def construct_mesh(input, filename, verbose=False):
"""
The following function is taking parsed values from the XML to:
- build model grids & meshes,
- initialise Finite Volume discretisation,
- define the partitioning when parallelisation is enable.
"""
rank = mpi.COMM_WORLD.rank
size = mpi.COMM_WORLD.size
comm = mpi.COMM_WORLD
cumflex = None
flex = None
wave = None
tinFlex = None
strata = None
mapero = None
# Get DEM regular grid and create Badlands TIN.
recGrid = raster2TIN.raster2TIN(filename, areaDelFactor=input.Afactor)
fixIDs = recGrid.boundsPt + recGrid.edgesPt
force = forceSim.forceSim(
input.seafile, input.seapos, input.rainMap, input.rainTime,
input.rainVal, input.orographic, input.orographiclin, input.rbgd,
input.rmin, input.rmax, input.rzmax, input.windx, input.windy,
input.tauc, input.tauf, input.nm, input.cw, input.hw, input.ortime,
input.tectFile, input.tectTime, recGrid.regX, recGrid.regY,
input.riverPos, input.riverTime, input.riverQws, input.riverRck,
input.riverNb, input.rockNb, input.tDisplay)
if input.disp3d:
force.time3d = input.time3d
if input.merge3d == 0. or input.merge3d > recGrid.resEdges:
force.merge3d = input.Afactor * recGrid.resEdges * 0.5
else:
force.merge3d = input.merge3d
# Partition the TIN
walltime = time.clock()
FVmesh = FVmethod.FVmethod(recGrid.tinMesh['vertices'],
recGrid.tinMesh['triangles'],
recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(
recGrid.tinMesh['vertices'][:, 0], recGrid.tinMesh['vertices'][:, 1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == rank)[0]
# Build Finite Volume discretisation
# Define overlapping partitions
lGIDs, localTIN = partitionTIN.overlap(recGrid.tinMesh['vertices'][:, 0],
recGrid.tinMesh['vertices'][:, 1],
RowProc, ColProc,
2 * recGrid.resEdges, verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'],
localTIN['edges'])
if rank == 0 and size > 1 and verbose:
print " - partition TIN amongst processors and create local TINs", time.clock(
) - walltime
# Define Finite Volume parameters
walltime = time.clock()
totPts = len(recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32, order='F')
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float, order='F')
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float, order='F')
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(
inGIDs, lGIDs, totPts, recGrid.resEdges * input.Afactor, verbose)
FVmesh.neighbours[tGIDs, :tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs, :tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs, :tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if rank == 0 and verbose:
print " - FV mesh ", time.clock() - walltime
# Define TIN parameters
if input.flexure:
elevation, cumdiff, cumhill, cumflex, inIDs, parentIDs = _define_TINparams(
totPts, input, FVmesh, recGrid, verbose)
else:
elevation, cumdiff, cumhill, inIDs, parentIDs = _define_TINparams(
totPts, input, FVmesh, recGrid, verbose)
# Build stratigraphic and erodibility meshes
if input.laytime > 0 and input.erolays >= 0:
strata, mapero = _build_strateroMesh(input, FVmesh, recGrid, cumdiff,
rank, verbose)
elif input.laytime > 0:
strata = _build_strateroMesh(input, FVmesh, recGrid, cumdiff, rank,
verbose)
elif input.erolays >= 0:
mapero = _build_strateroMesh(input, FVmesh, recGrid, cumdiff, rank,
verbose)
# Set default to no rain
force.update_force_TIN(FVmesh.node_coords[:, :2])
# Flexural isostasy initialisation
if input.flexure:
flex, tinFlex, cumflex = _init_flexure(FVmesh, input, recGrid, force,
elevation, cumdiff, cumflex,
totPts, rank, verbose)
# Wave grid initialisation
if input.waveOn:
wave = _init_wave(input, recGrid, force, rank, verbose)
# Stratigraphic TIN initialisation
if input.rockNb > 0:
layNb = int((input.tEnd - input.tStart) / input.laytime) + 2
bPts = recGrid.boundsPt
ePts = recGrid.edgesPt
if input.restart:
straTIN = stratiWedge.stratiWedge(
layNb, input.initlayers, FVmesh.node_coords[:, :2], bPts, ePts,
input.layersData, input.actlay, input.outDir,
input.strath5file, input.rockNb, recGrid.regX, recGrid.regY,
elevation, input.rockCk, cumdiff, input.rfolder, input.rstep)
else:
straTIN = stratiWedge.stratiWedge(
layNb, input.initlayers, FVmesh.node_coords[:, :2], bPts, ePts,
input.layersData, input.actlay, input.outDir,
input.strath5file, input.rockNb, recGrid.regX, recGrid.regY,
elevation, input.rockCk)
else:
straTIN = None
# Stratigraphic grid in case of carbonate and/or pelagic growth functions
if input.carbonate or input.pelagic:
layNb = int((input.tEnd - input.tStart) / input.tDisplay) + 2
bPts = recGrid.boundsPt
ePts = recGrid.edgesPt
if input.restart:
carbTIN = carbMesh.carbMesh(layNb, input.initlayers,
FVmesh.node_coords[:, :2], bPts, ePts,
input.layersData, input.outDir,
input.strath5file, recGrid.regX,
recGrid.regY, elevation, input.rfolder,
input.rstep)
else:
carbTIN = carbMesh.carbMesh(layNb, input.initlayers,
FVmesh.node_coords[:, :2], bPts, ePts,
input.layersData, input.outDir,
input.strath5file, recGrid.regX,
recGrid.regY, elevation)
else:
carbTIN = None
return recGrid, FVmesh, force, tMesh, lGIDs, fixIDs, \
inIDs, parentIDs, inGIDs, totPts, elevation, cumdiff, \
cumhill, cumflex, strata, mapero, tinFlex, flex, wave, \
straTIN, carbTIN
def reconstruct_mesh(recGrid, input, verbose=False):
"""
The following function is used after 3D displacements to:
- rebuild model grids & meshes,
- reinitialise Finite Volume discretisation,
- redefine the partitioning when parallelisation is enable.
"""
rank = mpi.COMM_WORLD.rank
size = mpi.COMM_WORLD.size
comm = mpi.COMM_WORLD
walltime = time.clock()
FVmesh = FVmethod.FVmethod(recGrid.tinMesh['vertices'],
recGrid.tinMesh['triangles'],
recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(
recGrid.tinMesh['vertices'][:, 0], recGrid.tinMesh['vertices'][:, 1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == rank)[0]
if rank == 0 and verbose:
print " - partition TIN amongst processors ", time.clock() - walltime
# Define overlapping partitions
walltime = time.clock()
lGIDs, localTIN = partitionTIN.overlap(recGrid.tinMesh['vertices'][:, 0],
recGrid.tinMesh['vertices'][:, 1],
RowProc, ColProc,
2 * recGrid.resEdges, verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'],
localTIN['edges'])
# Define Finite Volume parameters
totPts = len(recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32, order='F')
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float, order='F')
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float, order='F')
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(
inGIDs, lGIDs, totPts, recGrid.resEdges * input.Afactor, verbose)
FVmesh.neighbours[tGIDs, :tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs, :tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs, :tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if rank == 0 and verbose:
print " - reconstructed FV mesh ", time.clock() - walltime
inIDs = np.where(FVmesh.partIDs[recGrid.boundsPt:] == rank)[0]
inIDs += recGrid.boundsPt
elevationTIN.assign_parameter_pit(FVmesh.neighbours,
FVmesh.control_volumes, input.diffnb,
input.diffprop, recGrid.boundsPt,
input.fillmax)
return FVmesh, tMesh, lGIDs, inIDs, inGIDs, totPts
def load_dem(self, filename, verbose=False):
"""
Load a DEM input file.
