def run_EMUS(self):
# Load data
psis, cv_trajs, neighbors = uu.data_from_meta(self.meta_file_name,
self.dim,
T=self.T,
k_B=self.k_B,
period=None)
# Calculate the partition function for each window
z, F = emus.calculate_zs(psis, neighbors=neighbors)
# Calculate error in each z value from the first iteration.
zerr, zcontribs, ztaus = avar.calc_partition_functions(
psis, z, F, iat_method='acor')
# Calculate the PMF from EMUS
domain = ((-0.5, 6)) # Range of dihedral angle values
pmf, edges = emus.calculate_pmf(cv_trajs,
psis,
domain,
z,
nbins=self.num_bins,
kT=self.kT,
use_iter=False) # Calculate the pmf
# Calculate z using the MBAR iteration.
z_iter_1, F_iter_1 = emus.calculate_zs(psis, n_iter=1)
z_iter_2, F_iter_2 = emus.calculate_zs(psis, n_iter=2)
z_iter_5, F_iter_5 = emus.calculate_zs(psis, n_iter=5)
z_iter_1k, F_iter_1k = emus.calculate_zs(psis, n_iter=1000)
# Calculate new PMF
iterpmf, edges = emus.calculate_pmf(cv_trajs,
psis,
domain,
nbins=self.num_bins,
z=z_iter_1k,
kT=self.kT)
# Get the asymptotic error of each histogram bin.
pmf_av_mns, pmf_avars = avar.calc_pmf(cv_trajs,
psis,
domain,
z,
F,
nbins=self.num_bins,
kT=self.kT,
iat_method=np.average(ztaus,
axis=0))
### Data Output Section ###
# Plot the EMUS, Iterative EMUS pmfs.
pmf_centers = (edges[0][1:] + edges[0][:-1]) / 2.
self.x = pmf_centers
self.y = pmf_av_mns / self.tau
self.err = 1 / self.tau * np.sqrt(pmf_avars)
self.y_iter = iterpmf / self.tau
# Define Simulation Parameters
T = 300 # Temperature in Kelvin
k_B = 1.9872041E-3 # Boltzmann factor in kcal/mol
kT = k_B * T
meta_file = 'metadata.dat' # Path to Meta File
dim = 1 # 1 Dimensional CV space.
#period = 360 # Dihedral Angles periodicity
# Load data
#psis, cv_trajs, neighbors = uu.data_from_meta(meta_file,dim,T=T,k_B=k_B,period=period)
psis, cv_trajs, neighbors = uu.data_from_meta(meta_file, dim, T=T, k_B=k_B)
#psis, cv_trajs, neighbors = uu.data_from_meta(meta_file,dim,T=T,k_B=k_B,nsig=6)
nbins = 200 # Number of Histogram Bins.
# Calculate the partition function for each window
z, F = emus.calculate_zs(psis, neighbors=neighbors)
# Calculate error in each z value from the first iteration.
zerr, zcontribs, ztaus = avar.calc_partition_functions(psis,
z,
F,
iat_method='acor')
#zerr, zcontribs, ztaus = avar.calc_partition_functions(psis,z,F,neighbors,iat_method='acor')
# Calculate the PMF from EMUS
#domain = ((-180.0,180.)) # Range of dihedral angle values
domain = ((3.0, 25.0)) # Range of length values
pmf, edges = emus.calculate_pmf(cv_trajs,
psis,
domain,
z,
def main():
a = _parse_args() # Get Dictionary of Arguments
kT = a['k_B'] * a['T']
domain = np.reshape(a['domain'], (-1, 2))
# Load data
psis, cv_trajs, neighbors = uu.data_from_meta(a['meta_file'],
a['n_dim'],
T=a['T'],
k_B=a['k_B'],
period=a['period'],
nsig=a['sigma'])
if a['fxn_file'] is not None:
fdata = uu.fxn_data_from_meta(a['fxn_file'])
else:
fdata = None
# Calculate the partition function for each window
z, F = emus.calculate_zs(psis, neighbors=neighbors, n_iter=a['n_iter'])
# Calculate the PMF
pmf, edges = emus.calculate_pmf(cv_trajs,
psis,
domain,
z,
neighbors=neighbors,
nbins=a['nbins'],
kT=kT)
