def test_dHdlam(self):
ha = pot.harmonicOsc(k=1.0, x_shift=-5.0)
hb = pot.harmonicOsc(k=1.0, x_shift=5.0)
potential = pot.expCoupledHosc(ha=ha, hb=hb, lam=0)
positions = np.linspace(-10, 10, num=5)
# energies only for pot HA
lam = 0
potential.set_lam(lam=lam)
expected_result = np.array([
4.009080e-001, 4.009080e-001, 0.000, -5.846620e+053, -8.526387e+107
])
energies = potential.dhdlam(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_allclose(desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) +
"!\n\tPositions: " + str(positions) +
"\n\tEnergies: " + str(energies))
def test_dHdpos(self):
phase_shift = 0.0
multiplicity = 1.0
amplitude = 1.0
y_offset = 0.0
radians = False
positions = [0, 90, 180, 270, 360]
expected_result = np.array([0, 2, 0, -2, 0])
WavePotential = pot.wavePotential(phase_shift=phase_shift,
multiplicity=multiplicity,
amplitude=amplitude,
y_offset=y_offset,
radians=radians)
WavePotential2 = pot.wavePotential(phase_shift=phase_shift,
multiplicity=multiplicity,
amplitude=amplitude,
y_offset=y_offset,
radians=radians)
potential = pot.torsionPotential(
wave_potentials=[WavePotential, WavePotential2])
energies = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=list(expected_result),
actual=list(energies),
err_msg="The results of " +
potential.name + " are not correct!",
decimal=8)
def test_dhdpos1DNPos(self):
ha = pot1.harmonicOsc(x_shift=-5)
hb = pot1.harmonicOsc(x_shift=5)
setattr(ha, "nDim", 1)
setattr(hb, "nDim", 1)
positions = [5, -5, 2, 0]
expected_result = np.array(
[[[10.], [0.], [10.]], [[0.], [0.], [0.]],
[[7.], [1.0862069], [5.9137931]], [[5.], [2.5], [2.5]]],
ndmin=2)
potential = pot.envelopedPotential(V_is=[ha, hb])
dhdpos = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(dhdpos),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=expected_result,
actual=dhdpos,
err_msg="The results of " +
potential.name + " are not correct!",
decimal=8)
def test_check_positions_1DNPosSameState_Iterable_multiPos(self):
ha = pot1.harmonicOsc(x_shift=-5)
hb = pot1.harmonicOsc(x_shift=5)
potential = pot.envelopedPotential(V_is=[ha, hb])
positions = np.array([4, 2, 3])
expected = np.array([[[4], [4]], [[2], [2]], [[3], [3]]], ndmin=3)
checked = potential._check_positions_type_multiPos(positions=positions)
#print(checked)
np.testing.assert_equal(checked, expected, "not the same sorry.")
def testTraj(self):
integrator = metropolisMonteCarloIntegrator()
ha = OneD.harmonicOscillatorPotential(x_shift=-5)
hb = OneD.harmonicOscillatorPotential(x_shift=5)
pot = OneD.linearCoupledPotentials(Va=ha, Vb=hb)
sys = perturbedSystem(temperature=300.0,
potential=pot,
sampler=integrator)
lam = 0.5
sys.lam = lam
ens = self.convBelt(0.0, 1, system=sys)
def test_energies_1DNPos(self):
ha = pot1.harmonicOsc(x_shift=-5)
hb = pot1.harmonicOsc(x_shift=5)
potential = pot.envelopedPotential(V_is=[ha, hb])
positions = [0, 0.5, 1, 2]
expected = np.array([11.80685282, 10.11828465, 7.9999546, 4.5])
energies = potential.ene(positions)
np.testing.assert_almost_equal(energies,
expected,
err_msg="not the same sorry.",
decimal=5)
def test_check_positions1DNPos(self):
ha = pot1.harmonicOsc(x_shift=-5)
hb = pot1.harmonicOsc(x_shift=5)
potential = pot.envelopedPotential(V_is=[ha, hb])
positions = [0, 0.5, 1, 2]
expected = np.array(
[[[0], [0]], [[0.5], [0.5]], [[1], [1]], [[2], [2]]], ndmin=2)
checked = potential._check_positions_type(positions=positions)
#print(checked)
np.testing.assert_equal(checked, expected, "not the same sorry.")
