def test(natoms=40, boxl=4.0):
import pele.potentials.ljpshiftfast as ljpshift
from pele.optimize import mylbfgs
from pele.utils.neighbor_list import makeBLJNeighborListPot
ntypeA = int(natoms * 0.8)
ntypeB = natoms - ntypeA
rcut = 2.5
freezelist = range(ntypeA / 2) + range(ntypeA, ntypeA + ntypeB / 2)
nfrozen = len(freezelist)
print "nfrozen", nfrozen
coords = np.random.uniform(-1, 1, natoms * 3) * (natoms) ** (1.0 / 3) / 2
NLblj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
blj = FreezePot(NLblj, freezelist, natoms)
pot = makeBLJNeighborListPotFreeze(natoms, freezelist, ntypeA=ntypeA, rcut=rcut, boxl=boxl)
# pot = FreezePot(NLpot, freezelist)
eblj = blj.getEnergy(coords)
print "blj energy", eblj
epot = pot.getEnergy(coords)
print "mcpot energy", epot
print "difference", (epot - eblj) / eblj
pot.test_potential(coords)
print "\n"
ret1 = mylbfgs(coords, blj, iprint=-11)
np.savetxt("out.coords", ret1.coords)
print "energy from quench1", ret1.energy
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "ret1 evaluated in both potentials", pot.getEnergy(ret1.coords), blj.getEnergy(ret1.coords)
print "ret2 evaluated in both potentials", pot.getEnergy(ret2.coords), blj.getEnergy(ret2.coords)
coords = ret1.coords
e1, g1 = blj.getEnergyGradient(coords)
e2, g2 = pot.getEnergyGradient(coords)
print "energy difference from getEnergyGradient", (e2 - e1)
print "largest gradient difference", np.max(np.abs(g2 - g1))
print "rms gradients", np.linalg.norm(g1) / np.sqrt(len(g1)), np.linalg.norm(g2) / np.sqrt(len(g1))
if True:
for subpot in pot.pot.potentials:
nl = subpot
print "number of times neighbor list was remade:", nl.buildcount, "out of", nl.count
if False:
try:
import pele.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(np.reshape(coords, [-1, 3]), "A", 1)
pym.draw_spheres(np.reshape(ret1.coords, [-1, 3]), "A", 2)
pym.draw_spheres(np.reshape(ret2.coords, [-1, 3]), "A", 3)
except ImportError:
print "Could not draw using pymol, skipping this step"
def test(natoms=40, boxl=4.): # pragma: no cover
import pele.potentials.ljpshiftfast as ljpshift
from pele.optimize import mylbfgs
from pele.utils.neighbor_list import makeBLJNeighborListPot
ntypeA = int(natoms * 0.8)
ntypeB = natoms - ntypeA
rcut = 2.5
freezelist = list(range(old_div(ntypeA, 2))) + list(range(ntypeA, ntypeA + old_div(ntypeB, 2)))
nfrozen = len(freezelist)
print("nfrozen", nfrozen)
coords = old_div(np.random.uniform(-1, 1, natoms * 3) * natoms ** (1. / 3), 2)
NLblj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
blj = FreezePot(NLblj, freezelist, natoms)
pot = makeBLJNeighborListPotFreeze(natoms, freezelist, ntypeA=ntypeA, rcut=rcut, boxl=boxl)
eblj = blj.getEnergy(coords)
print("blj energy", eblj)
epot = pot.getEnergy(coords)
print("mcpot energy", epot)
print("difference", old_div((epot - eblj), eblj))
pot.test_potential(coords)
print("\n")
ret1 = mylbfgs(coords, blj, iprint=-11)
np.savetxt("out.coords", ret1.coords)
print("energy from quench1", ret1.energy)
ret2 = mylbfgs(coords, pot, iprint=-1)
print("energy from quench2", ret2.energy)
print("ret1 evaluated in both potentials", pot.getEnergy(ret1.coords), blj.getEnergy(ret1.coords))
print("ret2 evaluated in both potentials", pot.getEnergy(ret2.coords), blj.getEnergy(ret2.coords))
coords = ret1.coords
e1, g1 = blj.getEnergyGradient(coords)
e2, g2 = pot.getEnergyGradient(coords)
