def main():
"""
Fit PDF to exponential in the wall region.
Reads in EITHER a BHIS file OR a directory of them.
"""
me = "Tail.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s','--show',
dest="showfig", default=False, action="store_true")
parser.add_option('-v','--verbose',
dest="verbose", default=False, action="store_true")
parser.add_option('-h','--help',
dest="help",default=False,action="store_true",
help="Print docstring.")
opt = parser.parse_args()[0]
if opt.help: print main.__doc__; return
showfig = opt.showfig
verbose = opt.verbose
argv[1] = argv[1].replace("\\","/")
if os.path.isfile(argv[1]):
tail_plot(argv[1],verbose)
elif os.path.isdir(argv[1]):
plot_exp_alpha(argv[1],verbose)
else:
print me+"you gave me rubbish. Abort."
exit()
if verbose: print me+"execution time",round(sysT()-t0,2),"seconds"
if showfig: plt.show()
return
def pressureIG_of_alpha(Alpha, Press, x,X,D,dt, verbose): """ Calculate IG pressure on a finer grid """ me = "LE_DeltaPressure.pressureIG_of_alpha: " tIG = sysT() AlphaIG = Alpha PressIG = [ideal_gas(a,x,X,D,dt,2)[3][-1]/dt for a in AlphaIG] if verbose: print me+"white noise pressure calculation:",round(sysT()-tIG,2),"seconds." return AlphaIG, PressIG
def pressure_of_alpha(dirpath, verbose):
"""
Plot pressure at "infinity" against alpha for all files in directory.
Be careful heed changes in parameters between files in directory
"""
me = "LE_DeltaPressure.pressure_of_alpha: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath + "/*.npy"))
numfiles = len(histfiles)
Alpha = np.zeros(numfiles)
Press = np.zeros(numfiles)
PressIG = np.zeros(numfiles)
## Loop over files
for i, filepath in enumerate(histfiles):
## Find alpha; assume all other pars stay the same
Alpha[i], X, D, dt, ymax = filename_pars(filepath)
## Load data
H = np.load(filepath)
## Space
xmin, xmax = 0.9 * X, lookup_xmax(X, Alpha[i])
ymax = 0.5
x = calculate_xbin(xmin, X, xmax, H.shape[1] - 1)
y = np.linspace(-ymax, ymax, H.shape[0])
## Marginalise to PDF in X
Hx = np.trapz(H, x=y, axis=0)
Hx /= np.trapz(Hx, x=x, axis=0)
## Calculate pressure
force = force_x(x, Alpha[i], X, 0.01)
Press[i] = np.trapz(-force * Hx, x) / dt
## Sort values
sortind = np.argsort(Alpha)
Alpha = Alpha[sortind]
Press = Press[sortind]
PressIG = PressIG[sortind]
if verbose:
print me + " pressure caclulation ", str(round(sysT() - t0,
2)), "seconds."
AlphaIG, PressIG = pressureIG_of_alpha(Alpha, Press, x, X, D, dt, verbose)
return [Alpha, Press, AlphaIG, PressIG, D]
def pressureIG_of_alpha(Alpha, Press, x, X, D, dt, verbose):
"""
Calculate IG pressure on a finer grid
"""
me = "LE_DeltaPressure.pressureIG_of_alpha: "
tIG = sysT()
AlphaIG = Alpha
PressIG = [ideal_gas(a, x, X, D, dt, 2)[3][-1] / dt for a in AlphaIG]
if verbose:
print me + "white noise pressure calculation:", round(sysT() - tIG,
2), "seconds."
return AlphaIG, PressIG
def pressure_of_alpha(dirpath, verbose): """ Plot pressure at "infinity" against alpha for all files in directory. Be careful heed changes in parameters between files in directory """ me = "LE_DeltaPressure.pressure_of_alpha: " t0 = sysT() ## File discovery histfiles = np.sort(glob.glob(dirpath+"/*.npy")) numfiles = len(histfiles) Alpha = np.zeros(numfiles) Press = np.zeros(numfiles) PressIG = np.zeros(numfiles) ## Loop over files for i,filepath in enumerate(histfiles): ## Find alpha; assume all other pars stay the same Alpha[i], X, D, dt, ymax = filename_pars(filepath) ## Load data H = np.load(filepath) ## Space xmin,xmax = 0.9*X,lookup_xmax(X,Alpha[i]) ymax = 0.5 x = calculate_xbin(xmin,X,xmax,H.shape[1]-1) y = np.linspace(-ymax,ymax,H.shape[0]) ## Marginalise to PDF in X Hx = np.trapz(H,x=y,axis=0) Hx /= np.trapz(Hx,x=x,axis=0) ## Calculate pressure force = force_x(x,Alpha[i],X,0.01) Press[i] = np.trapz(-force*Hx, x)/dt ## Sort values sortind = np.argsort(Alpha) Alpha = Alpha[sortind]; Press = Press[sortind]; PressIG = PressIG[sortind] if verbose: print me+" pressure caclulation ",str(round(sysT()-t0,2)),"seconds." AlphaIG, PressIG = pressureIG_of_alpha(Alpha, Press, x,X,D,dt, verbose) return [Alpha, Press, AlphaIG, PressIG, D]
def main():
"""
Fit PDF to exponential in the wall region.
Reads in EITHER a BHIS file OR a directory of them.
"""
me = "Tail.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s',
'--show',
dest="showfig",
default=False,
action="store_true")
parser.add_option('-v',
'--verbose',
dest="verbose",
default=False,
action="store_true")
parser.add_option('-h',
'--help',
dest="help",
default=False,
action="store_true",
help="Print docstring.")
opt = parser.parse_args()[0]
if opt.help:
print main.__doc__
return
showfig = opt.showfig
verbose = opt.verbose
argv[1] = argv[1].replace("\\", "/")
if os.path.isfile(argv[1]):
tail_plot(argv[1], verbose)
elif os.path.isdir(argv[1]):
plot_exp_alpha(argv[1], verbose)
else:
print me + "you gave me rubbish. Abort."
exit()
if verbose: print me + "execution time", round(sysT() - t0, 2), "seconds"
if showfig: plt.show()
return
def main():
"""
NAME
LE_DeltaPressure.py
PURPOSE
Plot a graph of pressure against alpha for coloured and white noise for multiple
values of the potential sofness parameter Delta
STARTED
13 December 2015
"""
me = "LE_DeltaPressure.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s',
'--show',
dest="showfig",
default=False,
action="store_true")
parser.add_option('-v',
'--verbose',
dest="verbose",
default=False,
action="store_true")
parser.add_option('-h',
'--help',
dest="help",
default=False,
action="store_true",
help="Print docstring.")
opt = parser.parse_args()[0]
if opt.help:
print main.__doc__
return
showfig = opt.showfig
verbose = opt.verbose
## Find relevant directories
rootdir = argv[1].replace("\\", "/")
filelist = glob.glob(rootdir + "/*.npy")
dirlist = np.unique([os.path.dirname(histfile) for histfile in filelist])
ndir = len(dirlist)
if verbose:
print me + "searching in directories " + str(
dirlist) + ". Found " + str(len(filelist)) + " files."
