def metaDataScalarField(name, time, cycle, dim):
optlistDef = None
optlistMV = silo.DBoptlist()
optlistVar = silo.DBoptlist()
for optlist in (optlistMV, optlistVar):
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlist.addOption(SA._DBOPT_TENSOR_RANK, SA._DB_VARTYPE_SCALAR) == 0
return (None, SA._DB_VARTYPE_SCALAR, optlistDef, optlistMV, optlistVar)
def metaDataVectorField(name, time, cycle, dim):
assert dim in (2,3)
optlistDef = silo.DBoptlist()
optlistMV = silo.DBoptlist()
optlistVar = silo.DBoptlist()
for optlist in (optlistDef, optlistMV, optlistVar):
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlistMV.addOption(SA._DBOPT_TENSOR_RANK, SA._DB_VARTYPE_VECTOR) == 0
assert optlistVar.addOption(SA._DBOPT_HIDE_FROM_GUI, 1) == 0
assert optlistVar.addOption(SA._DBOPT_TENSOR_RANK, SA._DB_VARTYPE_SCALAR) == 0
if dim == 2:
return ("{<CELLS/%s_x>, <CELLS/%s_y>}" % (name, name), SA._DB_VARTYPE_VECTOR,
optlistDef, optlistMV, optlistVar)
else:
return ("{<CELLS/%s_x>, <CELLS/%s_y>, <CELLS/%s_z>}" % (name, name, name), SA._DB_VARTYPE_VECTOR,
optlistDef, optlistMV, optlistVar)
def metaDataTensorField(name, time, cycle, dim):
assert dim in (2, 3)
optlistDef = silo.DBoptlist()
optlistMV = silo.DBoptlist()
optlistVar = silo.DBoptlist()
for optlist in (optlistDef, optlistMV, optlistVar):
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlistMV.addOption(SA._DBOPT_TENSOR_RANK,
SA._DB_VARTYPE_TENSOR) == 0
assert optlistVar.addOption(SA._DBOPT_HIDE_FROM_GUI, 1) == 0
assert optlistVar.addOption(SA._DBOPT_TENSOR_RANK,
SA._DB_VARTYPE_SCALAR) == 0
if dim == 2:
return ("{{%s_xx, %s_xy}, {%s_yx, %s_yy}}" % (name, name, name, name),
SA._DB_VARTYPE_TENSOR, optlistDef, optlistMV, optlistVar)
else:
return (
"{{%s_xx, %s_xy, %s_xz}, {%s_yx, %s_yy, %s_yz}, {%s_zx, %s_zy, %s_zz}}"
% (name, name, name, name, name, name, name, name, name),
SA._DB_VARTYPE_TENSOR, optlistDef, optlistMV, optlistVar)
def writeDomainSiloFile(ndim, maxproc, baseDirectory, baseName,
procDirBaseName, materials, rhosamp, xminblock,
xmaxblock, nblock, jsplit, label, time, cycle,
pretendRZ):
assert jsplit < ndim
# Make sure the directories are there.
if mpi.rank == 0:
for iproc in xrange(maxproc):
pth = os.path.join(baseDirectory, procDirBaseName)
if not os.path.exists(pth):
os.makedirs(pth)
mpi.barrier()
# Is there anything to do?
if mpi.rank < maxproc:
numZones = 1
numNodes = 1
nblocknodes = list(nblock)
for i, x in enumerate(nblock):
numZones *= x
numNodes *= x + 1
nblocknodes[i] = x + 1
assert numZones > 0
assert len(rhosamp) == numZones
# Make a vector<int> version of nblock
nblock_vec = Spheral.vector_of_int(ndim)
for jdim in xrange(ndim):
nblock_vec[jdim] = nblock[jdim]
# Create the file.
fileName = os.path.join(baseDirectory, procDirBaseName,
"domain%i.silo" % mpi.rank)
f = silo.DBCreate(fileName, SA._DB_CLOBBER, SA._DB_LOCAL, label,
SA._DB_HDF5)
nullOpts = silo.DBoptlist()
# Make the hblk0 directory.
assert silo.DBMkDir(f, "hblk0") == 0
# Write the domain mesh.
coords = Spheral.vector_of_vector_of_double(ndim)
for jdim in xrange(ndim):
coords[jdim] = Spheral.vector_of_double(nblocknodes[jdim])
dx = (xmaxblock[jdim] - xminblock[jdim]) / nblock[jdim]
for i in xrange(nblocknodes[jdim]):
coords[jdim][i] = xminblock[jdim] + i * dx
optlist = silo.DBoptlist()
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
if pretendRZ:
assert optlist.addOption(SA._DBOPT_COORDSYS,
SA._DB_CYLINDRICAL) == 0
else:
