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rAKA akantu
mesh.cc
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/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 22 2016
*
* @brief class handling meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace
akantu
{
const
Element
ElementNull
(
_not_defined
,
0
);
/* -------------------------------------------------------------------------- */
void
Element
::
printself
(
std
::
ostream
&
stream
,
int
indent
)
const
{
std
::
string
space
;
for
(
Int
i
=
0
;
i
<
indent
;
i
++
,
space
+=
AKANTU_INDENT
)
;
stream
<<
space
<<
"Element ["
<<
type
<<
", "
<<
element
<<
", "
<<
ghost_type
<<
"]"
;
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
const
ID
&
id
,
const
MemoryID
&
memory_id
,
StaticCommunicator
&
communicator
)
:
Memory
(
id
,
memory_id
),
GroupManager
(
*
this
,
id
+
":group_manager"
,
memory_id
),
nodes
(
NULL
),
nodes_global_ids
(
NULL
),
nodes_type
(
0
,
1
,
id
+
":nodes_type"
),
nb_global_nodes
(
0
),
created_nodes
(
true
),
connectivities
(
"connectivities"
,
id
,
memory_id
),
normals
(
"normals"
,
id
,
memory_id
),
spatial_dimension
(
spatial_dimension
),
types_offsets
(
Array
<
UInt
>
((
UInt
)
_max_element_type
+
1
,
1
)),
ghost_types_offsets
(
Array
<
UInt
>
((
UInt
)
_max_element_type
+
1
,
1
)),
lower_bounds
(
spatial_dimension
,
0.
),
upper_bounds
(
spatial_dimension
,
0.
),
size
(
spatial_dimension
,
0.
),
local_lower_bounds
(
spatial_dimension
,
0.
),
local_upper_bounds
(
spatial_dimension
,
0.
),
mesh_data
(
"mesh_data"
,
id
,
memory_id
),
mesh_facets
(
NULL
),
mesh_parent
(
NULL
),
is_mesh_facets
(
false
),
is_distributed
(
false
),
communicator
(
&
communicator
),
element_synchronizer
(
NULL
),
node_synchronizer
(
NULL
)
{
AKANTU_DEBUG_IN
();
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
StaticCommunicator
&
communicator
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
id
,
memory_id
,
communicator
)
{
AKANTU_DEBUG_IN
();
this
->
nodes
=
&
(
alloc
<
Real
>
(
id
+
":coordinates"
,
memory_id
,
spatial_dimension
));
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
StaticCommunicator
::
getStaticCommunicator
(),
id
,
memory_id
)
{}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
const
ID
&
nodes_id
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
id
,
memory_id
,
StaticCommunicator
::
getStaticCommunicator
())
{
this
->
nodes
=
&
(
this
->
getArray
<
Real
>
(
nodes_id
));
this
->
nb_global_nodes
=
this
->
nodes
->
getSize
();
this
->
computeBoundingBox
();
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
Array
<
Real
>
&
nodes
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
id
,
memory_id
,
StaticCommunicator
::
getStaticCommunicator
())
{
this
->
nodes
=
&
nodes
;
this
->
nb_global_nodes
=
this
->
nodes
->
getSize
();
this
->
computeBoundingBox
();
}
/* -------------------------------------------------------------------------- */
Mesh
&
Mesh
::
initMeshFacets
(
const
ID
&
id
)
{
AKANTU_DEBUG_IN
();
if
(
!
mesh_facets
)
{
mesh_facets
=
new
Mesh
(
spatial_dimension
,
*
(
this
->
nodes
),
getID
()
+
":"
+
id
,
getMemoryID
());
mesh_facets
->
mesh_parent
=
this
;
mesh_facets
->
is_mesh_facets
=
true
;
}
AKANTU_DEBUG_OUT
();
return
*
mesh_facets
;
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
defineMeshParent
(
const
Mesh
&
mesh
)
{
AKANTU_DEBUG_IN
();
this
->
mesh_parent
=
&
mesh
;
this
->
is_mesh_facets
=
true
;
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
Mesh
::~
Mesh
()
{
AKANTU_DEBUG_IN
();
delete
mesh_facets
;
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
read
(
const
std
::
string
&
filename
,
const
MeshIOType
&
mesh_io_type
)
{
MeshIO
mesh_io
;
mesh_io
.
read
(
filename
,
*
this
,
mesh_io_type
);
type_iterator
it
=
this
->
firstType
(
spatial_dimension
,
_not_ghost
,
_ek_not_defined
);
type_iterator
last
=
this
->
lastType
(
spatial_dimension
,
_not_ghost
,
_ek_not_defined
);
if
(
it
==
last
)
AKANTU_EXCEPTION
(
"The mesh contained in the file "
<<
filename
<<
" does not seem to be of the good dimension."