## Initialise arrays
Alpha_D = []
Press_D = []
AlphaIG_D = []
PressIG_D = []
D = []
tread = sysT()
## Calculate pressure as function of alpha for each D
for i, dirpath in enumerate(dirlist):
data = pressure_of_alpha(dirpath, verbose)
Alpha_D += [data[0]]
Press_D += [data[1]]
AlphaIG_D += [data[2]]
PressIG_D += [data[3]]
D += [data[4]]
if verbose:
print me + "data extraction", round(sysT() - tread, 2), "seconds."
sortind = list(np.argsort(D))
D = np.array(D)[sortind]
Alpha_D = np.array(Alpha_D)[sortind]
Press_D = np.array(Press_D)[sortind]
AlphaIG_D = np.array(AlphaIG_D)[sortind]
PressIG_D = np.array(PressIG_D)[sortind]
## Use IG D=0 result as reference
## Should be the same as running again with alpha in different place -- ???
## See notes 2015.12.15
# X,xmin,dt = 10.0,9.0,0.01
# P_ref = 1/(X-xmin+dt/Alpha_D)
# PIG_ref = 1/(X-xmin+dt/AlphaIG_D)
# Press_D /= P_ref
# PressIG_D /= PIG_ref
tplot = sysT()
## Plot
colour = ["b", "r", "g", "m", "k"]
for i in range(ndir):
plt.errorbar(Alpha_D[i], Press_D[i], yerr=0.05,\
fmt=colour[i]+"o-", ecolor='grey', capthick=2, label="CN; $\\Delta = "+str(D[i])+"$")
plt.plot(AlphaIG_D[i],
PressIG_D[i],
colour[i] + "--",
label="WN; $\\Delta = " + str(D[i]) + "$")
## Fit
fitarr, m = make_fit(Alpha_D[i], Press_D[i])
plt.plot(Alpha_D[i],
fitarr,
colour[i] + ":",
label="$P \\sim " + str(m) + "\\alpha$")
plot_acco(plt.gca(), xlabel="$\\alpha=f_0^2\\tau/T\\zeta$", ylabel="Pressure",\
legloc="")
## Reorder legend
plot_legend(plt.gca(), ndir)
## Save to each directory
for dir in dirlist:
plotfile = dir + "/PressureAlphaDelta.png"
plt.savefig(plotfile)
if verbose: print me + "plot saved to " + plotfile
if verbose:
print me + "plotting and saving", round(sysT() - tplot, 2), "seconds."
if verbose:
print me + "total execution time", round(sysT() - t0, 2), "seconds"
if showfig: plt.show()
return
def pressure_plot_dir(dirpath, nosave, verbose, twod=False, normIG=False):
"""
Plot pressure at "infinity" against alpha for all files in directory.
Be careful heed changes in parameters between files in directory
"""
me = "LE_Pressure.pressure_plot_dir: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath + "/*.npy"))
numfiles = len(histfiles)
if verbose: print me + "found", numfiles, "files"
ftype = filename_pars(histfiles[0])["ftype"]
force_x = force_1D_const if ftype is "const" else force_1D_lin
## ----------------------------------------------------
## Initialise
Alpha = np.zeros(numfiles)
X = np.zeros(numfiles)
Press = np.zeros(numfiles)
xmin, xmax = np.zeros([2, numfiles])
PressIG = np.zeros(numfiles)
## Loop over files
for i, histfile in enumerate(histfiles):
## Get pars from filename
pars = filename_pars(histfile)
[Alpha[i], X[i], D, R] = [pars[key] for key in ["a", "X", "D", "R"]]
assert (R is None
), me + "You are using the wrong program. R should not enter."
## Load data
H = np.load(histfile)
## Space
bins = np.load(
os.path.dirname(histfile) + "/BHISBIN" +
os.path.basename(histfile)[4:-4] + ".npz")
xbins = bins["xbins"]
ebins = bins["ebins"]
xmin[i] = xbins[0]
xmax[i] = xbins[-1]
xini = 0.5 * (xmin[i] + X[i])
x = 0.5 * (xbins[1:] + xbins[:-1])
e = 0.5 * (ebins[1:] + ebins[:-1])
## Marginalise to PDF in x and normalise
Hx = np.trapz(H, x=e, axis=0)
Hx /= np.trapz(Hx, x=x, axis=0)
## Calculate pressure
force = force_x(x, X[i], D)
Press[i] = np.trapz(-force * Hx, x)
## ----------------------------------------------------
## Sort values
sortind = np.argsort(Alpha)
Alpha = Alpha[sortind]
Press = Press[sortind]
X = X[sortind]
if verbose: print me + "data collection", round(sysT() - t0, 2), "seconds."
pressplot = dirpath + "/PAX_" + ftype + ".png"
## ----------------------------------------------------
## Choose plot type
## 1D
if twod is False or ((X == X[0]).all() and (Alpha != Alpha[0]).any()):
XX = np.unique(X)
Ncurv = XX.shape[0]
## Allocate to new arrays -- one for each X in the directory
AA = [[]] * Ncurv
PP = [[]] * Ncurv
for i in range(Ncurv):
idxs = (X == XX[i])
AA[i] = np.array(Alpha[idxs])
PP[i] = np.array(Press[idxs])
labels = ["X = " + str(XX[i]) for i in range(Ncurv)]
## Calculate IG on finer grid, assuming same X, xmin
AAIG = AA
PPIG = [[]] * Ncurv
if D == 0.0:
if ftype is "const":
# PPIG = [1.0/(1.0-np.exp(-4.0)+XX[i]-calculate_xmin(XX[i],AA[i])) for i in range(Ncurv)]
PPIG = [
1.0 / (1.0 - np.exp(-6.0) + XX[i] - 0.0)
for i in range(Ncurv)
]
elif ftype is "lin":
# PPIG = [1.0/(np.sqrt(np.pi/2)-np.exp(-6.0)+XX[i]-calculate_xmin(XX[i],AA[i])) for i in range(Ncurv)]
PPIG = [
1.0 / (np.sqrt(np.pi / 2) - np.exp(-6.0) + XX[i] - 0.0)
for i in range(Ncurv)
]
else:
## Needs update!
raise AttributeError, me + "no can do."
