import unittest
import numpy as np
from polymers import physics
from ..test import Parameters
from ...test import integrate
parameters = Parameters()
FJC = physics.single_chain.fjc.thermodynamics.FJC
class Base(unittest.TestCase):
def test_init(self):
for _ in range(parameters.number_of_loops):
_ = FJC(
parameters.number_of_links_minimum,
parameters.link_length_reference,
parameters.hinge_mass_reference
)
def test_number_of_links(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
np.random.randint(
parameters.number_of_links_minimum,
high=parameters.number_of_links_maximum
)
self.assertEqual(
number_of_links,
FJC(
number_of_links,
parameters.link_length_reference,
parameters.hinge_mass_reference
).number_of_links
)
def test_link_length(self):
for _ in range(parameters.number_of_loops):
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
self.assertEqual(
link_length,
FJC(
parameters.number_of_links_minimum,
link_length,
parameters.hinge_mass_reference
).link_length
)
def test_hinge_mass(self):
for _ in range(parameters.number_of_loops):
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
self.assertEqual(
hinge_mass,
FJC(
parameters.number_of_links_minimum,
parameters.link_length_reference,
hinge_mass
).hinge_mass
)
def test_all_parameters(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
np.random.randint(
parameters.number_of_links_minimum,
high=parameters.number_of_links_maximum
)
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
self.assertEqual(
number_of_links,
model.number_of_links
)
self.assertEqual(
link_length,
model.link_length
)
self.assertEqual(
hinge_mass,
model.hinge_mass
)
class Legendre(unittest.TestCase):
def test_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
force_out = \
model.isometric.legendre.force(
np.array(end_to_end_length),
temperature
)
residual_abs = \
force \
- force_out
residual_rel = residual_abs/force
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_nondimensional_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_force_out = \
model.isometric.legendre.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
residual_abs = \
nondimensional_force \
- nondimensional_force_out
residual_rel = residual_abs/nondimensional_force
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
helmholtz_free_energy_legendre = \
model.isotensional.gibbs_free_energy(
np.array(force),
temperature
) + force*end_to_end_length
helmholtz_free_energy_legendre_out = \
model.isometric.legendre.helmholtz_free_energy(
np.array(end_to_end_length),
temperature
)
residual_abs = \
helmholtz_free_energy_legendre \
- helmholtz_free_energy_legendre_out \
+ parameters.boltzmann_constant*temperature*np.log(
8*np.pi**2*hinge_mass*link_length**2 *
parameters.boltzmann_constant*temperature /
parameters.planck_constant**2
)
residual_rel = residual_abs/helmholtz_free_energy_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
end_to_end_length_per_link = \
model.isotensional.end_to_end_length_per_link(
np.array(force),
temperature
)
helmholtz_free_energy_per_link_legendre = \
model.isotensional.gibbs_free_energy_per_link(
np.array(force),
temperature
) + force*end_to_end_length_per_link
helmholtz_free_energy_per_link_legendre_out = \
model.isometric.legendre.helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
)
residual_abs = \
helmholtz_free_energy_per_link_legendre \
- helmholtz_free_energy_per_link_legendre_out \
+ parameters.boltzmann_constant*temperature*np.log(
8*np.pi**2*hinge_mass*link_length**2 *
parameters.boltzmann_constant*temperature /
parameters.planck_constant**2
)/number_of_links
residual_rel = residual_abs/helmholtz_free_energy_per_link_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
relative_helmholtz_free_energy_legendre = \
model.isotensional.relative_gibbs_free_energy(
np.array(force),
temperature
) + force*end_to_end_length
relative_helmholtz_free_energy_legendre_out = \
model.isometric.legendre.relative_helmholtz_free_energy(
np.array(end_to_end_length),
temperature
)
residual_abs = \
relative_helmholtz_free_energy_legendre \
- relative_helmholtz_free_energy_legendre_out
residual_rel = residual_abs/relative_helmholtz_free_energy_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
end_to_end_length_per_link = \
model.isotensional.end_to_end_length_per_link(
np.array(force),
temperature
)
relative_helmholtz_free_energy_per_link_legendre = \
model.isotensional.relative_gibbs_free_energy_per_link(
np.array(force),
temperature
) + force*end_to_end_length_per_link
relative_helmholtz_free_energy_per_link_legendre_out = \
model.isometric.legendre. \
relative_helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
)
residual_abs = \
relative_helmholtz_free_energy_per_link_legendre \
- relative_helmholtz_free_energy_per_link_legendre_out
residual_rel = residual_abs / \
