From 0249d5bf3853a0aa002a75a97b8408e899b29af4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Fri, 20 May 2016 17:01:52 +0200
Subject: [PATCH] Fix some tests (failed since previous commit) + pep8 things
---
examples/NSDebug_faux2D.py | 2 +-
examples/testCurl.py | 4 +-
examples/testVisu.py | 2 +-
hysop/domain/mesh.py | 45 +++++++-----
hysop/domain/submesh.py | 16 ++---
hysop/domain/subsets.py | 2 +-
hysop/domain/tests/test_mesh.py | 6 +-
hysop/domain/tests/test_porous.py | 10 +--
hysop/domain/tests/test_regular_subset.py | 2 +-
hysop/domain/tests/test_submesh.py | 2 +-
hysop/domain/tests/test_subset.py | 8 +--
hysop/fields/discrete.py | 4 +-
.../tests/test_gpu_multiresolution_filter.py | 32 ++++-----
hysop/mpi/bridge_inter.py | 4 +-
hysop/mpi/topology.py | 4 +-
hysop/numerics/differential_operations.py | 6 +-
hysop/numerics/finite_differences.py | 4 +-
hysop/numerics/tests/test_diffOp.py | 4 +-
hysop/numerics/tests/test_update_ghosts.py | 2 +-
hysop/numerics/utils.py | 2 +-
hysop/operator/discrete/baroclinic.py | 68 +++++++++----------
.../operator/discrete/baroclinic_from_rhs.py | 4 +-
hysop/operator/discrete/density.py | 8 +--
hysop/operator/discrete/energy_enstrophy.py | 12 ++--
hysop/operator/discrete/monitoringPoints.py | 10 +--
hysop/operator/discrete/multiphase_gradp.py | 34 +++++-----
.../discrete/multiresolution_filter.py | 12 ++--
hysop/operator/discrete/profiles.py | 10 +--
hysop/operator/discrete/residual.py | 10 +--
.../operator/discrete/velocity_correction.py | 4 +-
hysop/operator/energy_enstrophy.py | 4 +-
hysop/operator/hdf_io.py | 2 +-
hysop/operator/monitoringPoints.py | 4 +-
hysop/operator/profiles.py | 4 +-
hysop/operator/residual.py | 2 +-
hysop/operator/tests/test_differential.py | 2 +-
hysop/operator/tests/test_hdf5_io.py | 16 ++---
hysop/operator/tests/test_multiphase_gradp.py | 8 +--
.../tests/test_multiresolution_filter.py | 26 +++----
hysop/operator/tests/test_penalization.py | 4 +-
hysop/operator/tests/test_redistribute.py | 18 ++---
41 files changed, 218 insertions(+), 205 deletions(-)
diff --git a/examples/NSDebug_faux2D.py b/examples/NSDebug_faux2D.py
index a6540feed..16902a658 100755
--- a/examples/NSDebug_faux2D.py
+++ b/examples/NSDebug_faux2D.py
@@ -373,7 +373,7 @@ cb2 = op['correction'].cb
def pseudo_norm(topo, var):
sloc = npw.zeros(3)
gloc = npw.zeros(3)
- sl = topo.mesh.iCompute
+ sl = topo.mesh.compute_index
for i in xrange(3):
sloc[i] = np.sum((var[i][sl]))
# sfft[i] = la.norm((vfft[i][slfft]))
diff --git a/examples/testCurl.py b/examples/testCurl.py
index 7b0b93cc9..0a08866ab 100644
--- a/examples/testCurl.py
+++ b/examples/testCurl.py
@@ -98,8 +98,8 @@ curlFD.apply(simulation)
printer.apply(simulation)
printer2.apply(simulation)
-ind = topo3.mesh.iCompute
-indfft = topofft.mesh.iCompute
+ind = topo3.mesh.compute_index
+indfft = topofft.mesh.compute_index
for i in xrange(3):
diff --git a/examples/testVisu.py b/examples/testVisu.py
index e2c7504a4..a7b10a5e1 100755
--- a/examples/testVisu.py
+++ b/examples/testVisu.py
@@ -125,7 +125,7 @@ for pref in filelist[1:]:
simu.advance()
## #print scalRef.norm(topo)
## #print scal3D.norm(topo)
-## #assert np.allclose(sc3D.data[0][topo.mesh.iCompute], scRef.data[0][topo.mesh.iCompute])
+## #assert np.allclose(sc3D.data[0][topo.mesh.compute_index], scRef.data[0][topo.mesh.compute_index])
velo = Field(domain=dom, name='Velocity', is_vector=True)
diff --git a/hysop/domain/mesh.py b/hysop/domain/mesh.py
index 4b0ec7576..01ea25d86 100644
--- a/hysop/domain/mesh.py
+++ b/hysop/domain/mesh.py
@@ -111,8 +111,8 @@ class Mesh(object):
# the number of ghost points on each subdomain.
self.discretization = discretization
# Mesh step size
- self.space_step = self.domain.length / (self.discretization.resolution
- - 1)
+ self.space_step = self.domain.length / (
+ self.discretization.resolution - 1)
# Coordinates of the origin of the mesh
self.global_origin = self.domain.origin
# Length of this mesh
@@ -133,6 +133,10 @@ class Mesh(object):
start = npw.asdimarray(global_start)
# last computational point, global index
ghosts = self.discretization.ghosts
+ # resolution of the computational grid (i.e. grid without ghosts)
+ self.compute_resolution = tuple(npw.const_dimarray(resolution) -
+ 2 * ghosts)
+
# shift between local and global index,
# such that: iglobal + shift = ilocal.
# Usefull for start() and end() methods.
@@ -149,16 +153,20 @@ class Mesh(object):
start = self.discretization.ghosts
# last computational point, local index
stop = self.resolution - start
- # Local position of the computational points
- self.iCompute = [slice(start[d], stop[d])
- for d in xrange(self._dim)]
+ # Local indices of the computational points
+ self.compute_index = [slice(start[d], stop[d])
+ for d in xrange(self._dim)]
+ # Local indices of all points
+ self.local_index = [slice(0, self.resolution[d])
+ for d in xrange(self._dim)]
# coordinates of the points of the grid
self.coords = np.ix_(*(np.linspace(self.origin[d],
self.end[d], self.resolution[d])
for d in xrange(self._dim)))
# coordinates of the 'computational' points, i.e. excluding ghosts.
- self.compute_coords = self.reduce_coords(self.coords, self.iCompute)
+ self.compute_coords = self.reduce_coords(self.coords,
+ self.compute_index)
gend = self.discretization.resolution - 1
# Is this mesh on the last process in some direction in the
@@ -166,7 +174,7 @@ class Mesh(object):
is_last = np.asarray([gend[d] < self.position[d].stop
for d in xrange(self._dim)])
# indices of points that must be used to compute integrals on this mesh
- self.ind4integ = self.compute_integ_point(is_last, self.iCompute)
+ self.ind4integ = self.compute_integ_point(is_last, self.compute_index)
self.coords4int = self.reduce_coords(self.coords, self.ind4integ)
# True if the current mesh is locally defined on the current mpi proc.
self.on_proc = True
@@ -195,8 +203,7 @@ class Mesh(object):
if n_dir is not None:
stops[n_dir] = npw.asdimarray([ic[d].start + 1 for d in n_dir])
- return [slice(ic[d].start,
- stops[d]) for d in xrange(dim)]
+ return [slice(ic[d].start, stops[d]) for d in xrange(dim)]
@staticmethod
def reduce_coords(coords, reduced_index):
@@ -227,20 +234,24 @@ class Mesh(object):
def local_indices(self, point):
"""
- returns indices of the point of coordinates (close to) tab = x, y, z
+ returns indices of the point of coordinates (close to) point = x, y, z
If (x, y, z) is not a grid point, it returns the closest grid point.
