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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| #include <sstream> | ||
| #include <string> | ||
| #include <ctime> | ||
| #include <atomic> | ||
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| #include "DataStruct.H" | ||
| #include "NCInterface.H" | ||
| #include "NCWpsFile.H" | ||
| #include "AMReX_IArrayBox.H" | ||
| #include "AMReX_IndexType.H" | ||
| #include "AMReX_Print.H" | ||
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| using namespace amrex; | ||
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| using IARRAY = NDArray<int>; | ||
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| void | ||
| fill_iab_from_arrays (int iv, Vector<IARRAY>& nc_arrays, | ||
| const std::string& var_name, | ||
| NC_Data_Dims_Type& NC_dim_type, | ||
| IArrayBox& temp); | ||
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| /** | ||
| * Function to read NetCDF variables and fill the corresponding Array4's | ||
| * | ||
| * @param fname Name of the NetCDF file to be read | ||
| * @param nc_var_names Variable names in the NetCDF file | ||
| * @param NC_dim_types NetCDF data dimension types | ||
| * @param fab_vars Fab data we are to fill | ||
| */ | ||
| void | ||
| BuildIABsFromNetCDFFile (const Box& domain, | ||
| const std::string &fname, | ||
| Vector<std::string> nc_var_names, | ||
| Vector<enum NC_Data_Dims_Type> NC_dim_types, | ||
| Vector<amrex::IArrayBox*> fab_vars) | ||
| { | ||
| int ioproc = ParallelDescriptor::IOProcessorNumber(); // I/O rank | ||
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| amrex::Vector<IARRAY> nc_arrays(nc_var_names.size()); | ||
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| if (amrex::ParallelDescriptor::IOProcessor()) | ||
| { | ||
| ReadNetCDFFile(fname, nc_var_names, nc_arrays); | ||
| } | ||
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| for (int iv = 0; iv < nc_var_names.size(); iv++) | ||
| { | ||
| amrex::IArrayBox tmp; | ||
| if (amrex::ParallelDescriptor::IOProcessor()) { | ||
| fill_iab_from_arrays(iv, nc_arrays, nc_var_names[iv], NC_dim_types[iv], tmp); | ||
| } | ||
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| Box box = tmp.box(); | ||
| int ncomp = tmp.nComp(); | ||
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| ParallelDescriptor::Bcast(&box, 1, ioproc); | ||
| ParallelDescriptor::Bcast(&ncomp, 1, ioproc); | ||
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| if (!amrex::ParallelDescriptor::IOProcessor()) { | ||
| #ifdef AMREX_USE_GPU | ||
| tmp.resize(box,ncomp, The_Pinned_Arena()); | ||
| #else | ||
| tmp.resize(box,ncomp); | ||
| #endif | ||
| } | ||
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| ParallelDescriptor::Bcast(tmp.dataPtr(), tmp.size(), ioproc); | ||
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| // Shift box by the domain lower corner | ||
| Box fab_bx = tmp.box(); | ||
| Dim3 dom_lb = lbound(domain); | ||
| fab_bx += IntVect(dom_lb.x,dom_lb.y,dom_lb.z); | ||
| // fab_vars points to data on device | ||
| fab_vars[iv]->resize(fab_bx,1); | ||
| #ifdef AMREX_USE_GPU | ||
| Gpu::copy(Gpu::hostToDevice, tmp.dataPtr(), tmp.dataPtr() + tmp.size(), fab_vars[iv]->dataPtr()); | ||
| #else | ||
| // Provided by BaseFab inheritance through FArrayBox | ||
| fab_vars[iv]->copy(tmp,tmp.box(),0,fab_bx,0,1); | ||
| #endif | ||
| } | ||