relative_helmholtz_free_energy_per_link_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_nondimensional_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_end_to_end_length = \
model.isotensional.nondimensional_end_to_end_length(
np.array(nondimensional_force),
)
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force),
)
nondimensional_helmholtz_free_energy_legendre = \
model.isotensional.nondimensional_gibbs_free_energy(
np.array(nondimensional_force),
temperature
) + nondimensional_force*nondimensional_end_to_end_length
nondimensional_helmholtz_free_energy_legendre_out = \
model.isometric.legendre.nondimensional_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link),
temperature
)
residual_abs = \
nondimensional_helmholtz_free_energy_legendre \
- nondimensional_helmholtz_free_energy_legendre_out \
+ np.log(
8*np.pi**2*hinge_mass*link_length**2 *
parameters.boltzmann_constant*temperature /
parameters.planck_constant**2
)
residual_rel = residual_abs / \
nondimensional_helmholtz_free_energy_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_nondimensional_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force),
)
nondimensional_helmholtz_free_energy_per_link_legendre = \
model.isotensional.nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_force),
temperature
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link
nondimensional_helmholtz_free_energy_per_link_legendre_out = \
model.isometric.legendre. \
nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link),
temperature
)
residual_abs = \
nondimensional_helmholtz_free_energy_per_link_legendre \
- nondimensional_helmholtz_free_energy_per_link_legendre_out \
+ np.log(
8*np.pi**2*hinge_mass*link_length**2 *
parameters.boltzmann_constant*temperature /
parameters.planck_constant**2
)/number_of_links
residual_rel = residual_abs / \
nondimensional_helmholtz_free_energy_per_link_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_nondimensional_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length = \
model.isotensional.nondimensional_end_to_end_length(
np.array(nondimensional_force),
)
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force),
)
nondimensional_relative_helmholtz_free_energy_legendre = \
model.isotensional.nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_force)
) + nondimensional_force*nondimensional_end_to_end_length
nondimensional_relative_helmholtz_free_energy_legendre_out = \
model.isometric.legendre. \
nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link)
)
residual_abs = \
nondimensional_relative_helmholtz_free_energy_legendre \
- nondimensional_relative_helmholtz_free_energy_legendre_out
residual_rel = residual_abs / \
nondimensional_relative_helmholtz_free_energy_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
def test_nondimensional_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force),
)
nondim_relative_helmholtz_free_energy_per_link_legendre = \
model.isotensional. \
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_force)
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link
nondim_relative_helmholtz_free_energy_per_link_legendre_out = \
model.isometric.legendre. \
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link)
)
residual_abs = \
nondim_relative_helmholtz_free_energy_per_link_legendre \
- nondim_relative_helmholtz_free_energy_per_link_legendre_out
residual_rel = residual_abs / \
nondim_relative_helmholtz_free_energy_per_link_legendre
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
class ThermodynamicLimit(unittest.TestCase):
def test_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
end_to_end_length_out = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
residual_abs = \
end_to_end_length \
- end_to_end_length_out
residual_rel = residual_abs/end_to_end_length
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
end_to_end_length_per_link = \
nondimensional_end_to_end_length_per_link*link_length
end_to_end_length_per_link_out = \
model.isotensional.end_to_end_length_per_link(
np.array(force),
temperature
)
residual_abs = \
end_to_end_length_per_link \
- end_to_end_length_per_link_out
residual_rel = residual_abs/end_to_end_length_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_end_to_end_length = \
nondimensional_end_to_end_length_per_link*number_of_links
nondimensional_end_to_end_length_out = \
model.isotensional.nondimensional_end_to_end_length(
np.array(nondimensional_force)
)
residual_abs = \
nondimensional_end_to_end_length \
- nondimensional_end_to_end_length_out
residual_rel = residual_abs/nondimensional_end_to_end_length
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_end_to_end_length_per_link_out = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
residual_abs = \
nondimensional_end_to_end_length_per_link \
- nondimensional_end_to_end_length_per_link_out
residual_rel = residual_abs / \
nondimensional_end_to_end_length_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