print("energy difference from getEnergyGradient", (e2 - e1))
print("largest gradient difference", np.max(np.abs(g2 - g1)))
print("rms gradients", old_div(np.linalg.norm(g1), np.sqrt(len(g1))), old_div(np.linalg.norm(g2), np.sqrt(len(g1))))
if True:
for subpot in pot.pot.potentials:
nl = subpot
print("number of times neighbor list was remade:", nl.buildcount, "out of", nl.count)
if False:
try:
import pele.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(np.reshape(coords, [-1, 3]), "A", 1)
pym.draw_spheres(np.reshape(ret1.coords, [-1, 3]), "A", 2)
pym.draw_spheres(np.reshape(ret2.coords, [-1, 3]), "A", 3)
except ImportError:
print("Could not draw using pymol, skipping this step")
def minima_from_ts(pot, xt, n=None, quench=None, stepmin=0.01, **kwargs):
"""
step off either side of a transition state and quench to find the minima
Parameters
----------
pot : potential object
xt : array
transition state coords
n : array
direction to step off
quench : callable
routine to use to do the quenching
kwargs : dict
parameters to pass to determine_pushoff
"""
if n is None:
# if no direction is given, choose random direction
n = vec_random_ndim(xt.size)
if quench is None:
quench = lambda coords: mylbfgs(coords, pot)
x1 = determine_pushoff(pot, xt, n, stepmin=stepmin, **kwargs)
x2 = determine_pushoff(pot, xt, -n, stepmin=stepmin, **kwargs)
minimum1 = quench(x1)
minimum2 = quench(x2)
return minimum1, minimum2
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 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 minima_from_ts(pot, xt, n=None, quench=None, stepmin=0.01, **kwargs):
"""
step off either side of a transition state and quench to find the minima
Parameters
----------
pot : potential object
xt : array
transition state coords
n : array
direction to step off
quench : callable
routine to use to do the quenching
kwargs : dict
parameters to pass to determine_pushoff
"""
if n is None:
# if no direction is given, choose random direction
n = vec_random_ndim(xt.size)
if quench:
quenchRoutine = lambda coords: quench(coords, pot=pot, **kwargs)
else:
quenchRoutine = lambda coords: mylbfgs(coords, pot=pot, **kwargs)
x1 = determine_pushoff(pot, xt, n, stepmin=stepmin, **kwargs)
x2 = determine_pushoff(pot, xt, -n, stepmin=stepmin, **kwargs)
minimum1 = quench(x1)
minimum2 = quench(x2)
return minimum1, minimum2
def test():
pi = np.pi
nspins = 6
#phases = np.zeros(nspins)
pot = XYModel(nspins, phi = np.pi/8.) #, phases=phases)
angles = np.random.uniform(-pi/4, pi/4, nspins)
print angles
e = pot.getEnergy(angles)
print e
print "numerical gradient"
ret = pot.getEnergyGradientNumerical(angles)
print ret[1]
print "analytical gradient"
ret2 = pot.getEnergyGradient(angles)
print ret2[1]
print ret[0]
print ret2[0]
#try a quench
from pele.optimize import mylbfgs
ret = mylbfgs(angles, pot)
print "quenched e = ", ret.energy
print ret.coords
test_basin_hopping(pot, angles)
def setUp(self):
self.natoms = 18
self.pot = _lj.LJ()
self.pot_comp = LJ()
x = np.random.uniform(-1, 1, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 18
self.pot = _lj.LJ()
self.pot_comp = LJ()
x = np.random.uniform(-1,1, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
from pele.optimize import mylbfgs
self.natoms = 10
self.coords = np.random.uniform(-1,1.,3*self.natoms) * self.natoms**(-1./3)
self.pot = LJ()
ret = mylbfgs(self.coords, self.pot, tol=2.)
