Fixing compile errors on Titan
This commit is contained in:
Mark Berrill
parent
90ffb5b9d0
commit
15d48e03c7
415
IO/silo.cpp
415
IO/silo.cpp
@ -14,41 +14,6 @@
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namespace silo {
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namespace silo {
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/****************************************************
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* Helper functions *
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****************************************************/
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template<class TYPE> static constexpr int getType();
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template<> constexpr int getType<double>() { return DB_DOUBLE; }
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template<> constexpr int getType<float>() { return DB_FLOAT; }
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template<> constexpr int getType<int>() { return DB_INT; }
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VariableDataType varDataType( DBfile *fid, const std::string& name )
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{
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auto type = DBGetVarType( fid, name.c_str() );
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VariableDataType type2 = VariableDataType::UNKNOWN;
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if ( type == DB_DOUBLE )
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type2 = VariableDataType::DOUBLE;
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else if ( type == DB_FLOAT )
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type2 = VariableDataType::FLOAT;
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else if ( type == DB_INT )
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type2 = VariableDataType::INT;
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return type2;
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}
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template<class TYPE>
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static inline void copyData( Array<TYPE>& data, int type, const void *src )
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{
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if ( type == getType<TYPE>() )
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memcpy( data.data(), src, data.length()*sizeof(TYPE) );
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else if ( type == DB_DOUBLE )
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data.copy<double>( static_cast<const double*>(src) );
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else if ( type == DB_FLOAT )
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data.copy<float>( static_cast<const float*>(src) );
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else if ( type == DB_INT )
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data.copy<int>( static_cast<const int*>(src) );
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else
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ERROR("Unknown type");
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}
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/****************************************************
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/****************************************************
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* Open/close a file *
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* Open/close a file *
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****************************************************/
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****************************************************/
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@ -71,113 +36,25 @@ void close( DBfile* fid )
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/****************************************************
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/****************************************************
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* Write/read an arbitrary vector *
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* Helper functions *
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****************************************************/
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****************************************************/
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template<class TYPE> int getSiloType();
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VariableDataType varDataType( DBfile *fid, const std::string& name )
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template<> int getSiloType<int>() { return DB_INT; }
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template<> int getSiloType<float>() { return DB_FLOAT; }
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template<> int getSiloType<double>() { return DB_DOUBLE; }
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template<class TYPE>
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void write( DBfile* fid, const std::string& varname, const std::vector<TYPE>& data )
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{
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{
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int dims = data.size();
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auto type = DBGetVarType( fid, name.c_str() );
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int err = DBWrite( fid, varname.c_str(), (void*) data.data(), &dims, 1, getSiloType<TYPE>() );
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VariableDataType type2 = VariableDataType::UNKNOWN;
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ASSERT( err == 0 );
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if ( type == DB_DOUBLE )
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}
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type2 = VariableDataType::DOUBLE;
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template<class TYPE>
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else if ( type == DB_FLOAT )
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std::vector<TYPE> read( DBfile* fid, const std::string& varname )
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type2 = VariableDataType::FLOAT;
