def randomVelocity(self, T):
"""
Assign random velocities.
@type T: float
@param T: Kelvin temperature.
"""
TopologyUtilities.randomVelocity(T, self.myTop, self.velvec, self.seed)
def executePropagator(prop, phys, forces, io, numsteps):
"""
Run and finish the propagator.
@type prop: Propagator
@param prop: MDL Propagator object
@type phys: Physical
@param phys: The physical system.
@type forces: Forces
@param forces: MDL Forces object
@type io: IO
@param io: MDL IO object
@type numsteps: int
@param numsteps: Number of steps to run
"""
# RUN
if (prop.myStep == 0 and prop.myLevel == 0):
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.prerunmodifiers, phys, forces,
prop, prop.myPropagator)
ii = 0
#prop.myPropagator.run(numsteps)
#return
while (ii < numsteps):
nextstop = int(
numpy.minimum(numsteps, io.computeNext(ii, phys.remcom,
phys.remang)))
if (prop.isMDL(prop.myPropagator)):
while (ii < nextstop):
prop.myPropagator.run(phys, forces, prop)
ii += 1
phys.myTop.time = prop.myStep * prop.myPropagator.getTimestep(
) * Constants.invTimeFactor()
phys.updateCOM_Momenta()
else:
prop.myPropagator.run(nextstop - ii)
ii = nextstop
if (prop.myLevel == 0):
prop.myStep = nextstop
phys.myTop.time = prop.myStep * prop.myPropagator.getTimestep()
io.run(phys, forces, prop.myStep, prop.myTimestep,
prop.myPropagator)
if (phys.remcom > 0 and ii % phys.remcom == 0):
TopologyUtilities.remLin(phys.velvec, phys.myTop)
if (phys.remang > 0 and ii % phys.remang >= 0):
TopologyUtilities.remAng(phys.posvec, phys.velvec, phys.myTop)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.postrunmodifiers, phys, forces,
prop, prop.myPropagator)
prop.myPropagator.finish(phys, forces, prop)
def executePropagator(prop, phys, forces, io, numsteps):
"""
Run and finish the propagator.
@type prop: Propagator
@param prop: MDL Propagator object
@type phys: Physical
@param phys: The physical system.
@type forces: Forces
@param forces: MDL Forces object
@type numsteps: int
@param numsteps: Number of steps to run
"""
# RUN
if (prop.myStep == 0 and prop.myLevel == 0):
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.prerunmodifiers, phys, forces,
prop, prop.myPropagator)
ii = 0
while (ii < numsteps):
if (io.pmvMODE == 0): # STOP CODE
return
elif (io.pmvMODE != 2): # RUN CODE
if (prop.isMDL(prop.myPropagator)):
prop.myPropagator.run(phys, forces, prop)
phys.myTop.time = prop.myStep * prop.myPropagator.getTimestep(
) * Constants.invTimeFactor()
phys.updateCOM_Momenta()
else:
prop.myPropagator.run(1)
if (io.doPmv):
io.pmvPlot()
ii = ii + 1
if (prop.myLevel == 0):
prop.myStep += 1
phys.myTop.time = prop.myStep * prop.myPropagator.getTimestep()
io.run(phys, forces, prop.myStep, prop.myTimestep,
prop.myPropagator)
if (phys.remcom >= 0):
TopologyUtilities.removeLinearMomentum(phys.velvec,
phys.myTop).disown()
if (phys.remang >= 0):
TopologyUtilities.removeAngularMomentum(
phys.posvec, phys.velvec, phys.myTop).disown()
else: # PAUSE CODE
io.pmvPlot()
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.postrunmodifiers, phys, forces,
prop, prop.myPropagator)
prop.myPropagator.finish(phys, forces, prop)
def pressure(self, forces):
"""
Pressure of the system.
@type forces: Forces
@param forces: MDL Forces object
@rtype: float
@return: System pressure
"""
TopologyUtilities.addVelocityVirial(forces.energies, self.myTop, self.velvec)
return TopologyUtilities.velocityVirial(self.myTop, self.velvec).pressure(self.myTop.getVolume(self.posvec))
def executePropagator(prop, phys, forces, io, numsteps):
"""
Run and finish the propagator.
@type prop: Propagator
@param prop: MDL Propagator object
@type phys: Physical
@param phys: The physical system.
