExact(__pyx_1))) {
|
|||
|
|
if (__pyx_5 >= PyList_GET_SIZE(__pyx_1)) break;
|
|||
|
|
__pyx_2 = PyList_GET_ITEM(__pyx_1, __pyx_5); Py_INCREF(__pyx_2); __pyx_5++;
|
|||
|
|
} else if (likely(PyTuple_CheckExact(__pyx_1))) {
|
|||
|
|
if (__pyx_5 >= PyTuple_GET_SIZE(__pyx_1)) break;
|
|||
|
|
__pyx_2 = PyTuple_GET_ITEM(__pyx_1, __pyx_5); Py_INCREF(__pyx_2); __pyx_5++;
|
|||
|
|
} else {
|
|||
|
|
__pyx_2 = PyIter_Next(__pyx_1);
|
|||
|
|
if (!__pyx_2) {
|
|||
|
|
if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
break;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
if (PyTuple_CheckExact(__pyx_2) && PyTuple_GET_SIZE(__pyx_2) == 2) {
|
|||
|
|
PyObject* tuple = __pyx_2;
|
|||
|
|
__pyx_4 = PyTuple_GET_ITEM(tuple, 0);
|
|||
|
|
Py_INCREF(__pyx_4);
|
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|
|
Py_DECREF(__pyx_v_i);
|
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|
|
__pyx_v_i = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
__pyx_4 = PyTuple_GET_ITEM(tuple, 1);
|
|||
|
|
Py_INCREF(__pyx_4);
|
|||
|
|
Py_DECREF(__pyx_v_line);
|
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|
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__pyx_v_line = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
}
|
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|
|
else {
|
|||
|
|
__pyx_3 = PyObject_GetIter(__pyx_2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
__pyx_4 = __Pyx_UnpackItem(__pyx_3, 0); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_i);
|
|||
|
|
__pyx_v_i = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
__pyx_4 = __Pyx_UnpackItem(__pyx_3, 1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_line);
|
|||
|
|
__pyx_v_line = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
if (__Pyx_EndUnpack(__pyx_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":55
|
|||
|
|
* print "Extracting electron radii per frame from %s ... "%(infile),
|
|||
|
|
* for i,line in enumerate(lines):
|
|||
|
|
* lo=(atoms+header)*framecnt+header # <<<<<<<<<<<<<<
|
|||
|
|
* hi=lo+atoms
|
|||
|
|
* if (i<lo):
|
|||
|
|
*/
|
|||
|
|
__pyx_4 = PyNumber_Add(__pyx_v_atoms, __pyx_v_header); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyNumber_Multiply(__pyx_4, __pyx_v_framecnt); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
__pyx_3 = PyNumber_Add(__pyx_2, __pyx_v_header); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_lo);
|
|||
|
|
__pyx_v_lo = __pyx_3;
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":56
|
|||
|
|
* for i,line in enumerate(lines):
|
|||
|
|
* lo=(atoms+header)*framecnt+header
|
|||
|
|
* hi=lo+atoms # <<<<<<<<<<<<<<
|
|||
|
|
* if (i<lo):
|
|||
|
|
* continue
|
|||
|
|
*/
|
|||
|
|
__pyx_4 = PyNumber_Add(__pyx_v_lo, __pyx_v_atoms); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_hi);
|
|||
|
|
__pyx_v_hi = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":57
|
|||
|
|
* lo=(atoms+header)*framecnt+header
|
|||
|
|
* hi=lo+atoms
|
|||
|
|
* if (i<lo): # <<<<<<<<<<<<<<
|
|||
|
|
* continue
|
|||
|
|
* elif (i >= lo) and (i < hi):
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyObject_RichCompare(__pyx_v_i, __pyx_v_lo, Py_LT); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_2); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":58
|
|||
|
|
* hi=lo+atoms
|
|||
|
|
* if (i<lo):
|
|||
|
|
* continue # <<<<<<<<<<<<<<
|
|||
|
|
* elif (i >= lo) and (i < hi):
|
|||
|
|
* lparse=line.split()
|
|||
|
|
*/
|
|||
|
|
goto __pyx_L5;
|
|||
|
|
goto __pyx_L7;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":59
|
|||
|
|
* if (i<lo):
|
|||
|
|
* continue
|
|||
|
|
* elif (i >= lo) and (i < hi): # <<<<<<<<<<<<<<
|
|||
|
|
* lparse=line.split()
|
|||
|
|
* id=int(lparse[0])
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyObject_RichCompare(__pyx_v_i, __pyx_v_lo, Py_GE); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_3); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_3 = PyObject_RichCompare(__pyx_v_i, __pyx_v_hi, Py_LT); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
}
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_3); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":60
|
|||
|
|
* continue
|
|||
|
|
* elif (i >= lo) and (i < hi):
|
|||
|
|
* lparse=line.split() # <<<<<<<<<<<<<<
|
|||
|
|
* id=int(lparse[0])
|
|||
|
|
* r=float(lparse[6])
|
|||
|
|
*/
|
|||
|
|
__pyx_4 = PyObject_GetAttr(__pyx_v_line, __pyx_kp_split); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_Call(__pyx_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_lparse);
|
|||
|
|
__pyx_v_lparse = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":61
|
|||
|
|
* elif (i >= lo) and (i < hi):
|
|||
|
|
* lparse=line.split()
|
|||
|
|
* id=int(lparse[0]) # <<<<<<<<<<<<<<
|
|||
|
|
* r=float(lparse[6])
|
|||
|
|
* if (r!=0):
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = __Pyx_GetItemInt(__pyx_v_lparse, 0, 0); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_4, 0, __pyx_3);
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
__pyx_2 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_4), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_4)); __pyx_4 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_id);
|
|||
|
|
__pyx_v_id = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":62
|
|||
|
|
* lparse=line.split()
|
|||
|
|
* id=int(lparse[0])
|
|||
|
|
* r=float(lparse[6]) # <<<<<<<<<<<<<<
|
|||
|
|
* if (r!=0):
|
|||
|
|
* arry[id-1][framecnt]=r
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = __Pyx_GetItemInt(__pyx_v_lparse, 6, 0); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_4, 0, __pyx_3);
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
__pyx_2 = PyObject_Call(((PyObject*)&PyFloat_Type), ((PyObject *)__pyx_4), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_4)); __pyx_4 = 0;
|
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|
|
Py_DECREF(__pyx_v_r);
|
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|
|
__pyx_v_r = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":63
|
|||
|
|
* id=int(lparse[0])
|
|||
|
|
* r=float(lparse[6])
|
|||
|
|
* if (r!=0): # <<<<<<<<<<<<<<
|
|||
|
|
* arry[id-1][framecnt]=r
|
|||
|
|
* if (framecnt==0): ecount+=1
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyObject_RichCompare(__pyx_v_r, __pyx_int_0, Py_NE); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_3); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":64
|
|||
|
|
* r=float(lparse[6])
|
|||
|
|
* if (r!=0):
|
|||
|
|
* arry[id-1][framecnt]=r # <<<<<<<<<<<<<<
|
|||
|
|
* if (framecnt==0): ecount+=1
|
|||
|
|
* if (i==lo+1):
|
|||
|
|
*/
|
|||
|
|
__pyx_4 = PyNumber_Subtract(__pyx_v_id, __pyx_int_1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_GetItem(__pyx_v_arry, __pyx_4); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
if (PyObject_SetItem(__pyx_2, __pyx_v_framecnt, __pyx_v_r) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":65
|
|||
|
|
* if (r!=0):
|
|||
|
|
* arry[id-1][framecnt]=r
|
|||
|
|
* if (framecnt==0): ecount+=1 # <<<<<<<<<<<<<<
|
|||
|
|
* if (i==lo+1):
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b"))
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyObject_RichCompare(__pyx_v_framecnt, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