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{
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else if ( type == DB_INT )
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int N = DBGetVarLength( fid, varname.c_str() );
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type2 = VariableDataType::INT;
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std::vector<TYPE> data(N);
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return type2;
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int err = DBReadVar( fid, varname.c_str(), data.data() );
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ASSERT( err == 0 );
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return data;
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}
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/****************************************************
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* Helper function to get variable suffixes *
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****************************************************/
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static std::vector<std::string> getVarSuffix( int ndim, int nvars )
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{
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std::vector<std::string> suffix(nvars);
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if ( nvars == 1 ) {
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suffix[0] = "";
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} else if ( nvars == ndim ) {
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if ( ndim==2 ) {
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suffix[0] = "_x";
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suffix[1] = "_y";
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} else if ( ndim==3 ) {
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suffix[0] = "_x";
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suffix[1] = "_y";
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suffix[2] = "_z";
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} else {
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ERROR("Not finished");
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}
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} else if ( nvars == ndim*ndim ) {
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if ( ndim==2 ) {
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suffix[0] = "_xx";
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suffix[1] = "_xy";
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suffix[2] = "_yx";
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suffix[3] = "_yy";
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} else if ( ndim==3 ) {
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suffix[0] = "_xx";
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suffix[1] = "_xy";
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suffix[2] = "_xz";
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suffix[3] = "_yx";
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suffix[4] = "_yy";
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suffix[5] = "_yz";
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suffix[6] = "_zx";
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suffix[7] = "_zy";
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suffix[8] = "_zz";
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} else {
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ERROR("Not finished");
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}
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} else {
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for (int i=0; i<nvars; i++)
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suffix[i] = "_" + std::to_string(i+1);
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}
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return suffix;
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}
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}
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/****************************************************
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/****************************************************
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* Write/read a uniform mesh to silo *
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* Write/read a uniform mesh to silo *
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****************************************************/
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****************************************************/
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template<int NDIM>
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void writeUniformMesh( DBfile* fid, const std::string& meshname,
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const std::array<double,2*NDIM>& range, const std::array<int,NDIM>& N )
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{
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PROFILE_START("writeUniformMesh",2);
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int dims[NDIM];
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for (size_t d=0; d<N.size(); d++)
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dims[d] = N[d]+1;
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float *x = nullptr;
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if ( NDIM >= 1 ) {
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x = new float[dims[0]];
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for (int i=0; i<N[0]; i++)
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x[i] = range[0] + i*(range[1]-range[0])/N[0];
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x[N[0]] = range[1];
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}
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float *y = nullptr;
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if ( NDIM >= 2 ) {
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y = new float[dims[1]];
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for (int i=0; i<N[1]; i++)
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y[i] = range[2] + i*(range[3]-range[2])/N[1];
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y[N[1]] = range[3];
