Merge branch 'CleanUp' into 'master'

Clean-up

See merge request !85

lbmpy/boundaries/boundaryconditions.py

@@ -79,6 +79,14 @@ class LbBoundary:
     def name(self, new_value):
         self._name = new_value
 
+    def __hash__(self):
+        return hash(self.name)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        return self.__dict__ == other.__dict__
+
 
 # end class Boundary
 
@@ -99,15 +107,6 @@ class NoSlip(LbBoundary):
     def __call__(self, f_out, f_in, dir_symbol, inv_dir, lb_method, index_field):
         return Assignment(f_in(inv_dir[dir_symbol]), f_out(dir_symbol))
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, NoSlip):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class NoSlip
 
 
@@ -213,15 +212,6 @@ class UBB(LbBoundary):
             return [Assignment(f_in(inv_dir[direction]),
                                f_out(direction) - vel_term)]
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, UBB):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class UBB
 
 
@@ -269,15 +259,6 @@ class SimpleExtrapolationOutflow(LbBoundary):
 
         return Assignment(f_in.center(inv_dir[dir_symbol]), f_out[tangential_offset](inv_dir[dir_symbol]))
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, SimpleExtrapolationOutflow):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class SimpleExtrapolationOutflow
 
 
@@ -425,15 +406,6 @@ class ExtrapolationOutflow(LbBoundary):
 
         return AssignmentCollection(boundary_assignments, subexpressions=subexpressions)
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, ExtrapolationOutflow):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class ExtrapolationOutflow
 
 
@@ -487,15 +459,6 @@ class FixedDensity(LbBoundary):
         return subexpressions + [Assignment(f_in(inv_dir[dir_symbol]),
                                             2 * eq_component - f_out(dir_symbol))]
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, FixedDensity):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class FixedDensity
 
 
@@ -530,15 +493,6 @@ class DiffusionDirichlet(LbBoundary):
         return [Assignment(f_in(inv_dir[dir_symbol]),
                            2 * w_dir * self.concentration - f_out(dir_symbol))]
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, DiffusionDirichlet):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class DiffusionDirichlet
 
 
@@ -562,15 +516,6 @@ class NeumannByCopy(LbBoundary):
         return [Assignment(f_in(inv_dir[dir_symbol]), f_out(inv_dir[dir_symbol])),
                 Assignment(f_out[neighbour_offset](dir_symbol), f_out(dir_symbol))]
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, NeumannByCopy):
-            return False
-        return self.__dict__ == other.__dict__
-
-
 # end class NeumannByCopy
 
 
@@ -603,12 +548,4 @@ class StreamInConstant(LbBoundary):
         return [Assignment(f_in(inv_dir[dir_symbol]), self.constant),
                 Assignment(f_out[neighbour_offset](dir_symbol), self.constant)]
 
-    def __hash__(self):
-        return hash(self.name)
-
-    def __eq__(self, other):
-        if not isinstance(other, StreamInConstant):
-            return False
-        return self.__dict__ == other.__dict__
-
 # end class StreamInConstant

lbmpy/turbulence_models.py

@@ -18,6 +18,29 @@ def frobenius_norm(matrix, factor=1):
 
 
 def add_smagorinsky_model(collision_rule, smagorinsky_constant, omega_output_field=None):
+    r""" Adds a smagorinsky model to a lattice Boltzmann collision rule. To add the Smagorinsky model to a LB scheme
+        one has to first compute the strain rate tensor $S_{ij}$ in each cell, and compute the turbulent
+        viscosity :math:`nu_t` from it. Then the local relaxation rate has to be adapted to match the total viscosity
+        :math `\nu_{total}` instead of the standard viscosity :math `\nu_0`.
+
+        A fortunate property of LB methods is, that the strain rate tensor can be computed locally from the
+        non-equilibrium part of the distribution function. This is somewhat surprising, since the strain rate tensor
+        contains first order derivatives. The strain rate tensor can be obtained by
+
+        .. math ::
+            S_{ij} = - \frac{3 \omega_s}{2 \rho_{(0)}} \Pi_{ij}^{(neq)}
+
+        where :math `\omega_s` is the relaxation rate that determines the viscosity, :math `\rho_{(0)}` is :math `\rho`
+        in compressible models and :math `1` for incompressible schemes.
+        :math `\Pi_{ij}^{(neq)}` is the second order moment tensor of the non-equilibrium part of
+        the distribution functions
+        :math `f^{(neq)} = f - f^{(eq)}` and can be computed as
+
+        .. math ::
+            \Pi_{ij}^{(neq)} = \sum_q c_{qi} c_{qj} \; f_q^{(neq)}
+
+
+    """
     method = collision_rule.method
     omega_s = get_shear_relaxation_rate(method)
     if isinstance(omega_s, float) or isinstance(omega_s, int):

lbmpy/updatekernels.py

@@ -12,30 +12,32 @@ from pystencils.sympyextensions import fast_subs
 # -------------------------------------------- LBM Kernel Creation -----------------------------------------------------
 