"""
# 1. Get DEM regular grid and create Badlands TIN.
recGrid = raster2TIN.raster2TIN(filename,
areaDelFactor=self.input.Afactor)
self.fixIDs = recGrid.boundsPt + recGrid.edgesPt
force = forceSim.forceSim(
self.input.seafile, self.input.seapos, self.input.rainMap,
self.input.rainTime, self.input.rainVal, self.input.orographic,
self.input.rbgd, self.input.rmin, self.input.rmax,
self.input.windx, self.input.windy, self.input.tauc,
self.input.tauf, self.input.nm, self.input.cw, self.input.hw,
self.input.ortime, self.input.tectFile, self.input.tectTime,
recGrid.regX, recGrid.regY, self.input.tDisplay)
if self.input.disp3d:
force.time3d = self.input.time3d
if self.input.merge3d == 0. or self.input.merge3d > recGrid.resEdges:
force.merge3d = self.input.Afactor * recGrid.resEdges * 0.5
else:
force.merge3d = self.input.merge3d
# 2. Partition the TIN
walltime = time.clock()
FVmesh = FVmethod.FVmethod(recGrid.tinMesh['vertices'],
recGrid.tinMesh['triangles'],
recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(
recGrid.tinMesh['vertices'][:, 0], recGrid.tinMesh['vertices'][:,
1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == self._rank)[0]
if self._rank == 0 and self._size > 1 and verbose:
print " - partition TIN amongst processors ", time.clock(
) - walltime
# 3. Build Finite Volume discretisation
# Define overlapping partitions
allIDs, localTIN = partitionTIN.overlap(
recGrid.tinMesh['vertices'][:, 0], recGrid.tinMesh['vertices'][:,
1],
RowProc, ColProc, 2 * recGrid.resEdges, verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'],
localTIN['edges'])
walltime = time.clock()
# Define Finite Volume parameters
totPts = len(recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32, order='F')
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float)
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float)
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(
inGIDs, allIDs, totPts, recGrid.resEdges * self.input.Afactor,
verbose)
FVmesh.neighbours[tGIDs, :tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs, :tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs, :tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if self._rank == 0 and verbose:
print " - FV mesh ", time.clock() - walltime
# 4. Interpolate elevation
walltime = time.clock()
inIDs = np.where(FVmesh.partIDs[recGrid.boundsPt:] == self._rank)[0]
inIDs += recGrid.boundsPt
local_elev = np.zeros(totPts)
local_elev.fill(-1.e6)
if self.input.restart:
local_cum = np.zeros(totPts)
local_cum.fill(-1.e6)
if self.input.flexure:
local_cumflex = np.zeros(totPts)
local_cumflex.fill(-1.e6)
local_elev[inIDs], local_cum[inIDs], local_cumflex[
inIDs] = recGrid.load_hdf5_flex(
self.input.rfolder, self.input.rstep,
FVmesh.node_coords[inIDs, :2])
else:
local_elev[inIDs], local_cum[inIDs] = recGrid.load_hdf5(
self.input.rfolder, self.input.rstep,
FVmesh.node_coords[inIDs, :2])
self._comm.Allreduce(mpi.IN_PLACE, local_elev, op=mpi.MAX)
self._comm.Allreduce(mpi.IN_PLACE, local_cum, op=mpi.MAX)
self.cumdiff = local_cum
self.cumdiff[:recGrid.boundsPt] = 0.
if self.input.flexure:
self._comm.Allreduce(mpi.IN_PLACE, local_cumflex, op=mpi.MAX)
self.cumflex = local_cumflex
self.cumflex[:recGrid.boundsPt] = 0.