@type forces: Forces
@param forces: MDL Forces object
@type io: IO
@param io: MDL IO object
@type numsteps: int
@param numsteps: Number of steps to run
"""
# RUN
if (prop.myStep == 0 and prop.myLevel == 0):
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.prerunmodifiers, phys, forces, prop, prop.myPropagator)
ii = 0
#prop.myPropagator.run(numsteps)
#return
while (ii < numsteps):
nextstop = int(numpy.minimum(numsteps, io.computeNext(ii, phys.remcom, phys.remang)))
if (prop.isMDL(prop.myPropagator)):
while (ii < nextstop):
prop.myPropagator.run(phys, forces, prop)
ii += 1
phys.myTop.time = prop.myStep*prop.myPropagator.getTimestep()*Constants.invTimeFactor()
phys.updateCOM_Momenta()
else:
prop.myPropagator.run(nextstop-ii)
ii = nextstop
if (prop.myLevel == 0):
prop.myStep = nextstop
phys.myTop.time = prop.myStep*prop.myPropagator.getTimestep()
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (phys.remcom > 0 and ii % phys.remcom == 0):
TopologyUtilities.remLin(phys.velvec, phys.myTop)
if (phys.remang > 0 and ii % phys.remang >= 0):
TopologyUtilities.remAng(phys.posvec, phys.velvec, phys.myTop)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.postrunmodifiers, phys, forces, prop, prop.myPropagator)
prop.myPropagator.finish(phys, forces, prop)
def executePropagator(prop, phys, forces, io, numsteps):
"""
Run and finish the propagator.
@type prop: Propagator
@param prop: MDL Propagator object
@type phys: Physical
@param phys: The physical system.
@type forces: Forces
@param forces: MDL Forces object
@type numsteps: int
@param numsteps: Number of steps to run
"""
# RUN
if (prop.myStep == 0 and prop.myLevel == 0):
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.prerunmodifiers, phys, forces, prop, prop.myPropagator)
ii = 0
while (ii < numsteps):
if (io.pmvMODE == 0): # STOP CODE
return
elif (io.pmvMODE != 2): # RUN CODE
if (prop.isMDL(prop.myPropagator)):
prop.myPropagator.run(phys, forces, prop)
phys.myTop.time = prop.myStep*prop.myPropagator.getTimestep()*Constants.invTimeFactor()
phys.updateCOM_Momenta()
else:
prop.myPropagator.run(1)
if (io.doPmv):
io.pmvPlot()
ii = ii + 1
if (prop.myLevel == 0):
prop.myStep += 1
phys.myTop.time = prop.myStep*prop.myPropagator.getTimestep()
io.run(phys, forces, prop.myStep, prop.myTimestep, prop.myPropagator)
if (phys.remcom >= 0):
TopologyUtilities.removeLinearMomentum(phys.velvec, phys.myTop).disown()
if (phys.remang >= 0):
TopologyUtilities.removeAngularMomentum(phys.posvec, phys.velvec, phys.myTop).disown()
else: # PAUSE CODE
io.pmvPlot()
if (prop.isMDL(prop.myPropagator)):
prop.runModifiers(prop.myPropagator.postrunmodifiers, phys, forces, prop, prop.myPropagator)
prop.myPropagator.finish(phys, forces, prop)
def temperature(self):
"""
System temperature (K)
@rtype: float
@return: Kelvin temperature
"""
return TopologyUtilities.temperature(self.myTop, self.velvec)
def kineticEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Kinetic energy, as a sum of 0.5*m*v^2 for each atom.
"""
return TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def kineticEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Kinetic energy, as a sum of 0.5*m*v^2 for each atom.
"""
return TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def totalEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Total energy, as a sum of potential and kinetic.
"""
# potentialEnergy() is a member function of ScalarStructure
return phys.app.energies.potentialEnergy()+TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def totalEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Total energy, as a sum of potential and kinetic.
"""
# potentialEnergy() is a member function of ScalarStructure
return phys.app.energies.potentialEnergy(
) + TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def plotTotal(self, phys, forces, step):
"""
Similar, for total energy
@type phys: Physical
@param phys: The physical system
@type forces: Forces
@param forces: MDL Forces object
@type step: int
@param step: Simulation step number
"""
self.plotQuantity(step, forces.energies.potentialEnergy(phys)+TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec), 'totalenergy')
def plotTemperature(self, phys, forces, step):
"""
Similar, for temperature
@type phys: Physical
@param phys: The physical system
@type forces: Forces
@param forces: MDL Forces object
@type step: int
@param step: Simulation step number
"""
self.plotQuantity(step,
TopologyUtilities.temperature(phys.myTop, phys.velvec), 'temperature')
def dihedral(self, index):
"""
Dihedral angle (rad, -PI to PI) at passed index
@type index: int
@param index: Dihedral index
@rtype: float
@return: Dihedral angle in radians
"""
myPhi = TopologyUtilities.computePhiDihedral(self.myTop, self.posvec, index-1)
if (myPhi > numpy.pi):
myPhi -= 2*numpy.pi
elif (myPhi < -numpy.pi):
myPhi += 2*numpy.pi
return myPhi
def build(self):
"""
Build the physical data.
