def read_simulation(NEB, step_to_use, i, state):
'''
This function will read in the forces of atoms from a lammps simulation.
Further, it only reads in the forces associated with the benzene atoms.
**Parameters**
NEB: :class:`NEB`
An NEB container holding the main NEB simulation
step_to_use: *int*
Which iteration in the NEB sequence the output to be read in is on.
i: *int*
The index corresponding to which image on the frame is to be
simulated.
state: *list,* :class:`structures.Atom`
A list of atoms describing the image on the frame associated with
index *i*.
**Returns**
new_energy: *float*
The energy of the system in Hartree (Ha).
new_atoms: *list,* :class:`structures.Atom`
A list of atoms with the forces attached in units of Hartree per
Angstrom (Ha/Ang).
'''
new_atoms = lammps_job.read_dump("lammps/solv_box-%d-%d/forces.dump" %
(step_to_use, i),
extras=['fx', 'fy', 'fz'])[0]
for atom in new_atoms:
atom.fx = units.convert("kcal/ang", "Ha/ang", float(atom.extras['fx']))
atom.fy = units.convert("kcal/ang", "Ha/ang", float(atom.extras['fy']))
atom.fz = units.convert("kcal/ang", "Ha/ang", float(atom.extras['fz']))
energy = open("lammps/solv_box-%d-%d/energy.profile" % (step_to_use, i),
'r').read().strip().split("\n")[-1]
new_energy = float(energy.strip().split()[-1].strip())
# Add the forces onto our state
for a, b in zip(state, new_atoms):
a.fx, a.fy, a.fz = b.fx, b.fy, b.fz
return units.convert_energy("kcal/mol", "Ha", new_energy), new_atoms
def f(x):
return units.convert("Ha/Ang", "eV/Ang", x)