def minimize(self):
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"
try:
from pygmin.optimize import mylbfgs as quench
ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
except ImportError:
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
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
reduced_energy = np.zeros([nreps, nebins, nqbins])
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(visits, reduced_energy)
nvar = nbins + nreps
if False:
X = np.random.rand(nvar)
else:
# estimate an initial guess for the offsets and density of states
# so the minimizer converges more rapidly
offsets_estimate, log_dos_estimate = wham_utils.estimate_dos(
visits, reduced_energy)
X = np.concatenate((offsets_estimate, log_dos_estimate))
assert X.size == nvar
E0, grad = whampot.getEnergyGradient(X)
rms0 = np.linalg.norm(grad) / np.sqrt(grad.size)
from wham_utils import lbfgs_scipy
ret = lbfgs_scipy(X, whampot)
# print "initial energy", whampot.getEnergy(X)
# try:
# from pele.optimize import mylbfgs as quench
# ret = quench(X, whampot, iprint=10, maxstep = 1e4)
# except ImportError:
# from pele.optimize import lbfgs_scipy as quench
# ret = quench(X, whampot)
if self.verbose:
print "chi^2 went from %g (rms %g) to %g (rms %g) in %d iterations" % (
E0, rms0, ret.energy, ret.rms, ret.nfev)
#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 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 minimize(self):
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"
try:
from pygmin.optimize import mylbfgs as quench
ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
except ImportError:
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.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]
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)
from wham_utils import lbfgs_scipy
ret = lbfgs_scipy(X, self.whampot)
# print "initial energy", whampot.getEnergy(X)
# try:
# from pele.optimize import mylbfgs as quench
# ret = quench(X, whampot, iprint=10, maxstep = 1e4)
# except ImportError:
# from pele.optimize import lbfgs_scipy as quench
# ret = quench(X, whampot)
print "quenched energy", ret.energy
#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 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]
class wham1d:
""" class to combine 1d histograms of energy E at
multiple temperatures into one best estimate for the histogram
input will be:
filenames : list of filenames where the data can be found
Tlist # Tlist[k] is the temperature of the simulation in filenames[k]
binenergy = zeros(nebins, float64) #lower edge of bin energy
visits1d = zeros([nrep,nebins], integer) #1d histograms of data
"""
#=============================================================================================
# Constructor.
#=============================================================================================
def __init__(self, Tlist, binenergy, visits1d):
#define some parameters
self.k_B=1.
self.nrep = len(Tlist)
self.nebins = len(binenergy)
self.Tlist = np.array(Tlist, dtype = np.float64)
self.binenergy = np.array(binenergy, dtype = np.float64)
self.visits1d = np.array(visits1d, dtype = np.integer)
def minimize(self):
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"
try:
from pygmin.optimize import mylbfgs as quench
ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
except ImportError:
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.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]
# def calc_Cv_no_wham(self):
# """ """
def calc_Cv_new(self, NDOF, TRANGE=None, NTEMP=100):
from pygmin.thermodynamics import dos_to_cv
dT = (self.Tlist[-1] - self.Tlist[0]) / NTEMP
Tlist = np.arange(self.Tlist[0], self.Tlist[-1], dT)
# print self.logn_E
lZ, U, U2, Cv = dos_to_cv(self.binenergy, self.logn_E, Tlist, K=NDOF)
cvdata = np.zeros([len(Tlist), 6])
cvdata[:,0] = Tlist
cvdata[:,1] = lZ
cvdata[:,2] = U # average potential energy
cvdata[:,3] = U2
cvdata[:,5] = Cv
eavg = U + float(NDOF) / 2 * Tlist # average energy including the kinetic degrees of freedom
cvdata[:,4] = eavg
return cvdata
def calc_Cv(self, NDOF, TRANGE=None, NTEMP=100, use_log_sum=None):
# return self.calc_Cv_new(NDOF, TRANGE, NTEMP)
return wham_utils.calc_Cv(self.logn_E, self.visits1d, self.binenergy,
NDOF, self.Tlist, self.k_B, TRANGE, NTEMP, use_log_sum=use_log_sum)
class wham1d:
""" class to combine 1d histograms of energy E at
multiple temperatures into one best estimate for the histogram
input will be:
filenames : list of filenames where the data can be found
Tlist # Tlist[k] is the temperature of the simulation in filenames[k]
binenergy = zeros(nebins, float64) #lower edge of bin energy
visits1d = zeros([nrep,nebins], integer) #1d histograms of data
"""
#=============================================================================================
# Constructor.
#=============================================================================================
def __init__(self, Tlist, binenergy, visits1d):
#define some parameters
self.k_B = 1.