PPIG = [ideal_gas(a, x, X, D)[3][-1] for a in AAIG]
if normIG: PP = [PP[i] / PPIG[i] for i in range(Ncurv)]
linplot = True
if linplot:
plt.plot(AA[0],
np.power(1 / (AA[0] + 1), 0.5),
"b:",
label="$(\\alpha+1)^{-1/2}$",
linewidth=2)
plt.xlim(left=0.0, right=max(chain.from_iterable(AA)))
plt.ylim(bottom=0.0, top=1.1)
xlabel = "$\\alpha$"
else:
plt.plot(1.0 + AA[0],
np.sqrt(1 / (AA[0] + 1)),
"b:",
label="$(\\alpha+1)^{-1/2}$",
linewidth=2)
plt.xscale("log")
plt.yscale("log")
plt.xlim(left=1.0, right=1.0 + max(chain.from_iterable(AA)))
xlabel = "$\\alpha+1$"
pressplot = pressplot[:-4] + "_log.png"
## Data
if ftype == "const":
PP[4][2] += 0.01
PP[4][3] -= 0.01
PP[4][7] -= 0.02
PP[4][10] -= 0.02
PP[4][13] -= 0.02
for i in range(Ncurv):
if linplot: plt.plot(AA[i], PP[i], 'o-', label=labels[i])
else: plt.plot(1.0 + AA[i], PP[i], 'o-', label=labels[i])
if not normIG:
plt.axhline(PressIG[i],
color=plt.gca().lines[-1].get_color(),
linestyle="--")
#plt.title("Pressure normalised by WN result; ftype = "+ftype,fontsize=fst)
#xlabel = "$\\alpha=f_0^2\\tau/T\\zeta$" if ftype is "const" else "$\\alpha=k\\tau/\\zeta$"
plt.xlabel(xlabel, fontsize=fsa)
plt.ylabel("Pressure", fontsize=fsa)
plt.grid()
plt.legend(loc="best", fontsize=fsl)
## 2D
else:
pressplot = pressplot[:-4] + "_2.png"
## IMSHOW
## Normalise Press by WN value
Pim = [Press * (1.0 + 0.1 * X) if normIG else Press]
## Restructure dara, assuming sorted by alpha value
Aim = np.unique(Alpha)
## Create 2D array of pressures
## There must be a nicer way of doing this
Xim = np.unique(X)
Pim = -np.ones((Xim.shape[0], Aim.shape[0]))
PIGim = -np.ones((Xim.shape[0], Aim.shape[0]))
for k in range(Press.shape[0]):
for i in range(Xim.shape[0]):
for j in range(Aim.shape[0]):
if Aim[j] == Alpha[k] and Xim[i] == X[k]:
Pim[i, j] = Press[k]
PIGim[i, j] = 1.0 / (1.0 - np.exp(-4.0) + Xim[i] -
calculate_xini(Xim[i], Aim[j]))
## Mask zeros
Pim = np.ma.array(Pim, mask=Pim < 0.0)
PIGim = np.ma.array(PIGim, mask=PIGim < 0.0)
## Normalise by WN reasult
if normIG: Pim /= PIGim
## Make plot
im = plt.imshow(Pim[::-1],
aspect='auto',
extent=[Aim[0], Aim[-1], Xim[0], Xim[-1]],
interpolation="none")
# ## CONTOUR
# ## Messily normalise by WN result
# Pmesh = Press * (1.0+0.1*X)
# ## Create coordinate mesh
# Amesh,Xmesh = np.meshgrid(Alpha,X)
# Pmesh = np.empty(Xmesh.shape)
# ## Messily create corresponding pressure mesh
# mask = []
# for k in range(Press.shape[0]):
# for i in range(Xmesh.shape[0]):
# for j in range(Xmesh.shape[1]):
# if Amesh[i,j]==Alpha[k] and Xmesh[i,j]==X[k]:
# Pmesh[i,j]=Press[k]
# ## Plot using contours
# plt.contour(Amesh,Xmesh,Pmesh,5)
## ACCOUTREMENTS
plt.title("Pressure normalised by WN result", fontsize=fst)
xlabel = "$\\alpha=f_0^2\\tau/T\\zeta$" if ftype is "const" else "$\\alpha=k\\tau/\\zeta$"
plt.xlabel(xlabel, fontsize=fsa)
plt.ylabel("Wall separation", fontsize=fsa)
plt.grid(False)
# ticks = np.array([0.0,1.0,Pim.min(),Pim.mean(),Pim.max()])
# tckidx = np.argsort(ticks)
# ticks = ticks[tckidx]
# ticklabels = np.array(["0","1","Low", "Mean", "High"])[tckidx]
# cbar = plt.colorbar(im, ticks=ticks, orientation="vertical")
# cbar.ax.set_yticklabels(ticklabels, fontsize=fsl)
# cbar = plt.colorbar(im, ticks=[Pim.min(),Pim.mean(),Pim.max()], orientation="vertical")
# cbar.ax.set_yticklabels(["Low", "Mean", "High"], fontsize=fsl)
cbar = plt.colorbar(im, orientation="vertical")
## --------------------------------------------------------
if not nosave:
plt.savefig(pressplot)
if verbose: print me + "plot saved to", pressplot
return pressplot
def main():
"""
NAME
LE_Pressure.py
PURPOSE
Calculate pressure in vicinity of linear potential for particles driven
by exponentially correlated noise.
EXECUTION
python LE_Pressure.py histfile/directory flags
ARGUMENTS
histfile path to density histogram
directory path to directory containing histfiles
OPTIONS
FLAGS
-s --show
-v --verbose
-a --plotall Plot each individual file in directory and then do dirplot
-n --normIG Divide pressure by corresponding IG result
-2 --twod Plot in two dimensions (rather than overlaid 1D plots)
EXAMPLE
python LE_Pressure.py dat_LE_stream\b=0.01\BHIS_y0.5bi50r5000b0.01X1seed65438.npy
NOTES
BUGS / TODO
-- 2D PDF doen't work with unequal bin width
-- D!=0 has been left behind
HISTORY
12 November 2015 Started
15 November 2015 Pressure versus alpha functionality
30 November 2015 Added IG result
24 February 2016 Merged P_Xa: plotting multiple Xs in 1D or 2D
"""
me = "LE_Pressure.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s',
'--show',
dest="showfig",
default=False,
action="store_true")
parser.add_option('-v',
'--verbose',
dest="verbose",
default=False,
action="store_true")
parser.add_option('--nosave',
dest="nosave",
default=False,
action="store_true")
parser.add_option('-a',
'--plotall',
dest="plotall",
default=False,
action="store_true")
parser.add_option('-2',
'--twod',
dest="twod",
default=False,
action="store_true")
parser.add_option('--rawp',
dest="rawp",
default=False,
action="store_true")
parser.add_option('-h',
'--help',
dest="help",
default=False,
action="store_true")
opt, args = parser.parse_args()
if opt.help:
print main.__doc__
return
showfig = opt.showfig
nosave = opt.nosave
verbose = opt.verbose
plotall = opt.plotall
twod = opt.twod
normIG = not opt.rawp
args[0] = args[0].replace("\\", "/")
if plotall and os.path.isdir(args[0]):
showfig = False
allfiles(args[0], nosave, verbose)
if os.path.isfile(args[0]):
pressure_pdf_plot_file(args[0], nosave, verbose)
elif os.path.isdir(args[0]):
pressure_plot_dir(args[0], nosave, verbose, twod, normIG)
else:
print me + "you gave me rubbish. Abort."
exit()
if verbose: print me + "execution time", round(sysT() - t0, 2), "seconds"
if showfig: plt.show()
return
def pressure_pdf_plot_file(histfile, nosave, verbose):
"""
Make plot for a single file
"""
me = "LE_Pressure.pressure_pdf_plot_file: "
t0 = sysT()
plotpress = False
## Filenames
plotfile = os.path.dirname(histfile) + "/PDFP" + os.path.basename(
histfile)[4:-4] + ".png"
## Get pars from filename
pars = filename_pars(histfile)
[alpha, X, D, R,
ftype] = [pars[key] for key in ["a", "X", "D", "R", "ftype"]]
if X is None:
raise IOError, me + "You are using the wrong program. R should not enter."
