Changeset 934

Timestamp:

09/22/16 10:58:44 (7 years ago)

Author:

mhnguyen

Message:

Adding new transformation: Compute_connectivity_domain

Test
+) On Curie
+) Test passes

Location:

XIOS/trunk

Files:

• inputs/Unstruct/iodef.xml (modified) (1 diff)
• src/config/compute_connectivity_domain_attribute.conf (added)
• src/config/node_type.conf (modified) (1 diff)
• src/generate_fortran_interface.cpp (modified) (2 diffs)
• src/group_factory_decl.cpp (modified) (1 diff)
• src/group_template_decl.cpp (modified) (1 diff)
• src/interface/c/iccompute_connectivity_domain.cpp (added)
• src/interface/c/icxml_tree.cpp (modified) (2 diffs)
• src/interface/c_attr/iccompute_connectivity_domain_attr.cpp (added)
• src/interface/fortran/compute_connectivity_domain_interface.f90 (added)
• src/interface/fortran/icompute_connectivity_domain.F90 (added)
• src/interface/fortran/ixios.F90 (modified) (1 diff)
• src/interface/fortran/ixios_interfaces.F90 (modified) (7 diffs)
• src/interface/fortran/ixml_tree.F90 (modified) (3 diffs)
• src/interface/fortran_attr/compute_connectivity_domain_interface_attr.F90 (added)
• src/interface/fortran_attr/icompute_connectivity_domain_attr.F90 (added)
• src/node/compute_connectivity_domain.cpp (added)
• src/node/compute_connectivity_domain.hpp (added)
• src/node/domain.cpp (modified) (1 diff)
• src/node/field.cpp (modified) (1 diff)
• src/node/node_enum.hpp (modified) (1 diff)
• src/node/node_type.hpp (modified) (1 diff)
• src/node/transformation.hpp (modified) (1 diff)
• src/node/transformation_enum.hpp (modified) (1 diff)
• src/object_factory_decl.cpp (modified) (2 diffs)
• src/object_template_decl.cpp (modified) (2 diffs)
• src/test/test_unstruct_complete.f90 (modified) (4 diffs)
• src/transformation/algo_types.hpp (modified) (1 diff)
• src/transformation/axis_algorithm_transformation.hpp (modified) (1 diff)
• src/transformation/domain_algorithm_compute_connectivity.cpp (added)
• src/transformation/domain_algorithm_compute_connectivity.hpp (added)
• src/transformation/grid_transformation_selector.cpp (modified) (2 diffs)
• src/type/type_util.hpp (modified) (2 diffs)
• src/xml_parser_decl.cpp (modified) (1 diff)

XIOS/trunk/inputs/Unstruct/iodef.xml

@@ -20 +20 @@
 
    <domain_definition>
-     <domain id="domain_srf" />
+     <domain id="domain_srf" >
+       <compute_connectivity_domain id="compute" type="edge" />
+     </domain>
    </domain_definition>
 

XIOS/trunk/src/config/node_type.conf

@@ -71 +71 @@
 #endif //__XIOS_CExtractDomainToAxis__
 
+#ifdef __XIOS_CComputeConnectivityDomain__
+   DECLARE_NODE(ComputeConnectivityDomain, compute_connectivity_domain)
+#endif //__XIOS_CComputeConnectivityDomain__
+
+
 #ifdef __XIOS_CContext__
    DECLARE_NODE_PAR(Context, context)

XIOS/trunk/src/generate_fortran_interface.cpp

@@ -33 +33 @@
   CZoomDomain zoomDomain;
   CGenerateRectilinearDomain genDomain;
+  CComputeConnectivityDomain compConDomain;
 
   CInterpolateAxis interpolateAxis;
@@ -290 +291 @@
   file.close();
 
+  file.open((path+"compute_connectivity_domain_interface_attr.F90").c_str());
+  compConDomain.generateFortran2003Interface(file);
+  file.close();
+
+  file.open((path+"iccompute_connectivity_domain_attr.cpp").c_str());
+  compConDomain.generateCInterface(file);
+  file.close();
+
+  file.open((path+"icompute_connectivity_domain_attr.F90").c_str());
+  compConDomain.generateFortranInterface(file);
+  file.close();
+
+
+
+
   file.open((path+"inverse_axis_interface_attr.F90").c_str());
   inverseAxis.generateFortran2003Interface(file);

