def build_refinementboxes(domain_box, **kwargs):
refinement_ratio = kwargs["refinement_ratio"]
boxes = {}
for ilvl, boxes_data in kwargs["refinement_boxes"].items():
level_number = int(ilvl.strip("L")) + 1
if level_number not in boxes:
boxes[level_number] = []
assert isinstance(boxes_data, (list, dict))
if isinstance(boxes_data, list):
for _, refinement_box in enumerate(boxes_data):
refined_box = boxm.refine(refinement_box, refinement_ratio)
boxes[level_number].append(refined_box)
else:
for boxname, lower_upper in boxes_data.items():
refinement_box = Box(lower_upper[0][0], lower_upper[1][0])
refined_box = boxm.refine(refinement_box, refinement_ratio)
boxes[level_number].append(refined_box)
# coarse level boxes are arbitrarily divided in 2 patches in the middle
middle_cell = np.round(domain_box.upper / 2)
lower_box = Box(0, middle_cell)
upper_box = Box(middle_cell + 1, domain_box.upper)
boxes[0] = [lower_box, upper_box]
return boxes
def build_boxes(domain_box, **kwargs):
refinement_ratio = kwargs["refinement_ratio"]
ndim = domain_box.ndim
boxes = {}
for ilvl, boxes_data in kwargs["refinement_boxes"].items():
level_number = int(ilvl.strip("L")) + 1
if level_number not in boxes:
boxes[level_number] = []
assert isinstance(boxes_data, (list, dict))
if isinstance(boxes_data, list):
for _, refinement_box in enumerate(boxes_data):
refined_box = boxm.refine(refinement_box, refinement_ratio)
boxes[level_number].append(refined_box)
else:
for boxname, box in boxes_data.items():
if isinstance(box, Box):
refinement_box = Box(box.lower, box.upper)
else:
refinement_box = Box(box[0], box[1])
refined_box = boxm.refine(refinement_box, refinement_ratio)
boxes[level_number].append(refined_box)
# coarse level boxes are arbitrarily divided in 2 patches in the middle
if (
"largest_patch_size" in kwargs
and (kwargs["largest_patch_size"] == domain_box.upper + 1).all()
):
boxes[0] = [Box(domain_box.lower, domain_box.upper + 1)]
else:
if ndim == 1:
middle_cell = np.round(domain_box.upper / 2)
lower_box = Box(0, middle_cell)
upper_box = Box(middle_cell + 1, domain_box.upper)
if ndim >= 2:
middle_cell = np.round(domain_box.upper / 2)
lower_box = Box([0] * ndim, middle_cell - 1)
upper_box = Box(middle_cell, domain_box.upper)
boxes[0] = [lower_box, upper_box]
if ndim >= 2:
boxes[0].append(
Box([0, middle_cell[1]], [middle_cell[0] - 1, domain_box.upper[1]])
)
boxes[0].append(
Box([middle_cell[0], 0], [domain_box.upper[0], middle_cell[1] - 1])
)
return boxes
def refine(field, **kwargs):
"""
optional kwargs
data : for overriding the field dataset so you don't have to make a temporary copy of a field just to have a different dataset
"""
assert isinstance(field, FieldData)
kwarg_keys = ["data"]
assert any([key in kwarg_keys for key in list(kwargs.keys())])
refinement_ratio = 2
primal_directions = field.primal_directions()
data = kwargs.get("data", field.dataset[:])
if "data" in kwargs:
assert data.shape == field.dataset.shape
fine_box = boxm.refine(field.box, refinement_ratio)
fine_layout = GridLayout(fine_box, field.origin, field.layout.dl/refinement_ratio, interp_order=field.layout.interp_order)
assert field.box.ndim == 1
fine_data = np.zeros(fine_box.shape + primal_directions + (field.ghosts_nbr[0] * 2))
ghostX = field.ghosts_nbr[0]
assert ghostX > 0
