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NCFile_8H_source.html
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<a href="NCFile_8H.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef _NCFILE_H_</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#define _NCFILE_H_</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span>  </div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include <sstream></span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include <ctime></span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include <atomic></span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span>  </div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "AMReX_FArrayBox.H"</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "AMReX_IArrayBox.H"</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "<a class="code" href="NCInterface_8H.html">NCInterface.H</a>"</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  </div>
<div class="line"><a name="l00013"></a><span class="lineno"><a class="line" href="NCFile_8H.html#a60014a8d74bed0d5ae984e600c68dc85"> 13</a></span> <span class="keyword">using</span> <a class="code" href="REMORA__PhysBCFunct_8H.html#a60014a8d74bed0d5ae984e600c68dc85">PlaneVector</a> = amrex::Vector<amrex::FArrayBox>;</div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  </div>
<div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06"> 15</a></span> <span class="keyword">enum class</span> <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> {</div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b">Time_BT_SN_WE</a>,</div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4">Time_SN_WE</a>,</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb">SN_WE</a>,</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> };</div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  </div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">//</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// NDArray is the datatype designed to hold any data, including scalars, multidimensional</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// arrays, that read from the NetCDF file.</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">//</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// The data read from NetCDF file are stored in a continuous memory, and the data layout is descriped</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// by using a vector (shape). AMRex Box can be constructed using the data shape information, and MultiFab</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// data array can be setup using the data that stored in the NDArray.</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">//</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">template</span> <<span class="keyword">typename</span> DataType></div>
<div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="structNDArray.html"> 30</a></span> <span class="keyword">struct </span><a class="code" href="structNDArray.html">NDArray</a></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> {</div>
<div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="structNDArray.html#a96033b69f69ea0ae537a24288715752d"> 32</a></span>  <span class="keyword">using</span> <a class="code" href="structNDArray.html#a96033b69f69ea0ae537a24288715752d">DType</a> = <span class="keyword">typename</span> std::remove_const<DataType>::type;</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  </div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="comment">// constructor</span></div>
<div class="line"><a name="l00035"></a><span class="lineno"><a class="line" href="structNDArray.html#a7bd19397e539424afc06e9fe12760434"> 35</a></span>  <span class="keyword">explicit</span> <a class="code" href="structNDArray.html#a7bd19397e539424afc06e9fe12760434">NDArray</a> (<span class="keyword">const</span> std::string vname, <span class="keyword">const</span> std::vector<size_t>& vshape)</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  : <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>{vname}, <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>{vshape}, <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>{1}, <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a>{true} {</div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a> = <span class="keyword">new</span> <a class="code" href="structNDArray.html#a96033b69f69ea0ae537a24288715752d">DType</a> [this-><a class="code" href="structNDArray.html#a1b3ece1ab109568fcb919d1af8f14eee">ndim</a>()];</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  }</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="comment">// default constructor</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="structNDArray.html#a1f33dbd861944bc1494f4790f4f8543d"> 41</a></span>  <a class="code" href="structNDArray.html#a1f33dbd861944bc1494f4790f4f8543d">NDArray</a> () : <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>{<span class="stringliteral">"null"</span>}, <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>{1}, <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a>{false}, <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>{nullptr} {}</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="comment">// copy constructor</span></div>
