def _detect_equilibration(self, A_t):
"""
Automatically detect equilibrated region.
ARGUMENTS
A_t (numpy.array) - timeseries
RETURNS
t (int) - start of equilibrated data
g (float) - statistical inefficiency of equilibrated data
Neff_max (float) - number of uncorrelated samples
"""
T = A_t.size
# Special case if timeseries is constant.
if A_t.std() == 0.0:
return (0, 1, T)
g_t = numpy.ones([T-1], numpy.float32)
Neff_t = numpy.ones([T-1], numpy.float32)
print T
for t in range(T-1):
print t
g_t[t] = timeseries.statisticalInefficiency(A_t[t:T])
Neff_t[t] = (T-t+1) / g_t[t]
Neff_max = Neff_t.max()
t = Neff_t.argmax()
g = g_t[t]
return (t, g, Neff_max)
def detect_equilibration(A_t):
"""
Automatically detect equilibrated region.
ARGUMENTS
A_t (numpy.array) - timeseries
RETURNS
t (int) - start of equilibrated data
g (float) - statistical inefficiency of equilibrated data
Neff_max (float) - number of uncorrelated samples
"""
T = A_t.size
# Special case if timeseries is constant.
if A_t.std() == 0.0:
return (0, 1, T)
g_t = numpy.ones([T - 1], numpy.float32)
Neff_t = numpy.ones([T - 1], numpy.float32)
for t in range(T - 1):
g_t[t] = timeseries.statisticalInefficiency(A_t[t:T])
Neff_t[t] = (T - t + 1) / g_t[t]
Neff_max = Neff_t.max()
t = Neff_t.argmax()
g = g_t[t]
return (t, g, Neff_max)
def subsample(Q_n,localQ):
print 'Subsampling the data'
g = timeseries.statisticalInefficiency(Q_n)
indices = numpy.array(timeseries.subsampleCorrelatedData(Q_n,g))
print '%i uncorrelated samples found of %i original samples' %(len(indices),len(Q_n))
localQ = localQ[:,indices]
return localQ
def EXPgauss(w_F, compute_uncertainty=True, is_timeseries=False):
"""
Estimate free energy difference using gaussian approximation to one-sided (unidirectional) exponential averaging.
ARGUMENTS
w_F (numpy array) - w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
OPTIONAL ARGUMENTS
compute_uncertainty (boolean) - if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries (boolean) - if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
RETURNS
DeltaF (float) - DeltaF is the free energy difference between the two states.
dDeltaF (float) - dDeltaF is the uncertainty, and is only returned if compute_uncertainty is set to True
NOTE
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
EXAMPLES
Compute the free energy difference given a sample of forward work values.
>>> import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> [DeltaF, dDeltaF] = EXPgauss(w_F)
>>> print 'Forward Gaussian approximated free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Forward Gaussian approximated free energy difference is 1.049 +- 0.089 kT
>>> [DeltaF, dDeltaF] = EXPgauss(w_R)
>>> print 'Reverse Gaussian approximated free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Reverse Gaussian approximated free energy difference is -1.073 +- 0.080 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
var = np.var(w_F)
# Estimate free energy difference by Gaussian approximation, dG = <U> - 0.5*var(U)
DeltaF = np.average(w_F) - 0.5*var
if compute_uncertainty:
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
T_eff = T
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(w_F, w_F)
T_eff = T/g
# Estimate standard error of E[x].
dx2 = var/ T_eff + 0.5*var*var/(T_eff - 1)
dDeltaF = np.sqrt(dx2)
# Return estimate of free energy difference and uncertainty.
return (DeltaF, dDeltaF)
else:
return DeltaF
def EXPgauss(w_F, compute_uncertainty=True, is_timeseries=False):
"""
Estimate free energy difference using gaussian approximation to one-sided (unidirectional) exponential averaging.
ARGUMENTS
w_F (numpy array) - w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
OPTIONAL ARGUMENTS
compute_uncertainty (boolean) - if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries (boolean) - if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
RETURNS
DeltaF (float) - DeltaF is the free energy difference between the two states.
dDeltaF (float) - dDeltaF is the uncertainty, and is only returned if compute_uncertainty is set to True
NOTE
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
EXAMPLES
Compute the free energy difference given a sample of forward work values.
>>> import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> [DeltaF, dDeltaF] = EXPgauss(w_F)
>>> print 'Forward Gaussian approximated free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Forward Gaussian approximated free energy difference is 1.049 +- 0.089 kT
>>> [DeltaF, dDeltaF] = EXPgauss(w_R)
>>> print 'Reverse Gaussian approximated free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Reverse Gaussian approximated free energy difference is -1.073 +- 0.080 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
var = np.var(w_F)
# Estimate free energy difference by Gaussian approximation, dG = <U> - 0.5*var(U)
DeltaF = np.average(w_F) - 0.5 * var
if compute_uncertainty:
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
T_eff = T
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(w_F, w_F)
T_eff = T / g
# Estimate standard error of E[x].
dx2 = var / T_eff + 0.5 * var * var / (T_eff - 1)
dDeltaF = np.sqrt(dx2)
# Return estimate of free energy difference and uncertainty.
return (DeltaF, dDeltaF)
else:
return DeltaF
def getNkandUkln(do_dhdl=False):
"""Identifies uncorrelated samples and updates the arrays of the reduced potential energy and dhdlt retaining data entries of these samples only.
Assumes that 'dhdlt' and 'u_klt' are in memory, as well as proper values for 'sta' and 'fin', i.e. the starting and
final snapshot positions to be read, both are arrays of dimension K."""
u_kln = numpy.zeros([K,K,max(fin-sta)], numpy.float64) # u_kln[k,m,n] is the reduced potential energy of uncorrelated sample index n from state k evaluated at state m
N_k = numpy.zeros(K, int) # N_k[k] is the number of uncorrelated samples from state k
g = numpy.zeros(K,float) # autocorrelation times for the data
if do_dhdl:
dhdl = numpy.zeros([K,n_components,max(fin-sta)], float) #dhdl is value for dhdl for each component in the file at each time.
print "\n\nNumber of correlated and uncorrelated samples:\n\n%6s %12s %12s %12s\n" % ('State', 'N', 'N_k', 'N/N_k')
for k in range(K):
# Sum up over the energy components; notice, that only the relevant data is being used in the third dimension.
dhdl_sum = numpy.sum(dhdlt[k,:,sta[k]:fin[k]], axis=0)
# Determine indices of uncorrelated samples from potential autocorrelation analysis at state k
# (alternatively, could use the energy differences -- here, we will use total dhdl).
g[k] = timeseries.statisticalInefficiency(dhdl_sum)
indices = numpy.array(timeseries.subsampleCorrelatedData(dhdl_sum, g=g[k])) # indices of uncorrelated samples
N = len(indices) # number of uncorrelated samples
# Handle case where we end up with too few.
if N < 50:
if do_dhdl:
print "WARNING: Only %s uncorrelated samples found at lambda number %s; proceeding with analysis using correlated samples..." % (N, k)
indices = numpy.arange(len(dhdl_sum))
N = len(indices)
N_k[k] = N # Store the number of uncorrelated samples from state k.