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}
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float *z = nullptr;
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if ( NDIM >= 3 ) {
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z = new float[dims[2]];
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for (int i=0; i<N[2]; i++)
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z[i] = range[4] + i*(range[5]-range[4])/N[2];
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z[N[2]] = range[5];
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}
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float *coords[] = { x, y, z };
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int err = DBPutQuadmesh( fid, meshname.c_str(), nullptr, coords, dims, NDIM, DB_FLOAT, DB_COLLINEAR, nullptr );
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ASSERT( err == 0 );
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PROFILE_STOP("writeUniformMesh",2);
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}
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void readUniformMesh( DBfile* fid, const std::string& meshname,
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void readUniformMesh( DBfile* fid, const std::string& meshname,
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std::vector<double>& range, std::vector<int>& N )
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std::vector<double>& range, std::vector<int>& N )
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{
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{
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@ -194,240 +71,6 @@ void readUniformMesh( DBfile* fid, const std::string& meshname,
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}
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}
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/****************************************************
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* Write a vector/tensor quad variable *
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****************************************************/
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template<int NDIM,class TYPE>
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void writeUniformMeshVariable( DBfile* fid, const std::string& meshname, const std::array<int,NDIM>& N,
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const std::string& varname, const Array<TYPE>& data, VariableType type )
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{
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PROFILE_START("writeUniformMeshVariable",2);
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int nvars=1, dims[NDIM]={1};
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const TYPE *vars[NDIM] = { nullptr };
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int vartype = 0;
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if ( type == VariableType::NodeVariable ) {
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ASSERT( data.ndim()==NDIM || data.ndim()==NDIM+1 );
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for (int d=0; d<NDIM; d++)
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ASSERT(N[d]+1==(int)data.size(d));
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vartype = DB_NODECENT;
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nvars = data.size(NDIM);
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size_t N = data.length()/nvars;
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for (int d=0; d<NDIM; d++)
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dims[d] = data.size(d);
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for (int i=0; i<nvars; i++)
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vars[i] = &data(i*N);
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} else if ( type == VariableType::EdgeVariable ) {
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ERROR("Not finished");
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} else if ( type == VariableType::SurfaceVariable ) {
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ERROR("Not finished");
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} else if ( type == VariableType::VolumeVariable ) {
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ASSERT( data.ndim()==NDIM || data.ndim()==NDIM+1 );
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for (int d=0; d<NDIM; d++)
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ASSERT(N[d]==(int)data.size(d));
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vartype = DB_ZONECENT;
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nvars = data.size(NDIM);
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size_t N = data.length()/nvars;
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for (int d=0; d<NDIM; d++)
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dims[d] = data.size(d);
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for (int i=0; i<nvars; i++)
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vars[i] = &data(i*N);
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} else {
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ERROR("Invalid variable type");
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}
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auto suffix = getVarSuffix( NDIM, nvars );
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std::vector<std::string> var_names(nvars);
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for (int i=0; i<nvars; i++)
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var_names[i] = varname + suffix[i];
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std::vector<char*> varnames(nvars,nullptr);
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for (int i=0; i<nvars; i++)
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varnames[i] = const_cast<char*>(var_names[i].c_str());
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int err = DBPutQuadvar( fid, varname.c_str(), meshname.c_str(), nvars,
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varnames.data(), vars, dims, NDIM, nullptr, 0, getType<TYPE>(), vartype, nullptr );
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ASSERT( err == 0 );
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PROFILE_STOP("writeUniformMeshVariable",2);
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}
