def plot(self, show_IDs=False):
'''
Method of ED class
Plot the energy diagram. Use show_IDs=True for showing the IDs of the
energy levels and allowing an easy linking.
E| 4__
n| 2__ / \
e|1__/ \__/5 \
r| 3\__/ 6\__
g|
y|
Parameters
----------
show_IDs : bool
show the IDs of the energy levels; is False by default
Returns
-------
fig (plt.figure) and ax (fig.add_subplot())
'''
fig = plt.figure()
ax = fig.add_subplot(111, aspect=self.aspect)
ax.set_ylabel(self.ylabel)
ax.axes.get_xaxis().set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
self.__auto_adjust()
data = zip(
self.energies, # 0
self.positions, # 1
self.bottom_texts, # 2
self.top_texts, # 3
self.colors, # 4
self.left_texts, # 5
self.right_texts) # 6
for level in data:
start = level[1] * (self.dimension + self.space
) # Start x position
# Plot the state's energy level line
ax.hlines(level[0], start, start + self.dimension, color=level[4])
# Label the energy level line
ax.text(
start + self.dimension / 2., # X
level[0] + self.offset, # Y
level[3], # self.top_texts
horizontalalignment='center',
verticalalignment='bottom')
ax.text(
start + self.dimension, # X
level[0], # Y
level[5], # self.left_texts
horizontalalignment='left',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start, # X
level[0], # Y
level[6], # self.right_texts
horizontalalignment='right',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start + self.dimension / 2., # X
level[0] - self.offset * 2, # Y
level[2], # self.bottom_text
horizontalalignment='center',
verticalalignment='top',
color=self.color_bottom_text)
if show_IDs:
# for showing the ID allowing the user to identify the level
# csera: This wasn't working with the 'data' zip, so I rewrote this to work directly
# with the self.[props]
for l in range(len(self.energies)):
objNum = l + 1
start = self.positions[l] * (self.dimension + self.space)
ax.text(start,
self.energies[l] + self.offset,
self.positions[l],
horizontalalignment='right',
color='red')
for idx, arrow in enumerate(self.arrows):
# by Kalyan Jyoti Kalita: put arrows between to levels
# x1, x2 y1, y2
for i in arrow:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + 0.5 * self.dimension
x2 = start + 0.5 * self.dimension
y1 = self.energies[idx]
y2 = self.energies[i]
gap = y1 - y2
gapnew = '{0:.2f}'.format(gap)
middle = y1 - 0.5 * gap #warning: this way works for negative H**O/LUMO energies
ax.annotate("",
xy=(x1, y1),
xytext=(x2, middle),
arrowprops=dict(color='green',
width=1.5,
headwidth=5))
ax.annotate(s=gapnew,
xy=(x2, y2),
xytext=(x1, middle),
color='green',
arrowprops=dict(width=6,
headwidth=15,
color='green'),
bbox=dict(boxstyle='round', fc='white'),
ha='center',
va='center')
for idx, link in enumerate(self.links):
# here we connect the levels with the links
# x1, x2 y1, y2
for i in link:
# i is a tuple: (end_level_id,ls,linewidth,color)
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + self.dimension
x2 = self.positions[i[0]] * (self.dimension + self.space)
y1 = self.energies[idx]
y2 = self.energies[i[0]]
line = Line2D([x1, x2], [y1, y2],
ls=i[1],
linewidth=i[2],
color=i[3])
ax.add_line(line)
for box in self.electons_boxes:
# here we add the boxes
# x,y,boxes,electrons,side,spacing_f
x, y, boxes, electrons, side, spacing_f = box
plot_orbital_boxes(ax, x, y, boxes, electrons, side, spacing_f)
# Return fig and ax
self.ax = ax
self.fig = fig
def plot(self, show_IDs=False):
'''
Method of ED class
Plot the energy diagram. Use show_IDs=True for showing the IDs of the
energy levels and allowing an easy linking.
