def ecut_convergence_study(ecuts=range(10, 40, 5)):
"""
H2 molecule in a big box
Generate a flow to compute the total energy and forces as a function of the interatomic distance
"""
inputs = []
for ecut in ecuts:
inputs += h2_h_input(ecut=ecut)
flow = flowtk.Flow.from_inputs("flow_h2h_ecut", inputs)
flow.make_scheduler().start()
import matplotlib.pyplot as plt
import pandas as pd
with abilab.abirobot(flow, "GSR") as robot:
frame = robot.get_dataframe()
frame = frame[["formula", "ecut", "energy"]]
print(frame)
grouped = frame.groupby("ecut")
rows = []
for ecut, group in grouped:
group = group.set_index("formula")
atomization = 2 * group["energy"]["H1"] - group["energy"]["H2"]
atomization = abilab.Energy(atomization, "eV").to("Ha")
rows.append(dict(ecut=ecut, atomization=atomization))
atomization_frame = pd.DataFrame(rows)
print(atomization_frame)
atomization_frame.plot("ecut", "atomization")
plt.show()
def acell_convergence_study(acell_list=range(8, 20, 2), ecut=10):
"""
H2 molecule in a big box
Generate a flow to compute the total energy and the forces as function of the interatomic distance
"""
inputs = []
for acell in acell_list:
inputs += h2_h_input(ecut=ecut, acell=3 * [acell])
flow = flowtk.Flow.from_inputs("flow_h2h_acell", inputs)
flow.make_scheduler().start()
def hh_dist(gsr):
"""This function receives a GSR file and computes the H-H distance"""
if len(gsr.structure) == 1:
l = None
else:
cart_coords = gsr.structure.cart_coords
l = np.sqrt(np.linalg.norm(cart_coords[1] - cart_coords[0]))
return "hh_dist", l
import matplotlib.pyplot as plt
import pandas as pd
with abilab.abirobot(flow, "GSR") as robot:
frame = robot.get_dataframe(funcs=hh_dist)
frame = frame[["formula", "a", "energy", "hh_dist"]]
print(frame)
grouped = frame.groupby("a")
rows = []
for a, group in grouped:
group = group.set_index("formula")
atomization = 2 * group["energy"]["H1"] - group["energy"]["H2"]
atomization = abilab.Energy(atomization, "eV").to("Ha")
# FIXME Values for hh_dist are wrong! why?
rows.append(
dict(a=a,
atomization=atomization,
hh_dist=group["hh_dist"]["H2"]))
atomization_frame = pd.DataFrame(rows)
print(atomization_frame)
atomization_frame.plot("a", "atomization")
plt.show()