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template<class TYPE>
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Array<TYPE> readUniformMeshVariable( DBfile* fid, const std::string& varname )
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{
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auto var = DBGetQuadvar( fid, varname.c_str() );
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ASSERT( var != nullptr );
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Array<TYPE> data( var->nels, var->nvals );
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int type = var->datatype;
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for (int i=0; i<var->nvals; i++) {
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Array<TYPE> data2( var->nels );
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copyData<TYPE>( data2, type, var->vals[i] );
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memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
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}
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DBFreeQuadvar( var );
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std::vector<size_t> dims( var->ndims+1, var->nvals );
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for (int d=0; d<var->ndims; d++)
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dims[d] = var->dims[d];
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data.reshape( dims );
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return data;
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}
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/****************************************************
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* Read/write a point mesh/variable to silo *
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****************************************************/
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template<class TYPE>
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void writePointMesh( DBfile* fid, const std::string& meshname,
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int ndim, int N, const TYPE *coords[] )
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{
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int err = DBPutPointmesh( fid, meshname.c_str(), ndim, coords, N, getType<TYPE>(), nullptr );
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ASSERT( err == 0 );
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}
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template<class TYPE>
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Array<TYPE> readPointMesh( DBfile* fid, const std::string& meshname )
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{
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auto mesh = DBGetPointmesh( fid, meshname.c_str() );
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int N = mesh->nels;
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int ndim = mesh->ndims;
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Array<TYPE> coords(N,ndim);
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int type = mesh->datatype;
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for (int d=0; d<ndim; d++) {
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Array<TYPE> data2( N );
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copyData<TYPE>( data2, type, mesh->coords[d] );
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memcpy( &coords(0,d), data2.data(), N*sizeof(TYPE) );
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}
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DBFreePointmesh( mesh );
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return coords;
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}
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template<class TYPE>
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void writePointMeshVariable( DBfile* fid, const std::string& meshname,
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const std::string& varname, const Array<TYPE>& data )
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{
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int N = data.size(0);
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int nvars = data.size(1);
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std::vector<const TYPE*> vars(nvars);
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for (int i=0; i<nvars; i++)
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vars[i] = &data(0,i);
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int err = DBPutPointvar( fid, varname.c_str(), meshname.c_str(), nvars, vars.data(), N, getType<TYPE>(), nullptr );
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ASSERT( err == 0 );
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}
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template<class TYPE>
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Array<TYPE> readPointMeshVariable( DBfile* fid, const std::string& varname )
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{
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auto var = DBGetPointvar( fid, varname.c_str() );
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ASSERT( var != nullptr );
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Array<TYPE> data( var->nels, var->nvals );
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int type = var->datatype;
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for (int i=0; i<var->nvals; i++) {
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Array<TYPE> data2( var->nels );
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copyData<TYPE>( data2, type, var->vals[i] );
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memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
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}
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DBFreeMeshvar( var );
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return data;
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}
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/****************************************************
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* Read/write a triangle mesh *
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****************************************************/
