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/* 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";
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static char __pyx_k_6[] = "Usage: python lmp2radii.pyx test.lammpstrj\n";
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static PyObject *__pyx_kp_10;
static PyObject *__pyx_kp_11;
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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 ...  ";
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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*/
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  /* "/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
 */
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  /* "/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;}
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  /* "/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):
 */
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/* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":32
 *     return
 * 
 * def makeradii(infile):             # <<<<<<<<<<<<<<
 * 
 *     print "Reading %s ... [WAIT]"%infile,
 */

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  /* "/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()
 */
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  /* "/Users/Andres/Documents/software/MD/eFF/pEFF/tools/eff/lmp2radii.pyx":35
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 *     header=9
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 *     framecnt=0
 *     header=9             # <<<<<<<<<<<<<<
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  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);
    }
}

