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Merge pull request #102 from sandialabs/ralberd/add_exodus_block_maps
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Draft: Adds element global ID map to Mesh named tuple
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@ralberd
ralberd authored Dec 20, 2024
2 parents 81ccef8 + 1e7ffb1 commit 04b7883
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Showing 5 changed files with 223 additions and 6 deletions.
6 changes: 4 additions & 2 deletions optimism/Mesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@

Mesh = namedtuple('Mesh', ['coords','conns','simplexNodesOrdinals',
'parentElement', 'parentElement1d', 'blocks',
'nodeSets', 'sideSets'],
defaults=(None,None,None))
'nodeSets', 'sideSets', 'block_maps'],
defaults=(None,None,None,None))
Mesh.__doc__ = \
"""Triangle mesh representing a domain.
Expand All @@ -25,6 +25,8 @@
edge data structure is a tuple of the element index and the local
number of the edge within that element. For example, triangle
elements will have edge 0, 1, or 2 for this entry.
block_maps: An optional dictionary mapping element block names to global
element ID maps that may be present in the mesh.
"""


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13 changes: 12 additions & 1 deletion optimism/ReadExodusMesh.py
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Expand Up @@ -11,6 +11,7 @@ def read_exodus_mesh(fileName):
with netCDF4.Dataset(fileName) as exData:
coords = _read_coordinates(exData)
conns, blocks = _read_blocks(exData)
blockMaps = _read_block_maps(exData, blocks)
nodeSets = _read_node_sets(exData)
sideSets = _read_side_sets(exData)

Expand All @@ -26,7 +27,7 @@ def read_exodus_mesh(fileName):
raise

return Mesh.Mesh(coords, conns, simplexNodesOrdinals, basis, basis1d,
blocks, nodeSets, sideSets)
blocks, nodeSets, sideSets, blockMaps)


def read_exodus_mesh_element_properties(fileName, varNames, blockNum=1):
Expand Down Expand Up @@ -89,6 +90,16 @@ def _read_blocks(exodusDataset):
conns = np.vstack(blockConns)
return conns, blocks

def _read_block_maps(exodusDataset, blocks):
block_maps = {}
elementMap = exodusDataset.variables['elem_num_map']
firstElemInBlock = 0
for blockName, blockElems in blocks.items():
nElemsInBlock = len(blockElems)
block_maps[blockName] = elementMap[firstElemInBlock:firstElemInBlock+nElemsInBlock]
firstElemInBlock += nElemsInBlock

return block_maps

def _read_block_variable_values(exodusDataset, blockOrdinal, variableName):
# read element variables currently on mesh
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Binary file added optimism/test/patch_2_blocks.exo
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191 changes: 191 additions & 0 deletions optimism/test/patch_2_blocks.txt
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@@ -0,0 +1,191 @@
netcdf patch_2_blocks {
dimensions:
len_name = 256 ;
time_step = UNLIMITED ; // (0 currently)
num_dim = 2 ;
num_nodes = 45 ;
num_elem = 16 ;
num_el_blk = 2 ;
num_node_sets = 4 ;
num_side_sets = 2 ;
num_el_in_blk1 = 8 ;
num_nod_per_el1 = 6 ;
num_el_in_blk2 = 8 ;
num_nod_per_el2 = 6 ;
num_side_ss1 = 2 ;
num_df_ss1 = 6 ;
num_side_ss2 = 4 ;
num_df_ss2 = 12 ;
num_qa_rec = 2 ;
four = 4 ;
len_string = 33 ;
num_nod_ns1 = 5 ;
num_nod_ns2 = 9 ;
num_nod_ns3 = 5 ;
num_nod_ns4 = 9 ;
variables:
double time_whole(time_step) ;
int eb_status(num_el_blk) ;
int eb_prop1(num_el_blk) ;
eb_prop1:name = "ID" ;
int ns_status(num_node_sets) ;
int ns_prop1(num_node_sets) ;
ns_prop1:name = "ID" ;
int ss_status(num_side_sets) ;
int ss_prop1(num_side_sets) ;
ss_prop1:name = "ID" ;
double coordx(num_nodes) ;
double coordy(num_nodes) ;
char eb_names(num_el_blk, len_name) ;
eb_names:_FillValue = "" ;
char ns_names(num_node_sets, len_name) ;
ns_names:_FillValue = "" ;
char ss_names(num_side_sets, len_name) ;
ss_names:_FillValue = "" ;
char coor_names(num_dim, len_name) ;
coor_names:_FillValue = "" ;
int connect1(num_el_in_blk1, num_nod_per_el1) ;
connect1:elem_type = "TRI6" ;
int connect2(num_el_in_blk2, num_nod_per_el2) ;
connect2:elem_type = "TRI6" ;
int elem_ss1(num_side_ss1) ;
int side_ss1(num_side_ss1) ;
double dist_fact_ss1(num_df_ss1) ;
int elem_ss2(num_side_ss2) ;
int side_ss2(num_side_ss2) ;
double dist_fact_ss2(num_df_ss2) ;
char qa_records(num_qa_rec, four, len_string) ;
int elem_map(num_elem) ;
int elem_num_map(num_elem) ;
int node_num_map(num_nodes) ;
int node_ns1(num_nod_ns1) ;
double dist_fact_ns1(num_nod_ns1) ;
int node_ns2(num_nod_ns2) ;
double dist_fact_ns2(num_nod_ns2) ;
int node_ns3(num_nod_ns3) ;
double dist_fact_ns3(num_nod_ns3) ;
int node_ns4(num_nod_ns4) ;
double dist_fact_ns4(num_nod_ns4) ;