assert optlist.addOption(SA._DBOPT_COORDSYS, SA._DB_CARTESIAN) == 0
assert silo.DBPutQuadmesh(f, "hblk0/hydro_mesh", coords, optlist) == 0
# # Domain neighbors.
# if maxproc > 1 and mpi.rank < maxproc:
# domain_neighbors = Spheral.vector_of_vector_of_int(2)
# if mpi.rank > 0:
# domain_neighbors[1].append(mpi.rank - 1)
# if mpi.rank < maxproc - 1:
# domain_neighbors[1].append(mpi.rank + 1)
# domain_neighbors[0].append(len(domain_neighbors[1]))
# assert silo.DBPutCompoundarray(f, "DOMAIN_NEIGHBOR_NUMS", Spheral.vector_of_string(len(domain_neighbors), "dummy"), domain_neighbors, nullOpts) == 0
# # Domain shared nodes.
# if maxproc > 1 and mpi.rank < maxproc:
# for idomain in xrange(len(domain_neighbors[1])):
# commelements = Spheral.vector_of_vector_of_int(11)
# if mpi.rank == 0:
# face = nnodes[jsplit] - 1
# elif mpi.rank == maxproc - 1:
# face = 0
# elif idomain == 0:
# face = 0
# else:
# face = nnodes[jsplit] - 1
# if jsplit == 0:
# for j in xrange(nnodes[1]):
# for k in xrange(nnodes[2]):
# commelements[6].append(face + j*nnodes[0] + k*nnodes[0]*nnodes[1])
# elif jsplit == 1:
# for i in xrange(nnodes[0]):
# for k in xrange(nnodes[2]):
# commelements[6].append(i + face*nnodes[0] + k*nnodes[0]*nnodes[1])
# else:
# for i in xrange(nnodes[0]):
# for j in xrange(nnodes[1]):
# commelements[6].append(i + j*nnodes[0] + face*nnodes[0]*nnodes[1])
# assert silo.DBPutCompoundarray(f, "DOMAIN_NEIGHBOR%i" % idomain, Spheral.vector_of_string(11, "dummy"), commelements, nullOpts) == 0
# Write materials.
if materials:
matnos = Spheral.vector_of_int(1, 0)
for i in xrange(len(materials)):
matnos.append(i + 1)
assert len(matnos) == len(materials) + 1
matlist = Spheral.vector_of_int(numZones, 0)
matnames = Spheral.vector_of_string(1, "void")
for imat, nodeList in enumerate(materials):
for i in xrange(numZones):
if rhosamp[i] > 0.0:
matlist[i] = imat + 1
matnames.append(nodeList.name)
assert len(matlist) == numZones
assert len(matnames) == len(materials) + 1
matOpts = silo.DBoptlist(1024)
assert matOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert matOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert matOpts.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS,
matnames) == 0
assert silo.DBPutMaterial(f, "hblk0/Materials", "hydro_mesh",
matnos, matlist, nblock_vec,
Spheral.vector_of_int(),
Spheral.vector_of_int(),
Spheral.vector_of_int(),
Spheral.vector_of_double(), matOpts) == 0
# Write the field variables.
varOpts = silo.DBoptlist(1024)
assert varOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert varOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutQuadvar1(f, "hblk0/den", "hydro_mesh", rhosamp,
Spheral.vector_of_double(), SA._DB_ZONECENT,
nblock_vec, varOpts) == 0
# That's it.
assert silo.DBClose(f) == 0
del f
return
def writeMasterSiloFile(ndim, nblock, jsplit, baseDirectory, baseName,
procDirBaseName, materials, rhosamp, label, time,
cycle):
nullOpts = silo.DBoptlist()
# Decide which domains have information.
if len(rhosamp) > 0:
myvote = mpi.rank + 1
else:
myvote = 0
maxproc = mpi.allreduce(myvote, mpi.MAX)
assert maxproc <= mpi.procs
# Pattern for constructing per domain variables.
domainNamePatterns = [
os.path.join(procDirBaseName, "domain%i.silo:%%s" % i)
for i in xrange(maxproc)
]
domainVarNames = Spheral.vector_of_string()
for iproc, p in enumerate(domainNamePatterns):
domainVarNames.append(p % "/hblk0/den")