"""
point = npw.asrealarray(point)
if self.is_inside(point):
- return npw.asdimarray(np.rint((point - self.origin)
- / self.space_step))
+ return npw.asdimarray(np.rint((point - self.origin) /
+ self.space_step))
else:
return False
def global_indices(self, point):
+ """returns global indices of the point of coordinates
+ (close to) point = x, y, z
+ If (x, y, z) is not a grid point, it returns the closest grid point.
+ """
point = npw.asrealarray(point)
- return npw.asdimarray(np.rint((point - self.domain.origin)
- / self.space_step))
+ return npw.asdimarray(np.rint((point - self.domain.origin) /
+ self.space_step))
def is_inside(self, point):
"""True if the point belongs to volume or surface
@@ -261,7 +272,7 @@ class Mesh(object):
s += ' - resolution : ' + str(self.resolution) + '\n'
s += ' - position in global mesh: ' + str(self.position) + '\n'
s += ' - global discretization : ' + str(self.discretization) + '\n'
- s += ' - computation points :' + str(self.iCompute) + '\n'
+ s += ' - computation points :' + str(self.compute_index) + '\n'
return s
def convert2local(self, sl):
@@ -334,5 +345,7 @@ class Mesh(object):
return self.discretization.resolution - 1
def local_shift(self, indices):
- shift = [self.iCompute[d].start for d in xrange(self._dim)]
+ """Shift input indices with ghost layer size
+ """
+ shift = [self.compute_index[d].start for d in xrange(self._dim)]
return tuple([indices[d] + shift[d] for d in xrange(self._dim)])
diff --git a/hysop/domain/submesh.py b/hysop/domain/submesh.py
index 46b0735fe..412f5fb63 100644
--- a/hysop/domain/submesh.py
+++ b/hysop/domain/submesh.py
@@ -88,16 +88,16 @@ class SubMesh(object):
self.position_in_parent = [s for s in sl]
# Indices of the points of the submesh, relative to
# the LOCAL array
- self.iCompute = self.mesh.convert2local(self.position_in_parent)
+ self.compute_index = self.mesh.convert2local(self.position_in_parent)
# Resolution of the local submesh
- self.resolution = [self.iCompute[d].stop - self.iCompute[d].start
+ self.resolution = [self.compute_index[d].stop - self.compute_index[d].start
for d in xrange(self._dim)]
- # Same as self.iCompute but recomputed to be used
+ # Same as self.compute_index but recomputed to be used
# for integration on the submesh
self.ind4integ = self.mesh.compute_integ_point(is_last,
- self.iCompute,
+ self.compute_index,
self._n_dir)
start = [self.position_in_parent[d].start - self.substart[d]
for d in xrange(self._dim)]
@@ -108,16 +108,16 @@ class SubMesh(object):
else:
self.position_in_parent = None
self.position = None
- self.iCompute = [slice(0, 0), ] * self._dim
- self.ind4integ = self.iCompute
+ self.compute_index = [slice(0, 0), ] * self._dim
+ self.ind4integ = self.compute_index
self.resolution = [0, ] * self._dim
# Shift between local submesh and local parent mesh.
- self.local_start = [self.iCompute[d].start for d in xrange(self._dim)]
+ self.local_start = [self.compute_index[d].start for d in xrange(self._dim)]
# Coordinates of the points of the local submesh
self.coords = self.mesh.reduce_coords(self.mesh.coords,
- self.iCompute)
+ self.compute_index)
self.coords4int = self.mesh.reduce_coords(self.mesh.coords,
self.ind4integ)
diff --git a/hysop/domain/subsets.py b/hysop/domain/subsets.py
index 02a36beb2..5dbdd9b24 100644
--- a/hysop/domain/subsets.py
+++ b/hysop/domain/subsets.py
@@ -744,7 +744,7 @@ class SubBox(Subset):
self.mesh[topo] = SubMesh(topo.mesh, gstart, gend)
self.real_length[topo] = self.mesh[topo].global_length
self.real_orig[topo] = self.mesh[topo].global_origin
- self.ind[topo] = [self.mesh[topo].iCompute]
+ self.ind[topo] = [self.mesh[topo].compute_index]
self._reduce_topology(topo)
return self.ind[topo]
diff --git a/hysop/domain/tests/test_mesh.py b/hysop/domain/tests/test_mesh.py
index 0ae2b4868..261abb444 100755
--- a/hysop/domain/tests/test_mesh.py
+++ b/hysop/domain/tests/test_mesh.py
@@ -35,7 +35,7 @@ def create_mesh(discr):
# Test local grid
assert (mesh.resolution == resolution).all()
assert (mesh.origin == dom.origin + (shift - gh) * mesh.space_step).all()
- assert mesh.iCompute == [slice(gh[d], resolution[d] - gh[d])
+ assert mesh.compute_index == [slice(gh[d], resolution[d] - gh[d])
for d in xrange(dim)]
assert (mesh.global_indices(dom.origin) == [0, ] * dim).all()
assert (mesh.local_indices(mesh.origin) == [0, ] * dim).all()
@@ -97,9 +97,9 @@ def test_convert_local():
elif main_size == 8:
newstart = start - topo.rank * Nz / main_size
newend = end - topo.rank * Nz / main_size
- slref = slice(max(mesh.iCompute[-1].start, newstart + gh[-1]),
+ slref = slice(max(mesh.compute_index[-1].start, newstart + gh[-1]),
min(max(newend + gh[-1], gh[-1]),
- mesh.iCompute[-1].stop))
+ mesh.compute_index[-1].stop))
sl = [slice(start + gh[d], end + gh[d]) for d in xrange(dim)]
sl[-1] = slref
if res is not None:
diff --git a/hysop/domain/tests/test_porous.py b/hysop/domain/tests/test_porous.py
index 3ae7c79c9..39dd869dd 100755
--- a/hysop/domain/tests/test_porous.py
+++ b/hysop/domain/tests/test_porous.py
@@ -54,7 +54,7 @@ def assert_porous(dref, sourcename, filename):
for i in xrange(li):
sd.data[0][ind[i]] = 10 * i + 1
sdref = sref.discretize(topo)
- ic = topo.mesh.iCompute
+ ic = topo.mesh.compute_index
assert np.allclose(sd.data[0][ic], sdref.data[0][ic])
@@ -95,7 +95,7 @@ def assert_bipole(dref, sourcename, filename):
for i in xrange(li):
sd.data[0][ind[i]] = 10 * i + 1
sdref = sref.discretize(topo)
- ic = topo.mesh.iCompute
+ ic = topo.mesh.compute_index
assert np.allclose(sd.data[0][ic], sdref.data[0][ic])
@@ -136,7 +136,7 @@ def assert_quadripole(dref, sourcename, filename):
for i in xrange(li):
sd.data[0][ind[i]] = 10 * i + 1
sdref = sref.discretize(topo)
- ic = topo.mesh.iCompute
+ ic = topo.mesh.compute_index
assert np.allclose(sd.data[0][ic], sdref.data[0][ic])
@@ -161,7 +161,7 @@ def assert_ring(dref, sourcename, filename):
for i in xrange(li):
sd.data[0][ind[i]] = 10 * i + 1
sdref = sref.discretize(topo)
- ic = topo.mesh.iCompute
+ ic = topo.mesh.compute_index
assert np.allclose(sd.data[0][ic], sdref.data[0][ic])
@@ -194,7 +194,7 @@ def assert_ringpole(dref, sourcename, filename):
for i in xrange(li):
sd.data[0][ind[i]] = 10 * i + 1
sdref = sref.discretize(topo)
- ic = topo.mesh.iCompute
+ ic = topo.mesh.compute_index
assert np.allclose(sd.data[0][ic], sdref.data[0][ic])
diff --git a/hysop/domain/tests/test_regular_subset.py b/hysop/domain/tests/test_regular_subset.py
index f20de501d..78c161c9e 100755
--- a/hysop/domain/tests/test_regular_subset.py
+++ b/hysop/domain/tests/test_regular_subset.py
@@ -215,4 +215,4 @@ def test_full2d_in3d():
i1 = cub.integrate_dfield_allc(vd)
assert (np.abs(i1 - vref) < 1e-6).all()
print topo
- print cub.mesh[topo].iCompute
+ print cub.mesh[topo].compute_index
diff --git a/hysop/domain/tests/test_submesh.py b/hysop/domain/tests/test_submesh.py
index 9f427d7bc..b4efae725 100755
--- a/hysop/domain/tests/test_submesh.py
+++ b/hysop/domain/tests/test_submesh.py
@@ -47,7 +47,7 @@ def check_submesh(discr):
r2 = mesh.convert2local([s for s
in Utils.intersl(gpos, mesh.position)])
- assert subm.iCompute == r2
+ assert subm.compute_index == r2
pos = subm.position_in_parent
subpos = [slice(pos[d].start - gstart[d],
pos[d].stop - gstart[d]) for d in xrange(dim)]
diff --git a/hysop/domain/tests/test_subset.py b/hysop/domain/tests/test_subset.py
index 00bb7bcc7..8501fc3b4 100755
--- a/hysop/domain/tests/test_subset.py
+++ b/hysop/domain/tests/test_subset.py
@@ -58,7 +58,7 @@ def check_subset(discr, fileref, class_name):
scal = Field(domain=topo.domain, is_vector=False, name='s0')
sd = scal.discretize(topo)
sd[0][subs.ind[topo][0]] = 2.