for l in range(K):
u_kln[k,l,0:N] = u_klt[k,l,indices]
if do_dhdl:
print "%6s %12s %12s %12.2f" % (k, fin[k], N_k[k], g[k])
for n in range(n_components):
dhdl[k,n,0:N] = dhdlt[k,n,indices]
if do_dhdl:
return (dhdl, N_k, u_kln)
return (N_k, u_kln)
def compute_stat_inefficiency2D(pos_xkn,pos_ykn,N_k):
''' computes iacts
'''
logger.info("computing IACTS")
K = pos_xkn.shape[0]
ineff = np.zeros(K,dtype=np.float)
ineffx = np.zeros(K,dtype=np.float)
ineffy = np.zeros(K,dtype=np.float)
for i in range(K):
ineffx[i] = timeseries.statisticalInefficiency( pos_xkn[i,0:N_k[i]] )
ineffy[i] = timeseries.statisticalInefficiency( pos_ykn[i,0:N_k[i]] )
if ineffx[i] > ineffy[i]:
ineff[i] = ineffx[i]
else:
ineff[i] = ineffy[i]
#logger.debug("IACT X and Y %s %s %s",iactx,iacty,i )
logger.info("IACTS computed")
return ineff,ineffx,ineffy
def subsample_series(series, g_t=None, return_g_t=False):
if g_t is None:
g_t = timeseries.statisticalInefficiency(series)
state_indices = timeseries.subsampleCorrelatedData(series, g = g_t, conservative=True)
N_k = len(state_indices)
transfer_series = series[state_indices]
if return_g_t:
return state_indices, transfer_series, g_t
else:
return state_indices, transfer_series
def getefficiency(N_k, U_kn, V_kn, N_kn, type):
K = len(N_k)
g = numpy.ones(K)
ge = numpy.ones(K)
gv = numpy.ones(K)
gn = numpy.ones(K)
if (type != 'volume') and (type != 'number'):
for k in range(K):
ge[k] = timeseries.statisticalInefficiency(U_kn[k, 0:N_k[k]],
fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (ge[k])
print "] as the statistical inefficiencies of the energy"
if type in requireV:
for k in range(K):
gv[k] = timeseries.statisticalInefficiency(V_kn[k, 0:N_k[k]],
fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (gv[k])
print "] as the statistical inefficiencies of the volume"
if type in requireN:
for k in range(K):
gn[k] = timeseries.statisticalInefficiency(N_kn[k, 0:N_k[k]],
fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (gn[k])
print "] as the statistical inefficiencies of the particle number"
for k in range(K):
g[k] = numpy.max([ge[k], gv[k], gn[k]])
print "Using ["
for k in range(K):
print " %.3f " % (g[k])
print "] as the statistical inefficiencies"
return g
def compute_stat_inefficiency1D(pos_kn,N_k):
''' computes iacts
'''
logger.info("computing IACTS")
K = pos_kn.shape[0]
ineff = np.zeros(K,dtype=np.float)
for i in range(K):
ineff[i] = timeseries.statisticalInefficiency( pos_kn[i,0:N_k[i]] )
logger.debug("%d %f\n",i,ineff[i])
logger.info("IACTS computed")
return ineff
def getefficiency(N_k,U_kn,V_kn,N_kn,type):
K = len(N_k)
g = numpy.ones(K)
ge = numpy.ones(K);
gv = numpy.ones(K);
gn = numpy.ones(K);
if (type != 'volume') and (type != 'number'):
for k in range(K):
ge[k] = timeseries.statisticalInefficiency(U_kn[k,0:N_k[k]],fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (ge[k])
print "] as the statistical inefficiencies of the energy"
if type in requireV:
for k in range(K):
gv[k] = timeseries.statisticalInefficiency(V_kn[k,0:N_k[k]],fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (gv[k])
print "] as the statistical inefficiencies of the volume"
if type in requireN:
for k in range(K):
gn[k] = timeseries.statisticalInefficiency(N_kn[k,0:N_k[k]],fast=False)
print "Calculating ["
for k in range(K):
print " %.3f " % (gn[k])
print "] as the statistical inefficiencies of the particle number"
for k in range(K):
g[k] = numpy.max([ge[k],gv[k],gn[k]])
print "Using ["
for k in range(K):
print " %.3f " % (g[k])
print "] as the statistical inefficiencies"
return g
def compute_stat_inefficiency(observ):
''' computes iacts
'''
logger.info("computing IACTS")
ineff = []
for sim in observ:
simIneff = []
for j in range(sim.shape[1]):
simIneff.append( timeseries.statisticalInefficiency( sim[:,j] ) )
ineff.append(simIneff)
ineff = np.array(ineff,dtype=np.float)
logger.info("IACTS computed")
return ineff
def subsample(U_kn,Q_kn,K,N_max):
assume_uncorrelated = False
if assume_uncorrelated:
print 'Assuming data is uncorrelated'
N_k = numpy.zeros(K, numpy.int32)
N_k[:] = N_max
else:
print 'Subsampling the data...'
N_k = numpy.zeros(K,numpy.int32)
g = numpy.zeros(K,numpy.float64)
for k in range(K): # subsample the energies
g[k] = timeseries.statisticalInefficiency(Q_kn[k])#,suppress_warning=True)
indices = numpy.array(timeseries.subsampleCorrelatedData(Q_kn[k],g=g[k])) # indices of uncorrelated samples
N_k[k] = len(indices) # number of uncorrelated samplesadsf
U_kn[k,0:N_k[k]] = U_kn[k,indices]
Q_kn[k,0:N_k[k]] = Q_kn[k,indices]
return U_kn, Q_kn, N_k
def subsample(U_kn,Q_kn,K,N_max):
assume_uncorrelated = False
if assume_uncorrelated:
print 'Assuming data is uncorrelated'
N_k = numpy.zeros(K, numpy.int32)
N_k[:] = N_max
else:
print 'Subsampling the data...'
N_k = numpy.zeros(K,numpy.int32)
g = numpy.zeros(K,numpy.float64)
for k in range(K): # subsample the energies
g[k] = timeseries.statisticalInefficiency(Q_kn[k])#,suppress_warning=True)
indices = numpy.array(timeseries.subsampleCorrelatedData(Q_kn[k],g=g[k])) # indices of uncorrelated samples
N_k[k] = len(indices) # number of uncorrelated samplesadsf
U_kn[k,0:N_k[k]] = U_kn[k,indices]
Q_kn[k,0:N_k[k]] = Q_kn[k,indices]
return U_kn, Q_kn, N_k
def find_g_t_states(u_kln, states=None, nequil=None):
#Subsample multiple states, this assumes you want to subsample independent of what was fed in
if states is None:
states = numpy.array(range(nstates))
num_sample = len(states)
if nequil is None:
gen_nequil = True
nequil = numpy.zeroes(num_sample, dtype=numpy.int32)
else:
if len(nequil) != num_sample:
print "nequil length needs to be the same as length as states!"
raise
else:
gen_nequl = False
g_t = numpy.zeros([num_sample])
Neff_max = numpy.zeros([num_sample])
for state in states:
g_t[state] = timeseries.statisticalInefficiency(u_kln[k,k,nequil[state]:])
Neff_max[k] = (u_kln[k,k,:].size + 1) / g_t[state]
return g_t, Neff_max
def EXP(w_F, compute_uncertainty=True, is_timeseries=False):
"""Estimate free energy difference using one-sided (unidirectional) exponential averaging (EXP).
Parameters
----------
w_F : np.ndarray, float
w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
compute_uncertainty : bool, optional, default=True
if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries : bool, default=False
if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
Returns
-------
DeltaF : float
DeltaF is the free energy difference between the two states.
dDeltaF : float
dDeltaF is the uncertainty, and is only returned if compute_uncertainty is set to True
Notes
-----
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
Examples
--------
Compute the free energy difference given a sample of forward work values.
>>> from pymbar import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> [DeltaF, dDeltaF] = EXP(w_F)
>>> print('Forward free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF))
Forward free energy difference is 1.088 +- 0.076 kT
>>> [DeltaF, dDeltaF] = EXP(w_R)
>>> print('Reverse free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF))
Reverse free energy difference is -1.073 +- 0.082 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
# Estimate free energy difference by exponential averaging using DeltaF = - log < exp(-w_F) >
DeltaF = - (logsumexp(- w_F) - np.log(T))
if compute_uncertainty:
# Compute x_i = np.exp(-w_F_i - max_arg)
max_arg = np.max(-w_F) # maximum argument
x = np.exp(-w_F - max_arg)
# Compute E[x] = <x> and dx
Ex = x.mean()
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(x, x)
# Estimate standard error of E[x].
dx = np.std(x) / np.sqrt(T / g)
# dDeltaF = <x>^-1 dx
dDeltaF = (dx / Ex)
# Return estimate of free energy difference and uncertainty.
return (DeltaF, dDeltaF)
else:
return DeltaF
T_k = T[-2::] files = ['%s/energy%i.npy' % (direc, T[-2]), '%s/energy%i.npy' % (direc, T[-1])] #file=['/home/edz3fz/checkensemble_high/CE_high.txt','/home/edz3fz/checkensemble_low/CE_low.txt'] #file=[direc+'/energy426.txt',direc+'/energy442.txt'] #file = ['/home/edz3fz/surface_replica_exchange/replica0/energy300.txt', '/home/edz3fz/surface_replica_exchange/replica3/energy356.txt'] down=load(files[0]) up=load(files[1]) length = len(down) down = down[length/2::] up = up[length/2::] #up=up[-50000::] #down=down[-50000::] #up=up[::100] #down=down[::100] g_up = timeseries.statisticalInefficiency(up) indices_up = numpy.array(timeseries.subsampleCorrelatedData(up,g=g_up)) print len(indices_up), 'samples' g_down = timeseries.statisticalInefficiency(down) indices_down = numpy.array(timeseries.subsampleCorrelatedData(up,g=g_down)) print len(indices_down), 'samples' type='total' U_kn=zeros([2,len(up)]) U_kn[0,0:len(indices_down)] = down[indices_down] U_kn[1,0:len(indices_up)] = up[indices_up] #T_k=array([300.,336.8472786]) #T_k=array([426.81933819,442.13650313])
# dtau_end = tau_end_i.std() / numpy.sqrt(float(nblocks))
# Print.
print "tau_end = %.3f+-%.3f iterations" % (tau_end, dtau_end)
del states
# Compute statistical inefficiency for reduced potential
energies = ncfile.variables['energies'][:, :, :].copy()
states = ncfile.variables['states'][:, :].copy()
u_n = numpy.zeros([niterations], numpy.float64)
for iteration in range(niterations):
u_n[iteration] = 0.0
for replica in range(nstates):
state = states[iteration, replica]
u_n[iteration] += energies[iteration, replica, state]
del energies, states
g_u = timeseries.statisticalInefficiency(u_n)
tau_u = (g_u - 1.0) / 2.0
print "g_u = %8.1f iterations" % g_u
print "tau_u = %8.1f iterations" % tau_u
# DEBUG for lactalbumin
#continue
# Compute torsions.
print "Computing torsions..."