assert len(domainVarNames) == maxproc
# We need each domains nblock info.
nblocks = [nblock]
for sendproc in xrange(1, maxproc):
if mpi.rank == sendproc:
mpi.send(nblock, dest=0, tag=50)
if mpi.rank == 0:
nblocks.append(mpi.recv(source=sendproc, tag=50)[0])
# Create the master file.
if mpi.rank == 0:
fileName = os.path.join(baseDirectory, baseName + ".silo")
f = silo.DBCreate(fileName, SA._DB_CLOBBER, SA._DB_LOCAL, label,
SA._DB_HDF5)
nullOpts = silo.DBoptlist()
# Write the domain file names and types.
domainNames = Spheral.vector_of_string()
meshTypes = Spheral.vector_of_int(maxproc, SA._DB_QUADMESH)
for p in domainNamePatterns:
domainNames.append(p % "hblk0/hydro_mesh")
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutMultimesh(f, "hydro_mesh", domainNames, meshTypes,
optlist) == 0
# Write material names.
material_names = Spheral.vector_of_string()
matnames = Spheral.vector_of_string(1, "void")
matnos = Spheral.vector_of_int(1, 0)
for p in domainNamePatterns:
material_names.append(p % "/hblk0/Materials")
for i, name in enumerate([x.name for x in materials]):
matnames.append(name)
matnos.append(i + 1)
assert len(material_names) == maxproc
assert len(matnames) == len(materials) + 1
assert len(matnos) == len(materials) + 1
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlist.addOption(SA._DBOPT_MMESH_NAME, "hydro_mesh") == 0
assert optlist.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS,
matnames) == 0
assert optlist.addOption(SA._DBOPT_MATNOS, SA._DBOPT_NMATNOS,
matnos) == 0
assert silo.DBPutMultimat(f, "Materials", material_names, optlist) == 0
# Write the variables descriptors.
# We currently hardwire for the single density variable.
types = Spheral.vector_of_int(maxproc, SA._DB_QUADVAR)
assert len(domainVarNames) == maxproc
optlistMV = silo.DBoptlist()
assert optlistMV.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlistMV.addOption(SA._DBOPT_DTIME, time) == 0
#assert optlistMV.addOption(SA._DBOPT_TENSOR_RANK, SA._DB_VARTYPE_SCALAR) == 0
assert optlistMV.addOption(SA._DBOPT_BLOCKORIGIN, 0) == 0
assert optlistMV.addOption(SA._DBOPT_MMESH_NAME, "hydro_mesh") == 0
assert silo.DBPutMultivar(f, "den", domainVarNames, types,
optlistMV) == 0
# Write the dummy variable "akap_0" to tell Hades we're actually Hydra or something.
assert silo.DBPutQuadvar1(f, "akap_0", "hydro_mesh",
Spheral.vector_of_double(ndim * ndim, 0.0),
Spheral.vector_of_double(), SA._DB_ZONECENT,
Spheral.vector_of_int(ndim, ndim),
nullOpts) == 0
# Write domain and mesh size info.
assert silo.DBMkDir(f, "Decomposition") == 0
assert silo.DBWrite(f, "Decomposition/NumDomains", maxproc) == 0
assert silo.DBWrite(f, "Decomposition/NumLocalDomains", maxproc) == 0
assert silo.DBWrite(f, "Decomposition/NumBlocks", 1) == 0
#assert silo.DBWrite(f, "Decomposition/LocalName", "hblk") == 0
localDomains = Spheral.vector_of_int()
domainFiles = Spheral.vector_of_vector_of_int(1)
for i in xrange(maxproc):
localDomains.append(i)
domainFiles[0].append(i)
assert silo.DBWrite(f, "Decomposition/LocalDomains", localDomains) == 0
assert silo.DBWrite(f, "DomainFiles", domainFiles) == 0
for iproc in xrange(maxproc):
assert silo.DBMkDir(f, "Decomposition/gmap%i" % iproc) == 0
stuff = Spheral.vector_of_int(12, 0)
for jdim in xrange(ndim):
stuff[6 + jdim] = nblocks[iproc][jdim]
if iproc in (0, maxproc - 1):
assert silo.DBWrite(
f, "Decomposition/gmap%i/NumNeighbors" % iproc, 1) == 0
else:
assert silo.DBWrite(
f, "Decomposition/gmap%i/NumNeighbors" % iproc, 2) == 0
assert silo.DBWrite(f, "Decomposition/gmap%i/gmap" % iproc,
stuff) == 0
# Close the file.
if mpi.rank == 0:
assert silo.DBClose(f) == 0
del f
return maxproc
def writeDomainSiloFile(ndim, baseDirectory, baseName, procDirBaseName,
nodeLists, label, time, cycle, dumpGhosts, fieldwad):
# Create the file.
fileName = os.path.join(baseDirectory, procDirBaseName % mpi.rank,
baseName + ".silo")
db = silo.DBCreate(fileName, SA._DB_CLOBBER, SA._DB_LOCAL, label,
SA._DB_HDF5)
nullOpts = silo.DBoptlist()
# Read the per material info.
if dumpGhosts:
ntot = sum([n.numNodes for n in nodeLists])
else:
ntot = sum([n.numInternalNodes for n in nodeLists])
coords = vector_of_vector_of_double(ndim)
for nodes in nodeLists:
if dumpGhosts:
pos = nodes.positions().allValues()
else:
pos = nodes.positions().internalValues()
n = len(pos)
for j in xrange(ndim):
for i in xrange(n):
coords[j].append(pos[i][j])
for j in xrange(ndim):
assert len(coords[j]) == ntot
# Write the Pointmesh.
meshOpts = silo.DBoptlist(1024)
assert meshOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert meshOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutPointmesh(db, "mesh", coords, meshOpts) == 0
# Write materials.
matnos = vector_of_int()
for i in xrange(len(nodeLists)):
matnos.append(i)
assert len(matnos) == len(nodeLists)
matlist = vector_of_int()
matnames = vector_of_string()
for (nodeList, imat) in zip(nodeLists, xrange(len(nodeLists))):
if dumpGhosts:
matlist += vector_of_int(nodeList.numNodes, imat)
else:
matlist += vector_of_int(nodeList.numInternalNodes, imat)
matnames.append(nodeList.name)
assert len(matlist) == ntot
assert len(matnames) == len(nodeLists)
matOpts = silo.DBoptlist(1024)
assert matOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert matOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert matOpts.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS,
matnames) == 0
vecInt = vector_of_int(0)
vecDouble = vector_of_double(0)
assert silo.DBPutMaterial(db, "material", "mesh", matnos, matlist, vecInt,
vecInt, vecInt, vecInt, vecDouble, matOpts) == 0
# Write the variable descriptions for non-scalar variables (vector and tensors).
writeDefvars(db, fieldwad)
# Write the field components.
varOpts = silo.DBoptlist(1024)
assert varOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert varOpts.addOption(SA._DBOPT_DTIME, time) == 0
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
for subname, vals in subvars:
if len(vals) > 0:
assert silo.DBPutPointvar1(db, subname, "mesh", vals,
varOpts) == 0
# That's it.
assert silo.DBClose(db) == 0
del db
return
def writeMasterSiloFile(ndim, baseDirectory, baseName, procDirBaseName,
nodeLists, label, time, cycle, dumpGhosts, fieldwad):
nullOpts = silo.DBoptlist()
# Pattern for constructing per domain variables.
domainNamePatterns = [
os.path.join(procDirBaseName % i, baseName + ".silo:%s")
for i in xrange(mpi.procs)
]
# Create the master file.
if mpi.rank == 0:
fileName = os.path.join(baseDirectory, baseName + ".silo")
db = silo.DBCreate(fileName, SA._DB_CLOBBER, SA._DB_LOCAL, label,
SA._DB_HDF5)
# Write the domain file names and types.
domainNames = vector_of_string()
meshTypes = vector_of_int(mpi.procs, SA._DB_POINTMESH)
for p in domainNamePatterns:
domainNames.append(p % "mesh")
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutMultimesh(db, "MESH", domainNames, meshTypes,
optlist) == 0
# Extract the material names, and write per material info if any.
if len(nodeLists) > 0:
# Write material names.
if mpi.rank == 0:
materialNames = [x.name for x in nodeLists]
material_names = vector_of_string()
matnames = vector_of_string()
matnos = vector_of_int()
for p in domainNamePatterns:
material_names.append(p % "material")
for (name, i) in zip(materialNames, range(len(materialNames))):
matnames.append(name)
matnos.append(i)
assert len(material_names) == mpi.procs
assert len(matnames) == len(nodeLists)
assert len(matnos) == len(nodeLists)
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlist.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS,
