def plot_multi_energy_diagram(*args, **kwargs):
"""
Draw a potential energy diagram of a series of
elementary reaction equation and save or show it.
Return the Figure object.
Parameters
----------
args:
rxn_equations_list : list
a list containing a series of reaction equation string
according to rules in setup file.
e.g. ['HCOOH_g + 2*_s <-> HCOO-H_s + *_s -> HCOO_s + H_s',
'HCOO_s + *_s <-> H-COO_s + *_s -> COO_s + H_s',
'COO_s -> CO2_g + *_s',
'2H_s <-> H-H_s + *_s -> H2_g + 2*_s'].
energy_tuples : list of tuples
e.g. [
(0.0, 1.0, 0.5),
(3.0, 4.7, 0.7),
(0.0, 4.0),
(3.0, 4.7, 0.7),
]
subsection_length : int, optional
Length of each subsection(x_i, x_f), defualt to be 1.0.
line_color : str, optional
Color code of the line. Default to be '#000000'/'black'.
init_y_offset : float, optional
Initial offset value on y axis.
has_shadow : Bool
Whether to add shadow effect to the main line.
Default to be True.
show_note : bool
Whether to show species note on the main line.
Default to be True.
show_aux_line: bool
Whether to show auxiliary lines on the main line.
Default to be Ture.
show_arrow : bool
Whether to show annotation arrow.
Default to be True.
fmt : str, optional
The output format : ['pdf'|'jpeg'|'png'|'raw'|'pgf'|'ps'|'svg']
Default to be 'jpeg'
show_mode : str, 'show' or 'save'
'show' : show the figure in a interactive way.
'save' : save the figure automatically.
peak_widths : tuple of floats, (1.0, ...)(default)
peak widths if TS exists.
Other parameters
----------------
kwargs :
'fname' : str, optional
'dpi' : int, default to be 80
'offset_coeff' : float, default to be 1.0
shadow offset coefficient.
Examples
--------
"""
############### args setting before plotting ################
#for args
if len(args) != 2:
raise ValueError("Need at least 2 args: " +
"rxn_equations_list, energy_tuples.")
rxn_equations_list, energy_tuples = args
#for kwargs
# peak widths
if 'peak_widths' in kwargs:
peak_widths = kwargs['peak_widths']
if len(peak_widths) != len(rxn_equations_list):
raise ValueError('number of peak widths and ' +
'number of rxn equations are not matched.')
else: # set to (1.0, 1.0, ...)
peak_widths = tuple([1.0]*len(rxn_equations_list))
n = kwargs['n'] if 'n' in kwargs else 100
subsection_length = \
kwargs['subsection_length'] if 'subsection_length' in kwargs else 1.0
line_color = kwargs['line_color'] if 'line_color' in kwargs else '#000000'
has_shadow = kwargs['has_shadow'] if 'has_shadow' in kwargs else True
fmt = kwargs['fmt'] if 'fmt' in kwargs else 'png'
init_y_offset = kwargs['init_y_offset'] if 'init_y_offset' in kwargs else 0.0
show_note = kwargs['show_note'] if 'show_note' in kwargs else True
show_aux_line = kwargs['show_aux_line'] if 'show_aux_line' in kwargs else True
show_arrow = kwargs['show_arrow'] if 'show_arrow' in kwargs else True
show_mode = kwargs['show_mode'] if 'show_mode' in kwargs else 'show'
##################### args setting END #######################
#convert rxn_equation_list(str) to elementary_rxns_list alike list
rxns_list = [RxnEquation(rxn_equation).tolist()
for rxn_equation in rxn_equations_list]
x_offset, y_offset = 0.0, init_y_offset
total_x, total_y = [], []
piece_points = [] # collectors
for idx, (rxn_equation, peak_width) in \
enumerate(zip(rxn_equations_list, peak_widths)):
