def action(index, folder):
ax = axs[0]
gap= axs[1]
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax,atoms)
pu.plot2DBZ(gap,atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0],eigSteps[-1]
print initStep, finalStep
energy = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
popStart = dp.readEigFile('siesta'+str(finalStep)+'q.EIG')
popEnd = dp.readEigFile('siesta'+str(initStep)+'q.EIG')
part = np.abs(popStart - popEnd)
plotted = part[:,3]
plotted[plotted < 0.1*np.max(plotted)] = 0.0
norm = 100.0
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,2*np.pi*atoms.get_reciprocal_cell(),
repeat = [1,1,0], flatten = False)
diffEnergy = energy[:,4] - energy[:,3]
outRange = np.ones(diffEnergy.shape)*20
outRange[diffEnergy > 4.5] = 0.0
for k in kcoorAll:
ct1 = ax.scatter(k[:,0], k[:,1], norm*plotted, color = colors[index], marker='h',
alpha=1.0, lw=0.0)
ct2 = gap.scatter(k[:,0], k[:,1], outRange, cmap=cmap, c=diffEnergy,
vmin = 1.0, vmax = 5.0, marker='h', alpha=1.0, lw=0.00)
ax.scatter([], [], 60, color = colors[index], label=folder, alpha=1.0, lw=0.0)
if index ==0 :
#plt.colorbar(ct2,ax=ax,extendrect=False)
plt.colorbar(ct2,ax=gap,extendrect=False)
def action(index, folder):
ax = axs[0]
gap = axs[1]
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax, atoms)
pu.plot2DBZ(gap, atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0], eigSteps[-1]
print initStep, finalStep
energy = dp.readEigFile('siesta' + str(finalStep) + '.EIG')
popStart = dp.readEigFile('siesta' + str(finalStep) + 'q.EIG')
popEnd = dp.readEigFile('siesta' + str(initStep) + 'q.EIG')
part = np.abs(popStart - popEnd)
plotted = part[:, 3]
plotted[plotted < 0.1 * np.max(plotted)] = 0.0
norm = 100.0
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,
2 * np.pi *
atoms.get_reciprocal_cell(),
repeat=[1, 1, 0],
flatten=False)
diffEnergy = energy[:, 4] - energy[:, 3]
outRange = np.ones(diffEnergy.shape) * 20
outRange[diffEnergy > 4.5] = 0.0
for k in kcoorAll:
ct1 = ax.scatter(k[:, 0],
k[:, 1],
norm * plotted,
color=colors[index],
marker='h',
alpha=1.0,
lw=0.0)
ct2 = gap.scatter(k[:, 0],
k[:, 1],
outRange,
cmap=cmap,
c=diffEnergy,
vmin=1.0,
vmax=5.0,
marker='h',
alpha=1.0,
lw=0.00)
ax.scatter([], [],
60,
color=colors[index],
label=folder,
alpha=1.0,
lw=0.0)
if index == 0:
#plt.colorbar(ct2,ax=ax,extendrect=False)
plt.colorbar(ct2, ax=gap, extendrect=False)
def action(index, folder):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax,atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0],eigSteps[-1]
#eigenvalue = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
part = np.abs(dp.readEigFile('siesta'+str(finalStep)+'q.EIG') - dp.readEigFile('siesta'+str(initStep)+'q.EIG'))
norm = 100.0/max(part[:,3])
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,2*np.pi*atoms.get_reciprocal_cell(),repeat = [1,1,0])
#evolvingBands = range(3,5)
ax.scatter(kcoorAll[:,0], kcoorAll[:,1], s=norm*np.abs(part[:,3]),lw=0.0, color= color[index], label=folder)
def plotPart(num):
data = []
part = partAll[num] - partAll[0]
kcoor, kweight = dp.readKpoints()
kall = [kcoor[:, :2] + point for point in points]
kall.extend([-kcoor[:, :2] + point for point in points])
for k1 in kall:
for k in range(eigen.shape[0]):
x = eigen[k, :]
data.extend([(k1[k, 0], k1[k, 1], value, part[k, index])
for index, value in enumerate(x)
