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richardjgowers/readingXYZ.ipynb

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readingXYZ.ipynb
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"%load_ext cython"
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"warning: /home/richard/.cache/ipython/cython/_cython_magic_31dbdbe3155d800dfc8607685237be56.pyx:22:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.\n",
"warning: /home/richard/.cache/ipython/cython/_cython_magic_31dbdbe3155d800dfc8607685237be56.pyx:22:22: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.\n",
"warning: /home/richard/.cache/ipython/cython/_cython_magic_31dbdbe3155d800dfc8607685237be56.pyx:22:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.\n",
"warning: /home/richard/.cache/ipython/cython/_cython_magic_31dbdbe3155d800dfc8607685237be56.pyx:22:39: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.\n"
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"</pre><pre class=\"cython line score-2\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">34</span>: <span class=\"k\">cdef</span> <span class=\"kt\">double</span>[<span class=\"p\">::</span><span class=\"mf\">1</span><span class=\"p\">]</span> <span class=\"n\">c_arr</span> <span class=\"o\">=</span> <span class=\"n\">arr</span></pre>\n",
"<pre class='cython code score-2 '> __pyx_t_7 = <span class='pyx_c_api'>__Pyx_PyObject_to_MemoryviewSlice_dc_double</span>(__pyx_v_arr, PyBUF_WRITABLE);<span class='error_goto'> if (unlikely(!__pyx_t_7.memview)) __PYX_ERR(0, 34, __pyx_L1_error)</span>\n",
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"<pre class=\"cython line score-0\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">37</span>: <span class=\"n\">read</span> <span class=\"o\">=</span> <span class=\"n\">stdio</span><span class=\"o\">.</span><span class=\"n\">getline</span><span class=\"p\">(</span><span class=\"o\">&amp;</span><span class=\"n\">line</span><span class=\"p\">,</span> <span class=\"o\">&amp;</span><span class=\"n\">read</span><span class=\"p\">,</span> <span class=\"n\">fp</span><span class=\"p\">)</span></pre>\n",
"<pre class='cython code score-0 '> __pyx_v_read = getline((&amp;__pyx_v_line), (&amp;__pyx_v_read), __pyx_v_fp);\n",
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"<pre class='cython code score-0 '> __pyx_t_8 = __pyx_v_c_n_atoms;\n",
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"<pre class='cython code score-0 '> __pyx_v_read = getline((&amp;__pyx_v_line), (&amp;__pyx_v_read), __pyx_v_fp);\n",
"</pre><pre class=\"cython line score-0\">&#xA0;<span class=\"\">40</span>: </pre>\n",
"<pre class=\"cython line score-0\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">41</span>: <span class=\"n\">first</span> <span class=\"o\">=</span> <span class=\"n\">cstring</span><span class=\"o\">.</span><span class=\"n\">strtok</span><span class=\"p\">(</span><span class=\"n\">line</span><span class=\"p\">,</span> <span class=\"n\">delims</span><span class=\"p\">)</span> <span class=\"c\"># element</span></pre>\n",
"<pre class='cython code score-0 '> __pyx_v_first = strtok(__pyx_v_line, __pyx_v_delims);\n",
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"<pre class='cython code score-0 '> __pyx_v_second = strtok(NULL, __pyx_v_delims);\n",
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"<pre class='cython code score-0 '> __pyx_v_third = strtok(NULL, __pyx_v_delims);\n",
"</pre><pre class=\"cython line score-0\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">44</span>: <span class=\"n\">fourth</span> <span class=\"o\">=</span> <span class=\"n\">cstring</span><span class=\"o\">.</span><span class=\"n\">strtok</span><span class=\"p\">(</span><span class=\"bp\">NULL</span><span class=\"p\">,</span> <span class=\"n\">delims</span><span class=\"p\">)</span></pre>\n",
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"<pre class=\"cython line score-0\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">46</span>: <span class=\"n\">c_arr</span><span class=\"p\">[</span><span class=\"n\">i</span><span class=\"o\">*</span><span class=\"mf\">3</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"n\">stdlib</span><span class=\"o\">.</span><span class=\"n\">atof</span><span class=\"p\">(</span><span class=\"n\">second</span><span class=\"p\">)</span></pre>\n",
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"</pre><pre class=\"cython line score-0\" onclick=\"(function(s){s.display=s.display==='block'?'none':'block'})(this.nextElementSibling.style)\">+<span class=\"\">47</span>: <span class=\"n\">c_arr</span><span class=\"p\">[</span><span class=\"n\">i</span><span class=\"o\">*</span><span class=\"mf\">3</span> <span class=\"o\">+</span> <span class=\"mf\">1</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"n\">stdlib</span><span class=\"o\">.</span><span class=\"n\">atof</span><span class=\"p\">(</span><span class=\"n\">third</span><span class=\"p\">)</span></pre>\n",
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],
"text/plain": [
"<IPython.core.display.HTML object>"
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"execution_count": 111,
"metadata": {},
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],
"source": [
"%%cython -a\n",
"\n",
"import cython\n",
"import numpy as np\n",
"\n",
"from libc cimport stdio\n",
"from libc cimport string as cstring\n",
"from libc cimport stdlib\n",
"from cpython.int cimport PyInt_FromString\n",
"\n",
"\n",
"@cython.wraparound(False)\n",
"@cython.boundscheck(False)\n",
"def read_xyz(bytes filename):\n",
" cdef stdio.FILE* fp\n",
" cdef char* line = NULL\n",
" \n",
" cdef object n_atoms\n",
" cdef int i, c_n_atoms\n",
" \n",
" cdef size_t read = 0\n",
" cdef char* delims = \" \\t\\n\"\n",
" cdef char *first, *second, *third, *fourth\n",
" \n",
" fp = stdio.fopen(filename, \"r\")\n",
" if fp == NULL:\n",
" raise ValueError(\"could not open file\")\n",
" \n",
" read = stdio.getline(&line, &read, fp)\n",
" n_atoms = PyInt_FromString(line, NULL, 10)\n",
" c_n_atoms = stdlib.atoi(line)\n",
" \n",
" # Allocate memory in np.zeros, then create C-friendly view to this\n",
" cdef object arr = np.zeros(3 * n_atoms)\n",
" cdef double[::1] c_arr = arr\n",
" \n",
" # This tight inside loop is pure C (annotation has no yellow lines)\n",
" read = stdio.getline(&line, &read, fp) # comment line\n",
" for i in range(c_n_atoms):\n",
" read = stdio.getline(&line, &read, fp)\n",
" # TODO: error checking on read, if read==0, we didn't get a line\n",
" \n",
" first = cstring.strtok(line, delims) # element\n",
" second = cstring.strtok(NULL, delims)\n",
" third = cstring.strtok(NULL, delims)\n",
" fourth = cstring.strtok(NULL, delims)\n",
" \n",
" # TODO: Check second, third, fourth aren't NULL, if they are these tokens were missing\n",
" c_arr[i*3] = stdlib.atof(second)\n",
" c_arr[i*3 + 1] = stdlib.atof(third)\n",
" c_arr[i*3 + 2] = stdlib.atof(fourth)\n",
"\n",
" stdio.fclose(fp);\n",
" \n",
" return arr.reshape(n_atoms, 3)"
]
},
{
"cell_type": "code",
"execution_count": 110,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"528 µs ± 11.5 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)\n"
]
}
],
"source": [
"%timeit read_xyz(b'./2r9r-1b.xyz')"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
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