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template<class TYPE>
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void writeTriMesh( DBfile* fid, const std::string& meshName,
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int ndim, int ndim_tri, int N, const TYPE *coords[], int N_tri, const int *tri[] )
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{
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auto zoneName = meshName + "_zones";
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std::vector<int> nodelist( (ndim_tri+1)*N_tri );
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for (int i=0, j=0; i<N_tri; i++) {
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for (int d=0; d<ndim_tri+1; d++, j++)
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nodelist[j] = tri[d][i];
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}
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int shapetype = 0;
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if ( ndim_tri==1 )
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shapetype = DB_ZONETYPE_BEAM;
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else if ( ndim_tri==2 )
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shapetype = DB_ZONETYPE_TRIANGLE;
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else if ( ndim_tri==3 )
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shapetype = DB_ZONETYPE_PYRAMID;
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else
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ERROR("Unknown shapetype");
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int shapesize = ndim_tri+1;
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int shapecnt = N_tri;
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DBPutZonelist2( fid, zoneName.c_str(), N_tri, ndim_tri, nodelist.data(),
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nodelist.size(), 0, 0, 0, &shapetype, &shapesize, &shapecnt, 1, nullptr );
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DBPutUcdmesh( fid, meshName.c_str(), ndim, nullptr, coords, N,
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nodelist.size(), zoneName.c_str(), nullptr, getType<TYPE>(), nullptr );
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}
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template<class TYPE>
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void readTriMesh( DBfile* fid, const std::string& meshname, Array<TYPE>& coords, Array<int>& tri )
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{
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auto mesh = DBGetUcdmesh( fid, meshname.c_str() );
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int ndim = mesh->ndims;
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int N_nodes = mesh->nnodes;
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coords.resize(N_nodes,ndim);
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int mesh_type = mesh->datatype;
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for (int d=0; d<ndim; d++) {
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Array<TYPE> data2( N_nodes );
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copyData<TYPE>( data2, mesh_type, mesh->coords[d] );
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memcpy( &coords(0,d), data2.data(), N_nodes*sizeof(TYPE) );
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}
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auto zones = mesh->zones;
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int N_zones = zones->nzones;
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int ndim_zones = zones->ndims;
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ASSERT( zones->nshapes==1 );
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int shape_type = zones->shapetype[0];
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int shapesize = zones->shapesize[0];
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tri.resize(N_zones,shapesize);
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|
||||||
for (int i=0; i<N_zones; i++) {
|
|
||||||
for (int j=0; j<shapesize; j++)
|
|
||||||
tri(i,j) = zones->nodelist[i*shapesize+j];
|
|
||||||
}
|
|
||||||
DBFreeUcdmesh( mesh );
|
|
||||||
}
|
|
||||||
template<class TYPE>
|
|
||||||
void writeTriMeshVariable( DBfile* fid, int ndim, const std::string& meshname,
|
|
||||||
const std::string& varname, const Array<TYPE>& data, VariableType type )
|
|
||||||
{
|
|
||||||
int nvars = 0;
|
|
||||||
int vartype = 0;
|
|
||||||
const TYPE *vars[10] = { nullptr };
|
|
||||||
if ( type == VariableType::NodeVariable ) {
|
|
||||||
vartype = DB_NODECENT;
|
|
||||||
nvars = data.size(1);
|
|
||||||
for (int i=0; i<nvars; i++)
|
|
||||||
vars[i] = &data(0,i);
|
|
||||||
} else if ( type == VariableType::EdgeVariable ) {
|
|
||||||
ERROR("Not finished");
|
|
||||||
} else if ( type == VariableType::SurfaceVariable ) {
|
|
||||||
ERROR("Not finished");
|
|
||||||
} else if ( type == VariableType::VolumeVariable ) {
|
|
||||||
vartype = DB_ZONECENT;
|
|
||||||
nvars = data.size(1);
|
|
||||||
for (int i=0; i<nvars; i++)
|
|
||||||
vars[i] = &data(0,i);
|
|
||||||
} else {
|
|
||||||
ERROR("Invalid variable type");
|
|
||||||
}
|
|
||||||
auto suffix = getVarSuffix( ndim, nvars );
|
|
||||||
std::vector<std::string> var_names(nvars);
|
|
||||||
for (int i=0; i<nvars; i++)
|
|
||||||
var_names[i] = varname + suffix[i];
|
|
||||||
std::vector<char*> varnames(nvars,nullptr);
|
|
||||||
for (int i=0; i<nvars; i++)
|
|
||||||
varnames[i] = const_cast<char*>(var_names[i].c_str());
|
|
||||||
DBPutUcdvar( fid, varname.c_str(), meshname.c_str(), nvars,
|
|
||||||
varnames.data(), vars, data.size(0), nullptr, 0, getType<TYPE>(), vartype, nullptr );
|
|
||||||
}
|
|
||||||
template<class TYPE>
|
|
||||||
Array<TYPE> readTriMeshVariable( DBfile* fid, const std::string& varname )
|
|
||||||
{
|
|
||||||
auto var = DBGetUcdvar( fid, varname.c_str() );
|
|
||||||
ASSERT( var != nullptr );
|
|
||||||
Array<TYPE> data( var->nels, var->nvals );
|
|
||||||
int type = var->datatype;
|
|
||||||
for (int i=0; i<var->nvals; i++) {
|
|
||||||
Array<TYPE> data2( var->nels );
|
|
||||||
copyData<TYPE>( data2, type, var->vals[i] );
|
|
||||||
memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
|
|
||||||
}
|
|
||||||
DBFreeUcdvar( var );
|
|
||||||