if lb < value < rb and part[k, index] > 3E-6])
if len(data) != 0:
data = np.array(data)
sc.remove()
sc = ax.scatter(data[:, 0],
data[:, 1],
s=data[:, 3] * 3E3,
c=data[:, 2],
lw=0.0,
cmap='jet')
def action(index, folder):
from ase.calculators.siesta.import_functions import xv_to_atoms
atoms = xv_to_atoms('siesta.XV')
import pyramids.plot.PlotUtility as pu
pu.plot2DBZ(ax, atoms)
eigSteps = dp.getEIGSteps()
initStep, finalStep = eigSteps[0], eigSteps[-1]
#eigenvalue = dp.readEigFile('siesta'+str(finalStep)+'.EIG')
part = np.abs(
dp.readEigFile('siesta' + str(finalStep) + 'q.EIG') -
dp.readEigFile('siesta' + str(initStep) + 'q.EIG'))
norm = 100.0 / max(part[:, 3])
kcoor, kweight = dp.readKpoints()
kcoorAll, klistAll = dp.recoverAllKPoints(kcoor,
2 * np.pi *
atoms.get_reciprocal_cell(),
repeat=[1, 1, 0])
#evolvingBands = range(3,5)
ax.scatter(kcoorAll[:, 0],
kcoorAll[:, 1],
s=norm * np.abs(part[:, 3]),
lw=0.0,
color=color[index],
label=folder)
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
import pyramids.io.result as dp
fig = plt.figure(figsize=(7,7))
ax = fig.add_subplot(111)
kcoor, kweight = dp.readKpoints()
Berry = dp.getBerry(str(3))
quiverLine = ax.quiver(kcoor[:,0], kcoor[:,1], Berry[:,0],Berry[:,1],
units='x',lw=0.5, edgecolors=('k'), headaxislength=5,
color='b',zorder=10,pivot='middle',alpha = 0.5)
#for step in dp.getBerrySteps():
#Berry = dp.getBerry(str(step))
#print dp.getBerrySteps()
def update_quiver(num, quiverLine):
"""updates the horizontal and vertical vector components by a
fixed increment on each frame
"""
if num not in dp.getBerrySteps():
return
Berry = dp.getBerry(str(num))
quiverLine.set_UVC(Berry[:,0],Berry[:,1])
import matplotlib.pyplot as plt
import pyramids.io.result as dP
import pyramids.plot.setting as ma
import pyramids.plot.PlotUtility as pu
from ase.dft.kpoints import get_special_points
from ase.calculators.siesta.import_functions import xv_to_atoms
from ase.lattice import hexagonal
#------------------------------------------------------------------------------
kpath = []
cut = [0]
atom = xv_to_atoms('siesta.XV')
specialKPoints = [r'$M$', r'$\Gamma$', r'$K$', r'$M$']
kpoints, kwgt = dP.readKpoints()
nkpts = kpoints.shape[0]
for i in range(79, 2, -13):
print i
kpath.append(i)
cut.append(len(kpath))
kpath.append(6)
kpath.append(5)
for i in range(12, 45, 11):
print i
kpath.append(i)
kpath.append(i - 1)
cut.append(len(kpath))
from pyramids.plot.setting import getPropertyFromPosition, setProperty, getColors
from pyramids.io.fdf import tdapOptions
import pyramids.io.result as dp
import matplotlib.pyplot as plt
import os
import ase
from ase.calculators.siesta.import_functions import xv_to_atoms
atom_temp = xv_to_atoms('siesta.XV')
atoms = ase.atoms.Atoms(symbols=atom_temp.get_chemical_symbols(),
positions=atom_temp.get_positions(),
cell = atom_temp.get_cell())
reciprocal_vectors = 2*np.pi*atoms.get_reciprocal_cell()
kcoor, kweight = dp.readKpoints()
import matplotlib.pyplot as plt
cut = 1
fig = plt.figure()
from mpl_toolkits.mplot3d import Axes3D
ax = fig.add_subplot(1,1,1,projection='3d')
points=np.array([(reciprocal_vectors[0,0:2]*i+
reciprocal_vectors[1,0:2]*j+
reciprocal_vectors[2,0:2]*k)
for i in range(-1,2)
for j in range(-1,2)
for k in range(-1,2)])
print points[:,0].max(), points[:,0].min()
from scipy.spatial import Voronoi, voronoi_plot_2d, convex_hull_plot_2d
