def __init__(self,
system,
nodeGrid='auto',
cellGrid='auto',
nocheck=False):
if nocheck:
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
if check.System(system, 'bc'):
if nodeGrid == 'auto':
nodeGrid = decomp.nodeGrid(system.comm.rank)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
raise Exception(
'Automatic cell size calculation not yet implemented'
)
else:
cellGrid = toInt3DFromVector(cellGrid)
for k in xrange(3):
if nodeGrid[k] * cellGrid[k] == 1:
print(("Warning! cellGrid[{}] has been "
"adjusted to 2 (was={})".format(
k, cellGrid[k])))
cellGrid[k] = 2
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
raise Exception(
'Error: could not create DomainDecomposition object')
def __init__(self, system,
nodeGrid='auto',
cellGrid='auto',
halfCellInt = 'auto',
nocheck=False):
# do sanity checks for the system first
if nocheck:
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid, halfCellInt)
else:
if check.System(system, 'bc'):
if nodeGrid == 'auto':
nodeGrid = decomp.nodeGridSimple(system.comm.rank)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
cellGrid = Int3D(2,2,2)
else:
cellGrid = toInt3DFromVector(cellGrid)
if halfCellInt == 'auto':
halfCellInt = 1
# minimum image convention check:
for k in range(3):
if nodeGrid[k]*cellGrid[k] == 1 :
print(("Warning! cellGrid[{}] has been "
"adjusted to 2 (was={})".format(k, cellGrid[k])))
cellGrid[k] = 2
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid, halfCellInt)
else:
print('Error: could not create DomainDecomposition object')
def __init__(self,
system,
nodeGrid='auto',
cellGrid='auto',
neiListx='auto',
neiListy='auto',
neiListz='auto'):
if nodeGrid == 'auto':
nodeGrid = Int3D(system.comm.rank, 1, 1)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
# TODO: Implement
raise 'Automatic cell size calculation not yet implemented'
else:
cellGrid = toInt3DFromVector(cellGrid)
if neiListx == 'auto':
neiListx = 0
else:
neiListx = neiListx
if neiListy == 'auto':
neiListy = 0
else:
neiListy = neiListy
if neiListz == 'auto':
neiListz = 0
else:
neiListz = neiListz
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid, neiListx, neiListy,
neiListz)
def __init__(self, system,
nodeGrid='auto',
cellGrid='auto',
nocheck=False):
# do sanity checks for the system first
if nocheck:
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
if check.System(system, 'bc'):
if nodeGrid == 'auto':
nodeGrid = decomp.nodeGrid(system.comm.rank)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
cellGrid = Int3D(2,2,2)
else:
cellGrid = toInt3DFromVector(cellGrid)
# minimum image convention check:
for k in range(3):
if nodeGrid[k]*cellGrid[k] == 1 :
print(("Warning! cellGrid[{}] has been "
"adjusted to 2 (was={})".format(k, cellGrid[k])))
cellGrid[k] = 2
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
print 'Error: could not create DomainDecomposition object'
def __init__(self, system,
nodeGrid='auto',
cellGrid='auto'):
if nodeGrid == 'auto':
nodeGrid = Int3D(system.comm.rank, 1, 1)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
# TODO: Implement
raise 'Automatic cell size calculation not yet implemented'
else:
cellGrid = toInt3DFromVector(cellGrid)
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
def getFoldedPosition(self, pos, imageBox=None):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup() or pmi.isController:
if imageBox is None:
return self.cxxclass.getFoldedPosition(self, toReal3DFromVector(pos))
else:
return self.cxxclass.getFoldedPosition(
self, toReal3DFromVector(pos), toInt3DFromVector(imageBox))
def getFoldedPosition(self, pos, imageBox=None):
if not (pmi._PMIComm and pmi._PMIComm.isActive()
) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup(
) or pmi.isController:
if imageBox is None:
return self.cxxclass.getFoldedPosition(self,
toReal3DFromVector(pos))
else:
return self.cxxclass.getFoldedPosition(
self, toReal3DFromVector(pos), toInt3DFromVector(imageBox))
def __init__(self, system, nodeGrid='auto', cellGrid='auto', nocheck=False):
if nocheck:
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
if check.System(system, 'bc'):
if nodeGrid == 'auto':
nodeGrid = decomp.nodeGrid(system.comm.rank)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
if cellGrid == 'auto':
raise Exception('Automatic cell size calculation not yet implemented')
else:
cellGrid = toInt3DFromVector(cellGrid)
for k in xrange(3):
if nodeGrid[k]*cellGrid[k] == 1:
print(("Warning! cellGrid[{}] has been "
"adjusted to 2 (was={})".format(k, cellGrid[k])))
cellGrid[k] = 2
self.next_id = 0
self.pmiinit(system, nodeGrid, cellGrid)
else:
raise Exception('Error: could not create DomainDecomposition object')
def __init__(self,
system,
nodeGrid='auto',
neiListx='auto',
neiListy='auto',
neiListz='auto',
nocheck=False):
# do sanity checks for the system first
if nocheck:
self.next_id = 0
self.pmiinit(system, nodeGrid, neiListx, neiListy,
neiListz) # H check
else:
if check.System(system, 'bc'):
if nodeGrid == 'auto':
nodeGrid = decomp.nodeGrid(system.comm.rank)
else:
nodeGrid = toInt3DFromVector(nodeGrid)
#if cellGrid == 'auto':
# cellGrid = Int3D(2,2,2)
#else:
# cellGrid = cellGrid
if neiListx == 'auto':
neiListx = neiListx
else:
neiListx = neiListx
if neiListy == 'auto':
neiListy = neiListy
else:
neiListy = neiListy
if neiListz == 'auto':
neiListz = neiListz
else:
neiListz = neiListz
# minimum image convention check:
self.next_id = 0
self.pmiinit(system, nodeGrid, neiListx, neiListy,
neiListz)
else:
print 'Error: could not create DomainDecomposition object'
def imageBox(self, val):
self.__getTmp().imageBox = toInt3DFromVector(val)
def imageBox(self, val): self.__getTmp().imageBox = toInt3DFromVector(val)
@property
