def __init__(self, dt, mesh, atoms, mixTable, integrator, thermostat = None):
self.dt = dt
self.mesh = mesh
self.ensemble = atoms
self.integrator = integrator
if thermostat is None:
thermostat = thermostats.noThermostat()
self.thermostat = thermostat
self.ensemble.setSimulator(self)
self.ensemble.initialize(mixTable, self.mesh)
self.cwd = os.getcwd()
self.cleanFiles()
self.makeDCVizFile()
if useDCViz:
self.DCVizApp = DCVizThread(join(self.cwd, "DCVizFiles", "MD_out0.dat"), True, False, delay = 0.1)
signal.signal(signal.SIGINT, self.signal_handler)
self.stopped = False
class MDApp():
regions = []
fields = []
def __init__(self, dt, mesh, atoms, mixTable, integrator, thermostat = None):
self.dt = dt
self.mesh = mesh
self.ensemble = atoms
self.integrator = integrator
if thermostat is None:
thermostat = thermostats.noThermostat()
self.thermostat = thermostat
self.ensemble.setSimulator(self)
self.ensemble.initialize(mixTable, self.mesh)
self.cwd = os.getcwd()
self.cleanFiles()
self.makeDCVizFile()
if useDCViz:
self.DCVizApp = DCVizThread(join(self.cwd, "DCVizFiles", "MD_out0.dat"), True, False, delay = 0.1)
signal.signal(signal.SIGINT, self.signal_handler)
self.stopped = False
def addField(self, field, region):
#Make sure not to perform more than necessary tests if several fields share a region
if region not in self.regions:
self.regions.append(region)
else:
region = self.regions[self.regions.index(region)]
field.addRegion(region)
self.fields.append(field)
def cleanFiles(self):
os.chdir(join(self.cwd, "DCVizFiles"))
files = glob.glob("MD_out*.dat")
for _file in [join(self.cwd, "DCVizFiles", __file) for __file in files]:
os.remove(_file)
os.chdir(self.cwd)
def updateFields(self):
for region in self.regions:
region.reset()
for atom in self.ensemble.atoms:
for region in self.regions:
region.append(atom)
for field in self.fields:
field.update()
print field
def run(self, T):
n = int(T/self.dt)
self.thermalize()
if useDCViz:
self.DCVizApp.start()
i = 0
while i < n and not self.stopped:
self.integrator.updateAtoms(self.ensemble)
# self.ensemble.getKineticEnergy()
# self.ensemble.checkLinearMomentum()
# self.ensemble.getTemperature()
# self.ensemble.getPressure()
self.updateFields()
self.makeDCVizFile(i)
print "%d%%" % int((i+1.) / n * 100)
i += 1
self.clean()
def thermalize(self):
Tnew = self.ensemble.thermalizer.bathT
T = 0
while abs(T - Tnew)/Tnew > 1E-4:
self.integrator.updateAtoms(self.ensemble)
T = Tnew
Tnew = self.ensemble.thermalize()
print Tnew, self.ensemble.thermalizer.bathT
def clean(self):
if useDCViz:
self.DCVizApp.stop()
def makeDCVizFile(self, i=0):
out = "%g %g %g\n%s\n" % (tuple(self.mesh.shape) + (self.ensemble.T,) + (str([obj.T for obj in self.fields if obj._type == "thermostat"]),))
for atom in self.ensemble.atoms:
if atom.sticky:
out += "%d %g %g %g %g\n" % (self.ensemble.getColor(atom), atom.pos[0], atom.pos[1], 0, 0)
else:
out += "%d %g %g %g %g\n" % (self.ensemble.getColor(atom), atom.pos[0], atom.pos[1], atom.vel[0], atom.vel[1])
with open(join(self.cwd, "DCVizFiles", "MD_out%d.dat" % i), "w") as f:
f.write(out)
def signal_handler(self, signal, frame):
self.stopped = True
self.clean()