[DFTB-Plus-User] Increasing the distance between two atoms

[Timothy Kennedy]

Hi all,

I'm currently trying to replicate the results of a study in which they
simulated mechanical tensile force by moving two atoms apart in a molecule.
I'm not entirely sure what the best way to achieve this is using DFTB+. I'm
currently using this function in an attempt to increase the size of the
simulation box (the code was originally from my professor):

# Setup NPT dynamics
myNPT = NPT(
    atoms=atoms,
    timestep=0.1 * units.fs,
    externalstress=0,
    ttime=100 * 0.1 * units.fs,
    pfactor=1,
    temperature_K=300,
    mask=(0,0,0),
    logfile='mylog',
    trajectory='mytraj',
    append_trajectory=False,
    loginterval=1
)

# Define the strain rate
strain_rate = np.array([[.0001 / units.fs, 0, 0], [0, 0, 0], [0, 0, 0]])  #
strain x for Strauss unit cell
myNPT.set_strain_rate(strain_rate)

I'm not getting very useful results and I'm unsure what the problem is. I
can share my entire program if anybody would like to see it. Any help is
appreciated!
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