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 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():
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)
class ATLJ(BasePotential):
"""
Lennard Jones + three body Axilrod-Teller term
V = sum_ij VLJ_ij + sum_ijk Z * (1 + 3*cos(t1)*cos(t2)*cos(t3)) / (rij * rjk * rik)**3 )
where t1, t2, t3 are the internal angles of the triangle ijk
Z > 0 stabilizes linear vs. triangular geometries
"""
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
def getEnergySlow(self, coords):
Elj = self.lj.getEnergy(coords)
natoms = coords.size / 3
X = np.reshape(coords, [natoms, 3])
Z = self.Z
energy = 0.
for i in range(natoms):
for j in range(i):
for k in range(j):
drij = X[i, :] - X[j, :]
drik = X[i, :] - X[k, :]
drjk = X[j, :] - X[k, :]
rij = np.linalg.norm(drij)
rik = np.linalg.norm(drik)
rjk = np.linalg.norm(drjk)
energy += (Z * (1. + 3. *
np.dot(drij, -drjk) *
np.dot(-drij, -drik) *
np.dot(drik, drjk) / (rij * rik * rjk) ** 2)
/ (rij * rik * rjk) ** 3 )
energy += Elj
return energy
def getEnergyFortran(self, coords):
garbage, e = ATfort.axt(coords, False, self.Z)
Elj = self.lj.getEnergy(coords)
return e + Elj
def getEnergyGradientFortran(self, coords):
grad, e = ATfort.axt(coords, True, self.Z)
elj, gradlj = self.lj.getEnergyGradient(coords)
return e + elj, grad + gradlj
def getEnergy(self, coords):
return self.getEnergyFortran(coords)
def getEnergyGradient(self, coords):
return self.getEnergyGradientFortran(coords)
class ATLJ(BasePotential):
"""
Lennard Jones + three body Axilrod-Teller term
V = sum_ij VLJ_ij + sum_ijk Z * (1 + 3*cos(t1)*cos(t2)*cos(t3)) / (rij * rjk * rik)**3 )
where t1, t2, t3 are the internal angles of the triangle ijk
Z > 0 stabilizes linear vs. triangular geometries
"""
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
def getEnergySlow(self, coords):
Elj = self.lj.getEnergy(coords)
natoms = coords.size // 3
X = np.reshape(coords, [natoms, 3])
Z = self.Z
energy = 0.
for i in range(natoms):
for j in range(i):
for k in range(j):
drij = X[i, :] - X[j, :]
drik = X[i, :] - X[k, :]
drjk = X[j, :] - X[k, :]
rij = np.linalg.norm(drij)
rik = np.linalg.norm(drik)
rjk = np.linalg.norm(drjk)
energy += (Z * (1. + 3. * np.dot(drij, -drjk) *
np.dot(-drij, -drik) * np.dot(drik, drjk) /
(rij * rik * rjk)**2) /
(rij * rik * rjk)**3)
energy += Elj
return energy
def getEnergyFortran(self, coords):
garbage, e = ATfort.axt(coords, False, self.Z)
Elj = self.lj.getEnergy(coords)
return e + Elj
def getEnergyGradientFortran(self, coords):
grad, e = ATfort.axt(coords, True, self.Z)
elj, gradlj = self.lj.getEnergyGradient(coords)
return e + elj, grad + gradlj
def getEnergy(self, coords):
return self.getEnergyFortran(coords)
def getEnergyGradient(self, coords):
return self.getEnergyGradientFortran(coords)
def setup_aatopology(self):
water_sites, ref = water(self.xyzfile)
rbsystem = RBTopology()
rbsystem.add_sites(water_sites)
rbsystem.finalize_setup()
#print len(rbsystem.sites), len(rbsystem.indices)
print "I have %d water molecules in the system" % len(rbsystem.sites)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.atom_indices[0]] - site.atom_positions[0]
pot = LJ(eps=0.1550, sig=3.1536)
# get the flattened coordinate array
print "The initial energy is", pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print "rbpot.getEnergy(rbcoords.coords)", rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
# coords = rbpot.getCoords()
# nrigid = rbcoords.size / 6
# print "nrigid", nrigid
self.potential = rbpot
self.nrigid = len(rbsystem.sites)
self.render_scale = 0.3
self.atom_types = rbsystem.get_atomtypes()
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 = FrozenPotentialWrapper(pot, reference_coords, frozen_dof)
reduced_coords = fpot.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.get_full_coords(ret.coords)
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
print(len(rbsystem.sites), len(rbsystem.indices))
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites) * 6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.indices[0]] - site.atom_positions[0]
# for simplicity just use a lj potential here
pot = LJ(sigma=2.)
