diff --git a/pystencils/datahandling/datahandling_interface.py b/pystencils/datahandling/datahandling_interface.py
index ce153ff7a95e6a3e2875aa5b02566874c3238662..8b426ce5be1205aacdceafbc15017e18bc4acb39 100644
--- a/pystencils/datahandling/datahandling_interface.py
+++ b/pystencils/datahandling/datahandling_interface.py
@@ -36,7 +36,7 @@ class DataHandling(ABC):
@abstractmethod
def add_array(self, name: str, values_per_cell, dtype=np.float64,
latex_name: Optional[str] = None, ghost_layers: Optional[int] = None, layout: Optional[str] = None,
- cpu: bool = True, gpu: Optional[bool] = None, alignment=False) -> Field:
+ cpu: bool = True, gpu: Optional[bool] = None, alignment=False, staggered=False) -> Field:
"""Adds a (possibly distributed) array to the handling that can be accessed using the given name.
For each array a symbolic field is available via the 'fields' dictionary
diff --git a/pystencils/datahandling/parallel_datahandling.py b/pystencils/datahandling/parallel_datahandling.py
index 4e8d965d4335725e5e0a00b842bbffeab9497924..0fd8d71df11cd8569221b869db016223dba51d52 100644
--- a/pystencils/datahandling/parallel_datahandling.py
+++ b/pystencils/datahandling/parallel_datahandling.py
@@ -90,7 +90,7 @@ class ParallelDataHandling(DataHandling):
self._custom_data_names.append(name)
def add_array(self, name, values_per_cell=1, dtype=np.float64, latex_name=None, ghost_layers=None,
- layout=None, cpu=True, gpu=None, alignment=False):
+ layout=None, cpu=True, gpu=None, alignment=False, staggered=False):
if ghost_layers is None:
ghost_layers = self.default_ghost_layers
if gpu is None:
@@ -140,7 +140,8 @@ class ParallelDataHandling(DataHandling):
assert all(f.name != name for f in self.fields.values()), "Symbolic field with this name already exists"
self.fields[name] = Field.create_generic(name, self.dim, dtype, index_dimensions, layout,
- index_shape=(values_per_cell,) if index_dimensions > 0 else None)
+ index_shape=(values_per_cell,) if index_dimensions > 0 else None,
+ staggered=staggered)
self.fields[name].latex_name = latex_name
self._field_name_to_cpu_data_name[name] = name
if gpu:
diff --git a/pystencils/datahandling/serial_datahandling.py b/pystencils/datahandling/serial_datahandling.py
index 8c79a0931f06fad7c7ab58143cf7058a3f52dbac..be9a3f9672335e51e18123bb53c2861f77a7e36a 100644
--- a/pystencils/datahandling/serial_datahandling.py
+++ b/pystencils/datahandling/serial_datahandling.py
@@ -76,7 +76,7 @@ class SerialDataHandling(DataHandling):
return self._field_information[name]['values_per_cell']
def add_array(self, name, values_per_cell=1, dtype=np.float64, latex_name=None, ghost_layers=None, layout=None,
- cpu=True, gpu=None, alignment=False):
+ cpu=True, gpu=None, alignment=False, staggered=False):
if ghost_layers is None:
ghost_layers = self.default_ghost_layers
if layout is None:
@@ -128,7 +128,8 @@ class SerialDataHandling(DataHandling):
self.gpu_arrays[name] = gpuarray.to_gpu(cpu_arr)
assert all(f.name != name for f in self.fields.values()), "Symbolic field with this name already exists"
- self.fields[name] = Field.create_from_numpy_array(name, cpu_arr, index_dimensions=index_dimensions)
+ self.fields[name] = Field.create_from_numpy_array(name, cpu_arr, index_dimensions=index_dimensions,
+ staggered=staggered)
self.fields[name].latex_name = latex_name
return self.fields[name]
diff --git a/pystencils/field.py b/pystencils/field.py
index aa0d1d36318c334a2bda3eb6ba197a4213a1c374..f5f59824b81c40e4f9558f4f9ccdee2951e3f3ea 100644
--- a/pystencils/field.py
+++ b/pystencils/field.py
@@ -21,7 +21,7 @@ from pystencils.sympyextensions import is_integer_sequence
__all__ = ['Field', 'fields', 'FieldType', 'AbstractField']
-def fields(description=None, index_dimensions=0, layout=None, **kwargs):
+def fields(description=None, index_dimensions=0, layout=None, staggered=False, **kwargs):
"""Creates pystencils fields from a string description.
