Merge pull request #219 from mfem/attribute_sets_dev

Attribute sets dev

examples/ex5p.py

@@ -306,7 +306,7 @@ def EvalValue(self, x):
         u_sock << "parallel " << num_procs << " " << myid << "\n"
         u_sock.precision(8)
         u_sock << "solution\n" << pmesh << u << "window_title 'Velocity'\n"
-        MPI.Barrier()
+        MPI.COMM_WORLD.Barrier()
         p_sock = mfem.socketstream("localhost", 19916)
         p_sock << "parallel " << num_procs << " " << myid << "\n"
         p_sock.precision(8)

mfem/_par/arrays_by_name.i

@@ -0,0 +1,31 @@
+%module(package="mfem._par") arrays_by_name
+%{
+#include "mfem.hpp"
+#include "numpy/arrayobject.h"
+#include "../common/io_stream.hpp"
+#include "../common/pyoperator.hpp"
+#include "../common/pycoefficient.hpp"
+#include "../common/pyintrules.hpp"
+%}
+
+%include "../common/existing_mfem_headers.i"
+
+#ifdef FILE_EXISTS_GENERAL_ARRAYS_BY_NAME
+%init %{
+import_array();
+%}
+
+%include "exception.i"
+%include "../common/exception.i"
+
+%import "array.i"
+%import "../common/io_stream_typemap.i"
+OSTREAM_TYPEMAP(std::ostream&)
+ISTREAM_TYPEMAP(std::istream&)
+
+%include "general/arrays_by_name.hpp"
+%ignore mfem::ArraysByName::begin;
+%ignore mfem::ArraysByName::end;
+
+%template(intArraysByName) mfem::ArraysByName<int>;
+#endif

mfem/_par/attribute_sets.i

@@ -0,0 +1,29 @@
+%module(package="mfem._par") attribute_sets
+%{
+#include "mfem.hpp"
+#include "numpy/arrayobject.h"
+#include "../common/io_stream.hpp"
+#include "../common/pyoperator.hpp"
+#include "../common/pycoefficient.hpp"
+#include "../common/pyintrules.hpp"
+%}
+
+%include "../common/existing_mfem_headers.i"
+#ifdef FILE_EXISTS_MESH_ATTRIBUTE_SETS
+
+%init %{
+import_array();
+%}
+
+%include "exception.i"
+%include "../common/exception.i"
+
+%import "array.i"
+%import "arrays_by_name.i"
+%import "../common/io_stream_typemap.i"
+OSTREAM_TYPEMAP(std::ostream&)
+ISTREAM_TYPEMAP(std::istream&)
+
+%include "mesh/attribute_sets.hpp"
+
+#endif

mfem/_par/mesh.i

@@ -39,6 +39,7 @@ import_array();
 
 %import "matrix.i"
 %import "array.i"
+%import "attribute_sets.i"
 %import "sort_pairs.i"
 %import "ncmesh.i"
 %import "vector.i"
@@ -217,30 +218,34 @@ def GetFaceElements(self, Face):
     return Elem1.value(), Elem2.value()
 %}
 %feature("shadow") mfem::Mesh::GetElementTransformation %{
-def GetElementTransformation(self, i):
+def GetElementTransformation(self, i, Tr=None):
     from mfem.par import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetBdrElementTransformation %{
-def GetBdrElementTransformation(self, i):
+def GetBdrElementTransformation(self, i, Tr=None):
     from mfem.par import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetFaceTransformation %{
-def GetFaceTransformation(self, i):
+def GetFaceTransformation(self, i, Tr=None):
     from mfem.par import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetEdgeTransformation %{
-def GetEdgeTransformation(self, i):
+def GetEdgeTransformation(self, i, Tr=None):
     from mfem.par import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}

mfem/_par/setup.py

@@ -121,8 +121,8 @@ def get_extensions():
                "tmop", "tmop_amr", "tmop_tools", "qspace", "qfunction",
                "quadinterpolator", "quadinterpolator_face",
                "submesh", "transfermap", "staticcond","sidredatacollection",
-               "psubmesh", "ptransfermap", "enzyme"]
-
+               "psubmesh", "ptransfermap", "enzyme",
+               "attribute_sets", "arrays_by_name"]
     if add_pumi == '1':
         from setup_local import puminc, pumilib
         modules.append("pumi")

