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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_type
(
0
,
1
,
id
+
":nodes_type"
),
connectivities
(
"connectivities"
,
id
,
memory_id
),
ghosts_counters
(
"ghosts_counters"
,
id
,
memory_id
),
normals
(
"normals"
,
id
,
memory_id
),
spatial_dimension
(
spatial_dimension
),
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
),
communicator
(
&
communicator
)
{
AKANTU_DEBUG_IN
();
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
Communicator
&
communicator
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
id
,
memory_id
,
communicator
)
{
AKANTU_DEBUG_IN
();
this
->
nodes
=
std
::
make_shared
<
Array
<
Real
>>
(
0
,
spatial_dimension
,
id
+
":coordinates"
);
AKANTU_DEBUG_OUT
();
}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
Communicator
::
getStaticCommunicator
(),
id
,
memory_id
)
{}
/* -------------------------------------------------------------------------- */
Mesh
::
Mesh
(
UInt
spatial_dimension
,
std
::
shared_ptr
<
Array
<
Real
>>
nodes
,
const
ID
&
id
,
const
MemoryID
&
memory_id
)
:
Mesh
(
spatial_dimension
,
id
,
memory_id
,
Communicator
::
getStaticCommunicator
())
{
this
->
nodes
=
nodes
;
this
->
nb_global_nodes
=
this
->
nodes
->
size
();
this
->
nodes_to_elements
.
resize
(
nodes
->
size
());
for
(
auto
&
node_set
:
nodes_to_elements
)
{
node_set
=
std
::
make_unique
<
std
::
set
<
Element
>>
();
}
this
->
computeBoundingBox
();
}
/* -------------------------------------------------------------------------- */
Mesh
&
Mesh
::
initMeshFacets
(
const
ID
&
id
)
{
AKANTU_DEBUG_IN
();
if
(
!
mesh_facets
)
{
mesh_facets
=
std
::
make_unique
<
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
()
=
default
;
/* -------------------------------------------------------------------------- */
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."
);
this
->
nb_global_nodes
=
this
->
nodes
->
size
();
this
->
computeBoundingBox
();
this
->
nodes_to_elements
.
resize
(
nodes
->
size
());
for
(
auto
&
node_set
:
nodes_to_elements
)
{
node_set
=
std
::
make_unique
<
std
::
set
<
Element
>>
();
}
}
/* -------------------------------------------------------------------------- */
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
->
size
();
++
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
)
{
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
);
}
communicator
->
allReduce
(
reduce_bounds
,
SynchronizerOperation
::
_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
();
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
initNormals
()
{
normals
.
initialize
(
*
this
,
_nb_component
=
spatial_dimension
,
_spatial_dimension
=
spatial_dimension
,
_element_kind
=
_ek_not_defined
);
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
getGlobalConnectivity
(
ElementTypeMapArray
<
UInt
>
&
global_connectivity
,
UInt
dimension
,
GhostType
ghost_type
)
{
AKANTU_DEBUG_IN
();
for
(
auto
type
:
elementTypes
(
dimension
,
ghost_type
))
{
auto
&
local_conn
=
connectivities
(
type
,
ghost_type
);
auto
&
g_connectivity
=
global_connectivity
(
type
,
ghost_type
);
UInt
nb_nodes
=
local_conn
.
size
()
*
local_conn
.
getNbComponent
();
if
(
!
nodes_global_ids
&&
is_mesh_facets
)
{
std
::
transform
(
local_conn
.
begin_reinterpret
(
nb_nodes
),
local_conn
.
end_reinterpret
(
nb_nodes
),
g_connectivity
.
begin_reinterpret
(
nb_nodes
),
[
&
node_ids
=
*
mesh_parent
->
nodes_global_ids
](
UInt
l
)
->
UInt
{
return
node_ids
(
l
);
});
}
else
{
std
::
transform
(
local_conn
.
begin_reinterpret
(
nb_nodes
),
local_conn
.
end_reinterpret
(
nb_nodes
),
g_connectivity
.
begin_reinterpret
(
nb_nodes
),
[
&
node_ids
=
*
nodes_global_ids
](
UInt
l
)
->
UInt
{
return
node_ids
(
l
);
});
}
}
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
);
}
/* -------------------------------------------------------------------------- */
template
<
typename
T
>
ElementTypeMap
<
UInt
>
Mesh
::
getNbDataPerElem
(
ElementTypeMapArray
<
T
>
&
arrays
,
const
ElementKind
&
element_kind
)
{
ElementTypeMap
<
UInt
>
nb_data_per_elem
;
for
(
auto
type
:
elementTypes
(
spatial_dimension
,
_not_ghost
,
element_kind
))
{
UInt
nb_elements
=
this
->
getNbElement
(
type
);
auto
&
array
=
arrays
(
type
);
nb_data_per_elem
(
type
)
=
array
.
getNbComponent
()
*
array
.
size
();
nb_data_per_elem
(
type
)
/=
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
=
nullptr
;
ElementTypeMapArray
<
T
>
*
internal
=
nullptr
;
try
{
internal
=
&
(
this
->
getData
<
T
>
(
field_id
));
}
catch
(...)