XIOS/trunk/src/group_factory_decl.cpp

@@ -35 +35 @@
   macro(CReduceDomainToAxisGroup)
   macro(CExtractDomainToAxisGroup)
+  macro(CComputeConnectivityDomainGroup)
 }

XIOS/trunk/src/group_template_decl.cpp

@@ -24 +24 @@
   macro(ReduceDomainToAxis)
   macro(ExtractDomainToAxis)
+  macro(ComputeConnectivityDomain)
 
 }

XIOS/trunk/src/interface/c/icxml_tree.cpp

@@ -50 +50 @@
    typedef xios::CInterpolateDomain         *  XInterpolateDomainPtr;
    typedef xios::CGenerateRectilinearDomain *  XGenerateRectilinearDomainPtr;
+   typedef xios::CComputeConnectivityDomain *  XComputeConnectivityDomainPtr;
 
    typedef xios::CTransformation<CAxis>   *  XTransformationAxisPtr;
@@ -452 +453 @@
       }
       *child_ = static_cast<XGenerateRectilinearDomainPtr>(tmpChild_);
+      CTimer::get("XIOS").suspend() ;
+   }
+
+   void cxios_xml_tree_add_computeconnectivitydomaintodomain
+      (XDomainPtr parent_, XComputeConnectivityDomainPtr * child_, const char * child_id, int child_id_size)
+   {
+      std::string child_id_str;
+      XTransformationDomainPtr tmpChild_;
+      CTimer::get("XIOS").resume() ;
+      if (cstr2string(child_id, child_id_size, child_id_str))
+      {
+         tmpChild_ = parent_->addTransformation(TRANS_COMPUTE_CONNECTIVITY_DOMAIN, child_id_str);
+      }
+      else
+      {
+         tmpChild_ = parent_->addTransformation(TRANS_COMPUTE_CONNECTIVITY_DOMAIN);
+      }
+      *child_ = static_cast<XComputeConnectivityDomainPtr>(tmpChild_);
       CTimer::get("XIOS").suspend() ;
    }

XIOS/trunk/src/interface/fortran/ixios.F90

@@ -106 +106 @@
                                         xios(is_defined_reduce_axis_to_scalar_attr)
 
+USE icompute_connectivity_domain, ONLY : txios(compute_connectivity_domain), xios(is_valid_compute_connectivity_domain)
+
+USE icompute_connectivity_domain_attr, ONLY : xios(set_compute_connectivity_domain_attr), &
+                                              xios(get_compute_connectivity_domain_attr), &
+                                              xios(is_defined_compute_connectivity_domain_attr)
+
 USE XIOS_INTERFACES, ONLY : xios(set_attr), xios(get_attr), xios(is_defined_attr), xios(get_handle), xios(add_child), &
                             xios(send_field), xios(recv_field), xios(field_is_active), xios(getVar), xios(setVar)

XIOS/trunk/src/interface/fortran/ixios_interfaces.F90

@@ -88 +88 @@
                                               xios(get_generate_rectilinear_domain_attr_hdl), &
                                               xios(is_defined_generate_rectilinear_domain_attr_hdl)
+USE icompute_connectivity_domain, ONLY : xios(get_compute_connectivity_domain_handle)
+
+USE icompute_connectivity_domain_attr, ONLY : xios(set_compute_connectivity_domain_attr_hdl), &
+                                              xios(get_compute_connectivity_domain_attr_hdl), &
+                                              xios(is_defined_compute_connectivity_domain_attr_hdl)
 
 USE ireduce_axis_to_scalar, ONLY : xios(get_reduce_axis_to_scalar_handle)
@@ -103 +108 @@
                       xios(add_generatedomaintodomain), xios(add_zoomaxistoaxis),                          &
                       xios(add_interpolateaxistoaxis), xios(add_inverseaxistoaxis), xios(add_scalar),      &
-                      xios(add_scalargroup), xios(add_scalartogrid), xios(add_reduceaxistoscalartoscalar)
+                      xios(add_scalargroup), xios(add_scalartogrid), xios(add_reduceaxistoscalartoscalar), &
+                      xios(add_computeconnectivitydomaintodomain)
 