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__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_3); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
__pyx_4 = PyNumber_InPlaceAdd(__pyx_v_ecount, __pyx_int_1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_ecount);
|
|||
|
|
__pyx_v_ecount = __pyx_4;
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
goto __pyx_L9;
|
|||
|
|
}
|
|||
|
|
__pyx_L9:;
|
|||
|
|
goto __pyx_L8;
|
|||
|
|
}
|
|||
|
|
__pyx_L8:;
|
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|
|
|
|||
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|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":66
|
|||
|
|
* arry[id-1][framecnt]=r
|
|||
|
|
* if (framecnt==0): ecount+=1
|
|||
|
|
* if (i==lo+1): # <<<<<<<<<<<<<<
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b"))
|
|||
|
|
* sys.stdout.flush()
|
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|
*/
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|
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__pyx_2 = PyNumber_Add(__pyx_v_lo, __pyx_int_1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
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__pyx_3 = PyObject_RichCompare(__pyx_v_i, __pyx_2, Py_EQ); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_3); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
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|
|
if (__pyx_6) {
|
|||
|
|
|
|||
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|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":67
|
|||
|
|
* if (framecnt==0): ecount+=1
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|||
|
|
* if (i==lo+1):
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b")) # <<<<<<<<<<<<<<
|
|||
|
|
* sys.stdout.flush()
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* if (i == hi+1):
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*/
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__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_sys); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_4, __pyx_kp_stdout); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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__pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_kp_write); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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__pyx_4 = PyNumber_Add(__pyx_v_framecnt, __pyx_int_1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = __Pyx_GetName(__pyx_m, __pyx_kp_2); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
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__pyx_7 = PyNumber_Add(__pyx_v_framecnt, __pyx_int_1); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
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__pyx_8 = PyTuple_New(1); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_8, 0, __pyx_7);
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__pyx_7 = 0;
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__pyx_7 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_8), NULL); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
Py_DECREF(__pyx_2); __pyx_2 = 0;
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Py_DECREF(((PyObject *)__pyx_8)); __pyx_8 = 0;
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__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_7);
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__pyx_7 = 0;
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__pyx_8 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_2), NULL); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
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__pyx_7 = PyNumber_Add(__pyx_8, __pyx_int_3); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
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|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
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__pyx_2 = __Pyx_GetName(__pyx_m, __pyx_kp_2); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_8 = PyTuple_New(1); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_frames);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_8, 0, __pyx_v_frames);
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|
|
__pyx_9 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_8), NULL); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_8)); __pyx_8 = 0;
|
|||
|
|
__pyx_2 = PyTuple_New(1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_2, 0, __pyx_9);
|
|||
|
|
__pyx_9 = 0;
|
|||
|
|
__pyx_8 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_2), NULL); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
|
|||
|
|
__pyx_9 = PyNumber_Add(__pyx_7, __pyx_8); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
__pyx_2 = PyNumber_Multiply(__pyx_9, __pyx_kp_19); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
__pyx_7 = PyTuple_New(3); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_7, 0, __pyx_4);
|
|||
|
|
Py_INCREF(__pyx_v_frames);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_7, 1, __pyx_v_frames);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_7, 2, __pyx_2);
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
__pyx_8 = PyNumber_Remainder(__pyx_kp_18, ((PyObject *)__pyx_7)); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_7)); __pyx_7 = 0;
|
|||
|
|
__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_9, 0, __pyx_8);
|
|||
|
|
__pyx_8 = 0;
|
|||
|
|
__pyx_4 = PyObject_Call(__pyx_3, ((PyObject *)__pyx_9), NULL); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":68
|
|||
|
|
* if (i==lo+1):
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b"))
|
|||
|
|
* sys.stdout.flush() # <<<<<<<<<<<<<<
|
|||
|
|
* if (i == hi+1):
|
|||
|
|
* framecnt+=1
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = __Pyx_GetName(__pyx_m, __pyx_kp_sys); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_7 = PyObject_GetAttr(__pyx_2, __pyx_kp_stdout); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
__pyx_8 = PyObject_GetAttr(__pyx_7, __pyx_kp_flush); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
goto __pyx_L10;
|
|||
|
|
}
|
|||
|
|
__pyx_L10:;
|
|||
|
|
goto __pyx_L7;
|
|||
|
|
}
|
|||
|
|
__pyx_L7:;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":69
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(framecnt+1,frames,(int(log10(framecnt+1))+3+int(log10(frames)))*"\b"))
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* if (i == hi+1): # <<<<<<<<<<<<<<
|
|||
|
|
* framecnt+=1
|
|||
|
|
* print
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = PyNumber_Add(__pyx_v_hi, __pyx_int_1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyObject_RichCompare(__pyx_v_i, __pyx_9, Py_EQ); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_4); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
if (__pyx_6) {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":70
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* if (i == hi+1):
|
|||
|
|
* framecnt+=1 # <<<<<<<<<<<<<<
|
|||
|
|
* print
|
|||
|
|
* print "Writing radii/frame table to %s ... "%(infile+'.out'),
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = PyNumber_InPlaceAdd(__pyx_v_framecnt, __pyx_int_1); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_v_framecnt);
|
|||
|
|
__pyx_v_framecnt = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
goto __pyx_L11;