 
-def create_lbm_kernel(collision_rule, input_field, output_field, accessor):
+def create_lbm_kernel(collision_rule, src_field, dst_field=None, accessor=StreamPullTwoFieldsAccessor()):
     """Replaces the pre- and post collision symbols in the collision rule by field accesses.
 
     Args:
         collision_rule:  instance of LbmCollisionRule, defining the collision step
-        input_field: field used for reading pdf values
-        output_field: field used for writing pdf values
-                      if accessor.is_inplace this parameter is ignored
+        src_field: field used for reading pdf values
+        dst_field: field used for writing pdf values if accessor.is_inplace this parameter is ignored
         accessor: instance of PdfFieldAccessor, defining where to read and write values
-                  to create e.g. a fused stream-collide kernel
+                  to create e.g. a fused stream-collide kernel See 'fieldaccess.PdfFieldAccessor'
 
     Returns:
         LbmCollisionRule where pre- and post collision symbols have been replaced
     """
     if accessor.is_inplace:
-        output_field = input_field
+        dst_field = src_field
+
+    if not accessor.is_inplace and dst_field is None:
+        raise ValueError("For two field accessors a destination field has to be provided")
 
     method = collision_rule.method
     pre_collision_symbols = method.pre_collision_pdf_symbols
     post_collision_symbols = method.post_collision_pdf_symbols
     substitutions = {}
 
-    input_accesses = accessor.read(input_field, method.stencil)
-    output_accesses = accessor.write(output_field, method.stencil)
+    input_accesses = accessor.read(src_field, method.stencil)
+    output_accesses = accessor.write(dst_field, method.stencil)
 
     for (idx, offset), input_access, output_access in zip(enumerate(method.stencil), input_accesses, output_accesses):
         substitutions[pre_collision_symbols[idx]] = input_access
@@ -55,19 +57,26 @@ def create_lbm_kernel(collision_rule, input_field, output_field, accessor):
     return result
 
 
-def create_stream_only_kernel(stencil, src_field, dst_field, accessor=StreamPullTwoFieldsAccessor()):
+def create_stream_only_kernel(stencil, src_field, dst_field=None, accessor=StreamPullTwoFieldsAccessor()):
     """Creates a stream kernel, without collision.
 
     Args:
-        stencil: lattice Boltzmann stencil which is used
-        src_field: Field the pre-streaming values are read from
-        dst_field: Field the post-streaming values are written to
-        accessor: Field accessor which is used to create the update rule. See 'fieldaccess.PdfFieldAccessor'
+        stencil: lattice Boltzmann stencil which is used in the form of a tuple of tuples
+        src_field: field used for reading pdf values
+        dst_field: field used for writing pdf values if accessor.is_inplace this parameter is ignored
+        accessor: instance of PdfFieldAccessor, defining where to read and write values
+                  to create e.g. a fused stream-collide kernel See 'fieldaccess.PdfFieldAccessor'
 
     Returns:
         AssignmentCollection of the stream only update rule
     """
-    temporary_symbols = sp.symbols(f'tmp_:{len(stencil)}')
+    if accessor.is_inplace:
+        dst_field = src_field
+
+    if not accessor.is_inplace and dst_field is None:
+        raise ValueError("For two field accessors a destination field has to be provided")
+
+    temporary_symbols = sp.symbols(f'streamed_:{len(stencil)}')
     subexpressions = [Assignment(tmp, acc) for tmp, acc in zip(temporary_symbols, accessor.read(src_field, stencil))]
     main_assignments = [Assignment(acc, tmp) for acc, tmp in zip(accessor.write(dst_field, stencil), temporary_symbols)]
     return AssignmentCollection(main_assignments, subexpressions=subexpressions)
@@ -103,13 +112,34 @@ def create_stream_pull_only_kernel(stencil, numpy_arr=None, src_field_name="src"
     return create_stream_only_kernel(stencil, src, dst, accessor=StreamPullTwoFieldsAccessor())
 