energy_tuple = get_relative_energy_tuple(energy_tuples[idx])
x, y, x2 = get_potential_energy_points(
energy_tuple=energy_tuple, n=n,
subsection_length=subsection_length,
peak_width=peak_widths[idx],
)
x_scale = 2*subsection_length + peak_width
#get total y
offseted_y = y + y_offset
total_y.extend(offseted_y.tolist())
#get total x
offseted_x = x + x_offset
total_x.extend(offseted_x.tolist())
####### collect values for adding annotations #######
#there are 3 points in each part
p1 = (2*subsection_length+offseted_x[0], offseted_y[0])
p3 = (offseted_x[-1], offseted_y[-1])
if len(energy_tuple) == 3:
p2 = (2*subsection_length + x2 + offseted_x[0], # x2 is the x value of barrier
energy_tuple[1] + y_offset)
piece_points.append((p1, p2, p3))
elif len(energy_tuple) == 2:
piece_points.append((p1, p3))
################ Collection End ################
#update offset value for next loop
x_offset += x_scale
y_offset = offseted_y[-1]
#Add extral line
#add head horizontal line
head_extral_x = np.linspace(0.0, subsection_length, n).tolist()
offseted_total_x = (np.array(total_x)+subsection_length).tolist()
head_extral_y = [total_y[0]]*n
total_x = head_extral_x + offseted_total_x
total_y = head_extral_y + total_y
#add the last horizontal line
tail_extral_x = np.linspace(total_x[-1],
total_x[-1]+subsection_length,
n).tolist()
tail_extral_y = [total_y[-1]]*n
total_x += tail_extral_x
total_y += tail_extral_y
total_x, total_y = np.array(total_x), np.array(total_y)
#get extreme values of x and y
y_min, y_max = np.min(total_y), np.max(total_y)
x_min, x_max = total_x[0], total_x[-1]
y_scale = y_max-y_min
################### start Artist Mode! ######################
multi = len(rxn_equations_list)/2.2
fig = plt.figure(figsize=(multi*10, multi*5))
#fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(y_min - y_scale/10, y_max + y_scale/10)
ax.set_xlim(x_min-subsection_length, x_max+subsection_length)
ax.set_title('Energy Profile',
fontdict={
'fontsize': 15,
'weight': 100,
'verticalalignment': 'bottom'
})
ax.set_xlabel('Reaction Coordinate')
ax.set_ylabel('Free Energy(eV)')
#add shadow
if has_shadow:
add_line_shadow(ax, total_x, total_y, depth=8,
color='#595959')
#main line
ax.plot(total_x, total_y, color=line_color, linewidth=3)
#get state string list as notes
state_str_list = []
for rxn_list in rxns_list:
t = tuple([state_obj.texen() for state_obj in rxn_list[:-1]])
state_str_list.append(t)
#################### Main loop to add notes ###################
#This is the main loop to add extral info to main line
#For each single loop, we get 3 or 2 points(tuple) for each elementary rxn
#and the first 2 or 1 latex reaction state string(involved in list)
def add_state_note(pts, tex_states):
"function to add notes to a state"
start_point, end_point = pts[0], pts[-1]
# add horizontal lines and vertical arrowa
if show_aux_line:
# plot horizontal lines
hori_x = np.linspace(start_point[0],
end_point[0]+2*subsection_length, 50)
hori_y = np.linspace(start_point[-1], start_point[-1], 50)
ax.plot(hori_x, hori_y, color=line_color, linewidth=1,
linestyle='dashed')
# plot vertical arrows
if len(pts) == 3:
mid_point = pts[1]
#plot activation energy arrow
ax.annotate(
'',
xy=(mid_point[0], mid_point[-1]),
xycoords='data',
xytext=(mid_point[0], start_point[-1]),
textcoords='data',
arrowprops=dict(arrowstyle="<->")
