import unittest
import numpy as np
from polymers import physics
from ..test import Parameters
parameters = Parameters()
FJC = physics.single_chain.fjc.thermodynamics.isotensional.legendre.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 Nondimensional(unittest.TestCase):
def test_helmholtz_free_energy(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
)
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_helmholtz_free_energy = \
model.nondimensional_helmholtz_free_energy(
np.array(nondimensional_force),
temperature
)
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
helmholtz_free_energy = \
model.helmholtz_free_energy(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy / \
parameters.boltzmann_constant/temperature \
- nondimensional_helmholtz_free_energy
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy
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 = \
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
)
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_helmholtz_free_energy = \
model.nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_force),
temperature
)
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
helmholtz_free_energy = \
model.helmholtz_free_energy_per_link(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy / \
parameters.boltzmann_constant/temperature \
- nondimensional_helmholtz_free_energy
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy
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 = \
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
)
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_helmholtz_free_energy = \
model.nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_force)
)
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
helmholtz_free_energy = \
model.relative_helmholtz_free_energy(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy / \
parameters.boltzmann_constant/temperature \
- nondimensional_helmholtz_free_energy
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy
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 = \
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
)
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_helmholtz_free_energy = \
model.nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_force)
)
force = nondimensional_force * \
parameters.boltzmann_constant*temperature/link_length
helmholtz_free_energy = \
model.relative_helmholtz_free_energy_per_link(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy / \
parameters.boltzmann_constant/temperature \
- nondimensional_helmholtz_free_energy
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
class PerLink(unittest.TestCase):
def test_helmholtz_free_energy(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
)
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
helmholtz_free_energy = \
model.helmholtz_free_energy(
np.array(force),
temperature
)
helmholtz_free_energy_per_link = \
model.helmholtz_free_energy_per_link(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy / \
number_of_links \
- helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
helmholtz_free_energy_per_link
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 = \
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
)
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
relative_helmholtz_free_energy = \
model.relative_helmholtz_free_energy(
np.array(force),
temperature
)
relative_helmholtz_free_energy_per_link = \
model.relative_helmholtz_free_energy_per_link(
np.array(force),
temperature
)
residual_abs = \
relative_helmholtz_free_energy / \
number_of_links \
- relative_helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
relative_helmholtz_free_energy_per_link
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 = \
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
)
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_helmholtz_free_energy = \
model.nondimensional_helmholtz_free_energy(
np.array(nondimensional_force),
temperature
)
nondimensional_helmholtz_free_energy_per_link = \
model.nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_force),
temperature
)
residual_abs = \
nondimensional_helmholtz_free_energy / \
number_of_links \
- nondimensional_helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy_per_link
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 = \
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
)
nondimensional_force = \
parameters.nondimensional_force_reference + \
parameters.nondimensional_force_scale*(0.5 - np.random.rand())
nondimensional_relative_helmholtz_free_energy = \
model.nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_force)
)
nondimensional_relative_helmholtz_free_energy_per_link = \
model.nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_force)
)
residual_abs = \
nondimensional_relative_helmholtz_free_energy / \
number_of_links \
- nondimensional_relative_helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
nondimensional_relative_helmholtz_free_energy_per_link
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
class Relative(unittest.TestCase):
