Cleanups 2024

doc/upload-docs.sh

@@ -1,3 +1,3 @@
 #! /bin/sh
 
-rsync --verbose --archive --delete _build/html/* doc-upload:doc/pytential
+rsync --verbose --archive --delete _build/html/ doc-upload:doc/pytential

examples/layerpot-3d.py

@@ -85,7 +85,7 @@ def main(mesh_name="ellipsoid"):
 
     if 0:
         from random import randrange
-        sigma = actx.zeros(density_discr.ndofs, angle.entry_dtype)
+        sigma = actx.np.zeros(density_discr.ndofs, angle.entry_dtype)
         for _ in range(5):
             sigma[randrange(len(sigma))] = 1
 

examples/layerpot.py

@@ -77,7 +77,7 @@ def op(**kwargs):
 
     if 0:
         from random import randrange
-        sigma = actx.zeros(density_discr.ndofs, angle.entry_dtype)
+        sigma = actx.np.zeros(density_discr.ndofs, angle.entry_dtype)
         for _ in range(5):
             sigma[randrange(len(sigma))] = 1
 

pytential/linalg/skeletonization.py

@@ -140,7 +140,7 @@ def prg():
 
     waa = bind(places, sym.weights_and_area_elements(
         places.ambient_dim, dofdesc=domain))(actx)
-    result = actx.zeros((cluster_index.nclusters,), dtype=waa.entry_dtype)
+    result = actx.np.zeros((cluster_index.nclusters,), dtype=waa.entry_dtype)
 
     from arraycontext import flatten
     _, (waa_per_cluster,) = prg()(actx.queue,

pytential/qbx/__init__.py

@@ -910,7 +910,7 @@ def _flat_centers(dofdesc, qbx_forced_limit):
 
             qbx_tgt_numberer = self.get_qbx_target_numberer(
                     tgt_to_qbx_center.dtype)
-            qbx_tgt_count = actx.zeros((), np.int32)
+            qbx_tgt_count = actx.np.zeros((), np.int32)
             qbx_tgt_numbers = actx.np.zeros_like(tgt_to_qbx_center)
 
             qbx_tgt_numberer(

pytential/qbx/fmm.py

@@ -400,8 +400,7 @@ def make_container():
 
 # {{{ FMM top-level
 
-def drive_fmm(expansion_wrangler, src_weight_vecs, timing_data=None,
-        traversal=None):
+def drive_fmm(expansion_wrangler, src_weight_vecs, timing_data=None):
     """Top-level driver routine for the QBX fast multipole calculation.
 
     :arg geo_data: A :class:`pytential.qbx.geometry.QBXFMMGeometryData` instance.
@@ -419,10 +418,7 @@ def drive_fmm(expansion_wrangler, src_weight_vecs, timing_data=None,
     wrangler = expansion_wrangler
 
     geo_data = wrangler.geo_data
-
-    if traversal is None:
-        traversal = geo_data.traversal()
-
+    traversal = wrangler.traversal
     tree = traversal.tree
 
     template_ary = src_weight_vecs[0]

pytential/qbx/geometry.py

@@ -482,7 +482,7 @@ def target_info(self):
 
         target_discr_starts.append(ntargets)
 
-        targets = actx.zeros((self.ambient_dim, ntargets), self.coord_dtype)
+        targets = actx.np.zeros((self.ambient_dim, ntargets), self.coord_dtype)
         code_getter.copy_targets_kernel()(
                 actx.queue,
                 targets=targets[:, :self.ncenters],
@@ -511,7 +511,7 @@ def target_side_preferences(self):
         actx = self._setup_actx
         tgt_info = self.target_info()
 
-        target_side_preferences = actx.zeros(tgt_info.ntargets, dtype=np.int8)
+        target_side_preferences = actx.np.zeros(tgt_info.ntargets, dtype=np.int8)
         for tdstart, (target_discr, qbx_side) in zip(
                 tgt_info.target_discr_starts,
                 self.target_discrs_and_qbx_sides):
@@ -545,10 +545,10 @@ def tree(self):
 
         target_radii = None
         if lpot_source._expansions_in_tree_have_extent:
-            target_radii = actx.zeros(target_info.ntargets, self.coord_dtype)
+            target_radii = actx.np.zeros(target_info.ntargets, self.coord_dtype)
             target_radii[:self.ncenters] = self.flat_expansion_radii()
 
-        refine_weights = actx.zeros(nparticles, dtype=np.int32)
+        refine_weights = actx.np.zeros(nparticles, dtype=np.int32)
 
         # Assign a weight of 1 to all sources, QBX centers, and conventional
         # (non-QBX) targets. Assign a weight of 0 to all targets that need
@@ -624,7 +624,7 @@ def qbx_center_to_target_box(self):
                         tree.box_id_dtype,
                         )
 
