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Dynamic properties for ParticleSlice #1160

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merged 5 commits into from
May 11, 2017
Merged

Dynamic properties for ParticleSlice #1160

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00e346b
Fix ParticleSlice.__str__
mkuron May 8, 2017
1fb1bad
Dynamically add any properties into ParticleSlice that ParticleHandle…
mkuron May 8, 2017
0eed2c8
Cleanup ParticleSlice
mkuron May 8, 2017
6b4ecb0
Get rid of _InjectParticleProperty
mkuron May 9, 2017
06c858a
ParticleSlice getter straight into numpy array
mkuron May 11, 2017
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2 changes: 1 addition & 1 deletion src/python/espressomd/particle_data.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,7 @@ cdef class ParticleHandle(object):
cdef int update_particle_data(self) except -1


cdef class ParticleSlice:
cdef class _ParticleSliceImpl:

cdef particle particle_data
cdef int update_particle_data(self, id) except -1
Expand Down
280 changes: 60 additions & 220 deletions src/python/espressomd/particle_data.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1148,10 +1148,11 @@ cdef class ParticleHandle:
setattr(self, k, P[k])


cdef class ParticleSlice:
cdef class _ParticleSliceImpl:
"""
Handles slice inputs e.g. part[0:2]. Sets values for selected slices or returns values as a single list.

This is the base class that should not be used directly as it lacks some properties. Use :class:`espressomd.ParticleSlice` instead.
"""

def __cinit__(self, slice_):
Expand All @@ -1178,232 +1179,20 @@ cdef class ParticleSlice:
else:
return 0

# Particle Type
property type:
"""
Particle type.

"""
def __get__(self):
type_list = []
for id in self.id_selection:
type_list.append(ParticleHandle(id).type)
return type_list

def __set__(self, _type_list):
if isinstance(_type_list, int):
for id in self.id_selection:
ParticleHandle(id).type = _type_list
return
if len(self.id_selection) != len(_type_list):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_type_list), len(self.id_selection)))
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[i]).type = _type_list[i]

# Position
property pos:
"""
Particle position (not folded into central image).

"""
def __set__(self, _pos_array):
if len(self.id_selection) != len(_pos_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_pos_array), len(self.id_selection)))

cdef double mypos[3]
for i in range(len(_pos_array)):
ParticleHandle(self.id_selection[i]).pos = _pos_array[i]

def __get__(self):
pos_array = np.zeros((len(self.id_selection), 3))
for i in range(len(self.id_selection)):
pos_array[i, :] = ParticleHandle(self.id_selection[i]).pos
return pos_array

property pos_folded:
"""
Particle position (folded into central image).

"""

def __set__(self, d):
raise Exception("setting a folded position is not implemented.")

def __get__(self):
pos_array = np.zeros((len(self.id_selection), 3))
for i in range(len(self.id_selection)):
pos_array[i, :] = ParticleHandle(
self.id_selection[i]).pos_folded
return pos_array

# Velocity
property v:
"""
Particle velocity.

"""

def __set__(self, _v_array):
if len(np.array(_v_array).shape) == 1:
for id in self.id_selection:
ParticleHandle(id).v = _v_array
return

if len(self.id_selection) != len(_v_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_v_array), len(self.id_selection)))

for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[i]).v = _v_array[i]

def __get__(self):
v_array = np.zeros((len(self.id_selection), 3))
for i in range(len(self.id_selection)):
v_array[i, :] = ParticleHandle(self.id_selection[i]).v
return v_array

# Force
property f:
"""
Particle force.

"""

def __set__(self, _f_array):
if len(np.array(_f_array).shape) == 1:
for id in self.id_selection:
ParticleHandle(id).f = _f_array
return

if len(self.id_selection) != len(_f_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_f_array), len(self.id_selection)))
for i in range(len(_f_array)):
ParticleHandle(self.id_selection[i]).f = _f_array[i]

def __get__(self):
f_array = np.zeros((len(self.id_selection), 3))
for i in range(len(self.id_selection)):
f_array[i, :] = ParticleHandle(self.id_selection[i]).f
return f_array

property mass:
"""
Particle mass.