# get the flattened coordinate array
print(pot.getEnergy(ref.coords.flatten()))
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print(rbpot.getEnergy(rbcoords.coords))
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g - g_n)
print(cg.posRigid)
print(cg.rotRigid)
ret = lbfgs_py(rbcoords.coords, rbpot)
print(ret.energy)
xyz.write_xyz(open("quenched.xyz", "w"),
rbsystem.to_atomistic(ret.coords),
atomtypes=ref.atomtypes)
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
print len(rbsystem.sites), len(rbsystem.indices)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.indices[0]] - site.atom_positions[0]
# for simplicity just use a lj potential here
pot = LJ(sigma=2.)
# get the flattened coordinate array
print pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
print cg.posRigid
print cg.rotRigid
ret = lbfgs_py(rbcoords.coords, rbpot)
print ret.energy
xyz.write_xyz(open("quenched.xyz", "w"), rbsystem.to_atomistic(ret.coords), atomtypes=ref.atomtypes)
class ATLJ(BasePotential):
"""
Lennard Jones + three body Axilrod-Teller term
V = sum_ij VLJ_ij + sum_ijk Z * (1 + 3*cos(t1)*cos(t2)*cos(t3)) / (rij * rjk * rik)**3 )
where t1, t2, t3 are the internal angles of the triangle ijk
Z > 0 stabilizes linear vs. triangular geometries
"""
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
# def getEnergyWeave(self, coords):
# """
# use weave inline
# """
# Elj = self.lj.getEnergy(coords)
#
# natoms = coords.size/3
# coords = np.reshape(coords, [natoms,3])
# energy=0.
# Z = self.Z
# #support_code
# code = """
# double drij[3];
# double drik[3];
# double drjk[3];
# energy = 0.;
# for (int i=0; i < natoms; ++i){
# for (int j=0; j<i; ++j){
# for (int k=0; k<j; ++k){
#
# double rij = 0.;
# double rik = 0.;
# double rjk = 0.;
#
# for (int d=0; d<3; ++d){
# drij[d] = coords(i,d) - coords(j,d);
# rij += drij[d]*drij[d];
# }
# for (int d=0; d<3; ++d){
# drjk[d] = coords(j,d) - coords(k,d);
# rjk += drjk[d]*drjk[d];
# }
# for (int d=0; d<3; ++d){
# drik[d] = coords(i,d) - coords(k,d);
# rik += drik[d]*drik[d];
# }
#
# rij = sqrt(rij);
# rjk = sqrt(rjk);
# rik = sqrt(rik);
#
# double ctijk = ( -(drij[0]*drjk[0] + drij[1]*drjk[1] + drij[2]*drjk[2]) / (rij * rjk) );
# double ctjki = ( (drjk[0]*drik[0] + drjk[1]*drik[1] + drjk[2]*drik[2]) / (rjk * rik) );
# double ctkij = ( (drik[0]*drij[0] + drik[1]*drij[1] + drik[2]*drij[2]) / (rik * rij) );
#
# double r3 = rij*rjk*rik;
# energy += Z*(1. + 3. * ctijk * ctjki * ctkij) / (r3*r3*r3);
# }
# }
# }
# return_val= energy;
# """
# energy = weave.inline(code, ["coords", "energy", "Z", "natoms"], type_converters=converters.blitz, verbose=2)
# #print "fast energy", Elj, energy
# energy += Elj
# return energy
def getEnergySlow(self, coords):
Elj = self.lj.getEnergy(coords)
natoms = coords.size/3
X = np.reshape(coords, [natoms,3])
Z = self.Z
energy = 0.
for i in range(natoms):
for j in range(i):
for k in range(j):
#print i, j, k
drij = X[i,:] - X[j,:]
drik = X[i,:] - X[k,:]
drjk = X[j,:] - X[k,:]
rij = np.linalg.norm( drij )
rik = np.linalg.norm( drik )
rjk = np.linalg.norm( drjk )
energy += Z * (1. + 3.*\
np.dot( drij, -drjk ) * \
np.dot(-drij, -drik ) * \
np.dot( drik, drjk ) / (rij*rik*rjk)**2) \
/ (rij*rik*rjk)**3
#print "slow energy", Elj, energy
energy += Elj
return energy
def getEnergyFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords)/3
garbage, e = ATfort.axt(coords, False, self.Z)
Elj = self.lj.getEnergy(coords)
return e + Elj
def getEnergyGradientFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords)/3
grad, e = ATfort.axt(coords, True, self.Z)
elj, gradlj = self.lj.getEnergyGradient(coords)
return e + elj, grad + gradlj
def getEnergy(self, coords):
return self.getEnergyFortran(coords)
def getEnergyGradient(self, coords):
#return self.getEnergyGradientNumerical(coords)
return self.getEnergyGradientFortran(coords)
def getEnergy(self, coords):
atom_coords = self.aatopology.to_atomistic(coords)
return LJ.getEnergy(self, atom_coords.flatten())