matnames) == 0
assert optlist.addOption(SA._DBOPT_MATNOS, SA._DBOPT_NMATNOS,
matnos) == 0
assert silo.DBPutMultimat(db, "MATERIAL", material_names,
optlist) == 0
# Write the variable descriptions for non-scalar variables (vector and tensors).
writeDefvars(db, fieldwad)
# Write the variables descriptors.
types = vector_of_int(mpi.procs, SA._DB_POINTVAR)
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
domainVarNames = vector_of_string()
nlocalvals = sum([len(x[1]) for x in subvars])
if desc is None:
for iproc, p in enumerate(domainNamePatterns):
nvals = mpi.bcast(nlocalvals, root=iproc)
if nvals > 0:
domainVarNames.append(p % name)
else:
domainVarNames.append("EMPTY")
assert len(domainVarNames) == mpi.procs
if mpi.rank == 0:
assert silo.DBPutMultivar(db, name, domainVarNames, types,
optlistMV) == 0
else:
for subname, vals in subvars:
domainVarNames = vector_of_string()
for iproc, p in enumerate(domainNamePatterns):
nvals = mpi.bcast(nlocalvals, root=iproc)
if nvals > 0:
domainVarNames.append(p % subname)
else:
domainVarNames.append("EMPTY")
assert len(domainVarNames) == mpi.procs
if mpi.rank == 0:
assert silo.DBPutMultivar(db, subname, domainVarNames,
types, optlistVar) == 0
# That's it.
if mpi.rank == 0:
assert silo.DBClose(db) == 0
del db
return
def writeDomainMeshSiloFile(dirName, mesh, index2zone, label, nodeLists, time, cycle, fieldwad,
pretendRZ, nodeArrays, zoneArrays, faceArrays,
meshType = SA._DB_UCDMESH):
# Is there anything to do?
numZones = len(mesh.cells)
if numZones > 0:
# Create the file.
fileName = os.path.join(dirName, "domain%i.silo" % mpi.rank)
db = silo.DBCreate(fileName,
SA._DB_CLOBBER, SA._DB_LOCAL, label, SA._DB_HDF5)
nullOpts = silo.DBoptlist()
# Make directories for variables.
assert silo.DBMkDir(db, "CELLS") == 0
assert silo.DBMkDir(db, "POINTS") == 0 # HACK
# Determine our dimensionality
if isinstance(mesh, polytope.Tessellation2d):
nDim = 2
else:
assert isinstance(mesh, polytope.Tessellation3d)
nDim = 3
# Write a Polygonal zone list.
zonelistName = { 2 : "zonelist",
3 : "PHzonelist" }
if nDim == 2:
# Read out the zone nodes. We rely on these already being arranged
# counter-clockwise.
zoneNodes = vector_of_vector_of_int()
shapesize = vector_of_int()
for zoneID in xrange(numZones):
zone = mesh.cells[zoneID]
nodes = vector_of_int()
for iface in zone:
if iface < 0:
nodes.append(mesh.faces[~iface][1])
else:
nodes.append(mesh.faces[iface][0])
zoneNodes.append(nodes)
shapesize.append(len(nodes))
assert len(zoneNodes) == numZones
assert len(shapesize) == numZones
assert silo.DBPutZonelist2(db, zonelistName[nDim], nDim, zoneNodes, 0, 0,
vector_of_int(numZones, SA._DB_ZONETYPE_POLYGON),
shapesize,
vector_of_int(numZones, 1),
nullOpts) == 0
# Write a Polyhedral zone list.
if nDim == 3:
# Construct the face-node lists.
numFaces = len(mesh.faces)
faceNodes = vector_of_vector_of_int(numFaces)
for iface in xrange(numFaces):
for j in xrange(len(mesh.faces[iface])):
faceNodes[iface].append(mesh.faces[iface][j])
assert len(faceNodes[iface]) == len(mesh.faces[iface])