.. note::

If not set the particle mass is ``1`` in reduced units.

"""

def __set__(self, _mass_array):
IF MASS:
if isinstance(_mass_array, int) or isinstance(_mass_array, float):
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[i]).mass = _mass_array
return
if len(self.id_selection) != len(_mass_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_mass_array), len(self.id_selection)))
for i in range(len(_mass_array)):
ParticleHandle(self.id_selection[i]).mass = _mass_array[i]
ELSE:
raise Exception("You are trying to set the particle mass \
but the mass feature is not compiled in.")

def __get__(self):
mass_array = np.zeros_like(self.id_selection)
for i in range(len(self.id_selection)):
mass_array[i] = ParticleHandle(self.id_selection[i]).mass
return mass_array

IF ELECTROSTATICS == 1:
property q:
"""
Particle charge.

"""

def __set__(self, _q_array):
if isinstance(_q_array, int) or isinstance(_q_array, float):
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[i]).q = _q_array
return

if len(self.id_selection) != len(_q_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_q_array), len(self.id_selection)))
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[i]).q = _q_array[i]

def __get__(self):
q_array = np.zeros_like(self.id_selection)
for i in range(len(self.id_selection)):
q_array[i] = ParticleHandle(self.id_selection[i]).q
return q_array

IF EXTERNAL_FORCES:
property ext_force:
"""
External force on a particle defined by a vector.

"""

def __set__(self, _ext_f_array):
if len(np.array(_ext_f_array).shape) == 1:
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[
i]).ext_force = _ext_f_array
return

if len(self.id_selection) != len(_ext_f_array):
raise Exception("Input list size (%i) does not match slice size (%i)." % (
len(_ext_f_array), len(self.id_selection)))

for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[
i]).ext_force = _ext_f_array[i]

def __get__(self):
ext_f_array = np.zeros((len(self.id_selection), 3))
for i in range(len(self.id_selection)):
ext_f_array[i, :] = ParticleHandle(
self.id_selection[i]).ext_force

return ext_f_array

IF EXCLUSIONS:
property exclude:
"""
Exclude particle from interaction.

"""

def __set__(self, _partners):
if not isinstance(_partners, list):
raise Exception(
"List object expected for exclusion partners.")
if isinstance(_partners[0], list):
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[
i]).exclude = _partners[i]
elif isinstance(_partners[0], int):
for i in range(len(self.id_selection)):
ParticleHandle(self.id_selection[
i]).exclude = _partners
else:
raise TypeError("Unexpected exclusion partner type.")

def __get__(self):
_exclude_array = []
for i in range(len(self.id_selection)):
_exclude_array.append(ParticleHandle(
self.id_selection[i]).exclude)
return _exclude_array

def add_exclusion(self, _partners):
self.exclude = _partners

Expand All @@ -1430,9 +1219,9 @@ cdef class ParticleSlice:
pl = ParticleList()
for i in self.id_selection:
if pl.exists(i):
res += str(pl[i]) + "\n"
# Remove final newline
return res[:-1]
res += str(pl[i]) + ", "
# Remove final comma
return "ParticleSlice([" + res[:-2] + "])"
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No need for this awkward comma removal

pl = ParticleList()
return "ParticleSlice([" + ", ".join(str(pl[i]) for i in self.id_selection if pl.exists(i)) + "])"

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It's nicer, and it's more in line with how Python and Numpy print their own data types. Also, if I remove that space at the end, why not remove the trailing comma along with it.


def update(self, P):
if "id" in P:
Expand Down Expand Up @@ -1479,6 +1268,13 @@ cdef class ParticleSlice:
ParticleHandle(id).remove()


class ParticleSlice(_ParticleSliceImpl):
"""
Handles slice inputs e.g. part[0:2]. Sets values for selected slices or returns values as a single list.