- icompute = topo.mesh.iCompute
+ icompute = topo.mesh.compute_index
return np.allclose(sd[0][icompute], vd[0][icompute])
@@ -120,7 +120,7 @@ def init_obst_list(discr, fileref):
sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.union(obs_list, topo)
sd[0][indices] = 2.
- icompute = topo.mesh.iCompute
+ icompute = topo.mesh.compute_index
return np.allclose(sd[0][icompute], vd[0][icompute])
@@ -145,7 +145,7 @@ def init_subtract(discr, fileref):
sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.subtract(box, s1, topo)
sd[0][indices] = 2.
- icompute = topo.mesh.iCompute
+ icompute = topo.mesh.compute_index
return np.allclose(sd[0][icompute], vd[0][icompute])
@@ -183,7 +183,7 @@ def init_subtract_lists(discr, fileref):
sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.subtract_list_of_sets(box, obs, topo)
sd[0][indices] = 2.
- return np.allclose(sd[0][topo.mesh.iCompute], vd[0][topo.mesh.iCompute])
+ return np.allclose(sd[0][topo.mesh.compute_index], vd[0][topo.mesh.compute_index])
def test_subtract_list_3d():
diff --git a/hysop/fields/discrete.py b/hysop/fields/discrete.py
index 803abb2e9..264e1f5e4 100755
--- a/hysop/fields/discrete.py
+++ b/hysop/fields/discrete.py
@@ -192,7 +192,7 @@ class DiscreteField(object):
"""
result = npw.zeros((self.nb_components))
gresult = npw.zeros((self.nb_components))
- ind_ng = self.topology.mesh.iCompute
+ ind_ng = self.topology.mesh.compute_index
for d in range(self.nb_components):
result[d] = la.norm(self.data[d][ind_ng]) ** 2
self.topology.comm.Allreduce(result, gresult)
@@ -207,7 +207,7 @@ class DiscreteField(object):
"""
result = npw.zeros((self.nb_components))
gresult = npw.zeros((self.nb_components))
- ind_ng = self.topology.mesh.iCompute
+ ind_ng = self.topology.mesh.compute_index
step = self.topology.mesh.space_step
for d in range(self.nb_components):
result[d] = (step[d] * la.norm(self.data[d][ind_ng])) ** 2
diff --git a/hysop/gpu/tests/test_gpu_multiresolution_filter.py b/hysop/gpu/tests/test_gpu_multiresolution_filter.py
index b44201bbd..111b4e919 100755
--- a/hysop/gpu/tests/test_gpu_multiresolution_filter.py
+++ b/hysop/gpu/tests/test_gpu_multiresolution_filter.py
@@ -56,11 +56,11 @@ def test_filter_linear():
f_out.wait()
valid = [npw.zeros(f_out[0].shape), ]
valid = func(valid, *topo_coarse.mesh.coords)
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute],
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index],
atol=1e-4, rtol=1e-3), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
if PY_COMPARE:
f_py = Field(box, formula=func, name='fpy')
op_py = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
@@ -72,10 +72,10 @@ def test_filter_linear():
f_py.initialize(topo=topo_fine)
op_py.apply(simu)
valid = f_py.discreteFields[topo_coarse]
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute]), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index]), \
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
def test_filter_L2_1():
@@ -108,10 +108,10 @@ def test_filter_L2_1():
f_out.wait()
valid = [npw.zeros(f_out[0].shape), ]
valid = func(valid, *topo_coarse.mesh.coords)
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute]), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index]), \
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
if PY_COMPARE:
f_py = Field(box, formula=func, name='fpy')
op_py = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
@@ -122,7 +122,7 @@ def test_filter_L2_1():
f_py.initialize(topo=topo_fine)
op_py.apply(simu)
valid = f_py.discreteFields[topo_coarse]
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute]), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index]), \
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
diff --git a/hysop/mpi/bridge_inter.py b/hysop/mpi/bridge_inter.py
index ecc0af52f..85f37b8a2 100644
--- a/hysop/mpi/bridge_inter.py
+++ b/hysop/mpi/bridge_inter.py
@@ -116,8 +116,8 @@ class BridgeInter(object):
self.comm.bcast(current_indices, root=MPI.PROC_NULL)
# Convert numpy arrays to dict of slices ...
- current_indices = Utils.arrayToDict(current_indices)
- remote_indices = Utils.arrayToDict(remote_indices)
+ current_indices = Utils.array_to_dict(current_indices)
+ remote_indices = Utils.array_to_dict(remote_indices)
return current_indices, remote_indices
diff --git a/hysop/mpi/topology.py b/hysop/mpi/topology.py
index 1ab614715..11a8057b1 100644
--- a/hysop/mpi/topology.py
+++ b/hysop/mpi/topology.py
@@ -508,7 +508,7 @@ class TopoTools(object):
root=root)
if toslice:
- return Utils.arrayToDict(iglob_res)
+ return Utils.array_to_dict(iglob_res)
else:
return iglob_res
@@ -572,7 +572,7 @@ class TopoTools(object):
comm.Gather([iglob[:, rank], MPI.INT], [iglob_res, MPI.INT],
root=root)
if toslice:
- return Utils.arrayToDict(iglob_res)
+ return Utils.array_to_dict(iglob_res)
else:
return iglob_res
diff --git a/hysop/numerics/differential_operations.py b/hysop/numerics/differential_operations.py
index b6096a301..3f78337a6 100755
--- a/hysop/numerics/differential_operations.py
+++ b/hysop/numerics/differential_operations.py
@@ -51,7 +51,7 @@ class DifferentialOperation(object):
indices : list of slices, optional
Represents the local mesh on which the operation
will be applied,
- like iCompute in :class:`~hysop.domain.mesh.Mesh`.
+ like compute_index in :class:`~hysop.domain.mesh.Mesh`.
See details in notes.
reduce_output_shape : boolean, optional
True to return the result in a reduced array. See notes below.
@@ -68,7 +68,7 @@ class DifferentialOperation(object):
** 1 - either invar and outvar are arrays of the same shape, and
outvar[...] = op(invar[...]) will be computed. In that case
indices and reduce_output_shape are not required.
