Merge pull request #2245 from devitocodes/funcs_on_subdims

dsl: Introduce ability to define Functions on Subdomains

devito/data/data.py

@@ -238,11 +238,12 @@ def __getitem__(self, glb_idx, comm_type, gather_rank=None):
                     stop += sendcounts[i]
                     data_slice = recvbuf[slice(start, stop, step)]
                     shape = [r.stop-r.start for r in self._distributor.all_ranges[i]]
-                    idx = [slice(r.start, r.stop, r.step)
-                           for r in self._distributor.all_ranges[i]]
-                    for i in range(len(self.shape) - len(self._distributor.glb_shape)):
-                        shape.insert(i, glb_shape[i])
-                        idx.insert(i, slice(0, glb_shape[i]+1, 1))
+                    idx = [slice(r.start - d.glb_min, r.stop - d.glb_min, r.step)
+                           for r, d in zip(self._distributor.all_ranges[i],
+                                           self._distributor.decomposition)]
+                    for j in range(len(self.shape) - len(self._distributor.glb_shape)):
+                        shape.insert(j, glb_shape[j])
+                        idx.insert(j, slice(0, glb_shape[j]+1, 1))
                     retval[tuple(idx)] = data_slice.reshape(tuple(shape))
                 return retval
             else:
@@ -329,6 +330,7 @@ def __getitem__(self, glb_idx, comm_type, gather_rank=None):
     @_check_idx
     def __setitem__(self, glb_idx, val, comm_type):
         loc_idx = self._index_glb_to_loc(glb_idx)
+
         if loc_idx is NONLOCAL:
             # no-op
             return

devito/data/decomposition.py

@@ -204,9 +204,26 @@ def index_glb_to_loc(self, *args, rel=True):
         >>> d.index_glb_to_loc((1, 6), rel=False)
         (5, 6)
         """
+        # Offset the loc_abs_min, loc_abs_max, glb_min, and glb_max
+        # In the case of a Function defined on a SubDomain, the global indices
+        # for accessing the data associated with this Function will run from
+        # `ltkn` to `x_M-rtkn-1`. However, the indices for accessing this array
+        # will run from `0` to `x_M-ltkn-rtkn-1`. As such, the global minimum
+        # (`ltkn`) should be subtracted for the purpose of indexing into the local
+        # array.
+        if not self.loc_empty:
+            loc_abs_min = self.loc_abs_min - self.glb_min
+            loc_abs_max = self.loc_abs_max - self.glb_min
+            glb_max = self.glb_max - self.glb_min
+        else:
+            loc_abs_min = self.loc_abs_min
+            loc_abs_max = self.loc_abs_max
+            glb_max = self.glb_max
+
+        glb_min = 0
 
-        base = self.loc_abs_min if rel is True else 0
-        top = self.loc_abs_max
+        base = loc_abs_min if rel else 0
+        top = loc_abs_max
 
