def __init__(self, system, center=[]):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_TDforce, system)
# set center of TD force
if (center != []):
self.cxxclass.setCenter(self, center[0], center[1], center[2])
def __init__(self, system, cutoff, angular_momentum=6,
do_cluster_analysis=False, include_surface_particles=False,
ql_low=-1.0, ql_high=1.0):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_OrderParameter, system, cutoff, angular_momentum,
do_cluster_analysis, include_surface_particles,
ql_low, ql_high)
def __init__(self):
'Local Version object'
if pmi._PMIComm and pmi._PMIComm.isActive():
if pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, _espresso.Version)
else :
pass
else :
cxxinit(self, _espresso.Version)
def __init__(self):
'Local construction of a System'
if pmi._PMIComm and pmi._PMIComm.isActive():
if pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, _espresso.System, pmi._PMIComm.getMPIsubcomm())
else :
pass
else :
cxxinit(self, _espresso.System, pmi._MPIcomm)
def __init__(self, system, cutoff, exclusionlist=[]):
'Local construction of a verlet list'
if pmi.workerIsActive():
if (exclusionlist == []):
# rebuild list in constructor
cxxinit(self, _espresso.VerletList, system, cutoff, True)
else:
# do not rebuild list in constructor
cxxinit(self, _espresso.VerletList, system, cutoff, False)
# add exclusions
for pair in exclusionlist:
pid1, pid2 = pair
self.cxxclass.exclude(self, pid1, pid2)
# now rebuild list with exclusions
self.cxxclass.rebuild(self)
def __init__(self, system, cutoff, exclusionlist=[]):
'Local construction of a verlet triple list'
if pmi.workerIsActive():
'''
cxxinit(self, _espresso.VerletListTriple, system, cutoff, True)
if (exclusionlist != []):
print 'Warning! Exclusion list is not yet implemented to the triple verlet \
list. Nothing happend to exclusion list'
'''
if (exclusionlist == []):
# rebuild list in constructor
cxxinit(self, _espresso.VerletListTriple, system, cutoff, True)
else:
# do not rebuild list in constructor
cxxinit(self, _espresso.VerletListTriple, system, cutoff, False)
# add exclusions
for pid in exclusionlist:
self.cxxclass.exclude(self, pid)
# now rebuild list with exclusions
self.cxxclass.rebuild(self)
def __init__(self, system, cutoff, adrcut, dEx, dHy, adrCenter=[], pids=[], exclusionlist=[]):
'Local construction of a verlet list for AdResS'
if pmi.workerIsActive():
cxxinit(self, _espresso.VerletListAdress, system, cutoff, adrcut, False, dEx, dHy)
#self.cxxclass.setAtType(self, atType)
# check for exclusions
if (exclusionlist != []):
# add exclusions
for pair in exclusionlist:
pid1, pid2 = pair
self.cxxclass.exclude(self, pid1, pid2)
# add adress particles
if (pids != []):
for pid in pids:
self.cxxclass.addAdrParticle(self, pid)
# set adress center
if (adrCenter != []):
self.cxxclass.setAdrCenter(self, adrCenter[0], adrCenter[1], adrCenter[2])
# rebuild list now
self.cxxclass.rebuild(self)
def __init__(self, system, latticeboltzmann):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_LBInit_ConstForce, system, latticeboltzmann)
def __init__(self, system, nodeGrid, cellGrid):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, storage_DomainDecompositionNonBlocking, system, nodeGrid, cellGrid)
def __init__(self, system, chainlength=None):
if chainlength is None:
cxxinit(self, analysis_MeanSquareDispl, system)
else:
cxxinit(self, analysis_MeanSquareDispl, system, chainlength)
def __init__(self, _system, _verletlist, _fixedtuplelist, KTI = False):
'Local construction of a verlet list for AdResS'
if pmi.workerIsActive():
cxxinit(self, integrator_Adress, _system, _verletlist, _fixedtuplelist, KTI)
def __init__(self, system, dampingmass):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_VelocityVerletOnRadius, system, dampingmass)
def __init__(self, storage):
if pmi.workerIsActive():
cxxinit(self, _espresso.ParticleGroup, storage)
def __init__(self, system, latticeboltzmann):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_LBOutput_Screen, system, latticeboltzmann)
def __init__(self, storage, fixedtupleList):
'Local construction of a fixed pair list'
if pmi.workerIsActive():
cxxinit(self, _espresso.FixedPairListAdress, storage, fixedtupleList)
def __init__(self, system, radius):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_NeighborFluctuation, system, radius)
def __init__(self, system):
cxxinit(self, analysis_Velocities, system)
def __init__(self, system, group):
cxxinit(self, integrator_VelocityVerletOnGroup, system, group)
def __init__(self, system):
cxxinit(self, analysis_Configurations, system)
def __init__(self, system):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_ParticleRadiusDistribution, system)
def __init__(self, storage, integrator, mO=16.0, mH=1.0, distHH=1.58, distOH=1.0):
'Local construction of a settle class'
if pmi.workerIsActive():
cxxinit(self, _espresso.Settle, storage, integrator, mO, mH, distHH, distOH)
def __init__(self, system, integrator, filename='out.xyz', unfolded=False, length_factor=1.0, length_unit='LJ', append=True): cxxinit(self, io_DumpXYZ, system, integrator, filename, unfolded, length_factor, length_unit, append)
def __init__(self, system, Ni, a=1.0, tau=1.0, numDims=3, numVels=19):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_LatticeBoltzmann, system, Ni, a, tau, numDims, numVels)
def __init__(self, system): cxxinit(self, analysis_XPressure, system)
def __init__(self, system, capForce, particleGroup = None):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
if (particleGroup == None) or (particleGroup.size() == 0):
cxxinit(self, integrator_CapForce, system, capForce)
else:
cxxinit(self, integrator_CapForce, system, capForce, particleGroup)
def __init__(self, system):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_LangevinThermostat1D, system)
def __init__(self, storage):
"Local construction of a fixed triple list"
if pmi.workerIsActive():
cxxinit(self, _espresso.FixedTripleList, storage)
def __init__(self, system, n, dh):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_PressureTensorMultiLayer, system, n, dh)
def __init__(self, system, particleGroup, fixMask):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, integrator_FixPositions, system, particleGroup, fixMask)
def __init__(self, system):
if not pmi._PMIComm or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, analysis_MaxPID, system)