<div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="structNDArray.html#a54f69e355d97f10089f82fb1087fb0af"> 44</a></span>  <a class="code" href="structNDArray.html#a54f69e355d97f10089f82fb1087fb0af">NDArray</a> (<span class="keyword">const</span> <a class="code" href="structNDArray.html">NDArray</a>& array) {</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a> = array.<a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>;</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a> = array.<a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>;</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a> = array.<a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>;</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>.fetch_add(1, std::memory_order_relaxed);</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  }</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="comment">// copy assignment</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="structNDArray.html#a63dda01f8d55fd1fc75437b125eb27b3"> 53</a></span>  <a class="code" href="structNDArray.html">NDArray</a>& <a class="code" href="structNDArray.html#a63dda01f8d55fd1fc75437b125eb27b3">operator=</a>(<span class="keyword">const</span> <a class="code" href="structNDArray.html">NDArray</a>& array) {</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a> = array.<a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>;</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a> = array.<a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>;</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a> = array.<a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>;</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>.fetch_add(1, std::memory_order_relaxed);</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  }</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// destructor</span></div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="structNDArray.html#afb8008f414c4404e3a6b425c12401d9d"> 63</a></span>  <a class="code" href="structNDArray.html#afb8008f414c4404e3a6b425c12401d9d">~NDArray</a> () {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>.fetch_sub(1, std::memory_order_acq_rel);</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">if</span> (<a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a> == 1 && <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a>) <span class="keyword">delete</span>[] <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  }</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">// get the data pointer</span></div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="structNDArray.html#aa1c5762c2de2f4286d4f341b618df1e5"> 69</a></span>  decltype(<span class="keyword">auto</span>) <a class="code" href="structNDArray.html#aa1c5762c2de2f4286d4f341b618df1e5">get_data</a> () {</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>.fetch_add(1, std::memory_order_relaxed);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordflow">return</span> <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>;</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  }</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="comment">// get the variable name</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="structNDArray.html#a4d7550e3c00d13d8397f1cfbdfd2ab48"> 75</a></span>  std::string <a class="code" href="structNDArray.html#a4d7550e3c00d13d8397f1cfbdfd2ab48">get_vname</a> () {</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">return</span> <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>;</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  }</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="comment">// get the variable data shape</span></div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="structNDArray.html#ad839c3c65bd755311afb6f0dad08f336"> 80</a></span>  std::vector<size_t> <a class="code" href="structNDArray.html#ad839c3c65bd755311afb6f0dad08f336">get_vshape</a> () {</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">return</span> <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="comment">// return the total number of data</span></div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="structNDArray.html#a1b3ece1ab109568fcb919d1af8f14eee"> 85</a></span>  <span class="keywordtype">size_t</span> <a class="code" href="structNDArray.html#a1b3ece1ab109568fcb919d1af8f14eee">ndim</a> () {</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">size_t</span> num = 1;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">int</span> isize = <span class="keyword">static_cast<</span><span class="keywordtype">int</span><span class="keyword">></span>(<a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>.size());</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">for</span> (<span class="keyword">auto</span> i=0; i<isize; ++i) num *= <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>[i];</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordflow">return</span> num;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  }</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="comment">// set the data shape information</span></div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="structNDArray.html#a6a0a485b6da8ce09dda81fc51607da73"> 93</a></span>  <span class="keywordtype">void</span> <a class="code" href="structNDArray.html#a6a0a485b6da8ce09dda81fc51607da73">set_vshape</a> (std::vector<size_t> vshape) {</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a> = vshape;</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  }</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  </div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keyword">private</span>:</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09"> 98</a></span>  std::string <a class="code" href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">name</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5"> 99</a></span>  std::vector<size_t> <a class="code" href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">shape</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972"> 100</a></span>  <span class="keyword">mutable</span> std::atomic<size_t> <a class="code" href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">ref_counted</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9"> 101</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">owned</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e"> 102</a></span>  <a class="code" href="structNDArray.html#a96033b69f69ea0ae537a24288715752d">DType</a>* <a class="code" href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">data</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> };</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keyword">template</span><<span class="keyword">typename</span> DType></div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="NCFile_8H.html#aa682cd5b28ee9ffaf36c6944bd124af0"> 106</a></span> <span class="keywordtype">void</span> <a class="code" href="NCFile_8H.html#aa682cd5b28ee9ffaf36c6944bd124af0">ReadNetCDFFile</a> (<span class="keyword">const</span> std::string& fname, amrex::Vector<std::string> names,</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  amrex::Vector<<a class="code" href="structNDArray.html">NDArray<DType></a> >& arrays)</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> {</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  AMREX_ASSERT(arrays.size() == names.size());</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">if</span> (amrex::ParallelDescriptor::IOProcessor())</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keyword">auto</span> ncf = <a class="code" href="classncutils_1_1NCFile.html#a2881b70e450e11f01b474c538b8d6885">ncutils::NCFile::open</a>(fname, NC_CLOBBER | NC_NETCDF4);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="comment"> // get the dimension information</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="comment"> int Time = static_cast<int>(ncf.dim("Time").len());</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="comment"> int DateStrLen = static_cast<int>(ncf.dim("DateStrLen").len());</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="comment"> int west_east = static_cast<int>(ncf.dim("west_east").len());</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="comment"> int south_north = static_cast<int>(ncf.dim("south_north").len());</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="comment"> int bottom_top = static_cast<int>(ncf.dim("bottom_top").len());</span></div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="comment"> int bottom_top_stag = static_cast<int>(ncf.dim("bottom_top_stag").len());</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment"> int west_east_stag = static_cast<int>(ncf.dim("west_east_stag").len());</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="comment"> int south_north_stag = static_cast<int>(ncf.dim("south_north_stag").len());</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="comment"> int bdy_width = static_cast<int>(ncf.dim("bdy_width").len());</span></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  amrex::Print() << <span class="stringliteral">"Reading the dimensions from the netcdf file "</span> << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  </div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordflow">for</span> (<span class="keyword">auto</span> n=0; n<arrays.size(); ++n) {</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="comment">// read the data from NetCDF file</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  std::string vname_to_write = names[n];</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  std::string vname_to_read = names[n];</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  </div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// amrex::AllPrint() << "About to read " << vname_to_read</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">// << " while filling the array for " << vname_to_write << std::endl;</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  </div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  std::vector<size_t> shape = ncf.var(vname_to_read).shape();</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  arrays[n] = <a class="code" href="structNDArray.html">NDArray<DType></a>(vname_to_read,shape);</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  DType* dataPtr = arrays[n].get_data();</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  </div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  std::vector<size_t> start(shape.size(), 0);</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  </div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="comment">// auto numPts = arrays[n].ndim();</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="comment">// amrex::Print() << "NetCDF Variable name = " << vname_to_read << std::endl;</span></div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// amrex::Print() << "numPts read from NetCDF file/var = " << numPts << std::endl;</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="comment">// amrex::Print() << "Dims of the variable = (";</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="comment">// for (auto &dim:shape)</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="comment">// amrex::Print() << dim << ", " ;</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">// amrex::Print() << ")" << std::endl;</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  ncf.var(vname_to_read).get(dataPtr, start, shape);</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  }</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  ncf.close();</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> }</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="comment"></span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment">/**</span></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment"> * Helper function for reading a single variable attribute</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment"> * @param fname Name of NetCDF file</span></div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment"> * @param var_name Name of variable</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment"> * @param attr_name Name of attribute to read</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment"> * @returns attribute value</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> std::string <a class="code" href="NCFile_8H.html#af8eb0b5eb41bbbf48a6dbced8cd0d6ea">ReadNetCDFVarAttrStr</a> (<span class="keyword">const</span> std::string& fname,</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keyword">const</span> std::string& var_name,</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keyword">const</span> std::string& attr_name);</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="comment"></span> </div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="comment">/**</span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="comment"> * Helper function for reading data from NetCDF file into a</span></div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="comment"> * provided FAB.</span></div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> <span class="comment"> * @param iv Index for which variable we are going to fill</span></div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> <span class="comment"> * @param nc_arrays Arrays of data from NetCDF file</span></div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> <span class="comment"> * @param var_name Variable name</span></div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="comment"> * @param NC_dim_type Dimension type for the variable as stored in the NetCDF file</span></div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="comment"> * @param temp FAB where we store the variable data from the NetCDF Arrays</span></div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> <span class="keyword">template</span><<span class="keyword">class</span> FAB,<span class="keyword">typename</span> DType></div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> <span class="keywordtype">void</span></div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="NCFile_8H.html#a5fbca9044ab6c565786cf158ff9a6c0f"> 182</a></span> <a class="code" href="NCFile_8H.html#a5fbca9044ab6c565786cf158ff9a6c0f">fill_fab_from_arrays</a> (<span class="keywordtype">int</span> iv,</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  amrex::Vector<<a class="code" href="structNDArray.html">NDArray<float></a>>& nc_arrays,</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keyword">const</span> std::string& var_name,</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a>& NC_dim_type,</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  FAB& temp)</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> {</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordtype">int</span> nsx, nsy, nsz;</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">if</span> (NC_dim_type == <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb">NC_Data_Dims_Type::SN_WE</a>) {</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  nsz = 