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NCFile_8H.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
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<title>REMORA: /home/runner/work/REMORA/REMORA/Source/IO/NCFile.H File Reference</title>
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<div id="projectname">REMORA
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<div id="projectbrief">Energy Research and Forecasting: An Atmospheric Modeling Code</div>
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<a href="#nested-classes">Classes</a> |
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<div class="title">NCFile.H File Reference</div> </div>
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<div class="contents">
<div class="textblock"><code>#include <sstream></code><br />
<code>#include <string></code><br />
<code>#include <ctime></code><br />
<code>#include <atomic></code><br />
<code>#include "AMReX_FArrayBox.H"</code><br />
<code>#include "AMReX_IArrayBox.H"</code><br />
<code>#include "<a class="el" href="NCInterface_8H_source.html">NCInterface.H</a>"</code><br />
</div><div class="textblock"><div class="dynheader">
Include dependency graph for NCFile.H:</div>
<div class="dyncontent">
<div class="center"><img src="NCFile_8H__incl.png" border="0" usemap="#a_2home_2runner_2work_2REMORA_2REMORA_2Source_2IO_2NCFile_8H" alt=""/></div>
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This graph shows which files directly or indirectly include this file:</div>
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<div class="center"><img src="NCFile_8H__dep__incl.png" border="0" usemap="#a_2home_2runner_2work_2REMORA_2REMORA_2Source_2IO_2NCFile_8Hdep" alt=""/></div>
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<p><a href="NCFile_8H_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structNDArray.html">NDArray< DataType ></a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr class="memitem:a60014a8d74bed0d5ae984e600c68dc85"><td class="memItemLeft" align="right" valign="top">using </td><td class="memItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#a60014a8d74bed0d5ae984e600c68dc85">PlaneVector</a> = amrex::Vector< amrex::FArrayBox ></td></tr>
<tr class="separator:a60014a8d74bed0d5ae984e600c68dc85"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="enum-members"></a>
Enumerations</h2></td></tr>
<tr class="memitem:a147911bcb83952a10f7560fd4e9d8f06"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> { <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b">Time_BT_SN_WE</a>
, <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4">Time_SN_WE</a>
, <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb">SN_WE</a>
}</td></tr>
<tr class="separator:a147911bcb83952a10f7560fd4e9d8f06"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:aa682cd5b28ee9ffaf36c6944bd124af0"><td class="memTemplParams" colspan="2">template<typename DType > </td></tr>
<tr class="memitem:aa682cd5b28ee9ffaf36c6944bd124af0"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#aa682cd5b28ee9ffaf36c6944bd124af0">ReadNetCDFFile</a> (const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< <a class="el" href="structNDArray.html">NDArray</a>< DType > > &arrays)</td></tr>
<tr class="separator:aa682cd5b28ee9ffaf36c6944bd124af0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af8eb0b5eb41bbbf48a6dbced8cd0d6ea"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#af8eb0b5eb41bbbf48a6dbced8cd0d6ea">ReadNetCDFVarAttrStr</a> (const std::string &fname, const std::string &var_name, const std::string &attr_name)</td></tr>
<tr class="separator:af8eb0b5eb41bbbf48a6dbced8cd0d6ea"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5fbca9044ab6c565786cf158ff9a6c0f"><td class="memTemplParams" colspan="2">template<class FAB , typename DType > </td></tr>
<tr class="memitem:a5fbca9044ab6c565786cf158ff9a6c0f"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#a5fbca9044ab6c565786cf158ff9a6c0f">fill_fab_from_arrays</a> (int iv, amrex::Vector< <a class="el" href="structNDArray.html">NDArray</a>< float >> &nc_arrays, const std::string &var_name, <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> &NC_dim_type, FAB &temp)</td></tr>
<tr class="separator:a5fbca9044ab6c565786cf158ff9a6c0f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abcadbd0591038f7d3c9bb13c37df21f9"><td class="memTemplParams" colspan="2">template<class FAB , typename DType > </td></tr>
<tr class="memitem:abcadbd0591038f7d3c9bb13c37df21f9"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="NCFile_8H.html#abcadbd0591038f7d3c9bb13c37df21f9">BuildFABsFromNetCDFFile</a> (const amrex::Box &domain, const std::string &fname, amrex::Vector< std::string > nc_var_names, amrex::Vector< enum <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> > NC_dim_types, amrex::Vector< FAB * > fab_vars)</td></tr>
<tr class="separator:abcadbd0591038f7d3c9bb13c37df21f9"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<h2 class="groupheader">Typedef Documentation</h2>
<a id="a60014a8d74bed0d5ae984e600c68dc85"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a60014a8d74bed0d5ae984e600c68dc85">◆ </a></span>PlaneVector</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">using <a class="el" href="REMORA__PhysBCFunct_8H.html#a60014a8d74bed0d5ae984e600c68dc85">PlaneVector</a> = amrex::Vector<amrex::FArrayBox></td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<h2 class="groupheader">Enumeration Type Documentation</h2>
<a id="a147911bcb83952a10f7560fd4e9d8f06"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a147911bcb83952a10f7560fd4e9d8f06">◆ </a></span>NC_Data_Dims_Type</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">enum <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">strong</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a147911bcb83952a10f7560fd4e9d8f06aa3968158227ea04595d4003503cca22b"></a>Time_BT_SN_WE </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a147911bcb83952a10f7560fd4e9d8f06a5f93bace93896872075eae75770cadc4"></a>Time_SN_WE </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a147911bcb83952a10f7560fd4e9d8f06a6d24059efd6f8399a1f327f1d86a47cb"></a>SN_WE </td><td class="fielddoc"></td></tr>
</table>
<div class="fragment"><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  {</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="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><!-- fragment -->