)
# plot reaction energy arrow
ax.annotate(
'',
xy=(end_point[0]+subsection_length, end_point[-1]),
xycoords='data',
xytext=(end_point[0]+subsection_length, start_point[-1]),
textcoords='data',
arrowprops=dict(arrowstyle="<->")
)
if show_note:
# add species notes
if len(pts) == 3: # those who have TS
for state_idx, (pt, tex_state) in enumerate(zip(pts, tex_states)):
if state_idx == 0: # for initial or final state
note_x = pt[0] - 1.8*subsection_length
note_y = pt[-1] + y_scale/50
ax.text(note_x, note_y, r'$\bf{'+tex_state+r'}$',
fontdict={'fontsize': 13, 'color': '#1874CD'})
if state_idx == 1: # for transition state
note_x = pt[0] - subsection_length/2
note_y = pt[-1] + y_scale/50
ax.text(note_x, note_y, r'$\bf{'+tex_state+r'}$',
fontdict={'fontsize': 13, 'color': '#CD5555'})
if len(pts) == 2: # no TS
pt, tex_state = pts[0], tex_states[0]
note_x = pt[0] - 1.8*subsection_length
note_y = pt[-1] + y_scale/50
ax.text(note_x, note_y, r'$\bf{'+tex_state+r'}$',
fontdict={'fontsize': 13, 'color': '#1874CD'})
if show_arrow:
# add energy annotations
el = Ellipse((2, -1), 0.5, 0.5)
# annotation between IS and FS
rxn_energy = round(end_point[-1] - start_point[-1], 2)
rxn_energy_latex = r'$\bf{\Delta G = ' + str(rxn_energy) + r' eV}$'
ax.annotate(rxn_energy_latex, xy=(end_point[0]+subsection_length,
(start_point[-1]+end_point[-1])/2),
xycoords='data',
xytext=(-70, 30), textcoords='offset points',
size=13, color='#8E388E',
arrowprops=dict(arrowstyle="simple",
fc="0.6", ec="none",
patchB=el,
connectionstyle="arc3,rad=0.2"),
)
if len(pts) == 3:
# annotation between TS and IS
act_energy = round((mid_point[-1] - start_point[-1]), 2)
act_energy_latex = r'$\bf{G_{a} = '+str(act_energy)+r' eV}$'
ax.annotate(act_energy_latex,
xy=(mid_point[0], (mid_point[1]+start_point[1])/2),
xycoords='data', xytext=(30, 20),
textcoords='offset points',
size=13, color='#B22222',
arrowprops=dict(arrowstyle="simple",
fc="0.6", ec="none",
patchB=el,
connectionstyle="arc3,rad=-0.2"),
)
######### Main Loop END ########
#use multiple thread to add notes
note_threads = []
nstates = len(state_str_list)
for pts, tex_states in zip(piece_points, state_str_list):
t = NoteThread(add_state_note, (pts, tex_states))
note_threads.append(t)
for i in xrange(nstates):
note_threads[i].start()
for i in xrange(nstates):
note_threads[i].join()
#add species note at last section
if show_note:
pt = pts[-1]
tex_state = rxns_list[-1][-1].texen()
ax.text(pt[0]+0.2*subsection_length, pt[-1]+y_scale/50,
r'$\bf{'+tex_state+r'}$',
fontdict={'fontsize': 13, 'color': '#1874CD'})
#remove xticks
ax.set_xticks([])
##################### Artist Mode End #####################
#creat path
if not os.path.exists("./energy_profile"):
os.mkdir("./energy_profile")
#filename
if 'fname' in kwargs:
fname = kwargs['fname'] + '.' + fmt
else:
fname = 'multi_energy_diagram.' + fmt
fullname = "./energy_profile/" + fname
if show_mode == 'show':
fig.show()
elif show_mode == 'save':
if 'dpi' in kwargs:
fig.savefig(fullname, dpi=kwargs['dpi'])
fig.savefig(fullname)
else:
raise ValueError('Unrecognized show mode parameter : ' + show_mode)
return fig, total_x, total_y
def plot_single_energy_diagram(*args, **kwargs):
"""
Draw a potential energy diagram of a elementary reaction equation
and save it.
Return the Figure object.