1;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  nsy = nc_arrays[iv].get_vshape()[0];</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  nsx = nc_arrays[iv].get_vshape()[1];</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="comment">// amrex::Print() << "TYPE SN WE " << nsy << " " << nsx << std::endl;</span></div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (NC_dim_type == <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4">NC_Data_Dims_Type::Time_SN_WE</a>) {</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  nsz = 1;</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  nsy = nc_arrays[iv].get_vshape()[1];</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  nsx = nc_arrays[iv].get_vshape()[2];</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="comment">// amrex::Print() << "TYPE TIME SN WE " << nsy << " " << nsx << std::endl;</span></div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (NC_dim_type == <a class="code" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b">NC_Data_Dims_Type::Time_BT_SN_WE</a>) {</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  nsz = nc_arrays[iv].get_vshape()[1];</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  nsy = nc_arrays[iv].get_vshape()[2];</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  nsx = nc_arrays[iv].get_vshape()[3];</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="comment">// amrex::Print() << "TYPE TIME BT SN WE " << nsx << " " << nsy << " " << nsz << std::endl;</span></div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  amrex::Abort(<span class="stringliteral">"Dont know this NC_Data_Dims_Type"</span>);</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  amrex::Box my_box;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  </div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">if</span> (var_name == <span class="stringliteral">"u"</span> || var_name == <span class="stringliteral">"ubar"</span>)</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  {</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  my_box.setSmall(amrex::IntVect(0,-1,0));</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  my_box.setBig(amrex::IntVect(nsx-1,nsy-1,nsz-1));</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  my_box.setType(amrex::IndexType(amrex::IntVect(1,0,0)));</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  }</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (var_name == <span class="stringliteral">"v"</span> || var_name == <span class="stringliteral">"vbar"</span>)</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  {</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  my_box.setSmall(amrex::IntVect(-1,0,0));</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  my_box.setBig(amrex::IntVect(nsx-1,nsy-1,nsz-1));</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  my_box.setType(amrex::IndexType(amrex::IntVect(0,1,0)));</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  }</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordflow">else</span> <span class="comment">// everything cell-centered -- these have one ghost cell</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  {</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  my_box.setSmall(amrex::IntVect(-1,-1,0));</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  my_box.setBig(amrex::IntVect(nsx-2,nsy-2,nsz-1));</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  }</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="comment">// amrex::Print() <<" NAME and BOX for this VAR " << var_name << " " << my_box << std::endl;</span></div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  </div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="preprocessor">#ifdef AMREX_USE_GPU</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="comment">// Make sure temp lives on CPU since nc_arrays lives on CPU only</span></div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  temp.resize(my_box,1,amrex::The_Pinned_Arena());</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  temp.resize(my_box,1);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  amrex::Array4<DType> fab_arr = temp.array();</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  </div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordtype">int</span> ioff = temp.box().smallEnd()[0];</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordtype">int</span> joff = temp.box().smallEnd()[1];</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keyword">auto</span> num_pts_in_box = my_box.numPts();</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keyword">auto</span> num_pts_in_src = nsx*nsy*nsz;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="comment">// amrex::Print() <<" NUM PTS IN BOX " << num_pts_in_box << std::endl;</span></div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="comment">// amrex::Print() <<" NUM PTS IN SRC " << num_pts_in_src << std::endl;</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  AMREX_ALWAYS_ASSERT(num_pts_in_box >= num_pts_in_src);</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  </div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> n(0); n < num_pts_in_src; ++n) {</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordtype">int</span> nplane = nsx*nsy;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordtype">int</span> k = n / nplane;</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordtype">int</span> j = (n - k*nplane) / nsx + joff;</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="keywordtype">int</span> i = n - k*nplane - (j-joff) * nsx + ioff;</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  fab_arr(i,j,k,0) = <span class="keyword">static_cast<</span>DType<span class="keyword">></span>(*(nc_arrays[iv].get_data()+n));</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  }</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> }</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span> <span class="comment"></span> </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span> <span class="comment">/**</span></div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> <span class="comment"> * Function to read NetCDF variables and fill the corresponding Array4's</span></div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> <span class="comment"> * @param fname Name of the NetCDF file to be read</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> <span class="comment"> * @param nc_var_names Variable names in the NetCDF file</span></div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> <span class="comment"> * @param NC_dim_types NetCDF data dimension types</span></div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> <span class="comment"> * @param fab_vars Fab data we are to fill</span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> <span class="keyword">template</span><<span class="keyword">class</span> FAB,<span class="keyword">typename</span> DType></div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> <span class="keywordtype">void</span></div>
<div class="line"><a name="l00266"></a><span class="lineno"><a class="line" href="NCFile_8H.html#abcadbd0591038f7d3c9bb13c37df21f9"> 266</a></span> <a class="code" href="NCFile_8H.html#abcadbd0591038f7d3c9bb13c37df21f9">BuildFABsFromNetCDFFile</a> (<span class="keyword">const</span> amrex::Box& domain,</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keyword">const</span> std::string &fname,</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  amrex::Vector<std::string> nc_var_names,</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  amrex::Vector<enum NC_Data_Dims_Type> NC_dim_types,</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  amrex::Vector<FAB*> fab_vars)</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span> {</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordtype">int</span> ioproc = amrex::ParallelDescriptor::IOProcessorNumber(); <span class="comment">// I/O rank</span></div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  </div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  amrex::Vector<NDArray<float>> nc_arrays(nc_var_names.size());</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  </div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordflow">if</span> (amrex::ParallelDescriptor::IOProcessor())</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  {</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <a class="code" href="NCFile_8H.html#aa682cd5b28ee9ffaf36c6944bd124af0">ReadNetCDFFile</a>(fname, nc_var_names, nc_arrays);</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  }</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  </div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> iv = 0; iv < nc_var_names.size(); iv++)</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  {</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  FAB tmp;</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordflow">if</span> (amrex::ParallelDescriptor::IOProcessor()) {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  fill_fab_from_arrays<FAB,DType>(iv, nc_arrays, nc_var_names[iv], NC_dim_types[iv], tmp);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  }</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  </div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordtype">int</span> ncomp = tmp.nComp();</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  amrex::Box box = tmp.box();</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  </div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  amrex::ParallelDescriptor::Bcast(&box, 1, ioproc);</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  amrex::ParallelDescriptor::Bcast(&ncomp, 1, ioproc);</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  </div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keywordflow">if</span> (!amrex::ParallelDescriptor::IOProcessor()) {</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span> <span class="preprocessor">#ifdef AMREX_USE_GPU</span></div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  tmp.resize(box,ncomp,amrex::The_Pinned_Arena());</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  