return data;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/****************************************************
|
/****************************************************
|
||||||
* Write a multimesh *
|
* Write a multimesh *
|
||||||
****************************************************/
|
****************************************************/
|
||||||
@ -460,44 +103,10 @@ void writeMultiVar( DBfile* fid, const std::string& varname,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}; // silo namespace
|
}; // silo namespace
|
||||||
|
|
||||||
|
|
||||||
// Explicit instantiations
|
|
||||||
template std::vector<int> silo::read<int>( DBfile* fid, const std::string& varname );
|
|
||||||
template std::vector<float> silo::read<float>( DBfile* fid, const std::string& varname );
|
|
||||||
template std::vector<double> silo::read<double>( DBfile* fid, const std::string& varname );
|
|
||||||
template void silo::writeUniformMesh<1>( DBfile*, const std::string&, const std::array<double,2>&, const std::array<int,1>& );
|
|
||||||
template void silo::writeUniformMesh<2>( DBfile*, const std::string&, const std::array<double,4>&, const std::array<int,2>& );
|
|
||||||
template void silo::writeUniformMesh<3>( DBfile*, const std::string&, const std::array<double,6>&, const std::array<int,3>& );
|
|
||||||
|
|
||||||
namespace {
|
|
||||||
template<class TYPE>
|
|
||||||
static void siloClassInstantiator() {
|
|
||||||
// use **all** functions here so that they get instantiated
|
|
||||||
const auto type = silo::VariableType::NullVariable;
|
|
||||||
Array<TYPE> tmp;
|
|
||||||
Array<int> tri;
|
|
||||||
silo::write<TYPE>( nullptr, "", std::vector<TYPE>() );
|
|
||||||
silo::read<TYPE>( nullptr, "" );
|
|
||||||
silo::writeUniformMeshVariable<1,TYPE>( nullptr, "", std::array<int,1>(), "", Array<TYPE>(), type );
|
|
||||||
silo::writeUniformMeshVariable<2,TYPE>( nullptr, "", std::array<int,2>(), "", Array<TYPE>(), type );
|
|
||||||
silo::writeUniformMeshVariable<3,TYPE>( nullptr, "", std::array<int,3>(), "", Array<TYPE>(), type );
|
|
||||||
silo::writePointMesh( nullptr, "", 0, 0, (const TYPE**) nullptr );
|
|
||||||
silo::writePointMeshVariable<TYPE>( nullptr, "", "", Array<TYPE>() );
|
|
||||||
silo::writeTriMesh<TYPE>( nullptr, "", 0, 0, 0, (const TYPE**) nullptr, 0, (const int**) nullptr );
|
|
||||||
silo::writeTriMeshVariable<TYPE>( nullptr, 0, "", "", Array<TYPE>(), type );
|
|
||||||
silo::readUniformMeshVariable<TYPE>( nullptr, "" );
|
|
||||||
silo::readPointMesh<TYPE>( nullptr, "" );
|
|
||||||
silo::readPointMeshVariable<TYPE>( nullptr, "" );
|
|
||||||
silo::readTriMesh<TYPE>( nullptr, "", tmp, tri );
|
|
||||||
silo::readTriMeshVariable<TYPE>( nullptr, "" );
|
|
||||||
};
|
|
||||||
template void siloClassInstantiator<double>();
|
|
||||||
template void siloClassInstantiator<float>();
|
|
||||||
template void siloClassInstantiator<int>();
|
|
||||||
}
|
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -1,5 +1,5 @@
|
|||||||
#ifndef NETCDF_READER
|
#ifndef SILO_INTERFACE
|
||||||
#define NETCDF_READER
|
#define SILO_INTERFACE
|
||||||
|
|
||||||
#include <string>
|
#include <string>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
@ -259,5 +259,9 @@ void writeMultiVar( DBfile* fid, const std::string& varname,
|
|||||||
const std::vector<std::string>& subVarNames,
|
const std::vector<std::string>& subVarNames,
|
||||||
const std::vector<int>& subVarTypes );
|
const std::vector<int>& subVarTypes );
|
||||||
|
|
||||||
|
|
||||||
}; // silo namespace
|
}; // silo namespace
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
#include "IO/silo.hpp"
|
||||||
|
|
||||||
|
|||||||
392
IO/silo.hpp
Normal file
392
IO/silo.hpp
Normal file
@ -0,0 +1,392 @@
|
|||||||
|
#ifndef SILO_INTERFACE_HPP
|
||||||
|
#define SILO_INTERFACE_HPP
|
||||||
|
|
||||||
|
#include "IO/silo.h"
|
||||||
|
#include "common/Utilities.h"
|
||||||
|
#include "common/MPI_Helpers.h"
|
||||||
|
|
||||||
|
#include "ProfilerApp.h"
|
||||||
|
|
||||||
|
|
||||||
|
#ifdef USE_SILO
|
||||||
|
|
||||||
|
#include <silo.h>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
namespace silo {
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Helper functions *
|
||||||
|
****************************************************/
|
||||||
|
template<class TYPE> static constexpr int getType();
|
||||||
|
template<> constexpr int getType<double>() { return DB_DOUBLE; }
|
||||||
|
template<> constexpr int getType<float>() { return DB_FLOAT; }
|
||||||
|
template<> constexpr int getType<int>() { return DB_INT; }
|
||||||
|
template<class TYPE>
|
||||||
|
inline void copyData( Array<TYPE>& data, int type, const void *src )
|
||||||
|
{
|
||||||
|
if ( type == getType<TYPE>() )
|
||||||
|
memcpy( data.data(), src, data.length()*sizeof(TYPE) );
|
||||||
|
else if ( type == DB_DOUBLE )
|
||||||
|
data.copy<double>( static_cast<const double*>(src) );
|
||||||
|
else if ( type == DB_FLOAT )
|
||||||
|
data.copy<float>( static_cast<const float*>(src) );
|
||||||
|
else if ( type == DB_INT )
|
||||||
|
data.copy<int>( static_cast<const int*>(src) );
|
||||||
|
else
|
||||||
|
ERROR("Unknown type");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Write/read an arbitrary vector *
|
||||||
|
****************************************************/
|
||||||
|
template<class TYPE> constexpr int getSiloType();
|
||||||
|
template<> constexpr int getSiloType<int>() { return DB_INT; }
|
||||||
|
template<> constexpr int getSiloType<float>() { return DB_FLOAT; }
|
||||||
|
template<> constexpr int getSiloType<double>() { return DB_DOUBLE; }
|
||||||
|
template<class TYPE>
|
||||||
|
void write( DBfile* fid, const std::string& varname, const std::vector<TYPE>& data )
|
||||||
|
{
|
||||||
|
int dims = data.size();
|
||||||
|
int err = DBWrite( fid, varname.c_str(), (void*) data.data(), &dims, 1, getSiloType<TYPE>() );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
std::vector<TYPE> read( DBfile* fid, const std::string& varname )
|
||||||
|
{
|
||||||
|
int N = DBGetVarLength( fid, varname.c_str() );
|
||||||
|
std::vector<TYPE> data(N);
|
||||||
|
int err = DBReadVar( fid, varname.c_str(), data.data() );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
return data;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Helper function to get variable suffixes *
|
||||||
|
****************************************************/
|
||||||
|
inline std::vector<std::string> getVarSuffix( int ndim, int nvars )
