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ERF_NCWpsFile.H File Reference
#include <sstream>
#include <string>
#include <atomic>
#include "AMReX_FArrayBox.H"
#include "AMReX_IArrayBox.H"
#include "ERF_EpochTime.H"
#include "ERF_NCInterface.H"
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Classes

struct  NDArray< DataType >
 

Typedefs

using PlaneVector = amrex::Vector< amrex::FArrayBox >
 

Enumerations

enum class  NC_Data_Dims_Type {
  Time_BT_SN_WE , Time_SN_WE , Time_BT , Time ,
  Time_BdyWidth_BT_SN , Time_BdyWidth_BT_WE , Time_BdyWidth_SN , Time_BdyWidth_WE
}
 

Functions

int BuildFABsFromWRFBdyFile (const std::string &fname, amrex::Vector< amrex::Vector< amrex::FArrayBox >> &bdy_data_xlo, amrex::Vector< amrex::Vector< amrex::FArrayBox >> &bdy_data_xhi, amrex::Vector< amrex::Vector< amrex::FArrayBox >> &bdy_data_ylo, amrex::Vector< amrex::Vector< amrex::FArrayBox >> &bdy_data_yhi)
 
template<typename DType >
void ReadTimeSliceFromNetCDFFile (const std::string &fname, const int tidx, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays, amrex::Vector< int > &success)
 
template<typename DType >
void ReadNetCDFFile (const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays, amrex::Vector< int > &success)
 
template<class FAB , typename DType >
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)
 
template<class FAB , typename DType >
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, amrex::Vector< int > &success)
 

Typedef Documentation

◆ PlaneVector

using PlaneVector = amrex::Vector<amrex::FArrayBox>

Enumeration Type Documentation

◆ NC_Data_Dims_Type

enum NC_Data_Dims_Type
strong
Enumerator
Time_BT_SN_WE 
Time_SN_WE 
Time_BT 
Time 
Time_BdyWidth_BT_SN 
Time_BdyWidth_BT_WE 
Time_BdyWidth_SN 
Time_BdyWidth_WE 
30  {
31  Time_BT_SN_WE,
32  Time_SN_WE,
33  Time_BT,
34  Time,
35  Time_BdyWidth_BT_SN,
36  Time_BdyWidth_BT_WE,
37  Time_BdyWidth_SN,
38  Time_BdyWidth_WE
39 };
NC_Data_Dims_Type::Time_BdyWidth_WE
@ Time_BdyWidth_WE
NC_Data_Dims_Type::Time_BdyWidth_BT_SN
@ Time_BdyWidth_BT_SN
NC_Data_Dims_Type::Time_BT
@ Time_BT
NC_Data_Dims_Type::Time_SN_WE
@ Time_SN_WE
NC_Data_Dims_Type::Time_BdyWidth_SN
@ Time_BdyWidth_SN
NC_Data_Dims_Type::Time_BT_SN_WE
@ Time_BT_SN_WE
NC_Data_Dims_Type::Time
@ Time
NC_Data_Dims_Type::Time_BdyWidth_BT_WE
@ Time_BdyWidth_BT_WE

Function Documentation

◆ BuildFABsFromNetCDFFile()

template<class FAB , typename DType >
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,
amrex::Vector< int > &  success 
)