tmp.resize(box,ncomp);</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  }</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  </div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  amrex::ParallelDescriptor::Bcast(tmp.dataPtr(), tmp.size(), ioproc);</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  </div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="comment">// Shift box by the domain lower corner</span></div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  amrex::Box fab_bx = tmp.box();</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  amrex::Dim3 dom_lb = lbound(domain);</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  fab_bx += amrex::IntVect(dom_lb.x,dom_lb.y,dom_lb.z);</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="comment">// fab_vars points to data on device</span></div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  fab_vars[iv]->resize(fab_bx,1);</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> <span class="preprocessor">#ifdef AMREX_USE_GPU</span></div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  amrex::Gpu::copy(amrex::Gpu::hostToDevice,</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  tmp.dataPtr(), tmp.dataPtr() + tmp.size(),</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  fab_vars[iv]->dataPtr());</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="comment">// Provided by BaseFab inheritance through FArrayBox</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  fab_vars[iv]->copy(tmp,tmp.box(),0,fab_bx,0,1);</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  }</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> }</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  </div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="aNCFile_8H_html_a147911bcb83952a10f7560fd4e9d8f06"><div class="ttname"><a href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a></div><div class="ttdeci">NC_Data_Dims_Type</div><div class="ttdef"><b>Definition:</b> NCFile.H:15</div></div>
<div class="ttc" id="aNCFile_8H_html_a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4"><div class="ttname"><a href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4">NC_Data_Dims_Type::Time_SN_WE</a></div><div class="ttdeci">@ Time_SN_WE</div></div>
<div class="ttc" id="aNCFile_8H_html_a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb"><div class="ttname"><a href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb">NC_Data_Dims_Type::SN_WE</a></div><div class="ttdeci">@ SN_WE</div></div>
<div class="ttc" id="aNCFile_8H_html_a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b"><div class="ttname"><a href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b">NC_Data_Dims_Type::Time_BT_SN_WE</a></div><div class="ttdeci">@ Time_BT_SN_WE</div></div>
<div class="ttc" id="aNCFile_8H_html_a5fbca9044ab6c565786cf158ff9a6c0f"><div class="ttname"><a href="NCFile_8H.html#a5fbca9044ab6c565786cf158ff9a6c0f">fill_fab_from_arrays</a></div><div class="ttdeci">void fill_fab_from_arrays(int iv, amrex::Vector< NDArray< float >> &nc_arrays, const std::string &var_name, NC_Data_Dims_Type &NC_dim_type, FAB &temp)</div><div class="ttdef"><b>Definition:</b> NCFile.H:182</div></div>
<div class="ttc" id="aNCFile_8H_html_aa682cd5b28ee9ffaf36c6944bd124af0"><div class="ttname"><a href="NCFile_8H.html#aa682cd5b28ee9ffaf36c6944bd124af0">ReadNetCDFFile</a></div><div class="ttdeci">void ReadNetCDFFile(const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays)</div><div class="ttdef"><b>Definition:</b> NCFile.H:106</div></div>
<div class="ttc" id="aNCFile_8H_html_abcadbd0591038f7d3c9bb13c37df21f9"><div class="ttname"><a href="NCFile_8H.html#abcadbd0591038f7d3c9bb13c37df21f9">BuildFABsFromNetCDFFile</a></div><div class="ttdeci">void BuildFABsFromNetCDFFile(const amrex::Box &domain, const std::string &fname, amrex::Vector< std::string > nc_var_names, amrex::Vector< enum NC_Data_Dims_Type > NC_dim_types, amrex::Vector< FAB * > fab_vars)</div><div class="ttdef"><b>Definition:</b> NCFile.H:266</div></div>
<div class="ttc" id="aNCFile_8H_html_af8eb0b5eb41bbbf48a6dbced8cd0d6ea"><div class="ttname"><a href="NCFile_8H.html#af8eb0b5eb41bbbf48a6dbced8cd0d6ea">ReadNetCDFVarAttrStr</a></div><div class="ttdeci">std::string ReadNetCDFVarAttrStr(const std::string &fname, const std::string &var_name, const std::string &attr_name)</div><div class="ttdef"><b>Definition:</b> NCFile.cpp:7</div></div>
<div class="ttc" id="aNCInterface_8H_html"><div class="ttname"><a href="NCInterface_8H.html">NCInterface.H</a></div></div>
<div class="ttc" id="aREMORA__PhysBCFunct_8H_html_a60014a8d74bed0d5ae984e600c68dc85"><div class="ttname"><a href="REMORA__PhysBCFunct_8H.html#a60014a8d74bed0d5ae984e600c68dc85">PlaneVector</a></div><div class="ttdeci">amrex::Vector< amrex::FArrayBox > PlaneVector</div><div class="ttdef"><b>Definition:</b> REMORA_PhysBCFunct.H:19</div></div>
<div class="ttc" id="aclassncutils_1_1NCFile_html_a2881b70e450e11f01b474c538b8d6885"><div class="ttname"><a href="classncutils_1_1NCFile.html#a2881b70e450e11f01b474c538b8d6885">ncutils::NCFile::open</a></div><div class="ttdeci">static NCFile open(const std::string &name, const int cmode=NC_NOWRITE)</div><div class="ttdef"><b>Definition:</b> NCInterface.cpp:577</div></div>