self.coords = ret.coords
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
def setUp(self):
self.natoms = 18
ntypeA = 5
self.pot = _lj.BLJCut(self.natoms, ntypeA)
self.pot_comp = LJpshift(self.natoms, ntypeA)
x = np.random.uniform(-1, 1, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def testBLJ(self):
X1 = np.copy(self.X1)
X2 = np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3)/2
#run a quench so the structure is not crazy
ret = mylbfgs(X2, self.pot)
X2 = ret.coords
self.runtest(X1, X2, MinPermDistCluster(measure=MeasureAtomicCluster(permlist=self.permlist)))
def setUp(self):
self.natoms = 18
ntypeA = 5
self.pot = _lj.BLJCut(self.natoms, ntypeA)
self.pot_comp = LJpshift(self.natoms, ntypeA)
x = np.random.uniform(-1, 1, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.0)
self.x = ret.coords
def setUp(self):
self.natoms = 200
rcut = 2.5
self.pot = _lj.LJCut(rcut=rcut)
self.pot_comp = LJpshift(self.natoms, self.natoms, rcut=rcut)
x = np.random.uniform(-rcut*2,rcut*2, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 200
rcut = 2.5
self.pot = _lj.LJCut(rcut=rcut)
self.pot_comp = LJpshift(self.natoms, self.natoms, rcut=rcut)
x = np.random.uniform(-rcut * 2, rcut * 2, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def testBLJ(self):
X1 = np.copy(self.X1)
X2 = old_div(np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3),2)
#run a quench so the structure is not crazy
ret = mylbfgs(X2, self.pot)
X2 = ret.coords
self.runtest(X1, X2, MinPermDistCluster(measure=MeasureAtomicCluster(permlist=self.permlist)))
def setUp(self):
from pele.optimize import mylbfgs
self.natoms = 10
self.coords = np.random.uniform(-1, 1., 3 * self.natoms) * self.natoms ** (-1. / 3)
self.pot = LJ()
ret = mylbfgs(self.coords, self.pot, tol=2.)
self.coords = ret.coords
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
def setUp(self):
self.natoms = 200
boxl = 7.
self.boxvec = [boxl] * 3
self.pot = _lj.LJ(boxvec=self.boxvec)
self.pot_comp = LJ(boxl=boxl)
x = np.random.uniform(-1,1, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 200
boxl = 7.
self.boxvec = [boxl] * 3
self.pot = _lj.LJ(boxvec=self.boxvec)
self.pot_comp = LJ(boxl=boxl)
x = np.random.uniform(-1, 1, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def __init__(self,
coords,
potential,
takeStep,
storage=None,
event_after_step=None,
acceptTest=None,
temperature=1.0,
quench=None,
confCheck=None,
outstream=sys.stdout,
insert_rejected=False):
#########################################################################
# initialize MonteCarlo base class
#########################################################################
MonteCarlo.__init__(self,
coords,
potential,
takeStep,
storage=storage,
event_after_step=event_after_step,
acceptTest=acceptTest,
temperature=temperature,
confCheck=confCheck,
outstream=outstream,
store_initial=False)
if quench is None:
quench = lambda coords: mylbfgs(coords, self.potential)
self.quench = quench
#########################################################################
# do initial quench
#########################################################################
self.markovE_old = self.markovE
res = self.quench(self.coords)
self.result.nfev += res.nfev
self.coords = res.coords
self.markovE = res.energy
self.rms = res.rms
self.funcalls = res.nfev
self.insert_rejected = insert_rejected
if self.storage:
self.storage(self.markovE, self.coords)
# print the initial quench
self.acceptstep = True
self.trial_energy = self.markovE
self.printStep()
self.result.energy = self.markovE
self.result.coords = self.coords.copy()
def setUp(self):
self.natoms = 18
self.ilist = np.array([(i,j) for i in xrange(self.natoms) for j in xrange(i+1,self.natoms)]).reshape(-1)
assert self.ilist.size == self.natoms*(self.natoms-1)
# print self.ilist
self.pot = _lj.LJInteractionList(self.ilist)
self.pot_comp = LJ()
x = np.random.uniform(-1,1, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 200
rcut = 2.5
boxl = 7.