|
|||
|
|
}
|
|||
|
|
__pyx_L11:;
|
|||
|
|
__pyx_L5:;
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":71
|
|||
|
|
* if (i == hi+1):
|
|||
|
|
* framecnt+=1
|
|||
|
|
* print # <<<<<<<<<<<<<<
|
|||
|
|
* print "Writing radii/frame table to %s ... "%(infile+'.out'),
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
*/
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_empty_tuple), 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":72
|
|||
|
|
* framecnt+=1
|
|||
|
|
* print
|
|||
|
|
* print "Writing radii/frame table to %s ... "%(infile+'.out'), # <<<<<<<<<<<<<<
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* fout=open(infile+'.out','w')
|
|||
|
|
*/
|
|||
|
|
__pyx_7 = PyNumber_Add(__pyx_v_infile, __pyx_kp_21); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_8 = PyNumber_Remainder(__pyx_kp_20, __pyx_7); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
|
|||
|
|
__pyx_3 = PyTuple_New(1); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_8);
|
|||
|
|
__pyx_8 = 0;
|
|||
|
|
if (__Pyx_Print(((PyObject *)__pyx_3), 0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":73
|
|||
|
|
* print
|
|||
|
|
* print "Writing radii/frame table to %s ... "%(infile+'.out'),
|
|||
|
|
* sys.stdout.flush() # <<<<<<<<<<<<<<
|
|||
|
|
* fout=open(infile+'.out','w')
|
|||
|
|
* for i in range(frames):
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = __Pyx_GetName(__pyx_m, __pyx_kp_sys); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyObject_GetAttr(__pyx_9, __pyx_kp_stdout); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_4, __pyx_kp_flush); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":74
|
|||
|
|
* print "Writing radii/frame table to %s ... "%(infile+'.out'),
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* fout=open(infile+'.out','w') # <<<<<<<<<<<<<<
|
|||
|
|
* for i in range(frames):
|
|||
|
|
* fout.writelines('\tF'+str(i))
|
|||
|
|
*/
|
|||
|
|
__pyx_7 = PyNumber_Add(__pyx_v_infile, __pyx_kp_22); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_8 = PyTuple_New(2); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_8, 0, __pyx_7);
|
|||
|
|
Py_INCREF(__pyx_kp_23);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_8, 1, __pyx_kp_23);
|
|||
|
|
__pyx_7 = 0;
|
|||
|
|
__pyx_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_8), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_8)); __pyx_8 = 0;
|
|||
|
|
Py_DECREF(__pyx_v_fout);
|
|||
|
|
__pyx_v_fout = __pyx_3;
|
|||
|
|
__pyx_3 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":75
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* fout=open(infile+'.out','w')
|
|||
|
|
* for i in range(frames): # <<<<<<<<<<<<<<
|
|||
|
|
* fout.writelines('\tF'+str(i))
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_frames);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_9, 0, __pyx_v_frames);
|
|||
|
|
__pyx_4 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_9), NULL); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
|
|||
|
|
if (PyList_CheckExact(__pyx_4) || PyTuple_CheckExact(__pyx_4)) {
|
|||
|
|
__pyx_5 = 0; __pyx_2 = __pyx_4; Py_INCREF(__pyx_2);
|
|||
|
|
} else {
|
|||
|
|
__pyx_5 = -1; __pyx_2 = PyObject_GetIter(__pyx_4); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
for (;;) {
|
|||
|
|
if (likely(PyList_CheckExact(__pyx_2))) {
|
|||
|
|
if (__pyx_5 >= PyList_GET_SIZE(__pyx_2)) break;
|
|||
|
|
__pyx_1 = PyList_GET_ITEM(__pyx_2, __pyx_5); Py_INCREF(__pyx_1); __pyx_5++;
|
|||
|
|
} else if (likely(PyTuple_CheckExact(__pyx_2))) {
|
|||
|
|
if (__pyx_5 >= PyTuple_GET_SIZE(__pyx_2)) break;
|
|||
|
|
__pyx_1 = PyTuple_GET_ITEM(__pyx_2, __pyx_5); Py_INCREF(__pyx_1); __pyx_5++;
|
|||
|
|
} else {
|
|||
|
|
__pyx_1 = PyIter_Next(__pyx_2);
|
|||
|
|
if (!__pyx_1) {
|
|||
|
|
if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
break;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_v_i);
|
|||
|
|
__pyx_v_i = __pyx_1;
|
|||
|
|
__pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":76
|
|||
|
|
* fout=open(infile+'.out','w')
|
|||
|
|
* for i in range(frames):
|
|||
|
|
* fout.writelines('\tF'+str(i)) # <<<<<<<<<<<<<<
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
* e=1
|
|||
|
|
*/
|
|||
|
|
__pyx_7 = PyObject_GetAttr(__pyx_v_fout, __pyx_kp_writelines); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_8 = PyTuple_New(1); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_i);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_8, 0, __pyx_v_i);
|
|||
|
|
__pyx_3 = PyObject_Call(((PyObject*)&PyBytes_Type), ((PyObject *)__pyx_8), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_8)); __pyx_8 = 0;
|
|||
|
|
__pyx_9 = PyNumber_Add(__pyx_kp_24, __pyx_3); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_4, 0, __pyx_9);
|
|||
|
|
__pyx_9 = 0;
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_7, ((PyObject *)__pyx_4), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_4)); __pyx_4 = 0;
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":77
|
|||
|
|
* for i in range(frames):
|
|||
|
|
* fout.writelines('\tF'+str(i))
|
|||
|
|
* fout.writelines("\n") # <<<<<<<<<<<<<<
|
|||
|
|
* e=1
|
|||
|
|
* for a in range(atoms):
|
|||
|
|
*/
|
|||
|
|
__pyx_8 = PyObject_GetAttr(__pyx_v_fout, __pyx_kp_writelines); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_3 = PyTuple_New(1); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_kp_25);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_kp_25);
|
|||
|
|
__pyx_9 = PyObject_Call(__pyx_8, ((PyObject *)__pyx_3), NULL); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":78
|
|||
|
|
* fout.writelines('\tF'+str(i))
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
* e=1 # <<<<<<<<<<<<<<
|
|||
|
|
* for a in range(atoms):
|
|||
|
|
* if arry[a][0] == 0.0: continue
|
|||
|
|
*/
|
|||
|
|
Py_INCREF(__pyx_int_1);
|
|||
|
|
Py_DECREF(__pyx_v_e);
|
|||
|
|
__pyx_v_e = __pyx_int_1;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":79
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
* e=1
|
|||
|
|
* for a in range(atoms): # <<<<<<<<<<<<<<
|
|||
|
|
* if arry[a][0] == 0.0: continue
|
|||
|
|
* else:
|
|||
|
|
*/
|
|||
|
|
__pyx_7 = PyTuple_New(1); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_atoms);
|
|||
|
|
PyTuple_SET_ITEM(__pyx_7, 0, __pyx_v_atoms);
|
|||
|
|
__pyx_4 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_7), NULL); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_7)); __pyx_7 = 0;
|
|||
|
|
if (PyList_CheckExact(__pyx_4) || PyTuple_CheckExact(__pyx_4)) {
|
|||
|
|
__pyx_5 = 0; __pyx_1 = __pyx_4; Py_INCREF(__pyx_1);
|
|||
|
|
} else {
|
|||
|
|
__pyx_5 = -1; __pyx_1 = PyObject_GetIter(__pyx_4); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
for (;;) {
|
|||
|
|
if (likely(PyList_CheckExact(__pyx_1))) {
|
|||
|
|
if (__pyx_5 >= PyList_GET_SIZE(__pyx_1)) break;
|
|||
|
|
__pyx_2 = PyList_GET_ITEM(__pyx_1, __pyx_5); Py_INCREF(__pyx_2); __pyx_5++;
|
|||
|
|
} else if (likely(PyTuple_CheckExact(__pyx_1))) {
|
|||
|
|
if (__pyx_5 >= PyTuple_GET_SIZE(__pyx_1)) break;
|
|||
|
|
__pyx_2 = PyTuple_GET_ITEM(__pyx_1, __pyx_5); Py_INCREF(__pyx_2); __pyx_5++;
|
|||
|
|
} else {
|
|||
|
|
__pyx_2 = PyIter_Next(__pyx_1);
|
|||
|
|
if (!__pyx_2) {
|
|||
|
|