<div class="ttc" id="astructNDArray_html"><div class="ttname"><a href="structNDArray.html">NDArray</a></div><div class="ttdef"><b>Definition:</b> NCFile.H:31</div></div>
<div class="ttc" id="astructNDArray_html_a0a1c90304eddb4d078132a1c1f45bef9"><div class="ttname"><a href="structNDArray.html#a0a1c90304eddb4d078132a1c1f45bef9">NDArray::owned</a></div><div class="ttdeci">bool owned</div><div class="ttdef"><b>Definition:</b> NCFile.H:101</div></div>
<div class="ttc" id="astructNDArray_html_a0d3be2b45f3fb008d12ec17dfd6abf09"><div class="ttname"><a href="structNDArray.html#a0d3be2b45f3fb008d12ec17dfd6abf09">NDArray::name</a></div><div class="ttdeci">std::string name</div><div class="ttdef"><b>Definition:</b> NCFile.H:98</div></div>
<div class="ttc" id="astructNDArray_html_a1b3ece1ab109568fcb919d1af8f14eee"><div class="ttname"><a href="structNDArray.html#a1b3ece1ab109568fcb919d1af8f14eee">NDArray::ndim</a></div><div class="ttdeci">size_t ndim()</div><div class="ttdef"><b>Definition:</b> NCFile.H:85</div></div>
<div class="ttc" id="astructNDArray_html_a1f33dbd861944bc1494f4790f4f8543d"><div class="ttname"><a href="structNDArray.html#a1f33dbd861944bc1494f4790f4f8543d">NDArray::NDArray</a></div><div class="ttdeci">NDArray()</div><div class="ttdef"><b>Definition:</b> NCFile.H:41</div></div>
<div class="ttc" id="astructNDArray_html_a4d7550e3c00d13d8397f1cfbdfd2ab48"><div class="ttname"><a href="structNDArray.html#a4d7550e3c00d13d8397f1cfbdfd2ab48">NDArray::get_vname</a></div><div class="ttdeci">std::string get_vname()</div><div class="ttdef"><b>Definition:</b> NCFile.H:75</div></div>
<div class="ttc" id="astructNDArray_html_a54f69e355d97f10089f82fb1087fb0af"><div class="ttname"><a href="structNDArray.html#a54f69e355d97f10089f82fb1087fb0af">NDArray::NDArray</a></div><div class="ttdeci">NDArray(const NDArray &array)</div><div class="ttdef"><b>Definition:</b> NCFile.H:44</div></div>
<div class="ttc" id="astructNDArray_html_a63dda01f8d55fd1fc75437b125eb27b3"><div class="ttname"><a href="structNDArray.html#a63dda01f8d55fd1fc75437b125eb27b3">NDArray::operator=</a></div><div class="ttdeci">NDArray & operator=(const NDArray &array)</div><div class="ttdef"><b>Definition:</b> NCFile.H:53</div></div>
<div class="ttc" id="astructNDArray_html_a6a0a485b6da8ce09dda81fc51607da73"><div class="ttname"><a href="structNDArray.html#a6a0a485b6da8ce09dda81fc51607da73">NDArray::set_vshape</a></div><div class="ttdeci">void set_vshape(std::vector< size_t > vshape)</div><div class="ttdef"><b>Definition:</b> NCFile.H:93</div></div>
<div class="ttc" id="astructNDArray_html_a7bd19397e539424afc06e9fe12760434"><div class="ttname"><a href="structNDArray.html#a7bd19397e539424afc06e9fe12760434">NDArray::NDArray</a></div><div class="ttdeci">NDArray(const std::string vname, const std::vector< size_t > &vshape)</div><div class="ttdef"><b>Definition:</b> NCFile.H:35</div></div>
<div class="ttc" id="astructNDArray_html_a8a0bbff40020f6aea23346ac656bf972"><div class="ttname"><a href="structNDArray.html#a8a0bbff40020f6aea23346ac656bf972">NDArray::ref_counted</a></div><div class="ttdeci">std::atomic< size_t > ref_counted</div><div class="ttdef"><b>Definition:</b> NCFile.H:100</div></div>
<div class="ttc" id="astructNDArray_html_a96033b69f69ea0ae537a24288715752d"><div class="ttname"><a href="structNDArray.html#a96033b69f69ea0ae537a24288715752d">NDArray::DType</a></div><div class="ttdeci">typename std::remove_const< DataType >::type DType</div><div class="ttdef"><b>Definition:</b> NCFile.H:32</div></div>
<div class="ttc" id="astructNDArray_html_a99d704051dda7b5635b12cbe785d7bb5"><div class="ttname"><a href="structNDArray.html#a99d704051dda7b5635b12cbe785d7bb5">NDArray::shape</a></div><div class="ttdeci">std::vector< size_t > shape</div><div class="ttdef"><b>Definition:</b> NCFile.H:99</div></div>
<div class="ttc" id="astructNDArray_html_a9d3679c95b5bf1813a7edaedf221837e"><div class="ttname"><a href="structNDArray.html#a9d3679c95b5bf1813a7edaedf221837e">NDArray::data</a></div><div class="ttdeci">DType * data</div><div class="ttdef"><b>Definition:</b> NCFile.H:102</div></div>
<div class="ttc" id="astructNDArray_html_aa1c5762c2de2f4286d4f341b618df1e5"><div class="ttname"><a href="structNDArray.html#aa1c5762c2de2f4286d4f341b618df1e5">NDArray::get_data</a></div><div class="ttdeci">decltype(auto) get_data()</div><div class="ttdef"><b>Definition:</b> NCFile.H:69</div></div>
<div class="ttc" id="astructNDArray_html_ad839c3c65bd755311afb6f0dad08f336"><div class="ttname"><a href="structNDArray.html#ad839c3c65bd755311afb6f0dad08f336">NDArray::get_vshape</a></div><div class="ttdeci">std::vector< size_t > get_vshape()</div><div class="ttdef"><b>Definition:</b> NCFile.H:80</div></div>
<div class="ttc" id="astructNDArray_html_afb8008f414c4404e3a6b425c12401d9d"><div class="ttname"><a href="structNDArray.html#afb8008f414c4404e3a6b425c12401d9d">NDArray::~NDArray</a></div><div class="ttdeci">~NDArray()</div><div class="ttdef"><b>Definition:</b> NCFile.H:63</div></div>
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