class DensityProfiler:
def __init__(self,file):
self.file = file
# crunch through the density data
self.data = CDF(file)
# and scale it to be in units of g/mL instead of number density
self.ScaleDataToDensity()
# scale each data set to adjust the number density to density in terms of g/mL
def ScaleDataToDensity(self):
molecular_weight = {'O':18.01, 'C':153.82, 'C1':153.82, 'C18':153.82, 'NA':22.99, 'N':62.00, 'S':96.06, 'Cl':35.45, 'SI':28.0855}
scale = {'O':1.0, 'C':1.0, 'C1':1.0, 'C18':1.0, 'NA':10.0, 'N':5.0, 'S':5.0, 'Cl':5.0, 'SI':1.0}
conversion = 1.0/(30.0*30.0*BIN_WIDTH * 1.0e-24 * 6.02e23)
for k,v in self.data.iteritems():
if k in ATOMS:
self.data[k] = map(lambda x: x * molecular_weight[k] * scale[k] * conversion, v)
return
def PlotData(self,fit=True):
# Set up the plot parameters (labels, size, limits, etc)
self.fig = plt.figure(num=1, facecolor='w', edgecolor='w', frameon=True)
# some of the prelim stuff for our figure
ax = self.fig.add_subplot(1,1,1)
#ax.set_title(TITLE, size='x-large')
x = self.data['Position']
# take care of plotting the fitting functions for the water
if fit:
self.PlotWaterFit(ax, x, self.data['O'], 'k-')
x = self.ShiftAxis(x,self.shift)
# plot the desired atomic densities
for atom in ATOMS:
datum = self.data[atom]
if atom != "O" and atom != "C":
print "yeehaw"
print x[datum.index(max(datum[:DATA_LENGTH]))]
ax.axvline(x[datum.index(max(datum[:DATA_LENGTH]))], color=LINESTYLES[atom][0], linestyle=':', linewidth=5)
# sets the maximum of the graph
#dat_max = max(datum)
#if dat_max > YRANGE[1]:
#YRANGE[1] = dat_max
# plots the data
ax.plot(x, datum, color=LINESTYLES[atom][0], linestyle='--', linewidth=5, label=LINESTYLES[atom][1])
# Do some labeling of the water data curve extrema (max/min, peaks/troughs, etc) for various reasons
#self.LabelWaterExtrema(ax,x,self.data['O'])
ylim = YRANGE[1] * 1.1
ax.set_ylim(YRANGE)
ax.set_xlim(XRANGE)
ax.set_axis_bgcolor('w')
ax.set_xlabel(r'Distance to Interface ($\AA$)', size=40)
ax.set_ylabel(r'$\rho$ ($\frac{mg}{mL}$)', size=45)
for a in ax.get_xticklabels() + ax.get_yticklabels():
a.set_fontsize(40)
#self.SetLegend()
plt.show()
def ShiftAxis(self,axis,shift):
return map(lambda p: p-shift, axis)
def LabelWaterExtrema(self,ax,x,datum):
# Show the location of the maximum water density peak and
# the trough behind it
peak = max(datum)
peak_index = datum.index(peak)
ax.axhline(y=peak, color='b', linestyle=':')
#here's the trough
trough_region = datum[peak_index:peak_index+80]
trough = min(trough_region)
trough_index = datum.index(trough)
ax.axhline(y=trough, color='b', linestyle=':')
print "max density = %f\ntrough density = %f\n" % (peak, trough)
print "Max Location = %f\nTrough Location = %f\n" % (x[peak_index], x[trough_index])
def SetLegend (self):
# set some legend properties. All the code below is optional. The
# defaults are usually sensible but if you need more control, this
# shows you how
leg = plt.legend(loc='best', shadow=True)
# the matplotlib.patches.Rectangle instance surrounding the legend
frame = leg.get_frame()
frame.set_facecolor('0.80') # set the frame face color to light gray
# matplotlib.text.Text instances
for t in leg.get_texts():
t.set_fontsize('x-large') # the legend text fontsize
# matplotlib.lines.Line2D instances
for l in leg.get_lines():
l.set_linewidth(2.0) # the legend line width
def PlotWaterFit (self, ax, x, datum, linetype='k-'):
d = DF()
fit_x = x[:DATA_LENGTH]
(self.fit, self.params) = d.FitLowerWater(fit_x, datum[:DATA_LENGTH])
shift = self.params["gibbs"]
self.shift = shift
width = self.params["width"]
print "System: ", TITLE
print "Left-side gibb's surface is located at: ", shift
# plot the fit line for the water
fit_x = self.ShiftAxis(fit_x,shift)
ax.plot(fit_x, self.fit, linetype, linewidth=4, label=r'H$_2$O Fit')
### This is added to identify the water region with shading
plt.axvspan(-width/2.0,width/2.0, facecolor='b', alpha=0.2)
# some text to distinguish the water regions
# this adds a box that clearly labels the width and 90-10 thickness of the interface from the fitting tanh
gibbs_1 = matplotlib.patches.Ellipse ((shift, max(datum)/2.0), 0.5, 0.1, alpha=0.0, fc="none")
'''
ax.annotate("Water/Decane Interface\nThickness = %5.3f\n\"90-10\" = %5.3f" % (width, width*2.197), (shift, max(datum)/2.0),
xytext=(-200,80), textcoords='offset points', size=14,
bbox=dict(boxstyle="round", fc=(1.0, 0.7, 0.7), ec=(1., .5, .5)),
arrowprops=dict(arrowstyle="wedge,tail_width=1.",
fc=(1.0, 0.7, 0.7), ec=(1., .5, .5),
patchA=None,
patchB=gibbs_1,
relpos=(0.2, 0.8),
connectionstyle="arc3,rad=-0.1"),
)
gibbs_2 = matplotlib.patches.Ellipse ((params[6], max(datum)/2.0), 0.5, 0.1, alpha=0.0, fc="none")
ax.annotate("Water Interface #2\nThickness = %5.3f\n\"90-10\" = %5.3f" % (params[7], params[7]*2.197), (params[6], max(datum)/2.0),
xytext=(100,80), textcoords='offset points', size=14,
bbox=dict(boxstyle="round", fc=(1.0, 0.7, 0.7), ec=(1., .5, .5)),
arrowprops=dict(arrowstyle="wedge,tail_width=1.",
fc=(1.0, 0.7, 0.7), ec=(1., .5, .5),
patchA=None,
patchB=gibbs_1,
relpos=(0.2, 0.8),
connectionstyle="arc3,rad=-0.1"),
)
'''
'''
def __init__(self,file): self.file = file # crunch through the density data self.data = CDF(file) # and scale it to be in units of g/mL instead of number density self.ScaleDataToDensity()
def __init__(self,file,header=None): CDF.__init__(self,file,header)