self.boxvec = [boxl] * 3
self.pot = _lj.LJCut(rcut=rcut, boxvec=self.boxvec)
self.pot_comp = LJpshift(self.natoms, self.natoms, rcut=rcut, boxl=boxl)
x = np.random.uniform(-rcut*2,rcut*2, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 18
self.ilist = np.array([(i,j) for i in range(self.natoms) for j in range(i+1,self.natoms)]).reshape(-1)
assert self.ilist.size == self.natoms*(self.natoms-1)
# print self.ilist
self.pot = _lj.LJInteractionList(self.ilist)
self.pot_comp = LJ()
x = np.random.uniform(-1,1, 3*self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 18
frozen_atoms = np.array([1, 2, 5, 9], dtype=int)
reference_coords = np.random.uniform(-1, 1, 3 * self.natoms)
self.pot = _lj.LJFrozen(reference_coords, frozen_atoms)
system = LJClusterFrozen(self.natoms, frozen_atoms, reference_coords)
self.pot_comp = system.get_potential()
x = system.get_random_configuration()
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def setUp(self):
self.natoms = 18
frozen_atoms = np.array([1, 2, 5, 9], dtype=int)
reference_coords = np.random.uniform(-1,1, 3*self.natoms)
self.pot = _lj.LJFrozen(reference_coords, frozen_atoms)
system = LJClusterFrozen(self.natoms, frozen_atoms, reference_coords)
self.pot_comp = system.get_potential()
x = system.get_random_configuration()
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def calculate_spointE(pot, db, nsteps=1000):
min_energies = []
ts_energies = []
ts_id = []
for m1 in db.minima():
#pot = ase_ff(atoms.set_positions(m1.coords.reshape((7, -1))))
res1 = mylbfgs(m1.coords, pot, nsteps=nsteps)
E1 = res1.energy
min_energies.append(E1)
for m2 in db.minima():
if m1 == m2 or m1.id() > m2.id():
continue
try:
ts_coords = db.getTransitionState(m1, m2).coords
res1 = mylbfgs(ts_coords, pot, nsteps=0)
E1 = res1.energy
ts_energies.append(E1)
ts_id.append([m1.id(), m2.id()])
except:
pass
return np.array(min_energies), np.array(ts_energies), np.array(ts_id)
def setUp(self):
from pele.potentials.ljpshiftfast import LJpshift as BLJ
self.natoms = 25
self.ntypeA = int(self.natoms * .8)
self.pot = BLJ(self.natoms, self.ntypeA)
self.permlist = [list(range(self.ntypeA)), list(range(self.ntypeA, self.natoms))]
self.X1 = old_div(np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3),2)
#run a quench so the structure is not crazy
ret = mylbfgs(self.X1, self.pot)
self.X1 = ret.coords
def setUp(self):
from pele.potentials.ljpshiftfast import LJpshift as BLJ
self.natoms = 25
self.ntypeA = int(self.natoms * .8)
self.pot = BLJ(self.natoms, self.ntypeA)
self.permlist = [list(range(self.ntypeA)), list(range(self.ntypeA, self.natoms))]
self.X1 = np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3)/2
#run a quench so the structure is not crazy
ret = mylbfgs(self.X1, self.pot)
self.X1 = ret.coords
def setUp(self):
self.natoms = 200
rcut = 2.5
boxl = 7.
self.boxvec = [boxl] * 3
self.pot = _lj.LJCut(rcut=rcut, boxvec=self.boxvec)
self.pot_comp = LJpshift(self.natoms,
self.natoms,
rcut=rcut,
boxl=boxl)
x = np.random.uniform(-rcut * 2, rcut * 2, 3 * self.natoms)
ret = mylbfgs(x, self.pot_comp, tol=10.)
self.x = ret.coords
def minimise(self, cluster):
'''Minimise a cluster
parameters:
cluster- a Cluster object from bcga.cluster
Using this method will overwrite the coordinates and energy of the
supplied Cluster object.'''
