def minimize(self):
#shape(visits2d) is now (nqbins, nebins, nreps)
#we need it to be (nreps, nqbins*nebins)
#first reorder indices
nreps = self.nrep
nebins = self.nebins
nqbins = self.nqbins
nbins = self.nebins * self.nqbins
#visits = np.zeros([nreps, nebins, nqbins], np.integer)
reduced_energy = np.zeros([nreps, nebins, nqbins])
# for k in range(self.nrep):
# for j in range(self.nqbins):
# for i in range(self.nebins):
# #visits[k,i,j] = self.visits2d[i,j,k]
# reduced_energy[k,i,j] = self.binenergy[i] / (self.Tlist[k]*self.k_B)
for j in range(self.nqbins):
reduced_energy[:,:,j] = self.binenergy[np.newaxis,:] / (self.Tlist[:,np.newaxis]*self.k_B)
visits = self.visits2d
visits = np.reshape( visits, [nreps, nbins ])
reduced_energy = np.reshape( reduced_energy, [nreps, nbins])
self.logP = np.where( visits != 0, np.log( visits.astype(float) ), 0 )
from wham_potential import WhamPotential
whampot = WhamPotential( self.logP, reduced_energy )
nvar = nbins + nreps
X = np.random.rand(nvar)
print "initial energy", whampot.getEnergy(X)
try:
from pygmin.optimize import mylbfgs as quench
ret = quench(X, whampot, iprint=10, maxstep = 1e4)
except ImportError:
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, whampot)
print "quenched energy", ret.energy
global_min = False
if global_min:
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(stepsize=10.)
takestep.useAdaptiveStep()
takestep.adaptive_class.f = 2.
bh = BasinHopping(X, whampot, takestep)
bh.run(1000)
#self.logn_Eq = zeros([nebins,nqbins], float64)
X = ret.coords
self.logn_Eq = X[nreps:]
self.w_i_final = X[:nreps]
self.logn_Eq = np.reshape(self.logn_Eq, [nebins, nqbins])
self.logn_Eq = np.where( self.visits2d.sum(0) == 0, self.LOGMIN, self.logn_Eq )
def test_basin_hopping(pot, angles):
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
takestep = RandomDisplacement(stepsize = np.pi/4)
takestepa = AdaptiveStepsize(takestep, frequency = 20)
bh = BasinHopping( angles, pot, takestepa, temperature = 1.01)
bh.run(400)
def getInitialCoords(natoms, pot):
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(0.3)
X = np.random.uniform(-1,1,natoms*3)*(1.*natoms)**(1./3)*.1
bh = BasinHopping(X, pot, takestep)
bh.run(30)
X = bh.coords
return X
def test_basin_hopping(pot, angles):
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=20)
bh = BasinHopping(angles, pot, takestepa, temperature=1.01)
bh.run(20)
def getInitialCoords(natoms, pot):
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(0.3)
X = np.random.uniform(-1, 1, natoms * 3) * (1. * natoms)**(1. / 3) * .1
bh = BasinHopping(X, pot, takestep)
bh.run(30)
X = bh.coords
return X
def getSetOfMinLJ(natoms = 11): #for testing purposes
from pygmin.potentials.lj import LJ
pot = LJ()
coords = np.random.uniform(-1,1,natoms*3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage.savenlowest import SaveN
saveit = SaveN(10)
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit, outstream=None)
bh.run(100)
return pot, saveit
def guesstsLJ():
from pygmin.potentials.lj import LJ
pot = LJ()
natoms = 9
coords = np.random.uniform(-1,1,natoms*3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage.savenlowest import SaveN
saveit = SaveN(10)
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit, outstream=None)
bh.run(100)
coords1 = saveit.data[0].coords
coords2 = saveit.data[1].coords
return guessts(coords1, coords2, pot)
def guesstsLJ():
from pygmin.potentials.lj import LJ
pot = LJ()
natoms = 9
coords = np.random.uniform(-1, 1, natoms * 3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage.savenlowest import SaveN
saveit = SaveN(10)
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit, outstream=None)
bh.run(100)
coords1 = saveit.data[0].coords
coords2 = saveit.data[1].coords
return guessts(coords1, coords2, pot)
def getSetOfMinLJ(natoms = 32): #for testing purposes
from pygmin.potentials.lj import LJ
pot = LJ()
coords = np.random.uniform(-1,1,natoms*3)
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage.database import Database
import os
#dbfile = "test.db"
#os.remove(dbfile)
#saveit = Database(db=dbfile)
saveit = Database()
takestep1 = RandomDisplacement()
takestep = AdaptiveStepsize(takestep1, frequency=15)
bh = BasinHopping(coords, pot, takestep, storage=saveit.minimum_adder(), outstream=None)
bh.run(100)
return pot, saveit
