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 scaleVolume(self, *args):
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 scaleVolume(self, *args):
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 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 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 addParticlesArray(self, particleList, *properties):
if not (pmi._PMIComm and pmi._PMIComm.isActive()
) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
index_id = -1
index_posx = -1 ### Real3D
index_posy = -1
index_posz = -1
index_modeposx = -1 ### Real3D
index_modeposy = -1
index_modeposz = -1
index_vx = -1 ### Real3D
index_vy = -1
index_vz = -1
index_modemomx = -1 ### Real3D
index_modemomy = -1
index_modemomz = -1
index_fx = -1 ### Real3D
index_fy = -1
index_fz = -1
index_fmx = -1 ### Real3D
index_fmy = -1
index_fmz = -1
index_q = -1
index_radius = -1
index_fradius = -1
index_vradius = -1
index_type = -1
index_mass = -1
index_varmass = -1
index_adrAT = -1 # adress AT particle if 1
index_lambda_adr = -1
index_lambda_adrd = -1
index_state = -1
index_pib = -1
last_pos = toReal3DFromVector([-99, -99, -99])
if properties == None:
# default properties = (id, pos)
index_id = 0
index_posx = 1
index_posy = 2
index_posz = 3
nindex = 4
else:
for nindex, val in enumerate(properties):
if val.lower() == "id": index_id = nindex
elif val.lower() == "posx": index_posx = nindex
elif val.lower() == "posy": index_posy = nindex
elif val.lower() == "posz": index_posz = nindex
elif val.lower() == "modeposx": index_modeposx = nindex
elif val.lower() == "modeposy": index_modeposy = nindex
elif val.lower() == "modeposz": index_modeposz = nindex
elif val.lower() == "type": index_type = nindex
elif val.lower() == "mass": index_mass = nindex
elif val.lower() == "varmass": index_varmass = nindex
elif val.lower() == "vx": index_vx = nindex
elif val.lower() == "vy": index_vy = nindex
elif val.lower() == "vz": index_vz = nindex
elif val.lower() == "modemomx": index_modemomx = nindex
elif val.lower() == "modemomy": index_modemomy = nindex
elif val.lower() == "modemomz": index_modemomz = nindex
elif val.lower() == "fx": index_fx = nindex
elif val.lower() == "fy": index_fy = nindex
elif val.lower() == "fz": index_fz = nindex
elif val.lower() == "fmx": index_fmx = nindex
elif val.lower() == "fmy": index_fmy = nindex
elif val.lower() == "fmz": index_fmz = 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
elif val.lower() == "state":
index_state = nindex
elif val.lower() == "pib":
index_pib = nindex
else:
raise SyntaxError("unknown particle property: %s" %
val)
assert index_id >= 0, "particle property id is mandatory"
assert index_posx >= 0, "particle property posx is mandatory"
assert index_posy >= 0, "particle property posy is mandatory"
assert index_posz >= 0, "particle property posz is mandatory"
def check3DProperty(prop, ix, iy, iz):
assert ((ix>=0)==(iy>=0) and (iy>=0)==(iz>=0)), \
"Missing at least one of the 3d coordinates of property \"{}\"".format(prop)
check3DProperty("pos", index_posx, index_posy, index_posz)
check3DProperty("v", index_vx, index_vy, index_vz)
check3DProperty("f", index_fx, index_fy, index_fz)
check3DProperty("fm", index_fmx, index_fmy, index_fmz)
check3DProperty("modepos", index_modeposx, index_modeposy,
index_modeposz)
check3DProperty("modemom", index_modemomx, index_modemomy,
index_modemomz)
indices = np.array([
index_id, index_posx, index_posy, index_posz, index_modeposx,
index_modeposy, index_modeposz, index_vx, index_vy, index_vz,
index_modemomx, index_modemomy, index_modemomz, index_fx,
index_fy, index_fz, index_fmx, index_fmy, index_fmz, index_q,
index_radius, index_fradius, index_vradius, index_type,
index_mass, index_varmass, index_adrAT, index_lambda_adr,
index_lambda_adrd, index_state, index_pib
],
dtype=np.int32)
self.cxxclass.addParticlesFromArray(self, particleList, indices)
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_modepos = -1
index_v = -1
index_modemom = -1
index_f = -1
index_fm = -1
index_q = -1
index_radius = -1
index_fradius = -1
index_vradius = -1
index_type = -1
index_mass = -1
index_varmass = -1
index_adrAT = -1 # adress AT particle if 1
index_lambda_adr = -1
index_lambda_adrd = -1
index_state = -1
index_pib = -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() == "modepos": index_modepos = nindex
elif val.lower() == "type": index_type = nindex
elif val.lower() == "mass": index_mass = nindex
elif val.lower() == "varmass": index_varmass = nindex
elif val.lower() == "v": index_v = nindex
elif val.lower() == "modemom": index_modemom = nindex
elif val.lower() == "f": index_f = nindex
elif val.lower() == "fm": index_fm = 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
elif val.lower() == "state":
index_state = nindex
elif val.lower() == "pib":
index_pib = nindex
else:
raise SyntaxError("unknown particle property: %s" %
val)
nindex += 1
if index_id < 0:
raise Exception("particle property id is mandatory")
if index_pos < 0:
raise Exception("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:
storedParticle = self.cxxclass.addParticle(
self, id, pos, True)
last_pos = pos
else:
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, True)
if storedParticle is not 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 state=%i"
% (index_id, index_pos, index_type, index_mass,
index_v, index_f, index_q, index_radius,
index_lambda_adr, index_lambda_adrd, index_state))
# only the owner processor writes other properties
if index_v >= 0:
storedParticle.v = particle[index_v]
if index_modepos >= 0:
storedParticle.modepos = particle[index_modepos]
if index_modemom >= 0:
storedParticle.modemom = particle[index_modemom]
if index_f >= 0:
storedParticle.f = particle[index_f]
if index_fm >= 0:
storedParticle.fm = particle[index_fm]
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_pib >= 0:
storedParticle.pib = particle[index_pib]
if index_mass >= 0:
storedParticle.mass = particle[index_mass]
if index_varmass >= 0:
storedParticle.varmass = particle[index_varmass]
if index_lambda_adr >= 0:
storedParticle.lambda_adr = particle[index_lambda_adr]
if index_lambda_adrd >= 0:
storedParticle.lambda_adrd = particle[
index_lambda_adrd]
if index_state >= 0:
storedParticle.state = particle[index_state]
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))
def f(self, val):
self.__getTmp().f = toReal3DFromVector(val)
def pos(self, val):
self.__getTmp().pos = toReal3DFromVector(val)
def v(self, val):
self.__getTmp().v = toReal3DFromVector(val)
def pos(self, val): self.__getTmp().pos = 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
index_state = -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
elif val.lower() == "state": index_state = 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 state=%i"%(index_id,index_pos,index_type,index_mass,index_v,index_f,index_q,index_radius,index_lambda_adr,index_lambda_adrd,index_state))
# 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]
if index_state >= 0:
storedParticle.state = particle[index_state]
def f(self, val): self.__getTmp().f = toReal3DFromVector(val)
@property
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 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 modemom(self, val):
self.__getTmp().modemom = toReal3DFromVector(val)
def computeForce(self, position, bc):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.computeForce(self, toReal3DFromVector(position), bc)
def computeForce(self, position, bc):
if not (pmi._PMIComm and pmi._PMIComm.isActive()
) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.computeForce(self,
toReal3DFromVector(position), bc)
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)
)
