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()