- Indices will be set to topo.mesh.iCompute.
+ Indices will be set to topo.mesh.compute_index.
** 2 - or outvar is a smaller array than invar, and
outvar[...] = op(invar(indices))
To use case 2, set reduce_output_shape = True and provide indices.
@@ -88,7 +88,7 @@ class DifferentialOperation(object):
self.method = method
if indices is None:
- indices = topo.mesh.iCompute
+ indices = topo.mesh.compute_index
reduce_output_shape = False
self._indices = indices
self.fd_scheme = self._init_fd_method(topo, reduce_output_shape)
diff --git a/hysop/numerics/finite_differences.py b/hysop/numerics/finite_differences.py
index c724b4cfc..cecf24579 100644
--- a/hysop/numerics/finite_differences.py
+++ b/hysop/numerics/finite_differences.py
@@ -13,7 +13,7 @@ class FiniteDifference(object):
Usage :
>> step = topo.mesh_space_step
- >> scheme = FD_C_4(step, topo.mesh.iCompute)
+ >> scheme = FD_C_4(step, topo.mesh.compute_index)
For a given numpy array (obviously discretized on the topo
used to compute indices), to compute result as the derivative
@@ -48,7 +48,7 @@ class FiniteDifference(object):
resolution of the mesh
indices : list of slices
Represents the local mesh on which finite-differences
- will be applied, like iCompute in :class:`~hysop.domain.mesh.Mesh`.
+ will be applied, like compute_index in :class:`~hysop.domain.mesh.Mesh`.
reduce_output_shape : boolean, optional
True to return the result in a reduced array. See notes below.
diff --git a/hysop/numerics/tests/test_diffOp.py b/hysop/numerics/tests/test_diffOp.py
index 529542e01..555ea48a3 100755
--- a/hysop/numerics/tests/test_diffOp.py
+++ b/hysop/numerics/tests/test_diffOp.py
@@ -108,8 +108,8 @@ def init(discr, vform, wform):
# Init 2D and 3D
v3d, w3d, topo3, work3 = init(discr3D, computeVel, computeVort)
v2d, w2d, topo2, work2 = init(discr2D, computeVel2, computeVort2)
-ic3 = topo3.mesh.iCompute
-ic2 = topo2.mesh.iCompute
+ic3 = topo3.mesh.compute_index
+ic2 = topo2.mesh.compute_index
def build_op(op_class, len_result, topo, work):
diff --git a/hysop/numerics/tests/test_update_ghosts.py b/hysop/numerics/tests/test_update_ghosts.py
index 8ec8f843f..b4cfaf2ee 100755
--- a/hysop/numerics/tests/test_update_ghosts.py
+++ b/hysop/numerics/tests/test_update_ghosts.py
@@ -15,7 +15,7 @@ def _setup(ghosts, topo_dim):
df = f.discreteFields[topo]
for i, dfd in enumerate(df.data):
dfd[...] = 0.
- dfd[topo.mesh.iCompute] = 1. * (i + 1)
+ dfd[topo.mesh.compute_index] = 1. * (i + 1)
return df, topo
diff --git a/hysop/numerics/utils.py b/hysop/numerics/utils.py
index 2399a503c..34cd0b8ea 100644
--- a/hysop/numerics/utils.py
+++ b/hysop/numerics/utils.py
@@ -19,7 +19,7 @@ class Utils(object):
y : list of numpy arrays
represents a discrete field
sl : list of slices
- mesh points indices (like topo.mesh.iCompute)
+ mesh points indices (like topo.mesh.compute_index)
work: numpy array
temporary buffer
diff --git a/hysop/operator/discrete/baroclinic.py b/hysop/operator/discrete/baroclinic.py
index b02527fb2..607fa5597 100644
--- a/hysop/operator/discrete/baroclinic.py
+++ b/hysop/operator/discrete/baroclinic.py
@@ -58,10 +58,10 @@ class Baroclinic(DiscreteOperator):
self._laplacian = diff_op.Laplacian(
self.velocity.topology,
- indices=self.velocity.topology.mesh.iCompute)
+ indices=self.velocity.topology.mesh.compute_index)
self._gradOp = diff_op.GradS(
self.velocity.topology,
- indices=self.velocity.topology.mesh.iCompute,
+ indices=self.velocity.topology.mesh.compute_index,
method=self.method[SpaceDiscretisation])
# Gravity vector
@@ -73,9 +73,9 @@ class Baroclinic(DiscreteOperator):
def initialize_velocity(self):
"""Initialize the temporary array 'result' with the velocity"""
topo = self.velocity.topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] = -self.velocity[d][iCompute]
+ self._result[d][compute_index] = -self.velocity[d][compute_index]
@debug
def apply(self, simulation=None):
@@ -95,14 +95,14 @@ class Baroclinic(DiscreteOperator):
self._synchronizeRho(self.density.data)
topo = self.velocity.topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
# result = du/dt = (u^(n)-u^(n-1))/dt
# result has been initialized with -u^(n-1)
# and _old_dt equals to the previous dt
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] += self.velocity[d][iCompute]
- self._result[d][iCompute] /= self._old_dt
+ self._result[d][compute_index] += self.velocity[d][compute_index]
+ self._result[d][compute_index] /= self._old_dt
# result = result + (u . grad)u
# (u. grad)u = (u.du/dx + v.du/dy + w.du/dz ;
@@ -114,64 +114,64 @@ class Baroclinic(DiscreteOperator):
# result[X] = result[X] + ((u. grad)u)[X]
# = result[X] + u.du/dx + v.du/dy + w.du/dz
for d in xrange(self.velocity.dimension):
- self._result[XDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[XDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
self._tempGrad = self._gradOp(
self.velocity[YDIR:YDIR + 1], self._tempGrad)
# result[Y] = result[Y] + ((u. grad)u)[Y]
# = result[Y] + u.dv/dx + v.dv/dy + w.dv/dz
for d in xrange(self.velocity.dimension):
- self._result[YDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[YDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
self._tempGrad = self._gradOp(
self.velocity[ZDIR:ZDIR + 1], self._tempGrad)
# result[Z] = result[Z] + ((u. grad)u)[Z]
# = result[Z] + u.dw/dx + v.dw/dy + w.dw/dz
for d in xrange(self.velocity.dimension):
- self._result[ZDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[ZDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
# result = result - nu*\Laplacian u (-g) = gradP/rho
for d in xrange(self.velocity.dimension):
self._tempGrad[d:d + 1] = self._laplacian(
self.velocity[d:d + 1], self._tempGrad[d:d + 1])
for d in xrange(self.velocity.dimension):
- self._tempGrad[d][iCompute] *= self.viscosity
- self._result[d][iCompute] -= self._tempGrad[d][iCompute]
+ self._tempGrad[d][compute_index] *= self.viscosity
+ self._result[d][compute_index] -= self._tempGrad[d][compute_index]