-        box_to_target_box = actx.zeros(tree.nboxes, tree.box_id_dtype)
+        box_to_target_box = actx.np.zeros(tree.nboxes, tree.box_id_dtype)
         if self.debug:
             box_to_target_box.fill(-1)
 
@@ -641,7 +641,7 @@ def qbx_center_to_target_box(self):
                     dtype=user_target_from_tree_target.dtype)
                 )
 
-        qbx_center_to_target_box = actx.zeros(self.ncenters, tree.box_id_dtype)
+        qbx_center_to_target_box = actx.np.zeros(self.ncenters, tree.box_id_dtype)
 
         if self.debug:
             qbx_center_to_target_box.fill(-1)
@@ -676,7 +676,7 @@ def qbx_center_to_target_box_source_level(self, source_level):
         sep_smaller = traversal.from_sep_smaller_by_level[source_level]
         qbx_center_to_target_box = self.qbx_center_to_target_box()
 
-        target_box_to_target_box_source_level = actx.zeros(
+        target_box_to_target_box_source_level = actx.np.zeros(
             len(traversal.target_boxes), dtype=traversal.tree.box_id_dtype)
         target_box_to_target_box_source_level.fill(-1)
         target_box_to_target_box_source_level[sep_smaller.nonempty_indices] = (
@@ -708,7 +708,7 @@ def global_qbx_flags(self):
         """
         actx = self._setup_actx
 
-        result = actx.zeros(self.ncenters, np.int8)
+        result = actx.np.zeros(self.ncenters, np.int8)
         result.fill(1)
 
         return actx.freeze(result)
@@ -727,7 +727,7 @@ def global_qbx_centers(self):
         user_target_to_center = actx.thaw(self.user_target_to_center())
 
         tgt_assoc_result = user_target_to_center[self.ncenters:]
-        center_is_used = actx.zeros(self.ncenters, np.int8)
+        center_is_used = actx.np.zeros(self.ncenters, np.int8)
 
         self.code_getter.pick_used_centers(
                 actx.queue,
@@ -792,7 +792,7 @@ def user_target_to_center(self):
                     self.target_association_tolerance),
                 debug=self.debug)
 
-        result = actx.zeros(
+        result = actx.np.zeros(
                 target_info.ntargets, tgt_assoc_result.target_to_center.dtype
                 )
         result[:self.ncenters].fill(target_state.NO_QBX_NEEDED)
@@ -814,9 +814,9 @@ def center_to_tree_targets(self):
         tree_ttc = actx.np.zeros_like(user_ttc)
         tree_ttc[self.tree().sorted_target_ids] = user_ttc
 
-        filtered_tree_ttc = actx.zeros(tree_ttc.shape, dtype=tree_ttc.dtype)
-        filtered_target_ids = actx.zeros(tree_ttc.shape, dtype=tree_ttc.dtype)
-        count = actx.zeros(1, dtype=tree_ttc.dtype)
+        filtered_tree_ttc = actx.np.zeros(tree_ttc.shape, dtype=tree_ttc.dtype)
+        filtered_target_ids = actx.np.zeros(tree_ttc.shape, dtype=tree_ttc.dtype)
+        count = actx.np.zeros(1, dtype=tree_ttc.dtype)
 
         self.code_getter.filter_center_and_target_ids(tree_ttc.dtype)(
                 tree_ttc, filtered_tree_ttc, filtered_target_ids, count,

pytential/qbx/refinement.py

@@ -313,7 +313,7 @@ def check_expansion_disks_undisturbed_by_sources(self,
             nelements_to_refine_prev = actx.to_numpy(
                 actx.np.sum(refine_flags)).item()
 
-        found_element_to_refine = actx.zeros(1, dtype=np.int32)
+        found_element_to_refine = actx.np.zeros(1, dtype=np.int32)
         found_element_to_refine.finish()
         unwrap_args = AreaQueryElementwiseTemplate.unwrap_args
 
@@ -378,7 +378,7 @@ def check_sufficient_source_quadrature_resolution(self,
             nelements_to_refine_prev = actx.to_numpy(
                     actx.np.sum(refine_flags)).item()
 
-        found_element_to_refine = actx.zeros(1, dtype=np.int32)
+        found_element_to_refine = actx.np.zeros(1, dtype=np.int32)
         found_element_to_refine.finish()
 
         from pytential import bind, sym
@@ -486,7 +486,7 @@ def make_empty_refine_flags(actx, density_discr):
     :returns: A :class:`pyopencl.array.Array` suitable for use as refine flags,
         initialized to zero.
     """
-    result = actx.zeros(density_discr.mesh.nelements, np.int32)
+    result = actx.np.zeros(density_discr.mesh.nelements, np.int32)
     result.finish()
     return result
 

pytential/qbx/target_assoc.py

@@ -527,7 +527,7 @@ def mark_targets(self, places, dofdesc,
                 tree.particle_id_dtype,
                 max_levels)
 