"""
tm = -1
if (hasattr(self, "myTop")):
tm = self.myTop.time
if (self.bc == "Periodic"):
if (self.defaultCBV):
# TEMPORARY STRUCTURES USED TO COMPUTE
# BOUNDING BOX
v1 = numpy.ndarray(3)
v2 = numpy.ndarray(3)
v3 = numpy.ndarray(3)
v4 = numpy.ndarray(3)
v1.fill(sys.maxint)
v2.fill(-sys.maxint)
# BOUNDING BOX
i = 0
while (i < numpy.size(self.positions)):
if (self.positions[i] < v1[0]):
v1[0] = float(self.positions[i])
if (self.positions[i] > v2[0]):
v2[0] = float(self.positions[i])
if (self.positions[i+1] < v1[1]):
v1[1] = float(self.positions[i+1])
if (self.positions[i+1] > v2[1]):
v2[1] = float(self.positions[i+1])
if (self.positions[i+2] < v1[2]):
v1[2] = float(self.positions[i+2])
if (self.positions[i+2] > v2[2]):
v2[2] = float(self.positions[i+2])
i += 3
v4.fill(Constants.periodicBoundaryTolerance()/2.0)
v1 = v1 - v4
v2 = v2 + v4
v3 = v2 - v1
self.cB1[0] = v3[0]
self.cB2[1] = v3[1]
self.cB3[2] = v3[2]
self.cO = v1 + v3 * 0.5
self.myTop.setBC(self.cB1[0],self.cB1[1],self.cB1[2],self.cB2[0],self.cB2[1],self.cB2[2],self.cB3[0],self.cB3[1],self.cB3[2],self.cO[0],self.cO[1],self.cO[2])
self.myTop.setExclusion(self.exclude)
if (self.myPSF.numAtoms() > 0 and hasattr(self.myPAR, 'readFlag')):
GenericTopology.buildTopology(self.myTop, self.myPSF, self.myPAR, 0, self.myTop.makeSCPISM())
if (numpy.size(self.velocities) == 0):
# This function actually returns a value, since it is
# unused the runtime environment detects a memory leak.
# disown() removes this concern.
MathUtilities.randomNumber(self.seed)
# NOTE TO SELF: THIS WAS COMMENTED OUT FOR PM 3
# IT MAY EFFECT RANDOM NUMBER CONSISTENCY
#aaa = MathUtilities.randomNumberFirst(self.seed, 1)
TopologyUtilities.randomVelocity(self.temperature, self.myTop, self.velvec, self.seed)
if (self.remcom >= 0):
TopologyUtilities.removeLinearMomentum(self.velvec, self.myTop).disown()
if (self.remang >= 0):
TopologyUtilities.removeAngularMomentum(self.posvec, self.velvec, self.myTop).disown()
if (self.bc == "Periodic"):
self.myTop.setCellSize(self.cellsize)
# COMPUTE INV MASS MATRIX
temp = list()
ii = 0
while ii < self.numAtoms()*3:
temp.append(0.0)
ii += 1
ii = 0
self.invmasses.resize(self.numAtoms()*3)
while ii < self.numAtoms()*3:
im = 1.0 / self.myPSF.getMass(ii/3)
self.invmasses[ii] = im
self.invmasses[ii+1] = im
self.invmasses[ii+2] = im
ii += 3
# COMPUTE MASS MATRIX
temp = list()
ii = 0
while ii < self.numAtoms()*3:
temp.append(0.0)
ii += 1
ii = 0
self.masses.resize(self.numAtoms()*3)
while ii < self.numAtoms()*3:
m = self.myPSF.getMass(ii/3)
temp[ii] = m
self.masses[ii] = temp[ii]
temp[ii] = 0.0
temp[ii+1] = m
self.masses[ii+1] = temp[ii+1]
temp[ii+1] = 0.0
temp[ii+2] = m
self.masses[ii+2] = temp[ii+2]
temp[ii+2] = 0.0
ii += 3
# COMPUTE MASS SUM
self.masssum = 0
ii = 0
while ii < self.numAtoms():
self.masssum += self.myPSF.getMass(ii)
ii += 1
# SET SELFICAL TIME
if (tm != -1):
self.myTop.time = tm
self.dirty = 0 # clean now!
def updateCOM_Momenta(self):
"""
Update center of mass and angular momentum
"""
TopologyUtilities.buildMolecularCenterOfMass(self.posvec,self.myTop)
TopologyUtilities.buildMolecularMomentum(self.velvec,self.myTop)