# Set up pele minimiser
coords = cluster._coords.flatten()
quench = lambda coords: mylbfgs(coords, self.potential)
# Minimise
res = quench(coords)
# Get cluster properties back from pele
cluster.energy = res.energy
cluster._coords = np.reshape(res.coords, (-1, 3))
cluster.quenched = True
return cluster
def minima_from_ts(pot, xt, n=None, quench=None, **kwargs):
"""
step off either side of a transition state and quench to find the minima
Parameters
----------
pot : potential object
xt : array
transition state coords
stepmin : float
initial guess for size of pushoff when stepping off the transition state
stepmax : float
maximum size of pushoff when stepping off the transition state
gdiff : float
criterion for choosing a step size. Try to choose a stepsize so that::
(gradpar - gradpar_ts) / gradpar_ts >= gdiff
where gradpar and gradpar_ts is the parallel component of the gradient
after the step and at the top of the transition state
quenchRoutine : callable
routine to use to do the quenching
quenchParams : dict
parameters to pass to quenchRoutine
verbose : bool
"""
# if no direction is given, choose random direction
if n==None:
# TODO: replace by better algorithm with uniform sampling
n = np.random.random(xt.shape)-0.5
if quench is None:
quench = lambda coords : mylbfgs(coords, pot)
#x1 = xt - displace*n
x1 = determinePushoff(pot, xt, n, **kwargs)
x2 = determinePushoff(pot, xt, -n, **kwargs)
#x2 = xt + displace*n
#e1,g1 = getEnergyGradient(x1)
#e2,g2 = getEnergyGradient(x2)
#print np.dot(g1,g2)
minimum1 = quench(x1)
minimum2 = quench(x2)
return minimum1, minimum2
def __init__(self, coords, potential, takeStep, storage=None,
event_after_step=[], acceptTest=None, temperature=1.0,
quench=None, confCheck=[], outstream=sys.stdout,
insert_rejected=False
):
#########################################################################
# initialize MonteCarlo base class
#########################################################################
MonteCarlo.__init__(self, coords, potential, takeStep, storage=storage,
event_after_step=event_after_step,
acceptTest=acceptTest, temperature=temperature,
confCheck=confCheck, outstream=outstream,
store_initial=False)
if quench is None:
quench = lambda coords : mylbfgs(coords, self.potential)
self.quench = quench
#########################################################################
# do initial quench
#########################################################################
self.markovE_old = self.markovE
res = self.quench(self.coords)
self.coords = res.coords
self.markovE = res.energy
self.rms = res.rms
self.funcalls = res.nfev
self.insert_rejected = insert_rejected
if(self.storage):
self.storage(self.markovE, self.coords)
# print the initial quench
self.acceptstep = True
self.trial_energy = self.markovE
self.printStep()
self.result.energy = self.markovE
self.result.coords = self.coords.copy()
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)
pot = XYModel( dim = [L,L], phi = np.pi)
angles = np.random.uniform(-pi, pi, nspins)
print angles
e = pot.getEnergy(angles)
print "energy ", e
# try a quench
if False:
from pele.optimize import mylbfgs
ret = mylbfgs(angles, pot)
print ret
# set up and run basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
# should probably use a different take step routine which takes into account
# the cyclical periodicity of angles
takestep = RandomDisplacement(stepsize = np.pi/4)
takestepa = AdaptiveStepsize(takestep, frequency = 20)
coords = np.zeros([nspins, 2])
for i in range(nspins):
vec = rotations.vec_random()
coords[i, :] = make2dVector(vec)
coords = np.reshape(coords, [nspins * 2])
coordsinit = np.copy(coords)
print coords
e = pot.getEnergy(coords)
print "energy ", e
print "try a quench"
from pele.optimize import mylbfgs
ret = mylbfgs(coords, pot)
print "quenched e = ", ret.energy, "funcalls", ret.nfev
print ret.coords
m = getm(ret[0])
print "magnetization after quench", m
# do basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=10)
coords = np.zeros([nspins, 2])
for i in range(nspins):
vec = rotations.vec_random()
coords[i, :] = make2dVector(vec)
coords = np.reshape(coords, [nspins * 2])
coordsinit = np.copy(coords)
print coords
e = pot.getEnergy(coords)
print "energy ", e
print "try a quench"
from pele.optimize import mylbfgs
ret = mylbfgs(coords, pot)
print "quenched e = ", ret.energy, "funcalls", ret.nfev
print ret.coords
m = getm(ret[0])
print "magnetization after quench", m
# do basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
takestep = RandomDisplacement(stepsize=np.pi / 4)
ntypeA = int(natoms*0.8)
rcut = 2.5
print "natoms", natoms, "ntypea", ntypeA
bljslow = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl, sigBB=1.7)
blj = LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl, sigBB=1.7)
ebljslow = bljslow.getEnergy(coords)
print "blj energy slow", ebljslow
eblj = blj.getEnergy(coords)
print "blj energy ", eblj
blj.test_potential(coords)
print ""
print "partially quenching coords"
ret1 = mylbfgs(coords, blj, iprint=-11, tol=1.)