energies = potential.ene(positions)
def test_run_step(self):
integrator = metropolisMonteCarloIntegrator()
ha = OneD.harmonicOscillatorPotential(x_shift=-5)
hb = OneD.harmonicOscillatorPotential(x_shift=5)
pot = OneD.linearCoupledPotentials(Va=ha, Vb=hb)
sys = perturbedSystem(temperature=300.0,
potential=pot,
sampler=integrator)
ens = self.convBelt(0.0, 1, system=sys)
ens.calculate_total_ensemble_energy()
ens.run()
ens.calculate_total_ensemble_energy()
ens.get_replicas_positions()
def test_dHdpos(self):
Vmax = 100
a = 0
b = 8
positions = [0, 0.1, 0.2, 0.5, 1, 2, 3, 6]
expected_result = np.array([
0, -0.62490234, -1.24921875, -3.11279297, -6.15234375, -11.71875,
-16.11328125, -16.40625
])
potential = pot.doubleWellPot(Vmax=Vmax, a=a, b=b)
energies = potential.dhdpos(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=expected_result,
actual=energies,
err_msg="The results of " +
potential.name + " are not correct!",
decimal=2)
def redraw_states(self,nstates_event):
self.nstates = nstates_event["new"]
#Plotting stuff
for line in self.ax.lines:
if(line != self.eds_line):
self.ax.lines.remove(line)
del line
self.positions_state = np.arange(-4, 4*self.nstates, 0.5)
self.positions = [[x] for x in self.positions_state]
V_is=[pot.harmonicOsc(x_shift=state*4, k=10) for state in range(self.nstates)]
for state_e in [V.ene(self.positions_state) for V in V_is]:
self.ax.plot(self.positions_state, state_e, alpha=0.8, lw=5)
self.ax.set_xlim([-4,(4*self.nstates)])
#pot
self.Eoffs = self.eds_pot.Eoff_i
if(len(self.Eoffs)<self.nstates):
for x in range(len(self.Eoffs), self.nstates):
self.Eoffs.append(0)
elif(len(self.Eoffs)>self.nstates):
self.Eoffs= self.Eoffs[:self.nstates]
self.eoff_sliders_box.children=self.make_eoff_sliders(self.nstates)
self.eds_pot = potN.envelopedPotential(V_is=V_is, s=np.log10(1+(self.s**1.5/1000)), Eoff_i=self.Eoffs)
eds_enes = self.eds_pot.ene(self.positions)
self.eds_line.set_data(self.positions, eds_enes)
self.fig.canvas.draw()
self.fig.canvas.flush_events()
def test_dHdpos(self):
c6: float = 1**(-1)
c12: float = 1**(-1)
x_shift: float = 0
y_shift = 0
positions = [0, 0.1, 0.2, 0.5, 1, 2, 3, 6]
expected_result = np.array([
np.inf, 1.19999940 * 10**14, 1.46479687 * 10**10,
9.75360000 * 10**4, 6.00000000, -4.54101562 * 10**-2,
-2.73595752 * 10**-3, -2.14325517 * 10**-5
])
potential = pot.lennardJonesPotential(c6=c6,
c12=c12,
x_shift=x_shift,
y_shift=y_shift)
energies = potential.dhdpos(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_allclose(desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct!")