<<
" No element of dimension "
<<
spatial_dimension
<<
" where read."
);
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
write
(
const
std
::
string
&
filename
,
const
MeshIOType
&
mesh_io_type
)
{
MeshIO
mesh_io
;
mesh_io
.
write
(
filename
,
*
this
,
mesh_io_type
);
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
printself
(
std
::
ostream
&
stream
,
int
indent
)
const
{
std
::
string
space
;
for
(
Int
i
=
0
;
i
<
indent
;
i
++
,
space
+=
AKANTU_INDENT
)
;
stream
<<
space
<<
"Mesh ["
<<
std
::
endl
;
stream
<<
space
<<
" + id : "
<<
getID
()
<<
std
::
endl
;
stream
<<
space
<<
" + spatial dimension : "
<<
this
->
spatial_dimension
<<
std
::
endl
;
stream
<<
space
<<
" + nodes ["
<<
std
::
endl
;
nodes
->
printself
(
stream
,
indent
+
2
);
stream
<<
space
<<
" + connectivities ["
<<
std
::
endl
;
connectivities
.
printself
(
stream
,
indent
+
2
);
stream
<<
space
<<
" ]"
<<
std
::
endl
;
GroupManager
::
printself
(
stream
,
indent
+
1
);
stream
<<
space
<<
"]"
<<
std
::
endl
;
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
computeBoundingBox
()
{
AKANTU_DEBUG_IN
();
for
(
UInt
k
=
0
;
k
<
spatial_dimension
;
++
k
)
{
local_lower_bounds
(
k
)
=
std
::
numeric_limits
<
double
>::
max
();
local_upper_bounds
(
k
)
=
-
std
::
numeric_limits
<
double
>::
max
();
}
for
(
UInt
i
=
0
;
i
<
nodes
->
getSize
();
++
i
)
{
// if(!isPureGhostNode(i))
for
(
UInt
k
=
0
;
k
<
spatial_dimension
;
++
k
)
{
local_lower_bounds
(
k
)
=
std
::
min
(
local_lower_bounds
[
k
],
(
*
nodes
)(
i
,
k
));
local_upper_bounds
(
k
)
=
std
::
max
(
local_upper_bounds
[
k
],
(
*
nodes
)(
i
,
k
));
}
}
if
(
this
->
is_distributed
)
{
StaticCommunicator
&
comm
=
StaticCommunicator
::
getStaticCommunicator
();
Matrix
<
Real
>
reduce_bounds
(
spatial_dimension
,
2
);
for
(
UInt
k
=
0
;
k
<
spatial_dimension
;
++
k
)
{
reduce_bounds
(
k
,
0
)
=
local_lower_bounds
(
k
);
reduce_bounds
(
k
,
1
)
=
-
local_upper_bounds
(
k
);
}
comm
.
allReduce
(
reduce_bounds
,
_so_min
);
for
(
UInt
k
=
0
;
k
<
spatial_dimension
;
++
k
)
{
lower_bounds
(
k
)
=
reduce_bounds
(
k
,
0
);
upper_bounds
(
k
)
=
-
reduce_bounds
(
k
,
1
);
}
}
else
{
this
->
lower_bounds
=
this
->
local_lower_bounds
;
this
->
upper_bounds
=
this
->
local_upper_bounds
;
}
size
=
upper_bounds
-
lower_bounds
;
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
template
<
typename
T
>
void
Mesh
::
initElementTypeMapArray
(
ElementTypeMapArray
<
T
>
&
vect
,
UInt
nb_component
,
UInt
dim
,
const
bool
&
flag_nb_node_per_elem_multiply
,
ElementKind
element_kind
,
bool
size_to_nb_element
)
const
{
AKANTU_DEBUG_IN
();
for
(
UInt
g
=
_not_ghost
;
g
<=
_ghost
;
++
g
)
{
GhostType
gt
=
(
GhostType
)
g
;
this
->
initElementTypeMapArray
(
vect
,
nb_component
,
dim
,
gt
,
flag_nb_node_per_elem_multiply
,
element_kind
,
size_to_nb_element
);
}
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
template
<
typename
T
>
void
Mesh
::
initElementTypeMapArray
(
ElementTypeMapArray
<
T
>
&
vect
,
UInt
nb_component
,
UInt
dim
,
GhostType
gt
,
const
bool
&
flag_nb_node_per_elem_multiply
,
ElementKind
element_kind
,
bool
size_to_nb_element
)
const
{
AKANTU_DEBUG_IN
();
this
->
initElementTypeMapArray
(
vect
,
nb_component
,
dim
,
gt
,
T
(),
flag_nb_node_per_elem_multiply
,
element_kind
,
size_to_nb_element
);
