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optimized_strain_analysis.py
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from ase import Atoms
import ase
from ase.geometry.analysis import Analysis
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import LinearSegmentedColormap
from matplotlib.colors import Normalize
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.cm import ScalarMappable
from ase import build
import matplotlib.ticker as ticker
from matplotlib.collections import LineCollection
class StrainAnalysis:
def __init__(self):
self.bond_z_change = None
self.bondlist_left_coor_x = None
self.bondlist_right_coor_x = None
self.bondlist_left_coor_y = None
self.bondlist_right_coor_y = None
self.str_opt_x = None
self.str_opt_y = None
self.bond_diff = None
self.z_change = None
def d_interlayer(self,layer1,layer2):
coor_1 = [i[2] for i in layer1.get_positions()]
coor_2 = [i[2] for i in layer2.get_positions()]
interlayer_d = abs(np.mean(coor_1)-np.mean(coor_2))
return interlayer_d
def d_vacuum(self,layer):
coor = [i[2] for i in layer.get_positions()]
vacuum = abs(np.mean(coor))
return vacuum
def layer_sep(self,geometry,peoridicity): #geometry is Atoms object from ase
bond_list = Analysis(geometry).all_bonds[0]
collection = []
single_layer = []
trig = bond_list[0]
duplicate_check = []
single_layer = trig
while True:
trig_copy = trig
trig = []
for j in trig_copy:
for m in bond_list[j]:
trig.append(m)
trig = list(set(trig))
for atom in trig:
if atom in single_layer:
duplicate_check.append(0)
else:
single_layer.append(atom)
if len(duplicate_check) == len(trig):
output = list(set(single_layer))
duplicate_check = []
for ind in output:
bond_list[ind] = 0
single_layer = []
for i in bond_list:
if i!=0:
trig = i
for i,item in enumerate(output):
output[i] = geometry[item]
if peoridicity == True:
output_atoms = Atoms(output,pbc = True)
output_atoms.set_cell(geometry.get_cell())
collection.append(output_atoms)
else:
output_atoms = Atoms(output)
collection.append(output_atoms)
else:
duplicate_check = []
check = np.array(bond_list,dtype=object)
if (check== 0).all() == True:
break
return collection
def flake_generator(self,geometry,x,y,z):
#Atoms.center(geometry)
P = np.zeros([3,3])
P[0][0] = x
P[1][1] = y
P[2][2] = z
supercell = ase.build.make_supercell(geometry,P)
supercell.set_pbc(False)
supercell.set_cell(None)
return supercell
def mirror(self,geometry,plane):
positions = geometry.get_positions()
x = list(map(lambda x:x[0],positions))
y = list(map(lambda y:y[1],positions))
z = list(map(lambda z:z[2],positions))
x_mean = np.mean(x)
y_mean = np.mean(y)
z_mean = np.mean(z)
if plane == 'xy':
new_positions = list(map(lambda coor:[coor[0],coor[1],2*z_mean-coor[2]],positions))
geometry.positions = new_positions
if plane == 'xz':
new_positions = list(map(lambda coor:[coor[0],2*coor[1]-y_mean,coor[2]],positions))
geometry.positions = new_positions
if plane == 'yz':
new_positions = list(map(lambda coor:[2*x_mean-coor[0],coor[1],coor[2]],positions))
geometry.positions = new_positions
return
def prepare_G(self,str_orig,str_opt,refernece_d):
#python simple plot for strain
#prepare data of structure
#structures must be flake
#str_orig,str_opt are atoms objects of flakes
str_orig_x = []
str_orig_y = []
str_orig_z = []
str_opt_x = []
str_opt_y = []
str_opt_z = []
z_change = []
bond_length_orig = []
bond_length_opt = []
z_atoms_up = []
z_atoms_down = []
z_atoms_neutral = []
bondlist_left = []
bondlist_right = []
bondlist_left_coor_x = []
bondlist_right_coor_x = []
bondlist_left_coor_y = []
bondlist_right_coor_y = []
bondlist_left_coor_z = []
bondlist_right_coor_z = []
bond_z_change = []
str_orig_coor = str_orig.get_positions()
str_opt_coor = str_opt.get_positions()
for c1,c2 in zip(str_orig_coor,str_opt_coor):
str_orig_x.append(c1[0])
str_orig_y.append(c1[1])
str_orig_z.append(c1[2])
str_opt_x.append(c2[0])
str_opt_y.append(c2[1])
str_opt_z.append(c2[2])
str_orig_bond = Analysis(str_orig).all_bonds
str_opt_bond = Analysis(str_opt).all_bonds