|
||||||
|
{
|
||||||
|
std::vector<std::string> suffix(nvars);
|
||||||
|
if ( nvars == 1 ) {
|
||||||
|
suffix[0] = "";
|
||||||
|
} else if ( nvars == ndim ) {
|
||||||
|
if ( ndim==2 ) {
|
||||||
|
suffix[0] = "_x";
|
||||||
|
suffix[1] = "_y";
|
||||||
|
} else if ( ndim==3 ) {
|
||||||
|
suffix[0] = "_x";
|
||||||
|
suffix[1] = "_y";
|
||||||
|
suffix[2] = "_z";
|
||||||
|
} else {
|
||||||
|
ERROR("Not finished");
|
||||||
|
}
|
||||||
|
} else if ( nvars == ndim*ndim ) {
|
||||||
|
if ( ndim==2 ) {
|
||||||
|
suffix[0] = "_xx";
|
||||||
|
suffix[1] = "_xy";
|
||||||
|
suffix[2] = "_yx";
|
||||||
|
suffix[3] = "_yy";
|
||||||
|
} else if ( ndim==3 ) {
|
||||||
|
suffix[0] = "_xx";
|
||||||
|
suffix[1] = "_xy";
|
||||||
|
suffix[2] = "_xz";
|
||||||
|
suffix[3] = "_yx";
|
||||||
|
suffix[4] = "_yy";
|
||||||
|
suffix[5] = "_yz";
|
||||||
|
suffix[6] = "_zx";
|
||||||
|
suffix[7] = "_zy";
|
||||||
|
suffix[8] = "_zz";
|
||||||
|
} else {
|
||||||
|
ERROR("Not finished");
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
suffix[i] = "_" + std::to_string(i+1);
|
||||||
|
}
|
||||||
|
return suffix;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Write/read a uniform mesh to silo *
|
||||||
|
****************************************************/
|
||||||
|
template<int NDIM>
|
||||||
|
void writeUniformMesh( DBfile* fid, const std::string& meshname,
|
||||||
|
const std::array<double,2*NDIM>& range, const std::array<int,NDIM>& N )
|
||||||
|
{
|
||||||
|
PROFILE_START("writeUniformMesh",2);
|
||||||
|
int dims[NDIM];
|
||||||
|
for (size_t d=0; d<N.size(); d++)
|
||||||
|
dims[d] = N[d]+1;
|
||||||
|
float *x = nullptr;
|
||||||
|
if ( NDIM >= 1 ) {
|
||||||
|
x = new float[dims[0]];
|
||||||
|
for (int i=0; i<N[0]; i++)
|
||||||
|
x[i] = range[0] + i*(range[1]-range[0])/N[0];
|
||||||
|
x[N[0]] = range[1];
|
||||||
|
}
|
||||||
|
float *y = nullptr;
|
||||||
|
if ( NDIM >= 2 ) {
|
||||||
|
y = new float[dims[1]];
|
||||||
|
for (int i=0; i<N[1]; i++)
|
||||||
|
y[i] = range[2] + i*(range[3]-range[2])/N[1];
|
||||||
|
y[N[1]] = range[3];
|
||||||
|
}
|
||||||
|
float *z = nullptr;
|
||||||
|
if ( NDIM >= 3 ) {
|
||||||
|
z = new float[dims[2]];
|
||||||
|
for (int i=0; i<N[2]; i++)
|
||||||
|
z[i] = range[4] + i*(range[5]-range[4])/N[2];
|
||||||
|
z[N[2]] = range[5];
|
||||||
|
}
|
||||||
|
float *coords[] = { x, y, z };
|
||||||
|
int err = DBPutQuadmesh( fid, meshname.c_str(), nullptr, coords, dims, NDIM, DB_FLOAT, DB_COLLINEAR, nullptr );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
PROFILE_STOP("writeUniformMesh",2);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Write a vector/tensor quad variable *
|
||||||
|
****************************************************/
|
||||||
|
template<int NDIM,class TYPE>
|
||||||
|
void writeUniformMeshVariable( DBfile* fid, const std::string& meshname, const std::array<int,NDIM>& N,
|
||||||
|
const std::string& varname, const Array<TYPE>& data, VariableType type )
|
||||||
|
{
|
||||||
|
PROFILE_START("writeUniformMeshVariable",2);
|
||||||
|
int nvars=1, dims[NDIM]={1};
|
||||||
|
const TYPE *vars[NDIM] = { nullptr };
|
||||||
|
int vartype = 0;
|
||||||
|
if ( type == VariableType::NodeVariable ) {
|
||||||
|
ASSERT( data.ndim()==NDIM || data.ndim()==NDIM+1 );
|
||||||
|
for (int d=0; d<NDIM; d++)
|
||||||
|
ASSERT(N[d]+1==(int)data.size(d));
|
||||||
|
vartype = DB_NODECENT;
|
||||||
|
nvars = data.size(NDIM);
|
||||||
|
size_t N = data.length()/nvars;
|
||||||
|
for (int d=0; d<NDIM; d++)
|
||||||
|
dims[d] = data.size(d);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
vars[i] = &data(i*N);
|
||||||
|
} else if ( type == VariableType::EdgeVariable ) {
|
||||||
|
ERROR("Not finished");
|
||||||
|
} else if ( type == VariableType::SurfaceVariable ) {
|
||||||
|
ERROR("Not finished");
|
||||||
|
} else if ( type == VariableType::VolumeVariable ) {
|
||||||
|
ASSERT( data.ndim()==NDIM || data.ndim()==NDIM+1 );
|
||||||
|
for (int d=0; d<NDIM; d++)
|
||||||
|
ASSERT(N[d]==(int)data.size(d));
|
||||||
|
vartype = DB_ZONECENT;
|
||||||
|
nvars = data.size(NDIM);
|
||||||
|
size_t N = data.length()/nvars;
|
||||||
|
for (int d=0; d<NDIM; d++)
|
||||||
|
dims[d] = data.size(d);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
vars[i] = &data(i*N);
|
||||||
|
} else {
|
||||||
|
ERROR("Invalid variable type");
|
||||||
|
}
|
||||||
|
auto suffix = getVarSuffix( NDIM, nvars );
|
||||||
|
std::vector<std::string> var_names(nvars);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
var_names[i] = varname + suffix[i];
|
||||||
|
std::vector<char*> varnames(nvars,nullptr);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
varnames[i] = const_cast<char*>(var_names[i].c_str());
|
||||||
|
int err = DBPutQuadvar( fid, varname.c_str(), meshname.c_str(), nvars,
|
||||||
|
varnames.data(), vars, dims, NDIM, nullptr, 0, getType<TYPE>(), vartype, nullptr );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
PROFILE_STOP("writeUniformMeshVariable",2);
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
Array<TYPE> readUniformMeshVariable( DBfile* fid, const std::string& varname )
|
||||||
|
{
|
||||||
|
auto var = DBGetQuadvar( fid, varname.c_str() );
|
||||||
|
ASSERT( var != nullptr );
|
||||||
|
Array<TYPE> data( var->nels, var->nvals );
|
||||||
|
int type = var->datatype;
|
||||||
|
for (int i=0; i<var->nvals; i++) {
|
||||||
|
Array<TYPE> data2( var->nels );
|
||||||
|
copyData<TYPE>( data2, type, var->vals[i] );
|
||||||
|
memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
|
||||||
|
}
|
||||||
|
DBFreeQuadvar( var );
|
||||||
|
std::vector<size_t> dims( var->ndims+1, var->nvals );
|
||||||
|
for (int d=0; d<var->ndims; d++)
|
||||||
|
dims[d] = var->dims[d];
|
||||||
|
data.reshape( dims );
|
||||||
|
return data;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Read/write a point mesh/variable to silo *
|
||||||
|
****************************************************/
|
||||||
|
template<class TYPE>
|
||||||
|
void writePointMesh( DBfile* fid, const std::string& meshname,
|
||||||
|
int ndim, int N, const TYPE *coords[] )
|
||||||
|
{
|
||||||
|
int err = DBPutPointmesh( fid, meshname.c_str(), ndim, coords, N, getType<TYPE>(), nullptr );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
Array<TYPE> readPointMesh( DBfile* fid, const std::string& meshname )
|
||||||
|
{
|
||||||
|
auto mesh = DBGetPointmesh( fid, meshname.c_str() );