force_out = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
residual_abs = \
force \
- force_out
residual_rel = residual_abs/force
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_force_out = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
residual_abs = \
nondimensional_force \
- nondimensional_force_out
residual_rel = residual_abs/nondimensional_force
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
helmholtz_free_energy = \
model.isometric.helmholtz_free_energy(
np.array(end_to_end_length),
temperature
)
helmholtz_free_energy_out = \
model.isotensional.gibbs_free_energy(
np.array(force),
temperature
) + force*end_to_end_length
residual_abs = \
helmholtz_free_energy \
- helmholtz_free_energy_out
residual_rel = residual_abs/helmholtz_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
helmholtz_free_energy_per_link = \
model.isometric.helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
)
helmholtz_free_energy_per_link_out = \
model.isotensional.gibbs_free_energy_per_link(
np.array(force),
temperature
) + force*end_to_end_length/number_of_links
residual_abs = \
helmholtz_free_energy_per_link \
- helmholtz_free_energy_per_link_out
residual_rel = residual_abs/helmholtz_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
relative_helmholtz_free_energy = \
model.isometric.relative_helmholtz_free_energy(
np.array(end_to_end_length),
temperature
)
relative_helmholtz_free_energy_out = \
model.isotensional.relative_gibbs_free_energy(
np.array(force),
temperature
) + force*end_to_end_length
residual_abs = \
relative_helmholtz_free_energy \
- relative_helmholtz_free_energy_out
residual_rel = residual_abs/relative_helmholtz_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
end_to_end_length = nondimensional_end_to_end_length_per_link * \
number_of_links*link_length
force = \
model.isometric.force(
np.array(end_to_end_length),
temperature
)
relative_helmholtz_free_energy_per_link = \
model.isometric.relative_helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
)
relative_helmholtz_free_energy_per_link_out = \
model.isotensional.relative_gibbs_free_energy_per_link(
np.array(force),
temperature
) + force*end_to_end_length/number_of_links
residual_abs = \
relative_helmholtz_free_energy_per_link \
- relative_helmholtz_free_energy_per_link_out
residual_rel = residual_abs/relative_helmholtz_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_helmholtz_free_energy = \
model.isometric.nondimensional_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link),
temperature
)
nondimensional_helmholtz_free_energy_out = \
model.isotensional.nondimensional_gibbs_free_energy(
np.array(nondimensional_force),
temperature
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link*number_of_links
residual_abs = \
nondimensional_helmholtz_free_energy \
- nondimensional_helmholtz_free_energy_out
residual_rel = residual_abs / \
nondimensional_helmholtz_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_helmholtz_free_energy_per_link = \
model.isometric.nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link),
temperature
)
nondimensional_helmholtz_free_energy_per_link_out = \
model.isotensional.nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_force),
temperature
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link
residual_abs = \
nondimensional_helmholtz_free_energy_per_link \
- nondimensional_helmholtz_free_energy_per_link_out
residual_rel = residual_abs / \
nondimensional_helmholtz_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_relative_helmholtz_free_energy = \
model.isometric. \
nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_relative_helmholtz_free_energy_out = \
model.isotensional. \
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_force)
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link*number_of_links
residual_abs = \
nondimensional_relative_helmholtz_free_energy \
- nondimensional_relative_helmholtz_free_energy_out
residual_rel = residual_abs / \
nondimensional_relative_helmholtz_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_end_to_end_length_per_link = \
parameters. \
nondimensional_end_to_end_length_per_link_reference + \
parameters. \
nondimensional_end_to_end_length_per_link_scale * \
(0.5 - np.random.rand())
nondimensional_force = \
model.isometric.nondimensional_force(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_relative_helmholtz_free_energy_per_link = \
model.isometric. \
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link)
)
nondimensional_relative_helmholtz_free_energy_per_link_out = \
model.isotensional. \
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_force)
) + nondimensional_force * \
nondimensional_end_to_end_length_per_link
residual_abs = \
nondimensional_relative_helmholtz_free_energy_per_link \
- nondimensional_relative_helmholtz_free_energy_per_link_out