positions = ncfile.variables['positions'][:, :, :, :]
coordinates = units.Quantity(
numpy.zeros([natoms, ndim], numpy.float32), units.angstroms)
phi_it = units.Quantity(
numpy.zeros([nstates, niterations], numpy.float32), units.radians)
psi_it = units.Quantity(
) # N_k[k] is the number of uncorrelated samples from simulation index k
reduced_expectation_data = []
if len(expectation_columns) > 0:
for i in range(len(expectation_columns)):
reduced_expectation_data.append(
numpy.zeros([K, N_samples], numpy.float64))
reduced_fep_data = []
if len(fep_columns) > 0:
for i in range(len(fep_columns)):
reduced_fep_data.append(numpy.zeros([K, N_samples], numpy.float64))
for k in range(K):
# Extract timeseries.
A_t = biasing_variable_kt[0][k, :]
# Compute statistical inefficiency.
try:
g = timeseries.statisticalInefficiency(A_t)
except Exception as e:
print str(e)
print A_t
# Subsample data.
if subsample_trajectories:
indices = timeseries.subsampleCorrelatedData(A_t, g=g)
else:
indices = timeseries.subsampleCorrelatedData(A_t, g=1)
N = len(indices) # number of uncorrelated samples
print "k = %5d : g = %.1f, N = %d" % (k, g, N)
for i in range(nbiases):
biasing_variable_kn[i][k, 0:N] = biasing_variable_kt[i][k, indices]
for i in range(nperturbations + 1):
U_kn[i][k, 0:N] = U_kt[i][k, indices]
#!/usr/bin/python
import string
import os
import sys
import numpy as np
import timeseries
dat1 = np.loadtxt("t1.dat", delimiter=None)
dat2 = np.loadtxt("t2.dat", delimiter=None)
g1 = timeseries.statisticalInefficiency(dat1, fast=True)
g2 = timeseries.statisticalInefficiency(dat2, fast=True)
nsamp1 = dat1.size / g1
nsamp2 = dat1.size / g2
avg1 = np.mean(dat1)
avg2 = np.mean(dat2)
sig1 = np.power(np.var(dat1) / nsamp1, 0.5)
sig2 = np.power(np.var(dat2) / nsamp2, 0.5)
print avg1, 3. * sig1
print avg2, 3. * sig2
def _subsample_kln(self, u_kln):
#Try to load in the data
if self.save_equil_data: #Check if we want to save/load equilibration data
try:
equil_data = numpy.load(
os.path.join(
self.source_directory, self.save_prefix + self.phase +
'_equil_data_%s.npz' % self.subsample_method))
if self.nequil is None:
self.nequil = equil_data['nequil']
elif type(self.nequil
) is int and self.subsample_method == 'per-state':
print "WARRNING: Per-state subsampling requested with only single value for equilibration..."
try:
self.nequil = equil_data['nequil']
print "Loading equilibration from file with %i states read" % self.nstates
except:
print "Assuming equal equilibration per state of %i" % self.nequil
self.nequil = numpy.array([self.nequil] * self.nstates)
self.g_t = equil_data['g_t']
Neff_max = equil_data['Neff_max']
#Do equilibration if we have not already
if self.subsample_method == 'per-state' and (
len(self.g_t) < self.nstates
or len(self.nequil) < self.nstates):
equil_loaded = False
raise IndexError
else:
equil_loaded = True
except:
if self.subsample_method == 'per-state':
self.nequil = numpy.zeros([self.nstates],
dtype=numpy.int32)
self.g_t = numpy.zeros([self.nstates])
Neff_max = numpy.zeros([self.nstates])
for k in xrange(self.nstates):
if self.verbose:
print "Computing timeseries for state %i/%i" % (
k, self.nstates - 1)
self.nequil[k] = 0
self.g_t[k] = timeseries.statisticalInefficiency(
u_kln[k, k, :])
Neff_max[k] = (u_kln[k, k, :].size + 1) / self.g_t[k]
#[self.nequil[k], self.g_t[k], Neff_max[k]] = self._detect_equilibration(u_kln[k,k,:])
else:
if self.nequil is None:
[self.nequil, self.g_t,
Neff_max] = self._detect_equilibration(self.u_n)
else:
[self.nequil_timeseries, self.g_t,
Neff_max] = self._detect_equilibration(self.u_n)
equil_loaded = False
if not equil_loaded:
numpy.savez(os.path.join(
self.source_directory, self.save_prefix + self.phase +
'_equil_data_%s.npz' % self.subsample_method),
nequil=self.nequil,
g_t=self.g_t,
Neff_max=Neff_max)
elif self.nequil is None:
if self.subsample_method == 'per-state':
self.nequil = numpy.zeros([self.nstates], dtype=numpy.int32)
self.g_t = numpy.zeros([self.nstates])
Neff_max = numpy.zeros([self.nstates])
for k in xrange(self.nstates):
[self.nequil[k], self.g_t[k],
Neff_max[k]] = self._detect_equilibration(u_kln[k, k, :])
if self.verbose:
print "State %i equilibrated with %i samples" % (
k, int(Neff_max[k]))
else:
[self.nequil, self.g_t,
Neff_max] = self._detect_equilibration(self.u_n)
if self.verbose: print[self.nequil, Neff_max]
# 1) Discard equilibration data
# 2) Subsample data to obtain uncorrelated samples
self.N_k = numpy.zeros(self.nstates, numpy.int32)
if self.subsample_method == 'per-state':
# Discard samples
nsamples_equil = self.niterations - self.nequil
self.u_kln = numpy.zeros(
[self.nstates, self.nstates,
nsamples_equil.max()])
for k in xrange(self.nstates):
self.u_kln[k, :, :nsamples_equil[k]] = u_kln[k, :,
self.nequil[k]:]
#Subsample
transfer_retained_indices = numpy.zeros(
[self.nstates, nsamples_equil.max()], dtype=numpy.int32)
for k in xrange(self.nstates):
state_indices = timeseries.subsampleCorrelatedData(
self.u_kln[k, k, :], g=self.g_t[k])
self.N_k[k] = len(state_indices)
transfer_retained_indices[k, :self.N_k[k]] = state_indices
transfer_kln = numpy.zeros(
[self.nstates, self.nstates,
self.N_k.max()])
self.retained_indices = numpy.zeros(
[self.nstates, self.N_k.max()], dtype=numpy.int32)
for k in xrange(self.nstates):
self.retained_indices[
k, :self.N_k[k]] = transfer_retained_indices[
k, :self.N_k[k]] #Memory reduction
transfer_kln[k, :, :self.N_k[k]] = self.u_kln[
k, :, self.retained_indices[k, :self.N_k[
k]]].T #Have to transpose since indexing in this way causes issues
#Cut down on memory, once function is done, transfer_kln should be released
self.u_kln = transfer_kln
self.retained_iters = self.N_k
else:
#Discard Samples
self.u_kln = u_kln[:, :, self.nequil:]
self.u_n = self.u_n[self.nequil:]
#Subsamples
indices = timeseries.subsampleCorrelatedData(
self.u_n, g=self.g_t) # indices of uncorrelated samples
self.u_kln = self.u_kln[:, :, indices]
self.N_k[:] = len(indices)
self.retained_indices = indices
self.retained_iters = len(indices)
return
mask_kt[k,0:T_k[k]] = True
# Create a list from this mask.
all_data_indices = where(mask_kt)
# Construct equal-frequency extension bins
print "binning data..."
bin_kt = zeros([K, T_max], int32)
(bin_left_boundary_i, bin_center_i, bin_width_i, bin_assignments) = construct_nonuniform_bins(x_kt[all_data_indices], nbins)
bin_kt[all_data_indices] = bin_assignments
# Compute correlation times.
N_max = 0
g_k = zeros([K], float64)
for k in range(K):
# Compute statistical inefficiency for extension timeseries
g = timeseries.statisticalInefficiency(x_kt[k,0:T_k[k]], x_kt[k,0:T_k[k]])
# store statistical inefficiency
g_k[k] = g
print "timeseries %d : g = %.1f, %.0f uncorrelated samples (of %d total samples)" % (k+1, g, floor(T_k[k] / g), T_k[k])
N_max = max(N_max, ceil(T_k[k] / g) + 1)
# Subsample trajectory position data.
x_kn = zeros([K, N_max], float64)
bin_kn = zeros([K, N_max], int32)
N_k = zeros([K], int32)
for k in range(K):
# Compute correlation times for potential energy and chi timeseries.
indices = timeseries.subsampleCorrelatedData(x_kt[k,0:T_k[k]])
