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PyInt_FromLong(i) : PyLong_FromUnsignedLongLong((sizeof(unsigned long long) > sizeof(Py_ssize_t) ? (1ULL << (sizeof(Py_ssize_t)*8)) : 0) + i); if (!j) return 0; r = PyObject_GetItem(o, j); Py_DECREF(j); } return r; } static int __Pyx_Print(PyObject *, int); /*proto*/ #if PY_MAJOR_VERSION >= 3 static PyObject* __pyx_print = 0; static PyObject* __pyx_print_kwargs = 0; #endif static void __Pyx_AddTraceback(const char *funcname); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Type declarations */ /* Module declarations from lmp2radii */ /* Implementation of lmp2radii */ 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"; static char __pyx_k_5[] = "-h"; static PyObject *__pyx_int_1; static PyObject *__pyx_int_7; 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static char __pyx_k_4[] = "h"; static PyObject *__pyx_kp_4; static char __pyx_k_opts[] = "opts"; static PyObject *__pyx_kp_opts; static char __pyx_k_printHelp[] = "printHelp"; static PyObject *__pyx_kp_printHelp; static char __pyx_k_exit[] = "exit"; static PyObject *__pyx_kp_exit; static char __pyx_k_infile[] = "infile"; static PyObject *__pyx_kp_infile; static char __pyx_k_opt[] = "opt"; static PyObject *__pyx_kp_opt; static char __pyx_k_arg[] = "arg"; static PyObject *__pyx_kp_arg; static char __pyx_k_makeradii[] = "makeradii"; static PyObject *__pyx_kp_makeradii; static char __pyx_k_open[] = "open"; static PyObject *__pyx_kp_open; static char __pyx_k_8[] = "r"; static PyObject *__pyx_kp_8; static char __pyx_k_xreadlines[] = "xreadlines"; static PyObject *__pyx_kp_xreadlines; static char __pyx_k_system[] = "system"; static PyObject *__pyx_kp_system; static char __pyx_k_12[] = "frames"; static PyObject *__pyx_kp_12; static char __pyx_k_13[] = "r"; static PyObject *__pyx_kp_13; static char __pyx_k_readline[] = "readline"; 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[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 ... 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#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); } }