Function to read NetCDF variables and fill the corresponding Array4's

Parameters
fnameName of the NetCDF file to be read
nc_var_namesVariable names in the NetCDF file
NC_dim_typesNetCDF data dimension types
fab_varsFab data we are to fill
345 {
346  int ioproc = amrex::ParallelDescriptor::IOProcessorNumber(); // I/O rank
347 
348  amrex::Vector<NDArray<float>> nc_arrays(nc_var_names.size());
349 
350  if (amrex::ParallelDescriptor::IOProcessor())
351  {
352  ReadNetCDFFile(fname, nc_var_names, nc_arrays, success);
353  }
354 
355  amrex::ParallelDescriptor::Bcast(success.dataPtr(), success.size(), ioproc);
356 
357  for (int iv = 0; iv < nc_var_names.size(); iv++)
358  {
359  if (success[iv] == 1) {
360  FAB tmp;
361  if (amrex::ParallelDescriptor::IOProcessor()) {
362  fill_fab_from_arrays<FAB,DType>(iv, nc_arrays, nc_var_names[iv], NC_dim_types[iv], tmp);
363  }
364 
365  int ncomp = tmp.nComp();
366  amrex::Box box = tmp.box();
367 
368  amrex::ParallelDescriptor::Bcast(&box, 1, ioproc);
369  amrex::ParallelDescriptor::Bcast(&ncomp, 1, ioproc);
370 
371  if (!amrex::ParallelDescriptor::IOProcessor()) {
372 #ifdef AMREX_USE_GPU
373  tmp.resize(box,ncomp,amrex::The_Pinned_Arena());
374 #else
375  tmp.resize(box,ncomp);
376 #endif
377  }
378 
379  amrex::ParallelDescriptor::Bcast(tmp.dataPtr(), tmp.size(), ioproc);
380 
381  // Shift box by the domain lower corner
382  amrex::Box fab_bx = tmp.box();
383  amrex::Dim3 dom_lb = lbound(domain);
384  fab_bx += amrex::IntVect(dom_lb.x,dom_lb.y,dom_lb.z);
385  // fab_vars points to data on device
386  fab_vars[iv]->resize(fab_bx,1);
387 #ifdef AMREX_USE_GPU
388  amrex::Gpu::copy(amrex::Gpu::hostToDevice,
389  tmp.dataPtr(), tmp.dataPtr() + tmp.size(),
390  fab_vars[iv]->dataPtr());
391 #else
392  // Provided by BaseFab inheritance through FArrayBox
393  fab_vars[iv]->copy(tmp,tmp.box(),0,fab_bx,0,1);
394 #endif
395  } // success
396  } // iv
397 }
ReadNetCDFFile
void ReadNetCDFFile(const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays, amrex::Vector< int > &success)
Definition: ERF_NCWpsFile.H:179
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◆ BuildFABsFromWRFBdyFile()

int BuildFABsFromWRFBdyFile ( const std::string &  fname,
amrex::Vector< amrex::Vector< amrex::FArrayBox >> &  bdy_data_xlo,
amrex::Vector< amrex::Vector< amrex::FArrayBox >> &  bdy_data_xhi,
amrex::Vector< amrex::Vector< amrex::FArrayBox >> &  bdy_data_ylo,
amrex::Vector< amrex::Vector< amrex::FArrayBox >> &  bdy_data_yhi 
)

◆ fill_fab_from_arrays()

template<class FAB , typename DType >
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 
)

Helper function for reading data from NetCDF file into a provided FAB.