if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
break;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_v_a);
|
|||
|
|
__pyx_v_a = __pyx_2;
|
|||
|
|
__pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":80
|
|||
|
|
* e=1
|
|||
|
|
* for a in range(atoms):
|
|||
|
|
* if arry[a][0] == 0.0: continue # <<<<<<<<<<<<<<
|
|||
|
|
* else:
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b"))
|
|||
|
|
*/
|
|||
|
|
__pyx_8 = PyObject_GetItem(__pyx_v_arry, __pyx_v_a); if (!__pyx_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_3 = __Pyx_GetItemInt(__pyx_8, 0, 0); if (!__pyx_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
__pyx_9 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_7 = PyObject_RichCompare(__pyx_3, __pyx_9, Py_EQ); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
__pyx_6 = __Pyx_PyObject_IsTrue(__pyx_7); if (unlikely(__pyx_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
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|
if (__pyx_6) {
|
|||
|
|
goto __pyx_L14;
|
|||
|
|
goto __pyx_L16;
|
|||
|
|
}
|
|||
|
|
/*else*/ {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":82
|
|||
|
|
* if arry[a][0] == 0.0: continue
|
|||
|
|
* else:
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b")) # <<<<<<<<<<<<<<
|
|||
|
|
* sys.stdout.flush()
|
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|
|
* e+=1
|
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|
|
*/
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__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_sys); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
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__pyx_2 = PyObject_GetAttr(__pyx_4, __pyx_kp_stdout); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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__pyx_8 = PyObject_GetAttr(__pyx_2, __pyx_kp_write); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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__pyx_3 = __Pyx_GetName(__pyx_m, __pyx_kp_2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
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__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
Py_INCREF(__pyx_v_e);
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PyTuple_SET_ITEM(__pyx_9, 0, __pyx_v_e);
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|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
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Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
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__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_4, 0, __pyx_7);
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__pyx_7 = 0;
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__pyx_2 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_4), NULL); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(((PyObject *)__pyx_4)); __pyx_4 = 0;
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__pyx_3 = __Pyx_GetName(__pyx_m, __pyx_kp_2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_INCREF(__pyx_v_ecount);
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PyTuple_SET_ITEM(__pyx_9, 0, __pyx_v_ecount);
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__pyx_7 = PyObject_Call(__pyx_3, ((PyObject *)__pyx_9), NULL); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
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|
Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
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__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
PyTuple_SET_ITEM(__pyx_4, 0, __pyx_7);
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__pyx_7 = 0;
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__pyx_3 = PyObject_Call(((PyObject*)&PyInt_Type), ((PyObject *)__pyx_4), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(((PyObject *)__pyx_4)); __pyx_4 = 0;
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__pyx_9 = PyNumber_Add(__pyx_2, __pyx_3); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
Py_DECREF(__pyx_2); __pyx_2 = 0;
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Py_DECREF(__pyx_3); __pyx_3 = 0;
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__pyx_7 = PyNumber_Add(__pyx_9, __pyx_int_3); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
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__pyx_4 = PyNumber_Multiply(__pyx_7, __pyx_kp_27); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
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__pyx_2 = PyTuple_New(3); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_INCREF(__pyx_v_e);
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PyTuple_SET_ITEM(__pyx_2, 0, __pyx_v_e);
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|
Py_INCREF(__pyx_v_ecount);
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PyTuple_SET_ITEM(__pyx_2, 1, __pyx_v_ecount);
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PyTuple_SET_ITEM(__pyx_2, 2, __pyx_4);
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__pyx_4 = 0;
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__pyx_3 = PyNumber_Remainder(__pyx_kp_26, ((PyObject *)__pyx_2)); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
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Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
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__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
PyTuple_SET_ITEM(__pyx_9, 0, __pyx_3);
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__pyx_3 = 0;
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__pyx_7 = PyObject_Call(__pyx_8, ((PyObject *)__pyx_9), NULL); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
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Py_DECREF(__pyx_8); __pyx_8 = 0;
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Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
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Py_DECREF(__pyx_7); __pyx_7 = 0;
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|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":83
|
|||
|
|
* else:
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b"))
|
|||
|
|
* sys.stdout.flush() # <<<<<<<<<<<<<<
|
|||
|
|
* e+=1
|
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* fout.writelines("%d\t"%(a+1))
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|
|
*/
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|
|
__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_sys); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_GetAttr(__pyx_4, __pyx_kp_stdout); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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__pyx_3 = PyObject_GetAttr(__pyx_2, __pyx_kp_flush); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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__pyx_8 = PyObject_Call(__pyx_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
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|
Py_DECREF(__pyx_8); __pyx_8 = 0;
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|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":84
|
|||
|
|
* sys.stdout.write("%d/%d%s"%(e,ecount,(int(log10(e))+int(log10(ecount))+3)*"\b"))
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* e+=1 # <<<<<<<<<<<<<<