# Calculate any averages of functions.
if fdata is not None:
favgs = []
for n, fdata_i in enumerate(fdata):
favgs.append(
emus.calculate_obs(psis, z, fdata_i, neighbors=neighbors))
# Perform Error analysis if requested.
if a['error'] is not None:
zEMUS, FEMUS = emus.calculate_zs(psis, neighbors=neighbors, n_iter=0)
zvars, z_contribs, z_iats = avar.calc_partition_functions(
psis, zEMUS, FEMUS, neighbors=neighbors, iat_method=a['error'])
z_avg_taus = np.average(z_iats, axis=0)
pmf_EMUS, pmf_EMUS_avar = avar.calc_pmf(cv_trajs,
psis,
domain,
zEMUS,
FEMUS,
neighbors=neighbors,
nbins=a['nbins'],
kT=kT,
iat_method=z_avg_taus)
# Perform analysis on any provided functions.
if fdata is not None:
favgs_EM = []
ferrs = []
fcontribs = []
for fdata_i in fdata:
iat, mean, variances = avar.calc_avg_ratio(
psis,
zEMUS,
FEMUS,
fdata_i,
neighbors=neighbors,
iat_method=a['error'])
favgs_EM.append(mean)
fcontribs.append(variances)
ferrs.append(np.sum(variances))
# Save Data
f = h5py.File(a['output'] + '_out.hdf5', "w")
# Save PMF
pmf_grp = f.create_group("PMF")
pmf_dset = pmf_grp.create_dataset("pmf", pmf.shape, dtype='f')
dmn_dset = pmf_grp.create_dataset("domain",
np.array(domain).shape,
dtype='f')
pmf_dset[...] = pmf
dmn_dset[...] = np.array(domain)
for ie, edg in enumerate(edges):
edg_dset = pmf_grp.create_dataset("edge_%d" % ie, edg.shape, dtype='f')
edg_dset[...] = edg
if a['error'] is not None:
pmf_EMUS_dset = pmf_grp.create_dataset("pmf_no_iter",
pmf_EMUS.shape,
dtype='f')
pmf_EMUS_dset[...] = pmf_EMUS
pmf_EMUS_avar_dset = pmf_grp.create_dataset("pmf_no_iter_avars",
pmf_EMUS_avar.shape,
dtype='f')
pmf_EMUS_avar_dset[...] = pmf_EMUS_avar
# Save partition functions
z_grp = f.create_group("partition_function")
z_dset = z_grp.create_dataset("z", z.shape, dtype='f')
z_dset[...] = z
F_dset = z_grp.create_dataset("F", F.shape, dtype='f')
F_dset[...] = F
if a['error'] is not None:
zerr_dset = z_grp.create_dataset("z_avars",
np.array(zvars).shape,
dtype='f')
zerr_dset[...] = np.array(zvars)
zEMUS_dset = z_grp.create_dataset("z_no_iter", zEMUS.shape, dtype='f')
zEMUS_dset[...] = zEMUS
FEMUS_dset = z_grp.create_dataset("F_no_iter", FEMUS.shape, dtype='f')
FEMUS_dset[...] = FEMUS
# Save function data.
if fdata is not None:
f_grp = f.create_group('function_averages')
f_dset = f_grp.create_dataset("f", np.shape(favgs), dtype='f')
f_dset[...] = np.array(favgs)
if a['error'] is not None:
fvar_dset = f_grp.create_dataset("f_avars",
np.shape(ferrs),
dtype='f')
fvar_dset[...] = ferrs
f.close()
def main():
"""
"""
free_energy_cmap = plt.cm.get_cmap('Blues_r')
four_pi = 4.*np.pi
kT = parameters['k_B']*parameters['temperature']
beta = 1./(2.*kT)
# ----------------------------------------
# RUN EMUS ANALYSIS STEP
print('Starting EMUS analysis')
psis, cv_trajs, neighbors = usutils.data_from_meta(parameters['emus_meta_file'],parameters['num_biased_dimensions'],T=parameters['temperature'],k_B=parameters['k_B']) # psis is a list of arrays containing the relative weights of each window's cv values in all windows. cv_trajs is a list of arrays containing the raw cv values for each window. neighbors is an 2D array containing indices for neighboring windows to be used.