Parameters
ivIndex for which variable we are going to fill
nc_arraysArrays of data from NetCDF file
var_nameVariable name
NC_dim_typeDimension type for the variable as stored in the NetCDF file
tempFAB where we store the variable data from the NetCDF Arrays
271 {
272  int ns1, ns2, ns3; // bottom_top, south_north, west_east (these can be staggered or unstaggered)
273  if (NC_dim_type == NC_Data_Dims_Type::Time_BT) {
274  ns1 = nc_arrays[iv].get_vshape()[1];
275  ns2 = 1;
276  ns3 = 1;
277  // amrex::Print() << "TYPE BT " << ns1 << std::endl;
278  } else if (NC_dim_type == NC_Data_Dims_Type::Time_SN_WE) {
279  ns1 = 1;
280  ns2 = nc_arrays[iv].get_vshape()[1];
281  ns3 = nc_arrays[iv].get_vshape()[2];
282  // amrex::Print() << "TYPE SN WE " << ns2 << " " << ns3 << std::endl;
283  } else if (NC_dim_type == NC_Data_Dims_Type::Time_BT_SN_WE) {
284  ns1 = nc_arrays[iv].get_vshape()[1];
285  ns2 = nc_arrays[iv].get_vshape()[2];
286  ns3 = nc_arrays[iv].get_vshape()[3];
287  // amrex::Print() << "TYPE BT SN WE " << ns1 << " " << ns2 << " " << ns3 << std::endl;
288  } else {
289  amrex::Abort("Dont know this NC_Data_Dims_Type");
290  }
291 
292  // TODO: The box will only start at (0,0,0) at level 0 -- we need to generalize this
293  amrex::Box my_box(amrex::IntVect(0,0,0), amrex::IntVect(ns3-1,ns2-1,ns1-1));
294 
295  if (var_name == "PH" || var_name == "PHB") {
296  my_box.setType(amrex::IndexType(amrex::IntVect(0,0,1)));
297  }
298  else if (var_name == "U" || var_name == "UU" || var_name == "MAPFAC_U") {
299  my_box.setType(amrex::IndexType(amrex::IntVect(1,0,0)));
300  }
301  else if (var_name == "V" || var_name == "VV" || var_name == "MAPFAC_V") {
302  my_box.setType(amrex::IndexType(amrex::IntVect(0,1,0)));
303  }
304  else if (var_name == "W" || var_name == "WW") {
305  my_box.setType(amrex::IndexType(amrex::IntVect(0,0,1)));
306  }
307 
308  amrex::Arena* Arena_Used = amrex::The_Arena();
309 #ifdef AMREX_USE_GPU
310  // Make sure temp lives on CPU since nc_arrays lives on CPU only
311  Arena_Used = amrex::The_Pinned_Arena();
312 #endif
313  temp.resize(my_box,1, Arena_Used);
314  amrex::Array4<DType> fab_arr = temp.array();
315 
316  int ioff = temp.box().smallEnd()[0];
317  int joff = temp.box().smallEnd()[1];
318 
319  auto num_pts = my_box.numPts();
320 
321  for (int n(0); n < num_pts; ++n) {
322  int k = n / (ns2*ns3);
323  int j = (n - k*(ns2*ns3)) / ns3 + joff;
324  int i = n - k*(ns2*ns3) - (j-joff) * ns3 + ioff;
325  fab_arr(i,j,k,0) = static_cast<DType>(*(nc_arrays[iv].get_data()+n));
326  }
327 }

◆ ReadNetCDFFile()