# gravity term : result = result - g
for d in xrange(self.velocity.dimension):
- self._result[2][iCompute] -= self._gravity[d]
+ self._result[2][compute_index] -= self._gravity[d]
# baroclinicTerm = -(gradRho/rho) x (gradP/rho)
self._tempGrad = self._gradOp(self.density[0:1], self._tempGrad)
for d in xrange(self.velocity.dimension):
- self._tempGrad[d][iCompute] = \
- self._tempGrad[d][iCompute] / self.density[0][iCompute]
-
- self._baroclinicTerm[0][iCompute] = \
- - self._tempGrad[1][iCompute] * self._result[2][iCompute]
- self._baroclinicTerm[0][iCompute] += \
- self._tempGrad[2][iCompute] * self._result[1][iCompute]
- self._baroclinicTerm[1][iCompute] = \
- - self._tempGrad[2][iCompute] * self._result[0][iCompute]
- self._baroclinicTerm[1][iCompute] += \
- self._tempGrad[0][iCompute] * self._result[2][iCompute]
- self._baroclinicTerm[2][iCompute] = \
- - self._tempGrad[0][iCompute] * self._result[1][iCompute]
- self._baroclinicTerm[2][iCompute] += \
- self._tempGrad[1][iCompute] * self._result[0][iCompute]
+ self._tempGrad[d][compute_index] = \
+ self._tempGrad[d][compute_index] / self.density[0][compute_index]
+
+ self._baroclinicTerm[0][compute_index] = \
+ - self._tempGrad[1][compute_index] * self._result[2][compute_index]
+ self._baroclinicTerm[0][compute_index] += \
+ self._tempGrad[2][compute_index] * self._result[1][compute_index]
+ self._baroclinicTerm[1][compute_index] = \
+ - self._tempGrad[2][compute_index] * self._result[0][compute_index]
+ self._baroclinicTerm[1][compute_index] += \
+ self._tempGrad[0][compute_index] * self._result[2][compute_index]
+ self._baroclinicTerm[2][compute_index] = \
+ - self._tempGrad[0][compute_index] * self._result[1][compute_index]
+ self._baroclinicTerm[2][compute_index] += \
+ self._tempGrad[1][compute_index] * self._result[0][compute_index]
# vorti(n+1) = vorti(n) + dt * baroclinicTerm
for d in xrange(self.vorticity.dimension):
- self._baroclinicTerm[d][iCompute] *= dt
- self.vorticity[d][iCompute] += self._baroclinicTerm[d][iCompute]
+ self._baroclinicTerm[d][compute_index] *= dt
+ self.vorticity[d][compute_index] += self._baroclinicTerm[d][compute_index]
# reinitialise for next iteration
# velo(n-1) update
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] = -self.velocity.data[d][iCompute]
+ self._result[d][compute_index] = -self.velocity.data[d][compute_index]
self._old_dt = dt
diff --git a/hysop/operator/discrete/baroclinic_from_rhs.py b/hysop/operator/discrete/baroclinic_from_rhs.py
index c503edbd6..1434833bc 100644
--- a/hysop/operator/discrete/baroclinic_from_rhs.py
+++ b/hysop/operator/discrete/baroclinic_from_rhs.py
@@ -54,8 +54,8 @@ class BaroclinicFromRHS(DiscreteOperator):
#self._synchronizeRHS(self.rhs.data)
topo = self.vorticity.topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
# vorti(n+1) = vorti(n) + dt * baroclinicTerm
for d in xrange(self.vorticity.dimension):
- self.vorticity[d][iCompute] += self.rhs[d][iCompute] * dt
+ self.vorticity[d][compute_index] += self.rhs[d][compute_index] * dt
diff --git a/hysop/operator/discrete/density.py b/hysop/operator/discrete/density.py
index ffea3a72b..d72df5ca7 100644
--- a/hysop/operator/discrete/density.py
+++ b/hysop/operator/discrete/density.py
@@ -42,14 +42,14 @@ class DensityVisco_d(DiscreteOperator):
assert simulation is not None, \
"Missing simulation value for computation."
- iCompute = self.density.topology.mesh.iCompute
+ compute_index = self.density.topology.mesh.compute_index
# Density reconstruction
- if self.density[0][iCompute].all() <= np.absolute(
+ if self.density[0][compute_index].all() <= np.absolute(
self.densityVal[1] - self.densityVal[0]) / 2.0:
- self.density[0][iCompute] = self.densityVal[1]
+ self.density[0][compute_index] = self.densityVal[1]
else:
- self.density[0][iCompute] = self.densityVal[0]
+ self.density[0][compute_index] = self.densityVal[0]
# Viscosity reconstruction :
# nu = nu1 + (nu2 - nu1) * (density - rho1)/(rho2 - rho1)
diff --git a/hysop/operator/discrete/energy_enstrophy.py b/hysop/operator/discrete/energy_enstrophy.py
index b5101215f..e22512fca 100644
--- a/hysop/operator/discrete/energy_enstrophy.py
+++ b/hysop/operator/discrete/energy_enstrophy.py
@@ -50,8 +50,8 @@ class EnergyEnstrophy(DiscreteOperator):
def _set_work_arrays(self, rwork=None, iwork=None):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
# setup for rwork, iwork is useless.
@@ -75,8 +75,8 @@ class EnergyEnstrophy(DiscreteOperator):
def get_work_properties(self):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
if shape_v == shape_w:
@@ -94,7 +94,7 @@ class EnergyEnstrophy(DiscreteOperator):
vd = self.velocity
# get the list of computation points (no ghosts)
nbc = vd.nb_components
- v_ind = self.velocity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
# Integrate (locally) velocity ** 2
local_energy = 0.
for i in xrange(nbc):
@@ -104,7 +104,7 @@ class EnergyEnstrophy(DiscreteOperator):
# --- Enstrophy computation ---
vortd = self.vorticity
nbc = vortd.nb_components
- w_ind = self.vorticity.topology.mesh.iCompute
+ w_ind = self.vorticity.topology.mesh.compute_index
# Integrate (locally) vorticity ** 2
work = self._rwork[-1]
local_enstrophy = 0.
diff --git a/hysop/operator/discrete/monitoringPoints.py b/hysop/operator/discrete/monitoringPoints.py
index 74738987b..de8ae0e8b 100644
--- a/hysop/operator/discrete/monitoringPoints.py
+++ b/hysop/operator/discrete/monitoringPoints.py
@@ -35,7 +35,7 @@ class MonitoringPoints(DiscreteOperator):
super(MonitoringPoints, self).__init__(variables=[velocity, vorticity],
**kwds)
topo_v = self.velocity.topology
- self.shape_v = self.velocity.data[0][topo_v.mesh.iCompute].shape
+ self.shape_v = self.velocity.data[0][topo_v.mesh.compute_index].shape
self.space_step = topo_v.mesh.space_step
self.length = topo_v.domain.length
self.origin = topo_v.domain.origin
@@ -53,8 +53,8 @@ class MonitoringPoints(DiscreteOperator):
def _set_work_arrays(self, rwork=None, iwork=None):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