 PRIVATE
@@ -116 +122 @@
                    xios(set_interpolate_domain_attr_hdl), xios(set_inverse_axis_attr_hdl),                   &
                    xios(set_generate_rectilinear_domain_attr_hdl), xios(set_scalar_attr_hdl),                &
-                   xios(set_scalargroup_attr_hdl), xios(set_reduce_axis_to_scalar_attr_hdl)
+                   xios(set_scalargroup_attr_hdl), xios(set_reduce_axis_to_scalar_attr_hdl),                 &
+                   xios(set_compute_connectivity_domain_attr_hdl)
 END INTERFACE xios(set_attr)
 
@@ -128 +135 @@
                    xios(get_interpolate_domain_attr_hdl), xios(get_inverse_axis_attr_hdl),                   &
                    xios(get_generate_rectilinear_domain_attr_hdl), xios(get_scalar_attr_hdl),                &
-                   xios(get_scalargroup_attr_hdl), xios(get_reduce_axis_to_scalar_attr_hdl)
+                   xios(get_scalargroup_attr_hdl), xios(get_reduce_axis_to_scalar_attr_hdl),                 &
+                   xios(get_compute_connectivity_domain_attr_hdl)
 END INTERFACE xios(get_attr)
 
@@ -141 +149 @@
                    xios(is_defined_inverse_axis_attr_hdl), xios(is_defined_generate_rectilinear_domain_attr_hdl),                 &
                    xios(is_defined_scalar_attr_hdl), xios(is_defined_scalargroup_attr_hdl),                                       &
-                   xios(is_defined_reduce_axis_to_scalar_attr_hdl)
+                   xios(is_defined_reduce_axis_to_scalar_attr_hdl), xios(is_defined_compute_connectivity_domain_attr_hdl)
 END INTERFACE xios(is_defined_attr)
 
@@ -153 +161 @@
                    xios(get_interpolate_domain_handle), xios(get_inverse_axis_handle),              &
                    xios(get_generate_rectilinear_domain_handle), xios(get_scalar_handle),           &
-                   xios(get_scalargroup_handle), xios(get_reduce_axis_to_scalar_handle)
+                   xios(get_scalargroup_handle), xios(get_reduce_axis_to_scalar_handle),            &
+                   xios(get_compute_connectivity_domain_handle)
 END INTERFACE xios(get_handle)
 
@@ -164 +173 @@
                    xios(add_interpolatedomaintodomain), xios(add_generatedomaintodomain),                            &
                    xios(add_zoomaxistoaxis), xios(add_interpolateaxistoaxis), xios(add_inverseaxistoaxis),           &
-                   xios(add_scalar), xios(add_scalartogrid), xios(add_reduceaxistoscalartoscalar)
+                   xios(add_scalar), xios(add_scalartogrid), xios(add_reduceaxistoscalartoscalar),                   &
+                   xios(add_computeconnectivitydomaintodomain)
 END INTERFACE xios(add_child)
 

XIOS/trunk/src/interface/fortran/ixml_tree.F90

@@ -13 +13 @@
    USE IINTERPOLATE_DOMAIN
    USE IGENERATE_RECTILINEAR_DOMAIN
+   USE ICOMPUTE_CONNECTIVITY_DOMAIN
    USE IZOOM_AXIS
    USE IINTERPOLATE_AXIS
@@ -214 +215 @@
       END SUBROUTINE cxios_xml_tree_add_generatedomaintodomain
 
+      SUBROUTINE cxios_xml_tree_add_computeconnectivitydomaintodomain(parent_, child_, child_id, child_id_size) BIND(C)
+         USE ISO_C_BINDING
+         INTEGER  (kind = C_INTPTR_T), VALUE        :: parent_
+         INTEGER  (kind = C_INTPTR_T)               :: child_
+         CHARACTER(kind = C_CHAR)    , DIMENSION(*) :: child_id
+         INTEGER  (kind = C_INT)     , VALUE        :: child_id_size
+      END SUBROUTINE cxios_xml_tree_add_computeconnectivitydomaintodomain
+
       SUBROUTINE cxios_xml_tree_add_zoomaxistoaxis(parent_, child_, child_id, child_id_size) BIND(C)
          USE ISO_C_BINDING
@@ -582 +591 @@
    END SUBROUTINE xios(add_generatedomaintodomain)
 