mfem/_ser/arrays_by_name.i

@@ -0,0 +1,31 @@
+%module(package="mfem._ser") arrays_by_name
+%{
+#include "mfem.hpp"
+#include "numpy/arrayobject.h"
+#include "../common/io_stream.hpp"
+#include "../common/pyoperator.hpp"
+#include "../common/pycoefficient.hpp"
+#include "../common/pyintrules.hpp"
+%}
+
+%include "../common/existing_mfem_headers.i"
+
+#ifdef FILE_EXISTS_GENERAL_ARRAYS_BY_NAME
+%init %{
+import_array();
+%}
+
+%include "exception.i"
+%include "../common/exception.i"
+
+%import "array.i"
+%import "../common/io_stream_typemap.i"
+OSTREAM_TYPEMAP(std::ostream&)
+ISTREAM_TYPEMAP(std::istream&)
+
+%include "general/arrays_by_name.hpp"
+%ignore mfem::ArraysByName::begin;
+%ignore mfem::ArraysByName::end;
+
+%template(intArraysByName) mfem::ArraysByName<int>;
+#endif

mfem/_ser/attribute_sets.i

@@ -0,0 +1,29 @@
+%module(package="mfem._ser") attribute_sets
+%{
+#include "mfem.hpp"
+#include "numpy/arrayobject.h"
+#include "../common/io_stream.hpp"
+#include "../common/pyoperator.hpp"
+#include "../common/pycoefficient.hpp"
+#include "../common/pyintrules.hpp"
+%}
+
+%include "../common/existing_mfem_headers.i"
+#ifdef FILE_EXISTS_MESH_ATTRIBUTE_SETS
+
+%init %{
+import_array();
+%}
+
+%include "exception.i"
+%include "../common/exception.i"
+
+%import "array.i"
+%import "arrays_by_name.i"
+%import "../common/io_stream_typemap.i"
+OSTREAM_TYPEMAP(std::ostream&)
+ISTREAM_TYPEMAP(std::istream&)
+
+%include "mesh/attribute_sets.hpp"
+
+#endif

mfem/_ser/mesh.i

@@ -31,6 +31,7 @@ import_array();
 %import "matrix.i"
 %import "mem_manager.i"
 %import "array.i"
+%import "attribute_sets.i"
 %import "sort_pairs.i"
 %import "ncmesh.i"
 %import "vector.i"
@@ -222,30 +223,34 @@ def GetFaceElements(self, Face):
     return Elem1.value(), Elem2.value()
 %}
 %feature("shadow") mfem::Mesh::GetElementTransformation %{
-def GetElementTransformation(self, i):
+def GetElementTransformation(self, i, Tr=None):
     from mfem.ser import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetBdrElementTransformation %{
-def GetBdrElementTransformation(self, i):
+def GetBdrElementTransformation(self, i, Tr=None):
     from mfem.ser import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetFaceTransformation %{
-def GetFaceTransformation(self, i):
+def GetFaceTransformation(self, i, Tr=None):
     from mfem.ser import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}
 %feature("shadow") mfem::Mesh::GetEdgeTransformation %{
-def GetEdgeTransformation(self, i):
+def GetEdgeTransformation(self, i, Tr=None):
     from mfem.ser import IsoparametricTransformation
-    Tr = IsoparametricTransformation()
+    if Tr is None:
+       Tr = IsoparametricTransformation()
     $action(self, i, Tr)
     return Tr
 %}

mfem/_ser/setup.py

@@ -103,7 +103,8 @@ def get_extensions():
                "tmop", "tmop_amr", "tmop_tools", "qspace", "qfunction",
                "quadinterpolator", "quadinterpolator_face",
                "submesh", "transfermap", "staticcond",
-               "sidredatacollection", "enzyme"]
+               "sidredatacollection", "enzyme",
+               "attribute_sets", "arrays_by_name"]
 
     if add_cuda == '1':
         from setup_local import cudainc

mfem/common/bilininteg_ext.i

@@ -255,6 +255,10 @@ namespace mfem {
     self._coeff = args
 %}
 
+%pythonappend ElasticityComponentIntegrator::ElasticityComponentIntegrator %{
+    self._coeff = parent_
+%}
+
 %pythonappend DGTraceIntegrator::DGTraceIntegrator %{
     self._coeff = args
 %}