Parameters
----------
energy_tuple : tuple of float, essential
energy data for profile plotting.
e.g. (0.0, 1.2, 0.7)
rxn_equation : str, essential
reaction equation string according to rules in setup file.
e.g. 'HCOOH_g + 2*_s <-> HCOO-H_s + *_s -> HCOO_s + H_s'.
subsection_length : int, optional
Length of each subsection(x_i, x_f), defualt to be 1.0.
line_color : str, optional
Color code of the line. Default to be '#000000'/'black'.
has_shadow : Bool
Whether to add shadow effect to the main line.
Default to be False.
fmt : str, optional
The output format : ['pdf'|'jpeg'|'png'|'raw'|'pgf'|'ps'|'svg']
Default to be 'jpeg'
show_mode : str, 'show' or 'save'
'show' : show the figure in a interactive way.
'save' : save the figure automatically.
peak_width : float, 1.0(default)
peak width if TS exists.
Other parameters
----------------
kwargs :
'fname' : str, optional
'offset_coeff' : float, default to be 1.0
shadow offset coefficient.
Examples
--------
>>> plot_single_energy_diagram((0.0, 1.2, 0.6),
'COO_s -> CO2_g + *_s',
has_shadow=True,
fname='pytlab')
>>> <matplotlib.figure.Figure at 0x5659f30>
"""
############### args setting before plotting ################
#for args
if len(args) != 2:
raise ValueError("Need at least 2 args: energy_tuple, rxn_equation.")
energy_tuple, rxn_equation = args
#for kwargs
n = kwargs['n'] if 'n' in kwargs else 100
subsection_length = \
kwargs['subsection_length'] if 'subsection_length' in kwargs else 1.0
line_color = kwargs['line_color'] if 'line_color' in kwargs else '#000000'
has_shadow = kwargs['has_shadow'] if 'has_shadow' in kwargs else True
fmt = kwargs['fmt'] if 'fmt' in kwargs else 'png'
show_mode = kwargs['show_mode'] if 'show_mode' in kwargs else 'show'
peak_width = kwargs['peak_width'] if 'peak_width' in kwargs else 1.0
##################### args setting END #######################
rxn_list = RxnEquation(rxn_equation).tolist()
energy_tuple = get_relative_energy_tuple(energy_tuple)
#energy info
rxn_energy = round(energy_tuple[-1] - energy_tuple[0], 2)
if len(energy_tuple) == 3:
act_energy = round(energy_tuple[1] - energy_tuple[0], 2)
#get x, y array
x, y, x2 = get_potential_energy_points(energy_tuple, n=n,
subsection_length=subsection_length,
peak_width=peak_width)
# get maximum and minimum values of x and y axis
y_min, y_max = np.min(y), np.max(y)
x_max = 3.7*subsection_length
#scale of y
y_scale = abs(y_max - y_min)
################### start Artist Mode! #######################
fig = plt.figure(figsize=(10, 7))
ax = fig.add_subplot(111)
ax.set_ylim(y_min - y_scale/5, y_max + y_scale/5)
ax.set_xlim(-subsection_length/3, x_max)
xlabel = ax.set_xlabel('Reaction Coordinate')
ylabel = ax.set_ylabel('Free Energy(eV)')
title = ax.set_title(r'$\bf{'+RxnEquation(rxn_equation).texen()+r'}$',
fontdict={
'fontsize': 13,
'weight': 1000,
'verticalalignment': 'bottom'
})
#add shadow
if has_shadow:
add_line_shadow(ax, x, y, depth=8, color='#595959')
#main line
ax.plot(x, y, color=line_color, linewidth=3)
#energy latex string
if 'act_energy' in dir():
act_energy_latex = r'$\bf{G_{a} = ' + str(act_energy) + r' eV}$'
rxn_energy_latex = r'$\bf{\Delta G = ' + str(rxn_energy) + r' eV}$'
####################### annotates #######################
#add species annotation
#get annotate coordiantes
note_offset = y_scale/40