def test_energies(self):
c6: float = 1**(-1)
c12: float = 1**(-1)
x_shift: float = 0
y_shift = 0
positions = [0, 0.1, 0.2, 0.5, 1, 2, 3, 6]
expected_result = np.array([
np.nan, 9.99999000 * 10**11, 2.44125000 * 10**8,
4.03200000 * 10**3, 0, -1.53808594 * 10**-2, -1.36986044 * 10**-3,
-2.14330111 * 10**-5
])
potential = pot.lennardJonesPotential(c6=c6,
c12=c12,
x_shift=x_shift,
y_shift=y_shift)
energies = potential.ene(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=expected_result,
actual=energies,
err_msg="The results of " +
potential.name + " are not correct!",
decimal=2)
def test_dHdpos(self):
q1 = 1
q2 = 1
epsilon = 1
positions = [0, 0.2, 0.5, 1, 2, 360]
expected_result = np.array([
-np.inf, -1.98943679, -0.31830988, -0.0795774715, -0.0198943679,
-0.000000614023700
])
potential = pot.coulombPotential(q1=q1, q2=q2, epsilon=epsilon)
energies = potential.dhdpos(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=list(expected_result),
actual=list(energies),
err_msg="The results of " +
potential.name + " are not correct!",
decimal=8)
def test_energies(self):
q1 = 1
q2 = 1
epsilon = 1
positions = [0, 0.2, 0.5, 1, 2, 360]
expected_result = np.array([
np.inf, 0.397887358, 0.159154943, 0.0795774715, 0.0397887358,
0.000221048532
])
potential = pot.coulombPotential(q1=q1, q2=q2, epsilon=epsilon)
energies = potential.ene(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=list(expected_result),
actual=list(energies),
err_msg="The results of " +
potential.name + " are not correct!",
decimal=8)
def __init__(self, potential: pot.envelopedPotential = pot.envelopedPotential(
V_is=[pot.harmonicOscillatorPotential(x_shift=2), pot.harmonicOscillatorPotential(x_shift=-2)], eoff=[0, 0]),
sampler: samplerCls = metropolisMonteCarloIntegrator(),
conditions: Iterable[conditionCls] = [],
temperature: float = 298.0, start_position: Union[Number, Iterable[Number]] = None,
eds_s: float = 1, eds_Eoff: Iterable[Number] = [0, 0]):
"""
__init__
construct a eds-System that can be used to manage a simulation.
Parameters
----------
potential: pot.envelopedPotential, optional
potential function class to be explored by sampling
sampler: sampler, optional
sampling method, that allows exploring the potential function
conditions: Iterable[condition], optional
conditions that shall be applied to the system.
temperature: float, optional
The temperature of the system (default: 298K)
start_position:
starting position for the simulation and setup of the system.
eds_s: float, optional
is the S-value of the EDS-Potential
eds_Eoff: Iterable[Number], optional
giving the energy offsets for the
"""
################################
# Declare Attributes
#################################
self._currentEdsS = eds_s
self._currentEdsEoffs = eds_Eoff
self.state = data.envelopedPStstate
super().__init__(potential=potential, sampler=sampler, conditions=conditions, temperature=temperature,
start_position=start_position)
# Output
self.set_s(self._currentEdsS)
self.set_eoff(self._currentEdsEoffs)
def test_init(self):
integrator = stochastic.metropolisMonteCarloIntegrator()
potential = OneD.harmonicOscillatorPotential()
sys = system.system(potential=potential, sampler=integrator)
replicas = 22
nsteps = 100
T_range = range(288, 310)
setattr(self, "group", None)
group = replica_exchange.temperatureReplicaExchange(
system=sys, temperature_range=T_range)
def test_simulate_good_exchange(self):
integrator = stochastic.metropolisMonteCarloIntegrator()