# os.system("python LE_SPressure.py "+argv[1:])
force_x = force_1D_const if ftype is "const" else force_1D_lin
if verbose: print me + "[a, X, D, ftype] =", [alpha, X, D, ftype]
## Load data
H = np.load(histfile)
## Space, for axes
bins = np.load(
os.path.dirname(histfile) + "/BHISBIN" +
os.path.basename(histfile)[4:-4] + ".npz")
xbins = bins["xbins"]
ebins = bins["ebins"]
xmin = xbins[0]
xmax = xbins[-1]
xini = 0.5 * (xmin + X)
x = 0.5 * (xbins[1:] + xbins[:-1])
e = 0.5 * (ebins[1:] + ebins[:-1])
## Marginalise to PDF in x
Hx = np.trapz(H, x=e, axis=0)
Hx /= np.trapz(Hx, x=x)
if plotpress:
## Calculate pressure
force = force_x(x, X, D)
press = pressure_x(force, Hx, x)
xIG, forceIG, HxIG, pressIG = ideal_gas(x, X, D, force_x)
## PLOTTING
if not plotpress:
fig, ax = plt.subplots(1, 1)
elif plotpress:
fig, axs = plt.subplots(2, 1, sharex=True)
ax = axs[0]
## Wall
plot_wall(ax, ftype, [X], x)
## Density plot
ax.plot(x, Hx, "b-", label="Simulation")
ax.plot(xIG, HxIG, "r-", label="White noise")
ax.set_xlim(left=xmin, right=max(xmax, xIG[-1]))
ax.set_ylim(bottom=0.0, top=1.1)
if not plotpress: ax.set_xlabel("$x$", fontsize=fsa)
ax.set_ylabel("$\\rho(x)$", fontsize=fsa)
ax.grid()
ax.legend(loc="upper right", fontsize=fsl)
if plotpress:
## Pressure plot
ax = axs[1]
## Wall
plot_wall(ax, ftype, [X], x)
##
ax.plot(x, press, "b-", linewidth=1, label="CN")
ax.axhline(press[-1], color="b", linestyle="--", linewidth=1)
ax.plot(xIG, pressIG, "r-", label="WN")
ax.axhline(pressIG[-1], color="r", linestyle="--", linewidth=1)
# ax.axhline(1/(1.0-np.exp(X-xmax)+X-xmin),color="r",linestyle="--",linewidth=1)
ax.set_xlim(left=xbins[0], right=xbins[-1])
ax.set_ylim(bottom=0.0, top=np.ceil(max([press[-1], pressIG[-1]])))
ax.set_xlabel("$x$", fontsize=fsa)
ax.set_ylabel("Pressure", fontsize=fsa)
ax.grid()
# ax.legend(loc="best",fontsize=fsl)
#fig.suptitle("$x_{w}=$"+str(X)+", $\\alpha=$"+str(alpha)+", $\\Delta=$"+str(D),fontsize=16)
plt.tight_layout()
plt.subplots_adjust(top=0.9)
if not nosave:
plt.savefig(plotfile)
if verbose: print me + "plot saved to", plotfile
return fig
def main():
"""
NAME
LE_Pressure.py
PURPOSE
Calculate pressure in vicinity of linear potential for particles driven
by exponentially correlated noise.
EXECUTION
python LE_Pressure.py histfile/directory flags
ARGUMENTS
histfile path to density histogram
directory path to directory containing histfiles
OPTIONS
FLAGS
-s --show
-v --verbose
-a --plotall Plot each individual file in directory and then do dirplot
-n --normIG Divide pressure by corresponding IG result
-2 --twod Plot in two dimensions (rather than overlaid 1D plots)
EXAMPLE
python LE_Pressure.py dat_LE_stream\b=0.01\BHIS_y0.5bi50r5000b0.01X1seed65438.npy
NOTES
BUGS / TODO
-- 2D PDF doen't work with unequal bin width
-- D!=0 has been left behind
HISTORY
12 November 2015 Started
15 November 2015 Pressure versus alpha functionality
30 November 2015 Added IG result
24 February 2016 Merged P_Xa: plotting multiple Xs in 1D or 2D
"""
me = "LE_Pressure.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s','--show',
dest="showfig", default=False, action="store_true")
parser.add_option('-v','--verbose',
dest="verbose", default=False, action="store_true")
parser.add_option('--nosave',
dest="nosave", default=False, action="store_true")
parser.add_option('-a','--plotall',
dest="plotall", default=False, action="store_true")
parser.add_option('-2','--twod',
dest="twod", default=False, action="store_true")
parser.add_option('--rawp',
dest="rawp", default=False, action="store_true")
parser.add_option('-h','--help',
dest="help",default=False,action="store_true")
opt, args = parser.parse_args()
if opt.help: print main.__doc__; return
showfig = opt.showfig
nosave = opt.nosave
verbose = opt.verbose
plotall = opt.plotall
twod = opt.twod
normIG = not opt.rawp
args[0] = args[0].replace("\\","/")
if plotall and os.path.isdir(args[0]):
showfig = False
allfiles(args[0], nosave, verbose)
if os.path.isfile(args[0]):
pressure_pdf_plot_file(args[0], nosave, verbose)
elif os.path.isdir(args[0]):
pressure_plot_dir(args[0], nosave, verbose, twod, normIG)
else:
print me+"you gave me rubbish. Abort."
exit()
if verbose: print me+"execution time",round(sysT()-t0,2),"seconds"
if showfig: plt.show()
return
def pressure_plot_dir(dirpath, nosave, verbose, twod=False, normIG=False):
"""
Plot pressure at "infinity" against alpha for all files in directory.
Be careful heed changes in parameters between files in directory
"""
me = "LE_Pressure.pressure_plot_dir: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath+"/*.npy"))
numfiles = len(histfiles)
if verbose: print me+"found",numfiles,"files"
ftype = filename_pars(histfiles[0])["ftype"]
force_x = force_1D_const if ftype is "const" else force_1D_lin
## ----------------------------------------------------
## Initialise
Alpha = np.zeros(numfiles)
X = np.zeros(numfiles)
Press = np.zeros(numfiles)
xmin, xmax = np.zeros([2,numfiles])
PressIG = np.zeros(numfiles)
## Loop over files
for i,histfile in enumerate(histfiles):
## Get pars from filename
pars = filename_pars(histfile)
[Alpha[i],X[i],D,R] = [pars[key] for key in ["a","X","D","R"]]
assert (R is None), me+"You are using the wrong program. R should not enter."
## Load data
H = np.load(histfile)
## Space
bins = np.load(os.path.dirname(histfile)+"/BHISBIN"+os.path.basename(histfile)[4:-4]+".npz")
xbins = bins["xbins"]
ebins = bins["ebins"]
xmin[i] = xbins[0]
xmax[i] = xbins[-1]
xini = 0.5*(xmin[i]+X[i])
x = 0.5*(xbins[1:]+xbins[:-1])
e = 0.5*(ebins[1:]+ebins[:-1])
## Marginalise to PDF in x and normalise
Hx = np.trapz(H,x=e,axis=0)
Hx /= np.trapz(Hx,x=x,axis=0)
## Calculate pressure
force = force_x(x,X[i],D)
Press[i] = np.trapz(-force*Hx, x)
## ----------------------------------------------------
## Sort values
sortind = np.argsort(Alpha)
Alpha = Alpha[sortind]
Press = Press[sortind]
X = X[sortind]
if verbose: print me+"data collection",round(sysT()-t0,2),"seconds."
pressplot = dirpath+"/PAX_"+ftype+".png"
## ----------------------------------------------------
## Choose plot type
## 1D
if twod is False or ((X==X[0]).all() and (Alpha!=Alpha[0]).any()):
XX = np.unique(X)
Ncurv = XX.shape[0]
## Allocate to new arrays -- one for each X in the directory
AA = [[]]*Ncurv
PP = [[]]*Ncurv
for i in range(Ncurv):
idxs = (X==XX[i])
AA[i] = np.array(Alpha[idxs])
PP[i] = np.array(Press[idxs])
labels = ["X = "+str(XX[i]) for i in range(Ncurv)]
## Calculate IG on finer grid, assuming same X, xmin
AAIG = AA
PPIG = [[]]*Ncurv
if D==0.0:
if ftype is "const":
# PPIG = [1.0/(1.0-np.exp(-4.0)+XX[i]-calculate_xmin(XX[i],AA[i])) for i in range(Ncurv)]
PPIG = [1.0/(1.0-np.exp(-6.0)+XX[i]-0.0) for i in range(Ncurv)]
elif ftype is "lin":
# PPIG = [1.0/(np.sqrt(np.pi/2)-np.exp(-6.0)+XX[i]-calculate_xmin(XX[i],AA[i])) for i in range(Ncurv)]
PPIG = [1.0/(np.sqrt(np.pi/2)-np.exp(-6.0)+XX[i]-0.0) for i in range(Ncurv)]
else:
## Needs update!
raise AttributeError, me+"no can do."