         if len(args) == 1:
             glb_idx = args[0]
@@ -217,11 +234,11 @@ def index_glb_to_loc(self, *args, rel=True):
                     return None
                 # -> Handle negative index
                 if glb_idx < 0:
-                    glb_idx = self.glb_max + glb_idx + 1
+                    glb_idx = glb_max + glb_idx + 1
                 # -> Do the actual conversion
-                if self.loc_abs_min <= glb_idx <= self.loc_abs_max:
+                if loc_abs_min <= glb_idx <= loc_abs_max:
                     return glb_idx - base
-                elif self.glb_min <= glb_idx <= self.glb_max:
+                elif glb_min <= glb_idx <= glb_max:
                     return None
                 else:
                     # This should raise an exception when used to access a numpy.array
@@ -239,30 +256,32 @@ def index_glb_to_loc(self, *args, rel=True):
                 elif isinstance(glb_idx, slice):
                     if self.loc_empty:
                         return slice(-1, -3)
-                    if glb_idx.step >= 0 and glb_idx.stop == self.glb_min:
-                        glb_idx_min = self.glb_min if glb_idx.start is None \
+                    if glb_idx.step >= 0 and glb_idx.stop == glb_min:
+                        glb_idx_min = glb_min if glb_idx.start is None \
                             else glb_idx.start
-                        glb_idx_max = self.glb_min
+                        glb_idx_max = glb_min
                         retfunc = lambda a, b: slice(a, b, glb_idx.step)
                     elif glb_idx.step >= 0:
-                        glb_idx_min = self.glb_min if glb_idx.start is None \
+                        glb_idx_min = glb_min if glb_idx.start is None \
                             else glb_idx.start
-                        glb_idx_max = self.glb_max if glb_idx.stop is None \
+                        glb_idx_max = glb_max \
+                            if glb_idx.stop is None \
                             else glb_idx.stop-1
                         retfunc = lambda a, b: slice(a, b + 1, glb_idx.step)
                     else:
-                        glb_idx_min = self.glb_min if glb_idx.stop is None \
+                        glb_idx_min = glb_min if glb_idx.stop is None \
                             else glb_idx.stop+1
-                        glb_idx_max = self.glb_max if glb_idx.start is None \
+                        glb_idx_max = glb_max if glb_idx.start is None \
                             else glb_idx.start
                         retfunc = lambda a, b: slice(b, a - 1, glb_idx.step)
                 else:
                     raise TypeError("Cannot convert index from `%s`" % type(glb_idx))
                 # -> Handle negative min/max
                 if glb_idx_min is not None and glb_idx_min < 0:
-                    glb_idx_min = self.glb_max + glb_idx_min + 1
+                    glb_idx_min = glb_max + glb_idx_min + 1
                 if glb_idx_max is not None and glb_idx_max < 0:
-                    glb_idx_max = self.glb_max + glb_idx_max + 1
+                    glb_idx_max = glb_max + glb_idx_max + 1
+
                 # -> Do the actual conversion
                 # Compute loc_min. For a slice with step > 0 this will be
                 # used to produce slice.start and for a slice with step < 0 slice.stop.
@@ -271,19 +290,19 @@ def index_glb_to_loc(self, *args, rel=True):
                 # coincide with loc_abs_min.
                 if isinstance(glb_idx, slice) and glb_idx.step is not None \
                         and glb_idx.step > 1:
-                    if glb_idx_min > self.loc_abs_max:
+                    if glb_idx_min > loc_abs_max:
                         return retfunc(-1, -3)
                     elif glb_idx.start is None:  # glb start is zero.
-                        loc_min = self.loc_abs_min - base \
+                        loc_min = loc_abs_min - base \
                             + np.mod(glb_idx.step - np.mod(base, glb_idx.step),
                                      glb_idx.step)
                     else:  # glb start is given explicitly
-                        loc_min = self.loc_abs_min - base \
+                        loc_min = loc_abs_min - base \
                             + np.mod(glb_idx.step - np.mod(base - glb_idx.start,
                                                            glb_idx.step), glb_idx.step)
-                elif glb_idx_min is None or glb_idx_min < self.loc_abs_min:
-                    loc_min = self.loc_abs_min - base
-                elif glb_idx_min > self.loc_abs_max:
+                elif glb_idx_min is None or glb_idx_min < loc_abs_min:
+                    loc_min = loc_abs_min - base
+                elif glb_idx_min > loc_abs_max:
                     return retfunc(-1, -3)
                 else:
                     loc_min = glb_idx_min - base
@@ -294,19 +313,19 @@ def index_glb_to_loc(self, *args, rel=True):
                 # coincide with loc_abs_max.
                 if isinstance(glb_idx, slice) and glb_idx.step is not None \
                         and glb_idx.step < -1:
-                    if glb_idx_max < self.loc_abs_min:
+                    if glb_idx_max < loc_abs_min:
                         return retfunc(-1, -3)
                     elif glb_idx.start is None:
                         loc_max = top - base \
-                            + np.mod(glb_idx.step - np.mod(top - self.glb_max,
+                            + np.mod(glb_idx.step - np.mod(top - glb_max,
                                                            glb_idx.step), glb_idx.step)
                     else:
                         loc_max = top - base \
                             + np.mod(glb_idx.step - np.mod(top - glb_idx.start,
                                                            glb_idx.step), glb_idx.step)
-                elif glb_idx_max is None or glb_idx_max > self.loc_abs_max:
-                    loc_max = self.loc_abs_max - base
-                elif glb_idx_max < self.loc_abs_min:
+                elif glb_idx_max is None or glb_idx_max > loc_abs_max:
+                    loc_max = loc_abs_max - base
+                elif glb_idx_max < loc_abs_min:
                     return retfunc(-1, -3)
                 else:
                     loc_max = glb_idx_max - base
@@ -321,19 +340,19 @@ def index_glb_to_loc(self, *args, rel=True):
                 return None
             abs_ofs, side = args
             if side == LEFT:
-                rel_ofs = self.glb_min + abs_ofs - base
+                rel_ofs = glb_min + abs_ofs - base
                 if abs_ofs >= base and abs_ofs <= top:
                     return rel_ofs
                 elif abs_ofs > top:
                     return top + 1
                 else:
                     return None
             else:
-                rel_ofs = abs_ofs - (self.glb_max - top)
-                if abs_ofs >= self.glb_max - top and abs_ofs <= self.glb_max - base:
+                rel_ofs = abs_ofs - (glb_max - top)
+                if abs_ofs >= glb_max - top and abs_ofs <= glb_max - base:
                     return rel_ofs
-                elif abs_ofs > self.glb_max - base:
-                    return self.glb_max - base + 1
+                elif abs_ofs > glb_max - base:
+                    return glb_max - base + 1
                 else:
                     return None
         else:

devito/deprecations.py

@@ -7,14 +7,23 @@ class DevitoDeprecation():
     @cached_property
     def coeff_warn(self):
         warn("The Coefficient API is deprecated and will be removed, coefficients should"
-             "be passed directly to the derivative object `u.dx(weights=...)",
+             " be passed directly to the derivative object `u.dx(weights=...)",
              DeprecationWarning, stacklevel=2)
         return
 
     @cached_property
     def symbolic_warn(self):
         warn("coefficients='symbolic' is deprecated, coefficients should"
-             "be passed directly to the derivative object `u.dx(weights=...)",
+             " be passed directly to the derivative object `u.dx(weights=...)",
+             DeprecationWarning, stacklevel=2)
+        return
+
+    @cached_property
+    def subdomain_warn(self):
+        warn("Passing `SubDomain`s to `Grid` on instantiation using `mygrid ="
+             " Grid(..., subdomains=(mydomain, ...))` is deprecated. The `Grid`"
+             " should instead be passed as a kwarg when instantiating a subdomain"
+             " `mydomain = MyDomain(grid=mygrid)`",
              DeprecationWarning, stacklevel=2)
         return
 

devito/finite_differences/differentiable.py

@@ -64,6 +64,7 @@ def time_order(self):
     @cached_property
     def grid(self):
         grids = {getattr(i, 'grid', None) for i in self._args_diff} - {None}
+        grids = {g.root for g in grids}
         if len(grids) > 1:
             warning("Expression contains multiple grids, returning first found")
         try:
@@ -86,6 +87,11 @@ def dimensions(self):
         return tuple(filter_ordered(flatten(getattr(i, 'dimensions', ())
                                             for i in self._args_diff)))
 
+    @cached_property
+    def root_dimensions(self):
+        """Tuple of root Dimensions of the physical space Dimensions."""
+        return tuple(d.root for d in self.dimensions if d.is_Space)
+
     @property
     def indices_ref(self):
         """The reference indices of the object (indices at first creation)."""
@@ -317,7 +323,7 @@ def laplacian(self, shift=None, order=None, method='FD', **kwargs):
         """
         w = kwargs.get('weights', kwargs.get('w'))
         order = order or self.space_order
-        space_dims = [d for d in self.dimensions if d.is_Space]
+        space_dims = self.root_dimensions
         shift_x0 = make_shift_x0(shift, (len(space_dims),))
         derivs = tuple('d%s2' % d.name for d in space_dims)
         return Add(*[getattr(self, d)(x0=shift_x0(shift, space_dims[i], None, i),
@@ -344,7 +350,7 @@ def div(self, shift=None, order=None, method='FD', **kwargs):
             Custom weights for the finite difference coefficients.
         """
         w = kwargs.get('weights', kwargs.get('w'))
-        space_dims = [d for d in self.dimensions if d.is_Space]
+        space_dims = self.root_dimensions
         shift_x0 = make_shift_x0(shift, (len(space_dims),))
         order = order or self.space_order
         return Add(*[getattr(self, 'd%s' % d.name)(x0=shift_x0(shift, d, None, i),
@@ -371,7 +377,7 @@ def grad(self, shift=None, order=None, method='FD', **kwargs):
             Custom weights for the finite
         """
         from devito.types.tensor import VectorFunction, VectorTimeFunction
-        space_dims = [d for d in self.dimensions if d.is_Space]
+        space_dims = self.root_dimensions
         shift_x0 = make_shift_x0(shift, (len(space_dims),))
         order = order or self.space_order
         w = kwargs.get('weights', kwargs.get('w'))
@@ -387,7 +393,7 @@ def biharmonic(self, weight=1):
         Generates a symbolic expression for the weighted biharmonic operator w.r.t.
         all spatial Dimensions Laplace(weight * Laplace (self))
         """
-        space_dims = [d for d in self.dimensions if d.is_Space]
+        space_dims = self.root_dimensions
         derivs = tuple('d%s2' % d.name for d in space_dims)
         return Add(*[getattr(self.laplace * weight, d) for d in derivs])
 