# Store subsampled positions.
N_k[k] = len(indices)
x_kn[k,0:N_k[k]] = x_kt[k,indices]
#!/usr/bin/env python
#Usage: calc_acf file [colnr [ndiscard] ]
import sys, timeseries
from numpy import *
if len(sys.argv) > 2:
colnr = int(sys.argv[2])
else:
colnr = 1
if len(sys.argv) > 3:
ndiscard = int(sys.argv[3])
else:
ndiscard = 0
lines = [line for line in open(sys.argv[1]).readlines() if line[0] != '#']
f = array([float(line.split()[colnr - 1]) for line in lines[ndiscard:]])
print timeseries.statisticalInefficiency(f)
infile = open(filename, 'r')
lines = infile.readlines()
infile.close()
# Parse data.
n = 0
for line in lines:
if line[0] != '#' and line[0] != '@':
tokens = line.split()
u_kn[k,n] = beta_k[k] * (float(tokens[2]) - float(tokens[1])) # reduced potential energy without umbrella restraint
n += 1
# Compute correlation times for potential energy and chi
# timeseries. If the temperatures differ, use energies to determine samples; otherwise, use the cosine of chi
if (DifferentTemperatures):
g_k[k] = timeseries.statisticalInefficiency(u_kn[k,:], u_kn[k,0:N_k[k]])
print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(u_kn[k,0:N_k[k]])
else:
chi_radians = chi_kn[k,0:N_k[k]]/(180.0/numpy.pi)
g_cos = timeseries.statisticalInefficiency(numpy.cos(chi_radians))
g_sin = timeseries.statisticalInefficiency(numpy.sin(chi_radians))
print "g_cos = %.1f | g_sin = %.1f" % (g_cos, g_sin)
g_k[k] = max(g_cos, g_sin)
print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(chi_radians, g=g_k[k])
# Subsample data.
N_k[k] = len(indices)
u_kn[k,0:N_k[k]] = u_kn[k,indices]
chi_kn[k,0:N_k[k]] = chi_kn[k,indices]
# infile = open(filename, 'r')
# lines = infile.readlines()
# infile.close()
# Parse data.
# n = 0
# for line in lines:
# if line[0] != '#' and line[0] != '@':
# tokens = line.split()
# u_kn[k,n] = beta_k[k] * (float(tokens[2]) - float(tokens[1])) # reduced potential energy without umbrella restraint
# n += 1
# Compute correlation times for potential energy and val
# timeseries. If the temperatures differ, use energies to determine samples; otherwise, use the cosine of val
if (DifferentTemperatures):
g_k[k] = timeseries.statisticalInefficiency(u_kn[k,:], u_kn[k,:])
print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(u_kn[k,:])
else:
#g_k[k] = timeseries.statisticalInefficiency(val_kn[k,:], val_kn[k,:])
#print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(val_kn[k,0:N_k[k]], fast=True, verbose=True)
# Subsample data.
N_k[k] = len(indices)
u_kn[k,0:N_k[k]] = u_kn[k,indices]
val_kn[k,0:N_k[k]] = val_kn[k,indices]
# print val_kn[k,0:N_k[k]]
# Set zero of u_kn -- this is arbitrary.
u_kn -= u_kn.min()
cluster_bin_kn = -1*numpy.ones([K,N_samples], numpy.int32) # cluster_bin_kn[k,n] is the cluster bin index of snapshot n of umbrella simulation k
N_k = numpy.zeros([K], numpy.int32) # N_k[k] is the number of uncorrelated samples from simulation index k
reduced_expectation_data = []
if len(expectation_columns) > 0:
for i in range(len(expectation_columns)):
reduced_expectation_data.append(numpy.zeros([K,N_samples], numpy.float64))
reduced_fep_data = []
if len(fep_columns) > 0:
for i in range(len(fep_columns)):
reduced_fep_data.append(numpy.zeros([K,N_samples], numpy.float64))
for k in range(K):
# Extract timeseries.
A_t = biasing_variable_kt[0][k,:]
# Compute statistical inefficiency.
try:
g = timeseries.statisticalInefficiency(A_t)
except Exception as e:
print str(e)
print A_t
# Subsample data.
if subsample_trajectories:
indices = timeseries.subsampleCorrelatedData(A_t, g=g)
else:
indices = timeseries.subsampleCorrelatedData(A_t, g=1)
N = len(indices) # number of uncorrelated samples
print "k = %5d : g = %.1f, N = %d" % (k, g, N)
for i in range(nbiases):
biasing_variable_kn[i][k,0:N] = biasing_variable_kt[i][k,indices]
for i in range(nperturbations+1):
U_kn[i][k,0:N] = U_kt[i][k,indices]
'%s/energy%i.npy' % (direc, T[-1]) ] #file=['/home/edz3fz/checkensemble_high/CE_high.txt','/home/edz3fz/checkensemble_low/CE_low.txt'] #file=[direc+'/energy426.txt',direc+'/energy442.txt'] #file = ['/home/edz3fz/surface_replica_exchange/replica0/energy300.txt', '/home/edz3fz/surface_replica_exchange/replica3/energy356.txt'] down = load(files[0]) up = load(files[1]) length = len(down) down = down[length / 2::] up = up[length / 2::] #up=up[-50000::] #down=down[-50000::] #up=up[::100] #down=down[::100] g_up = timeseries.statisticalInefficiency(up) indices_up = numpy.array(timeseries.subsampleCorrelatedData(up, g=g_up)) print len(indices_up), 'samples' g_down = timeseries.statisticalInefficiency(down) indices_down = numpy.array(timeseries.subsampleCorrelatedData(up, g=g_down)) print len(indices_down), 'samples' type = 'total' U_kn = zeros([2, len(up)]) U_kn[0, 0:len(indices_down)] = down[indices_down] U_kn[1, 0:len(indices_up)] = up[indices_up] #T_k=array([300.,336.8472786]) #T_k=array([426.81933819,442.13650313]) #T_k=array([424.67492585,450]) #T_k=array([437.99897735,450])
n_samples, n_bins = bp.shape
bi = np.arange(n_bins)
pmf = -0.6*np.log(bp)
pmf_mean = pmf.mean(axis=0)
pmf_mean -= np.min(pmf_mean)
pmf_std = pmf.std(axis=0)
# Calculate statistical inefficiency
try:
g = np.load(stat_ineff_file)
except:
g = np.zeros((n_bins,))
for k in xrange(n_bins):
g[k] = timeseries.statisticalInefficiency(pmf[:,k])
np.save(stat_ineff_file, g)
pmf_err = 1.96*g*pmf_std/np.sqrt(n_samples)
offset = np.min(pmf_mean - pmf_err)
pmf_mean -= offset
fig = plt.figure(1, figsize=fsize)
ax = fig.add_subplot(111)
ax.plot(bi, pmf_mean, color='black', lw=2, zorder=1000)
ax.fill_between(bi, pmf_mean + pmf_err, pmf_mean - pmf_err, alpha=.4, facecolor='gray', edgecolor='black', lw=1, zorder=900)
ax.set_xlabel(r'$\alpha$')
ax.set_ylabel(r'$G_{\alpha}$ (kcal/mol)')
def EXP(w_F, compute_uncertainty=True, is_timeseries=False):
"""
Estimate free energy difference using one-sided (unidirectional) exponential averaging (EXP).
ARGUMENTS
w_F (numpy array) - w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
OPTIONAL ARGUMENTS
compute_uncertainty (boolean) - if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries (boolean) - if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
RETURNS
DeltaF (float) - DeltaF is the free energy difference between the two states.
dDeltaF (float) - dDeltaF is the uncertainty, and is only returned if compute_uncertainty is set to True
NOTE
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
EXAMPLES
Compute the free energy difference given a sample of forward work values.
>>> import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> [DeltaF, dDeltaF] = EXP(w_F)
>>> print 'Forward free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Forward free energy difference is 1.088 +- 0.076 kT
>>> [DeltaF, dDeltaF] = EXP(w_R)
>>> print 'Reverse free energy difference is %.3f +- %.3f kT' % (DeltaF, dDeltaF)
Reverse free energy difference is -1.073 +- 0.082 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
# Estimate free energy difference by exponential averaging using DeltaF = - log < exp(-w_F) >
DeltaF = -(_logsum(-w_F) - np.log(T))
if compute_uncertainty:
# Compute x_i = np.exp(-w_F_i - max_arg)
max_arg = np.max(-w_F) # maximum argument
x = np.exp(-w_F - max_arg)
# Compute E[x] = <x> and dx
Ex = x.mean()
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(x, x)
# Estimate standard error of E[x].
dx = np.std(x) / np.sqrt(T / g)
# dDeltaF = <x>^-1 dx
dDeltaF = (dx / Ex)
# Return estimate of free energy difference and uncertainty.
return (DeltaF, dDeltaF)
else:
return DeltaF
def main():
options = parse_args()
kB = 0.00831447/4.184 #Boltzmann constant (Gas constant) in kJ/(mol*K)
dT = 2.5 # Temperature increment for calculating Cv(T)
T = numpy.loadtxt(options.tfile)
print 'Initial temperature states are', T
K = len(T)
U_kn, Q_kn, N_max = read_data(options,T,K)
print 'Subsampling Q...'
N_k = numpy.zeros(K,numpy.int32)
g = numpy.zeros(K,numpy.float64)
for k in range(K): # subsample the energies
g[k] = timeseries.statisticalInefficiency(Q_kn[k])#,suppress_warning=True)
indices = numpy.array(timeseries.subsampleCorrelatedData(Q_kn[k],g=g[k])) # indices of uncorrelated samples
N_k[k] = len(indices) # number of uncorrelated samplesadsf
print '%i uncorrelated samples out of %i total samples' %(len(indices),options.N_max/options.skip)
U_kn[k,0:N_k[k]] = U_kn[k,indices]
Q_kn[k,0:N_k[k]] = Q_kn[k,indices]
insert = True
if insert:
#------------------------------------------------------------------------
# Insert Intermediate T's and corresponding blank U's and E's
#------------------------------------------------------------------------
# Set up variables
Temp_k = T
currentT = T[0] + dT
maxT = T[-1]
i = 1
print("--Inserting intermediate temperatures...")