coords = ret1.coords
ebljslow = bljslow.getEnergy(coords)
print "blj energy slow", ebljslow
eblj = blj.getEnergy(coords)
print "blj energy ", eblj
blj.test_potential(coords, eps=1e-6)
print ""
print "quenching coords"
ret1 = mylbfgs(coords, blj, iprint=-11)
coords = ret1.coords
ebljslow = bljslow.getEnergy(coords)
print "blj energy slow", ebljslow
natoms = int(sys.argv[1])
print "benchmarking lennard jones potential, %d atoms, %d calls" % (natoms, N)
pot_old = LJ()
pot = _lj.LJ()
t0 = time.time()
for i in xrange(N):
x = 1. * (np.random.random(3 * natoms) - 0.5)
clbfgs = _lbfgs.LBFGS_CPP(pot, x, tol=1e-4)
ret = clbfgs.run()
t1 = time.time()
for i in xrange(N):
x = 1. * (np.random.random(3 * natoms) - 0.5)
ret = mylbfgs(x, pot_old, tol=1e-4)
t2 = time.time()
for i in xrange(N):
x = 1. * (np.random.random(3 * natoms) - 0.5)
clbfgs = _lbfgs.LBFGS_CPP(_lj_cython.LJ_cython(), x, tol=1e-4)
ret = clbfgs.run()
t3 = time.time()
for i in xrange(N):
x = 1. * (np.random.random(3 * natoms) - 0.5)
clbfgs = _lbfgs.LBFGS_CPP(pot_old, x, tol=1e-4)
ret = clbfgs.run()
L = 24
nspins = L**2
pot = XYModel(dim=[L, L], phi=np.pi)
angles = np.random.uniform(-pi, pi, nspins)
print(angles)
e = pot.getEnergy(angles)
print("energy ", e)
# try a quench
if False:
from pele.optimize import mylbfgs
ret = mylbfgs(angles, pot)
print(ret)
# set up and run basin hopping
from pele.basinhopping import BasinHopping
from pele.takestep.displace import RandomDisplacement
from pele.takestep.adaptive import AdaptiveStepsize
from pele.storage import savenlowest
# should probably use a different take step routine which takes into account
# the cyclical periodicity of angles
takestep = RandomDisplacement(stepsize=old_div(np.pi, 4))
takestepa = AdaptiveStepsize(takestep, frequency=20)
storage = savenlowest.SaveN(500)
import sys
import _lj
import _lbfgs
from pele.optimize import mylbfgs
N=100
natoms=[10, 13, 20, 30, 31, 38, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150]
print "benchmarking lennard jones potential, %d atoms, %d calls", natoms, N
pot_old = LJ()
pot = _lj.LJ()
clbfgs = _lbfgs.LBFGS(pot)
res = open("results.txt", "w")
for na in natoms:
t0 = time.time()
for i in xrange(N):
x = np.random.random(3*na) - 0.5
ret = clbfgs.run(x)
t1 = time.time()
for i in xrange(N):
x = np.random.random(3*na) - 0.5
ret = mylbfgs(x, pot_old, tol=1e-5)
res.write("%d %f %f\n"%(na, t1-t0, time.time()-t1))
print "%d %f %f\n"%(na, t1-t0, time.time()-t1)
res.close()
def test():
pi = np.pi
L = 8
nspins = L**2
#phases = np.zeros(nspins)
pot = HeisenbergModel( dim = [L,L], field_disorder = 1.) #, phases=phases)
coords = np.zeros([nspins, 2])
for i in range(nspins):
vec = rotations.vec_random()
coords[i,:] = make2dVector(vec)
coords = np.reshape(coords, [nspins*2])
if False:
normfields = np.copy(pot.fields)
for i in range(nspins): normfields[i,:] /= np.linalg.norm(normfields[i,:])
coords = coords3ToCoords2( np.reshape(normfields, [nspins*3] ) )
coords = np.reshape(coords, nspins*2)
#print np.shape(coords)
coordsinit = np.copy(coords)
#print "fields", pot.fields
print coords
if False:
coords3 = coords2ToCoords3(coords)
coords2 = coords3ToCoords2(coords3)
print np.reshape(coords, [nspins,2])
print coords2