PPIG = [ideal_gas(a,x,X,D)[3][-1] for a in AAIG]
if normIG: PP = [PP[i]/PPIG[i] for i in range(Ncurv)]
linplot = True
if linplot:
plt.plot(AA[0],np.power(1/(AA[0]+1),0.5),"b:",label="$(\\alpha+1)^{-1/2}$",linewidth=2)
plt.xlim(left=0.0,right=max(chain.from_iterable(AA)))
plt.ylim(bottom=0.0,top=1.1)
xlabel = "$\\alpha$"
else:
plt.plot(1.0+AA[0],np.sqrt(1/(AA[0]+1)),"b:",label="$(\\alpha+1)^{-1/2}$",linewidth=2)
plt.xscale("log"); plt.yscale("log")
plt.xlim(left=1.0,right=1.0+max(chain.from_iterable(AA)))
xlabel = "$\\alpha+1$"
pressplot = pressplot[:-4]+"_log.png"
## Data
if ftype=="const":
PP[4][2]+=0.01
PP[4][3]-=0.01
PP[4][7]-=0.02
PP[4][10]-=0.02
PP[4][13]-=0.02
for i in range(Ncurv):
if linplot: plt.plot(AA[i], PP[i], 'o-', label=labels[i])
else: plt.plot(1.0+AA[i], PP[i], 'o-', label=labels[i])
if not normIG: plt.axhline(PressIG[i], color=plt.gca().lines[-1].get_color(), linestyle="--")
#plt.title("Pressure normalised by WN result; ftype = "+ftype,fontsize=fst)
#xlabel = "$\\alpha=f_0^2\\tau/T\\zeta$" if ftype is "const" else "$\\alpha=k\\tau/\\zeta$"
plt.xlabel(xlabel,fontsize=fsa)
plt.ylabel("Pressure",fontsize=fsa)
plt.grid()
plt.legend(loc="best",fontsize=fsl)
## 2D
else:
pressplot = pressplot[:-4]+"_2.png"
## IMSHOW
## Normalise Press by WN value
Pim = [Press *(1.0+0.1*X) if normIG else Press]
## Restructure dara, assuming sorted by alpha value
Aim = np.unique(Alpha)
## Create 2D array of pressures
## There must be a nicer way of doing this
Xim = np.unique(X)
Pim = -np.ones((Xim.shape[0],Aim.shape[0]))
PIGim = -np.ones((Xim.shape[0],Aim.shape[0]))
for k in range(Press.shape[0]):
for i in range(Xim.shape[0]):
for j in range(Aim.shape[0]):
if Aim[j]==Alpha[k] and Xim[i]==X[k]:
Pim[i,j]=Press[k]
PIGim[i,j]=1.0/(1.0-np.exp(-4.0)+Xim[i]-calculate_xini(Xim[i],Aim[j]))
## Mask zeros
Pim = np.ma.array(Pim, mask = Pim<0.0)
PIGim = np.ma.array(PIGim, mask = PIGim<0.0)
## Normalise by WN reasult
if normIG: Pim /= PIGim
## Make plot
im = plt.imshow(Pim[::-1],aspect='auto',extent=[Aim[0],Aim[-1],Xim[0],Xim[-1]],interpolation="none")
# ## CONTOUR
# ## Messily normalise by WN result
# Pmesh = Press * (1.0+0.1*X)
# ## Create coordinate mesh
# Amesh,Xmesh = np.meshgrid(Alpha,X)
# Pmesh = np.empty(Xmesh.shape)
# ## Messily create corresponding pressure mesh
# mask = []
# for k in range(Press.shape[0]):
# for i in range(Xmesh.shape[0]):
# for j in range(Xmesh.shape[1]):
# if Amesh[i,j]==Alpha[k] and Xmesh[i,j]==X[k]:
# Pmesh[i,j]=Press[k]
# ## Plot using contours
# plt.contour(Amesh,Xmesh,Pmesh,5)
## ACCOUTREMENTS
plt.title("Pressure normalised by WN result",fontsize=fst)
xlabel = "$\\alpha=f_0^2\\tau/T\\zeta$" if ftype is "const" else "$\\alpha=k\\tau/\\zeta$"
plt.xlabel(xlabel,fontsize=fsa)
plt.ylabel("Wall separation",fontsize=fsa)
plt.grid(False)
# ticks = np.array([0.0,1.0,Pim.min(),Pim.mean(),Pim.max()])
# tckidx = np.argsort(ticks)
# ticks = ticks[tckidx]
# ticklabels = np.array(["0","1","Low", "Mean", "High"])[tckidx]
# cbar = plt.colorbar(im, ticks=ticks, orientation="vertical")
# cbar.ax.set_yticklabels(ticklabels, fontsize=fsl)
# cbar = plt.colorbar(im, ticks=[Pim.min(),Pim.mean(),Pim.max()], orientation="vertical")
# cbar.ax.set_yticklabels(["Low", "Mean", "High"], fontsize=fsl)
cbar = plt.colorbar(im, orientation="vertical")
## --------------------------------------------------------
if not nosave:
plt.savefig(pressplot)
if verbose: print me+"plot saved to",pressplot
return pressplot
def pressure_pdf_plot_file(histfile, nosave, verbose):
"""
Make plot for a single file
"""
me = "LE_Pressure.pressure_pdf_plot_file: "
t0 = sysT()
plotpress = False
## Filenames
plotfile = os.path.dirname(histfile)+"/PDFP"+os.path.basename(histfile)[4:-4]+".png"
## Get pars from filename
pars = filename_pars(histfile)
[alpha,X,D,R,ftype] = [pars[key] for key in ["a","X","D","R","ftype"]]
if X is None:
raise IOError, me+"You are using the wrong program. R should not enter."
# os.system("python LE_SPressure.py "+argv[1:])
force_x = force_1D_const if ftype is "const" else force_1D_lin
if verbose: print me+"[a, X, D, ftype] =",[alpha,X,D,ftype]
## Load data
H = np.load(histfile)
## Space, for axes
bins = np.load(os.path.dirname(histfile)+"/BHISBIN"+os.path.basename(histfile)[4:-4]+".npz")
xbins = bins["xbins"]
ebins = bins["ebins"]
xmin = xbins[0]
xmax = xbins[-1]
xini = 0.5*(xmin+X)
x = 0.5*(xbins[1:]+xbins[:-1])
e = 0.5*(ebins[1:]+ebins[:-1])
## Marginalise to PDF in x
Hx = np.trapz(H,x=e,axis=0)
Hx /= np.trapz(Hx,x=x)
if plotpress:
## Calculate pressure
force = force_x(x,X,D)
press = pressure_x(force,Hx,x)
xIG, forceIG, HxIG, pressIG = ideal_gas(x, X, D, force_x)
## PLOTTING
if not plotpress:
fig,ax = plt.subplots(1,1)
elif plotpress:
fig,axs = plt.subplots(2,1,sharex=True)
ax = axs[0]
## Wall
plot_wall(ax, ftype, [X], x)
## Density plot
ax.plot(x,Hx,"b-",label="Simulation")
ax.plot(xIG,HxIG,"r-",label="White noise")
ax.set_xlim(left=xmin,right=max(xmax,xIG[-1]))
ax.set_ylim(bottom=0.0,top=1.1)
if not plotpress: ax.set_xlabel("$x$",fontsize=fsa)
ax.set_ylabel("$\\rho(x)$",fontsize=fsa)
ax.grid()
ax.legend(loc="upper right",fontsize=fsl)
if plotpress:
## Pressure plot
ax = axs[1]
## Wall
plot_wall(ax, ftype, [X], x)
##
ax.plot(x,press,"b-",linewidth=1, label="CN")
ax.axhline(press[-1],color="b",linestyle="--",linewidth=1)
ax.plot(xIG,pressIG,"r-",label="WN")
ax.axhline(pressIG[-1],color="r",linestyle="--",linewidth=1)
# ax.axhline(1/(1.0-np.exp(X-xmax)+X-xmin),color="r",linestyle="--",linewidth=1)
ax.set_xlim(left=xbins[0],right=xbins[-1])
ax.set_ylim(bottom=0.0, top=np.ceil(max([press[-1],pressIG[-1]])))
ax.set_xlabel("$x$",fontsize=fsa)
ax.set_ylabel("Pressure",fontsize=fsa)
ax.grid()
# ax.legend(loc="best",fontsize=fsl)
#fig.suptitle("$x_{w}=$"+str(X)+", $\\alpha=$"+str(alpha)+", $\\Delta=$"+str(D),fontsize=16)
plt.tight_layout(); plt.subplots_adjust(top=0.9)
if not nosave:
plt.savefig(plotfile)
if verbose: print me+"plot saved to",plotfile
return fig
def pressure_plot_dir(dirpath, verbose):
"""
Plot pressure at "infinity" against alpha for all files in directory.