devito/ir/clusters/cluster.py

@@ -193,6 +193,7 @@ def functions(self):
     def grid(self):
         grids = set(f.grid for f in self.functions if f.is_AbstractFunction)
         grids.discard(None)
+        grids = {g.root for g in grids}
         if len(grids) == 0:
             return None
         elif len(grids) == 1:

devito/ir/equations/algorithms.py

@@ -3,7 +3,8 @@
 
 from devito.symbolics import (retrieve_indexed, uxreplace, retrieve_dimensions,
                               retrieve_functions)
-from devito.tools import Ordering, as_tuple, flatten, filter_sorted, filter_ordered
+from devito.tools import (Ordering, as_tuple, flatten, filter_sorted, filter_ordered,
+                          frozendict)
 from devito.types import (Dimension, Eq, IgnoreDimSort, SubDimension,
                           ConditionalDimension)
 from devito.types.array import Array
@@ -112,11 +113,7 @@ def lower_exprs(expressions, subs=None, **kwargs):
 def _lower_exprs(expressions, subs):
     processed = []
     for expr in as_tuple(expressions):
-        try:
-            dimension_map = expr.subdomain.dimension_map
-        except AttributeError:
-            # Some Relationals may be pure SymPy objects, thus lacking the subdomain
-            dimension_map = {}
+        dimension_map = _make_dimension_map(expr)
 
         # Handle Functions (typical case)
         mapper = {f: _lower_exprs(f.indexify(subs=dimension_map), subs)
@@ -160,6 +157,30 @@ def _lower_exprs(expressions, subs):
         return processed.pop()
 
 
+def _make_dimension_map(expr):
+    """
+    Make the dimension_map for an expression. In the basic case, this is extracted
+    directly from the SubDomain attached to the expression.
+
+    The indices of a Function defined on a SubDomain will all be the SubDimensions of
+    that SubDomain. In this case, the dimension_map should be extended with
+    `{ix_f: ix_i, iy_f: iy_i}` where `ix_f` is the SubDimension on which the Function is
+    defined, and `ix_i` is the SubDimension to be iterated over.
+    """
+    try:
+        dimension_map = {**expr.subdomain.dimension_map}
+    except AttributeError:
+        # Some Relationals may be pure SymPy objects, thus lacking the SubDomain
+        dimension_map = {}
+    else:
+        functions = [f for f in retrieve_functions(expr) if f._is_on_subdomain]
+        for f in functions:
+            dimension_map.update({d: expr.subdomain.dimension_map[d.root]
+                                  for d in f.space_dimensions if d.is_Sub})
+
+    return frozendict(dimension_map)
+
+
 def concretize_subdims(exprs, **kwargs):
     """
     Given a list of expressions, return a new list where all user-defined
@@ -206,7 +227,14 @@ def _(v, mapper, rebuilt, sregistry):
 
 @_concretize_subdims.register(Eq)
 def _(expr, mapper, rebuilt, sregistry):
-    for d in expr.free_symbols:
+    # Split and reorder symbols so SubDimensions are processed before lone Thicknesses
+    # This means that if a Thickness appears both in the expression and attached to
+    # a SubDimension, it gets concretised with the SubDimension.
+    thicknesses = {i for i in expr.free_symbols if isinstance(i, Thickness)}
+    symbols = expr.free_symbols.difference(thicknesses)
+
+    # Iterate over all other symbols before iterating over standalone thicknesses
+    for d in tuple(symbols) + tuple(thicknesses):
         _concretize_subdims(d, mapper, rebuilt, sregistry)
 
     # Subdimensions can be hiding in implicit dims