residual_rel = residual_abs / \
nondimensional_relative_helmholtz_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
gibbs_free_energy = \
model.isotensional.gibbs_free_energy(
np.array(force),
temperature
)
gibbs_free_energy_out = \
model.isometric.helmholtz_free_energy(
np.array(end_to_end_length),
temperature
) - force*end_to_end_length
residual_abs = \
gibbs_free_energy \
- gibbs_free_energy_out
residual_rel = residual_abs/gibbs_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
gibbs_free_energy_per_link = \
model.isotensional.gibbs_free_energy_per_link(
np.array(force),
temperature
)
gibbs_free_energy_per_link_out = \
model.isometric.helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
) - force*end_to_end_length/number_of_links
residual_abs = \
gibbs_free_energy_per_link \
- gibbs_free_energy_per_link_out
residual_rel = residual_abs/gibbs_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
relative_gibbs_free_energy = \
model.isotensional.relative_gibbs_free_energy(
np.array(force),
temperature
)
relative_gibbs_free_energy_out = \
model.isometric.relative_helmholtz_free_energy(
np.array(end_to_end_length),
temperature
) - force*end_to_end_length
residual_abs = \
relative_gibbs_free_energy \
- relative_gibbs_free_energy_out
residual_rel = residual_abs/relative_gibbs_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
end_to_end_length = \
model.isotensional.end_to_end_length(
np.array(force),
temperature
)
relative_gibbs_free_energy_per_link = \
model.isotensional.relative_gibbs_free_energy_per_link(
np.array(force),
temperature
)
relative_gibbs_free_energy_per_link_out = \
model.isometric.relative_helmholtz_free_energy_per_link(
np.array(end_to_end_length),
temperature
) - force*end_to_end_length/number_of_links
residual_abs = \
relative_gibbs_free_energy_per_link \
- relative_gibbs_free_energy_per_link_out
residual_rel = residual_abs/relative_gibbs_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_gibbs_free_energy = \
model.isotensional.nondimensional_gibbs_free_energy(
np.array(nondimensional_force),
temperature
)
nondimensional_gibbs_free_energy_out = \
model.isometric.nondimensional_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link),
temperature
) - nondimensional_force * \
nondimensional_end_to_end_length_per_link*number_of_links
residual_abs = \
nondimensional_gibbs_free_energy \
- nondimensional_gibbs_free_energy_out
residual_rel = residual_abs / \
nondimensional_gibbs_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_gibbs_free_energy_per_link = \
model.isotensional.nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_force),
temperature
)
nondimensional_gibbs_free_energy_per_link_out = \
model.isometric.nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link),
temperature
) - nondimensional_force * \
nondimensional_end_to_end_length_per_link
residual_abs = \
nondimensional_gibbs_free_energy_per_link \
- nondimensional_gibbs_free_energy_per_link_out
residual_rel = residual_abs / \
nondimensional_gibbs_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_relative_gibbs_free_energy = \
model.isotensional. \
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_force)
)
nondimensional_relative_gibbs_free_energy_out = \
model.isometric. \
nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_end_to_end_length_per_link)
) - nondimensional_force * \
nondimensional_end_to_end_length_per_link*number_of_links
residual_abs = \
nondimensional_relative_gibbs_free_energy \
- nondimensional_relative_gibbs_free_energy_out
residual_rel = residual_abs / \
nondimensional_relative_gibbs_free_energy
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
def test_nondimensional_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = parameters.number_of_links_maximum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_force = \
parameters. \
nondimensional_force_reference + \
parameters. \
nondimensional_force_scale * \
(0.5 - np.random.rand())
nondimensional_end_to_end_length_per_link = \
model.isotensional.nondimensional_end_to_end_length_per_link(
np.array(nondimensional_force)
)
nondimensional_relative_gibbs_free_energy_per_link = \
model.isotensional. \
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_force)
)
nondimensional_relative_gibbs_free_energy_per_link_out = \
model.isometric. \
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_end_to_end_length_per_link)
) - nondimensional_force * \
nondimensional_end_to_end_length_per_link
residual_abs = \
nondimensional_relative_gibbs_free_energy_per_link \
- nondimensional_relative_gibbs_free_energy_per_link_out
residual_rel = residual_abs / \
nondimensional_relative_gibbs_free_energy_per_link
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol_thermodynamic_limit
)
class ModifiedCanonicalStrongPotentialIsometric(unittest.TestCase):
def test_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.
