def test_rattle():
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i)
]:
dimer = s22('Water_dimer')
for m in [0, 3]:
dimer.set_angle(m + 1, m, m + 2, angleHOH)
dimer.set_distance(m, m + 1, rOH, fix=0)
dimer.set_distance(m, m + 2, rOH, fix=0)
fixOH1 = [(3 * i, 3 * i + 1) for i in range(2)]
fixOH2 = [(3 * i, 3 * i + 2) for i in range(2)]
fixHH = [(3 * i + 1, 3 * i + 2) for i in range(2)]
dimer.set_constraint(FixBondLengths(fixOH1 + fixOH2 + fixHH))
dimer.calc = calc
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
8.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=5)
md.run(25)
de = dimer.get_potential_energy() - e
assert abs(de - -0.028) < 0.001
def test_orca_qmmm():
from ase.calculators.tip4p import TIP4P, epsilon0, sigma0
from ase.calculators.orca import ORCA
from ase.calculators.qmmm import EIQMMM, LJInteractions
from ase.data import s22
atoms = s22.create_s22_system('Water_dimer')
qmcalc = ORCA(label='water', orcasimpleinput='BLYP def2-SVP')
lj = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
atoms.calc = EIQMMM(selection=[0, 1, 2],
qmcalc=qmcalc,
mmcalc=TIP4P(),
interaction=lj,
output='orca_qmmm.log')
e = atoms.get_potential_energy()
assert abs(e + 2077.45445852) < 1.0
def test_qmmm_tip4p():
from math import cos, sin, pi
import numpy as np
#import matplotlib.pyplot as plt
import ase.units as units
from ase import Atoms
from ase.calculators.tip4p import TIP4P, epsilon0, sigma0, rOH, angleHOH
from ase.calculators.qmmm import (SimpleQMMM, EIQMMM, LJInteractions,
LJInteractionsGeneral)
from ase.constraints import FixInternals
from ase.optimize import BFGS
r = rOH
a = angleHOH * pi / 180
# From https://doi.org/10.1063/1.445869
eexp = 6.24 * units.kcal / units.mol
dexp = 2.75
aexp = 46
D = np.linspace(2.5, 3.5, 30)
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
# General LJ interaction object
sigma_mm = np.array([sigma0, 0, 0])
epsilon_mm = np.array([epsilon0, 0, 0])
sigma_qm = np.array([sigma0, 0, 0])
epsilon_qm = np.array([epsilon0, 0, 0])
ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3)
for calc in [
TIP4P(),
SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P()),
SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P(), vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i),
EIQMMM([3, 4, 5], TIP4P(), TIP4P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig),
EIQMMM([3, 4, 5], TIP4P(), TIP4P(), ig, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig, vacuum=3.0)
]:
dimer = Atoms('OH2OH2', [(0, 0, 0), (r * cos(a), 0, r * sin(a)),
(r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[3, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
#plt.plot(D, E)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.01
dimer.constraints = FixInternals(bonds=[(r, (0, 1)), (r, (0, 2)),
(r, (3, 4)), (r, (3, 5))],
angles=[(a, (2, 0, 1)),
(a, (5, 3, 4))])
opt = BFGS(dimer,
maxstep=0.04,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(0, 3)
R = dimer.positions
v1 = R[2] - R[3]
v2 = R[3] - (R[5] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>23}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.006
assert abs(a0 - aexp) < 2.5
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
from ase.calculators.qmmm import (SimpleQMMM, EIQMMM, LJInteractions,
LJInteractionsGeneral)
from ase.constraints import FixInternals
from ase.optimize import GPMin
r = rOH
a = angleHOH * pi / 180
# From http://dx.doi.org/10.1063/1.445869
eexp = 6.50 * units.kcal / units.mol
dexp = 2.74
aexp = 27
D = np.linspace(2.5, 3.5, 30)
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
# General LJ interaction object
sigma_mm = np.array([0, 0, sigma0])
epsilon_mm = np.array([0, 0, epsilon0])
sigma_qm = np.array([0, 0, sigma0])
epsilon_qm = np.array([0, 0, epsilon0])
ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3)
for calc in [TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P(), vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i),
EIQMMM([3, 4, 5], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig),
def test_qmmm(testdir):
r = rOH
a = angleHOH * pi / 180
# From https://doi.org/10.1063/1.445869
eexp = 6.50 * units.kcal / units.mol
dexp = 2.74
aexp = 27
D = np.linspace(2.5, 3.5, 30)
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
# General LJ interaction object
sigma_mm = np.array([0, 0, sigma0])
epsilon_mm = np.array([0, 0, epsilon0])
sigma_qm = np.array([0, 0, sigma0])
epsilon_qm = np.array([0, 0, epsilon0])
ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3)
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P(), vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i),
EIQMMM([3, 4, 5], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig),
EIQMMM([3, 4, 5], TIP3P(), TIP3P(), ig, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig, vacuum=3.0)
]:
dimer = Atoms('H2OH2O',
[(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[5, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.01
dimer.constraints = FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)),
(r, (3, 5)), (r, (4, 5))],
angles_deg=[
(np.degrees(a), (0, 2, 1)),
(np.degrees(a), (3, 5, 4))
])
opt = GPMin(dimer,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.01
assert abs(a0 - aexp) < 4
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
def test_turbomole_qmmm():
"""Test the Turbomole calculator in simple QMMM and
explicit interaction QMMM simulations."""
r = rOH
a = angleHOH * pi / 180
D = np.linspace(2.5, 3.5, 30)
interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
qm_par = {'esp fit': 'kollman', 'multiplicity': 1}
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P()),
SimpleQMMM([0, 1, 2],
Turbomole(**qm_par),
TIP3P(),
TIP3P(),
vacuum=3.0),
EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction),
EIQMMM([3, 4, 5],
Turbomole(**qm_par),
TIP3P(),
interaction,
vacuum=3.0),
EIQMMM([0, 1, 2],
Turbomole(**qm_par),
TIP3P(),
interaction,
vacuum=3.0)
]:
dimer = Atoms('H2OH2O',
[(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[5, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.9
dimer.set_constraint(
FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)), (r, (3, 5)),
(r, (4, 5))],
angles_deg=[(angleHOH, (0, 2, 1)),
(angleHOH, (3, 5, 4))]))
opt = BFGS(dimer,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))