cadence = 2
if primal_directions[0]:
fine_data[ghostX:-ghostX:cadence] = data[ghostX:-ghostX] # coarse primal on top of fine
fine_data[ghostX + 1:-(ghostX - 1):cadence] = 0.5*data[ghostX:-ghostX] + 0.5*data[ghostX + 1:-(ghostX - 1)]
else:
fine_data[ghostX:-(ghostX + 1):cadence] = 0.25*data[ghostX - 1:-(ghostX + 1)] + 0.75*data[ghostX:-ghostX]
fine_data[ghostX + 1:-(ghostX - 1):cadence] = 0.25*data[ghostX + 1:-(ghostX - 1)] + 0.75*data[ghostX:-ghostX]
return FieldData(fine_layout, field.field_name, data=fine_data)
def make_fig(hier, fig_name, ilvl, extra_collections=[]):
if cpp.mpi_rank() == 0:
l0_in_l1 = [boxm.refine(p.box, 2) for p in hier.level(0).patches]
collections=[{
"boxes": l0_in_l1,
"facecolor": "grey",
}]
if 1 in hier.levels():
l1_over_l0 = [p.box for p in hier.level(1).patches]
collections += [{
"boxes": l1_over_l0,
"facecolor": "yellow",
}]
hier.plot_2d_patches(1,
collections=collections + extra_collections,
).savefig(fig_name+".png")
def build_patch_datas(domain_box, boxes, **kwargs):
quantities = kwargs["quantities"]
origin = kwargs["origin"]
interp_order = kwargs["interp_order"]
domain_size = kwargs["domain_size"]
cell_width = kwargs["cell_width"]
refinement_ratio = kwargs["refinement_ratio"]
skip_particles = False
if "particles" in quantities:
del quantities[quantities.index("particles")]
else:
skip_particles = True
domain_layout = GridLayout(domain_box, origin, cell_width, interp_order)
coarse_particles = Particles(box=domain_box)
# copy domain particles and put them in ghost cells
particle_ghost_nbr = domain_layout.particleGhostNbr(interp_order)
box_extend = particle_ghost_nbr - 1
upper_slct_box = Box(domain_box.upper - box_extend, domain_box.upper)
lower_slct_box = Box(domain_box.lower, domain_box.lower + box_extend)
if not skip_particles:
coarse_particles = Particles(box=domain_box)
upper_cell_particles = coarse_particles.select(upper_slct_box)
lower_cell_particles = coarse_particles.select(lower_slct_box)
coarse_particles.add(
upper_cell_particles.shift_icell(-domain_box.shape()))
coarse_particles.add(
lower_cell_particles.shift_icell(domain_box.shape()))
patch_datas = {}
for ilvl, lvl_box in boxes.items():
lvl_cell_width = cell_width / (refinement_ratio**ilvl)
if not skip_particles:
if ilvl == 0:
lvl_particles = coarse_particles
else:
level_domain_box = boxm.refine(domain_box, refinement_ratio)
lvl_ghost_domain_box = boxm.grow(
level_domain_box,
domain_layout.particleGhostNbr(interp_order))
lvl_particles = Particles(box=lvl_ghost_domain_box)
if ilvl not in patch_datas:
patch_datas[ilvl] = []
for box in lvl_box:
ghost_box = boxm.grow(box, 5)
origin = box.lower * lvl_cell_width
layout = GridLayout(box, origin, lvl_cell_width, interp_order)
datas = {
qty: globals()[qty](ghost_box, layout, domain_size)
for qty in quantities
}
if not skip_particles:
datas["particles"] = lvl_particles.select(ghost_box)
boxed_patch_datas = {}
for qty_name, data in datas.items():
if qty_name == 'particles':
pdata = ParticleData(layout, data, "pop_name")
else:
pdata = FieldData(layout, qty_name, data)
boxed_patch_datas[qty_name] = pdata
patch_datas[ilvl].append(boxed_patch_datas)
return patch_datas
def test_box_refinement(self, coarse, exp_refined):
actual_refined = boxm.refine(coarse, 2)
self.assertEqual(actual_refined, exp_refined)
