dw = 5000.,
nbands = -10,
kpts=(1, 1, 1),
xc = 'BEEF',
outdir='outdir',
psppath = "/scratch/users/colinfd/psp/gbrv",
sigma = 10e-4)
atoms.set_calculator(calc)
dyn = QuasiNewton(atoms,logfile='out.log',trajectory='out.traj')
dyn.run(fmax=0.01)
electronicenergy = atoms.get_potential_energy()
vib = Vibrations(atoms) # run vibrations on all atoms
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=electronicenergy,
atoms=atoms,
geometry='linear', # linear/nonlinear
symmetrynumber=2, spin=0) # symmetry numbers from point group
G = thermo.get_free_energy(temperature=300, pressure=101325.) # vapor pressure of water at room temperature
e = open('e_energy.out','w')
g = open('g_energy.out','w')
e.write(str(electronicenergy))
g.write(str(G))
outdir='calcdir',
psppath="/scratch/users/colinfd/psp/gbrv",
sigma=10e-4)
atoms.set_calculator(calc)
dyn = QuasiNewton(atoms, logfile='out.log', trajectory='out.traj')
dyn.run(fmax=0.01)
electronicenergy = atoms.get_potential_energy()
vib = Vibrations(atoms) # run vibrations on all atoms
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(
vib_energies=vib_energies,
electronicenergy=electronicenergy,
atoms=atoms,
geometry='linear', # linear/nonlinear
symmetrynumber=2,
spin=0) # symmetry numbers from point group
G = thermo.get_free_energy(
temperature=300,
pressure=101325.) # vapor pressure of water at room temperature
e = open('e_energy.out', 'w')
g = open('g_energy.out', 'w')
e.write(str(electronicenergy))
g.write(str(G))
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
n2 = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
print vib.get_frequencies()
vib.summary()
print vib.get_mode(-1)
vib.write_mode(-1, nimages=20)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=n2, symmetrynumber=2, spin=0)
thermo.get_free_energy(temperature=298.15, pressure=2*101325.)
CO2_t = IdealGasThermo(vib_energies=CO2_vib_energies[0:4],
electronicenergy=E_CO2, atoms=CO2,
geometry='linear', symmetrynumber=2,
spin=0)
H2_t = IdealGasThermo(vib_energies=H2_vib_energies[0:0],
electronicenergy=E_H2, atoms=H2,
geometry='linear', symmetrynumber=2,
spin=0)
H2O_t = IdealGasThermo(vib_energies=H2O_vib_energies[0:3],
electronicenergy=E_H2O, atoms=H2O,
geometry='nonlinear', symmetrynumber=2,
spin=0)
# now we can compute G_rxn for a range of temperatures from 298 to 1000 K
Trange = np.linspace(298, 1000, 20) # K
P = 101325. # Pa
Grxn = np.array([(CO2_t.get_free_energy(temperature=T, pressure=P)
+ H2_t.get_free_energy(temperature=T, pressure=P)
- H2O_t.get_free_energy(temperature=T, pressure=P)
- CO_t.get_free_energy(temperature=T, pressure=P)) * 96.485 for T in Trange])
Hrxn = np.array([(CO2_t.get_enthalpy(temperature=T)
+ H2_t.get_enthalpy(temperature=T)
- H2O_t.get_enthalpy(temperature=T)
- CO_t.get_enthalpy(temperature=T)) * 96.485
for T in Trange])
plt.plot(Trange, Grxn, 'bo-', label='$\Delta G_{rxn}$')
plt.plot(Trange, Hrxn, 'ro:', label='$\Delta H_{rxn}$')
plt.xlabel('Temperature (K)')
plt.ylabel(r'$\Delta G_{rxn}$ (kJ/mol)')
plt.legend(loc='best')
plt.savefig('images/wgs-dG-T.png')
plt.figure()
ibrion=2,
nsw=5,
atoms=atoms) as calc:
electronicenergy = atoms.get_potential_energy()
# next, we get vibrational modes
with jasp('molecules/n2-vib',
xc='PBE',
encut=300,
ibrion=6,
nfree=2,
potim=0.15,
nsw=1,
atoms=atoms) as calc:
calc.calculate()
vib_freq = calc.get_vibrational_frequencies() # in cm^1
#convert wavenumbers to energy
h = 4.1356675e-15 # eV*s
c = 3.0e10 #cm/s
vib_energies = [h*c*nu for nu in vib_freq]
print('vibrational energies\n====================')
for i,e in enumerate(vib_energies):
print('{0:02d}: {1} eV'.format(i,e))
# # now we can get some properties. Note we only need one vibrational
# energy since there is only one mode. This example does not work if
# you give all the energies because one energy is zero.
thermo = IdealGasThermo(vib_energies=vib_energies[0:0],
electronicenergy=electronicenergy, atoms=atoms,
geometry='linear', symmetrynumber=2, spin=0)
# temperature in K, pressure in Pa, G in eV
G = thermo.get_free_energy(temperature=298.15, pressure=101325.)
H2_t = IdealGasThermo(vib_energies=H2_vib_energies[0:0],
electronicenergy=E_H2,
atoms=H2,
geometry='linear',
symmetrynumber=2,
spin=0)
H2O_t = IdealGasThermo(vib_energies=H2O_vib_energies[0:3],
electronicenergy=E_H2O,
atoms=H2O,
geometry='nonlinear',
symmetrynumber=2,
spin=0)
# now we can compute G_rxn for a range of temperatures from 298 to 1000 K
Trange = np.linspace(298, 1000, 20) # K
P = 101325. # Pa
Grxn = np.array([(CO2_t.get_free_energy(temperature=T, pressure=P) +
H2_t.get_free_energy(temperature=T, pressure=P) -
H2O_t.get_free_energy(temperature=T, pressure=P) -
CO_t.get_free_energy(temperature=T, pressure=P)) * 96.485
for T in Trange])
Hrxn = np.array([
(CO2_t.get_enthalpy(temperature=T) + H2_t.get_enthalpy(temperature=T) -
H2O_t.get_enthalpy(temperature=T) - CO_t.get_enthalpy(temperature=T)) *
96.485 for T in Trange
])
plt.plot(Trange, Grxn, 'bo-', label='$\Delta G_{rxn}$')
plt.plot(Trange, Hrxn, 'ro:', label='$\Delta H_{rxn}$')
plt.xlabel('Temperature (K)')
plt.ylabel(r'$\Delta G_{rxn}$ (kJ/mol)')
plt.legend(loc='best')
plt.savefig('images/wgs-dG-T.png')