# setup for rwork, iwork is useless.
@@ -78,8 +78,8 @@ class MonitoringPoints(DiscreteOperator):
def get_work_properties(self):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
if shape_v == shape_w:
diff --git a/hysop/operator/discrete/multiphase_gradp.py b/hysop/operator/discrete/multiphase_gradp.py
index 0a2697b62..b15e780f5 100644
--- a/hysop/operator/discrete/multiphase_gradp.py
+++ b/hysop/operator/discrete/multiphase_gradp.py
@@ -54,10 +54,10 @@ class GradP(DiscreteOperator):
self._laplacian = diff_op.Laplacian(
self.velocity.topology,
- indices=self.velocity.topology.mesh.iCompute)
+ indices=self.velocity.topology.mesh.compute_index)
self._gradOp = diff_op.GradS(
self.velocity.topology,
- indices=self.velocity.topology.mesh.iCompute,
+ indices=self.velocity.topology.mesh.compute_index,
method=self.method[SpaceDiscretisation])
# Gravity vector
@@ -70,9 +70,9 @@ class GradP(DiscreteOperator):
def initialize_velocity(self):
"""Initialize the temporary array 'result' with the velocity"""
topo = self.velocity.topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] = -self.velocity[d][iCompute]
+ self._result[d][compute_index] = -self.velocity[d][compute_index]
@debug
def apply(self, simulation=None):
@@ -89,14 +89,14 @@ class GradP(DiscreteOperator):
self._synchronizeVel(self.velocity.data)
topo = self.velocity.topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
# result = du/dt = (u^(n)-u^(n-1))/dt
# result has been initialized with -u^(n-1)
# and _old_dt equals to the previous dt
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] += self.velocity[d][iCompute]
- self._result[d][iCompute] /= self._old_dt
+ self._result[d][compute_index] += self.velocity[d][compute_index]
+ self._result[d][compute_index] /= self._old_dt
# result = result + (u . grad)u
# (u. grad)u = (u.du/dx + v.du/dy + w.du/dz ;
@@ -108,36 +108,36 @@ class GradP(DiscreteOperator):
# result[X] = result[X] + ((u. grad)u)[X]
# = result[X] + u.du/dx + v.du/dy + w.du/dz
for d in xrange(self.velocity.dimension):
- self._result[XDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[XDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
self._tempGrad = self._gradOp(
self.velocity[YDIR:YDIR + 1], self._tempGrad)
# result[Y] = result[Y] + ((u. grad)u)[Y]
# = result[Y] + u.dv/dx + v.dv/dy + w.dv/dz
for d in xrange(self.velocity.dimension):
- self._result[YDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[YDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
self._tempGrad = self._gradOp(
self.velocity[ZDIR:ZDIR + 1], self._tempGrad)
# result[Z] = result[Z] + ((u. grad)u)[Z]
# = result[Z] + u.dw/dx + v.dw/dy + w.dw/dz
for d in xrange(self.velocity.dimension):
- self._result[ZDIR][iCompute] += \
- self.velocity[d][iCompute] * self._tempGrad[d][iCompute]
+ self._result[ZDIR][compute_index] += \
+ self.velocity[d][compute_index] * self._tempGrad[d][compute_index]
# result = result - nu*\Laplacian u (-g) = gradP/rho
for d in xrange(self.velocity.dimension):
self._tempGrad[d:d + 1] = self._laplacian(
self.velocity[d:d + 1], self._tempGrad[d:d + 1])
for d in xrange(self.velocity.dimension):
- self._tempGrad[d][iCompute] *= self.viscosity
- self._result[d][iCompute] -= self._tempGrad[d][iCompute]
+ self._tempGrad[d][compute_index] *= self.viscosity
+ self._result[d][compute_index] -= self._tempGrad[d][compute_index]
# gravity term : result = result - g
for d in xrange(self.velocity.dimension):
- self._result[2][iCompute] -= self._gravity[d]
+ self._result[2][compute_index] -= self._gravity[d]
for d in xrange(self.velocity.dimension):
self.gradp[d][...] = self._result[d]
@@ -145,5 +145,5 @@ class GradP(DiscreteOperator):
# reinitialise for next iteration
# velo(n-1) update
for d in xrange(self.velocity.dimension):
- self._result[d][iCompute] = -self.velocity.data[d][iCompute]
+ self._result[d][compute_index] = -self.velocity.data[d][compute_index]
self._old_dt = dt
diff --git a/hysop/operator/discrete/multiresolution_filter.py b/hysop/operator/discrete/multiresolution_filter.py
index b35f3229c..4639aa25b 100644
--- a/hysop/operator/discrete/multiresolution_filter.py
+++ b/hysop/operator/discrete/multiresolution_filter.py
@@ -113,19 +113,19 @@ class FilterFineToCoarse(DiscreteOperator):
for i_y in xrange(len(self._rmsh_method.weights)):
for i_z in xrange(len(self._rmsh_method.weights)):
self._sl_coarse.append((
- slice(self._mesh_out.iCompute[0].start -
+ slice(self._mesh_out.compute_index[0].start -
self._rmsh_method.shift + i_x,
- self._mesh_out.iCompute[0].stop -
+ self._mesh_out.compute_index[0].stop -
self._rmsh_method.shift + i_x,
None),
- slice(self._mesh_out.iCompute[1].start -
+ slice(self._mesh_out.compute_index[1].start -
self._rmsh_method.shift + i_y,
- self._mesh_out.iCompute[1].stop -
+ self._mesh_out.compute_index[1].stop -
self._rmsh_method.shift + i_y,
None),
- slice(self._mesh_out.iCompute[2].start -
+ slice(self._mesh_out.compute_index[2].start -
self._rmsh_method.shift + i_z,
- self._mesh_out.iCompute[2].stop -
+ self._mesh_out.compute_index[2].stop -
self._rmsh_method.shift + i_z,
None)
))
diff --git a/hysop/operator/discrete/profiles.py b/hysop/operator/discrete/profiles.py
index 10c175f3d..74ca03e4f 100644
--- a/hysop/operator/discrete/profiles.py
+++ b/hysop/operator/discrete/profiles.py
@@ -41,7 +41,7 @@ class Profiles(DiscreteOperator):
super(Profiles, self).__init__(variables=[velocity, vorticity],
**kwds)
topo_v = self.velocity.topology
- self.shape_v = self.velocity.data[0][topo_v.mesh.iCompute].shape
+ self.shape_v = self.velocity.data[0][topo_v.mesh.compute_index].shape
self.space_step = topo_v.mesh.space_step
self.length = topo_v.domain.length
self.origin = topo_v.domain.origin
@@ -64,8 +64,8 @@ class Profiles(DiscreteOperator):
def _set_work_arrays(self, rwork=None, iwork=None):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
# setup for rwork, iwork is useless.
@@ -89,8 +89,8 @@ class Profiles(DiscreteOperator):
def get_work_properties(self):
- v_ind = self.velocity.topology.mesh.iCompute
- w_ind = self.vorticity.topology.mesh.iCompute
+ v_ind = self.velocity.topology.mesh.compute_index
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_v = self.velocity.data[0][v_ind].shape
shape_w = self.velocity.data[0][w_ind].shape
if shape_v == shape_w:
diff --git a/hysop/operator/discrete/residual.py b/hysop/operator/discrete/residual.py
index 498924fd0..2fa568b12 100644
--- a/hysop/operator/discrete/residual.py
+++ b/hysop/operator/discrete/residual.py
@@ -26,7 +26,7 @@ class Residual(DiscreteOperator):
assert 'variables' not in kwds, 'variables parameter is useless.'
super(Residual, self).__init__(variables=[vorticity], **kwds)
topo_w = self.vorticity.topology
- self.shape_w = self.vorticity.data[0][topo_w.mesh.iCompute].shape
+ self.shape_w = self.vorticity.data[0][topo_w.mesh.compute_index].shape
self.space_step = topo_w.mesh.space_step
self.length = topo_w.domain.length
self.origin = topo_w.domain.origin
@@ -41,7 +41,7 @@ class Residual(DiscreteOperator):
def _set_work_arrays(self, rwork=None, iwork=None):
- w_ind = self.vorticity.topology.mesh.iCompute
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_w = self.vorticity.data[0][w_ind].shape