def coarsen(qty, coarseField, fineField, coarseBox, fineData, coarseData):
coarseLayout = coarseField.layout
fineLayout = fineField.layout
ndim = coarseLayout.box.ndim
nGhosts = coarseLayout.nbrGhostFor(qty)
coarseStartIndex = coarseLayout.physicalStartIndices(qty)
fineOffset = fineLayout.box.lower - boxm.refine(coarseLayout.box, 2).lower
is_primal = []
for direction in directions[:ndim]:
is_primal += [gridlayout.yee_element_is_primal(qty, direction)]
def coarse_indices(dim):
return np.arange(coarseBox.lower[dim], coarseBox.upper[dim] + 1)
def fineLocal(coarse_index, dim):
return fineLayout.AMRIndexToLocal(dim, coarse_index * refinement_ratio)
def coarseLocal(index, dim):
return coarseLayout.AMRIndexToLocal(dim, index)
if ndim == 1:
for index in coarse_indices(0):
fineIndex = fineLocal(index, 0)
coarseLocalIndex = coarseLocal(index, 0)
if is_primal[0]:
coarseData[coarseLocalIndex] = (
fineData[fineIndex - 1] * .25 + fineData[fineIndex] * .5 + fineData[fineIndex + 1] * .25
)
else:
coarseData[coarseLocalIndex] = (
fineData[fineIndex] * .5 + fineData[fineIndex + 1] * .5
)
if ndim == 2:
for indexX in coarse_indices(0):
fineIndexX = fineLocal(indexX, 0)
coarseLocalIndexX = coarseLocal(indexX, 0)
for indexY in coarse_indices(1):
fineIndexY = fineLocal(indexY, 1)
coarseLocalIndexY = coarseLocal(indexY, 1)
left, middle, right = 0, 0, 0
if all(is_primal):
left += fineData[fineIndexX - 1][fineIndexY - 1] * .25
left += fineData[fineIndexX - 1][fineIndexY] * .5
left += fineData[fineIndexX - 1][fineIndexY + 1] * .25
middle += fineData[fineIndexX][fineIndexY - 1] * .25
middle += fineData[fineIndexX][fineIndexY] * .5
middle += fineData[fineIndexX][fineIndexY + 1] * .25
right += fineData[fineIndexX + 1][fineIndexY - 1] * .25
right += fineData[fineIndexX + 1][fineIndexY] * .5
right += fineData[fineIndexX + 1][fineIndexY + 1] * .25
coarseData[coarseLocalIndexX][coarseLocalIndexY] = (
left * .25 + middle * .5 + right * .25
)
if is_primal[0] and not is_primal[1]:
left += fineData[fineIndexX - 1][fineIndexY] * .5
left += fineData[fineIndexX - 1][fineIndexY + 1] * .5
middle += fineData[fineIndexX][fineIndexY] * .5
middle += fineData[fineIndexX][fineIndexY + 1] * .5
right += fineData[fineIndexX + 1][fineIndexY] * .5
right += fineData[fineIndexX + 1][fineIndexY + 1] * .5
coarseData[coarseLocalIndexX][coarseLocalIndexY] = (
left * .25 + middle * .5 + right * .25
)
if not is_primal[0] and is_primal[1]:
left += fineData[fineIndexX][fineIndexY - 1] * .25
left += fineData[fineIndexX][fineIndexY] * .5
left += fineData[fineIndexX][fineIndexY + 1] * .25
right += fineData[fineIndexX + 1][fineIndexY - 1] * .25
right += fineData[fineIndexX + 1][fineIndexY] * .5
right += fineData[fineIndexX + 1][fineIndexY + 1] * .25
coarseData[coarseLocalIndexX][coarseLocalIndexY] = (left * .5 + right * .5)
if not any(is_primal):
left += fineData[fineIndexX][fineIndexY] * .5
left += fineData[fineIndexX][fineIndexY + 1] * .5
right += fineData[fineIndexX + 1][fineIndexY] * .5
right += fineData[fineIndexX + 1][fineIndexY + 1] * .5
coarseData[coarseLocalIndexX][coarseLocalIndexY] = (left * .5 + right * .5)
def _test_field_coarsening_via_subcycles(self, dim, interp_order,
refinement_boxes, **kwargs):
print("test_field_coarsening_via_subcycles for dim/interp : {}/{}".