def test_helmholtz_free_energy(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
)
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
helmholtz_free_energy = \
model.helmholtz_free_energy(
np.array(force),
temperature
)
helmholtz_free_energy_0 = \
model.helmholtz_free_energy(
np.array(
parameters.zero *
parameters.boltzmann_constant*temperature/link_length
),
temperature
)
relative_helmholtz_free_energy = \
model.relative_helmholtz_free_energy(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy \
- helmholtz_free_energy_0 \
- relative_helmholtz_free_energy
residual_rel = \
residual_abs / \
helmholtz_free_energy_0
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol *
parameters.boltzmann_constant*temperature/link_length
)
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 = \
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
)
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
helmholtz_free_energy_per_link = \
model.helmholtz_free_energy_per_link(
np.array(force),
temperature
)
helmholtz_free_energy_per_link_0 = \
model.helmholtz_free_energy_per_link(
np.array(
parameters.zero *
parameters.boltzmann_constant*temperature/link_length
),
temperature
)
relative_helmholtz_free_energy_per_link = \
model.relative_helmholtz_free_energy_per_link(
np.array(force),
temperature
)
residual_abs = \
helmholtz_free_energy_per_link \
- helmholtz_free_energy_per_link_0 \
- relative_helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
helmholtz_free_energy_per_link_0
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol *
parameters.boltzmann_constant*temperature/link_length
)
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 = \
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
)
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_helmholtz_free_energy = \
model.nondimensional_helmholtz_free_energy(
np.array(nondimensional_force),
temperature
)
nondimensional_helmholtz_free_energy_0 = \
model.nondimensional_helmholtz_free_energy(
np.array(parameters.zero),
temperature
)
nondimensional_relative_helmholtz_free_energy = \
model.nondimensional_relative_helmholtz_free_energy(
np.array(nondimensional_force)
)
residual_abs = \
nondimensional_helmholtz_free_energy \
- nondimensional_helmholtz_free_energy_0 \
- nondimensional_relative_helmholtz_free_energy
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy_0
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 = \
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
)
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_helmholtz_free_energy_per_link = \
model.nondimensional_helmholtz_free_energy_per_link(
np.array(nondimensional_force),
temperature
)
nondimensional_helmholtz_free_energy_per_link_0 = \
model.nondimensional_helmholtz_free_energy_per_link(
np.array(parameters.zero),
temperature
)
nondimensional_relative_helmholtz_free_energy_per_link = \
model.nondimensional_relative_helmholtz_free_energy_per_link(
np.array(nondimensional_force)
)
residual_abs = \
nondimensional_helmholtz_free_energy_per_link \
- nondimensional_helmholtz_free_energy_per_link_0 \
- nondimensional_relative_helmholtz_free_energy_per_link
residual_rel = \
residual_abs / \
nondimensional_helmholtz_free_energy_per_link_0
self.assertLessEqual(
np.abs(residual_abs),
parameters.abs_tol
)
self.assertLessEqual(
np.abs(residual_rel),
parameters.rel_tol
)
class Zero(unittest.TestCase):
def test_relative_helmholtz_free_energy(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
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
relative_helmholtz_free_energy_0 = \
model.relative_helmholtz_free_energy(
np.array(
parameters.zero *
parameters.boltzmann_constant*temperature/link_length
),
temperature
)
self.assertLessEqual(
relative_helmholtz_free_energy_0,
parameters.abs_tol *
parameters.boltzmann_constant*temperature
)
def test_relative_helmholtz_free_energy_per_link(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
)
temperature = \
parameters.temperature_reference + \
parameters.temperature_scale*(0.5 - np.random.rand())
relative_helmholtz_free_energy_per_link_0 = \
model.relative_helmholtz_free_energy_per_link(
np.array(
parameters.zero *
parameters.boltzmann_constant*temperature/link_length
),
temperature
)
self.assertLessEqual(
relative_helmholtz_free_energy_per_link_0,
parameters.abs_tol *
parameters.boltzmann_constant*temperature
)
def test_nondimensional_relative_helmholtz_free_energy(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
)
nondimensional_relative_helmholtz_free_energy_0 = \
model.nondimensional_relative_helmholtz_free_energy(
np.array(parameters.zero)
)
self.assertLessEqual(
nondimensional_relative_helmholtz_free_energy_0,
parameters.abs_tol
)
def test_nondimensional_relative_helmholtz_free_energy_per_link(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
)
nondimensional_relative_helmholtz_free_energy_per_link_0 = \
model.nondimensional_relative_helmholtz_free_energy_per_link(
np.array(parameters.zero)
)
self.assertLessEqual(
nondimensional_relative_helmholtz_free_energy_per_link_0,
parameters.abs_tol
)