Examples:
@@ -61,23 +61,25 @@ def fields(description=None, index_dimensions=0, layout=None, **kwargs):
arr = kwargs[field_name]
idx_shape_of_arr = () if not len(idx_shape) else arr.shape[-len(idx_shape):]
assert idx_shape_of_arr == idx_shape
- f = Field.create_from_numpy_array(field_name, kwargs[field_name], index_dimensions=len(idx_shape))
+ f = Field.create_from_numpy_array(field_name, kwargs[field_name], index_dimensions=len(idx_shape),
+ staggered=staggered)
elif isinstance(shape, tuple):
f = Field.create_fixed_size(field_name, shape + idx_shape, dtype=dtype,
- index_dimensions=len(idx_shape), layout=layout)
+ index_dimensions=len(idx_shape), layout=layout, staggered=staggered)
elif isinstance(shape, int):
f = Field.create_generic(field_name, spatial_dimensions=shape, dtype=dtype,
- index_shape=idx_shape, layout=layout)
+ index_shape=idx_shape, layout=layout, staggered=staggered)
elif shape is None:
f = Field.create_generic(field_name, spatial_dimensions=2, dtype=dtype,
- index_shape=idx_shape, layout=layout)
+ index_shape=idx_shape, layout=layout, staggered=staggered)
else:
assert False
result.append(f)
else:
assert layout is None, "Layout can not be specified when creating Field from numpy array"
for field_name, arr in kwargs.items():
- result.append(Field.create_from_numpy_array(field_name, arr, index_dimensions=index_dimensions))
+ result.append(Field.create_from_numpy_array(field_name, arr, index_dimensions=index_dimensions,
+ staggered=staggered))
if len(result) == 0:
return None
@@ -158,6 +160,14 @@ class Field(AbstractField):
First specify the spatial offsets in [], then in case index_dimension>0 the indices in ()
e.g. ``f[-1,0,0](7)``
+ Staggered Fields:
+ Staggered fields are used to store a value on a second grid shifted by half a cell with respect to the usual
+ grid.
+
+ The first index dimension is used to specify the position on the staggered grid (e.g. 0 means half-way to the
+ eastern neighbor, 1 is half-way to the northern neighbor, etc.), while additional indices can be used to store
+ multiple values at each position.
+
Example using no index dimensions:
>>> a = np.zeros([10, 10])
>>> f = Field.create_from_numpy_array("f", a, index_dimensions=0)
@@ -172,7 +182,7 @@ class Field(AbstractField):
@staticmethod
def create_generic(field_name, spatial_dimensions, dtype=np.float64, index_dimensions=0, layout='numpy',
- index_shape=None, field_type=FieldType.GENERIC) -> 'Field':
+ index_shape=None, field_type=FieldType.GENERIC, staggered=False) -> 'Field':
"""
Creates a generic field where the field size is not fixed i.e. can be called with arrays of different sizes
@@ -189,6 +199,7 @@ class Field(AbstractField):
field_type: besides the normal GENERIC fields, there are INDEXED fields that store indices of the domain
that should be iterated over, and BUFFER fields that are used to generate
communication packing/unpacking kernels
+ staggered: enables staggered access (with half-integer offsets) and corresponding printing
"""
if index_shape is not None:
assert index_dimensions == 0 or index_dimensions == len(index_shape)
@@ -210,11 +221,14 @@ class Field(AbstractField):
raise ValueError("Structured arrays/fields are not allowed to have an index dimension")
shape += (1,)
strides += (1,)
+ if staggered and index_dimensions == 0:
+ raise ValueError("A staggered field needs at least one index dimension")
- return Field(field_name, field_type, dtype, layout, shape, strides)
+ return Field(field_name, field_type, dtype, layout, shape, strides, staggered)
@staticmethod
- def create_from_numpy_array(field_name: str, array: np.ndarray, index_dimensions: int = 0) -> 'Field':
+ def create_from_numpy_array(field_name: str, array: np.ndarray, index_dimensions: int = 0,
+ staggered=False) -> 'Field':
"""Creates a field based on the layout, data type, and shape of a given numpy array.