self.nrep = len(Tlist)
self.nebins = len(binenergy)
self.Tlist = np.array(Tlist, dtype=np.float64)
self.binenergy = np.array(binenergy, dtype=np.float64)
self.visits1d = np.array(visits1d, dtype=np.integer)
def minimize(self):
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"
try:
from pygmin.optimize import mylbfgs as quench
ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
except ImportError:
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.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]
# def calc_Cv_no_wham(self):
# """ """
def calc_Cv_new(self, NDOF, TRANGE=None, NTEMP=100):
from pygmin.thermodynamics import dos_to_cv
dT = (self.Tlist[-1] - self.Tlist[0]) / NTEMP
Tlist = np.arange(self.Tlist[0], self.Tlist[-1], dT)
# print self.logn_E
lZ, U, U2, Cv = dos_to_cv(self.binenergy, self.logn_E, Tlist, K=NDOF)
cvdata = np.zeros([len(Tlist), 6])
cvdata[:, 0] = Tlist
cvdata[:, 1] = lZ
cvdata[:, 2] = U # average potential energy
cvdata[:, 3] = U2
cvdata[:, 5] = Cv
eavg = U + float(
NDOF
) / 2 * Tlist # average energy including the kinetic degrees of freedom
cvdata[:, 4] = eavg
return cvdata
def calc_Cv(self, NDOF, TRANGE=None, NTEMP=100, use_log_sum=None):
# return self.calc_Cv_new(NDOF, TRANGE, NTEMP)
return wham_utils.calc_Cv(self.logn_E,
self.visits1d,
self.binenergy,
NDOF,
self.Tlist,
self.k_B,
TRANGE,
NTEMP,
use_log_sum=use_log_sum)
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
reduced_energy = np.zeros([nreps, nebins, nqbins])
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(visits, reduced_energy)
nvar = nbins + nreps
if False:
X = np.random.rand(nvar)
else:
# estimate an initial guess for the offsets and density of states
# so the minimizer converges more rapidly
offsets_estimate, log_dos_estimate = wham_utils.estimate_dos(visits, reduced_energy)
X = np.concatenate((offsets_estimate, log_dos_estimate))
assert X.size == nvar
E0, grad = whampot.getEnergyGradient(X)
rms0 = np.linalg.norm(grad) / np.sqrt(grad.size)
from wham_utils import lbfgs_scipy
ret = lbfgs_scipy(X, whampot)
# print "initial energy", whampot.getEnergy(X)
# try:
# from pele.optimize import mylbfgs as quench
# ret = quench(X, whampot, iprint=10, maxstep = 1e4)
# except ImportError:
# from pele.optimize import lbfgs_scipy as quench
# ret = quench(X, whampot)
if self.verbose:
print "chi^2 went from %g (rms %g) to %g (rms %g) in %d iterations" % (
E0,
rms0,
ret.energy,
ret.rms,
ret.nfev,
)
# 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)
class wham1d:
""" class to combine 1d histograms of energy E at
multiple temperatures into one best estimate for the histogram
input will be:
filenames : list of filenames where the data can be found
Tlist # Tlist[k] is the temperature of the simulation in filenames[k]
binenergy = zeros(nebins, float64) #lower edge of bin energy
visits1d = zeros([nrep,nebins], integer) #1d histograms of data
"""
#=============================================================================================
# Constructor.
#=============================================================================================
def __init__(self, Tlist, binenergy, visits1d):
#define some parameters
self.k_B = 1.