# calculate the partition function for each window
z, F = emus.calculate_zs(psis,neighbors=neighbors) # z is an 1D array that contains the normalization constant for each window. F is an 2D array (num windows by num windows) that contains the eigenvalues of the iterature EMUS process.
zerr, zcontribs, ztaus = avar.calc_partition_functions(psis,z,F,iat_method='acor')
np.savetxt(parameters['output_directory'] + 'emus_stitching_constants.dat',np.c_[list(range(int(parameters['nWindows']))),z,zerr], fmt='%15.10f')
r0_k_data, file_list = read_meta(parameters['emus_meta_file']) # file_list not being saved...
# ----------------------------------------
# FOR REWEIGHTING, ONLY NEED THE Z ARRAY
del psis
del cv_trajs
del neighbors
del F
del zerr
del zcontribs
del ztaus
# ----------------------------------------
# LOAD IN UNBIASED AND BIASED CV DATA
print('Starting to load in cv data (original and new)')
nWindows_range = range(int(parameters['nWindows'])) # assumes windows are numbered with zero-indexing
data = ['' for i in nWindows_range]
for i in nWindows_range:
print('loading window', i)
temp_biased_data = np.loadtxt(file_list[i])[:,1]
temp_unbiased_data = np.loadtxt(parameters['unbiased_data_files_naming']%(i))[:,:2]
if temp_biased_data.shape[0] != temp_unbiased_data.shape[0]:
print('unbiased data file', i, 'has different number of values than the biased cv data file from the respective window. This should not happen.', temp_unbiased_data.shape, temp_biased_data.shape)
sys.exit()
temp_data = np.c_[temp_biased_data,temp_unbiased_data[:,0],temp_unbiased_data[:,1]] # biased CV data is row's index 0; unbiased CV data is row's index 1
data[i] = temp_data
# ----------------------------------------
# prep 2d histogram arrays
xMin = float(parameters['xMin'])
xMax = float(parameters['xMax'])
yMin = float(parameters['yMin'])
yMax = float(parameters['yMax'])
xBins = int(parameters['xBins'])
yBins = int(parameters['yBins'])
delta_x = (xMax - xMin)/xBins
delta_y = (yMax - yMin)/yBins
print('Bin widths:', delta_x, delta_y)
x_half_bins = np.array([xMin + delta_x*(i+0.5) for i in range(xBins)])
y_half_bins = np.array([yMin + delta_y*(i+0.5) for i in range(yBins)])
x_edges = np.array([xMin + delta_x*i for i in range(xBins+1)])
y_edges = np.array([yMin + delta_y*i for i in range(yBins+1)])
# ----------------------------------------
# REWEIGHTING BIASED CV FE SURFACE INTO A 2D CV SPACE
nValues_total = 0
x_total_fe_counts = np.zeros(xBins)
y_total_fe_counts = np.zeros(yBins)
td_total_fe_counts = np.zeros((xBins,yBins))
for i in nWindows_range:
nValues = len(data[i])
nValues_total += nValues
x_window_counts = np.zeros(xBins)
y_window_counts = np.zeros(yBins)
x_window_fe_counts = np.zeros(xBins)
y_window_fe_counts = np.zeros(yBins)
with open(parameters['output_directory'] + 'window%03d.frame_weights.dat'%(i),'w') as W:
for j in range(nValues):
# ----------------------------------------
# HISTOGRAMMING DATA POINT
x_index = int((data[i][j][1] - xMin)/delta_x)
y_index = int((data[i][j][2] - yMin)/delta_y)
if x_index < 0 or x_index > xBins:
print('!!! 0 > x_index >= xBins ...', data[i][j][0], x_index, i, 'Histogram bounds are not wide enough in the x-dimension. Job failed.')