|
|||
|
|
* fout.writelines("%d\t"%(a+1))
|
|||
|
|
* for f in range(frames):
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = PyNumber_InPlaceAdd(__pyx_v_e, __pyx_int_1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
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Py_DECREF(__pyx_v_e);
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|
|
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|
__pyx_9 = 0;
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|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":85
|
|||
|
|
* sys.stdout.flush()
|
|||
|
|
* e+=1
|
|||
|
|
* fout.writelines("%d\t"%(a+1)) # <<<<<<<<<<<<<<
|
|||
|
|
* for f in range(frames):
|
|||
|
|
* fout.writelines("%f\t"%(arry[a][f]))
|
|||
|
|
*/
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|||
|
|
__pyx_7 = PyObject_GetAttr(__pyx_v_fout, __pyx_kp_writelines); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
__pyx_4 = PyNumber_Add(__pyx_v_a, __pyx_int_1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyNumber_Remainder(__pyx_kp_28, __pyx_4); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
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__pyx_3 = PyTuple_New(1); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
PyTuple_SET_ITEM(__pyx_3, 0, __pyx_2);
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|||
|
|
__pyx_2 = 0;
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|||
|
|
__pyx_8 = PyObject_Call(__pyx_7, ((PyObject *)__pyx_3), NULL); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_7); __pyx_7 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_3)); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
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|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":86
|
|||
|
|
* e+=1
|
|||
|
|
* fout.writelines("%d\t"%(a+1))
|
|||
|
|
* for f in range(frames): # <<<<<<<<<<<<<<
|
|||
|
|
* fout.writelines("%f\t"%(arry[a][f]))
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = PyTuple_New(1); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_INCREF(__pyx_v_frames);
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|||
|
|
PyTuple_SET_ITEM(__pyx_9, 0, __pyx_v_frames);
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|||
|
|
__pyx_4 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_9), NULL); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_9)); __pyx_9 = 0;
|
|||
|
|
if (PyList_CheckExact(__pyx_4) || PyTuple_CheckExact(__pyx_4)) {
|
|||
|
|
__pyx_10 = 0; __pyx_2 = __pyx_4; Py_INCREF(__pyx_2);
|
|||
|
|
} else {
|
|||
|
|
__pyx_10 = -1; __pyx_2 = PyObject_GetIter(__pyx_4); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
for (;;) {
|
|||
|
|
if (likely(PyList_CheckExact(__pyx_2))) {
|
|||
|
|
if (__pyx_10 >= PyList_GET_SIZE(__pyx_2)) break;
|
|||
|
|
__pyx_7 = PyList_GET_ITEM(__pyx_2, __pyx_10); Py_INCREF(__pyx_7); __pyx_10++;
|
|||
|
|
} else if (likely(PyTuple_CheckExact(__pyx_2))) {
|
|||
|
|
if (__pyx_10 >= PyTuple_GET_SIZE(__pyx_2)) break;
|
|||
|
|
__pyx_7 = PyTuple_GET_ITEM(__pyx_2, __pyx_10); Py_INCREF(__pyx_7); __pyx_10++;
|
|||
|
|
} else {
|
|||
|
|
__pyx_7 = PyIter_Next(__pyx_2);
|
|||
|
|
if (!__pyx_7) {
|
|||
|
|
if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
break;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_v_f);
|
|||
|
|
__pyx_v_f = __pyx_7;
|
|||
|
|
__pyx_7 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":87
|
|||
|
|
* fout.writelines("%d\t"%(a+1))
|
|||
|
|
* for f in range(frames):
|
|||
|
|
* fout.writelines("%f\t"%(arry[a][f])) # <<<<<<<<<<<<<<
|
|||
|
|
* fout.writelines("\n")
|
|||
|
|
* print
|
|||
|
|
*/
|
|||
|
|
__pyx_3 = PyObject_GetAttr(__pyx_v_fout, __pyx_kp_writelines); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_8 = PyObject_GetItem(__pyx_v_arry, __pyx_v_a); if (!__pyx_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_9 = PyObject_GetItem(__pyx_8, __pyx_v_f); if (!__pyx_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
__pyx_4 = PyNumber_Remainder(__pyx_kp_29, __pyx_9); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_9); __pyx_9 = 0;
|
|||
|
|
__pyx_7 = PyTuple_New(1); if (unlikely(!__pyx_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_7, 0, __pyx_4);
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
__pyx_8 = PyObject_Call(__pyx_3, ((PyObject *)__pyx_7), NULL); if (unlikely(!__pyx_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_3); __pyx_3 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_7)); __pyx_7 = 0;
|
|||
|
|
Py_DECREF(__pyx_8); __pyx_8 = 0;
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":88
|
|||
|
|
* for f in range(frames):
|
|||
|
|
* fout.writelines("%f\t"%(arry[a][f]))
|
|||
|
|
* fout.writelines("\n") # <<<<<<<<<<<<<<
|
|||
|
|
* print
|
|||
|
|
* print "DONE .... GOODBYE !!"
|
|||
|
|
*/
|
|||
|
|
__pyx_9 = PyObject_GetAttr(__pyx_v_fout, __pyx_kp_writelines); if (unlikely(!__pyx_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = PyTuple_New(1); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
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|||
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|
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|
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__pyx_builtin___name__ = __Pyx_GetName(__pyx_b, __pyx_kp___name__); if (!__pyx_builtin___name__) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_kp_open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_kp_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_kp_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
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|
|
return 0;
|
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|
|
__pyx_L1_error:;
|
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|
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|
|||
|
|
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|
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|
|
|
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|
|
static int __Pyx_InitGlobals(void) {
|
|||
|
|
__pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
|
|||
|
|
__pyx_int_7 = PyInt_FromLong(7); if (unlikely(!__pyx_int_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
|
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|
|
__pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
|
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|
|
__pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
|
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|
|
__pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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|
|
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
|
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|
|
return 0;
|
|||
|
|
__pyx_L1_error:;
|
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|
|
return -1;
|
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|
|
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|
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|
|
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
PyMODINIT_FUNC initlmp2radii(void); /*proto*/
|
|||
|
|
PyMODINIT_FUNC initlmp2radii(void)
|
|||
|
|
#else
|
|||
|
|
PyMODINIT_FUNC PyInit_lmp2radii(void); /*proto*/
|
|||
|
|
PyMODINIT_FUNC PyInit_lmp2radii(void)
|