# Loop, inserting T's at which we are interested in the properties
while (currentT < maxT) :
if (currentT < Temp_k[i]):
Temp_k = numpy.insert(Temp_k, i, currentT)
currentT = currentT + dT
else:
currentT = Temp_k[i] + dT
i = i + 1
# Update number of states
K = len(Temp_k)
print("--Inserting blank energies to match up with inserted temperatures...")
# Loop, inserting E's into blank matrix (leaving blanks only where new Ts are inserted)
Q_fromfile = Q_kn
Nall_k = numpy.zeros([K], numpy.int32) # Number of samples (n) for each state (k) = number of iterations/energies
E_kn = numpy.zeros([K, N_max], numpy.float64)
Q_kn = numpy.zeros([K, N_max], numpy.float64)
i = 0
for k in range(K):
if (Temp_k[k] == T[i]):
E_kn[k,0:N_k[i]] = U_kn[i,0:N_k[i]]
Q_kn[k,0:N_k[i]] = Q_fromfile[i,0:N_k[i]]
Nall_k[k] = N_k[i]
i = i + 1
else:
print 'Not inserting intermediate temperatures'
Temp_k = T
E_kn = U_kn
Nall_k = N_k
#------------------------------------------------------------------------
# Compute inverse temperatures
#------------------------------------------------------------------------
beta_k = 1 / (kB * Temp_k)
#------------------------------------------------------------------------
# Compute reduced potential energies
#------------------------------------------------------------------------
print "--Computing reduced energies..."
u_kln = numpy.zeros([K,K,N_max], numpy.float64) # u_kln is reduced pot. ener. of segment n of temp k evaluated at temp l
for k in range(K):
for l in range(K):
u_kln[k,l,0:Nall_k[k]] = beta_k[l] * E_kn[k,0:Nall_k[k]]
#------------------------------------------------------------------------
# Initialize MBAR
#------------------------------------------------------------------------
# Initialize MBAR with Newton-Raphson
print ""
print "Initializing MBAR:"
print "--K = number of Temperatures"
print "--L = number of Temperatures"
print "--N = number of Energies per Temperature"
# Use Adaptive Method (Both Newton-Raphson and Self-Consistent, testing which is better)
if insert:
mbar = pymbar.MBAR(u_kln, Nall_k, method = 'adaptive', verbose=True, relative_tolerance=1e-12)
else:
f_k = wham.histogram_wham(beta_k, U_kn, Nall_k, relative_tolerance = 1.0e-4)
mbar = pymbar.MBAR(u_kln, Nall_k, initial_f_k = f_k, verbose=True)
#------------------------------------------------------------------------
# Compute Expectations for E_kt and E2_kt as E_expect and E2_expect
#------------------------------------------------------------------------
print ""
print "Computing Expectations for E..."
(E_expect, dE_expect) = mbar.computeExpectations(u_kln)*(beta_k)**(-1)
print "Computing Expectations for E^2..."
(E2_expect,dE2_expect) = mbar.computeExpectations(u_kln*u_kln)*(beta_k)**(-2)
print "Computing Expectations for Q..."
(Q,dQ) = mbar.computeExpectations(Q_kn)
#------------------------------------------------------------------------
# Compute Cv for NVT simulations as <E^2> - <E>^2 / (RT^2)
#------------------------------------------------------------------------
#print ""
#print "Computing Heat Capacity as ( <E^2> - <E>^2 ) / ( R*T^2 )..."
Cv_expect = numpy.zeros([K], numpy.float64)
dCv_expect = numpy.zeros([K], numpy.float64)
for i in range(K):
Cv_expect[i] = (E2_expect[i] - (E_expect[i]*E_expect[i])) / ( kB * Temp_k[i] * Temp_k[i])
dCv_expect[i] = 2*dE_expect[i]**2 / (kB *Temp_k[i]*Temp_k[i]) # from propagation of error
#print "Temperature dA <E> +/- d<E> <E^2> +/- d<E^2> Cv +/- dCv"
#print "-------------------------------------------------------------------------------"
#for k in range(K):
# print "%8.3f %8.3f %9.3f +/- %5.3f %9.1f +/- %5.1f %7.4f +/- %6.4f" % (Temp_k[k],mbar.f_k[k],E_expect[k],dE_expect[k],E2_expect[k],dE2_expect[k],Cv_expect[k], dCv_expect[k])
#numpy.savetxt('/home/edz3fz/Qsurf_int.txt',Q)
#numpy.savetxt('/home/edz3fz/dQsurf_int.txt',dQ)
#numpy.savetxt('/home/edz3fz/dQsol.txt',dQ)
#numpy.savetxt('/home/edz3fz/Qtemp.tt',Temp_k)
import matplotlib.pyplot as plt
#ncavg = numpy.average(Q_fromfile, axis=1)
plt.figure(1)
#plt.plot(T, ncavg, 'ko')
plt.plot(Temp_k,Q,'k')
plt.errorbar(Temp_k, Q, yerr=dQ)
plt.xlabel('Temperature (K)')
plt.ylabel('Q fraction native contacts')
#plt.title('Heat Capacity from Go like model MC simulation of 1BSQ')
plt.savefig(options.direc+'/foldingcurve.png')
numpy.save(options.direc+'/foldingcurve',numpy.array([Temp_k, Q, dQ]))
numpy.save(options.direc+'/heatcap',numpy.array([Temp_k, Cv_expect, dCv_expect]))
if options.show:
plt.show()
# get state and reduced potentials
line = lines[t]
elements = line.split()
state = int(elements[1]) - 1 # state in range(K)
current_reduced_potential = float(elements[2])
for k in range(K):
u_tk[t, k] = float(elements[3 + k])
# store
state_t[t] = state
u_t[t] = current_reduced_potential - g_k[state]
print "u_t = "
# outfile = open('%s.out' % datafile_directory,'w')
# for t in range(T):
# outfile.write("%16d %16.8f\n" % (t, u_t[t]))
# outfile.close()
g = timeseries.statisticalInefficiency(u_t, u_t)
print "g = %16.8f" % g
# compute correlation function
print "Computing correlation function..."
C_t = timeseries.normalizedFluctuationCorrelationFunction(
u_t, u_t, int(3 * g))
# outfile = open('corrfun-%s.dat' % datafile_directory, 'w')
# for t in range(len(C_t)):
# outfile.write('%8d %16.8f\n' % (t, C_t[t]))
# outfile.close()
# Test MRS's hypothesis.
u_t_singlestate = zeros([T], float64)
for state in range(K):
# construct timeseries
Nstate = 0
#========================================================================
#------------------------------------------------------------------------
# Read Data From File
#------------------------------------------------------------------------
print("")
print("Preparing data:")
T_from_file = read_simulation_temps(simulation,NumTemps)
E_from_file = read_total_energies(simulation,TE_COL_NUM)
K = len(T_from_file)
N_k = numpy.zeros(K,numpy.int32)
g = numpy.zeros(K,numpy.float64)
for k in range(K): # subsample the energies
g[k] = timeseries.statisticalInefficiency(E_from_file[k])
indices = numpy.array(timeseries.subsampleCorrelatedData(E_from_file[k],g=g[k])) # indices of uncorrelated samples
N_k[k] = len(indices) # number of uncorrelated samples
E_from_file[k,0:N_k[k]] = E_from_file[k,indices]
#------------------------------------------------------------------------
# Insert Intermediate T's and corresponding blank U's and E's
#------------------------------------------------------------------------
Temp_k = T_from_file
minT = T_from_file[0]
maxT = T_from_file[len(T_from_file) - 1]
#beta = 1/(k*BT)
#T = 1/(kB*beta)
if dtype == 'temperature':
minv = minT
maxv = maxT
# get state and reduced potentials
line = lines[t]
elements = line.split()
state = int(elements[1]) - 1 # state in range(K)
current_reduced_potential = float(elements[2])
for k in range(K):
u_tk[t,k] = float(elements[3 + k])
# store
state_t[t] = state
u_t[t] = current_reduced_potential - g_k[state]
print "u_t = "
# outfile = open('%s.out' % datafile_directory,'w')
# for t in range(T):
# outfile.write("%16d %16.8f\n" % (t, u_t[t]))
# outfile.close()
g = timeseries.statisticalInefficiency(u_t, u_t)
print "g = %16.8f" % g
# compute correlation function
print "Computing correlation function..."
C_t = timeseries.normalizedFluctuationCorrelationFunction(u_t, u_t, int(3 * g))
# outfile = open('corrfun-%s.dat' % datafile_directory, 'w')
# for t in range(len(C_t)):
# outfile.write('%8d %16.8f\n' % (t, C_t[t]))
# outfile.close()
# Test MRS's hypothesis.
u_t_singlestate = zeros([T], float64)
for state in range(K):
# construct timeseries
Nstate = 0
for t in range(T):
def EXP(w_F, compute_uncertainty=True, is_timeseries=False):
"""Estimate free energy difference using one-sided (unidirectional) exponential averaging (EXP).