| } | ||
|
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| /** | ||
| * Helper function for reading data from NetCDF file into a | ||
| * provided IAB. | ||
| * | ||
| * @param iv Index for which variable we are going to fill | ||
| * @param nc_arrays Arrays of data from NetCDF file | ||
| * @param var_name Variable name | ||
| * @param NC_dim_type Dimension type for the variable as stored in the NetCDF file | ||
| * @param temp FAB where we store the variable data from the NetCDF Arrays | ||
| */ | ||
| void | ||
| fill_iab_from_arrays (int iv, | ||
| Vector<IARRAY>& nc_arrays, | ||
| const std::string& var_name, | ||
| NC_Data_Dims_Type& NC_dim_type, | ||
| IArrayBox& temp) | ||
| { | ||
| int ns1, ns2, ns3; | ||
| if (NC_dim_type == NC_Data_Dims_Type::Time_BT) { | ||
| ns1 = nc_arrays[iv].get_vshape()[1]; | ||
| ns2 = 1; | ||
| ns3 = 1; | ||
| // amrex::Print() << "TYPE BT " << ns1 << std::endl; | ||
| } else if (NC_dim_type == NC_Data_Dims_Type::Time_SN_WE) { | ||
| ns1 = 1; | ||
| ns2 = nc_arrays[iv].get_vshape()[1]; | ||
| ns3 = nc_arrays[iv].get_vshape()[2]; | ||
| // amrex::Print() << "TYPE SN WE " << ns2 << " " << ns3 << std::endl; | ||
| } else if (NC_dim_type == NC_Data_Dims_Type::Time_BT_SN_WE) { | ||
| ns1 = nc_arrays[iv].get_vshape()[1]; | ||
| ns2 = nc_arrays[iv].get_vshape()[2]; | ||
| ns3 = nc_arrays[iv].get_vshape()[3]; | ||
| // amrex::Print() << "TYPE BT SN WE " << ns1 << " " << ns2 << " " << ns3 << std::endl; | ||
| } else { | ||
| amrex::Abort("Dont know this NC_Data_Dims_Type"); | ||
| } | ||
|
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| // TODO: The box will only start at (0,0,0) at level 0 -- we need to generalize this | ||
| Box my_box(IntVect(0,0,0), IntVect(ns3-1,ns2-1,ns1-1)); | ||
| // amrex::Print() <<" MY BOX " << my_box << std::endl; | ||
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| if (var_name == "U" || var_name == "UU" || | ||
| var_name == "MAPFAC_U" || var_name == "MAPFAC_UY") my_box.setType(amrex::IndexType(IntVect(1,0,0))); | ||
| if (var_name == "V" || var_name == "VV" || | ||
| var_name == "MAPFAC_V" || var_name == "MAPFAC_VY") my_box.setType(amrex::IndexType(IntVect(0,1,0))); | ||
| if (var_name == "W" || var_name == "WW") my_box.setType(amrex::IndexType(IntVect(0,0,1))); | ||
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| #ifdef AMREX_USE_GPU | ||
| // Make sure temp lives on CPU since nc_arrays lives on CPU only | ||
| temp.resize(my_box,1,The_Pinned_Arena()); | ||
| #else | ||
| temp.resize(my_box,1); | ||
| #endif | ||
| Array4<int> iab_arr = temp.array(); | ||
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| int ioff = temp.box().smallEnd()[0]; | ||
| int joff = temp.box().smallEnd()[1]; | ||
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| auto num_pts = my_box.numPts(); | ||
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| // amrex::Print() <<" ns1 * ns2 * ns3 " << ns1 * ns2 * ns3 << std::endl; | ||
| // amrex::Print() <<" NUMPTS " << num_pts << std::endl; | ||
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| for (int n(0); n < num_pts; ++n) { | ||
| int k = n / (ns2*ns3); | ||
| int j = (n - k*(ns2*ns3)) / ns3 + joff; | ||
| int i = n - k*(ns2*ns3) - (j-joff) * ns3 + ioff; | ||
| iab_arr(i,j,k,0) = static_cast<int>(*(nc_arrays[iv].get_data()+n)); | ||
| } | ||
| } |
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