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lammps/tools/eff/lmp2radii.c
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lmp2radii.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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#include <math.h>
#define __PYX_HAVE_API__lmp2radii
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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";
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_7;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_9;
static PyObject *__pyx_int_3;
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static PyObject *__pyx_kp_Info;
static char __pyx_k_sys[] = "sys";
static PyObject *__pyx_kp_sys;
static char __pyx_k_os[] = "os";
static PyObject *__pyx_kp_os;
static char __pyx_k_math[] = "math";
static PyObject *__pyx_kp_math;
static char __pyx_k_2[] = "log10";
static PyObject *__pyx_kp_2;
static char __pyx_k_shutil[] = "shutil";
static PyObject *__pyx_kp_shutil;
static char __pyx_k_rmtree[] = "rmtree";
static PyObject *__pyx_kp_rmtree;
static char __pyx_k_getopt[] = "getopt";
static PyObject *__pyx_kp_getopt;
static char __pyx_k_gnu_getopt[] = "gnu_getopt";
static PyObject *__pyx_kp_gnu_getopt;
static char __pyx_k_numpy[] = "numpy";
static PyObject *__pyx_kp_numpy;
static char __pyx_k___name__[] = "__name__";
static PyObject *__pyx_kp___name__;
static char __pyx_k_3[] = "__main__";
static PyObject *__pyx_kp_3;
static char __pyx_k_argv[] = "argv";
static PyObject *__pyx_kp_argv;
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";
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static PyObject *__pyx_kp_makeradii;
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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";
static PyObject *__pyx_kp_readline;
static char __pyx_k_split[] = "split";
static PyObject *__pyx_kp_split;
static char __pyx_k_close[] = "close";
static PyObject *__pyx_kp_close;
static char __pyx_k_14[] = "atoms";
static PyObject *__pyx_kp_14;
static char __pyx_k_15[] = "r";
static PyObject *__pyx_kp_15;
static char __pyx_k_readlines[] = "readlines";
static PyObject *__pyx_kp_readlines;
static char __pyx_k_zeros[] = "zeros";
static PyObject *__pyx_kp_zeros;
static char __pyx_k_dtype[] = "dtype";
static PyObject *__pyx_kp_dtype;
static char __pyx_k_enumerate[] = "enumerate";
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;
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static PyObject *__pyx_kp_23;
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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;
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]"
*/
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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);
}
}
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