|
||||||
|
int N = mesh->nels;
|
||||||
|
int ndim = mesh->ndims;
|
||||||
|
Array<TYPE> coords(N,ndim);
|
||||||
|
int type = mesh->datatype;
|
||||||
|
for (int d=0; d<ndim; d++) {
|
||||||
|
Array<TYPE> data2( N );
|
||||||
|
copyData<TYPE>( data2, type, mesh->coords[d] );
|
||||||
|
memcpy( &coords(0,d), data2.data(), N*sizeof(TYPE) );
|
||||||
|
}
|
||||||
|
DBFreePointmesh( mesh );
|
||||||
|
return coords;
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
void writePointMeshVariable( DBfile* fid, const std::string& meshname,
|
||||||
|
const std::string& varname, const Array<TYPE>& data )
|
||||||
|
{
|
||||||
|
int N = data.size(0);
|
||||||
|
int nvars = data.size(1);
|
||||||
|
std::vector<const TYPE*> vars(nvars);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
vars[i] = &data(0,i);
|
||||||
|
int err = DBPutPointvar( fid, varname.c_str(), meshname.c_str(), nvars, vars.data(), N, getType<TYPE>(), nullptr );
|
||||||
|
ASSERT( err == 0 );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
Array<TYPE> readPointMeshVariable( DBfile* fid, const std::string& varname )
|
||||||
|
{
|
||||||
|
auto var = DBGetPointvar( fid, varname.c_str() );
|
||||||
|
ASSERT( var != nullptr );
|
||||||
|
Array<TYPE> data( var->nels, var->nvals );
|
||||||
|
int type = var->datatype;
|
||||||
|
for (int i=0; i<var->nvals; i++) {
|
||||||
|
Array<TYPE> data2( var->nels );
|
||||||
|
copyData<TYPE>( data2, type, var->vals[i] );
|
||||||
|
memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
|
||||||
|
}
|
||||||
|
DBFreeMeshvar( var );
|
||||||
|
return data;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/****************************************************
|
||||||
|
* Read/write a triangle mesh *
|
||||||
|
****************************************************/
|
||||||
|
template<class TYPE>
|
||||||
|
void writeTriMesh( DBfile* fid, const std::string& meshName,
|
||||||
|
int ndim, int ndim_tri, int N, const TYPE *coords[], int N_tri, const int *tri[] )
|
||||||
|
{
|
||||||
|
auto zoneName = meshName + "_zones";
|
||||||
|
std::vector<int> nodelist( (ndim_tri+1)*N_tri );
|
||||||
|
for (int i=0, j=0; i<N_tri; i++) {
|
||||||
|
for (int d=0; d<ndim_tri+1; d++, j++)
|
||||||
|
nodelist[j] = tri[d][i];
|
||||||
|
}
|
||||||
|
int shapetype = 0;
|
||||||
|
if ( ndim_tri==1 )
|
||||||
|
shapetype = DB_ZONETYPE_BEAM;
|
||||||
|
else if ( ndim_tri==2 )
|
||||||
|
shapetype = DB_ZONETYPE_TRIANGLE;
|
||||||
|
else if ( ndim_tri==3 )
|
||||||
|
shapetype = DB_ZONETYPE_PYRAMID;
|
||||||
|
else
|
||||||
|
ERROR("Unknown shapetype");
|
||||||
|
int shapesize = ndim_tri+1;
|
||||||
|
int shapecnt = N_tri;
|
||||||
|
DBPutZonelist2( fid, zoneName.c_str(), N_tri, ndim_tri, nodelist.data(),
|
||||||
|
nodelist.size(), 0, 0, 0, &shapetype, &shapesize, &shapecnt, 1, nullptr );
|
||||||
|
DBPutUcdmesh( fid, meshName.c_str(), ndim, nullptr, coords, N,
|
||||||
|
nodelist.size(), zoneName.c_str(), nullptr, getType<TYPE>(), nullptr );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
void readTriMesh( DBfile* fid, const std::string& meshname, Array<TYPE>& coords, Array<int>& tri )
|
||||||
|
{
|
||||||
|
auto mesh = DBGetUcdmesh( fid, meshname.c_str() );
|
||||||
|
int ndim = mesh->ndims;
|
||||||
|
int N_nodes = mesh->nnodes;
|
||||||
|
coords.resize(N_nodes,ndim);
|
||||||
|
int mesh_type = mesh->datatype;
|
||||||
|
for (int d=0; d<ndim; d++) {
|
||||||
|
Array<TYPE> data2( N_nodes );
|
||||||
|
copyData<TYPE>( data2, mesh_type, mesh->coords[d] );
|
||||||
|
memcpy( &coords(0,d), data2.data(), N_nodes*sizeof(TYPE) );
|
||||||
|
}
|
||||||
|
auto zones = mesh->zones;
|
||||||
|
int N_zones = zones->nzones;
|
||||||
|
int ndim_zones = zones->ndims;
|
||||||
|
ASSERT( zones->nshapes==1 );
|
||||||
|
int shape_type = zones->shapetype[0];
|
||||||
|
int shapesize = zones->shapesize[0];
|
||||||
|
tri.resize(N_zones,shapesize);
|
||||||
|
for (int i=0; i<N_zones; i++) {
|
||||||
|
for (int j=0; j<shapesize; j++)
|
||||||
|
tri(i,j) = zones->nodelist[i*shapesize+j];
|
||||||
|
}
|
||||||
|
DBFreeUcdmesh( mesh );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
void writeTriMeshVariable( DBfile* fid, int ndim, const std::string& meshname,
|
||||||
|
const std::string& varname, const Array<TYPE>& data, VariableType type )
|
||||||
|
{
|
||||||
|
int nvars = 0;
|
||||||
|
int vartype = 0;
|
||||||
|
const TYPE *vars[10] = { nullptr };
|
||||||
|
if ( type == VariableType::NodeVariable ) {
|
||||||
|
vartype = DB_NODECENT;
|
||||||
|
nvars = data.size(1);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
vars[i] = &data(0,i);
|
||||||
|
} else if ( type == VariableType::EdgeVariable ) {
|
||||||
|
ERROR("Not finished");
|
||||||
|
} else if ( type == VariableType::SurfaceVariable ) {
|
||||||
|
ERROR("Not finished");
|
||||||
|
} else if ( type == VariableType::VolumeVariable ) {
|
||||||
|
vartype = DB_ZONECENT;
|
||||||
|
nvars = data.size(1);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
vars[i] = &data(0,i);
|
||||||
|
} else {
|
||||||
|
ERROR("Invalid variable type");
|
||||||
|
}
|
||||||
|
auto suffix = getVarSuffix( ndim, nvars );
|
||||||
|
std::vector<std::string> var_names(nvars);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
var_names[i] = varname + suffix[i];
|
||||||
|
std::vector<char*> varnames(nvars,nullptr);
|
||||||
|
for (int i=0; i<nvars; i++)
|
||||||
|
varnames[i] = const_cast<char*>(var_names[i].c_str());
|
||||||
|
DBPutUcdvar( fid, varname.c_str(), meshname.c_str(), nvars,
|
||||||
|
varnames.data(), vars, data.size(0), nullptr, 0, getType<TYPE>(), vartype, nullptr );
|
||||||
|
}
|
||||||
|
template<class TYPE>
|
||||||
|
Array<TYPE> readTriMeshVariable( DBfile* fid, const std::string& varname )
|
||||||
|
{
|
||||||
|
auto var = DBGetUcdvar( fid, varname.c_str() );
|
||||||
|
ASSERT( var != nullptr );
|
||||||
|
Array<TYPE> data( var->nels, var->nvals );
|
||||||
|
int type = var->datatype;
|
||||||
|
for (int i=0; i<var->nvals; i++) {
|
||||||
|
Array<TYPE> data2( var->nels );
|
||||||
|
copyData<TYPE>( data2, type, var->vals[i] );
|
||||||
|
memcpy( &data(0,i), data2.data(), var->nels*sizeof(TYPE) );
|
||||||
|
}
|
||||||
|
DBFreeUcdvar( var );
|
||||||
|
return data;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}; // silo namespace
|
||||||
|
|
||||||
|
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#endif
|
||||||
Loading…
Reference in New Issue
Block a user