potential = OneD.harmonicOscillatorPotential()
sys = system.system(potential=potential, sampler=integrator)
replicas = 22
nsteps = 100
T_range = range(288, 310)
group = replica_exchange.temperatureReplicaExchange(
system=sys, temperature_range=T_range)
##print(group.get_Total_Energy())
group.nSteps_between_trials = nsteps
group.simulate(5)
def test_energiesND1Pos_singlePos(self):
ha = pot1.harmonicOsc(x_shift=-5)
hb = pot1.harmonicOsc(x_shift=5)
position = [5, -5]
expected_result = 61.80685281944005
potential = pot.envelopedPotential(V_is=[ha, hb])
potential._set_singlePos_mode()
energies = potential.ene(position)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=expected_result,
actual=energies,
err_msg="The results of " +
potential.name + " are not correct!",
decimal=8)
def main():
TRE = replica_exchange.temperatureReplicaExchange
integrator = stochastic.metropolisMonteCarloIntegrator()
potential = OneD.harmonicOscillatorPotential()
sys = system.system(potential=potential, sampler=integrator)
replicas = 2
nsteps = 10
T_range = np.linspace(288, 310, num=replicas)
group = replica_exchange.temperatureReplicaExchange(
system=sys, temperature_range=T_range)
print("TotENERGY:", group.get_replica_total_energies())
group.nSteps_between_trials = nsteps
group._run_parallel(1)
print("FINI: ",
[traj.shape for key, traj in group.get_trajectories().items()])
def test_dHdpos(self):
x_range = [0, 1]
y_max = 10
y_min = 0
positions = [0, 2, 1, 0.5]
potential = pot.flat_well(x_range=x_range, y_max=y_max, y_min=y_min)
expected_result = np.array([0, 0, 0, 0])
energies = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
self.assertListEqual(list(expected_result),
list(energies),
msg="The results of " + potential.name +
" are not correct!")
def test_energies(self):
fc = 1.0
x_shift = 0.0
y_shift = 0.0
positions = [0, 2, 1, 0.5]
expected_result = np.array([0, 2, 0.5, 0.125])
potential = pot.harmonicOsc(k=fc, x_shift=x_shift, y_shift=y_shift)
energies = potential.ene(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
self.assertListEqual(list(expected_result),
list(energies),
msg="The results of " + potential.name +
" are not correct!")
def test_exchange_all(self):
integrator = stochastic.metropolisMonteCarloIntegrator()
potential = OneD.harmonicOscillatorPotential()
sys = system.system(potential=potential, sampler=integrator)
T_range = range(1, 10)
nReplicas = len(T_range)
positions = {x: float(1) for x in range(nReplicas)}
velocities = {x: float(0) for x in range(nReplicas)}
group = replica_exchange.temperatureReplicaExchange(
system=sys, temperature_range=T_range)
group.set_replicas_positions(positions)
group.set_replicas_velocities(velocities)
group._defaultRandomness = lambda x, y: False
group.exchange()
all_exchanges = group._current_exchanges
finpositions = list(group.get_replicas_positions().values())
finvelocities = list(group.get_replicas_velocities().values())
# Checking:
##constant params?
self.assertEqual(len(group.replicas),
nReplicas,
msg="not enough trajectories were retrieved!")
self.assertListEqual(
finpositions,
list(positions.values()),
msg="Positions should not change during exchange!")
#self.assertListEqual(finvelocities, velocities, msg="Velocities should not change during exchange!")
##exchange process
self.assertEqual(nReplicas // 2,
len(all_exchanges),
msg="length of all exchanges is not correct!")
self.assertTrue(all(list(all_exchanges.values())),
msg="not all exchanges are True!!")