force(
end_to_end_length,
potential_stiffness,
temperature
) -
model.isometric.
force(
end_to_end_length,
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.modified_canonical.
force(
end_to_end_length,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_force(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_force(
nondimensional_end_to_end_length_per_link
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_force(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.
relative_helmholtz_free_energy(
end_to_end_length,
potential_stiffness,
temperature
) -
model.isometric.
relative_helmholtz_free_energy(
end_to_end_length,
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.modified_canonical.
relative_helmholtz_free_energy(
end_to_end_length,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
potential_stiffness,
temperature
) -
model.isometric.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.modified_canonical.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
class ModifiedCanonicalWeakPotentialIsotensional(unittest.TestCase):
def test_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
end_to_end_length(
potential_distance,
potential_stiffness,
temperature
) -
model.isotensional.
end_to_end_length(
force,
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
end_to_end_length(
potential_distance,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
end_to_end_length_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.isotensional.
end_to_end_length_per_link(
force,
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
end_to_end_length_per_link(
potential_distance,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_end_to_end_length(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_end_to_end_length(
nondimensional_force
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_end_to_end_length(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_end_to_end_length_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_end_to_end_length_per_link(
nondimensional_force
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_end_to_end_length_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical.force(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
gibbs_free_energy(
force,
temperature
) +
model.isotensional.
gibbs_free_energy(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical.force(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
gibbs_free_energy_per_link(
force,
temperature
) +
model.isotensional.
gibbs_free_energy_per_link(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical.force(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
relative_gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
relative_gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
relative_gibbs_free_energy(
force,
temperature
) +
model.isotensional.
relative_gibbs_free_energy(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
relative_gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
relative_gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical.force(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical.force(
potential_distance,
potential_stiffness,
temperature
)
return (
model.modified_canonical.
relative_gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
relative_gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
relative_gibbs_free_energy_per_link(
force,
temperature
) +
model.isotensional.
relative_gibbs_free_energy_per_link(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.
relative_gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.
relative_gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.
nondimensional_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
) -
model.isotensional.
nondimensional_gibbs_free_energy(
nondimensional_force,
temperature
) +
model.isotensional.
nondimensional_gibbs_free_energy(
np.array(nondimensional_force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.
nondimensional_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
) -
model.isotensional.
nondimensional_gibbs_free_energy_per_link(
nondimensional_force,
temperature
) +
model.isotensional.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_relative_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_relative_gibbs_free_energy(
nondimensional_force
) +
model.isotensional.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_force_ref)
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_relative_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_force
) +
model.isotensional.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_force_ref)
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
class ModifiedCanonicalAsymptoticStrongPotentialIsometric(unittest.TestCase):
def test_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.asymptotic.strong_potential.
force(
end_to_end_length,
potential_stiffness,
temperature
) -
model.isometric.
force(
end_to_end_length,
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.isometric.
force(
end_to_end_length,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_force(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.asymptotic.strong_potential.
nondimensional_force(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_force(
nondimensional_end_to_end_length_per_link
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.isometric.
nondimensional_force(
nondimensional_end_to_end_length_per_link
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.asymptotic.strong_potential.
helmholtz_free_energy(
end_to_end_length,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
potential_stiffness,
temperature
) -
model.isometric.
helmholtz_free_energy(
end_to_end_length,
temperature
) +
model.isometric.
helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.isometric.
helmholtz_free_energy(
end_to_end_length,
temperature
) -
model.isometric.
helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.asymptotic.strong_potential.
helmholtz_free_energy_per_link(
end_to_end_length,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
potential_stiffness,
temperature
) -
model.isometric.
helmholtz_free_energy_per_link(
end_to_end_length,
temperature
) +
model.isometric.
helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.isometric.
helmholtz_free_energy_per_link(
end_to_end_length,
temperature
) -
model.isometric.
helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.asymptotic.strong_potential.
relative_helmholtz_free_energy(
end_to_end_length,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
potential_stiffness,
temperature
) -
model.isometric.
relative_helmholtz_free_energy(
end_to_end_length,
temperature
) +
model.isometric.
relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.isometric.
relative_helmholtz_free_energy(
end_to_end_length,
temperature
) -
model.isometric.
relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(end_to_end_length):
return (
model.modified_canonical.asymptotic.strong_potential.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
potential_stiffness,
temperature
) -
model.isometric.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
temperature
) +
model.isometric.
relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
def integrand_denominator(end_to_end_length):
return (
model.isometric.
relative_helmholtz_free_energy_per_link(
end_to_end_length,
temperature
) -
model.isometric.
relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small *
number_of_links*link_length
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero*number_of_links*link_length,
parameters.nondimensional_potential_distance_small *
number_of_links*link_length,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.asymptotic.strong_potential.
nondimensional_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
nondimensional_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
),
nondimensional_potential_stiffness,
temperature
) -
model.isometric.
nondimensional_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
temperature
) +
model.isometric.
nondimensional_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
),
temperature
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.isometric.
nondimensional_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
temperature
) -
model.isometric.
nondimensional_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.asymptotic.strong_potential.
nondimensional_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.strong_potential.
nondimensional_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
),
nondimensional_potential_stiffness,
temperature
) -
model.isometric.
nondimensional_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
temperature
) +
model.isometric.
nondimensional_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
),
temperature
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.isometric.
nondimensional_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
temperature
) -
model.isometric.
nondimensional_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
),
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_helmholtz_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.asymptotic.strong_potential.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.strong_potential.
nondimensional_relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
),
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link
) +
model.isometric.
nondimensional_relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
)
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.isometric.
nondimensional_relative_helmholtz_free_energy(
nondimensional_end_to_end_length_per_link
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy(
np.array(
parameters.
nondimensional_potential_distance_small
)
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_helmholtz_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(
nondimensional_end_to_end_length_per_link
):
return (
model.modified_canonical.asymptotic.strong_potential.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.strong_potential.
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
),
nondimensional_potential_stiffness
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link
) +
model.isometric.
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
)
)
)**2
def integrand_denominator(
nondimensional_end_to_end_length_per_link
):
return (
model.isometric.
nondimensional_relative_helmholtz_free_energy_per_link(
nondimensional_end_to_end_length_per_link
) -
model.isometric.
nondimensional_relative_helmholtz_free_energy_per_link(
np.array(
parameters.
nondimensional_potential_distance_small
)
)
)**2
numerator = integrate(
integrand_numerator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.zero,
parameters.nondimensional_potential_distance_small,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_large
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_large *
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
class ModifiedCanonicalAsymptoticWeakPotentialIsotensional(unittest.TestCase):
def test_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
end_to_end_length(
potential_distance,
potential_stiffness,
temperature
) -
model.isotensional.
end_to_end_length(
force,
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
end_to_end_length(
potential_distance,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
end_to_end_length_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.isotensional.
end_to_end_length_per_link(
force,
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
end_to_end_length_per_link(
potential_distance,
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_end_to_end_length(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_end_to_end_length(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_end_to_end_length(
nondimensional_force
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_end_to_end_length(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_end_to_end_length_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
def residual_rel(nondimensional_potential_stiffness):
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_end_to_end_length_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_end_to_end_length_per_link(
nondimensional_force
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_end_to_end_length_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical. \
asymptotic.weak_potential. \
force(
np.array(potential_distance_ref),
potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
gibbs_free_energy(
force,
temperature
) +
model.isotensional.