coords3new = coords2ToCoords3(coords2)
print coords3
print coords3new
e = pot.getEnergy(coords)
print "energy ", e
if False:
print "numerical gradient"
ret = pot.getEnergyGradientNumerical(coords)
print ret[1]
if True:
print "analytical gradient"
ret2 = pot.getEnergyGradient(coords)
print ret2[1]
print ret[0]
print ret2[0]
print "ratio"
print ret2[1] / ret[1]
print "inverse sin"
print 1./sin(coords)
print cos(coords)
print "try a quench"
from pele.optimize import mylbfgs
ret = mylbfgs(coords, pot, iprint=1)
print "quenched e = ", ret.energy, "funcalls", ret.nfev
print ret.coords
with open("out.spins", "w") as fout:
s = coords2ToCoords3( ret.coords )
h = pot.fields
c = coords2ToCoords3( coordsinit )
for node in pot.G.nodes():
i = pot.indices[node]
fout.write( "%g %g %g %g %g %g %g %g %g %g %g\n" % (node[0], node[1], \
s[i,0], s[i,1], s[i,2], h[i,0], h[i,1], h[i,2], c[i,0], c[i,1], c[i,2] ) )
coords3 = coords2ToCoords3( ret.coords )
m = np.linalg.norm( coords3.sum(0) ) / nspins
print "magnetization after quench", m
test_basin_hopping(pot, coords)
def test2():
import pele.potentials.ljpshiftfast as ljpshiftfast
import pele.potentials.ljpshift as ljpshift
from pele.optimize import mylbfgs
fname = "/scratch/scratch2/js850/library/cluster/spherical/1620/PTMC/q4/oneatom/cavity200-8/ts/coords1.quench"
fname = "/scratch/scratch2/js850/library/cluster/spherical/1620/PTMC/q4/oneatom/cavity200-8/ts/test.coords"
# fname = "out.coords"
if False:
coords = np.array(np.loadtxt(fname))
coords = coords.reshape(-1)
boxl = 11.05209
else:
natoms = 200
coords = np.random.uniform(-1, 1, natoms * 3) * (natoms) ** (1.0 / 3) / 2
print "max, min coords", coords.max(), coords.min()
boxl = 5
natoms = len(coords) / 3
ntypeA = int(natoms * 0.8)
rcut = 2.5
print "natoms", natoms, "ntypea", ntypeA
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
bljfast = ljpshiftfast.LJpshift(natoms, ntypeA, rcut=rcut, boxl=boxl)
pot = makeBLJNeighborListPot(natoms, ntypeA=ntypeA, rcut=rcut, boxl=boxl)
eblj = blj.getEnergy(coords)
print "blj energy", eblj
epot = pot.getEnergy(coords)
print "mcpot energy", epot
print "energy difference", (epot - eblj)
e1, g1 = blj.getEnergyGradient(coords)
e2, g2 = pot.getEnergyGradient(coords)
print "energy difference from getEnergyGradient", (e2 - e1)
print "largest gradient difference", np.max(np.abs(g2 - g1))
print "rms gradients", np.linalg.norm(g1) / np.sqrt(len(g1)), np.linalg.norm(g2) / np.sqrt(len(g1))
if False:
print "quenching"
ret1 = mylbfgs(coords, blj, iprint=-11)
np.savetxt("out.coords", ret1.coords)
print "energy from quench1", ret1.energy
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "max, min quenched coords", coords.max(), coords.min()
print "ret1 evaluated in both potentials", pot.getEnergy(ret1.coords), blj.getEnergy(ret1.coords)
print "ret2 evaluated in both potentials", pot.getEnergy(ret2.coords), blj.getEnergy(ret2.coords)
elif True:
print "quenching"
ret2 = mylbfgs(coords, pot, iprint=-1)
print "energy from quench2", ret2.energy
print "max, min quenched coords", ret2.coords.max(), ret2.coords.min()
print "ret2 evaluated in both potentials", pot.getEnergy(ret2.coords), blj.getEnergy(ret2.coords)
print "and in blj fast ", bljfast.getEnergy(ret2.coords)