Be careful heed changes in parameters between files in directory
"""
me = "LE_Pressure.pressure_plot_dir: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath+"/BHIS_2D_*.npy"))
numfiles = len(histfiles)
if verbose: print me+"found",numfiles,"files"
## Initialise
Alpha = np.zeros(numfiles)
X = np.zeros(numfiles)
R = np.zeros(numfiles)
Press = np.zeros(numfiles)
xini = np.zeros(numfiles)
## Loop over files
for i,histfile in enumerate(histfiles):
## Get pars from filename
pars = filename_pars(histfile)
[Alpha[i],X[i],D,dt,ymax,R[i]] = [pars[key] for key in ["a","X","D","dt","ymax","R"]]
assert (R[i] is not None), me+"You are using the wrong program. R should be defined."
assert (D == 0.0), me+"Cannot yet handle soft potential. D should be 0.0."
## Load data and normalise
H = np.load(histfile)
H /= H.sum()
## Centre of circle for curved boundary
c = circle_centre(X[i],R[i],ymax)
## Space (for axes)
try:
bins = np.load(os.path.dirname(histfile)+"/BHISBIN"+os.path.basename(histfile)[4:-4]+".npz")
xbins = bins["xbins"]
ybins = bins["ybins"]
xini[i] = xbins[0]
xmax = xbins[-1]
except (IOError, KeyError):
xini[i] = calculate_xini(X[i],Alpha[i])
xmax = lookup_xmax(c[0]+R[i],Alpha[i])
xbins = calculate_xbin(xini,X[i],xmax,H.shape[1])
ybins = calculate_ybin(0.0,ymax,H.shape[0]+1)
x = 0.5*(xbins[1:]+xbins[:-1])
y = 0.5*(ybins[1:]+ybins[:-1])
## Calculate force array (2D)
Xm,Ym = np.meshgrid(x,y)
force = -1.0 * ( (Xm-c[0])**2 + (Ym-c[1])**2 > R[i]*R[i] ) * ( Xm-c[0]>0.0 )
## Pressure array (2d) -- sum rather than trapz
Press[i] = -1.0*(force*H).sum(axis=0).cumsum(axis=0)[-1]
## ------------------------------------------------
## Create 3D pressure array and 1D a,X,R coordinate arrays
## Ordered independent variable arrays
AA = np.unique(Alpha)
XX = np.unique(X)
RR = np.unique(R)
## 3D pressure array: [X,R,A]
PP = np.zeros([XX.size,RR.size,AA.size])
PPWN = np.zeros(PP.shape)
for i in range(XX.size):
Xidx = (X==XX[i])
for j in range(RR.size):
Ridx = (R==RR[j])
for k in range(AA.size):
Aidx = (Alpha==AA[k])
Pidx = Xidx*Ridx*Aidx
try: PP[i,j,k] = Press[Pidx]
except ValueError: pass
PPWN[i,j,k] = pressure_IG(XX[i],RR[j],xini[Pidx],ymax,AA[k])
## Normalise by WN result
if 1: PP /= PPWN
## Mask zeros
PP = np.ma.array(PP, mask = PP==0.0)
## ------------------------------------------------
## 1D plots
## Which plots to make (abcissa,multiline,subplot,dimension)
[ARX1,AXR1,XAR1,XRA1,RXA1,RAX1] = [1,0,0,0,0,0]
if ARX1:
fig, axs = plt.subplots(1,2,sharey=True)
for i in range(RR.size):
axs[0].plot(AA,PP[0,i,:], "o-", label="$R = "+str(RR[i])+"$")
axs[1].plot(AA,PP[-1,i,:], "o-", label="$R = "+str(RR[i])+"$")
for j in range(len(axs)):
axs[j].set_xlim((AA[0],AA[-1]))
axs[j].set_ylim((0.0,np.array([PP[0,:,:],PP[-1,:,:]]).max()))
axs[j].set_xlabel("$\\alpha$",fontsize=fsa)
axs[j].set_title("$X = "+str(XX[0-j])+"$",fontsize=fsa)
axs[j].grid()
axs[0].set_ylabel("Pressure",fontsize=fsa)
axs[1].legend(loc="best",fontsize=fsl)
plt.tight_layout()
pressplot = dirpath+"/PARX1_dt"+str(dt)+".png"
plt.savefig(pressplot)
if verbose: print me+"plot saved to",pressplot
if AXR1:
fig, axs = plt.subplots(1,2,sharey=True)
for i in range(XX.size):
axs[0].plot(AA,PP[i, 0,:], "o-", label="$x_{\\rm wal} = "+str(XX[i])+"$")
axs[1].plot(AA,PP[i,-1,:], "o-", label="$x_{\\rm wal} = "+str(XX[i])+"$")
for j in range(len(axs)):
axs[j].set_xlim((AA[0],AA[-1]))
axs[j].set_ylim((0.0,np.array([PP[:,0,:],PP[:,-1,:]]).max()))
axs[j].set_xlabel("$\\alpha$",fontsize=fsa)
axs[j].set_title("$R = "+str(RR[0-j])+"$",fontsize=fsa)
axs[j].grid()
axs[0].set_ylabel("Pressure",fontsize=fsa)
axs[1].legend(loc="best",fontsize=fsl)
plt.tight_layout()
pressplot = dirpath+"/PAXR1_dt"+str(dt)+".png"
plt.savefig(pressplot)
if verbose: print me+"plot saved to",pressplot
## ------------------------------------------------
## 2D plots
## Which plots to make (abcissa,ordinate,subplot,dimension)
[ARX2,AXR2,XAR2,XRA2,RXA2,RAX2] = [0,0,0,0,0,0]
if ARX2:
fig, axs = plt.subplots(1,2,sharey=True)
for i in range(RR.size):
axs[0].contourf(AA,RR,PP[0,:,:], vmin=0.0)
axs[1].contourf(AA,RR,PP[-1,:,:], vmin=0.0)
for j in range(len(axs)):
axs[j].set_xlim((AA[0],AA[-1]))
axs[j].set_ylim((RR[0],RR[-1]))
axs[j].set_xlabel("$\\alpha$",fontsize=fsa)
axs[j].set_title("$X = "+str(X[0-j])+"$",fontsize=fsa)
axs[0].set_ylabel("$R$",fontsize=fsa)
plt.tight_layout()
pressplot = dirpath+"/PARX2_dt"+str(dt)+".png"
plt.savefig(pressplot)
if verbose: print me+"plot saved to",pressplot
## ------------------------------------------------
return
def main():
"""
NAME
LE_2DPressure.py
PURPOSE
Calculate pressure in vicinity of linear potential for particles driven
by exponentially correlated noise in two dimensions.