 
-def create_stream_pull_with_output_kernel(lb_method, src_field, dst_field, output):
+def create_stream_pull_with_output_kernel(lb_method, src_field, dst_field=None, output=None,
+                                          accessor=StreamPullTwoFieldsAccessor()):
+    """Creates a stream kernel, without collision but macroscopic quantaties like density or velocity can be calculated.
+
+    Args:
+        lb_method: lattice Boltzmann method see 'creationfunctions.create_lb_method'
+        src_field: field used for reading pdf values
+        dst_field: field used for writing pdf values if accessor.is_inplace this parameter is ignored
+        output: dictonary which containes macroscopic quantities as keys which should be calculated and fields as
+                values which should be used to write the data e.g.: {'density': density_field}
+        accessor: instance of PdfFieldAccessor, defining where to read and write values
+                  to create e.g. a fused stream-collide kernel See 'fieldaccess.PdfFieldAccessor'
+
+    Returns:
+        AssignmentCollection of the stream only update rule
+    """
+    if accessor.is_inplace:
+        dst_field = src_field
+
+    if not accessor.is_inplace and dst_field is None:
+        raise ValueError("For two field accessors a destination field has to be provided")
+
     stencil = lb_method.stencil
     cqc = lb_method.conserved_quantity_computation
     streamed = sp.symbols(f"streamed_:{len(stencil)}")
-    accessor = StreamPullTwoFieldsAccessor()
     stream_assignments = [Assignment(a, b) for a, b in zip(streamed, accessor.read(src_field, stencil))]
-    output_eq_collection = cqc.output_equations_from_pdfs(streamed, output)
+    output_eq_collection = cqc.output_equations_from_pdfs(streamed, output) if output\
+        else AssignmentCollection(main_assignments=[])
     write_eqs = [Assignment(a, b) for a, b in zip(accessor.write(dst_field, stencil), streamed)]
 
     subexpressions = stream_assignments + output_eq_collection.subexpressions

lbmpy_tests/test_boundary_handling.py

@@ -120,33 +120,45 @@ def test_boundary_utility_functions():
     noslip = NoSlip("noslip")
     assert noslip == NoSlip("noslip")
     assert not noslip == NoSlip("test")
+    assert not noslip == UBB((0, 0), name="ubb")
+
+    assert noslip.name == "noslip"
+    noslip.name = "test name setter"
+    assert noslip.name == "test name setter"
 
     ubb = UBB((0, 0), name="ubb")
     assert ubb == UBB((0, 0), name="ubb")
     assert not noslip == UBB((0, 0), name="test")
+    assert not ubb == NoSlip("noslip")
 
     simple_extrapolation = SimpleExtrapolationOutflow(normal_direction=stencil[4], stencil=stencil, name="simple")
     assert simple_extrapolation == SimpleExtrapolationOutflow(normal_direction=stencil[4],
                                                               stencil=stencil, name="simple")
     assert not simple_extrapolation == SimpleExtrapolationOutflow(normal_direction=stencil[4],
                                                                   stencil=stencil, name="test")
+    assert not simple_extrapolation == NoSlip("noslip")
 
     outflow = ExtrapolationOutflow(normal_direction=stencil[4], lb_method=method, name="outflow")
     assert outflow == ExtrapolationOutflow(normal_direction=stencil[4], lb_method=method, name="outflow")
     assert not outflow == ExtrapolationOutflow(normal_direction=stencil[4], lb_method=method, name="test")
+    assert not outflow == simple_extrapolation
 
     density = FixedDensity(density=1.0, name="fixedDensity")
     assert density == FixedDensity(density=1.0, name="fixedDensity")
     assert not density == FixedDensity(density=1.0, name="test")
+    assert not density == UBB((0, 0), name="ubb")
 
     diffusion = DiffusionDirichlet(concentration=1.0, name="diffusion")
     assert diffusion == DiffusionDirichlet(concentration=1.0, name="diffusion")
     assert not diffusion == DiffusionDirichlet(concentration=1.0, name="test")
+    assert not diffusion == density
 
     neumann = NeumannByCopy(name="Neumann")
     assert neumann == NeumannByCopy(name="Neumann")
     assert not neumann == NeumannByCopy(name="test")
+    assert not neumann == diffusion
 
     stream = StreamInConstant(constant=1.0, name="stream")
     assert stream == StreamInConstant(constant=1.0, name="stream")
     assert not stream == StreamInConstant(constant=1.0, name="test")
+    assert not stream == noslip