#get the change along z axis and within horizontal plane
for i in str_opt_z:
z_change.append(i-refernece_d)
#z_change.append(i-refernece_d-np.average(str_opt_z))
for count,coor in enumerate(z_change):
if coor > 0:
z_atoms_up.append(count)
elif coor < 0:
z_atoms_down.append(count)
elif coor == 0:
z_atoms_neutral.append(count)
#bond length change
for atom,bonded_array in zip(range(len(str_orig_z)),str_orig_bond[0]):
for bonded in bonded_array:
bond_length_orig.append(str_orig.get_distance(atom,bonded))
for atom,bonded_array in zip(range(len(str_opt_z)),str_opt_bond[0]):
for bonded in bonded_array:
bond_length_opt.append(str_opt.get_distance(atom,bonded))
bond_diff = [i-j for i,j in zip(bond_length_opt,bond_length_orig)]
##create list for bonds of graphene, compare the center with average to determine up or down
for i in range(len(str_opt_bond[0])):
for index in str_opt_bond[0][i]:
bondlist_left.append(i)
bondlist_right.append(index)
for i,j in zip(bondlist_left,bondlist_right):
bondlist_left_coor_x.append(str_opt_x[i])
bondlist_right_coor_x.append(str_opt_x[j])
bondlist_left_coor_y.append(str_opt_y[i])
bondlist_right_coor_y.append(str_opt_y[j])
bondlist_left_coor_z.append(str_opt_z[i])
bondlist_right_coor_z.append(str_opt_z[j])
for i,j in zip(bondlist_left_coor_z,bondlist_right_coor_z):
bond_z_change.append((i+j)/2-refernece_d)
#bond_z_change.append((i+j)/2-np.average(str_opt_z))
self.bond_z_change = bond_z_change
self.bondlist_left_coor_x = bondlist_left_coor_x
self.bondlist_right_coor_x = bondlist_right_coor_x
self.bondlist_left_coor_y = bondlist_left_coor_y
self.bondlist_right_coor_y = bondlist_right_coor_y
self.str_opt_x = str_opt_x
self.str_opt_y = str_opt_y
self.bond_diff = bond_diff
self.z_change = z_change
return
def prepare_COF(self,str_orig,str_opt):
#python simple plot for strain
#prepare data of structure
#structures must be flake
#str_orig,str_opt are atoms objects of flakes
str_orig_x = []
str_orig_y = []
str_orig_z = []
str_opt_x = []
str_opt_y = []
str_opt_z = []
z_change = []
bond_length_orig = []
bond_length_opt = []
z_atoms_up = []
z_atoms_down = []
z_atoms_neutral = []
bondlist_left = []
bondlist_right = []
bondlist_left_coor_x = []
bondlist_right_coor_x = []
bondlist_left_coor_y = []
bondlist_right_coor_y = []
bondlist_left_coor_z = []
bondlist_right_coor_z = []
bond_z_change = []
str_orig_coor = str_orig.get_positions()
str_opt_coor = str_opt.get_positions()
for c1,c2 in zip(str_orig_coor,str_opt_coor):
str_orig_x.append(c1[0])
str_orig_y.append(c1[1])
str_orig_z.append(c1[2])
str_opt_x.append(c2[0])
str_opt_y.append(c2[1])
str_opt_z.append(c2[2])
str_orig_bond = Analysis(str_orig).all_bonds
str_opt_bond = Analysis(str_opt).all_bonds
#get the change along z axis and within horizontal plane
for i in str_opt_z:
z_change.append(i-np.average(str_opt_z))
for count,coor in enumerate(z_change):
if coor > 0:
z_atoms_up.append(count)
elif coor < 0:
z_atoms_down.append(count)
elif coor == 0:
z_atoms_neutral.append(count)
#bond length change
for atom,bonded_array in zip(range(len(str_orig_z)),str_orig_bond[0]):
for bonded in bonded_array:
bond_length_orig.append(str_orig.get_distance(atom,bonded))
for atom,bonded_array in zip(range(len(str_opt_z)),str_opt_bond[0]):
for bonded in bonded_array:
bond_length_opt.append(str_opt.get_distance(atom,bonded))
bond_diff = [i-j for i,j in zip(bond_length_opt,bond_length_orig)]
##create list for bonds of graphene, compare the center with average to determine up or down
for i in range(len(str_opt_bond[0])):
for index in str_opt_bond[0][i]:
bondlist_left.append(i)
bondlist_right.append(index)
for i,j in zip(bondlist_left,bondlist_right):
bondlist_left_coor_x.append(str_opt_x[i])
bondlist_right_coor_x.append(str_opt_x[j])
bondlist_left_coor_y.append(str_opt_y[i])
bondlist_right_coor_y.append(str_opt_y[j])
bondlist_left_coor_z.append(str_opt_z[i])
bondlist_right_coor_z.append(str_opt_z[j])
for i,j in zip(bondlist_left_coor_z,bondlist_right_coor_z):
bond_z_change.append((i+j)/2-np.average(str_opt_z))