assert len(faceNodes) == numFaces
# Construct the zone-face list. We use the ones complement of a face ID
# to indicate that face needs to be reversed in reference to this zone.
# This is the same convention as polytope, so just copy it.
zoneFaces = mesh.cells
assert len(zoneFaces) == numZones
assert silo.DBPutPHZonelist(db, zonelistName[nDim], faceNodes, zoneFaces, 0, (numZones - 1), nullOpts) == 0
# Construct the mesh node coordinates.
assert len(mesh.nodes) % nDim == 0
numNodes = len(mesh.nodes)/nDim
coords = vector_of_vector_of_double(nDim, vector_of_double(numNodes))
for nodeID in xrange(numNodes):
for idim in xrange(nDim):
coords[idim][nodeID] = mesh.nodes[nDim*nodeID + idim]
assert len(coords) == nDim
# Write the mesh itself.
meshOpts = silo.DBoptlist(1024)
assert meshOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert meshOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert meshOpts.addOption(SA._DBOPT_COORDSYS, SA._DB_CARTESIAN) == 0
assert meshOpts.addOption(SA._DBOPT_NSPACE, nDim) == 0
assert meshOpts.addOption(SA._DBOPT_TV_CONNECTIVITY, 1) == 0
if nDim == 2:
if pretendRZ:
assert meshOpts.addOption(SA._DBOPT_COORDSYS, SA._DB_CYLINDRICAL) == 0
assert meshOpts.addOption(SA._DBOPT_XLABEL, "z") == 0
assert meshOpts.addOption(SA._DBOPT_YLABEL, "r") == 0
assert silo.DBPutUcdmesh(db, "MESH", coords, numZones, zonelistName[nDim], "NULL", meshOpts) == 0
else:
assert meshOpts.addOption(SA._DBOPT_PHZONELIST, zonelistName[nDim]) == 0
assert silo.DBPutUcdmesh(db, "MESH", coords, numZones, "NULL", "NULL", meshOpts) == 0
# Write materials.
if nodeLists:
matnos = vector_of_int()
for i in xrange(len(nodeLists)):
matnos.append(i)
assert len(matnos) == len(nodeLists)
matlist = vector_of_int(numZones)
matnames = vector_of_string()
offset = 0
for (nodeList, imat) in zip(nodeLists, xrange(len(nodeLists))):
for i in xrange(nodeList.numInternalNodes):
for j in index2zone[offset + i]:
matlist[j] = imat
matnames.append(nodeList.name)
offset += nodeList.numInternalNodes
assert len(matlist) == numZones
assert len(matnames) == len(nodeLists)
matOpts = silo.DBoptlist(1024)
assert matOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert matOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert matOpts.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS, matnames) == 0
assert silo.DBPutMaterial(db, "MATERIAL", "MESH", matnos, matlist, vector_of_int(),
vector_of_int(), vector_of_int(), vector_of_int(), vector_of_double(),
matOpts) == 0
assert silo.DBPutMaterial(db, "PointMATERIAL", "PointMESH", matnos, matlist, vector_of_int(),
vector_of_int(), vector_of_int(), vector_of_int(), vector_of_double(),
matOpts) == 0
# Write the variable descriptions for non-scalar variables (vector and tensors).
#writeDefvars(db, fieldwad)
# Write the field components.
centering = SA._DB_ZONECENT
varOpts = silo.DBoptlist(1024)
assert varOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert varOpts.addOption(SA._DBOPT_DTIME, time) == 0
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
for subname, vals in subvars:
if len(vals) > 0:
if isinstance(vals, vector_of_double):
assert silo.DBPutUcdvar1(db, "CELLS_" + subname, "MESH", vals, vector_of_double(), centering, varOpts) == 0
elif isinstance(vals, vector_of_int):
assert silo.DBPutUcdvar1(db, "CELLS_" + subname, "MESH", vals, vector_of_int(), centering, varOpts) == 0
# HACK: Write the field components on the point mesh as well. Remove when the vardef version is working.
centering = SA._DB_ZONECENT
varOpts = silo.DBoptlist(1024)
assert varOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert varOpts.addOption(SA._DBOPT_DTIME, time) == 0
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
for subname, vals in subvars:
if len(vals) > 0:
assert silo.DBPutPointvar1(db, "POINTS_" + subname, "PointMESH", vals, varOpts) == 0
# Write the set of neighbor domains.
thpt = vector_of_vector_of_int()
thpt.append(vector_of_int(1, len(mesh.neighborDomains)))
thpt.append(vector_of_int())
for i in mesh.neighborDomains:
thpt[-1].append(i)
elemNames = vector_of_string()
elemNames.append("num neighbor domains")
elemNames.append("neighbor domains")
assert silo.DBPutCompoundarray(db, "DOMAIN_NEIGHBOR_NUMS", elemNames, thpt, nullOpts) == 0