// global attributes:
:api_version = 8.25f ;
:version = 8.25f ;
:floating_point_word_size = 8 ;
:file_size = 1 ;
:maximum_name_length = 32 ;
:int64_status = 0 ;
:title = "cubit(l2/optimism_dev/optimism/optimism/test/patch_2_blocks.exo): 12/04/2024: 11" ;
data:

eb_status = 1, 1 ;

eb_prop1 = 1, 2 ;

ns_status = 1, 1, 1, 1 ;

ns_prop1 = 1, 2, 3, 4 ;

ss_status = 1, 1 ;

ss_prop1 = 1, 2 ;

coordx = 0, -0.231415557451398, 0, -0.115707778725699, -0.115707778725699,
0, -0.25, 0, -0.125, 0, -0.125, -0.5, -0.5, -0.25, -0.5, -0.375, -0.375,
-0.125, -0.240707778725699, -0.5, -0.375, -0.375, -0.5,
-0.240707778725699, -0.365707778725699, 0.231415557451398,
0.115707778725699, 0.115707778725699, 0.25, 0.125, 0.125, 0.5, 0.5, 0.25,
0.5, 0.375, 0.375, 0.125, 0.240707778725699, 0.240707778725699,
0.365707778725699, 0.375, 0.5, 0.5, 0.375 ;

coordy = 0.25, 0.0185844425486017, 0, 0.134292221274301,
0.00929222127430085, 0.125, -0.25, -0.25, -0.25, -0.125, -0.125, 0.25, 0,
0.25, 0.125, 0.125, 0.25, 0.25, 0.134292221274301, -0.25, -0.25, -0.125,
-0.125, -0.115707778725699, 0.00929222127430085, -0.0185844425486018,
-0.134292221274301, -0.0092922212743009, 0.25, 0.25, 0.125, -0.25, 0,
-0.25, -0.125, -0.125, -0.25, -0.25, -0.134292221274301,
0.115707778725699, -0.0092922212743009, 0.125, 0.25, 0.125, 0.25 ;

eb_names =
"left_half",
"right_half" ;

ns_names =
"left",
"bottom",
"right",
"top" ;

ss_names =
"right",
"top" ;

coor_names =
"x",
"y" ;

connect1 =
1, 2, 3, 4, 5, 6,
7, 8, 3, 9, 10, 11,
12, 13, 14, 15, 16, 17,
1, 14, 2, 18, 19, 4,
20, 7, 13, 21, 22, 23,
7, 2, 13, 24, 25, 22,
2, 14, 13, 19, 16, 25,
2, 7, 3, 24, 11, 5 ;