self.bond_z_change_cof = bond_z_change
self.bondlist_left_coor_x_cof = bondlist_left_coor_x
self.bondlist_right_coor_x_cof = bondlist_right_coor_x
self.bondlist_left_coor_y_cof = bondlist_left_coor_y
self.bondlist_right_coor_y_cof = bondlist_right_coor_y
self.str_opt_x_cof = str_opt_x
self.str_opt_y_cof = str_opt_y
self.bond_diff_cof = bond_diff
self.z_change_cof = z_change
return
def out_plane(self, color, transparency=0.7, linewidth=0.5, vmin=None, vmax=None, labelsize=14, fontsize=16, colorbar_tick_locator=0.1):
# Convert bond coordinates to segments format for LineCollection
segments = np.array([
[[x1, y1], [x2, y2]] for x1, y1, x2, y2 in zip(
self.bondlist_left_coor_x,
self.bondlist_left_coor_y,
self.bondlist_right_coor_x,
self.bondlist_right_coor_y
)
])
# Set up color mapping
if vmin is None:
vmin = min(self.bond_z_change)
if vmax is None:
vmax = max(self.bond_z_change)
cmap = LinearSegmentedColormap.from_list('rgba', color, N=256)
norm = Normalize(vmin=vmin, vmax=vmax)
# Create figure and axis
fig, ax = plt.subplots()
ax.set_aspect('equal', adjustable='box')
# Create LineCollection for bonds
lc = LineCollection(segments, linewidths=linewidth, colors=cmap(norm(self.bond_z_change)))
ax.add_collection(lc)
# Plot atoms using scatter (more efficient than multiple plot calls)
scatter = ax.scatter(self.str_opt_x, self.str_opt_y, s=1,
c=self.z_change, cmap=cmap, alpha=transparency,
vmin=vmin, vmax=vmax, zorder=5)
# Set plot limits based on data
ax.set_xlim(np.min(self.str_opt_x) - 1, np.max(self.str_opt_x) + 1)
ax.set_ylim(np.min(self.str_opt_y) - 1, np.max(self.str_opt_y) + 1)
# Add colorbar
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad="3%")
cb = plt.colorbar(scatter, cax=cax)
cb.locator = ticker.MultipleLocator(base=colorbar_tick_locator)
cb.update_ticks()
cb.ax.tick_params(labelsize=labelsize)
cb.set_label('\u0394'+'d'+' / '+'$\AA$', fontsize=fontsize)
cb.ax.yaxis.set_ticks_position('right')
ax.set_xticks([])
ax.set_yticks([])
return fig, ax
def in_plane(self, color, linewidth, vmin=None, vmax=None):
# Convert bond coordinates to segments format
segments = np.array([
[[x1, y1], [x2, y2]] for x1, y1, x2, y2 in zip(
self.bondlist_left_coor_x,
self.bondlist_left_coor_y,
self.bondlist_right_coor_x,
self.bondlist_right_coor_y
)
])
# Set up color mapping
if vmin is None:
vmin = min(self.bond_diff)
if vmax is None:
vmax = max(self.bond_diff)
cmap_bond = LinearSegmentedColormap.from_list('rgba', color, N=256)
norm = Normalize(vmin=vmin, vmax=vmax)
# Create figure and axis
fig, ax = plt.subplots()
ax.set_aspect('equal', adjustable='box')
# Create and add LineCollection
lc = LineCollection(segments, linewidths=linewidth, cmap=cmap_bond, norm=norm)
lc.set_array(np.array(self.bond_diff))
ax.add_collection(lc)
# Set plot limits
ax.set_xlim(np.min(self.bondlist_left_coor_x) - 1, np.max(self.bondlist_right_coor_x) + 1)
ax.set_ylim(np.min(self.bondlist_left_coor_y) - 1, np.max(self.bondlist_right_coor_y) + 1)
# Add colorbar
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad="3%")
cb = plt.colorbar(lc, cax=cax)
cb.ax.tick_params(labelsize=12)
cb.set_label('\u0394'+'d'+' / '+'$\AA$', fontsize=13)
ax.set_xticks([])
ax.set_yticks([])
return fig, ax
#plot COF frame on top of graphene
def add_COF(self,fig,ax,color,name,path,show_atoms = 'False',clear_after = 'True',transparancy = 0.7,zorder = 10,linewidth = 0.5):
ax2 = fig.add_subplot(111,sharex = ax, sharey = ax)
ax2.set_position(ax.get_position())
ax2.patch.set_visible(False)
for i in range(len(self.bondlist_left_coor_x_cof)):
ax2.plot([self.bondlist_left_coor_x_cof[i],self.bondlist_right_coor_x_cof[i]],[self.bondlist_left_coor_y_cof[i],self.bondlist_right_coor_y_cof[i]],linewidth=linewidth,c=color,alpha = transparancy,zorder = zorder)
if show_atoms == 'True':
ax2.scatter(self.str_opt_x_cof, self.str_opt_y_cof,s=1,c=color,alpha = transparancy,zorder = zorder)
fig.savefig(f'{path}{name}.png',dpi = 600, bbox_inches = 'tight')
if clear_after == 'True':
ax2.cla()
return