[yt-svn] commit/yt: ngoldbaum: Merged in ngoldbaum/yt (pull request #2545)
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Mon Mar 27 09:41:56 PDT 2017
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/07a9a1ec3496/
Changeset: 07a9a1ec3496
Branch: yt
User: ngoldbaum
Date: 2017-03-27 16:41:51+00:00
Summary: Merged in ngoldbaum/yt (pull request #2545)
Don't process particle onto a grid if it's outside of the grid. Closes #1333
Approved-by: Desika Narayanan <desika.narayanan at gmail.com>
Approved-by: John ZuHone <jzuhone at gmail.com>
Approved-by: Matt Turk <matthewturk at gmail.com>
Affected #: 3 files
diff -r 89085b6421618adde7a4d1fbc07a88906ba5775f -r 07a9a1ec3496b1b859bb8a3dcc0cf6ab9aefd3c3 yt/data_objects/tests/test_covering_grid.py
--- a/yt/data_objects/tests/test_covering_grid.py
+++ b/yt/data_objects/tests/test_covering_grid.py
@@ -111,7 +111,18 @@
obj = ds.arbitrary_grid(LE, RE, dims)
deposited_mass = obj["deposit", "all_density"].sum() * volume
- yield assert_equal, deposited_mass, ds.quan(1.0, 'g')
+ assert_equal(deposited_mass, ds.quan(1.0, 'g'))
+
+ LE = np.array([0.00, 0.00, 0.00])
+ RE = np.array([0.05, 0.05, 0.05])
+ dims = np.array([ncells, ncells, ncells])
+
+ obj = ds.arbitrary_grid(LE, RE, dims)
+
+ deposited_mass = obj["deposit", "all_density"].sum()
+
+ assert_equal(deposited_mass, 0)
+
# Test that we get identical results to the covering grid for unigrid data.
# Testing AMR data is much harder.
diff -r 89085b6421618adde7a4d1fbc07a88906ba5775f -r 07a9a1ec3496b1b859bb8a3dcc0cf6ab9aefd3c3 yt/geometry/particle_deposit.pxd
--- a/yt/geometry/particle_deposit.pxd
+++ b/yt/geometry/particle_deposit.pxd
@@ -136,7 +136,7 @@
cdef kernel_func sph_kernel
cdef public object nvals
cdef public int update_values
- cdef void process(self, int dim[3], np.float64_t left_edge[3],
- np.float64_t dds[3], np.int64_t offset,
- np.float64_t ppos[3], np.float64_t[:] fields,
- np.int64_t domain_ind)
+ cdef int process(self, int dim[3], np.float64_t left_edge[3],
+ np.float64_t dds[3], np.int64_t offset,
+ np.float64_t ppos[3], np.float64_t[:] fields,
+ np.int64_t domain_ind) except -1
diff -r 89085b6421618adde7a4d1fbc07a88906ba5775f -r 07a9a1ec3496b1b859bb8a3dcc0cf6ab9aefd3c3 yt/geometry/particle_deposit.pyx
--- a/yt/geometry/particle_deposit.pyx
+++ b/yt/geometry/particle_deposit.pyx
@@ -122,10 +122,12 @@
cdef np.int64_t gid = getattr(gobj, "id", -1)
cdef np.float64_t dds[3]
cdef np.float64_t left_edge[3]
+ cdef np.float64_t right_edge[3]
cdef int dims[3]
for i in range(3):
dds[i] = gobj.dds[i]
left_edge[i] = gobj.LeftEdge[i]
+ right_edge[i] = gobj.RightEdge[i]
dims[i] = gobj.ActiveDimensions[i]
for i in range(positions.shape[0]):
# Now we process
@@ -133,15 +135,21 @@
field_vals[j] = field_pointers[j,i]
for j in range(3):
pos[j] = positions[i, j]
+ continue_loop = False
+ for j in range(3):
+ if pos[j] < left_edge[j] or pos[j] > right_edge[j]:
+ continue_loop = True
+ if continue_loop:
+ continue
self.process(dims, left_edge, dds, 0, pos, field_vals, gid)
if self.update_values == 1:
for j in range(nf):
field_pointers[j][i] = field_vals[j]
- cdef void process(self, int dim[3], np.float64_t left_edge[3],
- np.float64_t dds[3], np.int64_t offset,
- np.float64_t ppos[3], np.float64_t[:] fields,
- np.int64_t domain_ind):
+ cdef int process(self, int dim[3], np.float64_t left_edge[3],
+ np.float64_t dds[3], np.int64_t offset,
+ np.float64_t ppos[3], np.float64_t[:] fields,
+ np.int64_t domain_ind) except -1:
raise NotImplementedError
cdef class CountParticles(ParticleDepositOperation):
@@ -152,20 +160,21 @@
np.zeros(self.nvals, dtype="int64", order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset, # offset into IO field
- np.float64_t ppos[3], # this particle's position
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset, # offset into IO field
+ np.float64_t ppos[3], # this particle's position
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
# here we do our thing; this is the kernel
cdef int ii[3]
cdef int i
for i in range(3):
ii[i] = <int>((ppos[i] - left_edge[i])/dds[i])
self.count[ii[2], ii[1], ii[0], offset] += 1
+ return 0
def finalize(self):
arr = np.asarray(self.count)
@@ -188,14 +197,14 @@