sys.exit()
elif x_index == xBins:
x_index = -1
if y_index < 0 or y_index > yBins:
print('!!! 0 > y_index >= yBins ...', data[i][j][0], y_index, i, 'Histogram bounds are not wide enough in the y-dimension. Job failed.')
sys.exit()
elif y_index == yBins:
y_index = -1
# ----------------------------------------
# ANALYZING DATA POINT IN CONSIDERATION OF CURRENT WINDOW
w = np.exp((-beta*r0_k_data[i][1])*(data[i][j][0] - r0_k_data[i][0])**2)/z[i] # exp((-k/2*k_B*T)(r-r0)^2)/z; no volume correction...
#w = (data[i][j][0]**2)*np.exp((-beta*r0_k_data[i][1])*(data[i][j][0] - r0_k_data[i][0])**2)/z[i] # r^2 * exp((-k/2*k_B*T)(r-r0)^2)/z;
x_window_counts[x_index] += 1
x_window_fe_counts[x_index] += 1/w
y_window_counts[y_index] += 1
y_window_fe_counts[y_index] += 1/w
# ----------------------------------------
# ANALYZING DATA POINT IN CONSIDERATION OF ALL WINDOWS
w = 0
for k in nWindows_range:
w+= np.exp((-beta*r0_k_data[k][1])*(data[i][j][0] - r0_k_data[k][0])**2)/z[k] # exp((-k/2*k_B*T)(r-r0)^2)/z; no volume correction...
#w+= (data[i][j][0]**2)*np.exp((-beta*r0_k_data[k][1])*(data[i][j][0] - r0_k_data[k][0])**2)/z[k] # r^2 * exp((-k/2*k_B*T)(r-r0)^2)/z;
w /= parameters['nWindows'] # <r^2 * exp((-k/2*k_B*T)(r-r0)^2)/z>; average reciprocal boltzmann weight of data point in all possible windows;
weight = 1./w
W.write('%15d %15f\n'%(j,weight))
x_total_fe_counts[x_index] += weight
y_total_fe_counts[y_index] += weight
td_total_fe_counts[x_index][y_index] += weight
# ----------------------------------------
# FINISHING ANALYSIS OF THE REWEIGHTED PROB. DENSITY OF EACH INDIVIDUAL WINDOW - XDATA
x_window_prob_density = x_window_counts/(nValues*delta_x)
plt.figure(1)
plt.plot(x_half_bins[:],x_window_prob_density[:],zorder=3)
# ----------------------------------------
# FINISHING ANALYSIS OF THE REWEIGHTED FREE ENERGY OF EACH INDIVIDUAL WINDOW - XDATA
x_window_fe_counts = -kT*np.log(x_window_fe_counts/(nValues*delta_x)) # no volume correction
#x_window_fe_counts = np.array([-kT*np.log(x_window_fe_counts[j]/(nValues*delta_x*four_pi)) for j in range(xBins)])
plt.figure(2)
plt.plot(x_half_bins[x_window_counts > 10.], x_window_fe_counts[x_window_counts > 10],zorder=3)
# ----------------------------------------
# FINISHING ANALYSIS OF THE REWEIGHTED PROB. DENSITY OF EACH INDIVIDUAL WINDOW - YDATA
y_window_prob_density = y_window_counts/(nValues*delta_y)
plt.figure(3)
plt.plot(y_half_bins[:],y_window_prob_density[:],zorder=3)
# ----------------------------------------
# FINISHING ANALYSIS OF THE REWEIGHTED FREE ENERGY OF EACH INDIVIDUAL WINDOW - YDATA
y_window_fe_counts = -kT*np.log(y_window_fe_counts/(nValues*delta_y)) # no volume correction
#y_window_fe_counts = np.array([-kT*np.log(y_window_fe_counts[j]/(nValues*delta_y*four_pi)) for j in range(yBins)])
plt.figure(4)
plt.plot(y_half_bins[y_window_counts > 10.], y_window_fe_counts[y_window_counts > 10],zorder=3)
print('Done with window', i)
# ----------------------------------------
# FINISHED REWEIGHTING, RUNNING BOOTSTRAP ANALYSIS TO GET ERROR BARS
if parameters['bootstrap_bool']:
print('Beginning bootstrap analysis to approximate error in reweighted CVs')
original_data = np.empty((0,3))
for i in nWindows_range:
original_data = np.concatenate((original_data,np.array(data[i])))
if original_data.shape != (nValues_total,3):
print(original_data.shape, nValues_total, 'something went wrong during bootstrapping')
sys.exit()
x_bootstrap_results = []
y_bootstrap_results = []
td_bootstrap_results = []
for i in range(parameters['nIterations']):
print('Starting Step %d of %d steps in bootstrap analysis'%(i,parameters['nIterations']))
# create bootstrap data
sample_data = original_data[np.random.randint(nValues_total,size=nValues_total)]
x_total_fe_bootstrap = np.zeros(xBins)
y_total_fe_bootstrap = np.zeros(yBins)
td_total_fe_bootstrap = np.zeros((xBins,yBins))
# analyze new dataset to get reweighted FE of each bin
for j in range(nValues_total):
# ----------------------------------------
# HISTOGRAMMING DATA POINT
x_index = int((sample_data[j,1] - xMin)/delta_x)
y_index = int((sample_data[j,2] - yMin)/delta_y)
if x_index == xBins:
x_index = -1
if y_index == yBins:
y_index = -1
w = 0
for k in nWindows_range:
w+= np.exp((-beta*r0_k_data[k][1])*(sample_data[j,0] - r0_k_data[k][0])**2)/z[k] # exp((-k/2*k_B*T)(r-r0)^2)/z; no volume correction...
w /= parameters['nWindows'] # <r^2 * exp((-k/2*k_B*T)(r-r0)^2)/z>; average reciprocal boltzmann weight of data point in all possible windows;
x_total_fe_bootstrap[x_index] += 1/w
y_total_fe_bootstrap[y_index] += 1/w
td_total_fe_bootstrap[x_index][y_index] += 1/w
x_total_fe_bootstrap /= delta_x*nValues_total
x_total_fe_bootstrap = -kT*np.log(x_total_fe_bootstrap) # no volume correction
x_total_fe_bootstrap -= np.ndarray.min(x_total_fe_bootstrap)
x_bootstrap_results.append(x_total_fe_bootstrap)
y_total_fe_bootstrap /= delta_y*nValues_total
y_total_fe_bootstrap = -kT*np.log(y_total_fe_bootstrap) # no volume correction
y_total_fe_bootstrap -= np.ndarray.min(y_total_fe_bootstrap)
y_bootstrap_results.append(y_total_fe_bootstrap)
td_total_fe_bootstrap /= delta_x*delta_y*nValues_total # currently a stitched probability density; no volume correction
td_total_fe_bootstrap = -kT*np.log(td_total_fe_bootstrap)
td_total_fe_bootstrap -= np.ndarray.min(td_total_fe_bootstrap)
td_bootstrap_results.append(td_total_fe_bootstrap)
### NOTE: CALCS THE STANDARD DEVIATION OF THE BOOTSTRAPPED DATA
x_std_error = np.std(np.array(x_bootstrap_results),axis=0)
y_std_error = np.std(np.array(y_bootstrap_results),axis=0)
td_std_error = np.std(np.array(td_bootstrap_results),axis=0)
np.savetxt(parameters['output_directory'] + 'x_axis_error_analysis.dat', x_std_error, fmt='%.10f')
np.savetxt(parameters['output_directory'] + 'y_axis_error_analysis.dat', y_std_error, fmt='%.10f')
np.savetxt(parameters['output_directory'] + 'td_axis_error_analysis.dat', td_std_error, fmt='%.10f')
del sample_data
del x_total_fe_bootstrap
del y_total_fe_bootstrap
del td_total_fe_bootstrap
del x_bootstrap_results
del y_bootstrap_results
del td_bootstrap_results