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
template
<
typename
T
>
void
Mesh
::
initElementTypeMapArray
(
ElementTypeMapArray
<
T
>
&
vect
,
UInt
nb_component
,
UInt
dim
,
GhostType
gt
,
const
T
&
default_value
,
const
bool
&
flag_nb_node_per_elem_multiply
,
ElementKind
element_kind
,
bool
size_to_nb_element
)
const
{
AKANTU_DEBUG_IN
();
Mesh
::
type_iterator
it
=
firstType
(
dim
,
gt
,
element_kind
);
Mesh
::
type_iterator
end
=
lastType
(
dim
,
gt
,
element_kind
);
for
(;
it
!=
end
;
++
it
)
{
ElementType
type
=
*
it
;
UInt
nb_comp
=
nb_component
;
if
(
flag_nb_node_per_elem_multiply
)
nb_comp
*=
Mesh
::
getNbNodesPerElement
(
*
it
);
UInt
size
=
0
;
if
(
size_to_nb_element
)
size
=
this
->
getNbElement
(
type
,
gt
);
vect
.
alloc
(
size
,
nb_comp
,
type
,
gt
,
default_value
);
}
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
initNormals
()
{
this
->
initElementTypeMapArray
(
normals
,
spatial_dimension
,
spatial_dimension
,
false
,
_ek_not_defined
);
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
getGlobalConnectivity
(
ElementTypeMapArray
<
UInt
>
&
global_connectivity
,
UInt
dimension
,
GhostType
ghost_type
)
{
AKANTU_DEBUG_IN
();
Mesh
::
type_iterator
it
=
firstType
(
dimension
,
ghost_type
);
Mesh
::
type_iterator
end
=
lastType
(
dimension
,
ghost_type
);
for
(;
it
!=
end
;
++
it
)
{
ElementType
type
=
*
it
;
Array
<
UInt
>
&
local_conn
=
connectivities
(
type
,
ghost_type
);
Array
<
UInt
>
&
g_connectivity
=
global_connectivity
(
type
,
ghost_type
);
if
(
!
nodes_global_ids
)
nodes_global_ids
=
mesh_parent
->
nodes_global_ids
;
UInt
*
local_c
=
local_conn
.
storage
();
UInt
*
global_c
=
g_connectivity
.
storage
();
UInt
nb_terms
=
local_conn
.
getSize
()
*
local_conn
.
getNbComponent
();
for
(
UInt
i
=
0
;
i
<
nb_terms
;
++
i
,
++
local_c
,
++
global_c
)
*
global_c
=
(
*
nodes_global_ids
)(
*
local_c
);
}
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper
&
Mesh
::
getGroupDumper
(
const
std
::
string
&
dumper_name
,
const
std
::
string
&
group_name
)
{
if
(
group_name
==
"all"
)
return
this
->
getDumper
(
dumper_name
);
else
return
element_groups
[
group_name
]
->
getDumper
(
dumper_name
);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_INSTANTIATE_INIT(type) \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
const bool & flag_nb_elem_multiply, ElementKind element_kind, \
bool size_to_nb_element) const; \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
GhostType gt, const bool & flag_nb_elem_multiply, \
ElementKind element_kind, bool size_to_nb_element) const; \
template void Mesh::initElementTypeMapArray<type>( \
ElementTypeMapArray<type> & vect, UInt nb_component, UInt dim, \
GhostType gt, const type & default_value, \
const bool & flag_nb_elem_multiply, ElementKind element_kind, \
bool size_to_nb_element) const
AKANTU_INSTANTIATE_INIT
(
Real
);
AKANTU_INSTANTIATE_INIT
(
UInt
);
AKANTU_INSTANTIATE_INIT
(
Int
);
AKANTU_INSTANTIATE_INIT
(
bool
);
/* -------------------------------------------------------------------------- */
template
<
typename
T
>
ElementTypeMap
<
UInt
>
Mesh
::
getNbDataPerElem
(
ElementTypeMapArray
<
T
>
&
array
,
const
ElementKind
&
element_kind
)
{
ElementTypeMap
<
UInt
>
nb_data_per_elem
;
typename
ElementTypeMapArray
<
T
>::
type_iterator
it
=
array
.