E| 4__
n| 2__ / \
e|1__/ \__/5 \
r| 3\__/ 6\__
g|
y|
Parameters
----------
show_IDs : bool
show the IDs of the energy levels
Returns
-------
fig (plt.figure) and ax (fig.add_subplot())
'''
fig = plt.figure()
ax = fig.add_subplot(111, aspect='equal')
ax.set_ylabel("Energy / $kcal$ $mol^{-1}$")
ax.axes.get_xaxis().set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
data = zip(
self.energies, # 0
self.positions, # 1
self.bottom_texts, # 2
self.top_texts, # 3
self.colors) # 4
for level in data:
start = level[1] * (self.dimension + self.space)
ax.hlines(level[0], start, start + self.dimension, color=level[4])
ax.text(
start + self.dimension / 2., #X
level[0] + self.offset, #Y
level[3], # self.top_texts
horizontalalignment='center')
ax.text(
start + self.dimension / 2., # X
level[0] - self.offset * 2, # Y
level[2], # self.bottom_text
horizontalalignment='center',
color=self.color_bottom_text)
if show_IDs:
#for showing the ID allowing the user to identify the level
for ind, level in enumerate(data):
start = level[1] * (self.dimension + self.space)
ax.text(start,
level[0] + self.offset,
str(ind),
horizontalalignment='right',
color='red')
for idx, arrow in enumerate(self.arrows):
# by Kalyan Jyoti Kalita: put arrows between to levels
# x1, x2 y1, y2
for i in arrow:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + 0.5 * self.dimension
x2 = start + 0.5 * self.dimension
y1 = self.energies[idx]
y2 = self.energies[i]
gap = y1 - y2
gapnew = '{0:.2f}'.format(gap)
middle = y1 - 0.5 * gap #warning: this way works for negative H**O/LUMO energies
ax.annotate("",
xy=(x1, y1),
xytext=(x2, middle),
arrowprops=dict(color='green',
width=1.5,
headwidth=5))
ax.annotate(s=gapnew,
xy=(x2, y2),
xytext=(x1, middle),
color='green',
arrowprops=dict(width=1.5,
headwidth=5,
color='green'),
bbox=dict(boxstyle='round', fc='white'),
ha='center',
va='center')
for idx, link in enumerate(self.links):
#here we connect the levels with the links
# x1, x2 y1, y2
for i in link:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + self.dimension
x2 = self.positions[i] * (self.dimension + self.space)
y1 = self.energies[idx]
y2 = self.energies[i]
l = Line2D([x1, x2], [y1, y2],
ls='--',
linewidth=0.5,
color='k')
ax.add_line(l)
for box in self.electons_boxes:
#here we add the boxes
# x,y,boxes,electrons,side,spacing_f
x, y, boxes, electrons, side, spacing_f = box
plot_orbital_boxes(ax, x, y, boxes, electrons, side, spacing_f)
self.fig = fig
self.ax = ax
def plot(self, show_IDs=False):
'''
Method of ED class
Plot the energy diagram. Use show_IDs=True for showing the IDs of the
energy levels and allowing an easy linking.
E| 4__
n| 2__ / \
e|1__/ \__/5 \
r| 3\__/ 6\__
g|
y|
Parameters
----------
show_IDs : bool
show the IDs of the energy levels
Returns
-------
fig (plt.figure) and ax (fig.add_subplot())
'''
fig = plt.figure()
ax = fig.add_subplot(111, aspect=self.aspect)
ax.set_ylabel("Energy / $kcal$ $mol^{-1}$")
ax.axes.get_xaxis().set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
self.__auto_adjust()
# Set reaction steps labels if requested
if self.reaction_steps_labels:
xticks_positions = []
xticks_labels = []
# Search for defined labels
for position in set(self.positions):
# Retrieve associated label
try:
position_label = self.reaction_steps_labels[position - 1]
except IndexError:
continue
# Compute x-coordinates of reaction step position
start = position * (self.dimension + self.space)
xticks_positions.append(start + self.dimension / 2.)