np.zeros(self.nvals, dtype="float64", order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset,
- np.float64_t ppos[3],
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset,
+ np.float64_t ppos[3],
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
cdef int ii[3]
cdef int ib0[3]
cdef int ib1[3]
@@ -210,7 +219,7 @@
ib0[i] = ii[i] - half_len
ib1[i] = ii[i] + half_len
if ib0[i] >= dim[i] or ib1[i] <0:
- return
+ return 0
ib0[i] = iclip(ib0[i], 0, dim[i] - 1)
ib1[i] = iclip(ib1[i], 0, dim[i] - 1)
for i from ib0[0] <= i <= ib1[0]:
@@ -233,6 +242,7 @@
for k from ib0[2] <= k <= ib1[2]:
dist = self.temp[k,j,i,offset] / kernel_sum
self.data[k,j,i,offset] += fields[1] * dist
+ return 0
def finalize(self):
return self.odata
@@ -246,20 +256,20 @@
np.zeros(self.nvals, dtype="float64", order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset,
- np.float64_t ppos[3],
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset,
+ np.float64_t ppos[3],
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
cdef int ii[3]
cdef int i
for i in range(3):
ii[i] = <int>((ppos[i] - left_edge[i]) / dds[i])
self.sum[ii[2], ii[1], ii[0], offset] += fields[0]
- return
+ return 0
def finalize(self):
sum = np.asarray(self.sum)
@@ -288,14 +298,14 @@
np.zeros(self.nvals, dtype="float64", order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset,
- np.float64_t ppos[3],
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset,
+ np.float64_t ppos[3],
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
cdef int ii[3]
cdef int i, cell_index
cdef float k, mk, qk
@@ -313,6 +323,7 @@
self.qk[ii[2], ii[1], ii[0], offset] = \
qk + (k - 1.0) * (fields[0] - mk) * (fields[0] - mk) / k
self.i[ii[2], ii[1], ii[0], offset] += 1
+ return 0
def finalize(self):
# This is the standard variance
@@ -338,14 +349,14 @@
np.zeros(self.nvals, dtype="float64", order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset, # offset into IO field
- np.float64_t ppos[3], # this particle's position
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset, # offset into IO field
+ np.float64_t ppos[3], # this particle's position
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
cdef int i, j, k
cdef np.uint64_t ii
@@ -371,6 +382,8 @@
self.field[ind[2] - k, ind[1] - j, ind[0] - i, offset] += \
fields[0]*rdds[0][i]*rdds[1][j]*rdds[2][k]
+ return 0
+
def finalize(self):
rv = np.asarray(self.field)
rv.shape = self.nvals
@@ -390,20 +403,21 @@
np.zeros(self.nvals, dtype='float64', order='F'), 4)
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset,
- np.float64_t ppos[3],
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset,
+ np.float64_t ppos[3],
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
cdef int ii[3]
cdef int i
for i in range(3):
ii[i] = <int>((ppos[i] - left_edge[i]) / dds[i])
self.w[ii[2], ii[1], ii[0], offset] += fields[1]
self.wf[ii[2], ii[1], ii[0], offset] += fields[0] * fields[1]
+ return 0
def finalize(self):
wf = np.asarray(self.wf)
@@ -422,15 +436,16 @@
self.update_values = 1
@cython.cdivision(True)
- cdef void process(self, int dim[3],
+ cdef int process(self, int dim[3],
np.float64_t left_edge[3],
np.float64_t dds[3],
np.int64_t offset,
np.float64_t ppos[3],
np.float64_t[:] fields,
np.int64_t domain_ind
- ):
+ ) except -1:
fields[0] = domain_ind
+ return 0
def finalize(self):
return
@@ -448,14 +463,14 @@
self.distfield[:] = np.inf
@cython.cdivision(True)
- cdef void process(self, int dim[3],
- np.float64_t left_edge[3],
- np.float64_t dds[3],
- np.int64_t offset,
- np.float64_t ppos[3],
- np.float64_t[:] fields,
- np.int64_t domain_ind
- ):
+ cdef int process(self, int dim[3],
+ np.float64_t left_edge[3],
+ np.float64_t dds[3],
+ np.int64_t offset,
+ np.float64_t ppos[3],
+ np.float64_t[:] fields,
+ np.int64_t domain_ind
+ ) except -1:
# This one is a bit slow. Every grid cell is going to be iterated
# over, and we're going to deposit particles in it.
cdef int i, j, k
@@ -477,7 +492,7 @@
gpos[2] += dds[2]
gpos[1] += dds[1]
gpos[0] += dds[0]
- return
+ return 0
def finalize(self):
nn = np.asarray(self.nnfield)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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