format(dim, interp_order))
from tests.amr.data.field.coarsening.test_coarsen_field import coarsen
from pyphare.pharein import global_vars
time_step_nbr = 3
diag_outputs = f"subcycle_coarsening/{dim}/{interp_order}/{self.ddt_test_id()}"
datahier = self.getHierarchy(
interp_order,
refinement_boxes,
"eb",
cells=60,
diag_outputs=diag_outputs,
time_step=0.001,
extra_diag_options={"fine_dump_lvl_max": 10},
time_step_nbr=time_step_nbr,
largest_patch_size=30,
ndim=dim,
**kwargs)
lvl_steps = global_vars.sim.level_time_steps
print("LEVELSTEPS === ", lvl_steps)
assert len(lvl_steps) > 1, "this test makes no sense with only 1 level"
finestTimeStep = lvl_steps[-1]
secondFinestTimeStep = lvl_steps[-2]
finest_level_step_nbr = global_vars.sim.level_step_nbr[-1]
uniqTimes = set([0])
for step in range(1, finest_level_step_nbr + 1):
checkTime = datahier.format_timestamp(finestTimeStep * step)
self.assertIn(checkTime, datahier.times())
uniqTimes.add(checkTime)
self.assertEqual(len(uniqTimes), len(datahier.time_hier.items()))
syncSteps = global_vars.sim.level_step_nbr[
-2] # ignore finest subcycles
# FIX THIS AFTER NO MORE REGRIDS
# SEE: https://github.com/PHAREHUB/PHARE/issues/400
assert syncSteps % time_step_nbr == 0 # perfect division
startStep = int(
syncSteps /
time_step_nbr) + 1 # skip first coarsest step due to issue 400
for step in range(startStep, syncSteps + 1):
checkTime = datahier.format_timestamp(secondFinestTimeStep * step)
self.assertIn(checkTime, datahier.times())
nLevels = datahier.levelNbr(checkTime)
self.assertGreaterEqual(nLevels, 2)
levelNbrs = datahier.levelNbrs(checkTime)
finestLevelNbr = max(levelNbrs)
coarsestLevelNbr = min(levelNbrs)
for coarseLevelNbr in range(coarsestLevelNbr, finestLevelNbr):
coarsePatches = datahier.level(coarseLevelNbr,
checkTime).patches
finePatches = datahier.level(coarseLevelNbr + 1,
checkTime).patches
for coarsePatch in coarsePatches:
for finePatch in finePatches:
lvlOverlap = boxm.refine(coarsePatch.box,
2) * finePatch.box
if lvlOverlap is not None:
for EM in ["E", "B"]:
for xyz in ["x", "y", "z"]:
qty = f"{EM}{xyz}"
coarse_pd = coarsePatch.patch_datas[qty]
fine_pd = finePatch.patch_datas[qty]
coarseBox = boxm.coarsen(lvlOverlap, 2)
coarse_pdDataset = coarse_pd.dataset[:]
fine_pdDataset = fine_pd.dataset[:]
coarseOffset = coarseBox.lower - coarse_pd.layout.box.lower
dataBox_lower = coarseOffset + coarse_pd.layout.nbrGhostFor(
qty)
dataBox = Box(
dataBox_lower,
dataBox_lower + coarseBox.shape - 1)
afterCoarse = np.copy(coarse_pdDataset)
# change values that should be updated to make failure obvious
assert (dim < 3) # update
if dim == 1:
afterCoarse[dataBox.
