def main():
natoms = 4
pot = LJ()
reference_coords = np.random.uniform(-1, 1, [3 * natoms])
print reference_coords
# freeze the first two atoms (6 degrees of freedom)
frozen_dof = range(6)
fpot = FrozenPotWrapper(pot, reference_coords, frozen_dof)
reduced_coords = fpot.coords_converter.get_reduced_coords(reference_coords)
print "the energy in the full representation:"
print pot.getEnergy(reference_coords)
print "is the same as the energy in the reduced representation:"
print fpot.getEnergy(reduced_coords)
ret = mylbfgs(reduced_coords, fpot)
print "after a minimization the energy is ", ret.energy, "and the rms gradient is", ret.rms
print "the coordinates of the frozen degrees of freedom are unchanged"
print "starting coords:", reference_coords
print "minimized coords:", fpot.coords_converter.get_full_coords(
ret.coords)
def test2(): # pragma: no cover
import numpy as np
from pele.potentials import LJ
from pele.utils.frozen_atoms import FrozenPotWrapper
from pele.optimize import mylbfgs
natoms = 4
pot = LJ()
reference_coords = np.random.uniform(-1, 1, [3 * natoms])
print reference_coords
# freeze the first two atoms (6 degrees of freedom)
frozen_dof = range(6)
fpot = FrozenPotWrapper(pot, reference_coords, frozen_dof)
reduced_coords = fpot.coords_converter.get_reduced_coords(reference_coords)
print "the energy in the full representation:"
print pot.getEnergy(reference_coords)
print "is the same as the energy in the reduced representation:"
print fpot.getEnergy(reduced_coords)
ret = mylbfgs(reduced_coords, fpot)
print "after a minimization the energy is ", ret.energy, "and the rms gradient is", ret.rms
print "the coordinates of the frozen degrees of freedom are unchanged"
print "starting coords:", reference_coords
print "minimized coords:", fpot.coords_converter.get_full_coords(
ret.coords)
def test2():
import numpy as np
from pele.potentials import LJ
from pele.utils.frozen_atoms import FrozenPotWrapper
from pele.optimize import mylbfgs
natoms = 4
pot = LJ()
reference_coords = np.random.uniform(-1, 1, [3 * natoms])
print reference_coords
# freeze the first two atoms (6 degrees of freedom)
frozen_dof = range(6)
fpot = FrozenPotWrapper(pot, reference_coords, frozen_dof)
reduced_coords = fpot.coords_converter.get_reduced_coords(reference_coords)
print "the energy in the full representation:"
print pot.getEnergy(reference_coords)
print "is the same as the energy in the reduced representation:"
print fpot.getEnergy(reduced_coords)
ret = mylbfgs(reduced_coords, fpot)
print "after a minimization the energy is ", ret.energy, "and the rms gradient is", ret.rms
print "the coordinates of the frozen degrees of freedom are unchanged"
print "starting coords:", reference_coords
print "minimized coords:", fpot.coords_converter.get_full_coords(ret.coords)
def get_potential(self):
try:
return self.pot
except AttributeError:
if self.one_frozen:
# freeze one spin to remove the global rotational symmetry
base_pot = HeisenbergModel(dim=self.dims, field_disorder=0.)
reference_coords = np.zeros(base_pot.nspins * 2)
n = reference_coords.size
frozen_dof = np.array([n-2, n-1])
# self.coords_converter = FrozenCoordsConverter(reference_coords, frozen_dof)
self.pot = FrozenPotWrapper(base_pot, reference_coords, frozen_dof)
self.coords_converter = self.pot.coords_converter
self.pot.G = base_pot.G
self.pot.indices = base_pot.indices
return self.pot
else:
return HeisenbergModelRA(dim=self.dims, field_disorder=self.field_disorder)
def get_potential(self, phases=None):
try:
return self.pot
except AttributeError:
assert self.one_frozen
base_pot = XYModel(dim=self.dim,
phi=self.phi_disorder,
phases=phases)
reference_coords = np.zeros(base_pot.nspins)
n = reference_coords.size
frozen_node = (0, 0)
frozen_index = base_pot.indices[frozen_node]
frozen_dof = np.array([frozen_index])
print "making frozen spin at", self.node2xyz(
base_pot.index2node[frozen_index])
# self.coords_converter = FrozenCoordsConverter(reference_coords, frozen_dof)
self.pot = FrozenPotWrapper(base_pot, reference_coords, frozen_dof)
# self.coords_converter = self.pot.coords_converter
# self.pot.G = base_pot.G
# self.pot.indices = base_pot.indices
return self.pot
def get_potential(self):
pot = LJCluster.get_potential(self)
frozen_pot = FrozenPotWrapper(pot, self.reference_coords, self.frozen_dof)
return frozen_pot