+   SUBROUTINE xios(add_computeconnectivitydomaintodomain)(parent_hdl, child_hdl, child_id)
+      TYPE(txios(domain))                      , INTENT(IN) :: parent_hdl
+      TYPE(txios(compute_connectivity_domain)) , INTENT(OUT):: child_hdl
+      CHARACTER(len = *), OPTIONAL             , INTENT(IN) :: child_id
+
+      IF (PRESENT(child_id)) THEN
+         CALL cxios_xml_tree_add_computeconnectivitydomaintodomain(parent_hdl%daddr, child_hdl%daddr, child_id, len(child_id))
+      ELSE
+         CALL cxios_xml_tree_add_computeconnectivitydomaintodomain(parent_hdl%daddr, child_hdl%daddr, "NONE", -1)
+      END IF
+
+   END SUBROUTINE xios(add_computeconnectivitydomaintodomain)
+
    SUBROUTINE xios(add_zoomaxistoaxis)(parent_hdl, child_hdl, child_id)
       TYPE(txios(axis))                      , INTENT(IN) :: parent_hdl

XIOS/trunk/src/node/domain.cpp

@@ -73 +73 @@
      m["interpolate_domain"] = TRANS_INTERPOLATE_DOMAIN;
      m["generate_rectilinear_domain"] = TRANS_GENERATE_RECTILINEAR_DOMAIN;
+     m["compute_connectivity_domain"] = TRANS_COMPUTE_CONNECTIVITY_DOMAIN;
    }
 

XIOS/trunk/src/node/field.cpp

@@ -1021 +1021 @@
        }
      }
+     else if (grid && grid->hasTransform() && !grid->isTransformed())
+     {
+       grid->transformGrid(grid);
+     }
    }
 

XIOS/trunk/src/node/node_enum.hpp

@@ -29 +29 @@
          eReduceAxisToScalar,
          eReduceDomainToAxis,
-         eExtractDomainToAxis
+         eExtractDomainToAxis,
+         eComputeConnectivityDomain
 
       } ENodeType;

XIOS/trunk/src/node/node_type.hpp

@@ -20 +20 @@
 #include "reduce_domain_to_axis.hpp"
 #include "extract_domain_to_axis.hpp"
+#include "compute_connectivity_domain.hpp"
 
 

XIOS/trunk/src/node/transformation.hpp

@@ -3 +3 @@
 
 #include "xios_spl.hpp"
+#include "xml_node.hpp"
 #include "transformation_enum.hpp"
 

XIOS/trunk/src/node/transformation_enum.hpp

@@ -15 +15 @@
         TRANS_REDUCE_AXIS_TO_SCALAR = 6,
         TRANS_REDUCE_DOMAIN_TO_AXIS = 7,
-        TRANS_EXTRACT_DOMAIN_TO_AXIS = 8
+        TRANS_EXTRACT_DOMAIN_TO_AXIS = 8,
+        TRANS_COMPUTE_CONNECTIVITY_DOMAIN = 9
       } ETranformationType;
 

XIOS/trunk/src/object_factory_decl.cpp

@@ -36 +36 @@
   macro(CReduceDomainToAxis)
   macro(CExtractDomainToAxis)
+  macro(CComputeConnectivityDomain)
 
   macro(CFieldGroup)
@@ -54 +55 @@
   macro(CReduceDomainToAxisGroup)
   macro(CExtractDomainToAxisGroup)
+  macro(CComputeConnectivityDomainGroup)
 }

XIOS/trunk/src/object_template_decl.cpp

@@ -23 +23 @@
   template class CObjectTemplate<CReduceDomainToAxis>;
   template class CObjectTemplate<CExtractDomainToAxis>;
+  template class CObjectTemplate<CComputeConnectivityDomain>;
 
   template class CObjectTemplate<CContextGroup>;
@@ -41 +42 @@
   template class CObjectTemplate<CReduceDomainToAxisGroup>;
   template class CObjectTemplate<CExtractDomainToAxisGroup>;
+  template class CObjectTemplate<CComputeConnectivityDomainGroup>;
 }