"""
pass

cdef class ParticleList:
"""
Provides access to the particles via [i], where i is the particle id. Returns a ParticleHandle object.
Expand Down Expand Up @@ -1625,7 +1421,7 @@ cdef class ParticleList:
yield self[i]

def exists(self, idx):
if isinstance(idx, int):
if isinstance(idx, int) or issubclass(type(idx), np.integer):
return particle_exists(idx)
if isinstance(idx, slice) or isinstance(idx, tuple) or isinstance(idx, list) or isinstance(idx, np.ndarray):
tf_array = np.zeros(len(idx), dtype=np.bool)
Expand All @@ -1640,9 +1436,9 @@ cdef class ParticleList:
res = ""
for i in range(max_seen_particle + 1):
if self.exists(i):
res += str(self[i]) + "\n"
# Remove final newline
return res[:-1]
res += str(self[i]) + ", "
# Remove final comma
return "ParticleList([" + res[:-2] + "])"
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No need for this awkward comma removal

return "ParticleList([" + ", ".join(str(self[i]) for i in range(max_seen_particle + 1) if self.exists(i)) + "])"


def writevtk(self, fname, types='all'):
"""
Expand Down Expand Up @@ -1721,3 +1517,47 @@ cdef class ParticleList:
if not (self.exists(i) and self.exists(j)):
continue
yield (self[i], self[j])

class _InjectParticleProperty:
def __init__(injector, attribute):
injector.attribute = attribute

def set(injector, particle_slice, values):
target = getattr(ParticleHandle(particle_slice.id_selection[0]), injector.attribute)
target_shape = np.shape(target)
N = len(particle_slice.id_selection)

if not target_shape: # scalar quantity
if not np.shape(values): # one value provided
for i in range(N):
setattr(ParticleHandle(particle_slice.id_selection[i]), injector.attribute, values)
elif np.shape(values)[0] == N: # one value for each particle provided
for i in range(N):
setattr(ParticleHandle(particle_slice.id_selection[i]), injector.attribute, values[i])
else:
raise Exception("Shape of value (%s) does not broadcast to shape of attribute (%s)." % (
np.shape(values), target_shape))
return

if target_shape == np.shape(values): # one value provided
for i in range(N):
setattr(ParticleHandle(particle_slice.id_selection[i]), injector.attribute, values)
elif target_shape == tuple(np.shape(values)[1:]) and np.shape(values)[0] == N: # one value for each particle provided
for i in range(N):
setattr(ParticleHandle(particle_slice.id_selection[i]), injector.attribute, values[i])
else:
raise Exception("Shape of value (%s) does not broadcast to shape of attribute (%s)." % (
np.shape(values), target_shape))

def get(injector, particle_slice):
values = []
for i in particle_slice.id_selection:
values.append(getattr(ParticleHandle(i), injector.attribute))
return np.array(values)

# auto-add missing particle properties to ParticleSlice
for attribute in particle_attributes:
if not attribute in dir(ParticleSlice):
ipp = _InjectParticleProperty(attribute)
new_property = property(ipp.get, ipp.set, doc=getattr(ParticleHandle, attribute).__doc__)
setattr(ParticleSlice, attribute, new_property)
4 changes: 2 additions & 2 deletions src/python/espressomd/utils.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ cdef check_type_or_throw_except(x, n, t, msg):
if hasattr(x, "__getitem__"):
for i in range(len(x)):
if not isinstance(x[i], t):
if not (t == float and isinstance(x[i], int)):
if not (t == float and isinstance(x[i], int)) and not (t == int and issubclass(type(x[i]), np.integer)):
raise ValueError(
msg + " -- Item " + str(i) + " was of type " + type(x[i]).__name__)
else:
Expand All @@ -71,7 +71,7 @@ cdef check_type_or_throw_except(x, n, t, msg):
else:
# N=1 and a single value
if not isinstance(x, t):
if not (t == float and isinstance(x, int)):
if not (t == float and isinstance(x, int)) and not (t == int and issubclass(type(x), np.integer)):
raise ValueError(msg + " -- Got an " + type(x).__name__)


Expand Down
1 change: 1 addition & 0 deletions testsuite/python/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ set(py_tests bondedInteractions.py
observables.py
p3m_gpu.py
particle.py
particle_slice.py
rotational_inertia.py
lbgpu_remove_total_momentum.py
tabulated.py
Expand Down
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