self.nrep = len(Tlist)
self.nebins = len(binenergy)
self.Tlist = np.array(Tlist, dtype=np.float64)
self.binenergy = np.array(binenergy, dtype=np.float64)
self.visits1d = np.array(visits1d, dtype=np.integer)
def minimize(self):
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 wham_utils import lbfgs_scipy
ret = lbfgs_scipy(X, self.whampot)
# try:
# from pele.optimize import mylbfgs as quench
# ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
# except ImportError:
# from pele.optimize import lbfgs_scipy as quench
# ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
# def calc_Cv_new(self, NDOF, TRANGE=None, NTEMP=100):
# from pele.thermodynamics import dos_to_cv
# dT = (self.Tlist[-1] - self.Tlist[0]) / NTEMP
# Tlist = np.arange(self.Tlist[0], self.Tlist[-1], dT)
## print self.logn_E
# lZ, U, U2, Cv = dos_to_cv(self.binenergy, self.logn_E, Tlist, K=NDOF)
# cvdata = np.zeros([len(Tlist), 6])
# cvdata[:,0] = Tlist
# cvdata[:,1] = lZ
# cvdata[:,2] = U # average potential energy
# cvdata[:,3] = U2
# cvdata[:,5] = Cv
#
# eavg = U + float(NDOF) / 2 * Tlist # average energy including the kinetic degrees of freedom
# cvdata[:,4] = eavg
# return cvdata
def calc_Cv(self, NDOF, TRANGE=None, NTEMP=100, use_log_sum=None):
# return self.calc_Cv_new(NDOF, TRANGE, NTEMP)
return wham_utils.calc_Cv(self.logn_E,
self.visits1d,
self.binenergy,
NDOF,
self.Tlist,
self.k_B,
TRANGE,
NTEMP,
use_log_sum=use_log_sum)
class wham1d:
""" class to combine 1d histograms of energy E at
multiple temperatures into one best estimate for the histogram
input will be:
filenames : list of filenames where the data can be found
Tlist # Tlist[k] is the temperature of the simulation in filenames[k]
binenergy = zeros(nebins, float64) #lower edge of bin energy
visits1d = zeros([nrep,nebins], integer) #1d histograms of data
"""
#=============================================================================================
# Constructor.
#=============================================================================================
def __init__(self, Tlist, binenergy, visits1d):
#define some parameters
self.k_B=1.
self.nrep = len(Tlist)
self.nebins = len(binenergy)
self.Tlist = np.array(Tlist, dtype = np.float64)
self.binenergy = np.array(binenergy, dtype = np.float64)
self.visits1d = np.array(visits1d, dtype = np.integer)
def minimize(self):
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 wham_utils import lbfgs_scipy
ret = lbfgs_scipy(X, self.whampot)
# try:
# from pele.optimize import mylbfgs as quench
# ret = quench(X, self.whampot, iprint=-1, maxstep=1e4)
# except ImportError:
# from pele.optimize import lbfgs_scipy as quench
# ret = quench(X, self.whampot)
#print "quench energy", ret.energy
X = ret.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
# def calc_Cv_new(self, NDOF, TRANGE=None, NTEMP=100):
# from pele.thermodynamics import dos_to_cv
# dT = (self.Tlist[-1] - self.Tlist[0]) / NTEMP
# Tlist = np.arange(self.Tlist[0], self.Tlist[-1], dT)
## print self.logn_E
# lZ, U, U2, Cv = dos_to_cv(self.binenergy, self.logn_E, Tlist, K=NDOF)
# cvdata = np.zeros([len(Tlist), 6])
# cvdata[:,0] = Tlist
# cvdata[:,1] = lZ
# cvdata[:,2] = U # average potential energy
# cvdata[:,3] = U2
# cvdata[:,5] = Cv
#
# eavg = U + float(NDOF) / 2 * Tlist # average energy including the kinetic degrees of freedom
# cvdata[:,4] = eavg
# return cvdata
def calc_Cv(self, NDOF, TRANGE=None, NTEMP=100, use_log_sum=None):
# return self.calc_Cv_new(NDOF, TRANGE, NTEMP)
return wham_utils.calc_Cv(self.logn_E, self.visits1d, self.binenergy,
NDOF, self.Tlist, self.k_B, TRANGE, NTEMP, use_log_sum=use_log_sum)