# setup for rwork, iwork is useless.
if rwork is None:
@@ -56,13 +56,13 @@ class Residual(DiscreteOperator):
def get_work_properties(self):
- w_ind = self.vorticity.topology.mesh.iCompute
+ w_ind = self.vorticity.topology.mesh.compute_index
shape_w = self.vorticity.data[0][w_ind].shape
return {'rwork': [shape_w], 'iwork': None}
def initialize_vortPrev(self):
- w_ind = self.vorticity.topology.mesh.iCompute
+ w_ind = self.vorticity.topology.mesh.compute_index
for d in xrange(self.vorticity.dimension):
self._vortPrev[d][w_ind] = self.vorticity[d][w_ind]
@@ -85,7 +85,7 @@ class Residual(DiscreteOperator):
# get the list of computation points (no ghosts)
wd = self.vorticity
nbc = wd.nb_components
- w_ind = self.vorticity.topology.mesh.iCompute
+ w_ind = self.vorticity.topology.mesh.compute_index
for i in xrange(nbc):
self._rwork[0][...] = (wd[i][w_ind] -
self._vortPrev[i][w_ind]) ** 2
diff --git a/hysop/operator/discrete/velocity_correction.py b/hysop/operator/discrete/velocity_correction.py
index a720d6960..0053ecd9b 100755
--- a/hysop/operator/discrete/velocity_correction.py
+++ b/hysop/operator/discrete/velocity_correction.py
@@ -131,10 +131,10 @@ class VelocityCorrection_D(DiscreteOperator):
# Computation of the required velocity shift
# for the current state
self.computeCorrection()
- iCompute = self.topo.mesh.iCompute
+ compute_index = self.topo.mesh.compute_index
# Apply shift to velocity
- self.velocity[XDIR][iCompute] += self.velocity_shift[XDIR]
+ self.velocity[XDIR][compute_index] += self.velocity_shift[XDIR]
start = self.velocity.nb_components
# reminder : self.rates =[vx_shift, flowrates[Y], flowrate[Z],
# vort_mean[X], vort_mean[Y], vort_mean[Z]]
diff --git a/hysop/operator/energy_enstrophy.py b/hysop/operator/energy_enstrophy.py
index 4f0bd403a..a59c1edeb 100644
--- a/hysop/operator/energy_enstrophy.py
+++ b/hysop/operator/energy_enstrophy.py
@@ -52,8 +52,8 @@ class EnergyEnstrophy(Computational):
raise RuntimeError(msg)
vd = self.discreteFields[self.velocity]
wd = self.discreteFields[self.vorticity]
- v_ind = vd.topology.mesh.iCompute
- w_ind = wd.topology.mesh.iCompute
+ v_ind = vd.topology.mesh.compute_index
+ w_ind = wd.topology.mesh.compute_index
shape_v = vd[0][v_ind].shape
shape_w = wd[0][w_ind].shape
if shape_v == shape_w:
diff --git a/hysop/operator/hdf_io.py b/hysop/operator/hdf_io.py
index e0771b289..5653b0aa3 100755
--- a/hysop/operator/hdf_io.py
+++ b/hysop/operator/hdf_io.py
@@ -123,7 +123,7 @@ class HDF_IO(Computational):
# Global resolution for hdf5 output (warning : this must
# be the whole domain resolution, not the subset resolution)
self._global_resolution = list(refmesh.global_resolution())
- self._slices = refmesh.iCompute
+ self._slices = refmesh.compute_index
if refmesh.on_proc:
sl = list(refmesh.position)
else:
diff --git a/hysop/operator/monitoringPoints.py b/hysop/operator/monitoringPoints.py
index 3066fda28..d67adc99f 100644
--- a/hysop/operator/monitoringPoints.py
+++ b/hysop/operator/monitoringPoints.py
@@ -45,8 +45,8 @@ class MonitoringPoints(Computational):
raise RuntimeError(msg)
vd = self.discreteFields[self.velocity]
wd = self.discreteFields[self.vorticity]
- v_ind = vd.topology.mesh.iCompute
- w_ind = wd.topology.mesh.iCompute
+ v_ind = vd.topology.mesh.compute_index
+ w_ind = wd.topology.mesh.compute_index
shape_v = vd[0][v_ind].shape
shape_w = wd[0][w_ind].shape
if shape_v == shape_w:
diff --git a/hysop/operator/profiles.py b/hysop/operator/profiles.py
index a7ffb9e30..ac7dfbdfe 100644
--- a/hysop/operator/profiles.py
+++ b/hysop/operator/profiles.py
@@ -50,8 +50,8 @@ class Profiles(Computational):
raise RuntimeError(msg)
vd = self.discreteFields[self.velocity]
wd = self.discreteFields[self.vorticity]
- v_ind = vd.topology.mesh.iCompute
- w_ind = wd.topology.mesh.iCompute
+ v_ind = vd.topology.mesh.compute_index
+ w_ind = wd.topology.mesh.compute_index
shape_v = vd[0][v_ind].shape
shape_w = wd[0][w_ind].shape
if shape_v == shape_w:
diff --git a/hysop/operator/residual.py b/hysop/operator/residual.py
index 1a5de67ae..077f52632 100644
--- a/hysop/operator/residual.py
+++ b/hysop/operator/residual.py
@@ -34,7 +34,7 @@ class Residual(Computational):
msg += 'before any call to this function.'
raise RuntimeError(msg)
wd = self.discreteFields[self.vorticity]
- w_ind = wd.topology.mesh.iCompute
+ w_ind = wd.topology.mesh.compute_index
shape_w = wd[0][w_ind].shape
return {'rwork': [shape_w], 'iwork': None}
diff --git a/hysop/operator/tests/test_differential.py b/hysop/operator/tests/test_differential.py
index 7a217638b..2ab50a59a 100755
--- a/hysop/operator/tests/test_differential.py
+++ b/hysop/operator/tests/test_differential.py
@@ -103,7 +103,7 @@ def check(op, ref_formula, topo, op_dim=3, order=4):
res_d = result.discreteFields[topo]
# Compare results with reference
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
err = topo.mesh.space_step ** order
dim = topo.domain.dimension
for i in xrange(result.nb_components):
diff --git a/hysop/operator/tests/test_hdf5_io.py b/hysop/operator/tests/test_hdf5_io.py
index 368836fd2..3e338fbae 100755
--- a/hysop/operator/tests/test_hdf5_io.py
+++ b/hysop/operator/tests/test_hdf5_io.py
@@ -98,7 +98,7 @@ def test_write_read_scalar_3D():
reader.setup()
sc3d = scal3D.discretize(topo)
scref = scalRef.discretize(topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
for d in xrange(scal3D.nb_components):
sc3d.data[d][...] = 0.0
assert not np.allclose(scref.data[d][ind], sc3d.data[d][ind])
@@ -138,7 +138,7 @@ def test_write_read_scalar_3D_defaults():
sc3d = scal3D.discretize(topo)
scref = scalRef.discretize(topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
for d in xrange(scal3D.nb_components):
sc3d.data[d][...] = scref.data[d][...]
scref.data[d][...] = 0.0
@@ -194,7 +194,7 @@ def test_write_read_vectors_3D_defaults():
v3d = velo.discretize(topo)