Parameters
----------
w_F : np.ndarray, float
w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
compute_uncertainty : bool, optional, default=True
if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries : bool, default=False
if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
Returns
-------
result_vals : dictionary
Possible keys in the result_vals dictionary
'Delta_f' : float
Free energy difference
'dDelta_f': float
Estimated standard deviation of free energy difference
Notes
-----
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
Examples
--------
Compute the free energy difference given a sample of forward work values.
>>> from pymbar import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> results = EXP(w_F)
>>> print('Forward free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Forward free energy difference is 1.088 +- 0.076 kT
>>> results = EXP(w_R)
>>> print('Reverse free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Reverse free energy difference is -1.073 +- 0.082 kT
"""
result_vals = dict()
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
# Estimate free energy difference by exponential averaging using DeltaF = - log < exp(-w_F) >
DeltaF = -(logsumexp(-w_F) - np.log(T))
if compute_uncertainty:
# Compute x_i = np.exp(-w_F_i - max_arg)
max_arg = np.max(-w_F) # maximum argument
x = np.exp(-w_F - max_arg)
# Compute E[x] = <x> and dx
Ex = x.mean()
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(x, x)
# Estimate standard error of E[x].
dx = np.std(x) / np.sqrt(T / g)
# dDeltaF = <x>^-1 dx
dDeltaF = (dx / Ex)
# Return estimate of free energy difference and uncertainty.
result_vals['Delta_f'] = DeltaF
result_vals['dDelta_f'] = dDeltaF
else:
result_vals['Delta_f'] = DeltaF
return result_vals
def EXPGauss(w_F, compute_uncertainty=True, is_timeseries=False):
"""Estimate free energy difference using gaussian approximation to one-sided (unidirectional) exponential averaging.
Parameters
----------
w_F : np.ndarray, float
w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
compute_uncertainty : bool, optional, default=True
if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries : bool, default=False
if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
Returns
-------
result_vals : dictionary
Possible keys in the result_vals dictionary
'Delta_f' : float
Free energy difference between the two states
'dDelta_f': float
Estimated standard deviation of free energy difference between the two states.
Notes
-----
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
Examples
--------
Compute the free energy difference given a sample of forward work values.
>>> from pymbar import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> results = EXPGauss(w_F)
>>> print('Forward Gaussian approximated free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Forward Gaussian approximated free energy difference is 1.049 +- 0.089 kT
>>> results = EXPGauss(w_R)
>>> print('Reverse Gaussian approximated free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Reverse Gaussian approximated free energy difference is -1.073 +- 0.080 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
var = np.var(w_F)
# Estimate free energy difference by Gaussian approximation, dG = <U> - 0.5*var(U)
DeltaF = np.average(w_F) - 0.5 * var
result_vals = dict()
if compute_uncertainty:
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
T_eff = T
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(w_F, w_F)
T_eff = T / g
# Estimate standard error of E[x].
dx2 = var / T_eff + 0.5 * var * var / (T_eff - 1)
dDeltaF = np.sqrt(dx2)
# Return estimate of free energy difference and uncertainty.
result_vals['Delta_f'] = DeltaF
result_vals['dDelta_f'] = dDeltaF
else:
result_vals['Delta_f'] = DeltaF
return result_vals
infile = open(filename, 'r')
lines = infile.readlines()
infile.close()
# Parse data.
n = 0
for line in lines:
if line[0] != '#' and line[0] != '@':
tokens = line.split()
u_kn[k,n] = beta_k[k] * (float(tokens[2]) - float(tokens[1])) # reduced potential energy without umbrella restraint
n += 1
# Compute correlation times for potential energy and chi
# timeseries. If the temperatures differ, use energies to determine samples; otherwise, use the cosine of chi
if (DifferentTemperatures):
g_k[k] = timeseries.statisticalInefficiency(u_kn[k,:], u_kn[k,:])
print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(u_kn[k,:])
else:
g_k[k] = timeseries.statisticalInefficiency(numpy.cos(chi_kn[k,:]/(180.0/numpy.pi)),numpy.cos(chi_kn[k,:]/(180.0/numpy.pi)))
print "Correlation time for set %5d is %10.3f" % (k,g_k[k])
indices = timeseries.subsampleCorrelatedData(numpy.cos(chi_kn[k,:]/(180.0/numpy.pi)))
# Subsample data.
N_k[k] = len(indices)
u_kn[k,0:N_k[k]] = u_kn[k,indices]
chi_kn[k,0:N_k[k]] = chi_kn[k,indices]
# Set zero of u_kn -- this is arbitrary.
u_kn -= u_kn.min()
# Construct torsion bins
def analyze_data(store_filename, phipsi_outfile=None):
"""
Analyze output from parallel tempering simulations.
"""
temperature = 300.0 * units.kelvin # temperature
ndiscard = 100 # number of samples to discard to equilibration
# Allocate storage for results.
results = dict()
# Compute kappa
nbins = 10
kB = units.BOLTZMANN_CONSTANT_kB * units.AVOGADRO_CONSTANT_NA # Boltzmann constant
kT = (kB * temperature) # thermal energy
beta = 1.0 / kT # inverse temperature
delta = 360.0 / float(nbins) * units.degrees # bin spacing
sigma = delta/3.0 # standard deviation
kappa = (sigma / units.radians)**(-2) # kappa parameter (unitless)
# Open NetCDF file.
ncfile = netcdf.Dataset(store_filename, 'r', version=2)
# Get dimensions.
[niterations, nstates, natoms, ndim] = ncfile.variables['positions'][:,:,:,:].shape
print "%d iterations, %d states, %d atoms" % (niterations, nstates, natoms)
# Discard initial configurations to equilibration.
print "First %d iterations will be discarded to equilibration." % ndiscard
niterations -= ndiscard
# Print summary statistics about mixing in state space.
[tau2, dtau2] = show_mixing_statistics_with_error(ncfile)
# Compute correlation time of state index.
states = ncfile.variables['states'][:,:].copy()
A_kn = [ states[:,k].copy() for k in range(nstates) ]
g_states = timeseries.statisticalInefficiencyMultiple(A_kn)
tau_states = (g_states-1.0)/2.0
# Compute statistical error.
nblocks = 10
blocksize = int(niterations) / int(nblocks)
g_states_i = numpy.zeros([nblocks], numpy.float64)
tau_states_i = numpy.zeros([nblocks], numpy.float64)
for block_index in range(nblocks):
# Extract block
states = ncfile.variables['states'][(blocksize*block_index):(blocksize*(block_index+1)),:].copy()
A_kn = [ states[:,k].copy() for k in range(nstates) ]
g_states_i[block_index] = timeseries.statisticalInefficiencyMultiple(A_kn)
tau_states_i[block_index] = (g_states_i[block_index]-1.0)/2.0
dg_states = g_states_i.std() / numpy.sqrt(float(nblocks))
dtau_states = tau_states_i.std() / numpy.sqrt(float(nblocks))
# Print.
print "g_states = %.3f+-%.3f iterations" % (g_states, dg_states)
print "tau_states = %.3f+-%.3f iterations" % (tau_states, dtau_states)
del states, A_kn
# Compute end-to-end time.
states = ncfile.variables['states'][:,:].copy()
[tau_end, dtau_end] = average_end_to_end_time(states)
# Compute statistical inefficiency for reduced potential
energies = ncfile.variables['energies'][ndiscard:,:,:].copy()
states = ncfile.variables['states'][ndiscard:,:].copy()
u_n = numpy.zeros([niterations], numpy.float64)
for iteration in range(niterations):
u_n[iteration] = 0.0
for replica in range(nstates):
state = states[iteration,replica]
u_n[iteration] += energies[iteration,replica,state]
del energies, states
g_u = timeseries.statisticalInefficiency(u_n)
print "g_u = %8.1f iterations" % g_u
# Compute x and y umbrellas.
print "Computing torsions..."
positions = ncfile.variables['positions'][ndiscard:,:,:,:]
coordinates = units.Quantity(numpy.zeros([natoms,ndim], numpy.float32), units.angstroms)
phi_it = units.Quantity(numpy.zeros([nstates,niterations], numpy.float32), units.radians)
psi_it = units.Quantity(numpy.zeros([nstates,niterations], numpy.float32), units.radians)
for iteration in range(niterations):
for replica in range(nstates):
coordinates[:,:] = units.Quantity(positions[iteration,replica,:,:].copy(), units.angstroms)
phi_it[replica,iteration] = compute_torsion(coordinates, 4, 6, 8, 14)
psi_it[replica,iteration] = compute_torsion(coordinates, 6, 8, 14, 16)
# Run MBAR.
print "Grouping torsions by state..."
phi_state_it = numpy.zeros([nstates,niterations], numpy.float32)
psi_state_it = numpy.zeros([nstates,niterations], numpy.float32)
states = ncfile.variables['states'][ndiscard:,:].copy()
for iteration in range(niterations):
replicas = numpy.argsort(states[iteration,:])
for state in range(1,nstates):
replica = replicas[state]
phi_state_it[state,iteration] = phi_it[replica,iteration] / units.radians
psi_state_it[state,iteration] = psi_it[replica,iteration] / units.radians
print "Evaluating reduced potential energies..."
