Fix for #681 and #682

src/Diagnostic/DiagnosticFields.cpp

@@ -154,10 +154,11 @@ DiagnosticFields::DiagnosticFields( Params &params, SmileiMPI *smpi, VectorPatch
         for( unsigned int ipatch=0 ; ipatch<vecPatches.size() ; ipatch++ ) {
             vecPatches( ipatch )->EMfields->allFields_avg.resize( diag_n+1 );
             if( time_average > 1 ) {
-                for( unsigned int ifield=0; ifield<fields_names.size(); ifield++ )
+                for( unsigned int ifield=0; ifield<fields_names.size(); ifield++ ) {
                     vecPatches( ipatch )->EMfields->allFields_avg[diag_n].push_back(
                         vecPatches( ipatch )->EMfields->createField( fields_names[ifield], params )
                     );
+                }
             }
         }
     }
@@ -333,9 +334,16 @@ void DiagnosticFields::run( SmileiMPI *smpi, VectorPatch &vecPatches, int itime,
             // Write
             H5Write dset = writeField( iteration_group_, fields_names[ifield] );
             // Attributes for openPMD
+            Field *f = vecPatches( 0 )->EMfields->allFields[fields_indexes[ifield]];
+            vector<double> stagger( f->dims().size() );
+            for( unsigned int i = 0; i < stagger.size(); i++ ) {
+                stagger[i] = 0.5 * (double) f->isDual(i);
+            }
+            bool ends_with_m = 0 == fields_names[ifield].compare( fields_names[ifield].length()-2, 2, "_m" );
+            double stagger_t = ends_with_m ? vecPatches( 0 )->EMfields->timestep*0.5 : 0.;
             openPMD_->writeFieldAttributes( dset, subgrid_start_, subgrid_step_ );
-            openPMD_->writeRecordAttributes( dset, field_type[ifield] );
-            openPMD_->writeFieldRecordAttributes( dset );
+            openPMD_->writeRecordAttributes( dset, field_type[ifield], stagger_t );
+            openPMD_->writeFieldRecordAttributes( dset, stagger );
             openPMD_->writeComponentAttributes( dset, field_type[ifield] );
         }
         #pragma omp barrier 

src/ElectroMagn/ElectroMagn.h

@@ -305,7 +305,6 @@ class ElectroMagn
     //! Number of elements in arrays without duplicated borders
     unsigned int bufsize[3][2];
 
-    //!\todo should this be just an integer???
     //! Oversize domain to exchange less particles (from params)
     std::vector<unsigned int> oversize;
 
@@ -380,9 +379,6 @@ class ElectroMagn
     cField *p_AM_;
     cField *Ap_AM_;
 
-    //! \todo check time_dual or time_prim (MG)
-//    //! method used to solve Maxwell's equation (takes current time and time-step as input parameter)
-//    virtual void solveMaxwellAmpere() = 0;
     //! Maxwell Ampere Solver
     Solver *MaxwellAmpereSolver_;
     //! Maxwell Faraday Solver

src/Field/Field.h

@@ -86,7 +86,6 @@ class Field
     virtual void shift_x( unsigned int delta ) = 0;
 
     //! vector containing the dimensions of the Field
-    //! \todo private/friend/modify (JD)
     std::vector<unsigned int> dims_;
 
     //! keep track ofwich direction of the Field is dual

src/Params/OpenPMDparams.cpp

@@ -18,16 +18,12 @@ OpenPMDparams::OpenPMDparams( Params &p ):
 
     // Grid parameters
     string xyz = "xyz";
-    gridGlobalOffset.resize( params->nDim_field );
-    gridOffset      .resize( params->nDim_field );
-    position        .resize( params->nDim_field );
+    gridGlobalOffset.resize( params->nDim_field, 0. );
+    gridOffset      .resize( params->nDim_field, 0. );
     gridSpacing     .resize( params->nDim_field );
     for( unsigned int idim=0; idim<params->nDim_field; idim++ ) {
         axisLabels.addString( xyz.substr( idim, 1 ) );
-        gridGlobalOffset[idim] = 0.;
-        gridOffset      [idim] = 0.;
-        position        [idim] = 0.;
-        gridSpacing     [idim] = params->cell_length[idim];
+        gridSpacing[idim] = params->cell_length[idim];
     }
     fieldSolverParameters = "";
     if( params->maxwell_sol == "Yee" ) {
@@ -192,15 +188,15 @@ void OpenPMDparams::writeSpeciesAttributes( H5Write & )
 {
 }
 
-void OpenPMDparams::writeRecordAttributes( H5Write &location, unsigned int unit_type )
+void OpenPMDparams::writeRecordAttributes( H5Write &location, unsigned int unit_type, double timeOffset )
 {
     location.attr( "unitDimension", unitDimension[unit_type] );
-    location.attr( "timeOffset", 0. );
+    location.attr( "timeOffset", timeOffset );
 }
 
-void OpenPMDparams::writeFieldRecordAttributes( H5Write &location )
+void OpenPMDparams::writeFieldRecordAttributes( H5Write &location, vector<double> &stagger )
 {
-    location.attr( "position", position );
+    location.attr( "position", stagger );
 }
 
 void OpenPMDparams::writeComponentAttributes( H5Write &location, unsigned int unit_type )

src/Params/OpenPMDparams.h

@@ -49,8 +49,6 @@ class OpenPMDparams
     DividedString fieldBoundary, fieldBoundaryParameters, particleBoundary, particleBoundaryParameters;
     //! current smoothing description
     std::string currentSmoothing, currentSmoothingParameters;
-    //! position of the fields within a cell
-    std::vector<double> position;
 
     //! Returns a time string in the openPMD format
     std::string getLocalTime();
@@ -74,10 +72,10 @@ class OpenPMDparams
     void writeSpeciesAttributes( H5Write& );
 
     //! Write the attributes for a record
-    void writeRecordAttributes( H5Write&, unsigned int );
+    void writeRecordAttributes( H5Write&, unsigned int, double timeOffset = 0 );
 
     //! Write the attributes for a field record
-    void writeFieldRecordAttributes( H5Write& );
+    void writeFieldRecordAttributes( H5Write&, std::vector<double> &stagger );
 
     //! Write the attributes for a component
     void writeComponentAttributes( H5Write&, unsigned int );

src/PartCompTime/PartCompTimeFactory.h

@@ -70,7 +70,7 @@ class PartCompTimeFactory
             }
         }
         else {
-            ERROR_NAMELIST( "Unknwon parameters setting the particle computing time evaluation operator: "
+            ERROR_NAMELIST( "Unknown parameters setting the particle computing time evaluation operator: "
              << params.geometry << ", Order : " << params.interpolation_order,
             LINK_NAMELIST + std::string("#main-variables"));
         }