connect2 =
8, 26, 3, 27, 28, 10,
29, 1, 3, 30, 6, 31,
32, 33, 34, 35, 36, 37,
8, 34, 26, 38, 39, 27,
29, 26, 33, 40, 41, 42,
29, 33, 43, 42, 44, 45,
26, 34, 33, 39, 36, 41,
26, 29, 3, 40, 31, 28 ;

elem_ss1 = 11, 14 ;

side_ss1 = 1, 2 ;

dist_fact_ss1 = 1, 1, 1, 1, 1, 1 ;

elem_ss2 = 4, 3, 14, 10 ;

side_ss2 = 1, 3, 3, 1 ;

dist_fact_ss2 = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ;

qa_records =
"CUBIT",
"15.8",
"06/22/2021",
"12:52:26",
"CUBIT",
"17.02.0",
"12/04/2024",
"11:57:45" ;

elem_map = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ;

elem_num_map = 100, 2, 103, 4, 101, 6, 102, 8, 9, 10, 11, 12, 13, 14, 15, 104 ;

node_num_map = 1, 15, 7, 24, 25, 22, 13, 2, 32, 23, 26, 5, 12, 11, 33, 27,
21, 20, 28, 6, 34, 29, 35, 30, 31, 14, 36, 37, 10, 17, 38, 3, 9, 8, 44,
39, 19, 18, 40, 41, 42, 43, 4, 45, 16 ;

node_ns1 = 12, 15, 13, 23, 20 ;

dist_fact_ns1 = 1, 1, 1, 1, 1 ;

node_ns2 = 20, 8, 32, 21, 7, 9, 38, 34, 37 ;

dist_fact_ns2 = 1, 1, 1, 1, 1, 1, 1, 1, 1 ;

node_ns3 = 32, 35, 33, 44, 43 ;

dist_fact_ns3 = 1, 1, 1, 1, 1 ;

node_ns4 = 1, 12, 43, 18, 14, 17, 45, 29, 30 ;

dist_fact_ns4 = 1, 1, 1, 1, 1, 1, 1, 1, 1 ;
}
19 changes: 16 additions & 3 deletions optimism/test/test_ReadExodusMesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,7 @@
haveNetCDF = 'netCDF4' in sys.modules
skipMessage = 'netCDF4 not installed, exodus reader disabled'


TEST_FILE = pathlib.Path(__file__).parent.joinpath('patch_2_blocks.g')
TEST_FILE = pathlib.Path(__file__).parent.joinpath('patch_2_blocks.exo')


class TestMeshReadData(TestFixture.TestFixture):
Expand Down Expand Up @@ -91,6 +90,20 @@ def test_side_set_sizes(self):
self.assertEqual(self.mesh.sideSets["right"].shape[0], 2)
self.assertEqual(self.mesh.sideSets["top"].shape[0], 4)

@TestFixture.unittest.skipIf(not haveNetCDF, skipMessage)
def test_block_maps(self):
# ncdump output (see patch_2_blocks.txt)
# elem_num_map = 100, 2, 103, 4, 101, 6, 102, 8, 9, 10, 11, 12, 13, 14, 15, 104;
goldBlock1Map = [100, 2, 103, 4, 101, 6, 102, 8]
block1Map = self.mesh.block_maps['left_half']
self.assertEqual(block1Map.size, 8)
self.assertArrayEqual(block1Map, goldBlock1Map)

goldBlock2Map = [9, 10, 11, 12, 13, 14, 15, 104]
block2Map = self.mesh.block_maps['right_half']
self.assertEqual(block2Map.size, 8)
self.assertArrayEqual(block2Map, goldBlock2Map)



class TestMeshReadPatchTest(TestFixture.TestFixture):
Expand All @@ -113,7 +126,7 @@ def setUp(self):
self.internalVariables = mechBvp.compute_initial_state()


@TestFixture.unittest.skipIf(not haveNetCDF, skipMessage)
@TestFixture.unittest.skipIf(not haveNetCDF, skipMessage)
def test_dirichlet_patch_test(self):
ebcs = [FunctionSpace.EssentialBC(nodeSet='left', component=0),
FunctionSpace.EssentialBC(nodeSet='left', component=1),
Expand Down

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