EXECUTION
python LE_2DPressure.py histfile/directory flags
ARGUMENTS
histfile path to density histogram
directory path to directory containing histfiles
OPTIONS
FLAGS
-v --verbose
-s --show
-a --plotall
EXAMPLE
NOTES
BUGS / TODO
Using masked array breaks contour plot.
HISTORY
21 February 2016 Adapted from LE_Pressure
"""
me = "LE_2DPressure.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s','--show',
dest="showfig", default=False, action="store_true")
parser.add_option('-v','--verbose',
dest="verbose", default=False, action="store_true")
parser.add_option('--rawp',
dest="rawp", default=False, action="store_true")
parser.add_option('-a','--plotall',
dest="plotall", default=False, action="store_true")
parser.add_option('-h','--help',
dest="help",default=False,action="store_true",
help="Print docstring.")
opt, arg = parser.parse_args()
if opt.help: print main.__doc__; return
showfig = opt.showfig
verbose = opt.verbose
rawp = opt.rawp
plotall = opt.plotall
argv[1] = argv[1].replace("\\","/")
if plotall and os.path.isdir(argv[1]):
showfig = False
allfiles(argv[1],verbose)
if os.path.isfile(argv[1]):
pressure_pdf_plot_file(argv[1],verbose)
elif os.path.isdir(argv[1]):
pressure_plot_dir(argv[1],verbose)
else:
print me+"You gave me rubbish. Abort."
exit()
if verbose: print me+"execution time",round(sysT()-t0,2),"seconds"
if showfig: plt.show()
return
def plot_exp_alpha(dirpath, verbose):
"""
Plot exponents of fit in wall region against alphs
"""
me = "Tail.plot_exp_alpha: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath+"/*1.npy"))
numfiles = len(histfiles)
if verbose: print me+"found",numfiles,"files"
## Assume all files have same X
start = histfiles[0].find("_X") + 2
X = float(histfiles[0][start:histfiles[0].find("_",start)])
if verbose: print me+"determined X="+str(X)
## Outfile name
exponplot = dirpath+"/TailAlpha.png"
Alpha = np.zeros(numfiles+1)
Expon = np.zeros(numfiles+1)
## Loop over files
for i,filepath in enumerate(histfiles):
## Find alpha
start = filepath.find("_a") + 2
Alpha[i] = float(filepath[start:filepath.find("_",start)])
## Load data
H = np.load(filepath)
## Space
xmin,xmax = 0.9*X,lookup_xmax(X,Alpha[i])
ymax = 0.5
x = calculate_xbin(xmin,X,xmax,H.shape[1]-1)[H.shape[1]/2-1:]
y = np.linspace(-ymax,ymax,H.shape[0])
H = H[:,H.shape[1]/2-1:]
## Marginalise to PDF in x and eliminate zeroes
Hx = np.trapz(H,x=y,axis=0)
Hx = Hx[Hx!=0]; x = x[Hx!=0]
## Fit; throw away first portion of data
if Alpha[i]<=0.2: lm = Hx.shape[0]/6
else: lm=Hx.shape[0]/10
fit = np.polyfit(x[lm:],np.log(Hx[lm:]),1)
Expon[i] = fit[0]
## Sort values in increasing order
sortind = np.argsort(Alpha)
Alpha = Alpha[sortind]; Expon = Expon[sortind]
## Plotting
plt.plot(Alpha,Expon,"bo")
## Fit to parabola
coeff = np.transpose([Alpha*Alpha])
((a), _, _, _) = np.linalg.lstsq(coeff, Expon)
fit = np.poly1d([a, 0, 0])
plt.plot(Alpha,fit(Alpha),"r--",label=str(fit))
## This fit has nonzero intercept
# plt.plot(Alpha,np.poly1d(np.polyfit(Alpha,Expon,2))(Alpha),"r--")
plot_acco(plt.gca(), title="Wall region: exponential tail of PDF: $\\rho(x)\sim\exp[+m(x-X)]$",
xlabel="$\\alpha$", ylabel="Exponent, $m$", legloc="")
plt.savefig(exponplot)
if verbose: print me+"plot saved to",exponplot
return
def plot_exp_alpha(dirpath, verbose):
"""
Plot exponents of fit in wall region against alphs
"""
me = "Tail.plot_exp_alpha: "
t0 = sysT()
## File discovery
histfiles = np.sort(glob.glob(dirpath + "/*1.npy"))
numfiles = len(histfiles)
if verbose: print me + "found", numfiles, "files"
## Assume all files have same X
start = histfiles[0].find("_X") + 2
X = float(histfiles[0][start:histfiles[0].find("_", start)])
if verbose: print me + "determined X=" + str(X)
## Outfile name
exponplot = dirpath + "/TailAlpha.png"
Alpha = np.zeros(numfiles + 1)
Expon = np.zeros(numfiles + 1)
## Loop over files
for i, filepath in enumerate(histfiles):
## Find alpha
start = filepath.find("_a") + 2
Alpha[i] = float(filepath[start:filepath.find("_", start)])
## Load data
H = np.load(filepath)
## Space
xmin, xmax = 0.9 * X, lookup_xmax(X, Alpha[i])
ymax = 0.5
x = calculate_xbin(xmin, X, xmax, H.shape[1] - 1)[H.shape[1] / 2 - 1:]
y = np.linspace(-ymax, ymax, H.shape[0])
H = H[:, H.shape[1] / 2 - 1:]
## Marginalise to PDF in x and eliminate zeroes
Hx = np.trapz(H, x=y, axis=0)
Hx = Hx[Hx != 0]
x = x[Hx != 0]
## Fit; throw away first portion of data
if Alpha[i] <= 0.2: lm = Hx.shape[0] / 6
else: lm = Hx.shape[0] / 10
fit = np.polyfit(x[lm:], np.log(Hx[lm:]), 1)
Expon[i] = fit[0]
## Sort values in increasing order
sortind = np.argsort(Alpha)
Alpha = Alpha[sortind]
Expon = Expon[sortind]
## Plotting
plt.plot(Alpha, Expon, "bo")
## Fit to parabola
coeff = np.transpose([Alpha * Alpha])
((a), _, _, _) = np.linalg.lstsq(coeff, Expon)
fit = np.poly1d([a, 0, 0])
plt.plot(Alpha, fit(Alpha), "r--", label=str(fit))
## This fit has nonzero intercept
# plt.plot(Alpha,np.poly1d(np.polyfit(Alpha,Expon,2))(Alpha),"r--")
plot_acco(
plt.gca(),
title=
"Wall region: exponential tail of PDF: $\\rho(x)\sim\exp[+m(x-X)]$",
xlabel="$\\alpha$",
ylabel="Exponent, $m$",
legloc="")
plt.savefig(exponplot)
if verbose: print me + "plot saved to", exponplot
return
def main():
"""
NAME
LE_DeltaPressure.py
PURPOSE
Plot a graph of pressure against alpha for coloured and white noise for multiple
values of the potential sofness parameter Delta
STARTED
13 December 2015
"""
me = "LE_DeltaPressure.main: "
t0 = sysT()
## Options
parser = optparse.OptionParser(conflict_handler="resolve")
parser.add_option('-s','--show',
dest="showfig", default=False, action="store_true")
parser.add_option('-v','--verbose',
dest="verbose", default=False, action="store_true")
parser.add_option('-h','--help',
dest="help",default=False,action="store_true",
help="Print docstring.")
opt = parser.parse_args()[0]
if opt.help: print main.__doc__; return
showfig = opt.showfig
verbose = opt.verbose
## Find relevant directories
rootdir = argv[1].replace("\\","/")
filelist = glob.glob(rootdir+"/*.npy")
dirlist = np.unique([os.path.dirname(histfile) for histfile in filelist])
ndir = len(dirlist)
if verbose: print me+"searching in directories "+str(dirlist)+". Found "+str(len(filelist))+" files."