{
return
nullptr
;
}
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
(
Communicator
::
getStaticCommunicator
());
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
distribute
(
Communicator
&
communicator
)
{
AKANTU_DEBUG_ASSERT
(
is_distributed
==
false
,
"This mesh is already distribute"
);
this
->
communicator
=
&
communicator
;
this
->
element_synchronizer
=
std
::
make_unique
<
ElementSynchronizer
>
(
*
this
,
this
->
getID
()
+
":element_synchronizer"
,
this
->
getMemoryID
(),
true
);
this
->
node_synchronizer
=
std
::
make_unique
<
NodeSynchronizer
>
(
*
this
,
this
->
getID
()
+
":node_synchronizer"
,
this
->
getMemoryID
(),
true
);
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
,
0
,
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
->
element_synchronizer
->
buildPrankToElement
();
this
->
computeBoundingBox
();
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
getAssociatedElements
(
const
Array
<
UInt
>
&
node_list
,
Array
<
Element
>
&
elements
)
{
for
(
const
auto
&
node
:
node_list
)
for
(
const
auto
&
element
:
*
nodes_to_elements
[
node
])
elements
.
push_back
(
element
);
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
fillNodesToElements
()
{
Element
e
;
UInt
nb_nodes
=
nodes
->
size
();
for
(
UInt
n
=
0
;
n
<
nb_nodes
;
++
n
)
{
if
(
this
->
nodes_to_elements
[
n
])
this
->
nodes_to_elements
[
n
]
->
clear
();
else
this
->
nodes_to_elements
[
n
]
=
std
::
make_unique
<
std
::
set
<
Element
>>
();
}
for
(
auto
ghost_type
:
ghost_types
)
{
e
.
ghost_type
=
ghost_type
;
for
(
const
auto
&
type
:
elementTypes
(
spatial_dimension
,
ghost_type
,
_ek_not_defined
))
{
e
.
type
=
type
;
e
.
kind
=
getKind
(
type
);
UInt
nb_element
=
this
->
getNbElement
(
type
,
ghost_type
);
Array
<
UInt
>::
const_iterator
<
Vector
<
UInt
>>
conn_it
=
connectivities
(
type
,
ghost_type
)
.
begin
(
Mesh
::
getNbNodesPerElement
(
type
));
for
(
UInt
el
=
0
;
el
<
nb_element
;
++
el
,
++
conn_it
)
{
e
.
element
=
el
;
const
Vector
<
UInt
>
&
conn
=
*
conn_it
;
for
(
UInt
n
=
0
;
n
<
conn
.
size
();
++
n
)
nodes_to_elements
[
conn
(
n
)]
->
insert
(
e
);
}
}
}
}
/* -------------------------------------------------------------------------- */
void
Mesh
::
eraseElements
(
const
Array
<
Element
>
&
elements
)
{
ElementTypeMap
<
UInt
>
last_element
;
RemovedElementsEvent
event
(
*
this
);
auto
&
remove_list
=
event
.
getList
();
auto
&
new_numbering
=
event
.
getNewNumbering
();
for
(
auto
&&
el
:
elements
)
{
if
(
el
.
ghost_type
!=
_not_ghost
)
{
auto
&
count
=
ghosts_counters
(
el
);
--
count
;
if
(
count
>
0
)
continue
;
}
remove_list
.
push_back
(
el
);
if
(
not
last_element
.
exists
(
el
.
type
,
el
.
ghost_type
))
{
UInt
nb_element
=
mesh
.
getNbElement
(
el
.
type
,
el
.
ghost_type
);
last_element
(
nb_element
-
1
,
el
.
type
,
el
.
ghost_type
);
auto
&
numbering
=
new_numbering
.
alloc
(
nb_element
,
1
,
el
.
type
,
el
.
ghost_type
);
for
(
auto
&&
pair
:
enumerate
(
numbering
))
{
std
::
get
<
1
>
(
pair
)
=
std
::
get
<
0
>
(
pair
);
}
}
UInt
&
pos
=
last_element
(
el
.
type
,
el
.
ghost_type
);
auto
&
numbering
=
new_numbering
(
el
.
type
,
el
.
ghost_type
);
numbering
(
el
.
element
)
=
UInt
(
-
1
);
numbering
(
pos
)
=
el
.
element
;
--
pos
;
}
this
->
sendEvent
(
event
);
}
}
// namespace akantu
Event Timeline
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