def calcCvNoWHAM(binenergy, visits, Tlist, NDOF):
"""compute the heat capacity using the direct calculation, i.e. not WHAM
This method computes <E^2> - <E>^2 directly from the visits histogram.
The heat capacity is returned at the temperatures of the replicas.
Parameters
----------
binenergy : ndarray
the (lower bound) energy of the bins
visits : 2d array
visits[r,b] is the number of visits in replica r to energy bin b
Tlist : array
the temperatures of the replicas
ndof : int
the number of degrees of freedom in the system
"""
nreps, nbins = np.shape(visits)
cvdata = np.zeros([nreps, 6])
for i in range(nreps):
cvdata[i,0] = Tlist[i]
m, std = utils.wstd(binenergy, visits[i,:])
cvdata[i,4] = m
cvdata[i,3] = std
#print std, Tlist[i], NDOF, std**2, Tlist[i]**2
cv = float(NDOF)/2. + std**2 / Tlist[i]**2
cvdata[i,5] = cv
return cvdata
def calcCvNoWHAM(binenergy, visits, Tlist, NDOF):
"""compute the heat capacity using the direct calculation, i.e. not WHAM
This method computes <E^2> - <E>^2 directly from the visits histogram.
The heat capacity is returned at the temperatures of the replicas.
Parameters
----------
binenergy : ndarray
the (lower bound) energy of the bins
visits : 2d array
visits[r,b] is the number of visits in replica r to energy bin b
Tlist : array
the temperatures of the replicas
ndof : int
the number of degrees of freedom in the system
"""
nreps, nbins = np.shape(visits)
cvdata = np.zeros([nreps, 6])
for i in range(nreps):
cvdata[i, 0] = Tlist[i]
m, std = utils.wstd(binenergy, visits[i, :])
cvdata[i, 4] = m
cvdata[i, 3] = std
#print std, Tlist[i], NDOF, std**2, Tlist[i]**2
cv = float(NDOF) / 2. + std**2 / Tlist[i]**2
cvdata[i, 5] = cv
return cvdata
def readVisitsFiles():
#load a Visits.his file to get the energy histograms
dirlist = plotVisits.getDirList()
vis = plotVisits.listVisitsFiles(dirlist[0])
vis = vis[-1]
fname = vis.fname
allvisits = []
for d in dirlist:
visits = utils.VisitsHis( d+"/" + fname )
allvisits.append(visits)
means = []
stds = []
for v in allvisits:
v.read()
energies, visits = v.getHis()
m, std = utils.wstd(energies, visits)
means.append(m)
stds.append(std)
return np.array(means), np.array(stds)
def checkWHAM(binenergy, visits, cvdata, Tlist):
for i in range(len(Tlist)):
m, std = utils.wstd(binenergy, visits[i,:])
print "wham_check", Tlist[i], m, std
def checkWHAM(binenergy, visits, cvdata, Tlist):
for i in range(len(Tlist)):
m, std = utils.wstd(binenergy, visits[i, :])
print "wham_check", Tlist[i], m, std