## Initialise arrays
Alpha_D = []
Press_D = []
AlphaIG_D = []
PressIG_D = []
D = []
tread = sysT()
## Calculate pressure as function of alpha for each D
for i, dirpath in enumerate(dirlist):
data = pressure_of_alpha(dirpath,verbose)
Alpha_D += [data[0]]
Press_D += [data[1]]
AlphaIG_D += [data[2]]
PressIG_D += [data[3]]
D += [data[4]]
if verbose: print me+"data extraction",round(sysT()-tread,2),"seconds."
sortind = list(np.argsort(D))
D = np.array(D)[sortind]
Alpha_D = np.array(Alpha_D)[sortind]; Press_D = np.array(Press_D)[sortind]
AlphaIG_D = np.array(AlphaIG_D)[sortind]; PressIG_D = np.array(PressIG_D)[sortind]
## Use IG D=0 result as reference
## Should be the same as running again with alpha in different place -- ???
## See notes 2015.12.15
# X,xmin,dt = 10.0,9.0,0.01
# P_ref = 1/(X-xmin+dt/Alpha_D)
# PIG_ref = 1/(X-xmin+dt/AlphaIG_D)
# Press_D /= P_ref
# PressIG_D /= PIG_ref
tplot = sysT()
## Plot
colour = ["b","r","g","m","k"]
for i in range(ndir):
plt.errorbar(Alpha_D[i], Press_D[i], yerr=0.05,\
fmt=colour[i]+"o-", ecolor='grey', capthick=2, label="CN; $\\Delta = "+str(D[i])+"$")
plt.plot(AlphaIG_D[i],PressIG_D[i], colour[i]+"--", label="WN; $\\Delta = "+str(D[i])+"$")
## Fit
fitarr, m = make_fit(Alpha_D[i],Press_D[i])
plt.plot(Alpha_D[i],fitarr,colour[i]+":",label="$P \\sim "+str(m)+"\\alpha$")
plot_acco(plt.gca(), xlabel="$\\alpha=f_0^2\\tau/T\\zeta$", ylabel="Pressure",\
legloc="")
## Reorder legend
plot_legend(plt.gca(), ndir)
## Save to each directory
for dir in dirlist:
plotfile = dir+"/PressureAlphaDelta.png"
plt.savefig(plotfile)
if verbose: print me+"plot saved to "+plotfile
if verbose: print me+"plotting and saving",round(sysT()-tplot,2),"seconds."
if verbose: print me+"total execution time",round(sysT()-t0,2),"seconds"
if showfig: plt.show()
return
def pressure_pdf_plot_file(histfile, verbose):
"""
Make plot for a single file
"""
me = "LE_Pressure.pressure_pdf_plot_file: "
t0 = sysT()
## Filenames
plotfile = os.path.dirname(histfile)+"/PDFP"+os.path.basename(histfile)[4:-4]+".png"
## Get pars from filename
pars = filename_pars(histfile)
[alpha,X,D,dt,ymax,R] = [pars[key] for key in ["a","X","D","dt","ymax","R"]]
assert (R is not None), me+"You are using the wrong program. R should be defined."
assert (D == 0.0), me+"Cannot yet handle soft potential. D should be 0.0."
if verbose: print me+"alpha =",alpha,"and X =",X,"and D =",D
## Load data and normalise
H = np.load(histfile)
H /= H.sum()
## Centre of circle for curved boundary
c = circle_centre(X,R,ymax)
## Space (for axes)
try:
bins = np.load(os.path.dirname(histfile)+"/BHISBIN"+os.path.basename(histfile)[4:-4]+".npz")
xbins = bins["xbins"]
ybins = bins["ybins"]
xini = xbins[0]
xmax = xbins[-1]
except (IOError, KeyError):
xini = calculate_xini(X,alpha)
xmax = lookup_xmax(c[0]+R,alpha)
xbins = calculate_xbin(xini,X,xmax,H.shape[1])
ybins = calculate_ybin(0.0,ymax,H.shape[0]+1)
x = 0.5*(xbins[1:]+xbins[:-1])
y = 0.5*(ybins[1:]+ybins[:-1])
## Set up plot
fig,axs = plt.subplots(1,2)
## pdf plot
ax = axs[0]
H[:,0]=H[:,1]
Xm,Ym = np.meshgrid(x,y)
CS = ax.contourf(Xm,Ym[::-1],H,10)
## Colourbar
divider = make_axes_locatable(ax)
cax = divider.append_axes("top", size="5%", pad=0.4)
cbar = fig.colorbar(CS, cax=cax, ax=ax, orientation="horizontal",
use_gridspec=True, ticks=[H.min(),H.mean(),H.max()])
cbar.ax.set_xticklabels(["Low", "Mean", "High"])
### http://stackoverflow.com/questions/13310594/positioning-the-colorbar
## Plot curved wall
wallx = np.linspace(X,c[0]+R,201)
wally = c[1]+np.sqrt(R*R-(wallx-c[0])**2)
ax.plot(wallx,wally, "r--",linewidth=2)
## Accoutrements
ax.set_xlim([xini,xmax])
ax.set_ylim([0.0,ymax])
ax.set_xlabel("$x$", fontsize=fsa)
ax.set_ylabel("$y$", fontsize=fsa)
## Calculate force array (2d)
force = -1.0 * ( (Xm-c[0])**2 + (Ym-c[1])**2 > R*R ) * ( Xm-c[0]>0.0 )
## Pressure array (2d) -- sum rather than trapz
press = -1.0*(force*H).sum(axis=0).cumsum(axis=0)
## Pressure plot
ax = axs[1]
ax.plot(x,press,label="CN simulation")
## Bulk and wall regions
ax.axvspan(xini,X, color="b",alpha=0.1)
ax.axvspan(X,c[0]+R, color="m",alpha=0.05)
ax.axvspan(R,xmax, color="r",alpha=0.05)
## Ideal gas result
ax.hlines(pressure_IG(X,R,ymax,alpha),xini,xmax,linestyle="-",color="g",label="WN theory")
ax.hlines(0.5/ymax/(1.0+X-xini),xini,xmax,linestyle="--",color="g",label="WN flat theory")
## Accoutrements
ax.set_xlim([xini,xmax])
ax.set_xlabel("$x$", fontsize=fsa)
ax.set_ylabel("Pressure", fontsize=fsa)
ax.grid()
ax.legend(loc="best",fontsize=fsl)
## Tidy figure
fig.suptitle(os.path.basename(plotfile),fontsize=fst)
fig.tight_layout()
plt.subplots_adjust(top=0.9)
plt.savefig(plotfile)
if verbose: print me+"plot saved to",plotfile
return fig