-        found_target_close_to_element = actx.zeros(1, np.int32)
+        found_target_close_to_element = actx.np.zeros(1, np.int32)
         found_target_close_to_element.finish()
 
         # Perform a space invader query over the sources.
@@ -658,7 +658,7 @@ def find_centers(self, places, dofdesc,
         wait_for = [evt]
 
         def make_target_field(fill_val, dtype=tree.coord_dtype):
-            arr = actx.zeros(tree.nqbxtargets, dtype)
+            arr = actx.np.zeros(tree.nqbxtargets, dtype)
             arr.fill(fill_val)
             wait_for.extend(arr.events)
             return arr
@@ -729,7 +729,7 @@ def mark_elements_for_refinement(self, places, dofdesc,
                 tree.particle_id_dtype,
                 max_levels)
 
-        found_element_to_refine = actx.zeros(1, np.int32)
+        found_element_to_refine = actx.np.zeros(1, np.int32)
         found_element_to_refine.finish()
 
         # Perform a space invader query over the sources.
@@ -790,7 +790,7 @@ def make_target_flags(self, target_discrs_and_qbx_sides):
         actx = self.array_context
 
         ntargets = sum(discr.ndofs for discr, _ in target_discrs_and_qbx_sides)
-        target_flags = actx.zeros(ntargets, dtype=np.int32)
+        target_flags = actx.np.zeros(ntargets, dtype=np.int32)
 
         offset = 0
         for discr, flags in target_discrs_and_qbx_sides:
@@ -849,7 +849,7 @@ def associate_targets_to_qbx_centers(places, geometry, wrangler,
 
     peer_lists = wrangler.find_peer_lists(tree)
 
-    target_status = actx.zeros(tree.nqbxtargets, dtype=np.int32)
+    target_status = actx.np.zeros(tree.nqbxtargets, dtype=np.int32)
     target_status.finish()
 
     have_close_targets = wrangler.mark_targets(places, dofdesc,
@@ -892,7 +892,7 @@ def associate_targets_to_qbx_centers(places, geometry, wrangler,
             "the 'target_association_tolerance' parameter, but "
             "this could also cause an invalid center assignment.")
 
-        refine_flags = actx.zeros(tree.nqbxelements, dtype=np.int32)
+        refine_flags = actx.np.zeros(tree.nqbxelements, dtype=np.int32)
         have_element_to_refine = wrangler.mark_elements_for_refinement(
                 places, dofdesc,
                 tree, peer_lists, target_status, refine_flags,

pytential/qbx/utils.py

@@ -327,7 +327,7 @@ def _make_centers(discr):
 
     # Build tree with sources and centers. Split boxes
     # only because of sources.
-    refine_weights = actx.zeros(nparticles, np.int32)
+    refine_weights = actx.np.zeros(nparticles, np.int32)
     refine_weights[:nsources].fill(1)
 
     refine_weights.finish()
@@ -363,7 +363,7 @@ def _make_centers(discr):
     del box_to_class
 
     # Compute element => source relation
-    qbx_element_to_source_starts = actx.zeros(nelements + 1, tree.particle_id_dtype)
+    qbx_element_to_source_starts = actx.np.zeros(nelements + 1, tree.particle_id_dtype)
     el_offset = 0
     node_nr_base = 0
     for group in density_discr.groups:

pytential/unregularized.py

@@ -415,7 +415,7 @@ def tree(self):
         nsources = lpot_src.density_discr.ndofs
         nparticles = nsources + target_info.ntargets
 
-        refine_weights = actx.zeros(nparticles, dtype=np.int32)
+        refine_weights = actx.np.zeros(nparticles, dtype=np.int32)
         refine_weights[:nsources] = 1
         refine_weights.finish()
 
@@ -449,7 +449,7 @@ def target_info(self):
         actx = self.array_context
         target_discr_starts.append(ntargets)
 
-        targets = actx.zeros(
+        targets = actx.np.zeros(
                 (lpot_src.ambient_dim, ntargets),
                 self.coord_dtype)
 

test/test_cost_model.py

@@ -745,8 +745,8 @@ def test_cost_model_correctness(actx_factory, dim, off_surface,
     src_weights = np.ones(ndofs)
 
     timing_data = {}
-    potential = drive_fmm(wrangler, (src_weights,), timing_data,
-            traversal=wrangler.trav)[0][geo_data.ncenters:]
+    potential = drive_fmm(wrangler, (src_weights,), timing_data
+            )[0][geo_data.ncenters:]
 
     # Check constant one wrangler for correctness.
     assert np.all(potential == ndofs)