N_k = numpy.ones([nstates], numpy.int32) * niterations
u_kln = numpy.zeros([nstates, nstates, niterations], numpy.float32)
for l in range(1,nstates):
phi0 = ((numpy.floor((l-1)/nbins) + 0.5) * delta - 180.0 * units.degrees) / units.radians
psi0 = ((numpy.remainder((l-1), nbins) + 0.5) * delta - 180.0 * units.degrees) / units.radians
u_kln[:,l,:] = - kappa * numpy.cos(phi_state_it[:,:] - phi0) - kappa * numpy.cos(psi_state_it[:,:] - psi0)
# print "Running MBAR..."
# #mbar = pymbar.MBAR(u_kln, N_k, verbose=True, method='self-consistent-iteration')
# mbar = pymbar.MBAR(u_kln[1:,1:,:], N_k[1:], verbose=True, method='adaptive', relative_tolerance=1.0e-2) # only use biased samples
# f_k = mbar.f_k
# mbar = pymbar.MBAR(u_kln[1:,1:,:], N_k[1:], verbose=True, method='Newton-Raphson', initial_f_k=f_k) # only use biased samples
# #mbar = pymbar.MBAR(u_kln, N_k, verbose=True, method='Newton-Raphson', initialize='BAR')
# print "Getting free energy differences..."
# [df_ij, ddf_ij] = mbar.getFreeEnergyDifferences(uncertainty_method='svd-ew')
# print df_ij
# print ddf_ij
# print "ln(Z_ij / Z_55):"
# reference_bin = 4*nbins+4
# for psi_index in range(nbins):
# print " [,%2d]" % (psi_index+1),
# print ""
# for phi_index in range(nbins):
# print "[%2d,]" % (phi_index+1),
# for psi_index in range(nbins):
# print "%8.3f" % (-df_ij[reference_bin, phi_index*nbins+psi_index]),
# print ""
# print ""
# print "dln(Z_ij / Z_55):"
# reference_bin = 4*nbins+4
# for psi_index in range(nbins):
# print " [,%2d]" % (psi_index+1),
# print ""
# for phi_index in range(nbins):
# print "[%2d,]" % (phi_index+1),
# for psi_index in range(nbins):
# print "%8.3f" % (ddf_ij[reference_bin, phi_index*nbins+psi_index]),
# print ""
# print ""
# Compute statistical inefficiencies of various functions of the timeseries data.
print "Computing statistical infficiencies of cos(phi), sin(phi), cos(psi), sin(psi)..."
cosphi_kn = [ numpy.cos(phi_it[replica,:] / units.radians).copy() for replica in range(1,nstates) ]
sinphi_kn = [ numpy.sin(phi_it[replica,:] / units.radians).copy() for replica in range(1,nstates) ]
cospsi_kn = [ numpy.cos(psi_it[replica,:] / units.radians).copy() for replica in range(1,nstates) ]
sinpsi_kn = [ numpy.sin(psi_it[replica,:] / units.radians).copy() for replica in range(1,nstates) ]
g_cosphi = timeseries.statisticalInefficiencyMultiple(cosphi_kn)
g_sinphi = timeseries.statisticalInefficiencyMultiple(sinphi_kn)
g_cospsi = timeseries.statisticalInefficiencyMultiple(cospsi_kn)
g_sinpsi = timeseries.statisticalInefficiencyMultiple(sinpsi_kn)
tau_cosphi = (g_cosphi-1.0)/2.0
tau_sinphi = (g_sinphi-1.0)/2.0
tau_cospsi = (g_cospsi-1.0)/2.0
tau_sinpsi = (g_sinpsi-1.0)/2.0
# Compute relaxation times in each torsion.
print "Relaxation times for transitions among phi or psi bins alone:"
phibin_it = ((phi_it + 180.0 * units.degrees) / (delta + 0.1*units.degrees)).astype(numpy.int16)
tau_phi = compute_relaxation_time(phibin_it, nbins)
psibin_it = ((psi_it + 180.0 * units.degrees) / (delta + 0.1*units.degrees)).astype(numpy.int16)
tau_psi = compute_relaxation_time(psibin_it, nbins)
print "tau_phi = %8.1f iteration" % tau_phi
print "tau_psi = %8.1f iteration" % tau_psi
# Compute statistical error.
nblocks = 10
blocksize = int(niterations) / int(nblocks)
g_cosphi_i = numpy.zeros([nblocks], numpy.float64)
g_sinphi_i = numpy.zeros([nblocks], numpy.float64)
g_cospsi_i = numpy.zeros([nblocks], numpy.float64)
g_sinpsi_i = numpy.zeros([nblocks], numpy.float64)
tau_cosphi_i = numpy.zeros([nblocks], numpy.float64)
tau_sinphi_i = numpy.zeros([nblocks], numpy.float64)
tau_cospsi_i = numpy.zeros([nblocks], numpy.float64)
tau_sinpsi_i = numpy.zeros([nblocks], numpy.float64)
for block_index in range(nblocks):
# Extract block
slice_indices = range(blocksize*block_index,blocksize*(block_index+1))
cosphi_kn = [ numpy.cos(phi_it[replica,slice_indices] / units.radians).copy() for replica in range(1,nstates) ]
sinphi_kn = [ numpy.sin(phi_it[replica,slice_indices] / units.radians).copy() for replica in range(1,nstates) ]
cospsi_kn = [ numpy.cos(psi_it[replica,slice_indices] / units.radians).copy() for replica in range(1,nstates) ]
sinpsi_kn = [ numpy.sin(psi_it[replica,slice_indices] / units.radians).copy() for replica in range(1,nstates) ]
g_cosphi_i[block_index] = timeseries.statisticalInefficiencyMultiple(cosphi_kn)
g_sinphi_i[block_index] = timeseries.statisticalInefficiencyMultiple(sinphi_kn)
g_cospsi_i[block_index] = timeseries.statisticalInefficiencyMultiple(cospsi_kn)
g_sinpsi_i[block_index] = timeseries.statisticalInefficiencyMultiple(sinpsi_kn)
tau_cosphi_i[block_index] = (g_cosphi_i[block_index]-1.0)/2.0
tau_sinphi_i[block_index] = (g_sinphi_i[block_index]-1.0)/2.0
tau_cospsi_i[block_index] = (g_cospsi_i[block_index]-1.0)/2.0
tau_sinpsi_i[block_index] = (g_sinpsi_i[block_index]-1.0)/2.0
dtau_cosphi = tau_cosphi_i.std() / numpy.sqrt(float(nblocks))
dtau_sinphi = tau_sinphi_i.std() / numpy.sqrt(float(nblocks))
dtau_cospsi = tau_cospsi_i.std() / numpy.sqrt(float(nblocks))
dtau_sinpsi = tau_sinpsi_i.std() / numpy.sqrt(float(nblocks))
del cosphi_kn, sinphi_kn, cospsi_kn, sinpsi_kn
print "Integrated autocorrelation times"
print "tau_cosphi = %8.1f+-%.1f iterations" % (tau_cosphi, dtau_cosphi)
print "tau_sinphi = %8.1f+-%.1f iterations" % (tau_sinphi, dtau_sinphi)
print "tau_cospsi = %8.1f+-%.1f iterations" % (tau_cospsi, dtau_cospsi)
print "tau_sinpsi = %8.1f+-%.1f iterations" % (tau_sinpsi, dtau_sinpsi)
# Print LaTeX line.
print ""
print "%(store_filename)s & %(tau2).2f $\pm$ %(dtau2).2f & %(tau_states).2f $\pm$ %(dtau_states).2f & %(tau_end).2f $\pm$ %(dtau_end).2f & %(tau_cosphi).2f $\pm$ %(dtau_cosphi).2f & %(tau_sinphi).2f $\pm$ %(dtau_sinphi).2f & %(tau_cospsi).2f $\pm$ %(dtau_cospsi).2f & %(tau_sinpsi).2f $\pm$ %(dtau_sinpsi).2f \\\\" % vars()
print ""
if phipsi_outfile is not None:
# Write uncorrelated (phi,psi) data
outfile = open(phipsi_outfile, 'w')
outfile.write('# alanine dipeptide 2d umbrella sampling data\n')
# Write umbrella restraints
nbins = 10 # number of bins per torsion
outfile.write('# %d x %d grid of restraints\n' % (nbins, nbins))
outfile.write('# Each state was sampled from p_i(x) = Z_i^{-1} q(x) q_i(x) where q_i(x) = exp[kappa*cos(phi(x)-phi_i) + kappa*cos(psi(x)-psi_i)]\n')
outfile.write('# phi(x) and psi(x) are periodic torsion angles on domain [-180, +180) degrees.\n')
outfile.write('# kappa = %f\n' % kappa)
outfile.write('# phi_i = [-180 + (floor(i / nbins) + 0.5) * delta] degrees\n')
outfile.write('# psi_i = [-180 + ( (i % nbins) + 0.5) * delta] degrees\n')
outfile.write('# where i = 0...%d, nbins = %d, and delta = %f degrees\n' % (nbins*nbins-1, nbins, delta / units.degrees))
outfile.write('# Data has been subsampled to generate approximately uncorrelated samples.\n')
outfile.write('#\n')
# write data header
outfile.write('# ')
for replica in range(nstates):
outfile.write('state %06d ' % replica)
outfile.write('\n')
# write data
indices = timeseries.subsampleCorrelatedData(u_n, g=g_u) # indices of uncorrelated iterations
states = ncfile.variables['states'][ndiscard:,:].copy()
for iteration in indices:
outfile.write(' ')
replicas = numpy.argsort(states[iteration,:])
for state in range(1,nstates):
replica = replicas[state]
outfile.write('%+6.1f %+6.1f ' % (phi_it[replica,iteration] / units.degrees, psi_it[replica,iteration] / units.degrees))
outfile.write('\n')
outfile.close()
return results
# dtau_end = tau_end_i.std() / numpy.sqrt(float(nblocks))
# Print.
print "tau_end = %.3f+-%.3f iterations" % (tau_end, dtau_end)
del states
# Compute statistical inefficiency for reduced potential
energies = ncfile.variables['energies'][:,:,:].copy()
states = ncfile.variables['states'][:,:].copy()
u_n = numpy.zeros([niterations], numpy.float64)
for iteration in range(niterations):
u_n[iteration] = 0.0
for replica in range(nstates):
state = states[iteration,replica]
u_n[iteration] += energies[iteration,replica,state]
del energies, states
g_u = timeseries.statisticalInefficiency(u_n)
tau_u = (g_u-1.0)/2.0
print "g_u = %8.1f iterations" % g_u
print "tau_u = %8.1f iterations" % tau_u
# DEBUG for lactalbumin
#continue
# Compute torsions.
print "Computing torsions..."