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if (PyObject_SetAttr(__pyx_m, __pyx_kp_opts, __pyx_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyObject_SetAttr(__pyx_m, __pyx_kp_argv, __pyx_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":102
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":103
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Py_DECREF(__pyx_1); __pyx_1 = 0;
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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|
Py_INCREF(__pyx_int_1);
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PyTuple_SET_ITEM(__pyx_2, 0, __pyx_int_1);
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Py_DECREF(__pyx_1); __pyx_1 = 0;
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Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
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Py_DECREF(__pyx_4); __pyx_4 = 0;
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goto __pyx_L3;
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/*else*/ {
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|||
|
|
|
|||
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|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":106
|
|||
|
|
* sys.exit(1)
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|||
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|
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|
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*/
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__pyx_1 = __Pyx_GetName(__pyx_m, __pyx_kp_argv); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
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__pyx_2 = __Pyx_GetItemInt(__pyx_1, 0, 0); if (!__pyx_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|
Py_DECREF(__pyx_1); __pyx_1 = 0;
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if (PyObject_SetAttr(__pyx_m, __pyx_kp_infile, __pyx_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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Py_DECREF(__pyx_2); __pyx_2 = 0;
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/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":109
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|||
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|
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|
|||
|
|
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|
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*/
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__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_opts); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (likely(PyTuple_CheckExact(__pyx_1))) {
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if (__pyx_5 >= PyTuple_GET_SIZE(__pyx_1)) break;
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|
__pyx_2 = PyTuple_GET_ITEM(__pyx_1, __pyx_5); Py_INCREF(__pyx_2); __pyx_5++;
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|||
|
|
} else {
|
|||
|
|
__pyx_2 = PyIter_Next(__pyx_1);
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|||
|
|
if (!__pyx_2) {
|
|||
|
|
if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
break;
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|||
|
|
}
|
|||
|
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|||
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|
if (PyTuple_CheckExact(__pyx_2) && PyTuple_GET_SIZE(__pyx_2) == 2) {
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|||
|
|
PyObject* tuple = __pyx_2;
|
|||
|
|
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|||
|
|
Py_INCREF(__pyx_6);
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|||
|
|
if (PyObject_SetAttr(__pyx_m, __pyx_kp_opt, __pyx_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_6); __pyx_6 = 0;
|
|||
|
|
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|||
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Py_INCREF(__pyx_6);
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|
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if (PyObject_SetAttr(__pyx_m, __pyx_kp_arg, __pyx_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_6); __pyx_6 = 0;
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
}
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|||
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else {
|
|||
|
|
__pyx_4 = PyObject_GetIter(__pyx_2); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
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|||
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|
|||
|
|
if (PyObject_SetAttr(__pyx_m, __pyx_kp_opt, __pyx_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
Py_DECREF(__pyx_6); __pyx_6 = 0;
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|||
|
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__pyx_6 = __Pyx_UnpackItem(__pyx_4, 1); if (unlikely(!__pyx_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
if (PyObject_SetAttr(__pyx_m, __pyx_kp_arg, __pyx_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
Py_DECREF(__pyx_6); __pyx_6 = 0;
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|||
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if (__Pyx_EndUnpack(__pyx_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
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|||
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|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":110
|
|||
|
|
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|
|||
|
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* for opt, arg in opts:
|
|||
|
|
* if opt == '-h': # -h: print help # <<<<<<<<<<<<<<
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|||
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|
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|||
|
|
*
|
|||
|
|
*/
|
|||
|
|
__pyx_6 = __Pyx_GetName(__pyx_m, __pyx_kp_opt); if (unlikely(!__pyx_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_2 = PyObject_RichCompare(__pyx_6, __pyx_kp_5, Py_EQ); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
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Py_DECREF(__pyx_6); __pyx_6 = 0;
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__pyx_3 = __Pyx_PyObject_IsTrue(__pyx_2); if (unlikely(__pyx_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
if (__pyx_3) {
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":111
|
|||
|
|
* for opt, arg in opts:
|
|||
|
|
* if opt == '-h': # -h: print help
|
|||
|
|
* printHelp() # <<<<<<<<<<<<<<
|
|||
|
|
*
|
|||
|
|
* makeradii(infile)
|
|||
|
|
*/
|
|||
|
|
__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_printHelp); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_6 = PyObject_Call(__pyx_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_4); __pyx_4 = 0;
|
|||
|
|
Py_DECREF(__pyx_6); __pyx_6 = 0;
|
|||
|
|
goto __pyx_L6;
|
|||
|
|
}
|
|||
|
|
__pyx_L6:;
|
|||
|
|
}
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
|
|||
|
|
/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":113
|
|||
|
|
* printHelp()
|
|||
|
|
*
|
|||
|
|
* makeradii(infile) # <<<<<<<<<<<<<<
|
|||
|
|
*/
|
|||
|
|
__pyx_2 = __Pyx_GetName(__pyx_m, __pyx_kp_makeradii); if (unlikely(!__pyx_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_4 = __Pyx_GetName(__pyx_m, __pyx_kp_infile); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
__pyx_6 = PyTuple_New(1); if (unlikely(!__pyx_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
PyTuple_SET_ITEM(__pyx_6, 0, __pyx_4);
