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Fix conflicts between class properties and instance variables
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@vyasr
vyasr committed Feb 2, 2018
1 parent 61406dc commit f65fd62
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Showing 2 changed files with 41 additions and 41 deletions.
6 changes: 3 additions & 3 deletions freud/cluster.pxi
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Original file line number Diff line number Diff line change
Expand Up @@ -42,14 +42,14 @@ cdef class Cluster:
behavior.
"""
cdef cluster.Cluster *thisptr
cdef box
cdef m_box
cdef rmax

def __cinit__(self, box, float rcut):
cdef _box.Box cBox = _box.Box(box.getLx(), box.getLy(), box.getLz(),
box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new cluster.Cluster(cBox, rcut)
self.box = box
self.m_box = box
self.rmax = rcut

def __dealloc__(self):
Expand Down Expand Up @@ -84,7 +84,7 @@ cdef class Cluster:
if points.shape[1] != 3:
raise RuntimeError('Need a list of 3D points for computeClusters()')

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down
76 changes: 38 additions & 38 deletions freud/order.pxi
View file
Original file line number Diff line number Diff line change
Expand Up @@ -970,12 +970,12 @@ cdef class LocalQl:
.. todo:: move box to compute, this is old API
"""
cdef order.LocalQl *thisptr
cdef box
cdef m_box
cdef rmax

def __init__(self, box, rmax, l, rmin=0):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.box = box
self.m_box = box
self.rmax = rmax
self.thisptr = new order.LocalQl(l_box, rmax, l, rmin)

Expand All @@ -998,7 +998,7 @@ cdef class LocalQl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1021,7 +1021,7 @@ cdef class LocalQl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1045,7 +1045,7 @@ cdef class LocalQl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1069,7 +1069,7 @@ cdef class LocalQl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down Expand Up @@ -1271,7 +1271,7 @@ cdef class LocalQlNear(LocalQl):
def __init__(self, box, rmax, l, kn=12):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new order.LocalQl(l_box, rmax, l, 0)
self.box = box
self.m_box = box
self.rmax = rmax
self.num_neigh = kn

Expand All @@ -1287,7 +1287,7 @@ cdef class LocalQlNear(LocalQl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalQl.compute(self, points, nlist_)

Expand All @@ -1299,7 +1299,7 @@ cdef class LocalQlNear(LocalQl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalQl.computeAve(self, points, nlist_)

Expand All @@ -1311,7 +1311,7 @@ cdef class LocalQlNear(LocalQl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalQl.computeNorm(self, points, nlist_)

Expand All @@ -1323,7 +1323,7 @@ cdef class LocalQlNear(LocalQl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalQl.computeAveNorm(self, points, nlist_)

Expand Down Expand Up @@ -1353,13 +1353,13 @@ cdef class LocalWl:
.. todo:: move box to compute, this is old API
"""
cdef order.LocalWl *thisptr
cdef box
cdef m_box
cdef rmax

def __init__(self, box, rmax, l):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new order.LocalWl(l_box, rmax, l)
self.box = box
self.m_box = box
self.rmax = rmax

def __dealloc__(self):
Expand All @@ -1382,7 +1382,7 @@ cdef class LocalWl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1405,7 +1405,7 @@ cdef class LocalWl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1429,7 +1429,7 @@ cdef class LocalWl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1453,7 +1453,7 @@ cdef class LocalWl:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down Expand Up @@ -1667,7 +1667,7 @@ cdef class LocalWlNear(LocalWl):
def __init__(self, box, rmax, l, kn=12):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new order.LocalWl(l_box, rmax, l)
self.box = box
self.m_box = box
self.rmax = rmax
self.num_neigh = kn

Expand All @@ -1683,7 +1683,7 @@ cdef class LocalWlNear(LocalWl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalWl.compute(self, points, nlist_)

Expand All @@ -1695,7 +1695,7 @@ cdef class LocalWlNear(LocalWl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalWl.computeAve(self, points, nlist_)

Expand All @@ -1707,7 +1707,7 @@ cdef class LocalWlNear(LocalWl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalWl.computeNorm(self, points, nlist_)

Expand All @@ -1719,7 +1719,7 @@ cdef class LocalWlNear(LocalWl):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return LocalWl.computeAveNorm(self, points, nlist_)