XIOS/trunk/src/test/test_unstruct_complete.f90

@@ -30 +30 @@
   INTEGER,ALLOCATABLE :: i_index(:)
   LOGICAL,ALLOCATABLE :: mask_glo(:),mask(:)
+  INTEGER,ALLOCATABLE :: n_local(:),local_neighbor(:,:)
   DOUBLE PRECISION,ALLOCATABLE :: lon(:),lat(:),field_A_srf(:,:), lonvalue(:) ;
   DOUBLE PRECISION,ALLOCATABLE :: bounds_lon(:,:),bounds_lat(:,:) ;
   INTEGER :: ni,ibegin,iend,nj,jbegin,jend
-  INTEGER :: i,j,l,ts,n
+  INTEGER :: i,j,l,ts,n, nbMax
   INTEGER :: ncell_glo,ncell,ind
   REAL :: ilon,ilat
@@ -164 +165 @@
   ALLOCATE(field_A_srf(ncell,llm))
   ALLOCATE(mask(ncell))
+  ALLOCATE(n_local(ncell))
   ncell=0
   data_n_index=0
@@ -205 +207 @@
   CALL xios_set_domain_attr("domain_srf", lonvalue_1D=lon, latvalue_1D=lat)
   CALL xios_set_domain_attr("domain_srf", nvertex=4, bounds_lon_1D=bounds_lon, bounds_lat_1D=bounds_lat)
+!  CALL xios_set_compute_connectivity_domain_attr("compute", n_neighbor=n_local, local_neighbor=local_neighbor)
 
 
@@ -211 +214 @@
   CALL xios_set_timestep(dtime)
   CALL xios_close_context_definition()
+
+  CALL xios_get_compute_connectivity_domain_attr("compute", n_neighbor_max=nbMax)
+  ALLOCATE(local_neighbor(nbMax,ncell))
+  CALL xios_get_compute_connectivity_domain_attr("compute", n_neighbor=n_local, local_neighbor=local_neighbor)
 
    DO ts=1,24*10

XIOS/trunk/src/transformation/algo_types.hpp

@@ -23 +23 @@
 #include "axis_algorithm_extract_domain.hpp"
 #include "extract_domain_to_axis.hpp"
+#include "domain_algorithm_compute_connectivity.hpp"
+#include "compute_connectivity_domain.hpp"
+
 #endif // __XIOS_ALGORITHM_TRANSFORMATION_TYPES_HPP__

XIOS/trunk/src/transformation/axis_algorithm_transformation.hpp

@@ -11 +11 @@
 
 #include "generic_algorithm_transformation.hpp"
+#include "grid_transformation_factory_impl.hpp"
 
 namespace xios {

XIOS/trunk/src/transformation/grid_transformation_selector.cpp

@@ -18 +18 @@
 {
   if (0 == source)
-  {  gridSource_ = gridDestination_; isSameGrid_ = true; }
+  {  gridSource_ = gridDestination_; }
+  if (gridSource_ == gridDestination_) isSameGrid_ = true;
 
   //Verify the compatibity between two grids
@@ -321 +322 @@
 
   //! Domain
-//  CDomainAlgorithmComputeConnectivity::registerTrans();
+  CDomainAlgorithmComputeConnectivity::registerTrans();
   CDomainAlgorithmInterpolate::registerTrans();
   CDomainAlgorithmZoom::registerTrans();

XIOS/trunk/src/type/type_util.hpp

@@ -40 +40 @@
     class CExtractDomainToAxis;
     class CExtractDomainToAxisGroup;
+    class CComputeConnectivityDomain;
+    class CComputeConnectivityDomainGroup;
 
   template <typename T> inline string getStrType(void);
@@ -96 +98 @@
   macro(CExtractDomainToAxis)
   macro(CExtractDomainToAxisGroup)
+  macro(CComputeConnectivityDomain)
+  macro(CComputeConnectivityDomainGroup)
 #undef macro
 }

XIOS/trunk/src/xml_parser_decl.cpp

@@ -29 +29 @@
     macro( ReduceDomainToAxis )
     macro( ExtractDomainToAxis )
+    macro( ComputeConnectivityDomain )
   }
 }