def globalMinimization(self):
"""
in experimentation i've never been able to find more than
one minimum
"""
nreps = self.nrep
nbins = self.nebins
visitsT = (self.visits1d)
#print "min vis", np.min(visitsT)
self.logP = np.where( visitsT != 0, np.log( visitsT ), 0 )
#print "minlogp", np.min(self.logP)
self.reduced_energy = self.binenergy[np.newaxis,:] / (self.Tlist[:,np.newaxis] * self.k_B)
self.whampot = WhamPotential(self.logP, self.reduced_energy)
X = np.random.rand( nreps + nbins )
E = self.whampot.getEnergy(X)
print "energy", E
print "quenching"
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
print "quench energy", ret.energy
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(stepsize=10)
takestep.useAdaptiveStep()
takestep.adaptive_class.f = 1.5 #i have no idea what a good stepsize should be
bh = BasinHopping(X, self.whampot, takestep )
import matplotlib.pyplot as plt
for i in range(10):
bh.run(2000)
self.logn_E = bh.coords[nreps:]
cvdata = self.calc_Cv(400)
plt.plot(cvdata[:,0], cvdata[:,5], '-')
plt.show()
X = bh.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
def globalMinimization(self):
"""
in experimentation i've never been able to find more than
one minimum
"""
nreps = self.nrep
nbins = self.nebins
visitsT = (self.visits1d)
#print "min vis", np.min(visitsT)
self.logP = np.where(visitsT != 0, np.log(visitsT), 0)
#print "minlogp", np.min(self.logP)
self.reduced_energy = self.binenergy[np.newaxis, :] / (
self.Tlist[:, np.newaxis] * self.k_B)
self.whampot = WhamPotential(self.logP, self.reduced_energy)
X = np.random.rand(nreps + nbins)
E = self.whampot.getEnergy(X)
print "energy", E
print "quenching"
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
print "quench energy", ret.energy
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
takestep = RandomDisplacement(stepsize=10)
takestep.useAdaptiveStep()
takestep.adaptive_class.f = 1.5 #i have no idea what a good stepsize should be
bh = BasinHopping(X, self.whampot, takestep)
import matplotlib.pyplot as plt
for i in range(10):
bh.run(2000)
self.logn_E = bh.coords[nreps:]
cvdata = self.calc_Cv(400)
plt.plot(cvdata[:, 0], cvdata[:, 5], '-')
plt.show()
X = bh.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
print "magnetization after quench", m
#do basin hopping
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage import savenlowest
takestep = RandomDisplacement(stepsize = np.pi/4)
takestepa = AdaptiveStepsize(takestep, frequency = 10)
storage = savenlowest.SaveN(20)
bh = BasinHopping( coords, pot, takestepa, temperature = 1.01, storage = storage)
bh.run(200)
print "lowest structures fount:"
with open("out.spins", "w") as fout:
for min in storage.data:
m = getm( min.coords )
print "energy", min.energy, "magnetization", m
fout.write( "energy %g magnetization %g\n" % (min.energy, m) )
printspins(fout, pot, min.coords)
fout.write("\n\n")
"""
view the spins with gnuplot using the command
h = 2.
s = 0.7
splot 'out.spins' u 1:2:(0) w p pt 5, '' index 1 u 1:2:(0):($6/h):($7/h):($8/h) w vectors t "fields", '' index 1 u 1:2:(0):($3*s):($4*s):($5*s) w vectors t "spins"
coords = np.zeros(2 * 3 * nmol, np.float64)
coords[0:nmol *
3] = np.random.uniform(-1, 1, [nmol * 3]) * 1.3 * (nsites)**(1. / 3)
for i in range(nmol):
k = nmol * 3 + 3 * i
coords[k:k + 3] = rot.random_aa()
#set up the takestep routine
from pygmin.potentials.rigid_bodies.take_step import RBTakeStep
takestep = RBTakeStep()
#set up the class to save lowest energy structures
from pygmin.storage.savenlowest import SaveN
saveit = SaveN(100)
#set up basinhopping
from pygmin.basinhopping import BasinHopping
bh = BasinHopping(coords, mysys, takestep, storage=saveit.insert)
#run basin hopping
bh.run(40)
#print the saved coords
fname = "otp.xyz"
print "saving xyz coords to", fname
from pygmin.printing.print_atoms_xyz import printAtomsXYZ as printxyz
with open(fname, "w") as fout:
for minimum in saveit.data:
xyz = mysys.getxyz(minimum.coords)
printxyz(fout, xyz, atom_type=["N", "O", "O"])
coords[k : k + 3] = rot.random_aa()
#set up the takestep routine
from pygmin.potentials.rigid_bodies.take_step import RBTakeStep
takestep = RBTakeStep()
#set up the class to save lowest energy structures
from pygmin.storage.savenlowest import SaveN
saveit = SaveN(100)
#set up basinhopping
from pygmin.basinhopping import BasinHopping
