#!/usr/bin/python
# Plot E(V) curve.
from pwtools import sql, mpl, io
db = sql.SQLiteDB('calc.db')
data = db.get_array("select volume,etot from calc order by volume")
natoms = io.cpickle_load('results/0/traj.pk').natoms
# plotting
fig,ax = mpl.fig_ax()
ax.plot(data[:,0]/float(natoms), data[:,1]/float(natoms))
ax.set_ylabel('energy/atom [eV]')
ax.set_xlabel('volume/atom [Ang^3]')
mpl.plt.show()
db = sql.SQLiteDB('calc.db', table='calc')
idx_lst = db.get_list1d("select idx from calc")
cols = [
('etot', 'float'), # eV
('pressure', 'float'), # GPa
('volume', 'float'), # Ang**3
('forces_rms', 'float'), # eV / Ang
('sxx', 'float'), # GPa
('syy', 'float'), # GPa
('szz', 'float'), # GPa
]
db.add_columns(cols)
for idx in idx_lst:
print(idx)
struct = io.cpickle_load('results/%i/traj.pk' % idx)[-1]
db.execute("update calc set etot=? where idx==?", (struct.etot, idx))
db.execute("update calc set volume=? where idx==?", (struct.volume, idx))
db.execute("update calc set pressure=? where idx==?",
(struct.pressure, idx))
db.execute("update calc set sxx=? where idx==?",
(struct.stress[0, 0], idx))
db.execute("update calc set syy=? where idx==?",
(struct.stress[1, 1], idx))
db.execute("update calc set szz=? where idx==?",
(struct.stress[2, 2], idx))
db.execute("update calc set forces_rms=? where idx==?",
(num.rms(struct.forces), idx))
db.commit()
# Load parsed results and put some values in the database.
from pwtools import sql, io, num
db = sql.SQLiteDB('calc.db', table='calc')
idx_lst = db.get_list1d("select idx from calc")
cols = [('etot', 'float'), # eV
('pressure', 'float'), # GPa
('volume', 'float'), # Ang**3
('forces_rms', 'float'), # eV / Ang
('sxx', 'float'), # GPa
('syy', 'float'), # GPa
('szz', 'float'), # GPa
]
db.add_columns(cols)
for idx in idx_lst:
print idx
struct = io.cpickle_load('results/%i/traj.pk' %idx)[-1]
db.execute("update calc set etot=? where idx==?", (struct.etot, idx))
db.execute("update calc set volume=? where idx==?", (struct.volume, idx))
db.execute("update calc set pressure=? where idx==?", (struct.pressure, idx))
db.execute("update calc set sxx=? where idx==?", (struct.stress[0,0], idx))
db.execute("update calc set syy=? where idx==?", (struct.stress[1,1], idx))
db.execute("update calc set szz=? where idx==?", (struct.stress[2,2], idx))
db.execute("update calc set forces_rms=? where idx==?",
(num.rms(struct.forces), idx))
db.commit()
# Load parsed results and put some values in the database.
from pwtools import sql, io, num
db = sql.SQLiteDB('calc.db', table='calc')
idx_lst = db.get_list1d("select idx from calc")
cols = [('etot', 'float'), # eV
('pressure', 'float'), # GPa
('volume', 'float'), # Ang**3
('forces_rms', 'float'), # eV / Ang
('sxx', 'float'), # GPa
('syy', 'float'), # GPa
('szz', 'float'), # GPa
]
db.add_columns(cols)
for idx in idx_lst:
print idx
struct = io.cpickle_load('results/%i/struct.pk' %idx)
db.execute("update calc set etot=? where idx==?", (struct.etot, idx))
db.execute("update calc set volume=? where idx==?", (struct.volume, idx))
db.execute("update calc set pressure=? where idx==?", (struct.pressure, idx))
db.execute("update calc set sxx=? where idx==?", (struct.stress[0,0], idx))
db.execute("update calc set syy=? where idx==?", (struct.stress[1,1], idx))
db.execute("update calc set szz=? where idx==?", (struct.stress[2,2], idx))
db.execute("update calc set forces_rms=? where idx==?",
(num.rms(struct.forces), idx))
db.commit()
# Load parsed results and put some values in the database.
from pwtools import sql, io, num
db = sql.SQLiteDB('calc.db', table='calc')
idx_lst = db.get_list1d("select idx from calc")
cols = [('etot', 'float'), # eV
('pressure', 'float'), # GPa
('volume', 'float'), # Ang**3
('forces_rms', 'float'), # eV / Ang
('sxx', 'float'), # GPa
('syy', 'float'), # GPa
('szz', 'float'), # GPa
]
db.add_columns(cols)
for idx in idx_lst:
print(idx)
struct = io.cpickle_load('results/%i/struct.pk' %idx)
db.execute("update calc set etot=? where idx==?", (struct.etot, idx))
db.execute("update calc set volume=? where idx==?", (struct.volume, idx))
db.execute("update calc set pressure=? where idx==?", (struct.pressure, idx))
db.execute("update calc set sxx=? where idx==?", (struct.stress[0,0], idx))
db.execute("update calc set syy=? where idx==?", (struct.stress[1,1], idx))
db.execute("update calc set szz=? where idx==?", (struct.stress[2,2], idx))
db.execute("update calc set forces_rms=? where idx==?",
(num.rms(struct.forces), idx))
db.commit()
#!/usr/bin/python
# Plot E(V) curve.
from pwtools import sql, mpl, io
db = sql.SQLiteDB('calc.db')
data = db.get_array("select volume,etot from calc order by volume")
natoms = io.cpickle_load('results/0/traj.pk').natoms
# plotting
fig, ax = mpl.fig_ax()
ax.plot(data[:, 0] / float(natoms), data[:, 1] / float(natoms))
ax.set_ylabel('energy/atom [eV]')
ax.set_xlabel('volume/atom [Ang^3]')
mpl.plt.show()