|
|||
|
|
__pyx_4 = 0;
|
|||
|
|
__pyx_1 = PyObject_Call(__pyx_2, ((PyObject *)__pyx_6), NULL); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
|
|||
|
|
Py_DECREF(__pyx_2); __pyx_2 = 0;
|
|||
|
|
Py_DECREF(((PyObject *)__pyx_6)); __pyx_6 = 0;
|
|||
|
|
Py_DECREF(__pyx_1); __pyx_1 = 0;
|
|||
|
|
goto __pyx_L2;
|
|||
|
|
}
|
|||
|
|
__pyx_L2:;
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
return;
|
|||
|
|
#else
|
|||
|
|
return __pyx_m;
|
|||
|
|
#endif
|
|||
|
|
__pyx_L1_error:;
|
|||
|
|
Py_XDECREF(__pyx_1);
|
|||
|
|
Py_XDECREF(__pyx_2);
|
|||
|
|
Py_XDECREF(__pyx_4);
|
|||
|
|
Py_XDECREF(__pyx_6);
|
|||
|
|
__Pyx_AddTraceback("lmp2radii");
|
|||
|
|
#if PY_MAJOR_VERSION >= 3
|
|||
|
|
return NULL;
|
|||
|
|
#endif
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static const char *__pyx_filenames[] = {
|
|||
|
|
"lmp2radii.pyx",
|
|||
|
|
};
|
|||
|
|
|
|||
|
|
/* Runtime support code */
|
|||
|
|
|
|||
|
|
static void __pyx_init_filenames(void) {
|
|||
|
|
__pyx_f = __pyx_filenames;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
|
|||
|
|
PyObject *__import__ = 0;
|
|||
|
|
PyObject *empty_list = 0;
|
|||
|
|
PyObject *module = 0;
|
|||
|
|
PyObject *global_dict = 0;
|
|||
|
|
PyObject *empty_dict = 0;
|
|||
|
|
PyObject *list;
|
|||
|
|
__import__ = PyObject_GetAttrString(__pyx_b, "__import__");
|
|||
|
|
if (!__import__)
|
|||
|
|
goto bad;
|
|||
|
|
if (from_list)
|
|||
|
|
list = from_list;
|
|||
|
|
else {
|
|||
|
|
empty_list = PyList_New(0);
|
|||
|
|
if (!empty_list)
|
|||
|
|
goto bad;
|
|||
|
|
list = empty_list;
|
|||
|
|
}
|
|||
|
|
global_dict = PyModule_GetDict(__pyx_m);
|
|||
|
|
if (!global_dict)
|
|||
|
|
goto bad;
|
|||
|
|
empty_dict = PyDict_New();
|
|||
|
|
if (!empty_dict)
|
|||
|
|
goto bad;
|
|||
|
|
module = PyObject_CallFunction(__import__, "OOOO",
|
|||
|
|
name, global_dict, empty_dict, list);
|
|||
|
|
bad:
|
|||
|
|
Py_XDECREF(empty_list);
|
|||
|
|
Py_XDECREF(__import__);
|
|||
|
|
Py_XDECREF(empty_dict);
|
|||
|
|
return module;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
|
|||
|
|
PyObject *result;
|
|||
|
|
result = PyObject_GetAttr(dict, name);
|
|||
|
|
if (!result)
|
|||
|
|
PyErr_SetObject(PyExc_NameError, name);
|
|||
|
|
return result;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
|
|||
|
|
PyObject *item;
|
|||
|
|
if (!(item = PyIter_Next(iter))) {
|
|||
|
|
if (!PyErr_Occurred()) {
|
|||
|
|
PyErr_Format(PyExc_ValueError,
|
|||
|
|
#if PY_VERSION_HEX < 0x02050000
|
|||
|
|
"need more than %d values to unpack", (int)index);
|
|||
|
|
#else
|
|||
|
|
"need more than %zd values to unpack", index);
|
|||
|
|
#endif
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
return item;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static int __Pyx_EndUnpack(PyObject *iter) {
|
|||
|
|
PyObject *item;
|
|||
|
|
if ((item = PyIter_Next(iter))) {
|
|||
|
|
Py_DECREF(item);
|
|||
|
|
PyErr_SetString(PyExc_ValueError, "too many values to unpack");
|
|||
|
|
return -1;
|
|||
|
|
}
|
|||
|
|
else if (!PyErr_Occurred())
|
|||
|
|
return 0;
|
|||
|
|
else
|
|||
|
|
return -1;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
static PyObject *__Pyx_GetStdout(void) {
|
|||
|
|
PyObject *f = PySys_GetObject("stdout");
|
|||
|
|
if (!f) {
|
|||
|
|
PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
|
|||
|
|
}
|
|||
|
|
return f;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static int __Pyx_Print(PyObject *arg_tuple, int newline) {
|
|||
|
|
PyObject *f;
|
|||
|
|
PyObject* v;
|
|||
|
|
int i;
|
|||
|
|
|
|||
|
|
if (!(f = __Pyx_GetStdout()))
|
|||
|
|
return -1;
|
|||
|
|
for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
|
|||
|
|
if (PyFile_SoftSpace(f, 1)) {
|
|||
|
|
if (PyFile_WriteString(" ", f) < 0)
|
|||
|
|
return -1;
|
|||
|
|
}
|
|||
|
|
v = PyTuple_GET_ITEM(arg_tuple, i);
|
|||
|
|
if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
|
|||
|
|
return -1;
|
|||
|
|
if (PyString_Check(v)) {
|
|||
|
|
char *s = PyString_AsString(v);
|
|||
|
|
Py_ssize_t len = PyString_Size(v);
|
|||
|
|
if (len > 0 &&
|
|||
|
|
isspace(Py_CHARMASK(s[len-1])) &&
|
|||
|
|
s[len-1] != ' ')
|
|||
|
|
PyFile_SoftSpace(f, 0);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
if (newline) {
|
|||
|
|
if (PyFile_WriteString("\n", f) < 0)
|
|||
|
|
return -1;
|
|||
|
|
PyFile_SoftSpace(f, 0);
|
|||
|
|
}
|
|||
|
|
return 0;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
#else /* Python 3 has a print function */
|
|||
|
|
static int __Pyx_Print(PyObject *arg_tuple, int newline) {
|
|||
|
|
PyObject* kwargs = 0;
|
|||
|
|
PyObject* result = 0;
|
|||
|
|
PyObject* end_string;
|
|||
|
|
if (!__pyx_print) {
|
|||
|
|
__pyx_print = PyObject_GetAttrString(__pyx_b, "print");
|
|||
|
|
if (!__pyx_print)
|
|||
|
|
return -1;
|
|||
|
|
}
|
|||
|
|
if (!newline) {
|
|||
|
|
if (!__pyx_print_kwargs) {
|
|||
|
|
__pyx_print_kwargs = PyDict_New();
|
|||
|
|
if (!__pyx_print_kwargs)
|
|||
|
|
return -1;
|
|||
|
|
end_string = PyUnicode_FromStringAndSize(" ", 1);
|
|||
|
|
if (!end_string)
|
|||
|
|
return -1;
|
|||
|
|
if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
|
|||
|
|
Py_DECREF(end_string);
|
|||
|
|
return -1;
|
|||
|
|
}
|
|||
|
|
Py_DECREF(end_string);
|
|||
|
|
}
|
|||
|
|
kwargs = __pyx_print_kwargs;
|
|||
|
|
}
|
|||
|
|
result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
|
|||
|
|
if (!result)
|
|||
|
|
return -1;
|
|||
|
|
Py_DECREF(result);
|
|||
|
|
return 0;
|
|||
|
|
}
|
|||
|
|
#endif
|
|||
|
|
|
|||
|
|
#include "compile.h"
|
|||
|
|
#include "frameobject.h"
|
|||
|
|
#include "traceback.h"
|
|||
|
|
|
|||
|
|
static void __Pyx_AddTraceback(const char *funcname) {
|
|||
|
|
PyObject *py_srcfile = 0;
|
|||
|
|
PyObject *py_funcname = 0;
|
|||
|
|
PyObject *py_globals = 0;
|
|||
|
|
PyObject *empty_string = 0;
|
|||
|
|
PyCodeObject *py_code = 0;
|
|||
|
|
PyFrameObject *py_frame = 0;
|
|||
|
|
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
py_srcfile = PyString_FromString(__pyx_filename);
|
|||
|
|
#else
|
|||
|
|
py_srcfile = PyUnicode_FromString(__pyx_filename);
|
|||
|
|
#endif
|
|||
|
|
if (!py_srcfile) goto bad;
|
|||
|
|
if (__pyx_clineno) {
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
|
|||
|
|
#else
|
|||
|
|
py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
|
|||
|
|
#endif
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
py_funcname = PyString_FromString(funcname);
|
|||
|
|
#else
|
|||
|
|
py_funcname = PyUnicode_FromString(funcname);
|
|||
|
|
#endif
|
|||
|
|
}
|
|||
|
|
if (!py_funcname) goto bad;
|
|||
|
|
py_globals = PyModule_GetDict(__pyx_m);
|
|||
|
|
if (!py_globals) goto bad;
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
empty_string = PyString_FromStringAndSize("", 0);
|
|||
|
|
#else
|
|||
|
|
empty_string = PyBytes_FromStringAndSize("", 0);
|
|||
|
|
#endif
|
|||
|
|
if (!empty_string) goto bad;
|
|||
|
|
py_code = PyCode_New(
|
|||
|
|
0, /*int argcount,*/
|
|||
|
|
#if PY_MAJOR_VERSION >= 3
|
|||
|
|
0, /*int kwonlyargcount,*/
|
|||
|
|
#endif
|
|||
|
|
0, /*int nlocals,*/
|
|||
|
|
0, /*int stacksize,*/
|
|||
|
|
0, /*int flags,*/
|