Kernels created for these kind of fields can only be called with arrays of the same layout, shape and type.
@@ -223,6 +237,7 @@ class Field(AbstractField):
field_name: symbolic name for the field
array: numpy array
index_dimensions: see documentation of Field
+ staggered: enables staggered access (with half-integer offsets) and corresponding printing
"""
spatial_dimensions = len(array.shape) - index_dimensions
if spatial_dimensions < 1:
@@ -241,12 +256,15 @@ class Field(AbstractField):
raise ValueError("Structured arrays/fields are not allowed to have an index dimension")
shape += (1,)
strides += (1,)
+ if staggered and index_dimensions == 0:
+ raise ValueError("A staggered field needs at least one index dimension")
- return Field(field_name, FieldType.GENERIC, array.dtype, spatial_layout, shape, strides)
+ return Field(field_name, FieldType.GENERIC, array.dtype, spatial_layout, shape, strides, staggered)
@staticmethod
def create_fixed_size(field_name: str, shape: Tuple[int, ...], index_dimensions: int = 0,
- dtype=np.float64, layout: str = 'numpy', strides: Optional[Sequence[int]] = None) -> 'Field':
+ dtype=np.float64, layout: str = 'numpy', strides: Optional[Sequence[int]] = None,
+ staggered=False) -> 'Field':
"""
Creates a field with fixed sizes i.e. can be called only with arrays of the same size and layout
@@ -257,6 +275,7 @@ class Field(AbstractField):
dtype: numpy data type of the array the kernel is called with later
layout: full layout of array, not only spatial dimensions
strides: strides in bytes or None to automatically compute them from shape (assuming no padding)
+ staggered: enables staggered access (with half-integer offsets) and corresponding printing
"""
spatial_dimensions = len(shape) - index_dimensions
assert spatial_dimensions >= 1
@@ -277,13 +296,15 @@ class Field(AbstractField):
raise ValueError("Structured arrays/fields are not allowed to have an index dimension")
shape += (1,)
strides += (1,)
+ if staggered and index_dimensions == 0:
+ raise ValueError("A staggered field needs at least one index dimension")
spatial_layout = list(layout)
for i in range(spatial_dimensions, len(layout)):
spatial_layout.remove(i)
- return Field(field_name, FieldType.GENERIC, dtype, tuple(spatial_layout), shape, strides)
+ return Field(field_name, FieldType.GENERIC, dtype, tuple(spatial_layout), shape, strides, staggered)
- def __init__(self, field_name, field_type, dtype, layout, shape, strides):
+ def __init__(self, field_name, field_type, dtype, layout, shape, strides, staggered):
"""Do not use directly. Use static create* methods"""
self._field_name = field_name
assert isinstance(field_type, FieldType)
@@ -298,6 +319,7 @@ class Field(AbstractField):
0 for _ in range(self.spatial_dimensions)
)) # type: tuple[float,sp.Symbol]
self.coordinate_transform = sp.eye(self.spatial_dimensions)
+ self.is_staggered = staggered
def new_field_with_different_name(self, new_name):
if self.has_fixed_shape:
@@ -427,6 +449,51 @@ class Field(AbstractField):
address_mode,
allow_textures=allow_textures).at(offset)
+ def staggered_access(self, offset, index=None):
+ """If this field is a staggered field, it can be accessed using half-integer offsets.
+ For example, an offset of ``(0, sp.Rational(1,2))`` or ``"E"`` corresponds to the staggered point to the east
+ of the cell center, i.e. half-way to the eastern-next cell.
+ If the field stores more than one value per staggered point (e.g. a vector or a tensor), the index (integer or
+ tuple of integers) refers to which of these values to access.
