argument = arg.split("=")
if argument[0] == "basedir":
basedir = argument[1]
elif argument[0] == "mode":
mode = argument[1]
elif argument[0] == "dirnumber":
dirnumber = int(float(argument[1]))
else:
print "argument should be one of those: basedir,mode, startwith,rstartwith,runs"
if basedir !="":
if mode == 'initial':
dirstring = "%07d" % (dirnumber,)
newdirstring = "%07d" % (dirnumber + 1,)
sim = gtis.gromacstis(basedir,"tis",kernel="reverse")
sim.preperationReverse()
sim.shootingQueueReverse()
sim.finalizeReverse(dirstring,newdirstring)
for i in range(len(sim.reversePaths)):
sim.getFullTrajectoryReverse(i, newdirstring)
sim.reversePaths[i].lastAcceptedFullTrajectory = sim.reversePpaths[i].fullTrajectory[:]
sim.outputAllFullTrajectoriesReverse(newdirstring)
sim.deleteScratchFiles()
elif mode == 'tis':
sim = gtis.gromacstis(basedir,"tis",kernel="reverse")
dirstring = "%07d" % (dirnumber,)
newdirstring = "%07d" % (dirnumber + 1,)
argument = arg.split("=")
if argument[0] == "basedir":
basedir = argument[1]
elif argument[0] == "mode":
mode = argument[1]
elif argument[0] == "dirnumber":
dirnumber = int(float(argument[1]))
else:
print "argument should be one of those: basedir,mode, startwith,rstartwith,runs"
if basedir != "":
if mode == 'initial':
dirstring = "%07d" % (dirnumber, )
newdirstring = "%07d" % (dirnumber + 1, )
sim = gtis.gromacstis(basedir, "tis", kernel="reverse")
sim.preperationReverse()
sim.shootingQueueReverse()
sim.finalizeReverse(dirstring, newdirstring)
for i in range(len(sim.reversePaths)):
sim.getFullTrajectoryReverse(i, newdirstring)
sim.reversePaths[
i].lastAcceptedFullTrajectory = sim.reversePpaths[
i].fullTrajectory[:]
sim.outputAllFullTrajectoriesReverse(newdirstring)
sim.deleteScratchFiles()
elif mode == 'tis':
sim = gtis.gromacstis(basedir, "tis", kernel="reverse")
dirstring = "%07d" % (dirnumber, )
if argument[0] == "basedir":
basedir = argument[1]
elif argument[0] == "mode":
mode = argument[1]
elif argument[0] == "startwith":
dirnumber = int(float(argument[1]))
elif argument[0] == "rstartwith":
rdirnumber = int(float(argument[1]))
elif argument[0] == "runs":
runs = int(float(argument[1]))
else:
print "Arguments should be one of those: basedir, mode, startwith, rstartwith, runs"
if basedir != "":
if mode == 'initial':
sim = gtis.gromacstis(basedir, "initial", kernel="head")
for i in range(sim.kernels.nkernels):
pythonpath = sim.paths[0].options.paths["pythonpath"]
mqsubs = sim.paths[0].options.runoptions["qsubsystem"]
mwalltime = sim.paths[0].options.runoptions["qsubwalltime"]
filename = sim.qsubsystem.writeKernelQsubFile(
basedir,
i,
pythonpath,
"initial",
0,
qsubs=mqsubs,
walltime=mwalltime)
if mqsubs == "LL":
for arg in sys.argv[1:]:
argument = arg.split("=")
if argument[0] == "basedir":
basedir = argument[1]
elif argument[0] == "mode":
mode = argument[1]
elif argument[0] == "dirnumber":
dirnumber = int(float(argument[1]))
elif argument[0] == "kernel":
kernel = int(float(argument[1]))
else:
print "argument should be one of those: basedir,mode, startwith,rstartwith,runs"
if basedir != "":
if mode == 'initial':
sim = gtis.gromacstis(basedir,"initial",kernel)
successfull = [False for x in sim.kernels.kernelPaths]
k = 0
while(True):
sim.preperationFromStart()
sim.shootingInitialGroFiles()
sim.shootingQueue()
sim.checkAllTisPathsAccepted()
sim.finalizeInitial()
for i in range(len(sim.kernels.kernelPaths)):
if sim.paths[i].tisaccepted:
successfull[i] = True
print k, successfull
if all(successfull):
break
'''
Created on May 3, 2010
@author: Wolfgang Lechner
'''
import pygromacstps.tis as gtis
import sys
if __name__ == '__main__':
if len(sys.argv) == 1:
print 'excepted parameters are "initial" and "tis"'
else:
if sys.argv[1] == 'initial':
sim = gtis.gromacstis("/home/cpd/wolf/membranes/firsttis",
"initial")
sim.preperationFromStart()
sim.reverseBackwardGroFile()
for i in range(10):
sim.shootingGroFile()
sim.shootingQueue()
sim.finalizeShooting("%07d" % i)
elif sys.argv[1] == 'tis':
sim = gtis.gromacstis("/home/cpd/wolf/membranes/firsttis", "tis")
sim.getStartTrajectories()
#sim.trialReplicaExchange("0000000")
sim.preperationTIS()
sim.lastAcceptedToGro("start")
sim.pickConfigurationsTIS("start")
sim.shootingQueue()
'''
Created on May 3, 2010
@author: Wolfgang Lechner
'''
import pygromacstps.tis as gtis
import sys
if __name__ == '__main__':
if len(sys.argv) == 1:
print 'excepted parameters are "initial" and "tis"'
else:
if sys.argv[1] == 'initial':
sim = gtis.gromacstis("/home/cpd/wolf/membranes/firsttis","initial")
sim.preperationFromStart()
sim.reverseBackwardGroFile()
for i in range(10):
sim.shootingGroFile()
sim.shootingQueue()
sim.finalizeShooting("%07d" % i)
elif sys.argv[1] == 'tis':
sim = gtis.gromacstis("/home/cpd/wolf/membranes/firsttis","tis")
sim.getStartTrajectories()
#sim.trialReplicaExchange("0000000")
sim.preperationTIS()
sim.lastAcceptedToGro("start")
sim.pickConfigurationsTIS("start")
sim.shootingQueue()
sim.checkAllTisPathsAccepted()