firstType
(
spatial_dimension
,
_not_ghost
,
element_kind
);
typename
ElementTypeMapArray
<
T
>::
type_iterator
last_type
=
array
.
lastType
(
spatial_dimension
,
_not_ghost
,
element_kind
);
for
(;
it
!=
last_type
;
++
it
)
{
UInt
nb_elements
=
this
->
getNbElement
(
*
it
);
nb_data_per_elem
(
*
it
)
=
array
(
*
it
).
getNbComponent
()
*
array
(
*
it
).
getSize
();
nb_data_per_elem
(
*
it
)
/=
nb_elements
;
}
return
nb_data_per_elem
;
}
/* -------------------------------------------------------------------------- */
template
ElementTypeMap
<
UInt
>
Mesh
::
getNbDataPerElem
(
ElementTypeMapArray
<
Real
>
&
array
,
const
ElementKind
&
element_kind
);
template
ElementTypeMap
<
UInt
>
Mesh
::
getNbDataPerElem
(
ElementTypeMapArray
<
UInt
>
&
array
,
const
ElementKind
&
element_kind
);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template
<
typename
T
>
dumper
::
Field
*
Mesh
::
createFieldFromAttachedData
(
const
std
::
string
&
field_id
,
const
std
::
string
&
group_name
,
const
ElementKind
&
element_kind
)
{
dumper
::
Field
*
field
=
NULL
;
ElementTypeMapArray
<
T
>
*
internal
=
NULL
;
try
{
internal
=
&
(
this
->
getData
<
T
>
(
field_id
));
}
catch
(...)
{
return
NULL
;
}
ElementTypeMap
<
UInt
>
nb_data_per_elem
=
this
->
getNbDataPerElem
(
*
internal
,
element_kind
);
field
=
this
->
createElementalField
<
T
,
dumper
::
InternalMaterialField
>
(
*
internal
,
group_name
,
this
->
spatial_dimension
,
element_kind
,
nb_data_per_elem
);
return
field
;
}
template
dumper
::
Field
*
Mesh
::
createFieldFromAttachedData
<
Real
>
(
const
std
::
string
&
field_id
,
const
std
::
string
&
group_name
,
const
ElementKind
&
element_kind
);
template
dumper
::
Field
*
Mesh
::
createFieldFromAttachedData
<
UInt
>
(
const
std
::
string
&
field_id
,
const
std
::
string
&
group_name
,
const
ElementKind
&
element_kind
);
#endif
/* -------------------------------------------------------------------------- */
void
Mesh
::
distribute
()
{
this
->
distribute
(
StaticCommunicator
::
getStaticCommunicator
());
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
distribute
(
StaticCommunicator
&
communicator
)
{
AKANTU_DEBUG_ASSERT
(
is_distributed
==
false
,
"This mesh is already distribute"
);
this
->
communicator
=
&
communicator
;
this
->
element_synchronizer
=
new
ElementSynchronizer
(
*
this
,
this
->
getID
()
+
":element_synchronizer"
,
this
->
getMemoryID
(),
true
,
communicator
);
this
->
node_synchronizer
=
new
NodeSynchronizer
(
*
this
,
this
->
getID
()
+
":node_synchronizer"
,
this
->
getMemoryID
(),
true
,
communicator
);
Int
psize
=
this
->
communicator
->
getNbProc
();
#ifdef AKANTU_USE_SCOTCH
Int
prank
=
this
->
communicator
->
whoAmI
();
if
(
prank
==
0
)
{
MeshPartitionScotch
partition
(
*
this
,
spatial_dimension
);
partition
.
partitionate
(
psize
);
MeshUtilsDistribution
::
distributeMeshCentralized
(
*
this
,
partition
);
}
else
{
MeshUtilsDistribution
::
distributeMeshCentralized
(
*
this
,
0
);
}
#else
if
(
!
(
psize
==
1
))
{
AKANTU_DEBUG_ERROR
(
"Cannot distribute a mesh without a partitioning tool"
);
}
#endif
this
->
is_distributed
=
true
;
this
->
computeBoundingBox
();
}
/* -------------------------------------------------------------------------- */
}
// akantu
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