# ----------------------------------------
# FINISHED REWEIGHTING, CLEANING UP VARIABLE SPACE
del data
del x_window_counts
del y_window_counts
del x_window_prob_density
del y_window_prob_density
del x_window_fe_counts
del y_window_fe_counts
# ----------------------------------------
# FINISHING PLOTTING OF THE REWEIGHTED PROB. DENSITY OF EACH INDIVIDUAL WINDOW - XDATA
finish_plot(1,parameters['output_directory']+parameters['reweighted_x_axis_prob_density_plot_name'],parameters['x_axis_label'],'Probability Density',xlim=(xMin,xMax))
# ----------------------------------------
# FINISHING PLOTTING OF THE REWEIGHTED, UNSTITCHED FREE ENERGY - XDATA
finish_plot(2,parameters['output_directory']+parameters['reweighted_x_axis_unstitched_fe_plot_name'],parameters['x_axis_label'],r'Relative Free Energy (kcal mol$^{-1}$)',xlim=(xMin,xMax))
# ----------------------------------------
# FINISHING PLOTTING OF THE REWEIGHTED PROB. DENSITY OF EACH INDIVIDUAL WINDOW - YDATA
finish_plot(3,parameters['output_directory']+parameters['reweighted_y_axis_prob_density_plot_name'],parameters['y_axis_label'],'Probability Density',xlim=(yMin,yMax))
# ----------------------------------------
# FINISHING PLOTTING OF THE REWEIGHTED, UNSTITCHED FREE ENERGY - YDATA
finish_plot(4,parameters['output_directory']+parameters['reweighted_y_axis_unstitched_fe_plot_name'],parameters['y_axis_label'],r'Relative Free Energy (kcal mol$^{-1}$)',xlim=(yMin,yMax))
# ----------------------------------------
# PLOTTING REWEIGHTED X-DATA FE SURFACE
x_total_fe_counts /= delta_x*nValues_total # no volume correction
#x_total_fe_counts /= four_pi*delta_x*nValues_total
x_total_fe_counts = -kT*np.log(x_total_fe_counts) # no volume correction
x_total_fe_counts -= np.ndarray.min(x_total_fe_counts)
np.savetxt(parameters['output_directory'] + parameters['reweighted_x_axis_stitched_fe_data_file_name'], np.c_[range(xBins),x_half_bins,x_total_fe_counts], fmt='%.10f')
plt.figure(5)
if parameters['bootstrap_bool']:
plt.errorbar(x_half_bins[:],x_total_fe_counts[:],yerr=x_std_error,ecolor='r',elinewidth=0.5,zorder=3)
else:
plt.plot(x_half_bins[:],x_total_fe_counts[:],zorder=3)
finish_plot(5, parameters['output_directory']+parameters['reweighted_x_axis_stitched_fe_plot_name'], parameters['x_axis_label'], r'Relative Free Energy (kcal mol$^{-1}$)',xlim=(xMin,xMax),ylim=(-0.05,10)) # NOTE
# ----------------------------------------
# PLOTTING REWEIGHTED Y-DATA FE SURFACE
y_total_fe_counts /= delta_y*nValues_total # no volume correction
#y_total_fe_counts /= four_pi*delta_y*nValues_total
y_total_fe_counts = -kT*np.log(y_total_fe_counts)
y_total_fe_counts -= np.ndarray.min(y_total_fe_counts)
np.savetxt(parameters['output_directory'] + parameters['reweighted_y_axis_stitched_fe_data_file_name'], np.c_[range(yBins),y_half_bins,y_total_fe_counts], fmt='%.10f')
plt.figure(6)
if parameters['bootstrap_bool']:
plt.errorbar(y_half_bins[:],y_total_fe_counts[:],yerr=y_std_error,ecolor='r',elinewidth=0.5,zorder=3)
else:
plt.plot(y_half_bins[:],y_total_fe_counts[:],zorder=3)