else:
local_elev[inIDs] = elevationTIN.getElevation(
recGrid.regX, recGrid.regY, recGrid.regZ,
FVmesh.node_coords[inIDs, :2])
self._comm.Allreduce(mpi.IN_PLACE, local_elev, op=mpi.MAX)
self.cumdiff = np.zeros(totPts)
if self.input.flexure:
self.cumflex = np.zeros(totPts)
elevation = elevationTIN.update_border_elevation(
local_elev,
FVmesh.neighbours,
FVmesh.edge_length,
recGrid.boundsPt,
btype=self.input.btype)
# Set default to no rain
force.update_force_TIN(FVmesh.node_coords[:, :2])
self.rain = np.zeros(totPts, dtype=float)
# Define variables
self.hillslope = diffLinear()
self.hillslope.CDaerial = self.input.CDa
self.hillslope.CDmarine = self.input.CDm
self.flow = flowNetwork()
self.flow.erodibility = self.input.SPLero
self.flow.m = self.input.SPLm
self.flow.n = self.input.SPLn
self.flow.mindt = self.input.minDT
self.flow.bedrock = self.input.bedrock
self.flow.alluvial = self.input.alluvial
self.flow.esmooth = self.input.esmooth
self.flow.dsmooth = self.input.dsmooth
self.flow.xycoords = FVmesh.node_coords[:, :2]
self.flow.spl = self.input.spl
self.flow.capacity = self.input.capacity
self.flow.filter = self.input.filter
self.flow.depo = self.input.depo
if self._rank == 0 and verbose:
print " - interpolate elevation on grid ", time.clock() - walltime
# Flexural isostasy initialisation
if self.input.flexure:
walltime = time.clock()
nx = self.input.fnx
ny = self.input.fny
if nx == 0:
nx = recGrid.nx
if ny == 0:
ny = recGrid.ny
if self.input.elasticH is None:
elasticT = str(self.input.elasticGrid)
else:
elasticT = self.input.elasticH
self.flex = isoFlex.isoFlex()
self.flex.buildGrid(nx, ny, self.input.youngMod,
self.input.dmantle, self.input.dsediment,
elasticT, self.input.flexbounds,
FVmesh.node_coords[:, :2])
self.tinFlex = np.zeros(totPts, dtype=float)
force.getSea(self.tNow)
self.tinFlex = self.flex.get_flexure(elevation,
self.cumdiff,
force.sealevel,
recGrid.boundsPt,
initFlex=True)
self.tinFlex = force.disp_border(self.tinFlex, FVmesh.neighbours,
FVmesh.edge_length,
recGrid.boundsPt)
self.cumflex += self.tinFlex
if self._rank == 0:
print " - Compute flexural isostasy ", time.clock(
) - walltime
# Save state for subsequent calls
# TODO: there is a lot of stuff here. Can we reduce it?
self.recGrid = recGrid
self.elevation = elevation
self.FVmesh = FVmesh
self.allIDs = allIDs
self.inIDs = inIDs
self.inGIDs = inGIDs
self.tMesh = tMesh
self.force = force
self.totPts = totPts
def rebuildMesh(self, verbose=False):
"""
Build TIN after 3D displacements.
"""
# Build the Finite Volume representation
self.fixIDs = self.recGrid.boundsPt + self.recGrid.edgesPt
walltime = time.clock()
FVmesh = FVmethod.FVmethod(self.recGrid.tinMesh['vertices'],
self.recGrid.tinMesh['triangles'],
self.recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(
self.recGrid.tinMesh['vertices'][:, 0],
self.recGrid.tinMesh['vertices'][:, 1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == self._rank)[0]
if self._rank == 0 and verbose:
print " - partition TIN amongst processors ", time.clock(
) - walltime
# Define overlapping partitions
allIDs, localTIN = partitionTIN.overlap(
self.recGrid.tinMesh['vertices'][:, 0],
self.recGrid.tinMesh['vertices'][:, 1], RowProc, ColProc,
2 * self.recGrid.resEdges, verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'],
localTIN['edges'])
walltime = time.clock()
# Define Finite Volume parameters
totPts = len(self.recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32)
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float)
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float)
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(
inGIDs, allIDs, totPts, self.recGrid.resEdges * self.input.Afactor,
verbose)
FVmesh.neighbours[tGIDs, :tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs, :tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs, :tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if self._rank == 0 and verbose:
print " - FV mesh ", time.clock() - walltime
inIDs = np.where(
FVmesh.partIDs[self.recGrid.boundsPt:] == self._rank)[0]
inIDs += self.recGrid.boundsPt
# Set default with no rain
self.force.update_force_TIN(FVmesh.node_coords[:, :2])
self.rain = np.zeros(totPts, dtype=float)
self.rain[inIDs] = self.force.get_Rain(self.tNow, self.elevation,
inIDs)
# Update flexural isostasy
if self.input.flexure:
self.tinFlex = np.zeros(totPts, dtype=float)
self.flex.update_flexure_parameters(FVmesh.node_coords[:, :2])