del group
setattr(self, "group", None)
def test_energies(self):
Vmax = 100
a = 0
b = 8
positions = np.linspace(-10, 10, num=5)
expected_result = np.array(
[31.640625, 37.13378906, 100, 37.13378906, 31.640625])
potential = pot.doubleWellPot(Vmax=Vmax, a=a, b=b)
energies = potential.ene(positions)
#print(energies)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(desired=expected_result,
actual=energies,
err_msg="The results of " +
potential.name + " are not correct!",
decimal=2)
def test_constructor(self):
potential = pot.lennardJonesPotential()
def test_dHdpos(self):
fc = 1.0
alpha = 1.0
gamma = 0.0
lam = 0
potential = pot.pertHarmonicOsc(fc=fc,
alpha=alpha,
gamma=gamma,
lam=lam)
positions = np.linspace(-10, 10, num=5)
#energies only for pot HA
lam = 0
potential.set_lam(lam=lam)
expected_result = np.array([-10, -5, 0, 5, 10])
energies = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
#energies only for pot HB
lam = 1
expected_result = np.array([-20, -10, 0, 10, 20])
potential.set_lam(lam=lam)
energies = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
#energies merged for pot HB and HA
lam = 0.5
expected_result = np.array([-15, -7.5, 0, 7.5, 15])
potential.set_lam(lam=lam)
energies = potential.dhdpos(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
def test_constructor(self):
potential = pot.pertHarmonicOsc()
def test_dHdpos(self):
ha = pot.harmonicOsc(k=1.0, x_shift=-5.0)
hb = pot.harmonicOsc(k=1.0, x_shift=5.0)
potential = pot.expCoupledHosc(ha=ha, hb=hb, lam=0)
positions = np.linspace(-10, 10, num=5)
#energies only for pot HA
lam = 0
potential.set_lam(lam=lam)
expected_result = np.array([
-1304235.5118838537, 0.0, 1.9168317203608185e-05,
1.469697537672566e-10, 8.451488578640889e-16
])
energies = potential.dhdpos(positions)
##print("GOT", list(energies))
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
#np.testing.assert_almost_equal(desired=expected_result, actual=energies, err_msg="The results of "+potential.name+" are not correct wit lambda "+str(lam)+"!\n\tPositions: "+str(positions)+"\n\tEnergies: "+str(energies), decimal=2)
#energies only for pot HB
lam = 1
expected_result = np.array([
-2.6622529026263318e+17, -680412108183.5752, -1304235.5118838537,
0.0, 1.9168317203608185e-05
])
potential.set_lam(lam=lam)
energies = potential.dhdpos(positions)
##print("GOT2", list(energies))
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
#np.testing.assert_almost_equal(desired=expected_result, actual=energies, err_msg="The results of "+potential.name+" are not correct wit lambda "+str(lam)+"!\n\tPositions: "+str(positions)+"\n\tEnergies: "+str(energies), decimal=2)
#energies merged for pot HB and HA
lam = 0.5
expected_result = np.array([
-1.331126451319687e+17, -340206054091.7876, -652117.7559323427,
7.34848768836283e-11, 9.584158602226667e-06
])
potential.set_lam(lam=lam)
energies = potential.dhdpos(positions)
##print("GOT3", list(energies))
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
def test_energies(self):
ha = pot.harmonicOsc(k=1.0, x_shift=-5.0)
hb = pot.harmonicOsc(k=1.0, x_shift=5.0)
potential = pot.expCoupledHosc(ha=ha, hb=hb, lam=0)
positions = np.linspace(-10, 10, num=5)
# energies only for pot HA
lam = 0
expected_result = np.array([12.5, 0, 12.5, 50, 112.5])
potential.set_lam(lam=lam)
energies = potential.ene(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
# energies only for pot HB
lam = 1
expected_result = np.array([112.5, 50, 12.5, 0, 12.5])
potential.set_lam(lam=lam)
energies = potential.ene(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
# energies merged for pot HB and HA
lam = 0.5
expected_result = np.array([12.78, 0.28, 12.5, 0.28, 12.78])
potential.set_lam(lam=lam)
energies = potential.ene(positions)
self.assertEqual(
type(expected_result),
type(energies),
msg=
"returnType of potential was not correct! it should be an np.array"
)
np.testing.assert_almost_equal(
desired=expected_result,
actual=energies,
err_msg="The results of " + potential.name +
" are not correct wit lambda " + str(lam) + "!\n\tPositions: " +
str(positions) + "\n\tEnergies: " + str(energies),
decimal=2)
def test_constructor(self):
potential = pot.expCoupledHosc()
def test_constructor(self):
potential = pot.doubleWellPot()