</div>
</div>
<h2 class="groupheader">Function Documentation</h2>
<a id="abcadbd0591038f7d3c9bb13c37df21f9"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abcadbd0591038f7d3c9bb13c37df21f9">◆ </a></span>BuildFABsFromNetCDFFile()</h2>
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template<class FAB , typename DType > </div>
<table class="memname">
<tr>
<td class="memname">void BuildFABsFromNetCDFFile </td>
<td>(</td>
<td class="paramtype">const amrex::Box & </td>
<td class="paramname"><em>domain</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>fname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< std::string > </td>
<td class="paramname"><em>nc_var_names</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< enum <a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> > </td>
<td class="paramname"><em>NC_dim_types</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< FAB * > </td>
<td class="paramname"><em>fab_vars</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Function to read NetCDF variables and fill the corresponding Array4's</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">fname</td><td>Name of the NetCDF file to be read </td></tr>
<tr><td class="paramname">nc_var_names</td><td>Variable names in the NetCDF file </td></tr>
<tr><td class="paramname">NC_dim_types</td><td>NetCDF data dimension types </td></tr>
<tr><td class="paramname">fab_vars</td><td>Fab data we are to fill </td></tr>
</table>
</dd>
</dl>
<div class="fragment"><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="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>
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<h2 class="memtitle"><span class="permalink"><a href="#a5fbca9044ab6c565786cf158ff9a6c0f">◆ </a></span>fill_fab_from_arrays()</h2>
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template<class FAB , typename DType > </div>
<table class="memname">
<tr>
<td class="memname">void fill_fab_from_arrays </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>iv</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< <a class="el" href="structNDArray.html">NDArray</a>< float >> & </td>
<td class="paramname"><em>nc_arrays</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>var_name</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="NCFile_8H.html#a147911bcb83952a10f7560fd4e9d8f06">NC_Data_Dims_Type</a> & </td>
<td class="paramname"><em>NC_dim_type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">FAB & </td>
<td class="paramname"><em>temp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Helper function for reading data from NetCDF file into a provided FAB.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">iv</td><td>Index for which variable we are going to fill </td></tr>
<tr><td class="paramname">nc_arrays</td><td>Arrays of data from NetCDF file </td></tr>
<tr><td class="paramname">var_name</td><td>Variable name </td></tr>
<tr><td class="paramname">NC_dim_type</td><td>Dimension type for the variable as stored in the NetCDF file </td></tr>
<tr><td class="paramname">temp</td><td>FAB where we store the variable data from the NetCDF Arrays </td></tr>
</table>
</dd>
</dl>
<div class="fragment"><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>
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<a id="aa682cd5b28ee9ffaf36c6944bd124af0"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa682cd5b28ee9ffaf36c6944bd124af0">◆ </a></span>ReadNetCDFFile()</h2>
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template<typename DType > </div>
<table class="memname">
<tr>
<td class="memname">void ReadNetCDFFile </td>
<td>(</td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>fname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< std::string > </td>
<td class="paramname"><em>names</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">amrex::Vector< <a class="el" href="structNDArray.html">NDArray</a>< DType > > & </td>
<td class="paramname"><em>arrays</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
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</div><div class="memdoc">
<div class="fragment"><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="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>
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<p class="reference">Referenced by <a class="el" href="NCFile_8H.html#abcadbd0591038f7d3c9bb13c37df21f9">BuildFABsFromNetCDFFile()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af8eb0b5eb41bbbf48a6dbced8cd0d6ea">◆ </a></span>ReadNetCDFVarAttrStr()</h2>
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<table class="memname">
<tr>
<td class="memname">std::string ReadNetCDFVarAttrStr </td>
<td>(</td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>fname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>var_name</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>attr_name</em> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>Helper function for reading a single variable attribute</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">fname</td><td>Name of NetCDF file </td></tr>
<tr><td class="paramname">var_name</td><td>Name of variable </td></tr>
<tr><td class="paramname">attr_name</td><td>Name of attribute to read </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>attribute value </dd></dl>
<div class="fragment"><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> {</div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span>  std::string attr_val;</div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  <span class="keywordflow">if</span> (amrex::ParallelDescriptor::IOProcessor())</div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  {</div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</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="l00015"></a><span class="lineno"> 15</span>  attr_val = ncf.var(var_name).get_attr(attr_name);</div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  ncf.close();</div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  }</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keywordflow">return</span> attr_val;</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> }</div>
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