def scaleVolume(self, *args):
'scale the Volume of the system, which means in detail: scale all particle coordinates, scale box length, scale cellgrid (if it exists)'
if pmi.workerIsActive():
if len(args) == 1:
arg0 = args[0]
if isinstance(arg0, Real3D):
#print arg0," is a Real3D object"
self.cxxclass.scaleVolume( arg0 )
elif hasattr(arg0, '__iter__'):
if len(arg0) == 3:
#print args, " has iterator and length 3"
self.cxxclass.scaleVolume(self, toReal3DFromVector(arg0) )
elif len(arg0) == 1:
#print args, " has iterator and length 1"
self.cxxclass.scaleVolume(self, toReal3DFromVector(arg0[0], arg0[0], arg0[0]) )
else:
print args, " is invalid"
else:
#print args, " is scalar"
self.cxxclass.scaleVolume(self, toReal3DFromVector( [arg0, arg0, arg0] ) )
elif len(args) == 3:
#print args, " is 3 numbers"
self.cxxclass.scaleVolume(self, toReal3DFromVector(*args) )
else:
print args, " is invalid"
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 computeForce(self, *args):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
if len(args) == 1:
arg0 = args[0]
if isinstance(arg0, float) or isinstance(arg0, int):
newargs = [arg0, 0, 0]
return self.cxxclass.computeForce(self, toReal3DFromVector(*newargs))[0]
return self.cxxclass.computeForce(self, toReal3DFromVector(*args))
def computeForce(self, *args):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
if len(args) == 1: # in case theta is passed
arg0 = args[0]
if isinstance(arg0, float) or isinstance(arg0, int):
return self.cxxclass.computeForce(self, arg0)
return self.cxxclass.computeForce(self, toReal3DFromVector(*args))
def getMinimumImageVector(self, pos1, pos2):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup() or pmi.isController:
return self.cxxclass.getMinimumImageVector(
self, toReal3DFromVector(pos1), toReal3DFromVector(pos2))
def pos(self, val): self.__getTmp().pos = toReal3DFromVector(val) @property
def v(self, val): self.__getTmp().v = toReal3DFromVector(val)
@property
def addParticles(self, particleList, *properties):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
index_id = -1
index_pos = -1
index_v = -1
index_f = -1
index_q = -1
index_radius = -1
index_fradius = -1
index_vradius = -1
index_type = -1
index_mass = -1
index_adrAT = -1 # adress AT particle if 1
index_lambda_adr = -1
index_lambda_adrd = -1
last_pos = toReal3DFromVector([-99,-99,-99])
if properties == None:
# default properities = (id, pos)
index_id = 0
index_pos = 1
nindex = 2
else:
nindex = 0
for val in properties:
if val.lower() == "id": index_id = nindex
elif val.lower() == "pos": index_pos = nindex
elif val.lower() == "type": index_type = nindex
elif val.lower() == "mass": index_mass = nindex
elif val.lower() == "v": index_v = nindex
elif val.lower() == "f": index_f = nindex
elif val.lower() == "q": index_q = nindex
elif val.lower() == "radius": index_radius = nindex
elif val.lower() == "fradius": index_fradius = nindex
elif val.lower() == "vradius": index_vradius = nindex
elif val.lower() == "adrat": index_adrAT = nindex
elif val.lower() == "lambda_adr": index_lambda_adr = nindex
elif val.lower() == "lambda_adrd": index_lambda_adrd = nindex
else: raise SyntaxError("unknown particle property: %s"%val)
nindex += 1
if index_id < 0 : raise "particle property id is mandatory"
if index_pos < 0 : raise "particle property pos is mandatory"
# we should check at the begin whether all the particles do not exist.
doWeAddParticles = True
for particle in particleList:
pid = particle[index_id]
if( self.particleExists(pid) ):
doWeAddParticles = False
print "WARNING: Particle ", pid, " already exists"
if(not doWeAddParticles):
print 'WARNING: Some particles already exist. The list of particles was not added.'
return
for particle in particleList:
# verify that each particle has enough entries, avoids index errors
if len(particle) != nindex:
raise SyntaxError("particle has %d entries, but %d expected"%(len(particle), nindex))
id = particle[index_id]
pos = particle[index_pos]
if index_adrAT >= 0:
if particle[index_adrAT] == 0:
#print "%d: addParticle %d, last_pos=pos %f, %f, %f"%(pmi._MPIcomm.rank,id,pos[0], pos[1], pos[2])
storedParticle = self.cxxclass.addParticle(self, id, pos)
last_pos = pos
else:
#print "%d: addAdrATparticle %d, pos %f, %f, %f, last_pos %f, %f, %f"%(pmi._MPIcomm.rank,id,pos[0],pos[1],pos[2],last_pos[0], last_pos[1], last_pos[2])
storedParticle = self.cxxclass.addAdrATParticle(self, id, pos, last_pos)
else:
#print "%d: addParticle %d, last_pos=pos %f, %f, %f"%(pmi._MPIcomm.rank,id,pos[0], pos[1], pos[2])
storedParticle = self.cxxclass.addParticle(self, id, pos)
if storedParticle != None:
self.logger.debug("Processor %d stores particle id = %d"%(pmi.rank, id))
self.logger.debug("particle property indexes: id=%i pos=%i type=%i mass=%i v=%i f=%i q=%i radius=%i lambda_adr=%i lambda_adrd=%i"%(index_id,index_pos,index_type,index_mass,index_v,index_f,index_q,index_radius,index_lambda_adr,index_lambda_adrd))
# only the owner processor writes other properties
if index_v >= 0:
storedParticle.v = particle[index_v]
if index_f >= 0:
storedParticle.f = particle[index_f]
if index_q >= 0:
storedParticle.q = particle[index_q]
if index_radius >= 0:
storedParticle.radius = particle[index_radius]
if index_fradius >= 0:
storedParticle.fradius = particle[index_fradius]
if index_vradius >= 0:
storedParticle.vradius = particle[index_vradius]
if index_type >= 0:
storedParticle.type = particle[index_type]
if index_mass >= 0:
storedParticle.mass = particle[index_mass]
if index_lambda_adr >= 0:
storedParticle.lambda_adr = particle[index_lambda_adr]
if index_lambda_adrd >= 0:
storedParticle.lambda_adrd = particle[index_lambda_adrd]
def addAdrATParticle(self, pid, *args):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.addAdrATParticle(
self, pid, toReal3DFromVector(*args)
)