# Add reaction step label
xticks_labels.append(position_label)
# Set defined labels
if xticks_labels:
ax.axes.get_xaxis().set_visible(True)
ax.spines['bottom'].set_visible(True)
ax.set_xticks(xticks_positions)
ax.set_xticklabels(xticks_labels)
data = zip(
self.energies, # 0
self.positions, # 1
self.bottom_texts, # 2
self.top_texts, # 3
self.colors, # 4
self.left_texts, # 5
self.right_texts) # 6
for level in data:
start = level[1] * (self.dimension + self.space)
ax.hlines(level[0], start, start + self.dimension, color=level[4])
ax.text(
start + self.dimension / 2., # X
level[0] + self.offset, # Y
level[3], # self.top_texts
horizontalalignment='center',
verticalalignment='bottom')
ax.text(
start + self.dimension, # X
level[0], # Y
level[5], # self.bottom_text
horizontalalignment='left',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start, # X
level[0], # Y
level[6], # self.bottom_text
horizontalalignment='right',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start + self.dimension / 2., # X
level[0] - self.offset * 2, # Y
level[2], # self.bottom_text
horizontalalignment='center',
verticalalignment='top',
color=self.color_bottom_text)
if show_IDs:
# for showing the ID allowing the user to identify the level
for ind, level in enumerate(data):
start = level[1] * (self.dimension + self.space)
ax.text(start,
level[0] + self.offset,
str(ind),
horizontalalignment='right',
color='red')
for idx, arrow in enumerate(self.arrows):
# by Kalyan Jyoti Kalita: put arrows between to levels
# x1, x2 y1, y2
for i in arrow:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + 0.5 * self.dimension
x2 = start + 0.5 * self.dimension
y1 = self.energies[idx]
y2 = self.energies[i]
gap = y1 - y2
gapnew = '{0:.2f}'.format(gap)
middle = y1 - 0.5 * gap #warning: this way works for negative H**O/LUMO energies
ax.annotate("",
xy=(x1, y1),
xytext=(x2, middle),
arrowprops=dict(color='green',
width=1.5,
headwidth=5))
ax.annotate(s=gapnew,
xy=(x2, y2),
xytext=(x1, middle),
color='green',
arrowprops=dict(width=6,
headwidth=15,
color='green'),
bbox=dict(boxstyle='round', fc='white'),
ha='center',
va='center')
for idx, link in enumerate(self.links):
# here we connect the levels with the links
# x1, x2 y1, y2
for i in link:
# i is a tuple: (end_level_id,ls,linewidth,color)
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + self.dimension
x2 = self.positions[i[0]] * (self.dimension + self.space)
y1 = self.energies[idx]
y2 = self.energies[i[0]]
line = Line2D([x1, x2], [y1, y2],
ls=i[1],
linewidth=i[2],
color=i[3])
ax.add_line(line)
for box in self.electons_boxes:
# here we add the boxes
# x,y,boxes,electrons,side,spacing_f
x, y, boxes, electrons, side, spacing_f = box
plot_orbital_boxes(ax, x, y, boxes, electrons, side, spacing_f)
# Return fig and ax
self.ax = ax
self.fig = fig
def plot(self, show_IDs=False, show_labels=True):
'''
Method of ED class
Plot the energy diagram. Use show_IDs=True for showing the IDs of the
energy levels and allowing an easy linking.