template<typename DType >
void ReadNetCDFFile ( const std::string &  fname,
amrex::Vector< std::string >  names,
amrex::Vector< NDArray< DType > > &  arrays,
amrex::Vector< int > &  success 
)
181 {
182  AMREX_ASSERT(arrays.size() == names.size());
183 
184  if (amrex::ParallelDescriptor::IOProcessor())
185  {
186  auto ncf = ncutils::NCFile::open(fname, NC_CLOBBER | NC_NETCDF4);
187 
188  /*
189  // get the dimension information
190  int Time = static_cast<int>(ncf.dim("Time").len());
191  int DateStrLen = static_cast<int>(ncf.dim("DateStrLen").len());
192  int west_east = static_cast<int>(ncf.dim("west_east").len());
193  int south_north = static_cast<int>(ncf.dim("south_north").len());
194  int bottom_top = static_cast<int>(ncf.dim("bottom_top").len());
195  int bottom_top_stag = static_cast<int>(ncf.dim("bottom_top_stag").len());
196  int west_east_stag = static_cast<int>(ncf.dim("west_east_stag").len());
197  int south_north_stag = static_cast<int>(ncf.dim("south_north_stag").len());
198  int bdy_width = static_cast<int>(ncf.dim("bdy_width").len());
199  */
200 
201  // amrex::Print() << "Reading the dimensions from the netcdf file " << "\n";
202 
203  for (auto n=0; n<arrays.size(); ++n)
204  {
205  std::string vname_to_write = names[n];
206  std::string vname_to_read = names[n];
207 
208  if (vname_to_read.substr(0,2) == "R_") {
209  vname_to_read = names[n+4]; // This allows us to read "T" instead -- we will over-write this later
210  }
211 
212  /*
213  amrex::AllPrint() << "About to read " << vname_to_read
214  << " while filling the array for " << vname_to_write << std::endl;
215  */
216 
217  success[n] = ncf.has_var(vname_to_read);
218  // amrex::Print() << " HAS VAR " << vname_to_read << " " << success[n] << std::endl;
219 
220  if (success[n] == 1) {
221 
222  std::vector<std::string> dimnames = ncf.var(vname_to_read).dimnames();
223  AMREX_ALWAYS_ASSERT(dimnames[0] == "Time");
224 
225  std::vector<size_t> shape = ncf.var(vname_to_read).shape();
226  arrays[n] = NDArray<DType>(vname_to_read,shape);
227  DType* dataPtr = arrays[n].get_data();
228 
229  std::vector<size_t> start(shape.size(), 0);
230 
231 #if 0
232  auto numPts = arrays[n].ndim();
233  amrex::Print() << "NetCDF Variable name = " << vname_to_read << std::endl;
234  amrex::Print() << "numPts read from NetCDF file/var = " << numPts << std::endl;
235  amrex::Print() << "Dims in var = " << ncf.var(vname_to_read).ndim() << std::endl;
236  amrex::Print() << "Dim names = (";
237  for (auto &dim:dimnames)
238  amrex::Print() << dim << ", " ;
239  amrex::Print() << ")" << std::endl;
240  amrex::Print() << "Dims of the variable = (";
241  for (auto &dim:shape)
242  amrex::Print() << dim << ", " ;
243  amrex::Print() << ")" << std::endl;
244 #endif
245 
246  ncf.var(vname_to_read).get(dataPtr, start, shape);
247 
248  } // has_var
249  }
250  ncf.close();
251  }
252 }
ncutils::NCFile::open
static NCFile open(const std::string &name, const int cmode=NC_NOWRITE)
Definition: ERF_NCInterface.cpp:707
NDArray
Definition: ERF_NCWpsFile.H:51

Referenced by BuildFABsFromNetCDFFile().

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◆ ReadTimeSliceFromNetCDFFile()

template<typename DType >
void ReadTimeSliceFromNetCDFFile ( const std::string &  fname,
const int  tidx,
amrex::Vector< std::string >  names,
amrex::Vector< NDArray< DType > > &  arrays,
amrex::Vector< int > &  success 
)
137 {
138  amrex::Print() << "Reading time slice " << tidx << " from " << fname << std::endl;
139  AMREX_ASSERT(arrays.size() == names.size());
140 
141  if (amrex::ParallelDescriptor::IOProcessor())
142  {
143  auto ncf = ncutils::NCFile::open(fname, NC_CLOBBER | NC_NETCDF4);
144 
145  int ntimes = ncf.dim("Time").len();
146  AMREX_ALWAYS_ASSERT((tidx >= 0) && (tidx < ntimes));
147 
148  for (auto n=0; n<arrays.size(); ++n)
149  {
150  std::string vname_to_write = names[n];
151  std::string vname_to_read = names[n];
152  if (vname_to_read.substr(0,2) == "R_") {
153  vname_to_read = names[n+4]; // This allows us to read "T" instead -- we will over-write this later
154  }
155 
156  success[n] = ncf.has_var(vname_to_read);
157 
158  if (success[n] == 1)
159  {
160  std::vector<std::string> dimnames = ncf.var(vname_to_read).dimnames();
161  AMREX_ALWAYS_ASSERT(dimnames[0] == "Time");
162 
163  std::vector<size_t> count = ncf.var(vname_to_read).shape();
164  std::vector<size_t> start(count.size(), 0);
165  start[0] = tidx;
166  count[0] = 1;
167 
168  arrays[n] = NDArray<DType>(vname_to_read, count);
169  DType* dataPtr = arrays[n].get_data();
170 
171  ncf.var(vname_to_read).get(dataPtr, start, count);
172  } // has_var
173  }
174  ncf.close();
175  }
176 }
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