finish_plot(6, parameters['output_directory']+parameters['reweighted_y_axis_stitched_fe_plot_name'], parameters['y_axis_label'], r'Relative Free Energy (kcal mol$^{-1}$)',xlim=(yMin,yMax),ylim=(-0.05,10)) # NOTE
# ----------------------------------------
# PLOTTING REWEIGHTED 2D FE LANDSCAPE
td_total_fe_counts /= delta_x*delta_y*nValues_total # currently a stitched probability density; no volume correction
#td_total_fe_counts /= four_pi*delta_x*delta_y*nValues_total # currently a stitched probability density; with vol correction
td_total_fe_counts = -kT*np.log(td_total_fe_counts)
td_total_fe_counts -= np.ndarray.min(td_total_fe_counts)
np.savetxt(parameters['output_directory'] + parameters['reweighted_2d_heatmap_data_file_name'], td_total_fe_counts, fmt='%.10f')
masked_fe_counts = ma.masked_where(np.isinf(td_total_fe_counts),td_total_fe_counts)
fig, ax = plt.subplots(num=7)
plt.pcolormesh(x_edges,y_edges,masked_fe_counts.T,cmap=free_energy_cmap,zorder=3,vmax=10)
cb1 = plt.colorbar() #extend='max'
cb1.set_label(r'Relative Free Energy (kcal mol$^{-1}$)',size=14)
ax.set_aspect('equal')
finish_plot(7, parameters['output_directory']+parameters['reweighted_2d_heatmap_plot_name'], parameters['x_axis_label'], parameters['x_axis_label'],xlim=(xMin,xMax),ylim=(yMin,yMax)) # NOTE
plt.close()
print('Done plotting.')
# ----------------------------------------
# OUTPUT SUMMARY FILE
summary(parameters['output_directory'] + 'reweighting.summary',sys.argv,parameters)
k_B = 1.9872041E-3 # Boltzmann factor in kcal/mol
kT = k_B * T
meta_file = 'cv_meta.txt' # Path to Meta File
dim = 1 # 1 Dimensional CV space.
period = 360 # Dihedral Angles periodicity
nbins = 60 # Number of Histogram Bins.
# Load data
psis, cv_trajs, neighbors = uu.data_from_meta(meta_file,
dim,
T=T,
k_B=k_B,
period=period)
# Calculate the partition function for each window
z_iter, F_iter = emus.calculate_zs(psis, neighbors=neighbors, n_iter=5)
plt.plot(np.arange(len(z_iter)), -np.log(z_iter), label='Window Free Energies')
plt.xlabel(r'Window Index')
plt.ylabel('Window FE Unitless')
plt.legend()
plt.show()
domain = ((-180.0, 180.)) # Range of dihedral angle values
# Calculate new PMF
iterpmf, edges = emus.calculate_pmf(cv_trajs,
psis,
domain,
nbins=nbins,
z=z_iter,
kT=kT)
matplotlib.use('Qt4Agg')
import matplotlib.pyplot as plt
# Define Simulation Parameters
T = 310 # Temperature in Kelvin
k_B = 1.9872041E-3 # Boltzmann factor in kcal/mol
kT = k_B * T
meta_file = 'wham_meta.txt' # Path to Meta File
dim = 1 # 1 Dimensional CV space.
period = 360 # Dihedral Angles periodicity
# Load data
psis, cv_trajs, neighbors = uu.data_from_WHAMmeta('wham_meta.txt',dim,T=T,k_B=k_B,period=period)
# Calculate the partition function for each window
z, F = emus.calculate_zs(psis,neighbors=neighbors,)
# Calculate error in each z value from the first iteration.
zerr, zcontribs, ztaus = avar.partition_functions(psis,z,F,iat_method='acor')
# Calculate the PMF
domain = ((-180.0,180.)) # Range of dihedral angle values
pmf = emus.calculate_pmf(cv_trajs,psis,domain,z,nbins=60,kT=kT) # Calculate the pmf