Expand All @@ -1744,13 +1744,13 @@ cdef class SolLiq:
.. todo:: move box to compute, this is old API
"""
cdef order.SolLiq *thisptr
cdef box
cdef m_box
cdef rmax

def __init__(self, box, rmax, Qthreshold, Sthreshold, l):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new order.SolLiq(l_box, rmax, Qthreshold, Sthreshold, l)
self.box = box
self.m_box = box
self.rmax = rmax

def __dealloc__(self):
Expand All @@ -1773,7 +1773,7 @@ cdef class SolLiq:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1796,7 +1796,7 @@ cdef class SolLiq:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand All @@ -1819,7 +1819,7 @@ cdef class SolLiq:
cdef np.ndarray[float, ndim=2] l_points = points
cdef unsigned int nP = <unsigned int> points.shape[0]

defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down Expand Up @@ -2063,7 +2063,7 @@ cdef class SolLiqNear(SolLiq):
def __init__(self, box, rmax, Qthreshold, Sthreshold, l, kn=12):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(), box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr = new order.SolLiq(l_box, rmax, Qthreshold, Sthreshold, l)
self.box = box
self.m_box = box
self.rmax = rmax
self.num_neigh = kn

Expand All @@ -2079,7 +2079,7 @@ cdef class SolLiqNear(SolLiq):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return SolLiq.compute(self, points, nlist_)

Expand All @@ -2091,7 +2091,7 @@ cdef class SolLiqNear(SolLiq):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return SolLiq.computeSolLiqVariant(self, points, nlist_)

Expand All @@ -2103,7 +2103,7 @@ cdef class SolLiqNear(SolLiq):
:type points: :class:`numpy.ndarray`, shape= :math:`\\left(N_{particles}, 3\\right)`, dtype= :class:`numpy.float32`
:type nlist: :py:class:`freud.locality.NeighborList`
"""
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, True, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, True, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
return SolLiq.computeSolLiqNoNorm(self, points, nlist_)

Expand All @@ -2123,7 +2123,7 @@ cdef class MatchEnv:
cdef order.MatchEnv *thisptr
cdef rmax
cdef num_neigh
cdef box
cdef m_box

def __cinit__(self, box, rmax, k):
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(),
Expand All @@ -2132,7 +2132,7 @@ cdef class MatchEnv:

self.rmax = rmax
self.num_neigh = k
self.box = box
self.m_box = box

def __dealloc__(self):
del self.thisptr
Expand All @@ -2147,7 +2147,7 @@ cdef class MatchEnv:
cdef _box.Box l_box = _box.Box(box.getLx(), box.getLy(), box.getLz(), box.getTiltFactorXY(),
box.getTiltFactorXZ(), box.getTiltFactorYZ(), box.is2D())
self.thisptr.setBox(l_box)
self.box = box
self.m_box = box

def cluster(self, points, threshold, hard_r=False, registration=False, global_search=False, nlist=None):
"""Determine clusters of particles with matching environments.
Expand Down Expand Up @@ -2176,11 +2176,11 @@ cdef class MatchEnv:
cdef locality.NeighborList *nlist_ptr
cdef NeighborList nlist_
if hard_r:
defaulted_nlist = make_default_nlist(self.box, points, points, self.rmax, nlist, True)
defaulted_nlist = make_default_nlist(self.m_box, points, points, self.rmax, nlist, True)
nlist_ = defaulted_nlist[0]
nlist_ptr = nlist_.get_ptr()
else:
defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, None, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, None, self.rmax)
nlist_ = defaulted_nlist[0]
nlist_ptr = nlist_.get_ptr()

Expand Down Expand Up @@ -2217,7 +2217,7 @@ cdef class MatchEnv:
cdef unsigned int nP = <unsigned int> points.shape[0]
cdef unsigned int nRef = <unsigned int> refPoints.shape[0]

defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, None, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, None, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down Expand Up @@ -2256,7 +2256,7 @@ cdef class MatchEnv:
cdef unsigned int nP = <unsigned int> points.shape[0]
cdef unsigned int nRef = <unsigned int> refPoints.shape[0]

defaulted_nlist = make_default_nlist_nn(self.box, points, points, self.num_neigh, nlist, None, self.rmax)
defaulted_nlist = make_default_nlist_nn(self.m_box, points, points, self.num_neigh, nlist, None, self.rmax)
cdef NeighborList nlist_ = defaulted_nlist[0]
cdef locality.NeighborList *nlist_ptr = nlist_.get_ptr()

Expand Down

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