# Save state for subsequent calls
# TODO: there is a lot of stuff here. Can we reduce it?
self.flow.xycoords = FVmesh.node_coords[:, :2]
self.FVmesh = FVmesh
self.allIDs = allIDs
self.inIDs = inIDs
self.inGIDs = inGIDs
self.tMesh = tMesh
self.totPts = totPts
def construct_mesh(input, filename, verbose=False):
"""
The following function is taking parsed values from the XML to:
- build model grids & meshes,
- initialise Finite Volume discretisation,
- define the partitioning when parallelisation is enable.
"""
rank = mpi.COMM_WORLD.rank
size = mpi.COMM_WORLD.size
comm = mpi.COMM_WORLD
cumflex = None
flex = None
tinFlex = None
strata = None
mapero = None
# Get DEM regular grid and create Badlands TIN.
recGrid = raster2TIN.raster2TIN(filename, areaDelFactor=input.Afactor)
fixIDs = recGrid.boundsPt + recGrid.edgesPt
force = forceSim.forceSim(input.seafile, input.seapos, input.rainMap,
input.rainTime, input.rainVal, input.orographic,
input.rbgd, input.rmin, input.rmax , input.windx,
input.windy, input.tauc, input.tauf, input.nm,
input.cw, input.hw, input.ortime, input.tectFile,
input.tectTime, recGrid.regX, recGrid.regY, input.riverPos,
input.riverTime, input.riverQws, input.riverWidth, input.riverNb,
input.tDisplay)
if input.disp3d:
force.time3d = input.time3d
if input.merge3d == 0. or input.merge3d > recGrid.resEdges:
force.merge3d = input.Afactor * recGrid.resEdges * 0.5
else:
force.merge3d = input.merge3d
# Partition the TIN
walltime = time.clock()
FVmesh = FVmethod.FVmethod(recGrid.tinMesh['vertices'], recGrid.tinMesh['triangles'],
recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(recGrid.tinMesh['vertices'][:, 0],
recGrid.tinMesh['vertices'][:, 1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == rank)[0]
# Build Finite Volume discretisation
# Define overlapping partitions
lGIDs, localTIN = partitionTIN.overlap(recGrid.tinMesh['vertices'][:, 0], recGrid.tinMesh['vertices'][:, 1],
RowProc, ColProc, 2*recGrid.resEdges, verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'], localTIN['edges'])
if rank == 0 and size > 1 and verbose:
print " - partition TIN amongst processors and create local TINs", time.clock() - walltime
# Define Finite Volume parameters
walltime = time.clock()
totPts = len(recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32, order='F')
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float)
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float)
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(inGIDs, lGIDs, totPts,
recGrid.resEdges*input.Afactor, verbose)
FVmesh.neighbours[tGIDs,:tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs,:tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs,:tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if rank == 0 and verbose:
print " - FV mesh ", time.clock() - walltime
# Define TIN parameters
if input.flexure:
elevation, cumdiff, cumflex, inIDs = _define_TINparams(totPts, input, FVmesh, recGrid, verbose)
else:
elevation, cumdiff, inIDs = _define_TINparams(totPts, input, FVmesh, recGrid, verbose)
# Build stratigraphic and erodibility meshes
if input.laytime > 0 and input.erolays >= 0:
strata, mapero = _build_strateroMesh(input, FVmesh, recGrid, cumdiff, rank, verbose)
elif input.laytime > 0:
strata = _build_strateroMesh(input, FVmesh, recGrid, cumdiff, rank, verbose)
elif input.erolays >= 0:
mapero = _build_strateroMesh(input, FVmesh, recGrid, cumdiff, rank, verbose)
# Set default to no rain
force.update_force_TIN(FVmesh.node_coords[:,:2])
# Flexural isostasy initialisation
if input.flexure:
flex, tinFlex, cumflex = _init_flexure(FVmesh, input, recGrid, force, elevation,
cumdiff, cumflex, totPts, rank, verbose)
return recGrid, FVmesh, force, tMesh, lGIDs, fixIDs, \
inIDs, inGIDs, totPts, elevation, cumdiff, \
cumflex, strata, mapero, tinFlex, flex
def reconstruct_mesh(recGrid, input, verbose=False):
"""
The following function is used after 3D displacements to:
- rebuild model grids & meshes,
- reinitialise Finite Volume discretisation,
- redefine the partitioning when parallelisation is enable.
"""
rank = mpi.COMM_WORLD.rank
size = mpi.COMM_WORLD.size
comm = mpi.COMM_WORLD
walltime = time.clock()
FVmesh = FVmethod.FVmethod(recGrid.tinMesh['vertices'], recGrid.tinMesh['triangles'],
recGrid.tinMesh['edges'])
# Perform partitioning by equivalent domain splitting
partitionIDs, RowProc, ColProc = partitionTIN.simple(recGrid.tinMesh['vertices'][:, 0],
recGrid.tinMesh['vertices'][:, 1])
FVmesh.partIDs = partitionIDs
# Get each partition global node ID
inGIDs = np.where(partitionIDs == rank)[0]
if rank == 0 and verbose:
print " - partition TIN amongst processors ", time.clock() - walltime
# Define overlapping partitions
walltime = time.clock()
lGIDs, localTIN = partitionTIN.overlap(recGrid.tinMesh['vertices'][:, 0],
recGrid.tinMesh['vertices'][:, 1],
RowProc, ColProc, 2*recGrid.resEdges,
verbose)
# Set parameters of the finite volume mesh
tMesh = FVmethod.FVmethod(localTIN['vertices'], localTIN['triangles'], localTIN['edges'])
# Define Finite Volume parameters
totPts = len(recGrid.tinMesh['vertices'][:, 0])
FVmesh.neighbours = np.zeros((totPts, 20), dtype=np.int32)
FVmesh.neighbours.fill(-2)
FVmesh.edge_length = np.zeros((totPts, 20), dtype=np.float)
FVmesh.vor_edges = np.zeros((totPts, 20), dtype=np.float)
FVmesh.control_volumes = np.zeros(totPts, dtype=np.float)
# Compute Finite Volume parameters
tGIDs, tNgbh, tEdgs, tVors, tVols = tMesh.construct_FV(inGIDs, lGIDs, totPts,
recGrid.resEdges*input.Afactor, verbose)
FVmesh.neighbours[tGIDs,:tMesh.maxNgbh] = tNgbh
FVmesh.edge_length[tGIDs,:tMesh.maxNgbh] = tEdgs
FVmesh.vor_edges[tGIDs,:tMesh.maxNgbh] = tVors
FVmesh.control_volumes[tGIDs] = tVols
if rank == 0 and verbose:
print " - reconstructed FV mesh ", time.clock() - walltime
inIDs = np.where(FVmesh.partIDs[recGrid.boundsPt:] == rank)[0]
inIDs += recGrid.boundsPt
elevationTIN.assign_parameter_pit(FVmesh.neighbours, recGrid.boundsPt, input.fillmax)
return FVmesh, tMesh, lGIDs, inIDs, inGIDs, totPts