# Calculate z using the MBAR iteration.
z_MBAR_1, F_MBAR_1 = emus.calculate_zs(psis,nMBAR=1)
z_MBAR_2, F_MBAR_2 = emus.calculate_zs(psis,nMBAR=2)
z_MBAR_5, F_MBAR_5 = emus.calculate_zs(psis,nMBAR=5)
z_MBAR_1k, F_MBAR_1k = emus.calculate_zs(psis,nMBAR=1000)
# Calculate new PMF
MBARpmf = emus.calculate_pmf(cv_trajs,psis,domain,nbins=60,z=z_MBAR_1k,kT=kT)
def main():
a = _parse_args() # Get Dictionary of Arguments
kT = a['k_B'] * a['T']
# Load data
psis, cv_trajs, neighbors = uu.data_from_WHAMmeta(a['meta_file'],a['ndim'],T=a['T'], k_B=a['k_B'],period=a['period'],nsig=a['sigma'])
if a['fxn_file'] is not None:
fdata = uu.data_from_fxnmeta(a['fxn_file'])
else:
fdata = None
# Calculate the partition function for each window
z, F= emus.calculate_zs(psis,neighbors=neighbors,nMBAR=a['nMBAR'])
# Calculate the PMF
pmf = emus.calculate_pmf(cv_trajs,psis,a['domain'],z,nbins=a['nbins'],kT=kT)
# Calculate any averages of functions.
if fdata is not None:
favgs = []
for n, fdata_i in enumerate(fdata):
favgs.append(emus.calculate_obs(psis,z,fdata_i))
# Perform Error analysis if requested.
if a['error'] is not None:
zEMUS, FEMUS= emus.calculate_zs(psis,neighbors=neighbors,nMBAR=0)
zvars, z_contribs, z_iats = avar.partition_functions(psis,zEMUS,FEMUS,neighbors=neighbors,iat_method=a['error'])
# Perform analysis on any provided functions.
if fdata is not None:
favgs_EM = []
ferrs = []
fcontribs = []
nfxns = len(fdata[0][0])
for n in xrange(nfxns):
fdata_i = [fi[:,n] for fi in fdata]
iat, mean, variances = avar.average_ratio(psis,zEMUS,FEMUS,fdata_i,neighbors=neighbors,iat_method=a['error'])
favgs_EM.append(mean)
fcontribs.append(variances)
ferrs.append(np.sum(variances))
# Save Data
if a['ext'] == 'txt':
np.savetxt(a['output']+'_pmf.txt',pmf)
np.savetxt(a['output']+'_z.txt',z)
np.savetxt(a['output']+'_F.txt',F)
if fdata is not None:
np.savetxt(a['output']+'_f.txt',favgs)
if a['error'] is not None:
np.savetxt(a['output']+'_zvars.txt',zvars)
if fdata is not None:
np.savetxt(a['output']+'_fvars.txt',ferrs)
elif a['ext'] == 'hdf5':
import h5py
f = h5py.File(a['output']+'_out.hdf5',"w")
# Save PMF
pmf_grp = f.create_group("PMF")
pmf_dset = pmf_grp.create_dataset("pmf",pmf.shape,dtype='f')
dmn_dset = pmf_grp.create_dataset("domain",np.array(a['domain']).shape,dtype='f')
pmf_dset[...] = pmf
dmn_dset[...] = np.array(a['domain'])
# Save partition functions
z_grp = f.create_group("partition_function")
z_dset = z_grp.create_dataset("z",z.shape,dtype='f')
z_dset[...] = z
F_dset = z_grp.create_dataset("F",F.shape,dtype='f')
F_dset[...] = F
if a['error'] is not None:
zerr_dset = z_grp.create_dataset("z_vars",np.array(zvars).shape,dtype='f')
zerr_dset[...] = np.array(zvars)
if fdata is not None:
f_grp = f.create_group('function_averages')
f_dset = f_grp.create_dataset("f",np.shape(favgs),dtype='f')
f_dset[...] = np.array(favgs)
if a['error'] is not None:
fvar_dset = f_grp.create_dataset("f_variances",np.shape(fvars),dtype='f')
fvar_dset[...] = ferrs
f.close()
else:
raise Warning('No valid output method detected.')