w3d = vorti.discretize(topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
# Copy current values of v3 and w3 into buff1 and buff2, for comparison
# after reader.apply, below.
@@ -266,7 +266,7 @@ def test_write_read_vectors_3D():
v3d = velo.discretize(topo)
w3d = vorti.discretize(topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
buff1 = Field(domain=dom, name='buff1', is_vector=True)
buff2 = Field(domain=dom, name='buff2', is_vector=True)
@@ -323,8 +323,8 @@ def test_write_read_subset_1():
assert os.path.exists(fullpath + '_00001.h5')
v3d = velo.discretize(topo)
- ind = topo.mesh.iCompute
- indsubset = mybox.mesh[topo].iCompute
+ ind = topo.mesh.compute_index
+ indsubset = mybox.mesh[topo].compute_index
buff1 = Field(domain=dom, name='buff1', is_vector=True)
@@ -378,8 +378,8 @@ def test_write_read_subset_2():
assert os.path.exists(fullpath + '_00001.h5')
v3d = velo.discretize(topo)
- ind = topo.mesh.iCompute
- indsubset = mybox.mesh[topo].iCompute
+ ind = topo.mesh.compute_index
+ indsubset = mybox.mesh[topo].compute_index
buff1 = Field(domain=dom, name='buff1', is_vector=True)
diff --git a/hysop/operator/tests/test_multiphase_gradp.py b/hysop/operator/tests/test_multiphase_gradp.py
index 477c9e48c..f9a3a000c 100755
--- a/hysop/operator/tests/test_multiphase_gradp.py
+++ b/hysop/operator/tests/test_multiphase_gradp.py
@@ -59,7 +59,7 @@ def test_gradp():
op.discretize()
op.setup()
topo = op.discreteFields[velo].topology
- iCompute = topo.mesh.iCompute
+ compute_index = topo.mesh.compute_index
velo.initialize(topo=topo)
op.initialize_velocity()
res.initialize(topo=topo)
@@ -67,6 +67,6 @@ def test_gradp():
op.apply(simu)
d_res = res.discreteFields[topo]
d_true_res = true_res.discreteFields[topo]
- assert np.allclose(d_res[0][iCompute], d_true_res[0][iCompute], atol=8e-3)
- assert np.allclose(d_res[1][iCompute], d_true_res[1][iCompute], atol=8e-3)
- assert np.allclose(d_res[2][iCompute], d_true_res[2][iCompute])
+ assert np.allclose(d_res[0][compute_index], d_true_res[0][compute_index], atol=8e-3)
+ assert np.allclose(d_res[1][compute_index], d_true_res[1][compute_index], atol=8e-3)
+ assert np.allclose(d_res[2][compute_index], d_true_res[2][compute_index])
diff --git a/hysop/operator/tests/test_multiresolution_filter.py b/hysop/operator/tests/test_multiresolution_filter.py
index 44e3e5e7e..fbda089f3 100755
--- a/hysop/operator/tests/test_multiresolution_filter.py
+++ b/hysop/operator/tests/test_multiresolution_filter.py
@@ -55,11 +55,11 @@ def filter(d_fine, d_coarse, func, method, atol=1e-8, rtol=1e-5):
op.apply(simu)
valid = [npw.zeros(f_out[0].shape), ]
valid = func(valid, *topo_coarse.mesh.coords)
- e = np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
- err = atol + rtol * np.max(np.abs(valid[0][topo_coarse.mesh.iCompute]))
- return np.allclose(f_out[0][topo_coarse.mesh.iCompute],
- valid[0][topo_coarse.mesh.iCompute],
+ e = np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
+ err = atol + rtol * np.max(np.abs(valid[0][topo_coarse.mesh.compute_index]))
+ return np.allclose(f_out[0][topo_coarse.mesh.compute_index],
+ valid[0][topo_coarse.mesh.compute_index],
atol=atol, rtol=rtol), e, err
@@ -188,11 +188,11 @@ def test_filter_linear():
op.apply(simu)
valid = [npw.zeros(f_out[0].shape), ]
valid = func(valid, *topo_coarse.mesh.coords)
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute],
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index],
atol=1e-4, rtol=1e-3), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
def test_filter_l2_1():
@@ -214,8 +214,8 @@ def test_filter_l2_1():
op.apply(simu)
valid = [npw.zeros(f_out[0].shape), ]
valid = func(valid, *topo_coarse.mesh.coords)
- assert np.allclose(valid[0][topo_coarse.mesh.iCompute],
- f_out[0][topo_coarse.mesh.iCompute]), \
- np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
- f_out[0][topo_coarse.mesh.iCompute]))
+ assert np.allclose(valid[0][topo_coarse.mesh.compute_index],
+ f_out[0][topo_coarse.mesh.compute_index]), \
+ np.max(np.abs(valid[0][topo_coarse.mesh.compute_index] -
+ f_out[0][topo_coarse.mesh.compute_index]))
diff --git a/hysop/operator/tests/test_penalization.py b/hysop/operator/tests/test_penalization.py
index 9026e986b..75bd69718 100755
--- a/hysop/operator/tests/test_penalization.py
+++ b/hysop/operator/tests/test_penalization.py
@@ -100,7 +100,7 @@ def check_penal(penal, sref, vref, scal, velo):
sd = scal.discretize(topo)
simu = Simulation(nbIter=3)
penal.apply(simu)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
assert np.allclose(sd.data[0][ind], sref.data[0][ind])
for d in xrange(vd.nb_components):
assert np.allclose(vd.data[d][ind], vref.data[d][ind])
@@ -282,7 +282,7 @@ def check_penal_vort(penal, wref, vref, vorti, velo):
velo.initialize(topo=topo)
vd = velo.discretize(topo)
wd = vorti.discretize(topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
simu = Simulation(nbIter=200)
penal.apply(simu)
diff --git a/hysop/operator/tests/test_redistribute.py b/hysop/operator/tests/test_redistribute.py
index a8bae9037..f5450b9a1 100755
--- a/hysop/operator/tests/test_redistribute.py
+++ b/hysop/operator/tests/test_redistribute.py
@@ -76,7 +76,7 @@ def test_distribute_intra_1():
red.apply()
red.wait()
vd_2 = velocity.discretize(default_topo)
- ind_ng = default_topo.mesh.iCompute
+ ind_ng = default_topo.mesh.compute_index
for d in xrange(velocity.nb_components):
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
@@ -136,7 +136,7 @@ def test_distribute_intra_2():
red.apply()
red.wait()
vd_2 = velocity.discretize(default_topo)
- ind_ng = default_topo.mesh.iCompute
+ ind_ng = default_topo.mesh.compute_index
wd = vorticity.discretize(default_topo)
for d in xrange(velocity.nb_components):
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
@@ -182,7 +182,7 @@ def test_distribute_intra_3():
red.apply()
red.wait()
vd_2 = velocity.discretize(target_topo)
- ind_ng = target_topo.mesh.iCompute
+ ind_ng = target_topo.mesh.compute_index
for d in xrange(velocity.nb_components):
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
@@ -231,7 +231,7 @@ def test_distribute_intra_4():
red.apply()
red.wait()
vd_2 = velocity.discretize(target_topo)
- ind_ng = target_topo.mesh.iCompute
+ ind_ng = target_topo.mesh.compute_index
for d in xrange(velocity.nb_components):
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
@@ -284,7 +284,7 @@ def test_distribute_intra_5():
red.wait()
vd = velocity.discretize(target_topo)
wd = vorticity.discretize(target_topo)
- ind_ng = target_topo.mesh.iCompute
+ ind_ng = target_topo.mesh.compute_index
for d in xrange(velocity.nb_components):
assert np.allclose(vd.data[d][ind_ng], rd.data[d][ind_ng])
@@ -385,7 +385,7 @@ def test_distribute_overlap():
red.wait()
if target_topo is not None:
vd_2 = velocity.discretize(target_topo)
- ind_ng = target_topo.mesh.iCompute
+ ind_ng = target_topo.mesh.compute_index
for d in xrange(velocity.nb_components):
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
@@ -483,7 +483,7 @@ def test_distribute_inter_2():
vd = velocity.discretize(topo=topo_CPU)
wd = reference.discretize(topo=topo_CPU)
vnorm = velocity.norm(topo_CPU)
- ind = topo_CPU.mesh.iCompute
+ ind = topo_CPU.mesh.compute_index
wnorm = reference.norm(topo_CPU)
assert np.allclose(vnorm, wnorm)
for d in xrange(dom.dimension):
@@ -527,7 +527,7 @@ def test_distribute_inter_3():
wd = reference.discretize(topo=topo2)
vd = velocity.discretize(topo=topo2)
vnorm = velocity.norm(topo2)
- ind = topo2.mesh.iCompute
+ ind = topo2.mesh.compute_index
assert np.allclose(vnorm, wnorm)
for d in xrange(dom.dimension):
assert np.allclose(wd.data[d][ind], vd.data[d][ind])
@@ -567,7 +567,7 @@ def test_distribute_inter_4():
if dom_tasks.is_on_task(CPU):
wd = reference.discretize(topo=topo)
vd = velocity.discretize(topo=topo)
- ind = topo.mesh.iCompute
+ ind = topo.mesh.compute_index
for d in xrange(dom.dimension):
assert np.allclose(wd.data[d][ind], vd.data[d][ind])
--
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