|||
|
|
empty_string, /*PyObject *code,*/
|
|||
|
|
__pyx_empty_tuple, /*PyObject *consts,*/
|
|||
|
|
__pyx_empty_tuple, /*PyObject *names,*/
|
|||
|
|
__pyx_empty_tuple, /*PyObject *varnames,*/
|
|||
|
|
__pyx_empty_tuple, /*PyObject *freevars,*/
|
|||
|
|
__pyx_empty_tuple, /*PyObject *cellvars,*/
|
|||
|
|
py_srcfile, /*PyObject *filename,*/
|
|||
|
|
py_funcname, /*PyObject *name,*/
|
|||
|
|
__pyx_lineno, /*int firstlineno,*/
|
|||
|
|
empty_string /*PyObject *lnotab*/
|
|||
|
|
);
|
|||
|
|
if (!py_code) goto bad;
|
|||
|
|
py_frame = PyFrame_New(
|
|||
|
|
PyThreadState_Get(), /*PyThreadState *tstate,*/
|
|||
|
|
py_code, /*PyCodeObject *code,*/
|
|||
|
|
py_globals, /*PyObject *globals,*/
|
|||
|
|
0 /*PyObject *locals*/
|
|||
|
|
);
|
|||
|
|
if (!py_frame) goto bad;
|
|||
|
|
py_frame->f_lineno = __pyx_lineno;
|
|||
|
|
PyTraceBack_Here(py_frame);
|
|||
|
|
bad:
|
|||
|
|
Py_XDECREF(py_srcfile);
|
|||
|
|
Py_XDECREF(py_funcname);
|
|||
|
|
Py_XDECREF(empty_string);
|
|||
|
|
Py_XDECREF(py_code);
|
|||
|
|
Py_XDECREF(py_frame);
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
|
|||
|
|
while (t->p) {
|
|||
|
|
#if PY_MAJOR_VERSION < 3
|
|||
|
|
if (t->is_unicode && (!t->is_identifier)) {
|
|||
|
|
*t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
|
|||
|
|
} else if (t->intern) {
|
|||
|
|
*t->p = PyString_InternFromString(t->s);
|
|||
|
|
} else {
|
|||
|
|
*t->p = PyString_FromStringAndSize(t->s, t->n - 1);
|
|||
|
|
}
|
|||
|
|
#else /* Python 3+ has unicode identifiers */
|
|||
|
|
if (t->is_identifier || (t->is_unicode && t->intern)) {
|
|||
|
|
*t->p = PyUnicode_InternFromString(t->s);
|
|||
|
|
} else if (t->is_unicode) {
|
|||
|
|
*t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
|
|||
|
|
} else {
|
|||
|
|
*t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
|
|||
|
|
}
|
|||
|
|
#endif
|
|||
|
|
if (!*t->p)
|
|||
|
|
return -1;
|
|||
|
|
++t;
|
|||
|
|
}
|
|||
|
|
return 0;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
/* Type Conversion Functions */
|
|||
|
|
|
|||
|
|
static INLINE Py_ssize_t __pyx_PyIndex_AsSsize_t(PyObject* b) {
|
|||
|
|
Py_ssize_t ival;
|
|||
|
|
PyObject* x = PyNumber_Index(b);
|
|||
|
|
if (!x) return -1;
|
|||
|
|
ival = PyInt_AsSsize_t(x);
|
|||
|
|
Py_DECREF(x);
|
|||
|
|
return ival;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
|
|||
|
|
if (x == Py_True) return 1;
|
|||
|
|
else if (x == Py_False) return 0;
|
|||
|
|
else return PyObject_IsTrue(x);
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x) {
|
|||
|
|
if (PyInt_CheckExact(x)) {
|
|||
|
|
return PyInt_AS_LONG(x);
|
|||
|
|
}
|
|||
|
|
else if (PyLong_CheckExact(x)) {
|
|||
|
|
return PyLong_AsLongLong(x);
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
PY_LONG_LONG val;
|
|||
|
|
PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1;
|
|||
|
|
val = __pyx_PyInt_AsLongLong(tmp);
|
|||
|
|
Py_DECREF(tmp);
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
|
|||
|
|
if (PyInt_CheckExact(x)) {
|
|||
|
|
long val = PyInt_AS_LONG(x);
|
|||
|
|
if (unlikely(val < 0)) {
|
|||
|
|
PyErr_SetString(PyExc_TypeError, "Negative assignment to unsigned type.");
|
|||
|
|
return (unsigned PY_LONG_LONG)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else if (PyLong_CheckExact(x)) {
|
|||
|
|
return PyLong_AsUnsignedLongLong(x);
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
PY_LONG_LONG val;
|
|||
|
|
PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1;
|
|||
|
|
val = __pyx_PyInt_AsUnsignedLongLong(tmp);
|
|||
|
|
Py_DECREF(tmp);
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
|
|||
|
|
static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x) {
|
|||
|
|
if (sizeof(unsigned char) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
unsigned char val = (unsigned char)long_val;
|
|||
|
|
if (unlikely((val != long_val) || (long_val < 0))) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned char");
|
|||
|
|
return (unsigned char)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x) {
|
|||
|
|
if (sizeof(unsigned short) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
unsigned short val = (unsigned short)long_val;
|
|||
|
|
if (unlikely((val != long_val) || (long_val < 0))) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned short");
|
|||
|
|
return (unsigned short)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE char __pyx_PyInt_char(PyObject* x) {
|
|||
|
|
if (sizeof(char) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
char val = (char)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to char");
|
|||
|
|
return (char)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE short __pyx_PyInt_short(PyObject* x) {
|
|||
|
|
if (sizeof(short) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
short val = (short)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to short");
|
|||
|
|
return (short)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE int __pyx_PyInt_int(PyObject* x) {
|
|||
|
|
if (sizeof(int) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
int val = (int)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to int");
|
|||
|
|
return (int)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE long __pyx_PyInt_long(PyObject* x) {
|
|||
|
|
if (sizeof(long) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
long val = (long)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to long");
|
|||
|
|
return (long)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE signed char __pyx_PyInt_signed_char(PyObject* x) {
|
|||
|
|
if (sizeof(signed char) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
signed char val = (signed char)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed char");
|
|||
|
|
return (signed char)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE signed short __pyx_PyInt_signed_short(PyObject* x) {
|
|||
|
|
if (sizeof(signed short) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
signed short val = (signed short)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed short");
|
|||
|
|
return (signed short)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE signed int __pyx_PyInt_signed_int(PyObject* x) {
|
|||
|
|
if (sizeof(signed int) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
signed int val = (signed int)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed int");
|
|||
|
|
return (signed int)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE signed long __pyx_PyInt_signed_long(PyObject* x) {
|
|||
|
|
if (sizeof(signed long) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
signed long val = (signed long)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed long");
|
|||
|
|
return (signed long)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
static INLINE long double __pyx_PyInt_long_double(PyObject* x) {
|
|||
|
|
if (sizeof(long double) < sizeof(long)) {
|
|||
|
|
long long_val = __pyx_PyInt_AsLong(x);
|
|||
|
|
long double val = (long double)long_val;
|
|||
|
|
if (unlikely((val != long_val) )) {
|
|||
|
|
PyErr_SetString(PyExc_OverflowError, "value too large to convert to long double");
|
|||
|
|
return (long double)-1;
|
|||
|
|
}
|
|||
|
|
return val;
|
|||
|
|
}
|
|||
|
|
else {
|
|||
|
|
return __pyx_PyInt_AsLong(x);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|