positions = ncfile.variables['positions'][:,:,:,:]
coordinates = units.Quantity(numpy.zeros([natoms,ndim], numpy.float32), units.angstroms)
phi_it = units.Quantity(numpy.zeros([nstates,niterations], numpy.float32), units.radians)
psi_it = units.Quantity(numpy.zeros([nstates,niterations], numpy.float32), units.radians)
for iteration in range(niterations):
for replica in range(nstates):
def _subsample_kln(self, u_kln):
#Try to load in the data
if self.save_equil_data: #Check if we want to save/load equilibration data
try:
equil_data = numpy.load(os.path.join(self.source_directory, self.save_prefix + self.phase + '_equil_data_%s.npz' % self.subsample_method))
if self.nequil is None:
self.nequil = equil_data['nequil']
elif type(self.nequil) is int and self.subsample_method == 'per-state':
print "WARRNING: Per-state subsampling requested with only single value for equilibration..."
try:
self.nequil = equil_data['nequil']
print "Loading equilibration from file with %i states read" % self.nstates
except:
print "Assuming equal equilibration per state of %i" % self.nequil
self.nequil = numpy.array([self.nequil] * self.nstates)
self.g_t = equil_data['g_t']
Neff_max = equil_data['Neff_max']
#Do equilibration if we have not already
if self.subsample_method == 'per-state' and (len(self.g_t) < self.nstates or len(self.nequil) < self.nstates):
equil_loaded = False
raise IndexError
else:
equil_loaded = True
except:
if self.subsample_method == 'per-state':
self.nequil = numpy.zeros([self.nstates], dtype=numpy.int32)
self.g_t = numpy.zeros([self.nstates])
Neff_max = numpy.zeros([self.nstates])
for k in xrange(self.nstates):
if self.verbose: print "Computing timeseries for state %i/%i" % (k,self.nstates-1)
self.nequil[k] = 0
self.g_t[k] = timeseries.statisticalInefficiency(u_kln[k,k,:])
Neff_max[k] = (u_kln[k,k,:].size + 1 ) / self.g_t[k]
#[self.nequil[k], self.g_t[k], Neff_max[k]] = self._detect_equilibration(u_kln[k,k,:])
else:
if self.nequil is None:
[self.nequil, self.g_t, Neff_max] = self._detect_equilibration(self.u_n)
else:
[self.nequil_timeseries, self.g_t, Neff_max] = self._detect_equilibration(self.u_n)
equil_loaded = False
if not equil_loaded:
numpy.savez(os.path.join(self.source_directory, self.save_prefix + self.phase + '_equil_data_%s.npz' % self.subsample_method), nequil=self.nequil, g_t=self.g_t, Neff_max=Neff_max)
elif self.nequil is None:
if self.subsample_method == 'per-state':
self.nequil = numpy.zeros([self.nstates], dtype=numpy.int32)
self.g_t = numpy.zeros([self.nstates])
Neff_max = numpy.zeros([self.nstates])
for k in xrange(self.nstates):
[self.nequil[k], self.g_t[k], Neff_max[k]] = self._detect_equilibration(u_kln[k,k,:])
if self.verbose: print "State %i equilibrated with %i samples" % (k, int(Neff_max[k]))
else:
[self.nequil, self.g_t, Neff_max] = self._detect_equilibration(self.u_n)
if self.verbose: print [self.nequil, Neff_max]
# 1) Discard equilibration data
# 2) Subsample data to obtain uncorrelated samples
self.N_k = numpy.zeros(self.nstates, numpy.int32)
if self.subsample_method == 'per-state':
# Discard samples
nsamples_equil = self.niterations - self.nequil
self.u_kln = numpy.zeros([self.nstates,self.nstates,nsamples_equil.max()])
for k in xrange(self.nstates):
self.u_kln[k,:,:nsamples_equil[k]] = u_kln[k,:,self.nequil[k]:]
#Subsample
transfer_retained_indices = numpy.zeros([self.nstates,nsamples_equil.max()], dtype=numpy.int32)
for k in xrange(self.nstates):
state_indices = timeseries.subsampleCorrelatedData(self.u_kln[k,k,:], g = self.g_t[k])
self.N_k[k] = len(state_indices)
transfer_retained_indices[k,:self.N_k[k]] = state_indices
transfer_kln = numpy.zeros([self.nstates, self.nstates, self.N_k.max()])
self.retained_indices = numpy.zeros([self.nstates,self.N_k.max()], dtype=numpy.int32)
for k in xrange(self.nstates):
self.retained_indices[k,:self.N_k[k]] = transfer_retained_indices[k,:self.N_k[k]] #Memory reduction
transfer_kln[k,:,:self.N_k[k]] = self.u_kln[k,:,self.retained_indices[k,:self.N_k[k]]].T #Have to transpose since indexing in this way causes issues
#Cut down on memory, once function is done, transfer_kln should be released
self.u_kln = transfer_kln
self.retained_iters = self.N_k
else:
#Discard Samples
self.u_kln = u_kln[:,:,self.nequil:]
self.u_n = self.u_n[self.nequil:]
#Subsamples
indices = timeseries.subsampleCorrelatedData(self.u_n, g=self.g_t) # indices of uncorrelated samples
self.u_kln = self.u_kln[:,:,indices]
self.N_k[:] = len(indices)
self.retained_indices = indices
self.retained_iters = len(indices)
return
def EXPGauss(w_F, compute_uncertainty=True, is_timeseries=False):
"""Estimate free energy difference using gaussian approximation to one-sided (unidirectional) exponential averaging.
Parameters
----------
w_F : np.ndarray, float
w_F[t] is the forward work value from snapshot t. t = 0...(T-1) Length T is deduced from vector.
compute_uncertainty : bool, optional, default=True
if False, will disable computation of the statistical uncertainty (default: True)
is_timeseries : bool, default=False
if True, correlation in data is corrected for by estimation of statisitcal inefficiency (default: False)
Use this option if you are providing correlated timeseries data and have not subsampled the data to produce uncorrelated samples.
Returns
-------
result_vals : dictionary
Possible keys in the result_vals dictionary
'Delta_f' : float
Free energy difference between the two states
'dDelta_f': float
Estimated standard deviation of free energy difference between the two states.
Notes
-----
If you are prodividing correlated timeseries data, be sure to set the 'timeseries' flag to True
Examples
--------
Compute the free energy difference given a sample of forward work values.
>>> from pymbar import testsystems
>>> [w_F, w_R] = testsystems.gaussian_work_example(mu_F=None, DeltaF=1.0, seed=0)
>>> results = EXPGauss(w_F)
>>> print('Forward Gaussian approximated free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Forward Gaussian approximated free energy difference is 1.049 +- 0.089 kT
>>> results = EXPGauss(w_R)
>>> print('Reverse Gaussian approximated free energy difference is %.3f +- %.3f kT' % (results['Delta_f'], results['dDelta_f']))
Reverse Gaussian approximated free energy difference is -1.073 +- 0.080 kT
"""
# Get number of work measurements.
T = float(np.size(w_F)) # number of work measurements
var = np.var(w_F)
# Estimate free energy difference by Gaussian approximation, dG = <U> - 0.5*var(U)
DeltaF = np.average(w_F) - 0.5 * var
result_vals = dict()
if compute_uncertainty:
# Compute effective number of uncorrelated samples.
g = 1.0 # statistical inefficiency
T_eff = T
if is_timeseries:
# Estimate statistical inefficiency of x timeseries.
import timeseries
g = timeseries.statisticalInefficiency(w_F, w_F)
T_eff = T / g
# Estimate standard error of E[x].
dx2 = var / T_eff + 0.5 * var * var / (T_eff - 1)
dDeltaF = np.sqrt(dx2)
# Return estimate of free energy difference and uncertainty.
result_vals['Delta_f'] = DeltaF
result_vals['dDelta_f'] = dDeltaF
else:
result_vals['Delta_f'] = DeltaF
return result_vals