# Write the shared nodes for each neighbor domain.
sharedNodes = mesh.sharedNodes
for ineighborDomain in xrange(len(mesh.neighborDomains)):
nodes = vector_of_int()
for i in sharedNodes[ineighborDomain]:
nodes.append(i)
assert len(nodes) == len(sharedNodes[ineighborDomain])
assert silo.DBPutCompoundarray(db, "DOMAIN_NEIGHBOR%i" % ineighborDomain,
vector_of_string(1, "shared_nodes"),
vector_of_vector_of_int(1, nodes),
nullOpts) == 0
# If requested, write out annotations for the nodes, zones, and faces.
if (not (nodeArrays is None) or
not (zoneArrays is None) or
not (faceArrays is None)):
names = vector_of_string()
values = vector_of_vector_of_int()
if not (nodeArrays is None):
for pair in nodeArrays:
assert len(pair) == 2
if len(pair[1]) > 0:
names.append(pair[0] + "_node")
values.append(vector_of_int())
for i in pair[1]:
values[-1].append(i)
assert len(values[-1]) == len(pair[1])
if not (zoneArrays is None):
for pair in zoneArrays:
assert len(pair) == 2
if len(pair[1]) > 0:
names.append(pair[0] + "_zone")
values.append(vector_of_int())
for i in pair[1]:
values[-1].append(i)
assert len(values[-1]) == len(pair[1])
if not (faceArrays is None):
for pair in faceArrays:
assert len(pair) == 2
if len(pair[1]) > 0:
names.append(pair[0] + "_face")
values.append(vector_of_int())
for i in pair[1]:
values[-1].append(i)
assert len(values[-1]) == len(pair[1])
assert len(names) == len(values)
if len(names) > 0:
assert silo.DBPutCompoundarray(db, "ANNOTATION_INT", names, values, nullOpts) == 0
# Write the point mesh.
if nodeLists:
ntot = sum([n.numInternalNodes for n in nodeLists])
coords = vector_of_vector_of_double(nDim)
for nodes in nodeLists:
pos = nodes.positions().internalValues()
n = len(pos)
for j in xrange(nDim):
for i in xrange(n):
coords[j].append(pos[i][j])
for j in xrange(nDim):
assert len(coords[j]) == ntot
# Write the Pointmesh.
meshOpts = silo.DBoptlist(1024)
assert meshOpts.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert meshOpts.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutPointmesh(db, "PointMESH", coords, meshOpts) == 0
# That's it.
assert silo.DBClose(db) == 0
del db
return
def writeMasterMeshSiloFile(dirName, mesh, label, nodeLists, time, cycle, fieldwad,
meshType = SA._DB_UCDMESH):
# Figure out who has something to write. Silo can't handle empty variables...
numZonesPerDomain = mpi.allreduce([(mpi.rank, len(mesh.cells))], mpi.SUM)
numZonesPerDomain.sort()
numZonesPerDomain = [x[1] for x in numZonesPerDomain]
# Only processor 0 actually writes the file.
linkfile = None
if mpi.rank == 0:
nullOpts = silo.DBoptlist()
# Create the master file.
p0, p1 = os.path.split(dirName)
fileName = os.path.join(dirName, "OvlTop.silo")
db = silo.DBCreate(fileName,
SA._DB_CLOBBER, SA._DB_LOCAL, label, SA._DB_HDF5)
# Make directories for variables.
assert silo.DBMkDir(db, "CELLS") == 0
assert silo.DBMkDir(db, "POINTS") == 0 # HACK
# Pattern for constructing per domain variables.
domainNamePatterns = [("%s/domain%i.silo:" % (p1, i)) + "%s" for i in xrange(mpi.procs) if numZonesPerDomain[i] > 0]
numDomains = len(domainNamePatterns)
# Write the domain file names and types.
domainNames = vector_of_string()
meshTypes = vector_of_int()
i = 0
for p in domainNamePatterns:
domainNames.append(p % "MESH")
meshTypes.append(meshType)
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutMultimesh(db, "MMESH", domainNames, meshTypes, optlist) == 0
# Also write out the points as a point mesh.
if nodeLists and mpi.rank == 0:
domainNames = vector_of_string()
meshTypes = vector_of_int(mpi.procs, SA._DB_POINTMESH)
for p in domainNamePatterns:
domainNames.append(p % "PointMESH")
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert silo.DBPutMultimesh(db, "MPointMESH", domainNames, meshTypes, optlist) == 0