gibbs_free_energy(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical. \
asymptotic.weak_potential. \
force(
np.array(potential_distance_ref),
potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
gibbs_free_energy_per_link(
force,
temperature
) +
model.isotensional.
gibbs_free_energy_per_link(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical. \
asymptotic.weak_potential. \
force(
np.array(potential_distance_ref),
potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
relative_gibbs_free_energy(
force,
temperature
) +
model.isotensional.
relative_gibbs_free_energy(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)*number_of_links*link_length
def residual_rel(nondimensional_potential_stiffness):
potential_stiffness = nondimensional_potential_stiffness / \
link_length**2 * \
parameters.boltzmann_constant*temperature
force_ref = model.modified_canonical. \
asymptotic.weak_potential. \
force(
np.array(potential_distance_ref),
potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
force = model.modified_canonical. \
asymptotic.weak_potential. \
force(
potential_distance,
potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
) -
model.isotensional.
relative_gibbs_free_energy_per_link(
force,
temperature
) +
model.isotensional.
relative_gibbs_free_energy_per_link(
np.array(force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
potential_distance = nondimensional_potential_distance * \
number_of_links*link_length
return (
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy_per_link(
potential_distance,
potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
relative_gibbs_free_energy_per_link(
np.array(potential_distance_ref),
potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
) -
model.isotensional.
nondimensional_gibbs_free_energy(
nondimensional_force,
temperature
) +
model.isotensional.
nondimensional_gibbs_free_energy(
np.array(nondimensional_force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
) -
model.isotensional.
nondimensional_gibbs_free_energy_per_link(
nondimensional_force,
temperature
) +
model.isotensional.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_force_ref),
temperature
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness,
temperature
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness,
temperature
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_gibbs_free_energy(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_relative_gibbs_free_energy(
nondimensional_force
) +
model.isotensional.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_force_ref)
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)
def test_nondimensional_relative_gibbs_free_energy_per_link(self):
for _ in range(parameters.number_of_loops):
number_of_links = \
parameters.number_of_links_maximum - \
parameters.number_of_links_minimum
link_length = \
parameters.link_length_reference + \
parameters.link_length_scale*(0.5 - np.random.rand())
hinge_mass = \
parameters.hinge_mass_reference + \
parameters.hinge_mass_scale*(0.5 - np.random.rand())
model = FJC(
number_of_links,
link_length,
hinge_mass
)
nondimensional_potential_distance_ref = \
np.array(
parameters.nondimensional_potential_distance_large_1
)
def residual_rel(nondimensional_potential_stiffness):
nondimensional_force_ref = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
def integrand_numerator(nondimensional_potential_distance):
nondimensional_force = \
model.modified_canonical.asymptotic.weak_potential. \
nondimensional_force(
nondimensional_potential_distance,
nondimensional_potential_stiffness
)
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
) -
model.isotensional.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_force
) +
model.isotensional.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_force_ref)
)
)**2
def integrand_denominator(nondimensional_potential_distance):
return (
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy_per_link(
nondimensional_potential_distance,
nondimensional_potential_stiffness
) -
model.modified_canonical.asymptotic.weak_potential.
nondimensional_relative_gibbs_free_energy_per_link(
np.array(nondimensional_potential_distance_ref),
nondimensional_potential_stiffness
)
)**2
numerator = integrate(
integrand_numerator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
denominator = integrate(
integrand_denominator,
parameters.nondimensional_potential_distance_large_1,
parameters.nondimensional_potential_distance_large_2,
parameters.points)
return np.sqrt(numerator/denominator)
residual_rel_1 = residual_rel(
parameters.nondimensional_potential_stiffness_small
)
residual_rel_2 = residual_rel(
parameters.nondimensional_potential_stiffness_small /
parameters.log_log_scale
)
log_log_slope = np.log(residual_rel_2/residual_rel_1) / \
np.log(parameters.log_log_scale)
self.assertLessEqual(
np.abs(log_log_slope + 1.0),
parameters.log_log_tol
)