E| 4__
n| 2__ / \
e|1__/ \__/5 \
r| 3\__/ 6\__
g|
y|
Parameters
----------
show_IDs : bool
show the IDs of the energy levels
Returns
-------
fig (plt.figure) and ax (fig.add_subplot())
'''
fig = plt.figure()
ax = fig.add_subplot(111, aspect=self.aspect)
if self.eunit == 'kcalmol-1':
ax.set_ylabel("Energy / $kcal$ $mol^{-1}$")
elif self.eunit == 'kJmol-1':
ax.set_ylabel("Energy / $kJ$ $mol^{-1}$")
ax.axes.get_xaxis().set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
self.__auto_adjust()
data = zip(
self.energies, # 0
self.positions, # 1
self.bottom_texts, # 2
self.top_texts, # 3
self.colors, # 4
self.left_texts, # 5
self.right_texts) # 6
for level in data:
start = level[1] * (self.dimension + self.space)
ax.hlines(level[0], start, start + self.dimension, color=level[4])
if type(level[3]) == float:
toptxt = format(level[3],
'.1f') #self.top_text, formatfix for energy
else:
toptxt = level[3] #leave as if, if not float
ax.text(
start + self.dimension / 2., # X
level[0] + self.offset, # Y
toptxt, # self.top_text
horizontalalignment='center',
verticalalignment='bottom')
if show_labels:
ax.text(
start + self.dimension, # X
level[0], # Y
level[5], # self.bottom_text
horizontalalignment='left',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start, # X
level[0], # Y
level[6], # self.bottom_text
horizontalalignment='right',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start + self.dimension / 2., # X
level[0] - self.offset * 2, # Y
level[2], # self.bottom_text
horizontalalignment='center',
verticalalignment='top',
color=self.color_bottom_text)
if show_IDs:
# for showing the ID allowing the user to identify the level
for ind, level in enumerate(data):
start = level[1] * (self.dimension + self.space)
ax.text(start,
level[0] + self.offset,
str(ind),
horizontalalignment='right',
color='red')
for idx, arrow in enumerate(self.arrows):
# by Kalyan Jyoti Kalita: put arrows between to levels
# x1, x2 y1, y2
for i in arrow:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + 0.5 * self.dimension
x2 = start + 0.5 * self.dimension
y1 = self.energies[idx]
y2 = self.energies[i]
gap = y1 - y2
gapnew = '{0:.2f}'.format(gap)
middle = y1 - 0.5 * gap #warning: this way works for negative H**O/LUMO energies
ax.annotate("",
xy=(x1, y1),
xytext=(x2, middle),
arrowprops=dict(color='green',
width=1.5,
headwidth=5))
ax.annotate(s=gapnew,
xy=(x2, y2),
xytext=(x1, middle),
color='green',
arrowprops=dict(width=6,
headwidth=15,
color='green'),
bbox=dict(boxstyle='round', fc='white'),
ha='center',
va='center')
for idx, link in enumerate(self.links):
# here we connect the levels with the links
# x1, x2 y1, y2
for i in link:
# i is a tuple: (end_level_id,ls,linewidth,color)
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + self.dimension
x2 = self.positions[i[0]] * (self.dimension + self.space)
y1 = self.energies[idx]
y2 = self.energies[i[0]]
line = Line2D([x1, x2], [y1, y2],
ls=i[1],
linewidth=i[2],
color=i[3])
ax.add_line(line)
for box in self.electons_boxes:
# here we add the boxes
# x,y,boxes,electrons,side,spacing_f
x, y, boxes, electrons, side, spacing_f = box
plot_orbital_boxes(ax, x, y, boxes, electrons, side, spacing_f)
for t in self.bottom_labels:
level_id, y, text = t
#start = level_id*(self.dimension+self.space)
#print(start + self.dimension/2., y, text)
#ax.text(start + self.dimension/2., y, text)
ax.text(level_id, y, text, horizontalalignment='center')
# Return fig and ax
self.ax = ax
self.fig = fig
def plot(self, show_IDs=False, ylabel=None, yunit=None):
'''
Method of ED class
Plot the energy diagram. Use show_IDs=True for showing the IDs of the
energy levels and allowing an easy linking.