bh = BasinHopping(coords, mysys, takestep, storage=saveit.insert )
#run basin hopping
bh.run(40)
#print the saved coords
fname = "otp.xyz"
print "saving xyz coords to", fname
from pygmin.printing.print_atoms_xyz import printAtomsXYZ as printxyz
with open(fname, "w") as fout:
for minimum in saveit.data:
xyz = mysys.getxyz(minimum.coords)
printxyz( fout, xyz, atom_type=["N", "O", "O"])
rotate=0.),
frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0.,
rotate=parameters.rotate),
frequency=50)
group.addBlock(100, step1)
group.addBlock(100, step2)
# with a generate random configuration
genrandom = OXDNAReseed()
# in a reseeding takestep procedure
reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed)
# store all minima in a database
db = Database(db="storage.sqlite", accuracy=1e-2)
# create Basinhopping object
opt = BasinHopping(coords,
potential,
reseed,
db.minimum_adder(),
temperature=parameters.temperature)
# run for 100 steps
opt.run(parameters.nsteps)
# now dump all the minima
i = 0
for m in db.minima():
i += 1
GMIN.userpot_dump("lowest_%03d.dat" % (i), m.coords)
#set up and run basin hopping
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.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)
storage = savenlowest.SaveN(500)
bh = BasinHopping( angles, pot, takestepa, temperature = 1.01, storage = storage)
bh.run(400)
print "minima found"
with open("out.spin", "w") as fout:
for min in storage.data:
print "energy", min.energy
fout.write("#%g\n" % (min.energy))
printspins(fout, pot, min.coords)
fout.write('\n\n')
"""
view this in gnuplot with the command
set size ratio -1
plot 'out.spin' index 0 u 1:2 w p pt 5, '' index 0 u 1:2:($3*0.5):($4*0.5) w vectors
"""
with open("out.energies", "w") as fout:
#set up and run basin hopping
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.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)
storage = savenlowest.SaveN(500)
bh = BasinHopping(angles, pot, takestepa, temperature=1.01, storage=storage)
bh.run(400)
print "minima found"
with open("out.spin", "w") as fout:
for min in storage.data:
print "energy", min.energy
fout.write("#%g\n" % (min.energy))
printspins(fout, pot, min.coords)
fout.write('\n\n')
"""
view this in gnuplot with the command
set size ratio -1
plot 'out.spin' index 0 u 1:2 w p pt 5, '' index 0 u 1:2:($3*0.5):($4*0.5) w vectors
"""
with open("out.energies", "w") as fout:
m = getm(ret[0])
print "magnetization after quench", m
#do basin hopping
from pygmin.basinhopping import BasinHopping
from pygmin.takestep.displace import RandomDisplacement
from pygmin.takestep.adaptive import AdaptiveStepsize
from pygmin.storage import savenlowest
takestep = RandomDisplacement(stepsize=np.pi / 4)
takestepa = AdaptiveStepsize(takestep, frequency=10)
storage = savenlowest.SaveN(20)
bh = BasinHopping(coords, pot, takestepa, temperature=1.01, storage=storage)
bh.run(200)
print "lowest structures fount:"
with open("out.spins", "w") as fout:
for min in storage.data:
m = getm(min.coords)
print "energy", min.energy, "magnetization", m
fout.write("energy %g magnetization %g\n" % (min.energy, m))
printspins(fout, pot, min.coords)
fout.write("\n\n")
"""
view the spins with gnuplot using the command
h = 2.
s = 0.7
splot 'out.spins' u 1:2:(0) w p pt 5, '' index 1 u 1:2:(0):($6/h):($7/h):($8/h) w vectors t "fields", '' index 1 u 1:2:(0):($3*s):($4*s):($5*s) w vectors t "spins"
"""
coords=potential.getCoords()
coords=np.random.random(coords.shape)
# create takestep routine
# we combine a normal step taking
group = takestep.BlockMoves()
step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace, rotate=0.), frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0., rotate=parameters.rotate), frequency=50)
group.addBlock(100, step1)
group.addBlock(100, step2)
# with a generate random configuration
genrandom = OXDNAReseed()
# in a reseeding takestep procedure
reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed)
# store all minima in a database
db = Database(db="storage.sqlite", accuracy=1e-2)
# create Basinhopping object
opt = BasinHopping(coords, potential, reseed, db.minimum_adder(), temperature=parameters.temperature)
# run for 100 steps
opt.run(parameters.nsteps)
# now dump all the minima
i=0
for m in db.minima():
i+=1
GMIN.userpot_dump("lowest_%03d.dat"%(i), m.coords)