lower[0]:dataBox.upper[0] +
1] = -144123
if dim == 2:
afterCoarse[
dataBox.lower[0]:dataBox.upper[0] +
1,
dataBox.lower[1]:dataBox.upper[1] +
1] = -144123
coarsen(qty, coarse_pd, fine_pd, coarseBox,
fine_pdDataset, afterCoarse)
np.testing.assert_allclose(
coarse_pdDataset,
afterCoarse,
atol=1e-16,
rtol=0)
def refine(field, **kwargs):
"""
optional kwargs
data : for overriding the field dataset so you don't have to make a temporary copy of a field just to have a different dataset
"""
assert isinstance(field, FieldData)
kwarg_keys = ["data"]
assert any([key in kwarg_keys for key in list(kwargs.keys())])
refinement_ratio = 2
primal_directions = field.primal_directions()
data = kwargs.get("data", field.dataset[:])
if "data" in kwargs:
assert data.shape == field.dataset.shape
fine_layout = GridLayout(
boxm.refine(field.box, refinement_ratio),
field.origin,
field.layout.dl / refinement_ratio,
interp_order=field.layout.interp_order,
)
# fine box has extra ghosts for padding against coarser such that at the normal number of ghosts are filled
fine_box = boxm.shrink(boxm.refine(field.ghost_box, refinement_ratio),
field.ghosts_nbr)
fine_data = np.zeros(fine_box.shape + primal_directions +
(field.ghosts_nbr * 2))
ghostX = field.ghosts_nbr[0]
assert ghostX > 1
cadence = 2
assert cadence == refinement_ratio
gX = 2 # level 0 ghost buffer from edge of normal coarse data box
rgX = 4 # level 1 ghost buffer from edge of extra large fine data box
if field.box.ndim == 1:
if primal_directions[0]:
# coarse primal on top of fine
fine_data[rgX:-rgX:cadence] = data[gX:-gX]
fine_data[rgX +
1:-(rgX - 1):cadence] = (0.5 * data[gX:-gX] +
0.5 * data[gX + 1:-(gX - 1)])
else:
fine_data[rgX:-(rgX + 1):cadence] = (
0.25 * data[gX - 1:-(gX + 1)] + 0.75 * data[gX:-gX])
fine_data[rgX +
1:-(rgX - 1):cadence] = (0.25 * data[gX + 1:-(gX - 1)] +
0.75 * data[gX:-gX])
if fine_box.ndim > 1:
assert field.ghosts_nbr[1] > 1
gY = 2
rgY = 4
cad = cadence
if fine_box.ndim == 2:
if all(primal_directions):
fine_data[rgX:-rgX:cad, rgY:-rgY:cad] = data[gX:-gX, gY:-gY]
fine_data[rgX + 1:-(rgX - 1):cad,
rgY:-rgY:cad] = (0.5 * data[gX:-gX, gY:-gY] +
0.5 * data[gX + 1:-(gX - 1), gY:-gY])
fine_data[rgX:-rgX:cad, rgY + 1:-(rgY - 1):cad] = (
0.5 * data[gX:-gX, gY:-gY] +
0.5 * data[gX:-gX, gY + 1:-(gY - 1)])
fine_data[rgX + 1:-(rgX - 1):cad, rgY + 1:-(rgY - 1):cad] = (
0.25 * data[gX:-gX, gY:-gY] +
0.25 * data[gX + 1:-(gX - 1), gY:-gY] +
0.25 * data[gX:-gX, gY + 1:-(gY - 1)] +
0.25 * data[gX + 1:-(gX - 1), gY + 1:-(gY - 1)])
elif primal_directions[0] and not primal_directions[1]:
fine_data[rgX:-rgX:cad,
rgY:-rgY:cad] = (0.25 * data[gX:-gX, gY - 1:-(gY + 1)] +
0.75 * data[gX:-gX, gY:-gY])
fine_data[rgX + 1:-(rgX - 1):cad, rgY:-rgY:cad] = 0.75 * (
0.5 * data[gX + 1:-(gX - 1), gY:-gY] +