+ """
+ assert self.is_staggered
+
+ if type(offset) is np.ndarray:
+ offset = tuple(offset)
+ if type(offset) is str:
+ offset = tuple(direction_string_to_offset(offset, self.spatial_dimensions))
+ offset = tuple([o * sp.Rational(1, 2) for o in offset])
+ if type(offset) is not tuple:
+ offset = (offset,)
+ if len(offset) != self.spatial_dimensions:
+ raise ValueError("Wrong number of spatial indices: "
+ "Got %d, expected %d" % (len(offset), self.spatial_dimensions))
+
+ offset = list(offset)
+ for i, o in enumerate(offset):
+ if (o + sp.Rational(1, 2)).is_Integer:
+ offset[i] += sp.Rational(1, 2)
+ idx = i
+ offset = tuple(offset)
+
+ if self.index_dimensions == 1: # this field stores a scalar value at each staggered position
+ if index is not None:
+ raise ValueError("Cannot specify an index for a scalar staggered field")
+ return Field.Access(self, offset, (idx,))
+ else: # this field stores a vector or tensor at each staggered position
+ if index is None:
+ raise ValueError("Wrong number of indices: "
+ "Got %d, expected %d" % (0, self.index_dimensions - 1))
+ if type(index) is np.ndarray:
+ index = tuple(index)
+ if type(index) is not tuple:
+ index = (index,)
+ if self.index_dimensions != len(index) + 1:
+ raise ValueError("Wrong number of indices: "
+ "Got %d, expected %d" % (len(index), self.index_dimensions - 1))
+
+ return Field.Access(self, offset, (idx, *index))
+
def __call__(self, *args, **kwargs):
center = tuple([0] * self.spatial_dimensions)
return Field.Access(self, center)(*args, **kwargs)
@@ -544,6 +611,7 @@ class Field(AbstractField):
obj._indirect_addressing_fields.update(a.field for a in e.atoms(Field.Access))
obj._is_absolute_access = is_absolute_access
+ obj.is_staggered = field.is_staggered
return obj
def __getnewargs__(self):
@@ -676,25 +744,45 @@ class Field(AbstractField):
def _latex(self, _):
n = self._field.latex_name if self._field.latex_name else self._field.name
offset_str = ",".join([sp.latex(o) for o in self.offsets])
+ if self.is_staggered:
+ offset_str = ",".join([sp.latex(o - sp.Rational(int(i == self.index[0]), 2))
+ for i, o in enumerate(self.offsets)])
if self.is_absolute_access:
offset_str = "\\mathbf{}".format(offset_str)
elif self.field.spatial_dimensions > 1:
offset_str = "({})".format(offset_str)
- if self.index and self.index != (0,):
- return "{{%s}_{%s}^{%s}}" % (n, offset_str, self.index if len(self.index) > 1 else self.index[0])
+ if self.is_staggered:
+ if self.index and self.field.index_dimensions > 1:
+ return "{{%s}_{%s}^{%s}}" % (n, offset_str, self.index[1:]
+ if len(self.index) > 2 else self.index[1])
+ else:
+ return "{{%s}_{%s}}" % (n, offset_str)
else:
- return "{{%s}_{%s}}" % (n, offset_str)
+ if self.index and self.field.index_dimensions > 0:
+ return "{{%s}_{%s}^{%s}}" % (n, offset_str, self.index if len(self.index) > 1 else self.index[0])
+ else:
+ return "{{%s}_{%s}}" % (n, offset_str)
def __str__(self):
n = self._field.latex_name if self._field.latex_name else self._field.name
offset_str = ",".join([sp.latex(o) for o in self.offsets])
+ if self.is_staggered:
+ offset_str = ",".join([sp.latex(o - sp.Rational(int(i == self.index[0]), 2))
+ for i, o in enumerate(self.offsets)])
if self.is_absolute_access:
offset_str = "[abs]{}".format(offset_str)
- if self.index and self.index != (0,):
- return "%s[%s](%s)" % (n, offset_str, self.index if len(self.index) > 1 else self.index[0])
+
+ if self.is_staggered:
+ if self.index and self.field.index_dimensions > 1:
+ return "%s[%s](%s)" % (n, offset_str, self.index[1:] if len(self.index) > 2 else self.index[1])
+ else:
+ return "%s[%s]" % (n, offset_str)
else:
- return "%s[%s]" % (n, offset_str)
+ if self.index and self.field.index_dimensions > 0:
+ return "%s[%s](%s)" % (n, offset_str, self.index if len(self.index) > 1 else self.index[0])
+ else:
+ return "%s[%s]" % (n, offset_str)
def get_layout_from_strides(strides: Sequence[int], index_dimension_ids: Optional[List[int]] = None):
diff --git a/pystencils_tests/test_blocking_staggered.py b/pystencils_tests/test_blocking_staggered.py
index 207d05a280f790c5c0b74a50e7ecfb252bd04276..f333d4ed34a32cb16e3e7642f542c2e82ea6d2ec 100644
--- a/pystencils_tests/test_blocking_staggered.py
+++ b/pystencils_tests/test_blocking_staggered.py
@@ -4,7 +4,8 @@ import pystencils as ps
def test_blocking_staggered():
- f, stag = ps.fields("f, stag(3): double[3D]")
+ f = ps.fields("f: double[3D]")
+ stag = ps.fields("stag(3): double[3D]", staggered=True)
terms = [
f[0, 0, 0] - f[-1, 0, 0],
f[0, 0, 0] - f[0, -1, 0],
diff --git a/pystencils_tests/test_field.py b/pystencils_tests/test_field.py
index 49bd4486474b91caf90c7e405f1a2a2ac7d7e33d..494cc6ab0cb3e0f7b001ba571dc1ca9bd5e4d54d 100644
--- a/pystencils_tests/test_field.py
+++ b/pystencils_tests/test_field.py
@@ -127,3 +127,17 @@ def test_itemsize():
assert x.itemsize == 4
assert y.itemsize == 8
assert i.itemsize == 2
+
+
+def test_staggered():
+
+ j1, j2, j3 = ps.fields('j1(2), j2(2,2), j3(2,2,2) : double[2D]', staggered=True)
+
+ assert j1[0, 1](1) == j1.staggered_access((0, sp.Rational(1, 2)))
+ assert j1[0, 1](1) == j1.staggered_access("N")
+
+ assert j2[0, 1](1, 1) == j2.staggered_access((0, sp.Rational(1, 2)), 1)
+ assert j2[0, 1](1, 1) == j2.staggered_access("N", 1)
+
+ assert j3[0, 1](1, 1, 1) == j3.staggered_access((0, sp.Rational(1, 2)), (1, 1))
+ assert j3[0, 1](1, 1, 1) == j3.staggered_access("N", (1, 1))
diff --git a/pystencils_tests/test_loop_cutting.py b/pystencils_tests/test_loop_cutting.py
index 58126928daea4e7e6df5e0e71b3e57ac1491cff2..0a84db509602be16b1a3828c3a9cdc4d1b9b79e2 100644
--- a/pystencils_tests/test_loop_cutting.py
+++ b/pystencils_tests/test_loop_cutting.py
@@ -34,9 +34,9 @@ def test_staggered_iteration():
s_arr_ref = s_arr.copy()
fields_fixed = (Field.create_from_numpy_array('f', f_arr),
- Field.create_from_numpy_array('s', s_arr, index_dimensions=1))
+ Field.create_from_numpy_array('s', s_arr, index_dimensions=1, staggered=True))
fields_var = (Field.create_generic('f', 2),
- Field.create_generic('s', 2, index_dimensions=1))
+ Field.create_generic('s', 2, index_dimensions=1, staggered=True))
for f, s in [fields_var, fields_fixed]:
# --- Manual
@@ -70,7 +70,7 @@ def test_staggered_iteration_manual():
s_arr_ref = s_arr.copy()
f = Field.create_from_numpy_array('f', f_arr)
- s = Field.create_from_numpy_array('s', s_arr, index_dimensions=1)
+ s = Field.create_from_numpy_array('s', s_arr, index_dimensions=1, staggered=True)
eqs = []
@@ -107,7 +107,8 @@ def test_staggered_iteration_manual():
def test_staggered_gpu():
dim = 2
- f, s = ps.fields("f, s({dim}): double[{dim}D]".format(dim=dim))
+ f = ps.fields("f: double[{dim}D]".format(dim=dim))
+ s = ps.fields("s({dim}): double[{dim}D]".format(dim=dim), staggered=True)
expressions = [(f[0, 0] + f[-1, 0]) / 2,
(f[0, 0] + f[0, -1]) / 2]
kernel_ast = ps.create_staggered_kernel(s, expressions, target='gpu', gpu_exclusive_conditions=True)