E| 4__
n| 2__ / \
e|1__/ \__/5 \
r| 3\__/ 6\__
g|
y|
Parameters
----------
show_IDs : bool
show the IDs of the energy levels
ylabel : string
determines the y-axis label, if None is given "Energies" is selected
yunit : string
determines the y-axis unit, if None is given "kcal/mol" is selected
Returns
-------
fig (plt.figure) and ax (fig.add_subplot())
'''
# Check for unit and label
if ylabel == None:
label = "Energy"
elif ylabel == "g":
label = "$\Delta$G"
else:
label = ylabel
if yunit == None:
unit = "kcal/mol"
elif yunit == "kj":
unit = "kJ/mol"
elif yunit == "ha":
unit = "Ha"
else:
unit = yunit
# Check for figure size
fig = plt.figure(figsize=self.size)
ax = fig.add_subplot(111, aspect=self.aspect)
ax.set_ylabel(label + " [" + unit + "]")
ax.axes.get_xaxis().set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
self.__auto_adjust()
data = zip(
self.energies, # 0
self.positions, # 1
self.bottom_texts, # 2
self.top_texts, # 3
self.colors, # 4
self.left_texts, # 5
self.right_texts) # 6
for level in data:
start = level[1] * (self.dimension + self.space)
ax.hlines(level[0], start, start + self.dimension, color=level[4])
ax.text(
start + self.dimension / 2., # X
level[0] + self.offset, # Y
level[3], # self.top_texts
horizontalalignment='center',
verticalalignment='bottom')
ax.text(
start + self.dimension, # X
level[0], # Y
level[5], # self.bottom_text
horizontalalignment='left',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start, # X
level[0], # Y
level[6], # self.bottom_text
horizontalalignment='right',
verticalalignment='center',
color=self.color_bottom_text)
ax.text(
start + self.dimension / 2., # X
level[0] - self.offset * 2, # Y
level[2], # self.bottom_text
horizontalalignment='center',
verticalalignment='top',
color=self.color_bottom_text)
if show_IDs:
# for showing the ID allowing the user to identify the level
for ind, level in enumerate(data):
start = level[1] * (self.dimension + self.space)
ax.text(start,
level[0] + self.offset,
str(ind),
horizontalalignment='right',
color='red')
for idx, arrow in enumerate(self.arrows):
# by Kalyan Jyoti Kalita: put arrows between to levels
# x1, x2 y1, y2
for i in arrow:
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + 0.5 * self.dimension
x2 = start + 0.5 * self.dimension
y1 = self.energies[idx]
y2 = self.energies[i]
gap = y1 - y2
gapnew = '{0:.2f}'.format(gap)
middle = y1 - 0.5 * gap #warning: this way works for negative H**O/LUMO energies
ax.annotate("",
xy=(x1, y1),
xytext=(x2, middle),
arrowprops=dict(color='green',
width=1.5,
headwidth=5))
ax.annotate(s=gapnew,
xy=(x2, y2),
xytext=(x1, middle),
color='green',
arrowprops=dict(width=6,
headwidth=15,
color='green'),
bbox=dict(boxstyle='round', fc='white'),
ha='center',
va='center')
for idx, link in enumerate(self.links):
# here we connect the levels with the links
# x1, x2 y1, y2
for i in link:
# i is a tuple: (end_level_id,ls,linewidth,color)
start = self.positions[idx] * (self.dimension + self.space)
x1 = start + self.dimension
x2 = self.positions[i[0]] * (self.dimension + self.space)
y1 = self.energies[idx]
y2 = self.energies[i[0]]
line = Line2D([x1, x2], [y1, y2],
ls=i[1],
linewidth=i[2],
color=i[3])
ax.add_line(line)
for box in self.electons_boxes:
# here we add the boxes
# x,y,boxes,electrons,side,spacing_f
x, y, boxes, electrons, side, spacing_f = box
plot_orbital_boxes(ax, x, y, boxes, electrons, side, spacing_f)
# Return fig and ax
self.ax = ax
self.fig = fig