0.5 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.5 * data[gX + 1:-(gX - 1), gY - 1:-(gY + 1)] +
0.5 * data[gX:-gX, gY - 1:-(gY + 1)])
fine_data[rgX:-rgX:cad, rgY + 1:-(rgY - 1):cad] = (
0.25 * data[gX:-gX, gY + 1:-(gY - 1)] +
0.75 * data[gX:-gX, gY:-gY])
fine_data[rgX + 1:-(rgX - 1):cad,
rgY + 1:-(rgY - 1):cad] = 0.75 * (
0.5 * data[gX + 1:-(gX - 1), gY:-gY] +
0.5 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.5 * data[gX + 1:-(gX - 1), gY + 1:-(gY - 1)] +
0.5 * data[gX:-gX, gY + 1:-(gY - 1)])
elif not primal_directions[0] and primal_directions[1]:
fine_data[rgX:-rgX:cad,
rgY:-rgY:cad] = (0.25 * data[gX - 1:-(gX + 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY])
fine_data[rgX + 1:-(rgX - 1):cad,
rgY:-rgY:cad] = (0.25 * data[gX + 1:-(gX - 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY])
fine_data[rgX:-rgX:cad, rgY + 1:-(rgY - 1):cad] = 0.5 * (
0.25 * data[gX - 1:-(gX + 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.5 * (
0.25 * data[gX - 1:-(gX + 1), gY + 1:-(gY - 1)] +
0.75 * data[gX:-gX, gY + 1:-(gY - 1)])
fine_data[rgX + 1:-(rgX - 1):cad, rgY + 1:-(rgY - 1):cad] = 0.5 * (
0.25 * data[gX + 1:-(gX - 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.5 * (
0.25 * data[gX + 1:-(gX - 1), gY + 1:-(gY - 1)] +
0.75 * data[gX:-gX, gY + 1:-(gY - 1)])
elif not any(primal_directions):
fine_data[rgX:-rgX:cad, rgY:-rgY:cad] = 0.75 * (
0.25 * data[gX - 1:-(gX + 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.25 * data[gX - 1:-(gX + 1), gY - 1:-(gY + 1)] +
0.75 * data[gX:-gX, gY - 1:-(gY + 1)])
fine_data[rgX + 1:-(rgX - 1):cad, rgY:-rgY:cad] = 0.75 * (
0.25 * data[gX + 1:-(gX - 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.25 * data[gX + 1:-(gX - 1), gY - 1:-(gY + 1)] +
0.75 * data[gX:-gX, gY - 1:-(gY + 1)])
fine_data[rgX:-rgX:cad, rgY + 1:-(rgY - 1):cad] = 0.75 * (
0.25 * data[gX - 1:-(gX + 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.25 * data[gX - 1:-(gX + 1), gY + 1:-(gY - 1)] +
0.75 * data[gX:-gX, gY + 1:-(gY - 1)])
fine_data[rgX + 1:-(rgX - 1):cad,
rgY + 1:-(rgY - 1):cad] = 0.75 * (
0.25 * data[gX + 1:-(gX - 1), gY:-gY] +
0.75 * data[gX:-gX, gY:-gY]) + 0.25 * (
0.25 * data[gX + 1:-(gX - 1), gY + 1:-(gY - 1)] +
0.75 * data[gX:-gX, gY + 1:-(gY - 1)])
# the fine data is ghost_nbr larger than expected to include ghost values from the coarser, so we drop the outer values
if field.box.ndim == 1:
fine_data = fine_data[field.ghosts_nbr[0]:-field.ghosts_nbr[0]]
elif field.box.ndim == 2:
fine_data = fine_data[field.ghosts_nbr[0]:-field.ghosts_nbr[0],
field.ghosts_nbr[1]:-field.ghosts_nbr[1], ]
elif field.box.ndim == 3:
fine_data = fine_data[field.ghosts_nbr[0]:-field.ghosts_nbr[0],
field.ghosts_nbr[1]:-field.ghosts_nbr[1],
field.ghosts_nbr[2]:-field.ghosts_nbr[2], ]
return FieldData(fine_layout, field.field_name, data=fine_data)