def __init__(self,basedir=".",mode="initial",cores=-1):
self.basedir = basedir
self.mode = mode
self.lastAcceptedPath = "start"
if cores == -1:
self.cores = multiprocessing.cpu_count()
else:
self.cores = cores
self.wrapper = wrappers.gromacswrapper()
self.distparser = parser.gdistparser()
self.filesystem = filesystem.filesystem()
self.interfaces = interfaces.interfaces()
self.stablestates = stablestates.stablestates()
self.helper = helpers.helpers()
#Initialize the logger
self.log = gtpslogging.log("debug",basedir)
self.log.log.debug("logfile created")
self.log.log.info(str(self.cores) + " CPUs detected")
#read the stables states from a file
self.stablestates.readStates(os.path.join(basedir,"stablestates.txt"))
self.log.log.info("Read States : " + str(self.stablestates.states))
"""
This array holds all the information about the paths. Each trajectory consists of a
forward-part and a backward-part. The trajectory can either be a forward trajectory
or a backward trajectory. Forward trajectroies start in A.
"""
self.paths = []
self.paths.append(pathsimulation.pathdata(0,basedir,mode,forward=True,forwardpart=True))
self.paths.append(pathsimulation.pathdata(0,basedir,mode,forward=True,forwardpart=False))
def __init__(self,basedir=".",mode="initial",kernel=0):
self.basedir = basedir
self.mode = mode
self.cores = multiprocessing.cpu_count()
self.wrapper = wrappers.gromacswrapper()
self.distparser = parser.gdistparser()
self.filesystem = filesystem.filesystem()
self.helper = helpers.helpers()
self.kernels = kernels.kernels(kernel)
self.qsubsystem = qsubsystem.qsubsystem()
#Initialize the logger
if kernel=="head":
self.log = gtpslogging.log("info",basedir,kernel)
else:
self.log = gtpslogging.log("debug",basedir,kernel)
self.log.log.debug("logfile created")
self.log.log.info(str(self.cores) + " CPUs detected")
self.kernels.readKernelOptions(os.path.join(basedir,"options","kerneloptions.txt"))
#read the stables states from a file
self.stablestates.readStates(os.path.join(basedir,"options","stablestates.txt"))
self.log.log.info("Read States : " + str(self.stablestates.states))
"""
This array holds all the information about the paths. Each trajectory consists of a
forward-part and a backward-part. The trajectory can either be a forward trajectory
or a backward trajectory. Forward trajectroies start in A.
"""
self.paths = []
self.npaths = 0
for i in range(self.kernels.ntps):
self.paths.append(pathdata.pathdata(i,basedir,mode,forward=True,forwardpart=True,interface=0))
self.paths.append(pathdata.pathdata(i,basedir,mode,forward=True,forwardpart=False,interface=0))
self.npaths += 1
self.kernels.generateKernelLists(self.npaths)
def __init__(self,basedir=".",mode="initial",kernel=0):
self.basedir = basedir
self.mode = mode
self.cores = multiprocessing.cpu_count()
self.wrapper = wrappers.gromacswrapper()
self.distparser = parser.gdistparser()
self.filesystem = filesystem.filesystem()
self.interfaces = interfaces.interfaces()
self.orderparameters = orderparameters.orderparameters()
self.helper = helpers.helpers()
self.kernels = kernels.kernels(kernel)
self.qsubsystem = qsubsystem.qsubsystem()
#Initialize the logger
if kernel=="head":
self.log = gtpslogging.log("info",basedir,kernel)
elif kernel=="reverse":
self.log = gtpslogging.log("info",basedir,kernel)
else:
self.log = gtpslogging.log("info",basedir,kernel)
self.log.log.debug("logfile created")
self.log.log.info(str(self.cores) + " CPUs detected")
self.interfaces.readInterfaces(os.path.join(basedir,"options","interfaces.txt"))
self.log.log.info("Read Interfaces Forward : " + str(self.interfaces.interfaces[0]))
self.log.log.info("Read Interfaces Backward : " + str(self.interfaces.interfaces[1]))
self.kernels.readKernelOptions(os.path.join(basedir,"options","kerneloptions.txt"))
#read the stables states from a file
self.orderparameters.readOP(os.path.join(basedir,"options","orderparameters.txt"))
self.log.log.info("Read OP : " + str(self.orderparameters.op[0]))
"""
This array holds all the information about the paths. Each trajectory consists of a
forward-part and a backward-part. The trajectory can either be a forward trajectory
or a backward trajectory. Forward trajectroies start in A.
"""
self.paths = []
self.npaths = 0
for i in range(self.interfaces.ninterfaces[0]):
self.paths.append(pathdata.pathdata(i,basedir,mode,forward=True,forwardpart=True,interface=self.interfaces.interfaces[0][i]))
self.paths.append(pathdata.pathdata(i,basedir,mode,forward=True,forwardpart=False,interface=self.interfaces.interfaces[0][i]))
self.npaths += 1
for i in range(self.interfaces.ninterfaces[1]):
n = i + self.interfaces.ninterfaces[0]
self.paths.append(pathdata.pathdata(n,basedir,mode,forward=False,forwardpart=True,interface=self.interfaces.interfaces[1][i]))
self.paths.append(pathdata.pathdata(n,basedir,mode,forward=False,forwardpart=False,interface=self.interfaces.interfaces[1][i]))
self.npaths += 1
self.reversePaths = []
for rp in self.interfaces.reversepaths[0]:
self.reversePaths.append(pathdatareverse.pathdatareverse(0, basedir, mode, forward=True, forwardpart=True, interface=rp, state=0))
for rp in self.interfaces.reversepaths[1]:
self.reversePaths.append(pathdatareverse.pathdatareverse(0, basedir, mode, forward=True, forwardpart=True, interface=rp, state=1))
self.kernels.generateKernelLists(self.npaths)
self.interfacedir = int(float(self.paths[0].options.runoptions["interfacecoordinate"]))
print self.interfacedir