param_list = []
#initial state
note_x_i = subsection_length/10
note_y_i = energy_tuple[0] + note_offset
note_str_i = r'$\bf{' + rxn_list[0].texen() + r'}$'
param_list.append((note_x_i, note_y_i, note_str_i))
#final state
note_x_f = subsection_length/10 + subsection_length + peak_width
note_y_f = energy_tuple[-1] + note_offset
note_str_f = r'$\bf{' + rxn_list[-1].texen() + r'}$'
param_list.append((note_x_f, note_y_f, note_str_f))
if len(energy_tuple) == 3:
#transition state
note_y_b = np.max(y) + note_offset # equal to energy_tuple[1]
idx = np.argmax(y)
note_x_b = x[idx] - subsection_length/4
#####################
barrier_x = x[idx] # x value of TS point
#####################
note_str_b = r'$\bf' + rxn_list[1].texen() + r'}$'
param_list.append((note_x_b, note_y_b, note_str_b))
#add annotates
for idx, param_tuple in enumerate(param_list):
if idx == 2:
ax.text(*param_tuple, fontdict={'fontsize': 13,
'color': '#CD5555'})
else:
ax.text(*param_tuple, fontdict={'fontsize': 13,
'color': '#1874CD'})
######################################################
# #
# inflection points coordinates: #
# (subsection_length, energy_tuple[0]) #
# (barrier_x, np.max(y)) #
# (2*subsection_length, energy_tuple[-1]) #
# #
######################################################
#energy change annotation
#initial state horizontal line
hori_x_i = np.linspace(subsection_length,
peak_width + 2*subsection_length, 50)
hori_y_i = np.linspace(energy_tuple[0], energy_tuple[0], 50)
ax.plot(hori_x_i, hori_y_i, color=line_color, linewidth=1,
linestyle='dashed')
el = Ellipse((2, -1), 0.5, 0.5)
if len(energy_tuple) == 3: # for reaction with barrier
#arrow between barrier
ax.annotate('', xy=(barrier_x, energy_tuple[0]), xycoords='data',
xytext=(barrier_x, np.max(y)), textcoords='data',
arrowprops=dict(arrowstyle="<->"))
#text annotations of barrier
ax.annotate(act_energy_latex,
xy=(barrier_x, np.max(y)/2), xycoords='data',
xytext=(-150, 30), textcoords='offset points',
size=13, color='#B22222',
arrowprops=dict(arrowstyle="simple",
fc="0.6", ec="none",
patchB=el,
connectionstyle="arc3,rad=0.2"),
)
# arrow between reaction energy
ax.annotate(
'',
xy=(subsection_length*3/2 + peak_width, energy_tuple[-1]),
xycoords='data',
xytext=(subsection_length*3/2 + peak_width, energy_tuple[0]),
textcoords='data',
arrowprops=dict(arrowstyle="<->")
)
# text annotations of reaction energy
ax.annotate(
rxn_energy_latex,
xy=(subsection_length*3/2 + peak_width,
(energy_tuple[-1]+energy_tuple[0])/2),
xycoords='data',
xytext=(50, 30), textcoords='offset points',
size=13, color='#8E388E',
arrowprops=dict(arrowstyle="simple",
fc="0.6", ec="none",
patchB=el,
connectionstyle="arc3,rad=-0.2"),
)
############## annotates end ################
################# Artist Mode End ! #######################
#remove xticks
ax.set_xticks([])
#save the figure object
#creat path
if not os.path.exists("./energy_profile"):
os.mkdir("./energy_profile")
#filename
if 'fname' in kwargs:
fname = kwargs['fname'] + '.' + fmt
else:
fname = 'elementary_energy_diagram.' + fmt
fullname = "./energy_profile/" + fname
if show_mode == 'save':
if 'dpi' in kwargs:
fig.savefig(fullname, dpi=kwargs['dpi'])
fig.savefig(fullname)
elif show_mode == 'show':
plt.show()
else:
raise ValueError('Unrecognized show mode parameter : ' + show_mode)
return fig, x, y