[Xplor-nih] error message

[Charles at Schwieters.org]

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Hello Marco--

> 
> Is there an easy way to write the energies during the dynamic e.g. in a csv 
> file? So it would become very easy to make a graph out of them. One of the 
> molecular modelling guys here asked me this also a few days ago.
> 

sure. Place the definition of the PrintEnergyTraj class (below) before
the structure calculation loop. Then at the beginning of structure
calculation (in calcOneStructure in eginput/gb1_rdc/anneal.py)
initialize the ivm object before high-temperature dynamics like

    dyn.setTrajectory( PrintEnergyTraj("energy.out",dyn) )

on each line of energy.out are iteration number, time, potential and
total energy.

best regards--
Charles

class PrintEnergyTraj:
    """a trajectory object to be used with an <m ivm>.IVM object, used to
    print energy during a trajectory run.
    Use the IVM setTrajectory method to assign to view a given ivm
    trajectory.
    """
    def __init__(s,filename,ivm):
        """specify the filename to print energy in. The frequency of update is
        controlled via the saveInterval member (defaults to 1 [every frame]).
        """
        s.saveInterval = 1
        s.file=open(filename,"w")
        s.time=0
        s.ivm=ivm
        return
    def write(s,iter,stepsize):
        if iter%s.saveInterval != 0: return

        s.time += stepsize
        print >>s.file,iter,s.time,s.ivm.Epotential(), s.ivm.Etotal()

        return
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