# Extract the material names, and write per material info if any.
if nodeLists:
# Write material names (MESH)
materialNames = [x.name for x in nodeLists]
material_names = vector_of_string()
matnames = vector_of_string()
matnos = vector_of_int()
for p in domainNamePatterns:
material_names.append(p % "MATERIAL")
for i, name in enumerate(materialNames):
matnames.append(name)
matnos.append(i)
assert len(material_names) == numDomains
assert len(matnames) == len(nodeLists)
assert len(matnos) == len(nodeLists)
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlist.addOption(SA._DBOPT_MMESH_NAME, "MMESH") == 0
assert optlist.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS, matnames) == 0
assert optlist.addOption(SA._DBOPT_MATNOS, SA._DBOPT_NMATNOS, matnos) == 0
assert silo.DBPutMultimat(db, "MMATERIAL", material_names, optlist) == 0
# Write material names (PointMESH)
materialNames = [x.name for x in nodeLists]
material_names = vector_of_string()
matnames = vector_of_string()
matnos = vector_of_int()
for p in domainNamePatterns:
material_names.append(p % "PointMATERIAL")
for i, name in enumerate(materialNames):
matnames.append(name)
matnos.append(i)
assert len(material_names) == numDomains
assert len(matnames) == len(nodeLists)
assert len(matnos) == len(nodeLists)
optlist = silo.DBoptlist(1024)
assert optlist.addOption(SA._DBOPT_CYCLE, cycle) == 0
assert optlist.addOption(SA._DBOPT_DTIME, time) == 0
assert optlist.addOption(SA._DBOPT_MMESH_NAME, "MPointMESH") == 0
assert optlist.addOption(SA._DBOPT_MATNAMES, SA._DBOPT_NMATNOS, matnames) == 0
assert optlist.addOption(SA._DBOPT_MATNOS, SA._DBOPT_NMATNOS, matnos) == 0
assert silo.DBPutMultimat(db, "MPointMATERIAL", material_names, optlist) == 0
# Write the variable descriptions for non-scalar variables (vector and tensors).
writeDefvars(db, fieldwad)
# Write the attributes for each variable.
# This is largely an Overlink thing, which only needs the components of types like vectors.
if len(fieldwad) > 0:
attrNames = vector_of_string()
attrs = vector_of_vector_of_int()
thpt = vector_of_int()
thpt.append(OverlinkAttrs["ATTR_ZONAL"])
thpt.append(OverlinkAttrs["ATTR_INTENSIVE"])
thpt.append(OverlinkAttrs["ATTR_SECOND_ORDER"])
thpt.append(0)
thpt.append(OverlinkAttrs["ATTR_FLOAT"])
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
for subname, vals in subvars:
attrNames.append(subname)
attrs.append(thpt)
assert len(attrNames) == len(attrs)
silo.DBPutCompoundarray(db, "VAR_ATTRIBUTES", attrNames, attrs, nullOpts)
# Write the variables descriptors.
ucdTypes = vector_of_int(numDomains, SA._DB_UCDVAR)
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
domainVarNames = vector_of_string()
for p in domainNamePatterns:
domainVarNames.append(p % ("CELLS_" + name))
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "CELLS/" + name, domainVarNames, ucdTypes, optlistMV) == 0
if desc != None:
for subname, vals in subvars:
domainVarNames = vector_of_string()
for p in domainNamePatterns:
domainVarNames.append(p % ("CELLS_" + subname))
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "CELLS/" + subname, domainVarNames, ucdTypes, optlistVar) == 0
# HACK: repeating for point values -- remove when vardefs work
# Write the variables descriptors.
ptTypes = vector_of_int(numDomains, SA._DB_POINTVAR)
for name, desc, type, optlistDef, optlistMV, optlistVar, subvars in fieldwad:
domainVarNames = vector_of_string()
for p in domainNamePatterns:
domainVarNames.append(p % ("POINTS_" + name))
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "POINTS/" + name, domainVarNames, ptTypes, optlistMV) == 0
if desc != None:
for subname, vals in subvars:
domainVarNames = vector_of_string()
for p in domainNamePatterns:
domainVarNames.append(p % ("POINTS_" + subname))
assert len(domainVarNames) == numDomains
assert silo.DBPutMultivar(db, "POINTS/" + subname, domainVarNames, ptTypes, optlistVar) == 0
# Make a convenient symlink for the master file.
linkfile = p1 + ".silo"
fullpath = os.path.join(p0, linkfile)
if os.path.exists(fullpath):
os.remove(fullpath)
targetfile = os.path.join(p1, "OvlTop.silo")
os.symlink(targetfile, os.path.join(p0, linkfile))
# That's it.
assert silo.DBClose(db) == 0
del db
# Everyone gets the link file name.
linkfile = mpi.bcast(linkfile, root=0)
return linkfile